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Evolution Final Exam Lecture 1 Biological Evolution change in the genetic properties of groups of organisms (“populations”) over the course of generations Often referred to more simply as “descent with modification” or “genetic change over time” Evolution is about change in proportions through time Within populations change in gene frequencies between generations (e.g. shift in proportion of individuals with dark versus light wing coloration) Between populations (or species) change in proportion of genetically differentiated populations (e.g. shift in proportion of populations with dark versus light wingcoloration) Why is evolution interesting? 1) Morphological diversity why do whales have lungs and snakes lack legs? 2) Genetic diversity why do salamanders have 10x more DNA than humans? 3) Species diversity why are there so many species of beetles (400,000!)? 4) Medicine How do bacteria, viruses and parasites counter our immune system? How do they evolve resistance to our medicines? 5) Technology How do insects evolve resistance to pesticides? Evolution is the only scientific explanation for many observed anatomical traits Misconception #1 Evolution and natural selection are the same thing Natural Selection is one mechanism by which evolution occurs, but natural selection and evolution are NOT one and the same Evolution is simply genetic change through time, to deny evolution is to deny genetic change occurs But, much evolution occurs due to natural selection Misconception #2 Individual organisms undergo biological evolution Populations or groups of organisms undergo evolution In biology, the change of individual organisms through their lifetime is termed “development” Misconception #3 Evidence for evolution is limited, it is only an unsubstantiated theory Evidence for evolution is abundant, stemming from numerous sources such as from the fossil record, DNA and genomic data, and direct observations in contemporary time Three Examples of evidence for evolution (many more will follow in the course!) 1) Antibiotic resistance 2) Pesticide resistance 3) Experimental evolution studies in the laboratory Eg. A tuberculosis ward at a U.S. Army base hospital in France during World War I at this point in time it was thought that antibiotics has conquered this bacterial disease. Evolution of drug resistance by the bacterium Moraxella catarrhalisis Cumulative numbers of arthropod pest species known to have evolved resistance to five classes of insecticides Evolution has also been observed DIRECTLY numerous times in laboratory studies Misconception #4 ok, evolution occurs within species, but it cannot explain the origin of new species As for studies within species, there is abundant evidence that new species form via evolution Evolution for evolution through the fossil record There aren’t intermediate forms between major animal groups. There are few “missing links”. FALSE Many intermediates forms and “missing links” have been found, with more found all the time. Limestone tiger beetle (Cicindelidia politula) phylogeography Adults active July to early August (New Mexico) Adults active September to December (Texas) Lecture 2 History of Evolutionary Thought 1) Before Darwin (pre 1859) 2) Darwin (1859) 3) Theories after Darwin (early 1900’s) 4) The evolutionary synthesis (1930’s, 40’s) 5) Biology since the synthesis (1950 on) Before Darwin variation is accidental imperfection (ESSENTIALISM) Plato and Aristotle Concept of edios “form” or “idea” or “essence” e.g. horses have an immutable (unchangeable) essence, but each individual has its imperfections This view is called essentialism and under this view variation is accidental imperfection Uniformitarianism “The present is the key to the past” Championed by geologists Hutton and Lyell. Catastrophism Sudden violent and shortlived events were responsible for the current state of the earth. JeanBaptiste Pierre, Antione de Monet, Chevalier de Lamarck Developed theories of phenotypic evolution and of speciation Lamarck’s theory of phenotypic evolution: inheritance of acquired characteristics Traits acquired during the course of an individual’s lifetime were passed on to offspring. e.g. lengthening of giraffe’s necks and thickening of a blacksmith’s arms Lamarck’s theory of speciation: species originate by spontaneous generation, and have not originated from common ancestors Lamarck’s theories were largely ignored and attacked during his lifetime. Georges Cuvier Organisms were functional wholes; any change in one part would destroy the delicate balance. But the functional integration of organisms meant that each part of an organism, no matter how small, bore signs of the whole. Darwin’s Life Lived 18091882 Voyage of the Beagle lasted 18311836 Darwin became an accomplished naturalist Theory formulated via INDUCTION The process of deriving general principles from particular facts or instances. Model (Hypothesis) A formal (mathematical) statement of causal relationships among variables Induction= using logic to generate expected data patterns Predictions Measurement= collecting values of the variables Data Comparison (our data against modelDo the patterns fit the predictions? Decision (reject or fail to reject; Never “accept” or “prove”). Data can be bad, and Bad (incorrect) models can be supported by good data! Deduction=modify the model Model (Hypothesis) A formal (mathematical) statement of causal relationships among variables After formulating his theory, he spent much time trying to sort out flaws Published the Origin of Species in 1859 (>150 years ago!) The power and brilliance of Darwin’s idea of naturals selection is often underestimated The idea was one of the most important, general, and powerful ideas in the history of thought The “Origin of Species” actually has two major these (and five overall theories) 1) Descent with modification (evolution) a succinct term to describe biological evolution 2) Causal agent of evolutionary change (natural selection) a) Natural selection is differential survival or reproductive success of classes of entities that differ in one or more characteristics. Usually the differences are inherited (and must be inherited for evolution by natural selection) Natural Selection as a cause of evolution Early in generation 1: Heritable (genetic) differences in phenotype e.g. white moths and black moths living in the same population Later in generation 1: Natural selection acts e.g. white moths die down because black moths are more favored in the population Generation 2: Evolutionary change via natural selection e.g. black moths are left in the population Darwin’s book actually includes five theories 1) Evolution as such is the simple proposition that the characteristics of lineages or organisms change over time 2) Common descent suggested that all life could be portrayed as one great family tree, this was a radically new view of evolution 3) Gradualism is the proposition that differences between even radically different organisms have evolved incrementally, by small steps through intermediate forms. 4) Population change is the thesis that evolution occurs by changes in the proportions of individuals within that have different inherited characteristics 5) Natural selection is Darwin’s brilliant hypothesis (independently conceived by Wallace) that the proportional changes described above are caused by differences in their ability to survive and reproduce and that such changes result in the evolution of adaptations Darwinian View: Variation is adaptive, evolved by natural selection Alfred Russel Wallace “Father of Biogeography” Wallace Line also the “Wallace Effect” explanation for speciation. Wallace Effect Posits that natural selection can contribute to thereproductive isolation of incipientspecies by evolving barriers against hybridization. Evolutionary Theories after Darwin Theory was initially very controversial Idea of evolution by common descent eventually accepted But the cause of evolution? The idea that natural selection caused evolution was debated Led to the rise of mutationist theories which argues that discretely different organisms arose via mutation and that natural selection was not required for the origin of new species. Mutation seen as an alternative to natural selection Mendelian genetics “particulate inheritance” Ideas were published 1865 but nearly completely ignored… Richard Goldschmidt (1940) and ‘hopeful monster’. First to integrate genetics, development, and evolution. "The change from species to species is not a change involving more and more additional atomistic changes, but a complete change of the primary pattern or reaction system into a new one, which afterwards may again produce intraspecific variation by micromutation." Macroevolution through macromutation The modern evolutionary synthesis (1930’s and 40’s) Forged from the contributions of geneticists, ecologists, systematists, and paleontologists Reconciled Darwin’s theory with the facts of (Mendelian) genetics Has been extended, clarified and modified since 1940’s, but is still generally considered fundamentally valid Ronald A. Fisher, J.B.S. Haldane, Sewall Wright Developed a mathematical theory of population genetics, which showed that mutation and natural selection together cause adaptive evolution Mutation is not an alternative to natural selection, but is rather it’s raw material The relative importance of random genetic changes versus natural selection in evolution was debated Founder effect and genetic drift Founder effect the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. Genetic drift the change in the frequency of a gene variant (allele) in a population due to random sampling of organisms. Ernst Mayr "modern synthesis" in the 1930s and 1940s that integrated M endel's theory ofhereditywith Darwin's theory of evolution and natural selectin. The traits that evolve during the period of isolation are called "isolating mechanisms ," and they discourage the two populations from interbreeding. Three major contributions: 1) Biological species concept (BSC) 2) Theory of geographic (allopatric speciation) 3) Theory of founder effect speciation Biological species concept (BSC): species are groups which are reproductively isolated (do not exchange genes) from other groups. premating: black and black, white and white. postmating: black and black=hybrid, white and white=hybrid Theory of geographic (allopatric) speciation: new species form when populations become geographically isolated, and thus can undergo genetic divergence. Theory of founder effect speciationdrastic reductions in population size promote speciation (e.g. genetic revolutions) Fundamental principles of evolution (major tenets of modern synthesis) 1) The phenotype (observed characteristics) is different frgenotype (the set of genes in an individual’s DNA); phenotypic difference can be partly due to genetic differences and partly due to direct (within generation) effects of the environment 2) Heredity variation are based on particlsenes that retain their identity as they pass through generations 3) Evolutionary change is a populational process that entails changes in the proportions or frequencies of individual organisms with different genotypes 4) Genes mutate at a low rate, typically too low a rate to cause a population to shift from one genotype to another; thus shifts occur instead by random fluctuagenetic drif) and nonrandom changes due to atural selection 5) Even a slight amount of selection can bring about substantial genetic changes, thus selection can account for both slight and extreme genetic differences 6) Mutations can accumulate in populations, thus populations harbor genetic variation 7) Differences between populations and species are often adaptive (evolved due to natural selection) and are based on differences at several or many genes of small effect (evolution occurs by small steps) 8) Species are characterized by barriers to genetic exchange and interbreeding (reproductive isolation), and usually evolve in geographic isolation 9) All organisms form a great “tree of life” or phylogeny. All forms of life have descended from a single common ancestor in the remote past Biology since the synthesis (1950 on) Motoo Kimura and the Neutral Theory of Molecular Evolution Natural selection requires phenotypic variation to act upon Butmany genetic changes cause no phenotypic change (do not produce phenotypic variation) Led to the hypothesis that most of the evolution of DNA sequences occurs by genetic drift, rather than natural selection. But, it provides a foundation for detecting natural selection on DNA sequences “Wobble” position and DNA nucleotide substitutions which do NOT change the protein (amino acid) William D. Hamilton, Robert Trivers, and Social Theory CooperationKin selection (explains confusing altruistic behaviors and eusocilin selectiois evolutionary strategy that favours the reproductive success of an organism's relatives, even at a cost to the organism's own survival and reproduction. Conflictparent/offspring, sibling, male/female The age of genomics (a new age of INDUCTION) new insights into the side, organization, and structure of genomes in turn, this information yields insight into the causes and consequences of evolution Lecture 3 Taxonomy and Systematics Taxonomy the science of describing, naming, and classifying organisms. Used to organize groups of species into progressively smaller hierarchical groups. Originally Kingdom was the most inclusive taxonomic group. (Kingdom, Phylum, Class, Order, Family, Genus, Species). “Five Kingdom” system was used for many years. (Monera, Protista, Fungi, Plantae, Animalia) “Three domain” system: Eukarya, Archaea, Bacteria Our purpose of taxonomy is to name species Modern species taxonomy started with Carl Linnaeus. First introduced binomial nomenclature is his 1753 “Species Plantarum” and 1758 “Systema Naturae” editions. Each species has two parts: First part (genus) and second part (species inside the genus) Taxon (plural=taxa) a unit of taxonomic classification Systematics the study of biological diversity and the evolutionary relationships among organisms. Testing hypothesis about which groups have descended from a common ancestor Extinct no longer present Extanttaxa that exist today Phylogeny the history of descent of a group of taxa from their common ancestors. (phylogenetics = study of phylogenies). The diagrams that depict phylogenies arehylogenetic trees.A phylogenetic tree is a systematic hypothesis. How can studying systematics possibly be interesting? Relatedness? The resulting pathway is interesting of itself (who is most closely related to who? Are dogs more closely related to cats or to pigs?) Sometimes results are surprising… Trait evolution? Phylogenetic tree provide a foundation for understanding many aspects of evolutionary history, such as the pathways by which various characters evolved (how many times did wings evolve?) Cutting edge technology? Use of molecular data, including whole genome sequences Detective work? Unlike some aspects of evolution, we cannot often directly observe evolutionary history. Instead, we must infer it using phylogenetic methods, like Sherlock Holmes reconstructing the history of crime… Phylogenetic tree terminology Root: the common ancestor of all taxa Node: a branchpoint in a tree Clade: a group of two or more taxa that includes both their common ancestor and all their descendents Systematics and Phylogenetic trees Monophyletic group : A taxon that is a clade. A group that includes ALL of the descendants of a common ancestor. Paraphyletic group : A group that includes some, but not all, of the descendants of a common ancestor. Polyphyletic group : A group that consists of members of multiple evolutionary lineages, but not include most recent common ancestor and all of its descendants. How is a phylogenetic tree actually built? One consideration is “shared characters” homology = same character state found in different taxa due to shared common ancestry analogy (homoplasy)= same character state found in different taxa due to convergent evolution or reversal. e.g. shark(fish), ichthyosaur(reptile), dolphin(mammal) character= a feature or trait (e.g. color of snail shell) character states= one of the variant conditions of a character (e.g. brown or yellow shell; A or T at a nucleotide position) ancestral stat state found in common ancestor derived state= state that has evolved from the ancestral state outgroup= a taxon that is closely related to the study. comparisons of character states can inform as to which are ancestral and derived. Cladistic approach Willi Hennig is known as the founder of phylogenetic trees, known as cladistics Create phylogenetic trees based on shared character states Only certain types of character data can give useful information about relationships Symplesiomorphies are shared ancestral characters. They aren’t phylogenetically informative. Autapomorphies are unique derived characters. This type of character is distinctive for a taxon and it enables us to identify that taxon, but autapomorphies also tell us nothing about a taxon’s relationship to other groups. Synapomorphies are shared derived characters. These are the only characters that really help us to resolve relationships. (i.e. are phylogenetically informative) Maximum parsimony the principle, dating back at least the 14th century, that the simplest explanation, requiring the fewest undocumented assumptions, should be preferred over more complicated hypotheses that require more assumptions. When we create phylogeny using maximum parsimony, we choose the tree that involves the smallest number of character changes. We are basing this on the assumption most shared derived characters are due to common ancestry, not convergence. Phylogenies are created using computers because they are omputationally intens Maximum parsimony is one of the least computational methods, actually. However, there are many possibly alternative relationships between taxa. These are VERY computer intesnive methods! Other methods of phylogenetic analysis NeighboringJoining A clustering method that is not based on characters per se, but instead finds relationships based on the percent differences between taxa (‘distance’). Maximum Likelihood (ML) given a specific model of evolution and a possible tree, thisalculates the likelihood of observing the data. Bayesian maximizes the robability of observing a particul given the model and the data, unlike the ML method, Bayesian analysis provides the probability of a set of different trees so that they can be compared and summarized. Lecture 4 Molecular Clocks Mutations occur over time. If they occur at a fairly constant rate, we could look at the number of changes in two DNA sequences and estimate the amount of time since they shared a common ancestor. The rate at which a gene accumulates mutations can be calibrated by the fossil record or geological data. Genes do not always display characteristics of a molecular clock. Nucleotide substitutions may occur faster or slower in some lineages. Difficulties in Phylogenetic Analysis Character scoring difficulties: what is homologous? Do two organisms have the same anatomical character state? In genomes, there are insertions and deletions of DNA/RNA throughout evolution. How can we align our sequences to determine homologies? Patterns of Evolution 1) Evolutionary history and classification 2) Character evolution 3) Rates of evolutionary change Evolutionary History and Classification Evolution has two major features: Anagensis (phyletic evolution) is the gradual accumulation in changes in the characteristics of a lineage over time. Cladogenesis (branching evolution or speciation) is the splitting of a gene pool into two or more separate pools. The descendant lineages may exhibit different levels of anagensis. The classic natural history museum representation implies that the tiny Hyracotherium gradually changed into a series of other species until the lineage eventually evolved into the modern day horse, Equus Any modern account of horse evolution is otjust simple anagenesis. Character Evolution We can use phylogenies to reconstruct the history of evolutionary change of a character by “mapping” it onto a phylogenetic tree. May show that a particular trait has evolved multiple times throuonvergent evolution. One form of convergent evolution is mimicry. Batesian mimicry involves a toxic model species and a palatable mimic. Mullerian mimicry involves multiple toxic species which are all similar in appearance. Predators learn to avoid all similarlooking species. Evolutionary reversals occur when a character state changes from a derived or “advanced” state back to more primitive state. Wings on insects. Mantophasmatodea(Heel walkers), Grylloblatodea(Ice crawlers), and Siphonaptera(Fleas) all don’t lack wings. Dollo’s Law (of Irreversibilit states that complex characteristics, once lost, are unlikely to be regained. According to Louis Dolloe (1893): “An organism is unable to return, even partially, to a previous stage already realized in the ranks of its ancestors.” Different characters evolve at different rate Some characters change little over vast amounts of evolutionary time, while other characters change rapidly. This phenomenon of different rates of character change within lineages is referred to as mosaic evolution. The implication is that a species donot evolve as a whole, but rather that its parts evolve quasiindependently. A character state in an organism could be primitive or derived, but it is inaccurate or wrong to consider one living species more “advanced” than another! Character Evolution and Development Evolutionary biologists have noticed common patterns of morphological evolution across many species. These patterns can be expressed in terms of their underlying developmental changes. In organisms there are often “modules” that are distinct units that have distinct genetic specifications, development patterns, locations, and interactions with other units (e.g. vertebrae, leaves, teeth, body segments of a centipede). If organisms evolve distinct identities and specializations for such units, this process is called individualization. Heterochrony is an evolutionary change in the timing or rate of developmental evaedomorphosis is the evolution of a juvenilelike reproductive Peramorphosis is the evolution of “hyperadult” features due to extended development. Allometry refers to the differential growth of different parts or dimensions of an organism during ontogeny. Some morphological structures may grow dispropotionally faster or slower than other structures. In many lineages we observe simplification of morphology reduction and/or loss of structures. This occurs very commonly in module type morphologies. Adaptive radiations and rates of cladogenesis (speciation) Some evolutionary lineages have a LOT more species than others. They appear to have undergone more cladogenesis Why?? “Adaptive radiations” occur when species rapidly diversify to fill available ecological niches. “Evolutionary radiation, rather than sustained, directional evolutionary trends, is probably the most common pattern of longterm evolution” Futuyma Adaptive radiations can occur because of key innovation the evolution of a novel trait that enables species to adapt to new environments or lifestyles. .LYTRA ia modified, hardened forewing which is only found in coleoptera(Beetles). Also some lineages HAD diversified into many species, but different lineages have had very different rates of extinction… Pace of Evolution Is the rate of evolutionary change constant throughout time? Gradualism is when species evolve continuously over long periods of time. Large changes in phenotype are simply due to many small changes over time. Punctuated equilibrium is a scenario where the tempo of evolution is sporadic. There are short periods of evolutionary time where major phenotypic changes occur. Fossil record often supports PE. Lecture 5 Evolution in the Fossil Record Some general patterns in the history of the earth 1) The distribution of land masses and oceans have changed over time, affecting the geographic distributions of organisms. a) Permian Pangaea. Triassic Laurasia (Northern Hemisphere) and Gondwanaland (Southern Hemisphere) 2) Catastrophic events have occurred...repeatedly. These include meteorite impacts, volcanic eruptions, massive changes in sea levels. a) Mass extinctions catastrophic decline of species (Oldest to Earliest) i) Late Ordovician Biggest extinction rate overall, and in the Paleozoic ii) Late Devonian iii) Permian Triassic Next biggest after Late Ordovician iv) Late Triassic v) Cretaceous Tertiary Biggest extinction rate in the Mesozoic 3) Climates have changed. This includes glacial cycles (there were many) Land masses have moves, climates have changed, and species have moved. Species distributions have changed over time. 4) Especially after mass extinctions, the diversification of higher taxa has sometimes been relatively rapid. 5) The diversification of higher taxa has included increases both in the number of species and in the variety of their form and ecological habits. 6) Extinct taxa have sometimes been replaced by unrelated by ecologically similar taxa. 7) The geographic distributions of many taxa have changed greatly a) The Camelid family originated from North America during the Pleistocene. 8) Of the variety of forms in a higher taxon that were present in the remote past, usually only a few have persisted in the long term. 9) Over time, the composition of the biota increasingly resembles that of the present A lot of our knowledge about the past comes the fossil record The fossil record provides a great deal of information, however it is important to note that there are biases. Some common biases in the fossil record 1) Toward common, widespread species yet lots of biodiversity is globally rare or occupies geographically small ranges 2) Toward physically large species yet VAST majority of biodiversity is small to tiny in body size 3) Toward species that died in substrates that lent themselves to longterm preservation a) Insects in amber Eocene b) Insects in limestone 4) Towards hard body parts, shells, and other mineral based structures Origins of Higher Taxa Based on comparisons of extant (living) species we can often hypothesize what traits may have existed in the ancestor...even before any fossil is discovered. Later discovery of fossils can confirm an evolutionary hypothesis. Lecture 6 The Origin and History of Life on Earth Before life began: Universe came into existence 14 billion years ago The Emergence of Life Simplest living things were complex aggregations of molecules; left no fossil record and thus can only be studied theoretically and experimentally “Life” is a difficult concept to define, but generally it is agreed that an assemblage of molecules is “alive” if it can capture energy from the environment, and then use that energy to replicate itself, and thus be capable of evolving. Simple organic molecules have been found in space and have been produced by abiotic chemical reactions (e.g. MillerUrey. Theysimulated the conditions thought at the time to be present on the early Earth, and tested the chemical origin of life under those conditions.) The most likely early replicators were short RNA or RNAlike molecules (“RNA world”). Long RNA sequences would not replicate well because their mutation rate would be too high to allow them to maintain their identity. A larger genome might evolve if two or more macromolecules each catalyzed the replication of the other. Precambrian times (Archaean and Proterozoic Eras) 4.5 bya to 542 mya Early atmosphere had little oxygen, so earliest organisms were anaerobic, in the ocean. First known fossils at 3.03.5 bya. When photosynthesis evolved in cyanobacteria and other bacteria, it introduced oxygen into the atmosphere. Living things today are classified into three “empires” or “domains.” For two billion years, about half of the history of life on earth, only two prokaryotic empires existed, the Archaea and Bacteria. Major event in the history of l.72.0 bya origin of eukaryotes, which are distinguished by features such as cytoskeleton, a nucleus with multiple chromosomes and a mitotic spindle. Earliest confirmed fossils are 1.5 billions years old. Nearly all have mitochondria and many have chloroplasts. These organelles are descended from bacteria that were ingested and later became endosymbionts. Most eukaryotes undergo meiosis, basis of sex and recombination For approximately a billion years the eukaryotes were exclusively unicellular. Another major event was the evolution of multicellularity (oldest fossils 1.2 bya). Oldest confirmed fossils of multicellular animals are about 575 million years old. Multicellularity may have evolved because of the advantage of “division of labor” between different cell types with different functions (increased specialization leads to increased efficiency) Precambrian: Ediacaran Fauna (575542 mya) Charniodiscus, Tribrachidium, Dickinsonia Paleozoic Era: Cambrian Explosion (542 mya) Emergence of almost all modern phyla (taxonomic rank below Kingdom and above Class e.g. Mollusca, Echinoderma), as well as many extinct groups. Diversification referred to as the Cambrian explosion because it transpired over a short time (20 million years) relative to preceding and succeeding intervals. What caused this “explosion”? Possibly a perfect storm of favorable conditions, including a warm, wet planet with no major ice masses High atmospheric oxygen levels due to cyanobacteria respiration Developed ozone layer which shielded the planet from damaging ultraviolet radiation Evolution of Hox gene and subsequent modifications, gene duplication events Increased morphological diversity due to “evolutionary arms races” End of period marked by mass extinction Paleozoic Era: OrdovicianDevonian (488359 mya) Many animal phyla diversified greatly in the Ordovician giving rise to many new classes and orders, including many echinoderms Jawless fish (agnathans) reached their highest development and diversity during this time Included one of the major mass extinction events (OrdovicianSilurian) The only living agnathans are hagfishes and lampreys First jawed fish (gnathostomes) appear during the early part of this time Acanthodians had up to five pairs of ventral finlike structures that may represent an early stage in the evolution of paired appendages. Placoderms had jaws, paired limbs (fins), and heavy body armor. The gnathostomes are mostly fish (25,00030,000 species), but also include all of the terrestrial vertebrates. The key innovation of a jawed mouth opened up diverse array of feeding options, especially predation. Hox gene duplication and subsequent evolution were critical to this evolutionary development. Primitive fishes had nine gill arches supporting eight gill slits. In early gnathostomes (e.g. Placoderms) the first two gill arches were lost and the third became modified into the jawbones. In more modern fish species, the fourth gill arch also became modified into additional jaw support. Allowed for increased biting power. Paleozoic Era: Terrestrial Life a lot happened Ordovician to Devonian! First known terrestrial organisms were sporebearing structures of very small plants, related to today’s liverworts they were not fished crawling out of the sea). By end of Devonian, land plants had greatly diversified: there were ferns, club mosses and horsetails which resembled large trees The earliest known arthropods colonization of land happened about 420450 mya Then the first terrestrial vertebrates and tetrapods by the end of the Devonian Jaekelopteus appears to be the largest arthropod ever discovered (2.5 meters/8 ft. long excluding appendages) Lobefinned fishes (Sarcopterygii) first appeared in the early Devonian (400 mya). Species like Eusthenopteron were typical fish in many characteristics, but possessed paired fleshy fins with well developed lateral bones and jointed ray fins. Tiktaalik (“tetrapodomorph”) was a recent (2006) discovery that represents a key transitional “missing link” stage between earlier sarcopterygian species and early tetrapods. It lacked gill cover bones which enabled a greater range of motion of the head. It also appears to have had primitive lungs for amphibious lifestyle. Possesses tetrapodlike robust ribcage. Acanthostega and Ichthyostega are some of the earliest tetrapods. Acanthostega had four distinct limbs (with digits), but lacked wrists and was not welladapted for weightbearing or movement on land. Ichthyostega appears to have been much more adapted for land movement. General body plan was very amphibianlike. Late Paleozoic Era: CarboniferousPermian (359251 mya) Late Paleozoic seed plants begin to diversify and the first winged insects evolve and rapidly diversify into many orders, including primitive dragonflies, grasshoppers, true bugs, and beetles During the Permian the continents approached one another and formed a single world continent (Pangaea) Permian ended 251 mya with two episodes of extinction that together constitute the most massive extinction event in the history of earth so far Cause not totally agreed upon, but likely triggered by vast volcanic eruptions which released poisonous gases and carbon dioxide, which in turn caused acid rain and global warming Meganeuropsis permiana largest insect that ever lived. Had a 1m wingspan. EndPermian mass extinction (251 mya) “Great Dying” 96% of all marine species and 70% of land species became extinct, including only known mass extinction of insects, within a few hundred thousand years (“blink of an eye”) .0125% time since origin of life Mesozoic Era (25165 mya) “Age of Reptiles or “Age of Dinosaurs” Includes the riassic, Jurassic, Cretaceous periods Of major importance was the breakup of supercontinent Pangaea (started about 175 mya). First separated into Laurasia and Gondwana. Most of the earth was warm, and the highest temperatures ever recorded were during the Cretaceous In marine environments, many previously decimated groups diversified again. Intensified “arms race” led to the disappearance of many nonarmored lineages. First flowering plants (angiosperms) appeared in early Cretaceous (145 mya), but Gymnosperms dominated for most of the Mesozoic. Some groups that are uncommon today were once key components of Mesozoic ecosystems. These include cycads, ginkos. Did Angiosperm Radiation Lead to Beetle Radiation? A VERY large percentage (about 80%) of the diversity of life on Earth comes from the radiation of these two groups: Insects make up about 950,000 species (400,000 species of beetles) and Angiosperms contain about 250,000 species. There are about 1,500,000 described species of all organisms. Radiation of amniote tetrapods. First dinosaurs evolved from a diapsid lineage during the mid Triassic (230 mya). Dominated the land in many ecological roles for 165 million years. Synapsids include the pelycosaurs and therapsids and later on the mammals in the late Triassic (200 mya). Mammals remained small and ecologically unimportant throughout the Mesozoic. Synapsids Permian Pelycosaurs, therapsids, and transition to Mesozoic mammals Dimetrodon, Pristerognathus, Tetraceratops, Oligokyphus Dinosaurs diversified during Mesozoic, before Cenozoic Went extinct, save for one lineage, at the end of the Cretaceous Known as the K /T boundary 65.5 mya One surviving lineage then diversified into about 10,000 species, more familiarly known as birds! Birds are dinosaurs!!! Cenozoic Era is sometimes called “the age of mammals”, and on a rough scale, mammals did replace dinosaurs…….. One predator replaces another: Tyrannosaurids replaced by Sabertoothed cat One herbivore replaces another: Diplodocids replaced by a chalicothere, bizarre horse relative Late Cenozoic Era: Pliocene (5.31.8 mya) About 3.5 mya the Isthmus of Panama arose, creating a bridge between North and South America. This resulted in the “Great American Interchange” of fauna between the continents. Many placentals dispersed from North America to South America, and marsupials and Xenarthrans dispersed from South America to North America. The connection of the Isthmus and the resulting change in ocean currents may have contributed to the following ice age of the Pleistocene. Late Cenozoic Era: Pleistocene (last 1.8 million years) Embraces a short time period (1.8 my), but it critically important for understanding today’s organisms, due to its recency and dramatic effects Continents configured much as today Comprised of at least four major glacial advances, and many minor ones The most recent glacial advance reached its maximum 18,000 years ago and melted back 15,000 to 8,000 years ago Pleistocene: Ecological consequences Profound effects on organisms When sea level was lower, many organisms moved between land masses that are now isolated Distributions shifted according to advance and retreat of ice and changes in overall temperature, as habitats became available and unavailable Many species that were broadly distributed became isolated in separated areas (termed glacial refugia where favorable conditions persisted during glacial periods Lecture 7 The Geography of Evolution Geographical Patterns in Evolution An Evolutionary Perspective Biogeography: the study of the processes that form an organism's’ geographic distribution. Typically considers studies at higher taxonomic levels. i.e. at the species level and above. Phylogeography: the study of the processes that form the geographic distribution of genetic lineages within species. Often ties into the study of speciation. History of Biogeography Charles Darwin(18091882): stating that all species of organisms arise and develop through the natural selection of small, inherited variations that increase the individual's ability to compete, survive, and reproduce. Alfred Russel Wallace(18231913): Wallace supplied Darwin with birds for his studies and decided to seek Darwin's help in publishing his own ideas on evolution. Both well known for identifying natural selection as a means of evolutionary change. But they also laid the groundwork for the field of biogeography. NOTE: Evolutionary biologists accurately predicted historical processes of the earth BEFORE geologists were involved! MANY biogeographic facts make little sense except in light of evolution… and this struck them both. As Darwin stated, the idea that species exist through special creation is hard to reconcile with biogeographic facts. However the observations make a lot more sense if a species: 1) has a definite site or region of origin 2) achieves a broader distribution by dispersal 3) becomes modified and gives rise to descendant species in the various regions in which it migrates (or becomes isolated due to movement of land masses) “Neither the similarity or dissimilarity of the inhabitants of different regions can be wholly accounted for by climatal and other physical conditions” Griffin (Old World vulture) and Black vulture (New World vulture) African longclaw (Africa) and Meadowlark (North America) Darwin, like Wallace and many other biogeographers, based many of his observations and conclusions from patterns of species on islands. He noted that a species had a single region of origin and had spread from there. Most of the species on islands are most obviously related to species on the nearest mainland (the apparent source of origin) The most remote oceanic islands generally have only species which are excellent longdistance dispersers. Leads to the Theory of Island Biogeography, as formulated by Robert MacArthur and E. O. Wilson. The size and distance of the island to the mainland will impact the number of species via immigration and extinction rate. Some of the basic principles are as follows: 1) The closer the island to another land mass, the higher the probability of colonization. 2) The older the island, the more likely it will be colonized. 3) The larger the island, the more species are likely to be established. 4) Geographic isolation reduces gene flow between populations. 5) Over time, colonial populations become genetically divergent from their parent population due to natural selection, mutation, and/or genetic drift. Major Patterns of Distribution: Biogeographic Realms Nearctic: North America Neotropical: South America Palearctic: Europe and Asia Ethiopian: Africa Oriental: India and Islands Antarctic: Southernmost part of South America + Antarctica History is often more important than current climatic conditions Each region has e ndemic fauna Northern Spring Salamander: Year round range in (valley and ridge) and highlands in New Jersey Pine Barrens Treefrog: Species Range in the Coastal Plain of New Jersey Range of the chinese alligator (alligator sinensis): very small part of eastern china Range of the american alligator (alligator mississippiensis): covers many of the southern east states Often taxa have disjunct distributions that may be explained by a combination of historical and contemporary (i.e. ecological) factors. Major Factors in Biogeography Vicariance: separation of populations due to a barrier. Example: mountain Can be due to a number of factors: geology, climate, ecology. Vicariance is typically thought of as the default explanation for the origination and distribution of much of the world’s biodiversity. Example: Great Basin pocket mouse and San Joaquin pocket mouse Dispersal: movements of individuals and the establishments of a population in a previously unoccupied region. Examples include the colonization of the Galapagos Islands and the expansion of armadillos into North America. Differences between Vicariance and Dispersal Vicariance is often expected to affect a wide range of organisms in a similar fashion. occurs at the same point in time Dispersal can produce more idiosyncratic patterns in different organisms Phylogenetic patterns are expected to be different under scenarios of vicariance and dispersal Fossil data, phylogenetic data, and molecular clocks can be used to evaluate biogeographic scenarios Lecture 8 Evolutionary Studies of Vicariant Processes Wallace’s line A noted geographic break that separates subgroups of organisms in a variety of plant and animal groups. Hypothesized that this has resulted from the breakup of tectonic plates during the middle to late Mesozoic (75160 MYA). Agamid lizards found on both sides of Wallace's’ line. Conflicting hypotheses on the origin of Australian and PNG agamid fauna. Example: Calotes calotes (Green Garden Lizard) male Vicariance All species from Australia and PNG form a clade that is sister to the SE Asia species. Molecular Clock estimates of divergence between Australian +PNG species vs SE Asia species is 150 MYA consistent with a mesozoic tectonic breakup. Phylogenies for other lizard families show similar patterns and dates. Dispersal Hawaiian islands offer a great system to study the role of dispersal in evolution. Islands are of different ages due to the movement of the Pacific plate over a “hot spot.” Phylogenetic expectations under a dispersal scenario: most basal lineages should occur in Kauai and youngest lineages should occur in Hawaii Example: Tetragnatha spiders Historical Biogeography Phylogenies play a central role in studying biogeographic patterns. Vicariance and dispersal are not mutually exclusive explanations for the distribution of a group of organisms, both can be factors. A third factor, extinction, is also an important consideration. While you can’t use extinct species in molecular phylogenetic studies, you can hypothesize extinction events to account for patterns that deviate from a pure model of vicariance. Phylogeographic analysis Phylogeographic detection of cryptic genetic lineages Plethodon jordani species complex mtDNA gene tree A vs. B= 16% sequence divergence Detection of divergent lineages containing geographic assemblages of alleles. Strongly suggests the presence of at least 2 separate species that have been diverging for a long time. Phylogenetic analysis is important in uncovering major evolutionary patterns. A phylogeographic analysis is different from historical biogeography in that population sampling is necessary. Phylogeographic analysis Phylogeographic analysis of the movement of genes. Within (and between) divergent lineages (species) we can study how genes move across populations. Gene Flow Range Expansion At this level, phylogeography needs to utilize populationgenetic approaches. phylogenies are viewed in a different way. We can call this “historical demography” Restricted Gene Flow Older, ancestral alleles have been around longer than younger tip alleles and have had more time to spread throughout the range of a species or population Range Expansion Younger, tip alleles will have had an opportunity to cover a large distribution due to a range expansion event Phylogeographic analysis of the movement of genes in the Plethodon jordani complex. Genetic patterns of range expansions are common throughout the distribution and history of the P. jordani complex Contiguous Range Expansion Long Distance Colonization Hypothetical distribution of the P. jordani complex during Pleistocene glaciations Cooler climate facilitated the movement of populations to lower elevations Phylogeographic analysis Phylogeography bridges the fields of phylogenetics and population genetics to give insight into major evolutionary patterns as well as more recent processes. Can be important in the recognition of new species, especially in systems with limited morphological variation (i.e.ryptic species ). When integrated with information from other sources (climate, ecology) the results can be informative about the processes that have acted to shape geographic patterns of evolution. Phylogeography and historical demography Effective population size (Ne) “the number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequencies under random genetic drift” Sewall Wright … or the number of individuals in an idealized population that would exhibit a certain amount of genetic variation Haplotype diversity (H) a measure of the degree of variation of haplotypes (alleles) found within a population Nucleotide diversity (pi) a measure of the average of nucleotide differences between an two DNA sequences chosen from a population A word about DNA barcoding… The idea: A single gene (i.e. Cytochrome oxidase subunit I) could be used to identify all living things. No need for taxonomists because all we need to do is get a gene sequence and we’ll know what an organism is. “Deus ex machina” philosophy The problems: It fails much of the time at least 30% by conservative estimates (Funk and Omland 2003, Sperling 2003). If species recently separated, then it is likely to fail to distinguish them genetically. If species are closely related, they may occasionally hybridize and this method will fail to identify them. Unfortunately, it most often misidentifies species in the most important cases (i.e. difficult to identify closely related species). Opposite of scientific process, as it employs deductive rather than inductive reasoning. Assumes nature is incredibly simple and consistent. Uses arbitrary thresholds for determining new species (i.e. 3% genetic divergence) Takes resources away from more rigorous science and misleads the public. “Meadow Group” (C. longilabris, nebraskana) < 3.5% sequence divergence > “Forest Group” (C. sexguttata, patruela, denikei) Taxonomic species are NOT monophyletic Lecture 9 Hypotheses for species nonmonophyly 1) Polymorphism 2) not hybridization 3) not incomplete lineage sorting Geography of Evolution: What determines the limits of species ranges? Why does the range end where it does? Species have a fundamental ecological niche the set of all environmental conditions in which a species can maintain stable population size Species also have a realized ecological niche the range that a species actually occupies Ecological Niche Modeling (ENM) Methods How is it actually created? What do you need? Georeferenced locality data for species Environmental layers detailed relevant climatic data for region of interest Niche modeling algorithm MAXENT (Philips, et al 2006) is a computational program often used to generate ENMS and SDMs. MAXENT generation of model All known localities for species of interest Ecological niche model created based on training data Species distribution model Model compared to test data Predicting species distributions witEcological Niche Modeling Hypothesis Distributions are maintained by environmental factors Hypotheses to explain incongruence Competitive exclusion Historical barrier Recent extinction Ecological Niche Modeling may be used for a variety of conversation applications 1) Validation of a historic/dubious species locality 2) Discovery of unknown populations for rare species 3) Discovery of new species which share a nearly identical fundamental niche based on niche conservatism and allopatric speciation Lecture 10 The Agents of Evolutionary Change Genes Within Populations Evolution can result from any process that causes a change in the genetic composition of a population We cannot talk about evolution therefore without considering population genetics the study of the properties of genes in populations. Five Agents of Evolutionary Change 1. Mutation ultimate source of variation 2. Gene flow movement of alleles between populations 3. Nonrandom mating can affect proportion of homozygotes 4. Genetic drift the effect of chance on small populations 5. Selection some genotypes do better than others in their environment Any of these forces may bring about changes in allele frequencies. Multiple forces can act at once! All completely new genetic variation arises via m utation Mutation (general)= change in the genetic material carried by individual organisms Mutation (detailed)= an error in the replication of a nucleotide sequence, or any other alteration of the genome (except recombination) Mutations can be caused by radiation, chemical mutagens, viruses, transposable elements, or errors in the DNA replication machinery. In a molecular context a gene mutation is an alteration of a DNA sequence, independent from whether or not it has phenotypic effect Mutations have evolutionary consequences only if they are transmitted to succeeding generations Mutations are considered by most biologists to be errors. Thus, the process of mutation is generally thought to be not an adaptation, but a consequence of unrepaired DNA damage. What are the different kinds of DNA mutations? Mutations can have phenotypic effects if they occur in proteincoding regions However, even in this case, many mutations will not have phenotypic effects. Why? Redundancy of genetic code (remember neutral theory) Synonymous (‘silent’) mutations h ave no effect on the amino acid sequence of the protein, therefore no effect on phenotype and the mutation is “hidden from selection” Nonsynonymous mutations result in an amino acid change, this change may have little or no effect on the function of the protein, and thus little phenotypic effect, or there may be substantial functional and phenotypic effects Natural selection acts on phenotypic variation Even though genetic differences exist, selection cannot act on them, because there i no phenotypic variation Note: mutations are NOT more frequent in “wobble” positions… they are just more frequently observed because they survived Gene Flow movement of alleles between po
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