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Biological Sciences
Mark Fitzpatrick

BIOA01H3 – Lecture 31 st Chapter 18 18.2 Systematic Biology: An Overview  systematic biology, classification, and taxonomy help us organize and understand information about biological world Science of systematics has two major goals: 1. Reconstruct phylogeny or evolutionary history of a group of organisms  Presented as phylogenetic trees  formal hypotheses identifying likely relationships among species  Often revised as new data presented 2. Taxonomy  the identification and naming of species and their placement in a classification. Classification: arrangement of organisms into hierarchical groups reflecting relatedness.  Most systematics want classification to mirror phylogenetic history and, thus, adaptive radiation (evolutionary history) of group of organisms in question 18.3 the Linnaean System of Classification  Linnaeus described and named thousands of species on basis of similarities and differences; kept track by creating taxonomic hierarchy A family is a group of genera that closely resemble on another  orders, classes, phyla, kingdoms, and then into three domains.  Organisms included within any category of taxonomic hierarchy make up a taxon i.e. woodpeckers are a taxon (Picidae) at the family level, and pine trees are a taxon (Pinus) at the genus level 18.4 From Classification to Phylogeny  For at least 200 years, systematists relied on organismal traits (mainly morphology) when analyzing evolutionary relationships & classifying organisms  During Linnaeus, developed phylogenies based on characters such as chromosomal anatomy; details of physiological functioning; morphology of subcellular structures, cells, organ systems, and whole organisms; and patterns of behaviours  Systematists today now also use molecular sequences of nucleic acids and proteins 1 18.5 Evaluating Systematic Characters  Systematists seek characters that are independent markers of underlying genetic similarity and differentiation  Limbs of tetrapod vertebrates are homologous characters sharing the same embryological (developmental) history, and are useful in preparing phylogenies  Phenotypic similarities between organisms reflect underlying genetic similarities  Comparison of homologous characters used as indicators of common ancestry and genetic relatedness  Analogous characters have same fnc; they’re homoplasious (none form homoplasies), phenotypic similarities that evolved independently in different lineages  Systematists exclude homoplasies b/c don’t provide info on shared genetic ancestry  Mosaic evolution refers to the reality that in all evolutionary lineages, some characters evolves slowly, whereas others evolve rapidly  Every species displays mixture of ancestral characters and derived characters  Derived characters provide most useful information about evolutionary relationships b/c once derived traits established, it’s present in all descendants  Systematists frequently use outgroup comparisons to identify ancestral and derived characters; involves comparing group under study w/ more distantly related species noth otherwise included in analysis 18.6 Phylogenetic Inference and Classification  When converting phylogenetic tree into classification, systematists use principle of monophyly  try to define monopyletic taxa  those derived from a single ancestral species  polyphyletic taxa  include species from separate evolutionary lineages  if, based on the presence of wings, we placed bats, birds, pterosaurs, and insects in one taxonomic group, it would be polyphyletic  paraphyletic taxon  includes an ancestor and some, but not all, of its descendants  traditional taxon class Reptilia is paraphyletic b/c includes some “obvious” reptiles (i.e. turtles, lizards, crocodiles) but not other descendants (mammals and birds)  many systematists also create parsimonious phylogenetic hypotheses; include fewest possible evolutionary changes to account for diversity within lineage 2  justification of this approach is assumption of parsimony  simplest explanation should be most accurate  means that any particular evolutionary change is an unlikely event and presumably happened only once in any evolutionary lineage 18.6a Traditional Evolutionary Systematics Classifies Organisms According to Their Evolutionary History Using Phenotypic Similarities and Differences  most systematists followed Linnaeus’s practice of using phenotypic similarities and differences to infer evolutionary relationships  traditional evolutionary systematics; groups together species that share ancestral and derived characters  i.e. mammals defined by internal skeleton, vertebral column, and four limbs – ancestral characters among tetrapod vertebrates; mammals also have hair, mammary glands, and four-chambered heart – these are derived characters but four-chambered heart also occurs in birds and some reptiles 18.6b Cladistics Make Classifications Based on Shared Derived Characters  cladistics emerged when researches criticized lack of clarity in classifications based on two distinct phenomena; branching evolution and morphological divergence  Hennig argued that classifications should be based solely on evolutionary relationships Cladistics produces phylogenetic hypotheses and classifications that reflect only branching pattern of evolution. Ignores morphological divergence.  Group together species that share derived characters  Cladists argues that mammals form monophyletic lineage, a clade, b/c have unique set of derived characters, incl. hair, mammary glands, reduction of bones in lower jaw, and four-chamber heart  Ancestral characters found in mammals i.e. internal skeleton, vertebral column, and four legs don’t distinguish them from tetrapod vertebrates so these traits excluded from analysis  Phylogenetic trees produced by cladists (cladograms) illustrate hypothesized sequence of evolutionary branchings w/ hypothetical ancestor at each branching point  Cladograms strictly portray monophyletic groups & under assumption of parsimony  Most biologists use cladistics approach b/c evolutionary focus, clear goals, and precise methods  Propose using strictly cladistics system, called PhyloCode, that identifies and names clades instead of placing organisms into familiar taxonomic groups 3 18.7a Molecular Clocks Estimate Times of Divergences Using Shared Mutations  Molecular phylogenetics based on observation that many molecules been conserved by evolution  Mutations in some types of DNA appear to arise at relatively constant rate; differences in DNA sequences of two species can serve as molecular clock  indexing their times of divergence  Large differences suggests divergence in distant past, small differences suggest more recent common ancestor  Mosaic evolution occurs at molecular level, so diff. molecules exhibit individual rates of change  Mitochondrial DNA (mtDNA) evolves relatively quickly; useful for dating evolutionary divergences that occurred within last few million years  Chloroplast DNA (cpDNA) and genes that encode ribosomal RNA evolve slowly, providing info about divergence hundreds of millions of years ago 18.7b Molecular Data Are Extracted and Segments of Nucleic Acid Are Used for Analysis  Practice of molecular phylogenetics based on set of distinctive methods  After selecting protein molecule or segment of nucleic acid for analysis, systematists determine exact sequence of amino acids (in case of proteins) or nucleotide bases (in case of DNA or RNA)  Amino acid sequencing allows systematists to compare primary structure of protein molecules directly  Amino acid sequence of protein determined by sequence of nucleotide bases in gene encoding that protein  When two species exhibit similar amino acid sequences for same protein, infer genetic similarity and evolutionary relationship 18.7c Molecular Sequences Are Aligned to Correct for the Effects of Insertions and Deletions  Before comparing molecular sequences from different organisms, homologous sequences being compared must be properly aligned  Once aligned, comparison of nucleotide base or amino acid sequences can be used to determine whether mutations or other processes produced evolutionary changes in sequences  These similarities/differences can be used to create phylogenetic trees, each of which are hypothesis about evolutionary relationships  Different assumptions may yield alternative trees for any data set, therefore systematists developed several approaches for comparing molecular sequences and constructing trees  For DNA sequences, simplest approach is to count number of similarities and differences between
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