Evolution and Diversity of Life
Evolution and Diversity of Life
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Chapter 1 The Virus and the Whale Whales are the largest animals on earth They must rise to the oceans surface to breathe opening a blowhole to draw air into their lungs Another oddity about blue whales is that instead of laying eggs they give birth Viruses are the smallest living things on earth The virus that causes influenza has 10 genes Viruses replicate by invading cells and hijacking their molecules to assemble copies of themselves As they spread through their host they cause several diseases No predator can approach a blue whale but a virus can kill it Biological evolution is any change in the inherited traits of a population that occurs from one generation to the next Evolution explains the diversity of life Evoution provides scientific tools we can use to address some of the challenges we face as a society The viruses and bacteria that causes diseases are continually evolving rendering many drugs ineffective Insect populations that feed on crops can evolve resistance to pesticides and weed populations evolve resistance to herbicides We are altering the environment on a planetary scale by introducing invasive species to new habitats spreading pollutions and altering the climate All these changes are driving animals and plants into new evolution trajectories Evolutionary case studies 1 Whales Mammals gone to sea How do we know whales are mammals Whales share synapomorphies with mammals such as mammary glands Three middle ear bones hair in developing embryos Although they live in water and have fish like bodies they have mammal like qualities similarities with fish arose through Convergent evolution Charles Darwin in his book The Origin of Species written in 1859 proposed a straightfonivard explanation for this puzzling pattern of similarities and differences Cetaceans whaesampdophins defended from mammals that lived on land and their ineage evolved into marine mammals through natural selection Danivin argued that evolution was a gradual process Lineage A chain of ancestors that include their descendants A lineage may be the successive generations of organisms in a single population the members of an entire species during an interval of geological time or a group of related species descending from a common ancestor In a process of convergent evolution the ancestors of modern whales lost their hind limbs and their front legs and became shaped like their flippers The mammary glands of whales and land mammals are examples of homology Apomorphy A derived character Synapomorphy a shared derived character plesiomorphy a primitive character symplesiomorphy shared primitive character Homology the similarity of biological features genes structures behaviors in a different species or groups because their descent from a common ancestor Homologous genes do not necessarily produce the same features bc an ancestral gene may be recruited for different functions in different Hneages Homoplacy character similarity that arose independently in different groups through convergence or parallelism Phylogeny a visual representation of the revolutionary history of populations genes or species Used to analyze morphology genes and phenotypes Ontology The origin and development of an organism from conception until adult scientists found synapomorphy traits similar to the whale from a 40 million year old fossil named Dorudon It had both cetacean traits and fish traits Phillip Gingerrich discovered a 50 million year fossil that shared synamorphies with cetaceans they named it pakicetus It was found near a shallow stream proving that it lived on land First terrestrial whale Hans Thewissen found quotthe walking whaequot Fossils showed that losing legs took millions of years one way to tell if an animal was terrestrial or aquatic is to look at whether they drank freshwater or salt water Living whales drank seawater while land mammals on drink freshwater Both waters contain oxygen atoms but the oxygen atoms are slightly different Sea water has more oxygen atoms with 10 neutrons Therefore sea animals have larger percentage of heavy oxygen in their bones than do mammals on land Brain size in dolphins evolved as well They thrive in a large social group they form alliances compete for mates and build relationships thats persist for the duration of their long lives sadly small populations put cetaceans at risk Humans hunt them and since they produce small populations they are prone to bottlenecking inbreeding and genetic drift Key Note 11 Whales and fishes lineages evolving independently converged on body forms that are superficially similar Ambulocetus was a fossil whale that had legs This animal had traits that were intermediate between modern whales and their lineages The chemistry of fossil whales document a transition from land to estuaries to the open oceanthe same tradition documented in the changing shapes of their skeletons Studying limb development in dolphins has revealed some of the mechanisms responsible for the evolutionary loss of hind limbs The fact that whales start the process of hindlimb development is evidence for their evolution from terrestrial mammalian ancestors 2 Viruses The Deadly Escape Artists A virus is made up of around 10 genes shells made of protein A protein that studs the surface of a virus is called Hemagglutinin latches onto proteins on the host cell Once inside the virus genome recruits our cells genetic machinery to mass produce copies of itself Each infected cell can make thousands of new copies of the viral genome which are then packaged into new membrane envelopes that escape the cell to infect a new host all living things make copies of their genes but in each generation they make a few mistakes known as mutations so that ancestors and descendants do not haveiden calgenes Viruses with beneficial mutations reproduce more than other virus their descendants come to dominate the virus population This helps create a diversity of new strains that change over time Doctors create vaccines which are made up of hemagglutinin proteins which trigger the body to make antibodies to them Once these antibodies begin to circulate they enable the immune system to mount a swift defense against actual viruses with the same hemagglutinin proteins the flu virus evolves rapidly because they evolve so quickly vaccine designers have to generate a hypothesis about which strains will come to dominate the next flu season Viruses originally descended from strains that infected other animalsbirds Bird flu crosses over becoming adapted to replicating in humans This transition is aided by the ability of virus to swap genes in a process known as reassortment Key Concepts 12 Hemagglutinin is a protein on the surface of the influenza virus that latches it to a host cell it is also the protein that is recognized by our immune system and it is harvested to manufacture vaccines This viral protein evolves extremely rapidly rendering our vaccines obsolete months after they are made Reassortment of the influenza virus is terrifying because it could blend dangerous elements of pig or bird flu with the infectious potential of human flu instantaneously generating a deadly and infectious strain Reassortment events can occur in any bird pig or human individual that is simultaneously infected with more than one strain Mutations arise at a roughly steady rate and so the number of different mutations in two lineages provides a clue to how long ago they diverged from a common ancestor We change vaccines every year because viruses evolve so quickly and because the virus gets strains with beneficial mutations The new strains are no longer recognizable by the immune system molecular clock viruses that go unseen for months 3 Evolution A tapestry of Concepts Danivin observed the pattern of evolution in the fossil record and the morphology of living species He interoperated this pattern as the result of descent with modification from common ancestors He noted that there were variations in every generation Over time natural selection would drive large scale changes even rise to new species Genetic driftis evolution arising from random changes in the genetic composition of a population from one generation to the next 4 Common Misconceptions about Evolution Misconception 1 Evolution isjust a quottheoryquot A theory makes sense of what would othenivise seem like an arbitrary mysterious collection of data It is supported by independent lines of evidence Misconception 2 Evolutionary biology has a complete explanation for everything that has happened in the history of life Biologists are still discovering new things All evidence fits within context of evolution Misconception 3 Evolution explains the origin of life Evolution is a process that occurs when populations of organisms change genetically over time The origin of life is a vibrant field of research on its own Misconception 4 The study of evolution is the search for direct ancestors and missing links Biologists expect there to be missing links They know finding direct ancestors is unlikelyThe find relationships of species represented by fossils and by living individuals The phylogeny itself can shed light on how new traits evolved Misconception 5 Evolution violates the second law of thermodynamics Earth is not a closed system Sun provides energy Misconception 6 Evolution is a natural selection Natural selection is a crucial part of evolution but it is not the entirety of it others include genetic drift and sexual selection Misconception 7 Evolution is entirely random Whether a particular mutation arises in a particular individual is a matter of chance however how that mutation spreads is more than chance Misconception 8 Evolution provides species with the adaptations they need Evolution cannot identify what a species needs Natural selection is the cause Misconception 9 Evolution is a march of progress New species diverge like branches on a tree Misconception 10 Evolution always goes from simple to complex Ex bacteria lost most of the genes essential for surviving as freeliving bacteria Misconception 11 Individual adapt to their environment No populations adapt It requires changes in the frequency of alleles Misconception 12Evolution has made living things perfectly adapted to their enviroment natural selection can act only on what already exists and it operates under tight constraints of physics and development Misconception 13Evoution happens for the good of the species Evolution cannot recognize what is best for a large group of organisms natural selection operates at the level of genes and the reproductive success of individuals Misconception 14Evolution promotes selfishness and cruelty Natural selection favors behaviors that boost the spread of genes from one generation to the next ex flowering plants provide food to insects that pollinate them Misconception 15 Evolution seeks peaceful harmony in nature predators are exquisitely adapted to finding and killing prey so not peaceful Misconception 16 Some forms of life are higher on the ladder of life and some lower Every living species can boast many adaptation to its environment Humans have brains that allow to us think but that does not make us better adapted than other species Dolphins can communicate undenivater and we cannot We lack echolocation Misconception 17Evoution has produced a stable diversity of life More than 99 of species that ever existed have become extinct To Sum It Up Evolution is descentwith modification Mutations are errors that arise when DNA is replicated New mutations cause individuals to differ from each other geneticallygenerate variation within a population Natural selection and genetic drift are mechanisms of evolution because they can cause the genetic composition of a population to shift from generation to generation Natural selection occurs when some genetic types of individual survive and reproduce more successfully than others Evolution does not respond to an individuals need Evolution produces complex adaptations but it does not move toward a particular goal Evolutionary biologists test hypotheses about evolution using many different lines of evidence Whales evolved from land mammals about 50 Million years ago Evolution has shaped many aspects of their biology from their behavior to their aging THe rapid evolution of the influenza virus makes it difficult to fight QUESTIONS Which is a definition of evolution Descent with modification mutated genes becoming more or less common over the course of generations Change within a lineage due to natural selection and other mechanisms Which of the following is a true statement Having bigger brains gave both advantages and disadvantages to human ancestors Which of the following supports the concept of descent with modification All living organisms share a common code of genetic instructions many mammals have the same patter of bones in their forelimbs Which of the following is NOT a place that scientists look for evidence of evolution Change within an individual organism Which is the best explanation of why baleen whales still have genes for building teeth Their ancestors had teeth and they inherited these genes from them even though they no longer function Hemagglutinin is importnat in the evolution of influenza virus because It allows the virus to bind to the cells of its host Chapter 2 From Natural Philosophy to Danivin 21 Nature Before Danvin Danivin39s insights form the foundation evolutionary theory It explains how patterns of diversity came to be combined his ideas with work of many others He combined work of many others The urge to classify reached its most glorious form in the mid 170039s with the work of botanist Carl Linnaeus He organized all living things known at the time into a single hierarchy of groups Taxa He could assign every species to a particular genus family or order according to traits it shared with other species His system of taxonomy was so useful that biologist continue to use it today While Linnaeus studied diversity of life in present form other naturalists were looking back over life39s history Nicolaus Stenowas a anatomistHe proposed that after sharks died there teeth eventually were transformed to stone He argued that originally a seas must have covered the mountains He believed that the earth was just a few thousand years odbut he introduced a new idea that life and the planet that supported it had a history filled with change and the Earth itself kept a record of that history Key Notes Carl Linnaeus is the father of modern taxonomy Nicolaus Steno is the father of geology and stratigraphy the study of layering rock as a method for reconstructing the past 22 Evolution Before Danvin Georges Buffon was one of the earliest naturalists to argue that life had changed over time He believed that earth formed according to laws of physics and chemistry And that the earth was lower than previously thought Life emerged as distinct types and transformed when environment changed Fossils and Extinctions Because steno realized that fossils were the remains of living things a new science known as paleontology formed which is the study of prehistoric life Georges Cuvier said that fossils resemble but are not exactly the same as modern species Many past species are exstinct Geologists realized that change was gradual James Hutton realized that rocks formed through imperceptibly slow changes many of which we see today He realized the earth must be old Also William Smith realized that the same kinds of fossils tended to appear in older rocks but different ones appeared in younger layers Smith created the first geological map Geologists named rock formations from different periods Evolution as Striving Lamarck believed life was driven from simple to complex Complex species descended from microbes Microbes continually generated spontaneously Adaption occurs through inheritance of acquired changes To explain why there are microbes today Lamarck argued that primitive life was being spontaneously generated all the time Today39s bacteria are just the newest arrivals Lamarck also believed animals and plants could adapt to their environment He claimed these could be passed down Lamarck got shut down and died in poverty Key Concepts George Buffon proposed that new varieties of a species could arise in response to new habitats However he did not believe that species could arise this way Georges Cuvier conducted pioneering research in comparative anatomy and paleontology He provided some of the first compelling evidence for ex nc on James Hutton envisioned a world with a deep history shaded by gradual transformations of landscapes through imperceptibly slow changes William Smith was an English geologist who created the first geological map Lamarck was an early proponent of evolution as a process that obeyed natural laws 23 The Unof cial Naturalist Charles Danivin decided not to go to Medical school and instead further his knowledge in nature He sailed the HMS Beagle in 1831 On his voyage he collected many fossils and living organisms He read the book The Principles of Geology 183033 by Charles Lyell Lyell made the argument that the Earth39s landscapes had been created not by gigantic catastrophes but by a series of many small changes Uniformitarianism Which is the idea that the natural laws observable around us now are also responsible for events in the past One part of this view for example was the idea that the Earth had been shaped by the cumulative action of gradual processes like sediment deposition and erosion Danivin had observations that he collected that led him to believe that the earth had evolved He found birds that had dramatically different beaks which turned out to all be finches Danivin was prompted to go public with his ideas because he was afraid Alfred Russel Wallace would publish first and he would cast in Wallace39s shadows It was until Danivin published The Origin of Species in 1859 when he got lots of attention He said all species share a common ancestry and that changes occur through natural selection Common Descent Homologous traittraits are similar because they are inherited from a common ancestor exthe arms between a human seal and bat Analogous traits are similar because they have converged on a shared form They are not derived from a common ancestor exshark finsdolphin fins moth wingsbird wings Natural Selection Natural Selectionis a mechanism that can lead to evolution whereby differential reproduction of individuals causes some genetic types to replace others Adaptationsare inherited aspects of an individual that allows it to out complete other members of a population that lack the trait Adaptations are traits that have evolved through the mechanism of natural selection Sexual SelectionArises when individuals of one sex compete with each other over access to individuals of other sex It can lead to the evolution of traits like showy ornaments or weapons that improve the animals chances of mating Genetic Drift is a change in the frequency of traits ar genetic variants that arise across generations due to random events Drift is most pronounced in small populations To Sum It Up In the 17th and 18th centuries naturalists devised systems to classifying life and recognized fossils as the remains of living things Science is the use of evidence to construct testable explanations and predictions natural phenomena as well as the organization of knowledge generated through this process Georges Buffon proposed that the Earth was very old and that life had gradually changed during its history Georges Cuvier helped establish that many fossils were the remains of extinct species The geological record revealed a succession of different species that lived on the earth Lamarck developed an early theory of evolution based in part on the idea that acquired traits are passed down through a mechanism of heredity Charles Danlvin and Alfred Wallace independently developed a theory o fevolution by means of natural selection Homology is the similarity of characteristics in different species because of a common ancestor Thomas Malthus 1798 Essay on the principle of population said that populations increase exponentially and food resources increase arithmetically QUESTIONS Early scientists learned many things from fossils WHich of the following is one of those things The earth changes The history of an are can be found in its rocks Different organisms once lived on the planet Which of these statements is a concept found in Georges Buffons ideas about evolution but not in the way we understand evolution now Life is divided into a number of distinct types that are not related to each other What would Lamarck and Charles Danlvin Agreed on One Generation can pass on its trait to the next What is the correct definition of homology structure of limbs that are common among all mammals How does artificial selection differ from natural selection The strength of the selection is stronger it happens more rapidly and the selection is goal orientated What set Danlvin and Wallace39s concept of natural selection apart from earlier ideas of evolution THeir concept depended on a process that is observable Chapter 3 What the Rocks Say How Geology and Paleontology Reveal the History of Life 31 The Ancient Earth Danlvin rejected that the earth was only a few thousand years old At first he was most known for Geology because he made careful observations while on HMS Beagle HE recognized that these formations were the result of gradual changes spread over vast amounts of time He believed that the earth was billions of years old Lord Kelvin argued that the Earth could not be older than 20 million years old based on the temperture of rocks He was wrong Physicists finally found a way to measure the age of rocks They discovered that radioactive isotope atoms decay into other elements at a precise rate Found out the earth was 456 Billion Years Old through radiometric data 32 A Vast Museum The fossil record is far from complete especially because most animals do not fossilize Also it is very rare when tissues fossilize However places with soft tissue fossil deposits are called Lagerstatten They are some Lagerstattens located in the Burgess Shale found in canada The Burgess Shale has over 65000 specimen of mostly soft bodied animals representing at least 93 species 505 million years ago Bringing fossils to life Fossils provide clues about behavior development modes of reproduction Some fossils preserve evidence of predators eating prey bite marks on ancient relatives of humans demonstrate that our ancestors were regular eaten by carnivores ALso when animals walked on soft ground they sometimes left tracks behind and those cavities became preserved Scientists now can scan electron microscopes that allow them to examine the cellular structure of fossils A scientist used this technology to look at fossilized feathers they determined that the melanosomes in the a fossilized bird were the same as living birds Cat Scans help determine function of the hadrosaur crest They saw that the crest was connected to the nasal cavity This allowed sound greeted by blowing air The ears tuned to this frequency Traces of Vanished Life A fossil is not the only trace that an organism can leave behind Some rocks themselves are made from the remains of dead organisms Biomarkers Molecular evidence of life in the fossil record Biomarkers can include fragments of DNA molecules such as lipids or isotopic ratios A number of these biomarkers have been found in 164 billion year old rocks in Australia One of them is called Okenane the only organism known to produce this are purple sulfur bacteria We can hypothesize that since okenane is present in these rocks purple sulfur must have been around Even the individual atoms in rocks can offer scientists clues about ancient life Isotopes not only offer clues to the habitats in which organisms lived they also provide clues to their metabolism PLants obtain their carbon from the atmosphere carbon 12 carbon 13 the ratio is important Key Concepts Technology allows scientists to gain new insights into the behavior and appearance of extinct seizes from their fossils Isotopes and biomarker molecules carry information about the history of life 33 Life39s Earliest Marks Earliest life unlikely to preserved as fossils Since they are sure they won39t be able to find the earliest fossils they shifted their attention to the isotopes in ancient rocks in hopes of finding a chemical signature of early life presence of carbon in early rocks suggests life 36 billion years ago Earliest sign of life were known as stromatoites 345 billion years ago 34 The Rise of Life Cambrian period542 to 510 million years ago Bacteria One of two prokaryote domains of life Bacteria includes organisms such as E Coli and other familiar microbes 35 billion Archaea One of the two prokaryotes domains of life They are distinguished by a number of unique biochemical features 35 billion Eukarya A domain of life characterized by unique traits including membrane enclosed cell nuclei and mitochondrialncludes animals plants fungi and protists 18 billion 35 Life Gets Big The transition to multicellular life began at least 21 billion years ago but multicellularity likely evolved in a number of lineages 36 The Dawn of The Animal Kingdom Cambrian 550 million years ago500 million Ordovician 500 million years 450 million explosion in marine fishestetrapods Silvrian 450400 million Devonian 400350 million years ago Prokaryotes colonized terrestrial environments first fossils date to 26 billion years ago Terrestrial animals plants and fungi appeared much much later First terrestrial plant and fungal life Oldest terrestrial plant fossils are 475 million years ago early plants resembled mosses and livenivorts Large forest ecosystems within 100 million years Fungi appear 400 million years ago associated with plants they do not fossilize very well They are the decomposers of ecosystems that can be reused by other organisms Very important in the growth of plants Lignin is important to forming robust plants tall plants First terrestrial Animal life Invertebrate traclwvays date to 480 Million years ago porbably relatives of insect and spiders not clear whether they lived on land permanently Oldest fossil of fully terrestrial animal dates to 428 million years ago centipede like First territorial vertebrates Oldest traclwvays date to 390 million years ago Oldest fossils of tetrapods date to 370 million years ago Familiar forms of life did not emerge until recently Flowering plants birds mammals teleost fish 350 million years ago many currently existing lineages had yet to evolve Evolution of mammals Mammals evolved from synapsids have a hole in the skull All vertebrates have quadrate bone except for mammals defenastrate throw them out the window 280 million years ago synapsids first mammals emerged 150 million years ago Diversification of mammals Mammals diversified after dinosaurs went extinct 65 million years ago whales bats and primate all emerged around 50 million years ago oldest human fossils are 200000 years old Birds150 million years ago descendants of dinosaurs flowering plants132 million years ago grasses 20 million insects 400 million years ago but most current lineages appear much later KEY CONCEPTS 1Many of the most diverse existing plant animal lineages evolved instantly Early animal life resembles sponges Oldest fossils 650 million years ago Biomarkers also demonstrate existence of sponges during this time Search for early animals can be controversial Animal embryos or animal relatives Ediacaran fauna diverse and unique animals dominated the oceans from 575535 million years ago many hard to place taxonomically they are extinct now Most have no descendants Currently existing lineages recognizable during the early Cambrian 542511 million years ago diverse nothing like it today Chordates emerged during early cambrian found in china Protostomes insects mollusks Deuterstomes starfishetc 3 7 Climbing Ashore Prokaryotes dated to 26 billion years ago tetrapods vertebrates with four limbs Living tetrapods include mammals birdsetc 38 Recent Arrivals Most species of fish on Earth today belong to group known as the telosts They have the mobility of an upperjaw bone Synapsids are a lineage of tetrapods that emerged 300 million years ago and gave rise to mammals They have temporal fenestrae 20 million years ago grasses became a thing HomininHumans and all species more closely related to humans more than to chimps To Sum It Up Geologists use the breakdown of radioactive isotopes to estimate the age of rocks Organisms rarely become fossils Biomarkers such as molecules from cell walls can be preserved for hundreds of millions of years The ratio of isotopes in fossils can tie hints about the diet and ecology of extinct species The oldest proposed evidence of life is 37 billion Stromatolites and other fossils of microbes date back about 35 billion years The three main branches of life are Bacteria Archaea and Eukaryotes Mulitcellular eukaryotic fossils date back as far as 16 billion years ago biomarkers of animals date back as far as 650 Million years go The ediacaran fauna is a puzzling collection of animals that existed between about 575 and 535 million years ago QUESTIONS How did the fossils of the Burgess Shale Form The animals dropped into anoxic ocean depths and were covered by fine sediment Which of the following molecules has not been used as a biomarker an organic chemical signature of once living organisms Sodium Ions Which outcome would you predict if you could compare the isotopes of fossils of two species of human ancestors and found high ratios of carbon1312 in one and low ratios in the other The species with high ratios likely preferred eating shrubby vegetation Fossils of single celled grazers are important because they are early members of what group Eukarya Which of the following is not true about Archaea They store DNA in nucleus How can scientists determine that multicellular life arose more than once Animals are more closely related to singlecelled eukaryotes than to fungi Which fossils often took the form of disks fronds or blobs Ediacaran Fauna Why is a notochord an important adaption for understanding the evolution of humans A notochord is a characteristic of chordates hollow nerve cord What allows us to know that synapsids were tetrapods They had four legs that they used to walk with They lived on land They were dominate land animals They evolved into mammals Which of the following groups existed 350 Million Years Ago tetrapods Which group does not apply to the idea that quotmany of the most diverse animal and plant species alive today belong to young lineagesquot insects Chapter 4 The Tree Of Life Neil Shubin wanted to learn about how tetrapods evolved from marine ancestors and how they went from living undenivater to living on land He decided to search for fossils of extinct species that evolved during this transition He then found an outline of a jaw that looked more like those of a tetrapod than those of a fish This was a creature that lived 375 million years ago Looked like a fish without arms It had gills and scales but its front pair of appendages could bend at the elbow and could sport the weight of its body They named it Tiktaalik 41 Tree Thinking Evolution has a tree ike structure but no evolutionary biologist would try to draw the entire tree of life representing every species because there are so many Phylogeny A visual representation of the evolutionary history of populations genes or species Tips Terminal ends of an evolutionary tree representing species molecules or populations being compared Branches Lineages evolving through time between successive speciation events Node A point in a phylogeny where a lineage splits Internal nodes Nodes within a phylogeny representing ancestral populations or species Clade An organism and all of its descendants 42 Phylogeny and Taxonomy Monophyletic A term used to describe a group of organisms that form a clade Different conclusions can result from different lines of evidence Linnaeus39s system was built on an understanding of structural similarities that was relative basic compared with the tools of scientists today 43 Reconstructing Phylogenies Because we do not have direct knowledge of the past we must infer the branching patterns of a phylogeny from data Most of the time we gather that data by measuring characters of the taxa that will form the tips of th tree we want to draw Characters Heritable aspects of organisms that can be compared across taxa Taxa A group of organisms that a taxonomistjudges to be a taxonomic unit such as a species or order Homoplasy character state similarity not due to shared descent Convergent evolution The independent origin of similar traits in separate evolutionary lineages systematists identify synapomorphies to generate phylogenies Homoplasy can create the mistaken impression that species are closely related when they are not 44 Fossils Phylogeny and the Timing of Evolution Exaption A Trait that originates performing one function and which is later co opted for a new function New lines of evidence suggest some commonly used taxon names should be revised to reflect evolutionary history apomorphya deprived character synapomorphy a shared derived character Define species or genus pesiomorphy A primitive character 5 fingers symplesiomorphy shared primitive character Parsimony the fewest of steps in a tree Reconstruction of phylogenies is based on analysis of phylogentic trees clades are determined by synapomorphies Not all traits are similar due to common descent homoplasious traits can be misleading principle of parsimony used to find tree that is most likely to be correct phylogenies are created by indetifying synapomorphies fossils can be used to contain divergence times Fins to limbs homology through time Coelacanth fins are homolooug to tetrapod forelimbs Phylogenies generate hypotheses the coelacanth has fins and they found a fish that has similar features to a tetrapod Scientists predicted where transitional fossils would be found They found Tiktaalik transition fossil between fish and tetrapods limb is in between tetrapod and fins however shares more homologies with tetrapods for examplewrist The reason the fish began to evolve was because there was a lot of food sources on land or to escaped drying up land or predators Homology can be obvious or not ex the jawjoint bone of a reptile and ear bones of a mammal in everything but mammals that define the jaw bones are the quadrate articularjaw joint bone Fossils and phylogeny document transition of bones from jaw to ear jaw became more robust by eliminating the jaw bone began to become sound conducting bone feathers homologous to scalesderived why feathers evolved insuation help locomotion assisted them in traction Danivin proposed that humans most closely related to African Apes Fossil record should document transition to unique human traits wrote book descent of man bipedality larger bran size smaller canine teeth coccyx bones on both posterior to illium Transition to bipedality appears to have evolved before larger prawn position of foramen magnum weight bearing stance short stiff toes ardipithecus adapted to walking and arboreal life hominins became better adapted to walking upright over time Key Concepts living members of a clade may not reliably indicate origins of synapomorphies the mammalian inner ear is made up of modified parts of the jaw feathers are an expatiation our current understanding of human evolution is based on 20 different species bipedalism evolved before large brain size To Sum It Up A phylogeny is a branching diagram that shows the evolutionary relationships among groups of organisms Unique character states that arose in the common ancestor of a clade and are inherited by daughter species in that clade are called shared derived characters Phylogenies are constructed using shared derived characters a cladogram is a phylogeny constructed by grouping taxa into nested hierarchies using information from snyapomorphies scientists reconstruct evolutionary trees to develop and test hypotheses about how major evolutionary transformations took place character states in different species may be similar because they were derived from a common ancestor of the speciessynapomorphy or because the species were converged independently on the same character state homology evolutionary reversals occur when a derived character state reverts to its ancestral state such as loss of flight in some species of birds tetrapods belong to a clade called obe fins which include coelacanths and lung shes some tetrapod traits such as toes and legs evolved while the ancestors of tetrapods still lived in water the bones of the mammalian ear evolved from bones of the lowerjaw sometimes traits that arise for one function are later co opted for a different function exaptations and phylogenies can help reveal this feathers evolved before flight Dinosaurs used these early feathers for other functions perhaps for insulation courtship display and nest brooding human anatomy and behavior have evolved gradually over the past 7 million years Hominins were bipedal millions of years before they evolved large brains QUESTIONS Which of the following is not a synapomorphy The ability to swim in dolphins and sharks Which of the following can lead to homoplasy the reversion of a derived character state to its ancestral sate the independent origin of similar traits in separate lineages the evolution of wings in both birds and bats Why are bird feathers considered an expatiation Because they first evolved under different conditions than those under which they are currently found Chapter 5 Raw Material what makes someone tall a gene that if your homozygous to that gene it adds 1cm environment you grow ingenesfood even chemistry of your mothers uterus proteins are chains of amino acids forms ion channels break down molecules in food we eat stores hemoglobin 100000 types transport hemoglobin combinations of 20 amino acids DNA codes for protein mutation any change to the genomic sequence ATCG Messanger RNA T becomes U forms great long strings eukaryotic DNA is organized into chromosomes paraphyletic bacteria and archaea DNA is wrapped around histones manage contrapting DNA Code Letter AUCG in ran or ATCG in Dna Codonthe triplet of adjacent nucleotides in messenger ran that codes for a specific amino acid NOnoverlapping CODEcode in which only as many amino acids are coded as there are condons in the end t oend sequence eg for the triplet UUUCCC phenylalanine UUU and proline CCC redundant or degenerate presence of more that one codeon for a particular amino acid EG only 20 amino acids but more that 20 codes Comma less code absence of nucleotides UUUCCC Synonymous codons different condons that specify the same amino acids in the redundant code UUU UUC ambiguous codecircumstances when one condon can code for more than one amino acids none existing Frame Shift mutationchange in the reading frame because the insertion or deletion of nucleotides in numbersother that multiply of the conon length changes the previous partitioning of codons in the reading frames and causes a new sequence of codons to be read Replacement mutation change in nucleotide sequence either by deletion insertion or substitution resulting in the appearance of a codon that produces different amino acid in a particular proteinic Universial code use of the same genetic code in all organisms UUU is phyenlalnine in bacteria ice and tobacco mitochondria may have exceptions Chomosomes come in homologous pair we are diploid ploidy can vary number of copies of unique chromosomes in a cell snake plant has 100 production of protein from dan requires transcript and translation gene expression process by which information from a gene is transformed into product Ribosomes translate MRNA into protein Gene expression can be regulated in a number of ways RNA splicing can create multiple proteins from a single genes Regulation of gene expression is flexible READ THROUGH THE TABLE ON THE SLIDES noncoding regions make up most of the genome these include RNA genes pseudogenes mobile genetic elements Micro RNA can effect phenotypes KEYNOTES Most proteins function in 4 ways Enzymes Cellcell signaling receptors structural elements Mutations are the raw material for evolution In diploid organisms deleterious mutations may be masked by a functional gene copy All cells use mRNA to carry genetic info Noncoding RNA plays critical roles in gene regulation CHanges in coding sequences and gene expressions are heritable gene expression changes can affect when where and how much a gene is expressed heterchronytiming of expression of a gene when atagonny heterotopy change in where the gene is expressed heterometry change in the amount of product heterotypy change in protein that is synthesized changed in the product all create the same product but it39s the change exturtle shell enochondral bone formation Dermal bone between dermis and epidermisclavice its scapula is in its ribs one change Types of mutations point mutation is most common insertion deetion gene duplication inversion chromosome fusion genome duplication mutations Germ line mutation can alter the phenotype Different types of mutation can alter the phenotype Since there are so many genes there can be consequences to gene mutation Germ line mutations are heritable somatic mutations zaffect cells in the body of an organism not heritable germline mutations affect gametes heritable and relevant to evolution To Sum It Up Genetic information is stored in DNA DNA is copied into RNA which has many functions in the cell Some RNA molecules serve as templates for proteins Proteins are essential tools in the structure an function of an organism they can function as enzymes signals receptors or structural elements Mutations are changes in the genetic information of an organism they are the ultimate source of heritable genetic variation the raw material essential for evolution Offspring can inherit germ line mutations from there parents Mutations can affect the product of a gene such as protein or the levels of expression of that gene product Mutations are rare but they arise at a roughly steady rate Sexual reproduction adds the quantity of genetic variation within a population During meiosis independent assortment and genetic recombination separate mex and combine ales result in in sibling offspring from the same parents with different inherited characteristics The phenotype is the manifestation of the genotype but the link is not always straightfonlvard Some genetic polymorphisms exist because of a mutation to a single gene Some genotypes can produce multiple phenotypes spending on the environment Quantitative traits can reflect simultaneous effects of multiple genes and the environment so that it is misleading to speak of a gene quotfor a traitquot For instance there is no quotheight genequot any particular gene that effects height probably accounts for only a small amount of variation among the heights of individuals in a population This principle is true for other complex traits as well The environment can produce large variations in the expression of a trait phenotypic plasticity is the result of interactions between genotypes and environments QUESTIONS Which of the following is not a protein Nucleotides What role do histones play in eukaryotes Condensing the DNA and Controlling the transcription of genes What is one importantjob of a hormone To alther expression of target genes What is the name of DNA sequences that have lost their protein coding ability Pseudogenes What an organism incorporates genetic material from another organism that is not its parent that is known as Horizontal gene transfer Complete dominance occurs when The phenotype of a heterozygote is identical to the homozygote Which of these statements about the link between phenotypes and genotypes are not always true Diseases are caused by recessive genes Which of the following isare part of the environmental control of gene expression signals from outside body from other genes within the cell and signals from other cells Chapter 6 61 The Genetics of Populations Genetic locus loci The specific location of a gene or piece of DNA sequence on a chromosome When mutations modify the sequence at a locus they generate new aleles variants of a particular gene or DNA region Alleles are mutually exclusive alternative states for a genetic locus Population genetics The study of the distribution of alleles within populations and the mechanisms that can cause allele frequencies to change over time when studying loci geneticists usually focus on a few loci at a time considering their are millions Key Concepts Because diploid organisms carry two copies of each autosomal chromosome they can have as many and two alleles for each gene or locus Individuals carrying two different alleles are heterozygous for the locus Populations contain mixtures of individuals each with a unique genotype reflecting the alleles that they carry at all of their genetic loci At any time some alleles will be more common than others Evolution is defined as any change in the frequency of alleles from one generation to the next 62 Changes over Time Or Not Hardy Weinberg equiibrium Population alleles frequencies do not change if population is infinitely large genotypes do not differ in fitness there is no mutation mating is random there is no migration With these models they considered how many parents of each possible genotype were present in a population and how often each of the possible crosses of different pairs occurred p22pqq2 pfrequency of one allele qfrequency of the other allele 63 Evolution s Null Model The hardyWeinberg theorem is useful because it provides mathematical proof that evolution will not occur in the absence of selectiondrift migration or mutation May explicitly delineating the conditions under which allele frequencies do not change the theorem serves as a useful null model for studying the ways that allele frequencies do change Helps us understand explicitly how and why populations evolve Key Concepts Because it describes the conditions in which evolution will not occur the HardyWeinberg theorem serves as the fundamental null model of population genetics 64 A Random Sample Genetic drift occurs when a random nonrepresentative sample from a population produces the next generation The smaller the sample the bigger deviation you ll notice from the original Fixed AlleleAn allele becomes fixed in a population when all of the alternative alleles have disappeared No genetic variation exists at a fixed locus within a population because all individuals are genetically identical at that locus Drift reduces genetic variation in a population alleles are lost at a faster rate in small populations 65 Bottlenecks and Founder Effects Genetic Bottenecks Events in which the number of individuals in a population is reduced drastically Even if this dip in numbers is temporary It can have a lasting effect on the genetic variation of a population Rare alleles are likely to be lost during a bottleneck Genetic drift becomes stronger depends on the how small the population size becomes and the frequency of the allele Founder Effect A type of genetic drift describing the lose of allelic variation that accompanies founding of a new population from a very small number of individuals a small sample of a much larger source population This effect can cause the new population to differ considerably from the source population 6 6 Selection Winning and Losing Fitness The reproductive success of an individual with a particular phenotype Components of fitness w Survival to reproductive age mating success fecundity Relative fitness fitness of a genotype standardized by comparison to other genotypes To understand how selection leads to changes in the frequencies of alleles we can consider the contributions of an allele rather than a genotype to fitness Average excess of fitness The difference between the average fitness of individuals bearing the allele and the average fitness of the population as a whole Ap p x aA1w Apchange in allele frequency pfrequency of A1 waverage fitness aAaverage excess of tness Natura selection is more powerful in large populations Drift is weaker in large population Small advantages in fitness can lead to large changes over the long term Mutations often have more than one effect on an organism Pleiotropy The condition when a mutation in a single gene affects the expression of many different phenotypic traits Pleiotropy is considered to be antagonistic if a mutation with beneficial effects for one trait also causes detrimental effects on other traits ex mosquitos who had a mutation that helps them against pesticides made them more easily of getting caught by spiders Alleles that lower fitness experience negative selection Alleles that increase fitness experience positive selection Relationships among allele at at a locus Additive allee yields twice the phenotypic effect when two copies present there is no dominance Dominance Allele masks presence of recessive in heterozygote Mutation generates variation Mutation rates for given gene are low but considering genome size and population size many new mutations arise each generation humans have 98 billion new mutations Source of variation for selection and drift to act Mutationselection balance Equilibrium frequency reached through tugofwar between negative selection and new mutation explains persistence of rare deleterious mutations in populations Some forms of selection maintain diversity in populations negative frequency dependent seection Rare genotypes have higher fitness than common genotypes This process can maintain genetic variation within populations Heterozygote advantage Key Concepts Selection occurs when genotypes differ in fitness Outcome of selection depends on frequency of allele and effects on fitness Population size influences power of drift and selection drift more powerful in small populationselection more powerful in large population Both drift and selection are potent mechanisms of evolution and their relative importance depends critically on the size of the population When populations are very small the effect of drift can enhance the action of selection eg removing harmful alleles that have been driven to low frequency by selection or oppose it eg by removing alleles that are beneficial When populations are large the effects of drift are minimal and selection is more important force Alleles often affect the fitness of an organism in more than one way When these fitness effects oppose each other the balance between them will determine the net direction of selection acting on the allele This balance may tip one way in one environment and a different way in others pleiotropic effects Laboratory studies of experimental evolution help reveal how new alleles can arise and spread through a population in response to selection rare allele are almost always carried in heterozygous state When recessive alleles exist in heterozygous individuals they are invisible to the action of selection Selection cannot drive dominant beneficials alleles all the way to fixation because once the alternative recessive alleles become rare they can hide indefinitely in a heterozygous state The mutation rate for any specific locus may be extremely low but it is much higher when considering an entire genome or population The gradual accumulation of mutations within populations is the ultimate source of heritable variation Balancing selection actively maintains multiple alleles within a population Two mechanisms are heterozygote advantage where the heterozygotes for the alleles in question have higher fitness than either of the homozygotes and negative frequency dependent selection If the fitness of an allele is higher when the allele is rare then the selection can retain allelic diversity within a population 6 7 Inbreeding The Collapse of a Dynasty King charles II was a victim of inbreeding Inbreeding coefficient Probability that two alleles are identical by descent Inbreeding depression results in the reduced fitness rare deleterious alleles more likely to combine in homozygotes it does not change the frequency of alleles in a population It simply rearranges alleles such that homozygotes for rare recessive alleles become more common This mean that inbreeding on its own is not a mechanism of evolution Key Concepts Alleles are identical by descent if they both descended from a single mutational event Inbreeding increases percentage of loci that are homozygous for alleles identical by descent Genetic bottlenecks often go hand in hand with inbreeding and selection recessive alleles exposed to selection Chapter 7 71 Genetics of Quantitative Traits Polygenic trait influenced by many genetic loci interaction between alleles epistasis interaction with environment phenotypic plasticity Quantitive genetics study of the genetic mechanisms of continuous phenotypic traits To estimate the amount of variation for a trait in a population is known as variance VPVGVE VP total phenotypic variance in population VGvariance due to genetic differences VEvariance due to environmental differences Broad sense of heritabilityproportion of phenotypic variance explained by genetic differences among individuals Key Concepts When components of variation are additive genetic and environmental variance sum to total phenotypic variance Heritability is the proportion of phenotypic variance due to genetic difference broad sense of heritability includes additive effects dominance effects and epistatic effects 72 The Evolutionary Response to selection Modes of selection Directional Selection favors individuals at one end of a trait distribution such as animals with small body size large individuals have lower fitness than smaller individuals after selection and provided the trait is heritable the distribution of phenotypes should shift to the left towards a smaller mean body size Stabilizing Selection favors individuals with a trait near the population mean fish with the largest and smallest body sizes have the lowest fitness and in the generation after selection the variance of the population should be smaller than it was in the preceding generation Disruptive Selection selects against the population mean favoring individuals at either end of the distribution Here if selection is strong enough populations may begin to diverge in phenotype How much the population changes depends on Selection differential A measure of the strength of phenotypic selection The selection differential describes the difference between the mean of all members of a population and the mean of the individuals that reproduce contributing offspring to the next generation Heritability Selection differential measures the strength of selection high heritability results in larger change Calculating the evolutionary response to selection Rh2xS Key Concepts Evolution and selection are not the same selection can occur without evolution The magnitude of change depends on strength of selectionseection differential and heritability 73 Dissecting Complex Traits Quantitative Trait Loci QTL Stretches of DNA that are correlated with variation in a phenotypic trait These regions contain genes or are linked to genes that contribute to population differences in a phenotype Key Concepts QTL mapping studies permit quantitative geneticists to identify regions of the genome responsible for genetic variation in phenotypic traits This method can serve as a first step towards elucidating the genes responsible for phenotypic evolution 74 The Evolution of phenotypic plasticity A single genotype produces different phenotypes depending on the environment plasticity Reaction norm The pattern of phenotypic expression of a single genotype across a range of environments In a sense reaction norms depict how development maps the genotype into the phenotype as a function of the environment all genotypes may not respond to the environment in the same way Plasticity can evolve Rapid change can lead to mismatch between plastic traits and environment Key Concepts Sometimes organisms differ heritably for how they react to environmental situations When this occurs the response themselves can evolve This can lead to the evolution of adaptive phenotypic plasticity Chapter 8 81 Evolution in a Birds Beak Diversity in Darwin s Finches Medium ground finchVariation in beak size influences efficiency at eating different types of seeds Drought resulted in more hard woody seeds Large beaks were favored natural selection natural selection is variable over time Some years big beaks are favored while other years small beaks are favored Key Concepts Beak size influences fitness and is heritable Natural selection can cause change Directional selection favors increase or decrease the mean of a trait Stabilizing selection favors average values of a trait Long term studies reveal fluctuation in direction and strength of natural selection 82 Mice in Black and White Coat color variation affects fitness Light coat color evolved independently in different populations Key Concepts Gene Flow can bring alleles to new locations Alleles may increase or decrease fitness Evolution in response to natural selection is the inevitable outcome whenever three conditions are met individuals differ in their expression of a trait this variation is at least partially heritable and because of these differences some individuals survive and reproduce more effectively than others specific features of the environment can generate natural selection on a trait These agents of election can be even such as storms or droughts or environmental factors like predators or diet 83 The geography of fitness Natura selection can produce variation in time but it can also create variation in space across the geographical range of a population This is known as Gene Flow The amount of gene flow depends on how far individuals move and how far their gametes move It can raise or lower fitness Aposematism an antipredator strategy used by a potential prey item to signal danger or a lack of palatability The most commonly known for of aposematism is warning coloration in which bright coloration of prey that are potentially dangerous can act as a deterrent to potential predators ex scarlet kingsnakes mimic the venomous coral snakes where the ranges of the two species overlap But farther away from these regions the king snakes loo less like the coral snakes Natural selection favors genes for mimicry in the regions of overlap but as these genes flow to other regions they get eliminated Predators that live in the coral snakes territory learn to avoid the bright color pattern But in other regions they are more likely to attack kin snakes with this pattern because they are easy to spot Key Concepts natural selection can lead variation over the geographic range of a species 84 Predators versus Parasitoids When agents of selection act in opposing d ec ons Female gall flies lay eggs into the growing tips of goldenrod a plant that thrives in old farm fields After the eggs hatch each larva bores into the bud tissues to feed The larva secretes fluid containing proteins and other molecules that change the gene expression of cells in the plant The plant cells grow into a bulbous tumor like structure known as a gall that is hard on the outside and soft on the inside Cradled at the center of the gall the gall fly larva can feed on the plants fluids Ga diameter is variable and heritable Stabilizing selection on gall size Woodpeckers feed on goldenrod galls during the winter when old field vegetation has died back and the galls are most visible The find primarily large galls Tiny wasps inject their eggs into the smallest galls The result is a balance natural selection favors flies that produce intermediate gall sizes Key Concepts When agents of selection act in opposition the net effect can be a balance stabilizing selection for an intermediate trait value 8 5 Replicated Natural Experiments 3 spines sticklebacks are small fish that can be marine sticklebacks grow spines and bony plates that protect them from predators While the lake sticklebacks are less armored Low Eda Eda regulates the growth of the lateral armor plates therefore low Eda means little protection allele favored in the freshwater populations Little predation pressure to counterbalance However Low Eda allele present at low frequency in marine environment it was favored when introduced to freshwater Key Concepts Sometimes multiple populations independently experience the same change in their selection environment These populations are ideal for evolutionary studies because they act like replicated natural experiments The nature of the evolutionary response can be observed for each population and compared across the different populations 8 6 Drinking Milk A Fingerprint of Natural Selection The ability to digest lactose as adults found in certain populations Lactase expression persists into adulthood correlates with domestication of cattle Around the time young mammals are weaned they typically stop producing lactase in their guts because they stop drinking milk natural selection should favor this shift since it means that mammals don t waste energy making an enzyme with no advantage Depends on lactase gene To understand how 30 of people ended up with alleles for lactose tolerance we muct realize that humans began to domesticate cattle in europe leading to a dramatic change in their diet Now energyrich milk and milk based foods were available into adult hood Genetic Linkage The physical proximity of alleles at different loci Genetic loci that are physically close to one another on the same chromosome are less likely to be separated by recombination during meiosis and are thus said the be genetically linked Seective Sweep Strong selection can sweep a favorable allele to fixation within a population so fast that there is little opportunity for recombination In the absence of recombination late stretches of DNA flanking the favorable allele will reach high frequency In other words a mutation arose independently in each population that conferred lactose tolerance and then spread rapidly in both continents strong evidence for positive selection on lactase persistence alleles ln cattle herding cultures milk was plentiful and the ability to digest milk brought huge benefits People who could get protein and other nutrients from milk were most likely to survive and to pass on their mutant copy of LCT to their offspring 8 7 Humans as Agents of Selection Humandriven selection had its first huge impact on the world when we domesticated plants and animals 10000 years ago Artificial selection on wild cabbage resoled in the evolution of diverse plant forms including broccoli kale etc gradual increase in cob size documented by archaeologists Domestic dog diversity created in last 15000 years Chemical warfare When humans domesticated crops they created a new food supply not only for themselves but also for huge hordes of insects farmers had ridiculous ways to fight off insects It only takes a few years for resistance to a new pesticide to emerge rapid evolution of herbicide resistance Creation of refuges can slow the evolution of resistance Bt crops select for resistance in pests It comes at a cost when Bt is not present Creation of Bt free refuges favor Bt susceptibe insects Slows evolution of resistance Refuges are now required by law Altered Environments and invasive species introduced cane toads to australia they have expanded rapidly and are evolving to smaller body sizes in these new habitats The native snakes are killed by toxins in skin glands of cane toads and these predators also are evolving rapidly in response to this introduced species In response the snakes are getting larger to lower the concentration of toxin in the cane toads when they eat them Also smaller gape widths evolved making it harder to swallow the bigger toads which are also the most toxic and thus most likely to kill the snakes Hunting and Fishing as agents of Selection Evolution of shorter male horns due to hunting unnatural selection because hunters want big horned big bodied sheep Same goes with the atlantic cod They re body sizes are decreasing Key Concepts The speed of evolution depends on the amount of genetic variation and strength of the selection An understanding of evolutionary biology can lead to novel management practices which slow the evolution of resistance in populations Chapter 9 91 Coalescing Genes Molecular phylogenies are similar to morphological ones They compare homologous characters in a group of organisms to reconstruct their relationships In the case of molecular phylogenies the characters might be the presence of adenine in a certain gene genetic loci have their own genealogy The phylogeny shows a mutation where the ancestral state of G changed to T This derived allele is then transmitted on through that lineage GampT come from a common ancestor Alleles in populations coalesce to a common ancestor Coalescence The process by which looking back through time the genealogy of any pair of homologous alleles merges in a common ancestor time varies for different genes Coalescence process takes can vary a great deal It depends on factors such as whether alleles are under selection which can accelerate their rise in frequency The size of a population plays a role as well since it takes longer for drift to fix an allele in a big population Selection any natural or artificial process that results in differential reproduction among the me mbers ofa population so that the inheritable traits of only certain individuals are pass ed on or are passed on ingreater proportion to succeeding generations Key Concepts It is possible to trace the genealogies of genes back through time reconstructing when mutations generated new alleles and how these alleles subsequently spread 92 Gene Trees and Species Trees During speciation alleles will be passed from generation to generation accumulating mutations and forming branched genealogical lineages known as gene trees Gene tree The branched genealogical lineage of homologous alleles that traces their evolution back to an ancestral allele Gene trees do not always match species trees Key Concepts Gene trees and species trees do not always match data from multiple genes used in phylogeny construction 93 Methods of Molecular Phylogenetic Building a phylogeny with genetic data Each nucleotides a potentially informative character Homoplasy is common separate lineages can independently arrive at the same character state thus not part of the same phylogeny Morphological Homoplasy such as the hydrodynamic shape of dolphins and tuna is often the product of mutations to many interacting genes Molecular Homoplasy can evolve much more easy since DNA can exist in only 1 of4 states the probability that separate lineages will independently arrive at the same character state is high Maximum parsimony A statistical method for reconstructing phylogenies which identifies the tree topology that minimizes the total amount of change or the number of steps required to fit the data to the tree The tree with the fewest number of steps is the most parsimonious Purifying selection removes deleterious alleles from a population It is a common form of stabilizing selection Genes differ in rate of evolution slowly evolving genes useful for distantly related species rapidly evolving genes used for closely related lineages Common Methods maximum parsimony simplest explanation favored Distance matrix reconstructing phylogenies by clustering taxa based on genetic distance neighborjoining a distance method in which scientists pair together the two least distant species by joining there branches at a node maximum likelihood finds out most likely tree given specific model of molecular evolution Bayesian method looks at probability that a tree is correct given a specific model of molecular evolution Key Concepts phylogenetic trees are hypotheses that are constantly reevaluated when new data become available 94 Experimental phylogeny Experimental phylogenetic s validates methods Key Concepts Because constructing phylogenies and science more broadly is often a process of evaluating evidence scientists often test the effectiveness of the methodologies used to draw conclusions 9 5 Four case studies in molecular phylogeny 1 Tetrapods originated from obe finned fishes lungfishes are most closely related DNA proved 2 Humans evolved from extinct hominids 100000 closest relative lucy African ancestry Mulitregional model hominids across Old World were a single species connected by gene flow local adaptation Out of Africa modelall humans are derived from recent african ancestry most suppo ed 3 Darwins finches Only one does not live in galapagosz Cocos finch explanation they did not evolve from another species cocos finches most likely evolved from Darvvin s finches after migrating from the Galapagos Island Colonization most supported monophyletic clade 4 HIV 33 million effected came from lentiviruses which effect mammals closely related to strain that effects monkeys and apes not a monophyletic clade different viruses have different origins 3 separate introductions from chimps 9 6 Natural Selection versus Neutral Evolution Besides solving mysteries about taxa phylogenies also help scientist answer broad questions about evolution Such as how much of lives diversity can be explained by evolutionary mechanisms other than selection synonymous Substitutions Mutations that do not alter the amino acid sequence of a protein Because these mutations do not affect the protein an organism produces They are less prone to selection and often free from selection completely doesn t change protein Evolve at a neutral rate Replacement substitutions Mutations that alter the amino acids sequence of a protein These can affect the phenotype are are therefore more subject to selection faster evolution than synonymous sites indicate positive selection slower evolution than synonymous sites indicates purifying selection Motoo Kimura produced the first formal neutral theory of molecular evolution He said that most evolution at the molecular level is neutral due to drift neutral substitutions should accrue in a clock like fashion different types of DNA should evolve at different rates The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variability within species are not caused by natural selection but by random drift of mutant alleles that are neutral or nearly neutral The essential part of the neutral theory is not so much that molecular mutants are selectively neutral in the strict sense as that their fate is largely determined by random genetic drift more distantly related two species were the more mutations had accumulated in each lineage since they split from a common ancestor mutations became fixed in the lineages with almost clock like regularity rates of evolution in different types of DNA does differ The precise relationship between natural selection and neutral election is a complex one that scientists are still exploring But it is clear that neutral evolution has played a major role in how genomes got to the way way they are today Molecular ClockA method used to determine time based on base pair substitution Molecular clocks used the rates of molecular change to deduce the divergence time between two lineages in a phylogeny There are two peaks in mammalian diversification rates one was after the mass ex nc on estimate date of common ancestor can be used to estimate diversification events Signature of positive selection the accumulation of an unusually high level of substitutions that change the structure of proteins Synonymous substitutions alter a condon without changing the amino acid it encodes Replacement substitutions change the amino acid and potentially change the way a protein functions Scientists can look for evidence of selection by comparing substitutions of different genes Replacement substitutions in the this gene lowers the fitness of organisms so they are lost from populations however positive selection acquires replacement substitutions that raise fitness They are favored Molecular data allows scientists to detect natural selection that took place millions of years ago FOXP2 what makes us human language gene Key Concepts The neutral theory of molecular evolution describes the pattern of nucleotide sequence evolution under the forces of mutation and random genetic drift in the absence of selection Under these conditions the rate at which one nucleotide replaces another in a population should equal the rate of mutation at that site regardless of the size of the population The neutral theory predicts that neutral mutations will yield nucleotide substitutions in a population at a rate equivalent to the rate of mutation As long as mutations rates remain fairly constant through time neutral variation should accumulate at a steady rate generating a molecular signature that can be used date events in the distant past clock like fashion Both positive and purifying selection leave distinctive signatures in nucleotide or amino acid sequences that can be detected using statistical tests 9 7 Deciphering the Genome Genome alignments reveal conserved elements with important functions Sometimes genome comparisons can reveal new members of gene families that previously went undetected Scientists have identified some of those genes that control lipid levels by studying people with high and low levels of lipids searching for genetic markers that tend to show up in each group Mice have the same gene cluster Chapter 10 101 Innovation in Our Own Time Novel Traits Traits that arise not inherited from an ancestor within a lineage and have no obvious counterparts in related lineages Complex Adaptations They are novel traits that require multiple mutations to achieve a fitness advantage The ability to consume citrate Influenced by many environmental and genetic factors Involved in complex adaptations Hox Gene Gene duplication paralogs can produce novel functions One copy can continue to perform the genes original function while the other is free to evolve ex Promiscuous proteinsable to carry out more than one function Gene duplication and snake venoms After studying venoms Fry made a tree and realized that on one of these trees was a muscle destroying venom that reveals that the closest relatives of this are defensin genes which are found in the immune system to fight infections Gene duplication produced extra copies of the gene which became specialized for attacking different pathogens in the pancreas Todays snakes inherited these duplicate genes and one of them had a mutation that let them produce poison in their mouths Rose to an entire family of venomous snakes Key Concepts Venom evolved before snakes themselves Promiscuous proteins are often the starting point for novel traits Novel traits can arise when existing genes are expressed in new developmental contexts recruitment or co option Duplicated genes accumulate mutations rapidly because they are released from purifying selection Novel traits can evolve from duplication and co option of proteins involved in other functions 103 The Genetic Tool Kit Hox genes are part of a conserved genetic toolkit Development of each species is controlled by homologous Hox genes Dorsal ventralpatterning is conserved Fly legs and mouse legs patterned by same genetic cascade Expression differences in single gene give rise to limbs elongation These genes are orthologs Changes in limb patterning pathway result in limb loss Blocking of the Sonic hedgehog gene the vertebrate ortholog of the insect gene Hh can truncate activity of the limb patterning and block growth of the limbs Mutatn mice develop with only short stubs and humans are limbless interruption of the limp patterning pathway led to the evolutionary loss of legs in snakes There forelegs were lost due to Hox genes extended in the Trunk region Hind legs were lost due to Sonic hedgehog gene Gene expression changes in adaptive radiation Key Concepts Hox genes and other patterning genes participate in regulatory networks that demarcate the geography of developing animalsThese networks comprise an ancient genetic toolkit inherited by all animals with bilateral body symmetry Blocking or interrupting a patterning pathway can result in complete loss of a structure subtle expression changes can dramatically alter phenotypes 104 Recycling Networks Mutations to gene networks can produce additional appendages Types of mutations Truncate block pathway bocks growth eg loss Changes signal levels changes shape of structure cricket legs Deploy in new body region form outgrowth beetle horns Deploy at new time or stage new pattern elementeyespots Evolution of feathers 1Shh establish dorsal ventral polarity in epidermal cell thats will grow a shingle like scale 2genes began expressed a 2nd time after placed had formed 3 keep overlapping 4growth of feather tube 5feather peel open into branches 6gene expression caused the slits to form at an angle Key Concepts Changes in the timing and location of expression of developmental genes can alter the shape or properties of a structure 105 Evolving Eyes Complex eyes have evolved in several lineages All animal eyes capture light with cells known as photoreceptors Shapes of these photoreceptors take very different forms in different clades When light enters your eye it strikes a molecule known as opsin Opsins sit on the surface of photoreceptor cells Photons trigger chemical reactions that cause photoreceptors to send electrical message towards brain Copsins present in the common ancestor of all living vertebrates opsins evolved from serpentine proteins opsins evolved 650 million years ago crystains evolved through gene recruitment helped focus images Hypothesis for evolution of the vertebrate eye chordateeye spot expressing photoreceptor genes light sensitive regions bulge outward to the sides of the head now has opsins forms optic cup and retina lens evolve ability to focus an image eyes become spherical 106 Constraints on adaptation Law of physics Pleiotropy beneficia effect on one trait but a harmful one on another Antagonistic pleiotropy Almost all mammals have 7 vertebrate mutations that would lead to more or fewer cervical vertebrate may have deleterious effects as well Key Concepts Contraints on evolution arise when one evolutionary trajectory is more likely than another Genetic variation may be lacking because the resulting phenotypes are unsuccessful can t survive Antagonistic pleiotropy can constrain the direction of evolution because it causes some phenotypes to be unsuccessful 10 7 Building on History imperfection in complex adaptions They are not perfect laryngeal nerve 108 Convergent Evolution Convergent EvolutionThe process by which similar traits evolve in unrelated lineages Examining traits that converge can shed light on how each lineage arrived at the shared phenotype the genetic and developmental underpinning of similar adaptations It can reveal multiple solutions to a common challenge as well as the limitations imposed by history within each lineage Paraelism Convergent evolution that arises through mutation of the same genes Deep Homologytraits in different lineages arise from same inherited regulatory networks QUESTIONS 610 chapter 6 1lf two individual mate one of them heterozygous at a locus and the other homozygous for a recessive allele at the same locus what will be the outcome The offspring will be either heterozygous or homozygous for the recessive allele 2 The HardyWeinburg theorem is an important mathematical concept because It demonstrates that in the absence of outside forces allele frequencies of a population will not change from one generation to the next 3 Which population would be most likely to have allele frequencies in Hardy Weinburg equilibrium A large population that is currently not evolving 4 Which of these statements is NOT true about genetic drift Genetic drift happens faster in large populations than small ones 5 A genetic bottleneck in a population often results in what Loss of alleles loss of genetic diversity an increase in genetics drift 6 What do population geneticists mean when they refer to the fitness of an allele The contribution of an allele to a genotypes relative success at producing new individuals 7 When will an allele with a higher fitness than any other allele at the same locus become more common depends on both the strength of the selection and the population size 8 If a mutation that produces a new deleterious allele arises in a population what ill most likely happen to that frequency of that allele Depends on the alleles effect on phenotypes if the allele is recessive drift will determine and the allele will be rare enough that it is almost never expressed in a homozygous state 9 Which of these statements about balancing selection is true It is responsible for maintaining the S allele for sicklecell anemia within humans 10 Which of these statements about inbreeding is true Inbreeding is not a mechanism of evolution can effect the finiteness of individuals but not necessarily alter allele frequencies is a concern of conservation biologists and inbreeding increases the probability that two alleles at any locus will be identical by descent Chapter 7 1 Why does the variation of phenotypic traits often have a continuous distribution Because phenotypic traits are often polygenic 2 Which of these statements about narrow sense of heritability h2 is true The numerator of narrow sense heritability includes only the additive effects of the alleles 3 The breeders equation incorporates two of the conditions Danivin identified with that must be met for evolution by natural selection to take place Which 2 Differences in phenotypes that influence the probability of survival or reproduction s and the differences in phenotypic traits that must be at least partially heritable h2 4 If age of sexual maturation is a phenotypically plastic trait what relationships would you expect to find Environmental conditions such as nutrition affect the age at which individuals begin reproducing 5 Which of the following can be the result of evolution A decrease in the heritability of a trait and a change in the interaction between genes and the environment 6 Which of the following is an example of the process of evolution A population of snowshoe hares having a different frequency of alleles than the previous generation Chapter 8 1 How did Sacha Vignieri and Hopi Hoekstra test whether coat color affected old field mouse fitness They used dark and light models of mice to determine predation rates in forest and beach habitats 2 If gene flow were eliminated between northern and southern portions of the scarlet king snakes range what do you predict would happen to the frequency of alleles that produce a coral snake like pattern The frequencies of the alleles would decrease in the northern part of the range 3 What are extended phonotypes Phenotypes that are shared by multiple generations 4 How do selective sweeps on an allele affect flanking stretches on DNA Flanking regions are the same in many individuals in the population 5 Which is not a potential agent of selection Genetic drift 6 What is the best course of action for a farmer who wants to slow the evolution of resistance of a pest population feeding on his crops Allowing some nonresistant pests to survive 7 What is the likely reason for city populations of a plant to produce more non dispersing seeds than plants in the country side City plants with genes that make seeds drop are more likely to reproduce successfully 8 Which of these statements about selection is false selection in mammals always operates more strongly on surveil than on reproduction 9 What is the most likely reason that lactose tolerance alleles selectively swept through certain human populations Lactose tolerance had a large effect on survival Chapter 9 1 Why is understanding coalescence important when developing molecular phylogenies Because scientists can sample only a limited portion of the history in any allele 2 Experimental phylogenies are important for reconstructing phylogenetic trees because they allow scientists to make predictions about evolution and test them to examine the statistical hypotheses generated by different methods of phylogenetic tree reconstruction and to examine how restriction enzymes recognize different DNA sequences 3 Molecular phylogenies indicate that the Same mutation evolved in three separate lineages of HIV in each instance it improved the ability of the virus to infect humans 4 The theory of neutral evolution describes The rate of mutation at a site in the absence of selection regardless of the size of the population 5 Which of these is a true statement about molecular clocks they use neutral theory to date events within a phylogeny they can be calibrated using fossils of known age and are affected by the segments of DNA being examined and relative sizes of the populations 6 When KagtKs then Scientists would reject the null hypothesis of neutral evolution because the number of replacement substations is greater than expected Chapter 10 1 How do novel traits arise Through mutation leading to new phenotypes 2 What is a paralog A gene that has taken on a new function through gene duplication 3 Which process allowed sphingobium bacteria to break down toxic PCP Protein promiscuity 4 Which process led to the evolution of snake venom Gene recruitment natural selection and gene duplication 5 What is an ortholog Two genes in two different species that serve the same function and were inherited from a common ancestor 6 What do you predict would happen to the hind legs ofa fly if the gene Dpp were artificially over expressed The legs would grow longer 7 What role does Bmp4 play in the expression of finch beak phenotypes It is regulatory gene that turns on many other genes 8 Which of the following statements is true about evolution of feathers The development of feathers uses all the same genes that are used in the development of scales 9 Which organism does not use crystalline in its eyes to focus light rag worms 10 What is Not an example of antagonistic pleiotropy mutation that confer resistance to Bt also make insects more vulnerable to natural plant defensive chemicals 11 Why do giraffes have a recurrent laryngeal nerve that is 19 feet longer than it needs to be The route of that nerve was inherited from their ancestors 12 What do you predict would happen if you inserted a pax 6 gene from a mouse into the genome of an octopus extras eyes would develop but with octopus crystalline Chapter 11 111 Sex Mechanisms of reproduction are diverse Heterogamous 2 sex chromosomes determines if your male or female Hermaphroditic An organism is both male and female Sequential protogynus 1st female then male or protandrous male first Simutaneous both at same time ex Slug Parthenogenic Only females reproduce themselves Asexual reproduce themselves Why bother with sexual selection Twofold cost of sex If you are asexual reproducer you would be female You would always produce offspring that were female and they would reproduce only female If your a sexual reproducer you may produce a male If a male is produced then he has to find a female Only have a 14 of what you would have if you were a asexual female Asexual lineages multiply faster than sexual lineages because of all progeny are capable of producing offspring In sexual lineages half of the offspring are males who cannot themselves produce offspring This effectively halves the rate of replication of sexual species Mullers Ratchet The process by which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner Disadvantages of sexual twofold cost search cost reduced relatedness risk of stds Advantages of sexual Combining beneficial mutations generation of novel genotypes faster evolution clearance of deleterious mutations Sex creates new genotypes that can pass on beneficially Red Queen effect For coevolving populations to maintain relative fitness each population much constantly adapt to the other Arms races makes sex beneficial Resilient to parasites Persistence of asexual reproduction in Bdelloid rotifers 400 species of invertebrates that live in freshwater All female They can enter a state of metabolic dormancy and complete dehydration that can rehydrate Enter dormant phase during difficult conditions horizontal gene transfer shedding of parasites Key Concepts Sex is the combining and mixing of chromosomes during offspring production Hermaphrodites that self fertilize reproduce sexualy but do not create genetic vana on In models a strategy is a method of maximizing fitness that is contrasted with alternative methods Sex creates new genetic variation by mixing parental alleles The red queen effect has been used to explain the advantages of sex and constant coevolutionary arms races Ecological situations that require rapid evolution are likely to favor sex Asexual lineages have evolved mechanisms that compensate for lack of sex 112 Sexual Selection Anisogamyresults in differential investment in reproduction invest more in eggs than sperm Limitations on reproductive success differ for the sexes females are limited by fecundity eggs are few and expensive males are limited by the number of mates they can obtain lnvestment differences can extend past fertilization Uncertain paternity may explain why male parental care is rare Females have certain paternity Males dont parental care could be directed toward offspring not their own 113 The rules of Attraction Asymmetrical parents care alters operational sex ratio ratio of males to females capable of reproducing at a a given time slower rate of reproduction by females leads to male biased operational sex ratio Sexual selection differential reproductive success resulting from competition for mates intrasexual selection big muscles intersexual female picks some aspect of male sexual selection typically stronger on males maximize fitness by mating multiply males biased osr Sexual Dimorphic result from sexual selection Ornaments attractive traits that increase mating success note that ornaments can serve as handicaps Armaments weaponry used to outcompete other individuals Mae male competition leads to extreme variance in reproductive success competing for mates is costly Males may also compete for territory Benefits of female choice Direct benefits benefit the female directly ex food nest sites protection Femaes may benefit from cannibalism ex red back spiders Femaes choose flashy males to know that they are healthy female preferences are often consistent Development of weapons in males can involve trade offs Indirect benefits benefits that affect the genetic quality of the female s offspring Increase the fitness of the offspring 114 The evolution of mating systems Types of mating systems Monogamyone male pairs with one female sexual partners mate with each other exclusively social partners pair but may cheat Polygyny males mate with multiple females Polyandry females mate with multiple males Polyandry selects for male traits that increase paternity 115 Sperm Wars Sperm CompetitionA form of sexual selection that arises after mating when males compete for fertilization of femae s eggs Sperm competition drives evolution of larger testes Deer Mice A males sperm will join together to form aggregates that can swim faster together than they can individually The sperm can recognize other sperm from the same male so that the can preferentially aggregate with their kin Key Concepts When females mate with multiple males sperm from the different males must compete for opportunities to fertilize the females eggs 116 Sexual Conflict and Antagonistic Coevolution Sexual conflict results in antagonistic coevolution Sexual conflict traits that confer a fitness benefit on one sex but cost to the other Sexual conflict in ducks When male ducks cannot find a mate they harass other taken female ducks until they die Key Concepts Sexual conflict leads to antagonistic coevolution between males and female To Sum It Up Sex is widespread in nature but its success is puzzling due to the twofold reproductive cost it induces Benefits that outweigh this cost include allowing populations to adapt faster or keeping deleterious mutations from accumulating The Red Queen effect predicts an evolutionary arms race between hosts and their parasites because hosts have to evolve defenses at a rapid rate just to survive in the presence of parasites Although sexual reproduction may be one adaption that creates variation among individuals several adaptations in asexual bdelloid rotifers have evolved that confer similar advantages Females typically invest in limited number of eggs while males can produce vast numbers of sperm This imbalance explains most of the difference in the sexes in many species In many species males compete with rival males for access to females intrasexual selection In many species females choose males based on displays songs and other forms of courtship intersexual Females stand to gain directly by choosing males that provide food or protection as well as indirectly by choosing quality males In many species females have been shown to prefer males with certain traits over others Those traits in some cases signal good genes in the males Females in many species mate with more than one partner As a result sperm competition has evolved among males in these species Conflicts of interest over the control of fertilization can result in antagonistic coevolutionary arms races between males and females Chapter 12 After Conception 121 Selection across a Lifetime Life history theory explores how the schedule and duration of key events in an organisms lifetime are shaped by natural selection It helps explain variation in the age at which organisms begin reproducing the size and number of offspring produced the amount and type of parental care invested and the onset of senescence Some mutations that are beneficial in one context are harmful in another Antagonistic pleiotropy plays an important role in selection on mutations that affect an organisms life history eg a mutation that is beneficial early in life but then harmful later in life Since fitness effects are bigger earlier in life it may be favored by natural selection despite the harm it causes in old age Evolution of life history traits Life history traits involved in trade offs Limited amount of energy to invest in survival maintenance and reproduction Natural selection expected to optimize in light of tradeoffs Maximize number of offspring surviving to maturity Also depends on likelihood of survival to different age classes Data from opossums supports predictions from life history theory A female opossum during the course of her life has several litters She could potentially increase her fitness by giving birth to larger litters But larger litters require more resources from her during both pregnancy and nursing If she can t find enough food or resources to nurture her extra young They could die Now consider a female who does the opposite She gives birth to only a few small litters because fewer offspring require fewer resources she would be able to rear much healthier offspring and put herself at less risk than if she produced big litters But producing too few may mean a decline in her relative fitness because others would outbredd her Predation risk drives life history evolution in guppies Ones that do not face predators grow up slowly and females produce large offspring but few offspring per litter lfthey have predators the males are ready to mate much earlier than the males that are predator free and females produce twice as many offspring and are much smaller Key Concepts Tradeoffs arise when investment in one trait result in lower investment in another trait Investment in reproduction is often at the expense of investment in growth or maintenance Selection may favor alleles that are beneficial early in life even if they are deleterious late in life Investment in early reproduction ofter reduces reproduction late in life 12 2 Parental Investment Females are more likely than males to provide parental care Males have less investment Males have uncertain paternity Sex role reversal Females compete over access to males female jacanas lay their eggs with males near by and then abandon them The male protects the eggs and later the chicks Because females abandon their eggs and males take on parental care females are able to recycle faster than males pipefishmales get pregnant Adjusting the family Organisms may regulate the number of offspring to maximize fitness miscarriage cannibalism Organisms may regulate the sex ratio to maximize fitnesslf a female is in poor condition she may be better off having more daughters than sons Why are sex ratios often balanced production of each sex favored when rare rare sex has more mating opportunities TriversWillard hypothesis Mothers alter sex ratio depending on condition If a males in good condition males likely to benefit more from being large Females are favored with high resources Up to three helping daughters is beneficial Males favored with low resources disperse away from poor habitat Male birds tend to fly away from their natal home in search of other female and other territories Fig wasps produce female biased sex ratiosMales mate with sisters a singer male can inseminate multiple females Unfertilized eggs envelop into males and fertilized eggs develop into females Females can directly manipulate the sex of their offspring simply by fertilizing or not fertilizing there eggs Some species switch sex in predicted manner They start as females but switch to males when they are large Genomic imprinting Gene expression silenced by methylation by one parent Methylation The process by which methyl groups are added to certain nucleotides Methylation alters gene expression thereby reducing or eliminating the production of proteins or RNA molecules Genomic imprinting and parental conflict Fathers favor more investment in current offspring future offspring not likely to be his Mothers favor less investment than father saves it for future reproduction Key Concepts Females generally benefit more than males from providing parental care exceptions provide exciting tests Frequency dependent selection can lead to balanced sex ratios Predictions of the TriversWillard hypothesis produce females in poor condition Males in good condition Parental care is often rife with conflict sexes may maximize fitness differently Males benefit when mothers invests more in current offspring females benefit by saving resources for future offspring parental conflict can lead to battle of gene expression in offspring 123 Searching for immortality genes Senescence The deterioration in the biological functions of an organism as it ages Postponing senescence Calorie restriction can slow the aging process Genes involved in repair switched on under stress May involve tradeoffs Worm mutants that age more slowly have lower fitness Key Concepts Senescence results from a trade off between reproduction early in life and longevity 124 Menopause Why do Women stop having kids Menopause may be adaptive Older females benefit from rearing current children or helping rear grandchildren Menopause may be a life history trade off Other species also have post reproductive lifespan May be more common than currently known To Sum It Up The timing and duration of key events in an organisms lifetime are traits that can evolve through natural selection Trade offs can arise when the timing of one event such as age at first breeding reduces the duration of another even such as life span The number of offspring that females produce and the timing of their reproduction are also subject to selection When males invest more resources into offspring than females do the sex roles can reverse supporting sexual selection theory Females in some speices adjust the ratio of songs to daughters Males and females each have optimal strategies for reproductive success Sometimes those strategies come into conflict as when birds abandon a nest to find another mate Conflict between parents have been involved to explain the evolution of gene imprinting As a result of life history trade offs the biological functions of an organism change as the organism ages Unlike other primates human females experience menopause Whether menopause is adaptive or the result of life hisotry trade offs is still up for debate Chapter 13 Origin of Species 131 What is a species 3 Concepts of what is a species Phylogenetic species concept Species are the smallest possible groups whose members are descended from a common ancestor and recognizable by unique derived traits Biological species concept Species are groups of interbreeding populations that are reproductively isolated from other such groups General lineage species concept Species are metapopulations that exchange alleles frequently enough to comprise the same gene pool Metapopulation A group of spatially separated populations of the same species that interact at some level 132 Barriers to Gene Flow Keeping Species apart For sexually reproducing species to remain distinct they require isolating barriers to block gene flow with other species Barriers emerge and drive species to evolve into two separate species SpeciationThe evolutionary process by which new species arise Speciation causes one evolutionary lineage to split into two or more linages Isolating barriers Geographic Barrier Extrinsic properties of landscape that prevent gene flow Elk and Red deer mate in the zoo but they do not mate in the wild are they two different species or nah Allopatry Occurs when populations are in separate non overapping geographic barriers to gene flow Reproductive Barrierfeatures of organisms that prevent interbreeding Few or no genes are exchanged between the population eg fruit flies that lay eggs on blueberries won t mate with fruit flies that lay eggs on apples Also time can create a reproductive barrier SympatryOccurs when populations are in the same geographic area Premating Barrier Pollinator isoation many species depend on pollinators such as bees and birds to carry pollen the male gamete to other plants where it can fertilize the female gametesA breed of monkey flowers evolved to where bees and hummingbirds pollinate it Since the two had different pollinators they were never crossed bred even though they are so closely related Mismatched MorphologyTwo species of beetles have overlapping ranges One factor allowing them to live in sympatry is their differently shaped sexual organs The male genitalia developed differently shaped copulatory pieces The female beetles have sexual organs that can accommodate the copulatory pieces of males of their own species But the can be injured if they mate with males of other species Postmating prezygotic Barrier Gamete incompatibility occurs when sperm or pollen from one species fails to penetrate and fertilize the egg of another species In many species the male cannot simply deliver his sperm and leave He must engage in a copulatory courtship Some have to have the right frequency to mate If a male from a different speices carries out the wrong copulatory courtship while mating then she is less likely to fertilize her eggs with the sperm he has deposited inside her Postzygotic Barrier Happens after the fertilized zygote from successfully developing and reproducing themselves Embryos with two species for parents may fail to develop Some hybrids do develop successfully but may have deformities that leave them in poor health or become sterile Hybrid inviabilityHybrids die before or shortly after birth Hybrid sterility Hybrids suffer problems in the reproductive system or gametes Ecological inviabilityHybrids develop normally but they suffer lower viability because they cannot find an appropriate ecological niche Behavioral sterilityHybrids can produce normal gametes but cannot obtain mates LOOK AT CHART page 401 Key Concepts Geographic barriers to gene flow physically separate populations Important for all species concepts Reproductive barriers are intrinsic features of organisms that reduce likelihood of interbreeding geographic barriers are most common Separation of populations in space and time reduces interbreeding habitat preference timing of reproduction Divergent floral traits can cause pollinator isolation and reduce interbreeding Molecular incompatibilities between gametes can proven interbreeding Genetic incompatibilities can be important barriers to gene flow between populations if they cause hybrid offspring to be sterile or to perform poorly 133 The origin of isolating barriers how new species form The many different isolating barriers in nature help keep sexually reproducing species distinct But these barriers had to come from somewhere They either result from changes to the landscape that keep populations apart or they emerge she populations evolve and in the process become less and less likely to interbreed Allopatric speciationls the result of geographical isolation A Here a population begins with the continuous geographical range it contains genetic variation but gene flow ensures that new mutations can spread across the range once they arise B A river dives the population into two subpopulations C They change of allele frequencies in the two subpopulations is no longer linked they become increasingly divergent D The river later dries up allowing the two subpopulations to make contact During their separation reproductive barriers may evolve reducing the gene flow between the two subpopulations no longer can mate Ring SpeciesA connected series of populations each of which can interbreed with its neighboring populations that have diverged so that the populations at the ends of the series are too different to interbreed eg greenish warblers originally evolved sour hot the himalayas They later spread eastward and westward along obtain range and then expanded their range north Today ornithologists recognize six subspecies of these birds The populations of warblers have diverged in male song pattern and female preferences for those patterns Populations are also more genetically distant the farther they are from each other around the wing Speciation in sympatry flies named Rhagoletis in the US forms two sympatric but genetically distinct populations One lives on hawthorn trees one lives on apple trees The two races are specialized for their particular fruit Apples and hawthorns blossom at different times of the year and so they cannot mate This happened because english colonists brought apple trees with them to america Ecological speciationEvolution of reproductive barriers due to adaptation to divergent environments ex Danivin s Finches Key Concepts Populations become allopatric when new geographic barriers arise New species can form when geographic barriers arise Isolation by distance occurs because individuals tend to mate with individuals from the same or nearby populations Ring species demonstrate how species can form even with some gene flow Reproductive isolation can arise eve non sympatry because individuals in different subpopulations rarely interbreed Ecological speciation can lead to speciation in sympatry Reproductive isolation can arise as a byproduct of adaption to divergent environments 134 The speed of speciation Aopoyploidy polyploidy more than two paired chromosomes resulting from interspecific hybridization if polyploidy arises within a species its called autopolyploidy Can lead to extremely rapid speciation Key Concept The speed of speciation is highly dependent on the genetic architecture of organisms In plants mutations such as duplication events are common As a result interspecific hybridization and allopolyploidy can generate new speices rapidly In birds and mammals however reproductive isolation can take millions of years 135 Uncovering hidden species Giraffes form 6 separate species according to the phylogentic species concept Giraffes are choosing to mate only with other giraffes having the same pattern 13 6 The puzzle of microbial species Bacterial species often defined by specific adaptations Bacteria cannot be divided into species by using the same rules that work for animals A different way to define bacterial species is based on the way they are adapted to narrow ecological niches Horizontal Gene Transfer any process in which genetic material is transferred to another organism without descent Horizontal gene transfer in E Coli Scientists discovered that e coli only share a limited core of genes only 6 on the genes shared by all of the strains Key Concepts ultimately species concepts are human artifacts Methods for recognizing species continue to improve To Sum It Up Naturalists began classifying organisms into species before Danivin developed his theory of natural selection Speciation is the evolution of new species No single definition of species currently applies to all taxa The phylogentic species concept focuses on the phylogentic history of the organisms and the biological species concept on reproductive isolation The general lineage species concept emphasizes the frequency of allele exchange among metapopulations of organisms Gene flow can be interrupted by geographic and reproductive barriers Populations can be physically separated from each other by features of the environment and intrinsic properties of the organisms themselves can reduce the likelihood of interbreeding Reproductive barriers can evolve between populations isolated by space or time pre zygotic reproductive barriers reduce the likelihood that a zygote will form either before mating or before fertilization Pos tzygotic reproductive barriers prevent fertilized zygotes from successfully developing and reproducing themselves Allopatric speciation occurs when geographically isolated populations evolve independently as a result of drift mutation and different selection pressure Speciation can also take place without geographical isolation Ring species sympatric speciation and allopolyploidy are examples Complete reproductive isolation can take millions of years to evolve between two species of birds for example But in plants allopolyploidy can lead to new species quite rapidly Genetic studies sometimes reveal that what appears to be a single species may be several giraffes Species of bacteria and archaea are difficult to identify using concepts developed for sexually reproducing species Chapter 14 Macroevolution 141 Microevolution and macroevolution Microevolutionevolution occurring within populations including adaptive and neutral changes in allele frequencies from one generation to the next Occurs so rapidly that scientists can watch traits change from generation to generation and link the gene mutations that lead to the differences Scientists can also measure the strength of selection this gives them the opportunity to conduct controlled experiments providing powerful tests of evolutionary hypotheses Macroevoution evolution occurring above the species level including the origination diversification and extinction of species over long periods of evolutionary time Cannot be observed because scientists don t live for millions of years They instead explore the evidence left behind eg fossil record molecular clocks How it shapes the diversity of life lnterpay between speciation and extinction determines diversity D1 diversity orginations extinctions D2 new diversity We can calculate rates of origination and extinction The origination and extinction rates in a clade determine the total diversity at any given time This is known as Standing diversity If more species originate then become extinct the standing diversity will increase Diverse taxa have higher origination rate than extinction rate The total number of ordinations and extinctions in a given interval of time is known as a Turnover Extinction rate often tracks origination rate Diversity can decline when extinction increases or origination decreases Drop in the origination rate contributed to dinosaur extinction Key Concepts Extinction occurs when the last member of a clade dies The clade may be a single species or a higher group Mass extinction in a clade can have two causes Drop in origination rate or increase in extinction rate 142 Biogeography Mapping macroevolution BiogeographyThe study of the distribution of species across space and time Environmental conditions such as climate alone could not completely account for the distribution of species Biodiversity has complex geographical patterns The tropics have a higher density of species of vascular plants that the higher latitudes do When Danivin and Wallace first investigated biogeography the only way they could evinsion species getting where they are now was through dispersal DispersalThe movement of populations from one geographic region to the other eg birds flying to islands elephants walking over mountain ranges As geologists learned more about how the surface of the Earth changes it became clear that the formation of barriers can also shape biogeographical patterns this process is known as vicariance VicarianceThe formation of geographic barriers to dispersal and gene flow resulting in the separation of populations One of the most important ways that vicariance occurred was through plate tectonics lfa land mass breaks apart the lineages that live on it can become separated The most closely related clades should be found on the most recently separated landmasses This phylogenetic comparison of landmasses is called an area phylogeny Area Phylogeny A phylogenetic tree that relates the ordinations of lineages to each other Area phylogenies can be used to examine the approximate times when lineages separated by replacing the species names in a taxonomic phylogeny with the names of places where taxa of interest either live or lived Marsupials evolved through a mix of vicariance and dispersal Key Concepts Biogeography is a multidisciplinary field that explores the roles of geography and history in explaining the distribution of species 143 Measuring diversity through time Measuring diversity through time is a challenge because 1 paleontologists have found only a tiny fraction of all the species that ever lived 2 determining species from fossils alone like organ taxaa group of fossils of a particular part of an organism such as leaves or seeds whose parent organism remains unknown because the fossils were preserved unattached to the rest of the individual Three Evolutionary Faunas Cambrian fauna arose at the beginning of the paleozoic and quickly declined Dominated by trilobites inarticulate brachiopods and coil shelled mollusks The paleozoic fauna arose in the ordovician included coral crustaceans mollusks and others The modern fauna has its roots in the cambrian but came to dominate the planet 250 million years ago included clams and snails Caveats to diversity studies Most taxa studied are not species Assignments to higher taxonomic groups somewhat arbitrary Phylogenetic relationships among groups uncertain Large Scale Patterns may obscure interesting regional patterns 144 Adaptive Radiations When Alpha eclipses Omega Adaptive radiationsEvolutionary lineages that have undergone exceptionally rapid diversification into variety of lifestyles or ecological niches eg Hawaiian honeycreepers Adaptive radiations can often be recognized from phylogenies when parallel lineages of the same age differ strikingly in the number and diversity of species they contain After the ancestors of modern silverswords colonized the Hawaiin archipelago they diversified into many species with widely divergent phenotypes indicated here by the clade in red Adaptive radiations sometimes lead to impressive examples of convergent evolution The early evolution of animals represents one of the biggest adaptive raidiations in the history of life Fossils document the growing diversity of animals in the Cambrian The diversity of trace fossils of organisms that moved horizontally and vertically through substrates as well as small shelly fossils dominate the earliest Cambrian major groups of animals evolved from common ancestors Fossi records reveal how major transitions occurred Rapid diversification of animals corresponds to major environmental changes Warming and retreat ofglaciers Oxygenation of ocean new animals began burrowing crawling on the ocean floor and swimming rapidly after prey Key Concepts Most adaptive radiations involve exploitation of environments not occupied by competitors Key innovations can transform how organisms interact with their environment paves the way for adaptive radiation 145 The pace of extinctions a species can become extinct due to many different causes such as a change in the climate disappearance of its habitat competition from other species or the arrival of a new predator Background extinctionthe normal rate of extinction for a taxon or biota A clade can survive background extinctions only by continuing to produce new species Mass extinctiona statistically significant increase above background extinction rate Its the extinction of many species within a short period of time 146 The Big Five Mass extinctions mass extinction can result from climate change rising carbon dioxide from volcanic activity may have led to permian extinction asteroid impact etc The Ordovician Event 86 species lost cause climate The Devonian Event Gobal cooling The Permian Event Volcanism The Triassic Event Carbon diode levels The Cretaceous Event Impact Key Concepts The big five extinctions had different causes that impacted different organisms 14 7 Macroevoluton and the sixth mass extinction Humans may be driving a 6th mass extinction We kill them for food destroy their habitats increasing carbon dioxide leads to warming temperatures and acidifies the ocean Current extinction rates are on par with previous mass extinctions Key Concept Although a single extinction event may have minimal impacts on an ecosystem a mass extinction can have cascading effects To Sum It Up Microevolution describes the evolution of alleles and processes such as selection and drift Macroevolution describes evolution at a much larger scale it is evolution applied above the species level including the origination diversification and extinction of species and clades over long periods of time Changes in biodiversity can be examined using models that account for the number of originations immigrations extinctions and emigrations over a specific time period Lineages can produce new species at fast or slow rates Lineages can also experience status and burst of change Extinction can be caused by predation loss of habitat or other factors that reduce a species population Rates of origination alpha and extinction omega can be calculated using changes in their numbers over some unit of time The relationship between the two determines the fate of a particular clade Biogeography is the interdisciplinary study of the distribution of species around the world Dispersal and vicariance are important processes in species distributions Dispersal describes the movement of organisms from their place of origin for example a seed being transported to an island by wind Vicariance is the process of barrier formation such as the barriers that develop through plate tectonics Macroevolutionary biologists measuring diversity over time must be corrected for biases caused by discrepancies in the fossil record They have developed several models that have been extremely influential to our understanding of whether species diversity has increased over time Adaptive radiations occur when lineages diversify into many different species with disparate lifestyles behaviors and morphologies Opportunities for adaptive radiation can arise if a key innovation transforms how an organism interacts with its environment These key innovations can allow the organism to exploit new and under contested habitats or novel ways of life The early evolution of animals was a major radiation possibly triggered by world wide environmental changes The struggle between predators and prey accelerated the diversification of animal lineages The global extinction rate has varied over time On at least 5 occasions there have been mass extinctions but no clear ecological or taxonomic signal or cause unites all 5 Periods of high extinction rates coincide with major environmental changes including impacts volcanic eruptions and global warming Humans are the new agents of a pulse of extinction Chapter 15 Intimate Partnerships 151 The Web Of Life CoevolutionReciprocal evolutionary change between interacting species driven by natural selection Species exist in a web of interactions eg The Zebra The zebra does not generate its own organic carbon it grazes on grasses once the zebra swallows a mouthful of plant matter it does not digest this food by itself instead trillions of bacteria and archae in its digestive tract produce enzymes to break it down The zebra in return is prey for lion and others It may also become infected with deadly viruses Each of these effects the zebras fitness 152 Variation and populations Building blocks of coevolution Positive mutualismPositive effects on fitness Pollination Insects and other animals visit flowers to gather nectar Plants benefit because the animals spread their pollen allowing them to reproduce Coevolved adaptions Bright colors on flowers attract insects and birds Hummingbirds insert slender bills into flower tubes Seed Dispersal Birds eat fleshy fruits Seeds pass through their digestive tracts and released in their dropping The plant benefits from being dispersed across a wide range Nutrient exchange between mycorrhiza and plants Fungi in soil deliver minerals and other nutrients to plant roots Plants deliver organic carbon to fungi Farming Some species of ants rear mushroom gardens in their nest Co evolved adaptions Farmed fungi grow only inside ant nets Ants harbor bacteria on their skin that kill fungi that invade gardens Animals and microbiota Humans and other animals depend on microbes to help digest food and synthesize vitamins Cleaners Some species of fish eat ectoparasites on the skins of other fish PositiveNeutral commensalism A relationship in which one species benefits but the other suffers no loss of fnness Remora fish attach to larger fish and detach to feed on the prey killed by larger fish Coevolved adaptions Remora fish has structures to keep it attached to other fish NegativePositive Predators and prey a relationship in which an animal ingests another animalplant Coevolved adaptations Prey produce toxin to deter predators predators evolve defenses against toxins Plants produce sticky latex to stop insects insects avoid triggering latex production Deceptive pollination A flower tricks and insect into visiting it without providing nectar in exchange Coevolved adaptations Flowers produce pheromones and grow structures that appear like female insects Male insects learn to avoid flowers Host and parasite Virus intestinal worm or other organism lives in or on another organism often causing disease or death Coevolved adaptations Many species of parasites castrate hosts or alter their behavior Host immune systems attack the pathogens Coevolution requires genetic variation Genetic variation can fuel rapid evolution eg the soapberry bug It fed on balloon vine The beaks could not reach it so they evolved to longer lengths The plant also grew bigger The strengths of reciprocal selection varies geographically Variation can be maintained when traits have other costs Geographic mosaic theory of coevolution A theory that proposes that the geographic structure of populations is central to the dynamics of coevolution The direction and intensity of coevolution varies from population to population and co evolved genes from these populations mix together as a result of gene flow Three factors that the evolution of interaction between species 1Geographic variation in the type of selection on the interacting species In some places the interaction between species may be under mutalistic selection for example and antagonistic selection in other places 2Georgraphic variation in the strength of reciprocal election resulting from these interactions 3geographic variation in the distribution of traits that evolve in response to this selection When two species are in antagonistic reationships such as parasites and their hosts they can generate negative frequency dependent selection on each other parasites that are adapted for the most common host genotype will have the highest fitness They multiply the fitness of the common hosts goes down Rare host genotypes now have higher fitness than the common ones because they suffer less from parasite infections Over time these rare host genotypes will become more common Now the most common parasite genotype will be selected against while rare parasite genotypes are better adapted to the new dominate host genotype selected for Coevolutionary alteration can occur in interactions involving many species It occurs when one species is in an antagonistic relationship with several species A predator might attack several prey species Coevolutionary arms races species interact antagonistically in a way that results in each species exerting reciprocal directional selection on the other As one species evolves to overcome the weapon of the other it in turns selects for new weaponry on its opponent The adaptations that arise during coevolutionary escalations can impose a cost on each species example The TTX toxin of newts block the skeletal muscle sodium channels Garter snakes evolved resistance to the toxin through mutations to the gene for sodium channel Hot Spots Vs Cold Spots In some regions newts and garter snakes have mismatched levels of toxicity and resistance In some regions the newts do not produce enough toxins to harm the snakes Newts and snakes have hotspots and cold spots of coevolution Cold spots are where mismatch results in little convolution Hotspots are where closely matched toxin and resistance levels reflect coevolutionary escalation Decelerating Arms races ex Rabbits had a virus that was so strong it killed off droves of rabbits Because it was so strong it killed off so many rabbits that its host population thinned out Now the virus strains tended to become extinct because they killed rabbits without being transmitted to another one Selection began to favor less virulent drains Geographic mosaic also applies to mutualisms Mullerian mimicry Occurs when several harmful or distasteful species resemble each other in appearance facilitation the learned Batesian mimicry occurs when harmless species resemble harmful or distasteful species deriving protection from predators in the process Key Concepts The intensity and specificity of coevolutionary interactions can vary geographically and over time Antagonistic interactions may involve frequency dependent selection that maintains genetic variation Predator populations may switch prey generating alternating bouts of painivise interactions Arms races result when antagonistic interactions lad to directional selection on each species Strongly antagonistic interactions may evolve to be less antagonistic over time When mutualistic species exert positive frequency dependent selection rapid coevolution can result Mutualisms are vulnerable to cheating long standing mutualisms often have mechanisms to punish cheaters 153 Coevolution as an engine of biodiversity Coevolution process can drive to speciation Plants evolve innovations to escape predation allows for radiation Predators evolve to overcome defenses allows for radiation Diversifying coevouton An increase in genetic diversity caused by the heterogeneity of coevolutionary processes across the range of ecological partners Beetles diversity linked to coevolution with plants and angiosperms Familes of beetles that switched to feeding on angiosperms diversified much more rapidly yielding many more present day species Deception fosters diversity in orchids Some orchid species pollinate by deception They lure insects to them but do not offer any food The Australian tongue orchid attract male insects seeking mates Introduced predators can disrupt mutualism Key Concepts Highly specialized mutualisms make species dependent on each other Extinction of one species may drive extinction of another 154 Edosymbiosis How two species become one Endosymbiosis Mutualistic organisms that live within the body or cells of another organism It can span long evolutionary time spans eg Sharpshooters have co evolved with bacteria that supply the insects with essential nutrients The bacteria benefit by getting food and shelter from the insects The sharpshooters even developed special organs called bacteriomes Mitochondria generate energy for our cells They were originally free living bacteria that were later engulfed in our single celled ancestors Now they would not survive a second out of a cell The have evolved inside the cells of eukaryotes for billions of years Plant plastids are derived from freeliving bacteria Key Concepts Mitochondria and plastids are endosymbiotic bacteria that have coevolved with their hosts 155 Invasion of the genomic parasites Retrovirus An RNA virus that uses an enzyme called reverse transriptase to become part of the host cells DNA It causes aids Endogenous retroviruses make up 8 of the human genome To Sum It Up Species in ecological relationships adapt to one another in a process known as coevolution Species can have a range of relationships with each other from antagonistic to mutualistic Coevolution takes place in a geographic mosaic where the structure and intensity of selection varies from population to population The mosaic is defined as coevolved genes from various populations mix together as a result of gene flow Negative frequency dependent selection can maintain genetic variation within populations of interacting species Parasites and their hosts can evolve in arms races Predators and their can as well Mutualists can exert positive frequency dependent selections on each other ultimately leading to fixation of alleles that facilitate the interaction in each population Coevolution can promote biodiversity and the extinction of a species can endanger its coevolutionary partners During co speciation co evolving partners branch into new lineages together Some organisms have become permanent residents inside other organisms Mitochondria for example began as free living bacteria Some viruses can become established permanently in the genome of their host The human genome contains 100000 segments of DNA from vwuses Chapter 16 Minds and Microbes 16 1 Behavior Evolves The behavior of an organism is its tendency to react in a particular fashion to a specific situation or stimulus Behaviors are traits that vary just as height and other phenotypic traits do If you approach different squirrels for example they will wait different periods of time before running away This behavior variation is partly due to genetic variation Genes influence behavior at three timescales On a moment by moment basis gene expression changes brain function and vise versa Social interactions also interact with brain function to influence an individuals behavior Genes also influence behavior over the course of development Finally genes undergo selection in response to the social and physical environment This complex network of influence makes it challenging to pinpoint the effects of individuals genes on behavior Behavioral ecologyThe science that explores the relationship between behavior ecology and the evolution to elucidate the adaptive significance of animal actions Animals tend to resemble their parents in how exploratory or timid they are Scientists are now identifying candidate genes that affect the expression of behavior Selection experiments reveal how behavior can evolve eg an experiment that mice was spontaneously ran on a wheel for long periods of time were elected After 30 generations they ran about three times more each day than control mice Mice selected for aggression made more attacks The bird was selected for either a willingness or a reluctance to explore Their behavior shifted in both populations Bacteria may not have brains they may not be able to carry out sophisticated actions such as making tools but they can still respond to their environment in an adaptive fashion Mutations can alter their responses and some of those mutations are favored by natural selection Individuals may cheat The M xanthus Form mounds when food source exhausted A few random cells become spores only a fraction of the bacteria develop into spores that can disperse and survive The rest die in the moundThis behavior has led to the evolution of cheaters The proportion of cheaters among the spores in a mound is higher than would be predicted from their proportion in the entire population Evolution in high food environment led to loss of mounding behavior More likely to be spores when paired with a wild type There is also a cheating slime mold when its starving the cells join to form a slug which then grows into a stalk with a patch of spores on top during reproduction The stalk cells support the spires but die in the process Kin recognition has evolved as a way to overcoming cheating so only relatives are including in a slug formation Evolution of Neurons All animals except for sponges use neurons to control their behavior Spikes of voltage travel down the length of a neuron and then trigger the release of neurotransmitters at synapse which in turn trigger activity in neighboring neurons A neuron generates signals with pulses of electric charge that move from one end of the cell to the other The signal can move from one neuron to the next at specula junction of the two cells that is called a synapse The neuron sending the signal dumps chemicals known as neurotransmitters into the synapse and they re taken up by the receiver neuron Animal nervous systems vary tremendously The earliest animals probably did not have newborns It probably took 100000000 years The network of proteins in neurons evolved in a stepwise fashion in the ancestors of animals which lacked neurons Sponges lack nervous systems but make a number of proteins that are homologous to proteins found in neurons Its possible that sponge larvae use these preteens to build sensory cells that help them detect good places for them to settle to the seafloor to develop Earliest fossil evidence of brain 530 million year old Haikouicthys The oldest signs of the verb rate nervous system is found in that rock Those rocks contained hundreds of fossilized impressions of a tiny creature M It h as a spinal cored surrounded by vertebrae which are supported by a notochord As vertebrate lineages diverged their brains diverged as well Vertebrate brains are divided into specialized regions The human brain like other vertebrate brains is divided into many specialized regions each helping to carry out certain functions Vertebrate brain comes in many shapes and sizes And yet share the same basic organization Brain evolution is shaped by ecological adaption Sensory maps show the parts of the body that have the most concentration of nerve endings Complex behavior can be triggered by innate sensitivity stimuli Herring gull chicks respond to the sight of their parents by begging for food To determine what the chicks respond to He built cardboard cutouts of adult gull heads A cutout of the beak alone is almost as effective at triggering a response from a chick as a full head On the other hand a head without a red spot is less likely to trigger a pecking response These experiments show that the red beak spot is mainly responsible for a chicks response Key Concepts Proximate studies focus on how behaviors are elicited Ultimate studies focuses on why behaviors have evolved Behavior evolves just like any other trait The beginning of nervous systems evolved early in the animal lineage Animal nervous systems have diversified to become highly specialized filters of sensory information May behaviors are innate Innate behaviors provide clear examples of behavioral evolution 16 2 Shortsighted selection and sel shness Individual seection Differential performance fitness of individuals causes some genotypes to outcompete and replace other genotypes Group seection Differential performance fitness of groups of individuals causes some groups to outcompete and replace other groups Individual selection is more powerful than group selection It happens more rapidly than group selection Also organisms are reproductively selfish Key Concepts If individuals selection predominates then behaviors beneficial to individuals will evolve even if detrimental to groups Immediate fitness consequences determine the success of an allele irrespective of the ultimate outcome Organisms are reproductively selfish even if detrimental to group or species 163 Rock Paper Scissors Side Blotch Lizards Individual selection for behavior can produce an unexpectedly wide range of strategies because the fitness of an individuals social behaviors depend on what other animals around it are doing An example is the Male side botched lizards They produce 3 different kinds of males Orange are big and aggressive and guard large territories containing multiple females Blue are smaller and less aggressive They defend there territories well but their territories are only big enough to contain a single female Yellow lizards don t defend any territory at all intend they mimic female yellow lizards in order to sneak into the territories of the other males They can then surreptitiously mate with females passing on their alleles for yellow throats and sneaky behaviors The prevalence of each behavior type raises or lowers the fitness of the others As a result the types oscillate in frequency over time Game Theory A mathematical approach to studying behavior that doves for the optimal decision in strategic situations games where the payoff to a particular choice depends on the choices of others Its also when social conditions determine behavioral strategies Key Concepts An evolutionary stable strategy is a behavior that when adopted by a population of players cannot be invaded by an alternative strategy 164 Why Be Social Dilution effect The safety in numbers that arise through swamping the foraging capacity of local predators Individual selection can favor group living if the gains it brings to an individual outweigh the costs Benefits costs of sociality Increased vigilanceanteope in groups to spot predators increased conspicuousness to predators Dilution effectsafety in numbers increased competition for food Enhanced defense capabiitypenguinsjumping off ice together reduce being eaten Increased competition for mates Cooperative foraginghuntinghunting in groups Decreased certainty of paternity Improved defense of critical resource Cliff swallows build nests in dense colonies Increased transmission of disease Key Concepts The probability that any one individual will be attacked by a predator decreases with increasing group size The cost and benefits of behavior may not be the same for every individual sex status body condition 165 The importance of Kin Altruism Occurs whenever a helping individual behaves in a way that benefits another individual at a cost to its own fitness Helping other members of the group benefited the group as a whole Individuals often help relatives offspring and full siblings are the most then grandchildren Coefficient of relatedness rbetween two individuals is the probability that they share identical copies of a particular allele It can also be thought of as the proportion of alleles that are likely to be shared between the two individuals A child have 50 of a parent s genes There coefficient of relatedness is 05 Inclusive fitness explains altruism Inclusive fitness An individuals total fitness including its own reproduction as well as any increase in the reproduction of its relatives due specifically to its own ac ons Inclusive fitnessDirect fitness indirect fitness Kin selection selection arising from the indirect fitness benefits of helping relatives eg ground squirrelsindividuals give an alarm call when they detect the approach of a predator Alarm calling is risky because it draws attention of the predator towards the caerbut these calls give other individuals in the colony time to escape Females more likely to give call because they are often surrounded by close relatives Certainty of paternity makes parental care profitable Hamiltons rule describes when altruism is favored rB gt C rthe coefficient of relatedness between donor and recipient Bbenefiet to the recipient arising from help Ccost of donor from helping Individuals may recognize phenotypic markers females know that the baby is theirs males do not Physical proximity cannot be a reliable indicator Their certainty is low so there parental care is low Green Beard effect A situation in which an allele produces three things Recognizable phenotype ability to recognize phenotype preferential treatment of individuals with phenotype When Kin recognition fails Animals generally do not have direct phenotypic markers for the presence of particular alleles Instead they must rely on behavioral rules such as learning the doors or features of individuals in the nest The rules can be broken Ifthe cues are copied then cheaters can exploit the benefits of cooperative behavior to the detriment of the helping individuals In several clades of lycaenid butterflies for example the larvae produces chemicals that mimic those of certain ant species The ants carry the butterfly larva into their nests and feed it as if it were one of their own The larva pupates inside the ant colony and develops into an adult butterfly At that point it no longer bears ant kin recongintion chemicals Key Concepts Kin selection theory predicts that individuals should help relatives more than non relatives and they should help close relatives more than distinct one Parental care is the most widespread form of helping Physical proximity ensures high relatedness Certainty of paternity is rare for males Organisms sometimes recognize kin directly by phenotypic markers Kin recognition cues can be exploited 166 Rewiring Behavior The most important feature of animal nervous systems is that they allow the organism to learn Synaptic plasticity when the number or strength of synaptic connections between neurons is altered in response to stimuli Synapses change over the lifetime of an animal New synapses grow some die and some get strongerweaker They grow from learning Learning ability may involve trade offs There was an experiment with flies where the fast learning flies died quicker than the slower learning ones Learning imposes some kind of cost on an organism Forming a lot of connections between neurons may causes harmful side effects possibly by producing cell damagins molecules Its also possible that the proteins used by neurons during learning interfere with other chemical reactions such as the one that repairs cells Key Concepts Synaptic plasticity is thought to be the neural mechanism of learning and memory Learning can be costly closets can be offset by benefits in some circumstances 16 7 Animal Geniuses Some animals are capable of complex cognition It can allow animals to have sophisticated social interacting s with other members of their species Chimps use many different gestures to communicate with one another They fail the pointing test though lfyou put food under one cup and no food under the other The scientist points at the cup with the food and the chimp then gets to choose one of them They get it 50 of the time Dogs and humans are the only ones A dolphin wears a sponge to protect its head as it hunts for prey on the seafloor Dolphins are among the few lineages of animals known to make and use tools Social living can influence brain evolution The social lives of primates may have profoundly affected the evolution of their brains This graph shows how primate species that live in large groups tend to have a proportionally larger neocortex Key Concepts Tool use have evolved independently several times in birds and mammals To Sum It Up Behavior is shaped by evolution Scientists can observe the evolution of behavior in laboratory experiments and in the wild The building blocks of neurons evolved millions of years before neurons did The evolution of nervous systems allowed animals to develop more sophisticated behaviors than other taxa Nervous systems allow animals to learn Learning itself can evolve according to the tradeOoff between its costs and benefits Organisms are reproductively selfish they behave in ways that enhance the spread of their own genetic material even if this behavior is detrimental to their population Organisms share alleles with siblings and cousins as well as with parents and offspring for this reason they tend to help relatives more than non relatives and close relatives more than distant relatives The fitness consequences of a behavior often depends on what everyone else is doing Large brains in vertebrates allow them to solve complex ecological problems The behavior of primates is shaped by their highly social lives Chapter 17 Human evolution 171 An Origin among the apes Miocene apes gave rise to present day ape lineages Homininsmemebers of the human branch of the hominid clade including the genus homo and its close relatives Hominids Members of the clade containing humans chimps bonobos etc Commonly referred to as the great apes The phylogeny of primates is based on the combination of analysis of DNA and fossils Fossil calibration allows dating of common ancestors 172 Walking into a new kind of life Hominins first emerged at the end of the miocene period There was a decrease in rain and other environmental change during hominins evolution This is probably why new lineages began to form The earliest hominins were found in Africa We transitioned to bipedalism We have found fossils that document the transition to bipedalism Early homo were efficient walkers Also the diet of early hominins changed Chimps had large teeth in massive jaws however humans have much smallerjaws due to a shift in diet Also its possible that a reduction in male mae competition led to a reduction in canine teeth Tool use may have emerged as early as 34 mya Hominins developed a style of toolmaking called oldowan The shape of the tools show how they were made by striking off flakes form large round rocks Hominins used tools to scavenge meat and possibly to fashion wooden toosTools and hominid fossils were preserved We can tell the diet based off of the tools Australopithecus sediba sister to Homo The hominid in between lucy and a homo erectus Homo used relatively sophisticated tools Key Concepts Change to open habitat may have elected for bipedalism Oldowan tools are the earliest stone tools Humans did not evolve in a ladder like progression at least four species co existed 173 Out of Africa for the rst time First migration out of Africa did not include our own lineage Neanderthals evolved in Europe and Asia Relationships among some early hominids is uncertain Modern humans emerged 200000 year ago early Homo sapiens were culturally diverse They had there own language and tool styles Early Homo sapiens displayed increasing levels of creativity Brain is evolving and becoming more diverse and developing more complex tools such as needles and threads This allowed us to develop sophisticated trade networks We are visually oriented creatures not o fashioned It allows us to recognize facial expressions as social recognitions This allows us to become ultra social Neanderthals and modern humans form separate monophyletic groups DNA suggests some interbreeding between neanderthals and nonAfrican Humans Denisovans close relatives of Neanderthals also interbred with humans Current hypothesis for expansion out of Africa We moved out of africa bumped into neanderthals they went to western europe Then some colonized other americas 50000 years ago Key Concepts Both molecular and fossil evidence suggest that humans and neanderthals represent separate lineages descending from a common african ancestor The debates about the relationships among fossil hominins highlights the complexity of our evolutionary history Early art suggests considerable brain power fertility goddesses Social evolution may have driven increased brain size Human children display relatively advanced social skills Social domain watching someone take something out of a tube and then repeating it after watching Physical domain FOXP2 gene implicated in capacity for language If you have a deficiently of it they could not come up with a relative verb of a noun given to them They are not very good at speaking or using language FOXP2 is active in other animals too Broca s area of the brain Aso argued that the the nerve bundle arcuate fosicuous allows us to make rapid decisions with speech Evolution meets civilizationhaving these individual cultures we suffer from numerous bottlenecks Language evolution similar to biological evolution genetic structure reflects geography High altitude adaptation we sequence people with high elevation and they have evolved 2 genes that allow them to sense oxygen better because they are high in a ude Selection for malaria resistance Malaria kills a lot of africans Alleles are forming to protect against it Shows that humans are always evolving Chloestro affects fitness able to reproduce Human emotions result from modification of preexisting networks aka bonding between mother and offspring Oxytocinletting out milk Important to women bonding with their offspring Vasopressin plays critical role in pair bonding If you have a lot you tend to want to be monogamous Social stimuli interact with brain chemistry to produce emotion Human biases in economic decision making seen in monkeys Child abuse more likely by non biological parents If you have one natural parent and one stepparent you are subjected to child abuse Key Concepts Humans have adapted to recent environmental change Humans have modified environmental in ways that relax selection on some traits The chemistry of human emotions is the result of a history of selection and adaptation Decision making systems have been shaped by natural selection Evolutionary psychology explores the extent to which human behaviors are the result of adaptation and selection To Sum It Up Hominins include humans and all other species more closely related to them than chimps and bonobos To the hominid fossil record extends back 7million years agreeing roughly with molecular clock studies Hominins bipedalism gradually became more efficient Hypotheses for the evolution of bipedalism include efficient feeding and heating dissipation Hominins evolved a flexible foraging strategy The ability to make and use stone tools evolved perhaps as long ago as 34 million years Hominins used these tools to scavenge meat The genus Homo evolved about 18 million years go It was characterized by a tall body with long legs Homo soon developed a new stone tool industry called acheulean Members of the genus homo we re the first hominins to leave africa Neanderthals were sophisticated hunters who were adept at making tools and they may have had a brain capable of understanding symbols Homo sapiens evolved 200000 years ago in Africa and expand out of Africa about 50000 years ago Our species may have interbred with at least 4 other hominid lineages after they left Africa Human brain evolution may have been driven by social intelligence Language evolved as a tool for communication through changes in connections in the brain Language accelerated cultural evolution in humans which can also be analyzed like biological evolution The rise of civilization allowed for new opportunities for drift and natural selection to reshape the human genome Emotions such as love and fear have evolutionary roots in distant mammalian ancestors humans sometimes makes irrational decisions using neural circuits that evolved to evaluate rewards man that 30 million years ago Mate choice and parental care in juan can be explained to some extent by the same evolutionary principles used to study them in other species
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