UVA BIOL 2200 Lessons 10-11 Textbook Notes

L10&11 Textbook Notes: Phylogeny and the Tree of Life (C26) phylogeny and evolutionary relationships • phylogeny: the evolutionary history of a species or group of species • systematics: a discipline focused on classifying organisms and determining their evolutionary relationships binomial nomenclature • the first part of a binomial is the genus • the second part of a binomial is the specific epithet, which is unique for each species within a genus hierarchical classification • following genera in the linnaean system: • related genera are in the same family • related families are in the same order • related orders are in the same class • related classes are in the same phyla • related phyla are in the same kingdom • related kingdoms are in the same domain • taxon: a named group at any level of the hierarchy linking classification and phylogeny • phylogenetic tree: a branching diagram representing the evolutionary history of a group of organisms • some mistakes in classification can be made if shared features are lost throughout evolution, or new evidence can change classification • the linnaean system distinguishes groups but does not given information about their evolutionary relationships to one another phylogenetic trees • each branch point represents the common ancestor of the two evolutionary lineages diverging from it • evolutionary lineage: sequence of ancestral organisms leading to a particular descendant taxon • sister taxa: groups of organisms that share an immediate common ancestor that is not shared by any other group • members of a sister group are each other’s closest relatives • phylogenetic trees are rooted; a branch point within the tree represents the most recent common ancestor of all taxa in the tree • basal taxon: a lineage that diverges from all other members of its group early in its history • trees show patterns of descent rather than phenotypic similarity • the ages of taxa or branch points cannot be inferred • one taxon cannot be assumed to have evolved from the one next to it • if a species shares the same most recent common ancestor with one species as it does with other species, they are just as closely related applying phylogenies • phylogenies can identify a species’ closest living relatives, which can be used to transfer alleles from one to another • species identities can be determined by analyzing how related their dna sequences are to other organisms morphological and molecular homologies • homologies: phenotypic and genetic similarities due to shared ancestry • morphological divergence between related species can be great and their genetic divergence small (or vice versa) sorting homology from analogy • analogy: similarity between organisms that is due to convergent evolution • convergent evolution occurs when similar environmental pressures and natural selection produce similar adaptations in organisms from different evolutionary lineages • the more elements that are similar in two complex structures, the more likely that they came from a common ancestor • if genes in two organisms share many portions of their nucleotide sequences, it is likely that they are homologous evaluating molecular homologies • if the species are closely related, their dna sequences will probably differ at only one or a few sites • distantly related species usually have different bases and lengths because insertions and deletions accumulate over long periods • many differences in genes indicate great divergence in lineages since their common ancestor • in analogy, bases can be shared in otherwise very different sequences as coincidental matches cladistics • cladistics: an approach in which common ancestry is the primary criterion used to classify organisms • clades: groups including an ancestral species and all of its descendants • clades are nested within larger clades • a taxon is equivalent to a clade only if it is monophyletic, meaning that it consists of an ancestral species and all of its descendants • a paraphyletic group consists of an ancestral species and some, but not all, of its descendants • a polyphyletic group includes distantly related species but not their most recent common ancestor shared ancestral and shared derived characters • because of descent with modification, organisms have characters that are similar to and different from their ancestors • shared ancestral character: a trait that originated in an ancestor of the taxon • shared derived character: an evolutionary novelty unique to a clade (can also refer to the loss of a feature) inferring phylogenies using derived characters • outgroup: a species or group of species from an evolutionary lineage that is closely related to but not part of the group of species being studied (ingroup) • if all of the species in the ingroup have a certain trait, it was present in their ancestor but not the outgroup • the following trait that is present in, for example, all but one of the ingroup species, arose in a lineage leading to all members of the ingroup except for that one phylogenetic trees with proportional branch lengths • in some phylogenetic trees, branch lengths are proportional to the amount of evolutionary change or the times at which events occurred • if the total length of the horizontal lines from the base of the tree to one species is less than that leading to another, then fewer genetic changes in the former lineage (or vice versa) • if the two species are shown to have evolved for an certain amount of time after diverging from a common ancestor, the rate of change can also be inferred maximum parsimony and maximum likelihood • maximum parsimony: we should first investigate the simplest explanation that is consistent with the facts • the most parsimonious tree requires the fewest evolutionary events • maximum likelihood: identifies the tree most likely to have produced a given set of dna data based on certain probability rules about how dna sequences change over time phylogenetic trees as hypotheses • phylogenetic bracketing: predicting that features shared by two groups of closely related organisms are present in their common ancestor and all of its descendants unless independent data indicate otherwise molecular data and trees • molecular data uncovers evolutionary relationships between groups with little morphological similarities • molecular trees can represent short or long periods of time since different genes can evolve at different rates gene duplications and gene families • molecular techniques help to trace the phylogenies of gene duplications • molecular phylogenies must account for duplications that have resulted in gene families, groups of related genes within an organisms’s genome • orthologous genes: homology is the result of a speciation event and occurs between genes found in different species • • reflect the history of speciation events paralogous genes: homology is the result of gene duplication, so multiple copies have diverged from one another within a species genome evolution • disparate organisms can still share biochemical and developmental pathways due to orthologous genes • the number of genes a species has does not increase through duplication at the same rate as phenotypic complexity molecular clocks • molecular clock: an approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates • the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the genes branched from their common ancestor • the number of nucleotide substitutions in paralogous genes is proportional to the time since the ancestral gene was duplicated • these genetic differences are compared to the dates of evolutionary branch points from the fossil record differences in clock speed • if a mutation is selectively neutral, it is neither beneficial nor harmful • if it has no effect on fitness and is not removed by selection, the rate of evolution should be regular • if the sequence of amino acids is essential to survival, most mutations will be harmful, so the genes change slowly • if the sequence of amino acids is less critical, the genes change quickly potential problems with molecular clocks • most irregularities are likely the result of natural selection, making them non-neutral • molecular clocks can be made more accurate by calibrating them with the known rates at which many genes have evolved two kingdoms to three domains • three domains - bacteria, archaea, and eukarya - are used instead of the two kingdoms of plants and animals • the bacteria domain contains most of prokaryotes • archaea contains a diverse group of prokaryotic organisms • the eukaryotic domain includes all organisms with cells containing true nuclei horizontal gene transfer • the first major split in the history of life occurred when bacteria diverged from other organisms • different genes yield different results about relationships • horizontal gene transfer: a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection, and fusion of organisms • explains inconsistency in trees based on vertical gene transfer • horizontal transfer can occur between eukaryotes or between eukaryotes and prokaryotes