Chapter 25 Outline - Summary Campbell Biology PDF

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Chapter 25: Phylogeny and Systematics Overview “Investigating the Tree of Life” 

Phylogeny is the evolutionary history of a species or a group of species

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They use systematics, an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct

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Systematists have traditionally studied morphologically and biochemical resemblances among organism as a basis for inferring evolutionary relationships

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Systematists have gained a powerful new tool, molecular systematics, which uses comparisons of DNA, RNA, and other molecules to infer evolutionary relationships between individual genes and even between entire genomes

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This information allows evolutionary biologists to construct a universal tree of all life 25.1 “Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence”

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Fossils can establish relationships between living organisms because they reveal ancestral characteristics that may have been lost over time in certain lineages The Fossil Record

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Sedimentary rocks are the richest source of fossils

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Deposits pile up and compress the older sediments into layers called strata

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The fossil record is based on the sequence in which fossils have accumulated in such strata

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Fossils only inform phylogeny only if we can determine their ages, clarifying the order in which various characteristics appeared and disappeared Morphological and Molecular Homologies

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Certain morphological and molecular similarities among living organisms can indicate phylogenetic history Sorting Homology from Analogy

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A potential red herring in constructing a phylogeny is similarity due to convergent evolution—called analogy—rather than to shared ancestry (homology)

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Another clue to distinguishing between homology and analogy is to consider the complexity of the characters being compared

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If genes in two organisms share many portions of their nucleotide sequences, it is highly likely that the genes are homologous Evaluating Molecular Homologies

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Molecular comparisons of nucleic acid often pose technical challenges

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The first step is to align comparable nucleic acid sequences from the two species being studied. If the species are very closely related, the sequences likely differ at only one or a few sites

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Nucleic acid sequences in distantly related species usually have different bases at many sites and may even have different lengths

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Over longer periods of time, insertions and deletions accumulated, altering the lengths of the gene sequences

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Systematists use computer programs to analyze comparable DNA segments of differing lengths and realign them properly

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Scientists have developed mathematical tools that can distinguish “distant” homologies from such coincidental matches in extremely divergent sequences 25.2 “Phylogenetic systematics connects classification with evolutionary history”

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Taxonomy is an ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences Binomial Nomenclature

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To avoid ambiguity when communicating about organisms, biologists refer to each species by a specific name, called a binomial

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The first part of the species’ name is the genus to which the species belongs

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The second part is the specific epithet, which is unique for each species within the genus Hierarchical Classification

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Beyond genera, systematists employ progressively more comprehensive categories of classification

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They place related genera in the same family, families => orders, orders => classes, classes => phylum, phylum => kingdoms, and kingdoms => domains

Linking Classification and Phylogeny

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Systematists use branching diagrams called phylogenetic trees to depict their hypotheses about evolutionary relationships

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The branching of such trees reflects the hierarchical classification of groups nested within more inclusive groups

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A phylogenetic tree is often constructed from a series of dichotomies, or twoway branching points; each branch point represents the divergence of two species from a common ancestor

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Each of the “deeper” branch points represents progressively greater amounts of divergence

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The sequences of branching in a tree does not indicate the actual age of the particular species 25.3 “Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters”

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Patterns of shared characteristics can be depicted in a diagram called a cladogram

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A cladogram by itself does not imply evolutionary history, but if the shared characteristics are due to common ancestry, then the cladogram forms the basis of a phylogenetic tree

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A clade is defined as a group of species that includes an ancestral species and all its descendants. The analysis of how species may be grouped into clades is called cladistics

Cladistics

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A valid clade is monophyletic, signifying that it consists of the ancestral species and all its descendants

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A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

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A polyphyletic grouping consists of several species that lack a common ancestor Shared Primitive and Shared Derived Characters

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After systematists have separated homologous and analogous similarities, they must sort through the homologies to distinguish shared primitive and shared derived characters. Characters here refers to any feature that a particular taxon possesses

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A shared primitive character is shared beyond the taxon we are trying to define

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A shared derived character is an evolutionary novelty unique to a particular clade Outgroups

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Systematists use outgroup comparison to differentiate between shared derived characters and shared primitive characters

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An outgroup is a species or a group of species that is closely related to the ingroup, the various species we are studying

Phylogenetic Trees and Timing Phylograms

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In a phylogram, the length of a branch reflects the number of changes that taken have place in a particular DNA sequences in that lineage Ultrametric Trees

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Even though the branches in a phylogram may have different lengths, all the different lineages that descend from a common ancestor have survived for the same number of years

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The equal amounts of chronological time can be represented in an ultrametric tree

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The branching pattern is the same as in a phylogram, but all of the branches that can be traced from the common ancestor to the present are of equal length

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They can draw on data from the fossil record to place certain branch points in the context of geologic time Maximum Parsimony and Maximum Likelihood

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According to the principle of maximum parsimony, we should first investigate the simplest explanation that is consistent with the facts

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The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequences of evolutionary events

Phylogenetic Trees as Hypotheses

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Any phylogenetic tree represents a hypothesis about how the various organisms in the tree are related to one another. The best hypothesis is the one that fits all the available data

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Applying parsimony in molecular systematics is more reliable for a data set of many long DNA sequences than for a smaller data set

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The strongest phylogenetic hypotheses are those supported by multiple lines of molecular and morphological evidence as well as by fossil evidence 25.4 “Much of an organism’s evolutionary history is documented in its genome”

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The ability of molecular trees to encompass both short and long periods of time is based on the fact that different genes evolve at different rates, even in the same evolutionary lineage Gene Duplications and Gene Families

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Gene duplication increases the number of genes in the genome, providing opportunities for further evolutionary changes

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Orthologous genes refer to the homologous genes that are passed in a straight line from one generation to the next but have ended up in different gene pools because of speciation

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Paralogous genes result from gene duplication, so they are found in more than one copy in the same genome

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Orthologous genes can only diverge after speciation has taken place, with the result that the genes are found in separate gene pools

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Paralogous genes can diverge even while they are in the same gene pool, because they are present in more than one copy in the genome Genome Evolution

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Orthologous genes are widespread and can extend over huge evolutionary distances

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The number of genes seems not to have increased through duplication at the same rate of phenotypic complexity 25.5 “Molecular clocks can help track evolutionary time” Molecular Clocks

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The concept of a molecular clock is a yardstick 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

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The assumption underlying the molecular clock is that the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from their common ancestor

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You can calibrate the molecular clock of a gene that has a reliable average rate of evolution by graphing the number of nucleotide differences against the times of a series of evolutionary branch points that are known from the fossil record Neutral Theory

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Neutral theory is that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection

Difficulties with Molecular Clocks

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Molecular clocks does not run as smoothly as neutral theory predicts

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Many irregularities are likely to be the result of natural selection in which DNA changes are favored over others The Universal Tree of Life

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Investigators use two criteria to identify regions of DNA molecules that can demonstrate the branching pattern of this tree

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The regions must be able to be sequenced, and they must have evolved so slowly that homologies between even distantly related organisms can still be detected

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The tree of life consists of three great domains: Bacteria, Archaea, Eukarya

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Domain bacteria includes most of the currently known prokaryotes

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Archaea consists of a diverse group of prokaryotic organisms that inhabit a wide variety of environments

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Eukarya consists all of the organisms that have cells containing true nuclei

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The early history of these domains is not clear

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Horizontal gene transfer is when genes are transferred from one genome to another through mechanisms such as transposable elements, and perhaps through fusions of different organisms

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Because phylogenetic trees are based on the assumption that genes are passed vertically from one generation to the next, the occurrence of such horizontal events means that the universal trees built from different genes often give inconsistent results, particularly near the root of that tree...