Chapter 26 Notes
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Date Created: 02/18/16
Biology Chapter 26 Notes Investigating the tree of life 0 Legless lizards have evolved independently in several different groups Phylogeny is the evolutionary history of a species or group of related species For example a phylogeny shows that legless lizards and snakes evolved from different lineages of legged lizards The discipline of systematics classi es organisms and determines their evolutionary relationships 0 Concept 261 Phylogenies show evolutionary relationships 0 O Taxonomy is the scienti c discipline concerned with classifying and naming organisms Linking classi cation of phylogeny Binomial Nomenclature Twopart name for species and hierarchical classi cation The two part scienti c name of a species is called a binomial I The rst part of the name is the genus The second part is unique for each species within the genus Both parts together name the species not just the second part 0 Hierarchical Classi cation The taxonomic groups from broad to narrow are domain kingdom phylum class order family genus and species A taxonomic unit at any level of hierarchy is called a taxon The broader taxa are not comparable between lineages For example an order of snails has less genetic diversity that an order of mammals o Linking classi cation and phylogeny The evolutionary history of a group of organisms can be represented in a branching phylogenic tree Linnaean classi cation binomial nomenclature and phylogeny can differ from each other Systematists have proposed a classi cation system that would recognize only groups that include a common ancestor and all its descendants A phylogenic tree represents a hypothesis about evolutionary relationships Erarich paint Eastejineaees airEras GE LINEEGE This branch point represents the cummun ancestnr of taxa Each branch point represents the divergence of two spices Tree branches can be rotated around a branch point without changing the evolutionary relationships Sister taxa are groups that share an immediate common ancestor A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree A basal taxon diverges early in the history of a group and originates near the common ancestor of the group A polytomy is a branch form which more than two groupings emerge TextHi Tait Eister taxa Tax22in Cid Texan El Texan E Tamari F 1 asal Tam rl Tia n This branch paint farms 3 paly t my an unrescillyed pattern f divergence Concept 262 Phylogenies are inferred from morphological and molecular data 0 To infer phylogenies systematists gather information about morphologies genes and biochemistry of living organisms o Morphological and molecular homologies Phenotypic and genetic similarities due to shared ancestry are called homologies Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences 0 Sorting Homology from Analogy While constructing a phylogeny systematists need to distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry Analogy is similarity due to convergent evolution Convergent evolution occurs when similar environmental pressures and natural selection produce similar analogous adaptations in organisms from different evolutionary lineages Bat and bird wings are homologous as forelimbs but analogous as functional wings Analogous structures or molecular sequences that evolved independently are also called homoplasies Homology can be distinguished from analogy by comparing fossil evidence and degree of complexity The more elements that are similar in two complex structures the more likely it is that they are homologous 0 Evaluating molecular homologies Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms It is also important to distinguish homology from analogy in molecular similarities 0 Concept 263 Shared characters are used to construct phylogenic trees 0 Once homologous characters have been identi ed they can be used to infer a phylogeny o Cladistics Cladistics groups organisms by common descent monophyly A clade is a group of species that includes an ancestral species and all its descendants Clades can be nested in larger clades but not all groupings of organisms qualify as clades A clade is a monophyletic group signifying that it consists of the ancestor species and all its descendants A paraphyletic grouping consists of an ancestral species and some but not all of the descendants A polyphyletic grouping includes distantly related species but does not include their most recent common ancestor Sometimes this is a group de ned by an analogous character not a homology 0 For example the quotgroup of all vertebrates that can yquot Polyphyletic groups are distinguished from paraphyletic groups by the fact that they do not include the most recent common ancestor Biologists avoid de ned polyphyletic groups and instead reclassify organisms if evidence suggests they are polyphyletic a Ml ll39llilpihyl 39 gnaw cladEa E33 Fara hyletii rm Dz Pnnlyphyletie artistry A A IE39i Emu p I E El Emu p IIE I II D D E r E Emup Ii E F F F E El 393 0 Shared ancestral and shared derived characters 0 In comparison with its ancestor an organism has both shared and different characteristics 0 A shared ancestral character is a character that originated in an ancestor of the taxon Example the backbone for mammalsquot o A shared derived character synapomorphy is an evolutionary novelty unique to a particular cade This is the modern interpretation of homology Example quotIn mammals hair is considered a shared derived character an evolutionary novelty unique to a cadequot o A character can be both ancestral and derived depending on the context Inferring phylogenies using derived characteristics 0 When inferring evolutionary relationships it is useful to know in which cade a shared or derived rst appeared 0 An outgroup is a species or group of species that is closely related to the ingroup the various species being studied The outgroup is a group that has diverged before the ingroup Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics 0 Maximum parsimony and maximum likelihood o Systematists can never be sure of nding the best tree in a large data set 0 They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood 0 Maximum parsimony assumes that the tree that requires the fewest evolutionary events appearances of shared derived characters is the most likely o The principle of maximum likelihood states that given certain rules about how DNA changes over time a tree can be found that re ects the most likely sequence of evolutionary events 0 Computer programs are used to search for trees that are parsimonious and likely Phylogenetic trees as hypotheses o The best hypotheses for phylogenetic trees t the most data morphological molecular and fossil o Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendants For example phylogenetic bracketing allows us to infer characteristics of dinosaurs 0 Birds and crocodiles share several features four chambered hearts song nest building and brooding 0 These characteristics likely evolved in a common ancestor and were shared by all of its descendants including dinosaurs The fossil record supports nest building and brooding in dinosaurs Concept 264 An organism s evolutionary history is documented in its genome Comparing nucleic acids or other molecules to infer relatedness is a valuable approach for tracing organisms evolutionary history 0 DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago mtDNA evolves rapidly and can be used to explore recent evolutionary events Gene duplications and gene families 0 O 0 Gene duplication increases the number of genes in the genome providing more opportunities for evolutionary changes Repeated gene duplications result in gene families Like homologous genes duplicated genes can be traced to a common ancestor Orthologous genes are found in a single copy in the genome and are homologous between species They can diverge only after speciation occurs Paralogous genes result from gene duplication so are found in more than one copy in the genome They can diverge within the clade that carries them and often evolve new functions Genome evolution Orthologous genes are widespread and extend across many widely varied species For example humans and mice diverged about 65 million years ago and 99 of our genes are orthologous Gene number and the complexity of an organism are not strongly linked For example humans have only four times as many genes as yeast a singlecelled eukaryote Genes in complex organisms appear to be very versatile and each gene can encode multiple proteins that perform many different functions Concept 265 Molecular clocks help track evolutionary time To extend phylogenies beyond the fossil record we must make an assumption about how molecular change occurs over time Molecular clocks O A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change In orthologous genes nucleotide substitutions are assumed to be proportional to the time since they last shared a common ancestor In paralogous genes nucleotide substitutions are proportional to the time since the genes became duplicated Molecular clocks are calibrated against branches whose dates are known from the fossil record Individual genes vary in how clocklike they are 0 Differences in clock speed 0 If most of the evolutionary change in genes and proteins has no effect on tness then the rate of molecular change should be regular like a clock Differences in clock rate for different genes are a function of the importance of the gene and how critical the speci c amino acid is to protein function 0 Potential problems with molecular clocks O The molecular clock does not run as smoothly as expected if mutations were neutral lrregularities result from natural selection in which some DNA changes are favored over others Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty The use of multiple genes or genes that evolved in different taxa may improve estimates 0 Applying a molecular clocks dating the origin of HIV 0 O Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates HIV spread to humans more than once Comparison of HIV samples shows that the virus evolved in a very clocklike way 0 Application of a molecular clock to one strain of HIV 0 suggests that that strain spread to humans during the 1930s A more advanced molecular clock approach estimated the rst spread to humans around 1910 0 Concept 266 Our understanding of the tree of life continues to change based on new data 0 Recently we have gained insight into the very deepest branches of the tree of life through molecular systematics From two kingdoms to three domains 0 Early taxonomists classi ed all species as either plants or animals Later ve kingdoms were recognized Monera prokaryotes Protista Plantae Fungi and Animalia More recently the threedomain system has been adopted Bacteria Archaea and Eukarya The threedomain system is supported by data from many sequenced genomes The important role of horizontal gene transfer 0 The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria The tree of life is based largely on rRNA genes however some other genes reveal different relationships There have been substantial interchanges of genes between organisms in different domains Horizontal gene transfer is the movement of genes from one genome to another Horizontal gene transfer occurs by exchange of transposable elements and plasmids viral infection and fusion of organisms Disparities between gene trees can be explained by the occurrence of horizontal gene transfer Horizontal gene transfer has played a key role in the evolution of both prokaryotes and eukaryotes 0 Some biologists argue that horizontal gene transfer was so common that the early history of life should be represented as a tangled network of connected branches
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