1362-SP10-Lecture-11_41509

1362-SP10-Lecture-11_41509 - Phylogeny A snake or lizard...

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Unformatted text preview: Phylogeny A snake or lizard species? • Understanding of evolutionary relationships (phylogeny) allows one to compare traits of related species to answer such questions. • Constructing phylogenies occurs via systematics classifying organisms & determining evolutionary relationships. • Employ a range of data for systematics: fossils, molecules, genes, morphological data, and behavioral information. • Taxonomy: science of naming, describing, & classifying organisms – Binomial nomenclature: Linnaeus’ system of naming an organism genus & species (e.g., Homo sapiens); each term in Latin form. “sapiens” is one of several species in the genus “Homo” Taxonomic Classification • Linnaeus developed a hierarchical classification scheme: increasingly inclusive categories closely related species grouped in same genus & extending to domain (largest grouping) • Named taxonomic unit at any level is a taxon, i.e., Mammalia (class level) • Importance of taxonomy – Identification of organisms: medical applications; ecological studies – Taxonomy often reflects evolutionary relationships Biological Classification of Life Life Life on Earth Prokaryotes Domain Eubacteria Kingdom Eubacteria Domain Archaea Kingdom Archaebacteria Eukaryotes Simple multicells or unicells Domain Eukarya Multicellular Heterotrophic Autotrophic Kingdom Protista (photosynthetic) Kingdom Plantae • Constructed from comparison of cellular, metabolic, molecular data. Absorptive Ingestive nutrition nutrition Kingdom Fungi Kingdom Animalia • Linking classification & phylogeny: how would a phylogenetic tree of a human, a yeast, & a tomato look like based on the information in the given classification shown here? Reading a Phylogenetic Tree current species (descendants) Branch points (nodes) represent division of lineages; equate to speciation events. Root of the tree ancestral species Lines of descent Time component (relative or absolute) to a phylogenetic tree Linking Classification & Phylogeny • The evolutionary history of a group is represented by a phylogenetic tree. • Interpret solely in terms of patterns of descent • In some cases, the pattern matches the taxonomic classification, but not always. Example: classification of birds • Base classification solely on phylogeny ?– group descendants of common ancestors together. Utility of Phylogenetic Trees: Phylogeny of Immunodeficiency Virus • HIV is a zoonotic disease (transfer from animal host to human) • How & where did virus enter human population? • Compare genomes of immunodeficiency viral types to construct tree. • Discover HIV has two origins: – HIV‐1 from chimps (central Africa) and – HIV‐2 from mangabeys (west Africa) Reconstructing Phylogenies • In reconstructing phylogenies, one first distinguishes among homologous & homoplastic (analogies) features: – Homologous features: traits shared by species that have been inherit‐ ed from a common ancestor; reflects shared evolutionary history. • Example: limb bones of vertebrates – Homoplastic features: does not reflect shared history, rather similarity due to convergent evolution. • Animals from different lineages evolved similar (homoplastic) adaptations independently under similar selection pressures. • Example: insect wing v. bird wing • Closer view of homologies & homoplasies on next slide Homologies & Homoplasies Example: limbs evolved from a tetrapod ancestor; its’ decendants inherited this feature, and is a homology shared with crocs, birds, mice, bats, and others. In examining bird & bat (bats are mammals) ancestry, both have wings, does this imply they are more closely related to each other than to mice & crocodiles? Despite homologous bone structure, a bat wing is covered with skin; bird wing is covered with feathers. • Suggests an uncommon ancestry • Wings are a homoplastic feature, though as limbs they are homologous. • Evolved independently from different, non‐ flying ancestors by convergent evolution. Tetrapod ancestor • Once homologous features are established, then one infers phylogeny from these homologous characters. • Conversion of phylogenies into taxonomic classifications involves a form of systematics termed cladistics, in which organisms are classified based on common ancestry. • A taxonomic group is only considered as such if it is a monophyletic clade, i.e., consists of an ancestor and all its’ descendants. Contrast monophyletic clade with: – Paraphyletic: includes ancestor, but not all of the descendants – Polyphyletic: comprises taxa with different ancestors. Different ancestor for “C” Cladistics Common ancestor “G” excluded • Clades, as in taxonomic groupings, are nested within larger clades. Clades are identified using shared derived characters; these are differentiated from shared ancestral characters: All similar characters Homoplasies Homologies Ancestral Derived (unique to clade) • Shared ancestral characters: common to all members of a taxon – Defines a broad taxon; based on a more distant common ancestry • Shared derived characters: variation from ancestral form; separates larger taxon into smaller taxa – Based on more recent common ancestry (Tetrapod ancestor) • A single trait may be derived or ancestral, depending on the frame of reference, e.g., four limbs is an ancestral character of all tetrapods (green shaded area), but among vertebrates it is a derived trait that only tetrapods possess (fishes, sharks do not). Example on next slide. Comparing Ancestral & Derived Characters Reptiles & Mammals are in the subphylum Vertebrata, whose members are distinguished by the presence of a backbone: Reptiles & Mammals Vertebral column Subphylum is an ancestral Vertebrata character among reptiles & mammals; can’t use to differentiate them Vertebrate ancestor Reptiles Mammals 3 inner ear bones Vertebrate 3 inner ear bones is a derived character that Classes separates mammals from reptiles. This character is Vertebrate ancestor ancestral among mammals. Mammalian Lions, wolves Orders Bats Reptiles carnassials 3 inner ear bones Vertebrate ancestor Separate class Mammalia into orders: Example: lions, wolves,& bats; lions & wolves are carnivores with teeth called carnassials; this is a derived trait separating them from other mammals, but ancestral to all carnivores. Constructing a Phylogenetic Tree • As shown in the previous slide, a simple phylogenetic tree of a group of organisms can be constructed from a series of dichotomies (i.e., presence or absence of derived traits). • In an outgroup analysis, an outgroup is used for comparison and represents a lineage closely related to the group of interest, termed the ingroup, but diverged earlier than any other members in the ingroup. • The outgroup is used to differentiate shared ancestral characters ‐ those present in both the ingroup & outgroup, from shared derived ones ‐ those evolved in the ingroup since they separated from the outgroup lineage. • Example: relationship of 8 chordate species (lancet, lamprey, tuna, salamander, turtle, & leopard) All possess a notochord during development; this becomes the vertebral column as vertebrates mature; does not occur lancelets. Thus, lancelets separated from the lineage leading to vertebrates; they are the outgroup. Combine information of derived traits to construct phylogenetic tree: 0 = absent 1 = present These are shared derived characters among vertebrates Assumptions: each derived trait evolved only once and traits were not lost once they appeared. • Phylogenetic trees are hypotheses about how the organisms in the tree are related to one another. • The hypothesis may be challenged by new data resulting in modification of the tree. • Can use trees to test predictions : example – bird phylogeny Evidence shows birds descended from dinosaurs as shown; the closest living relatives to birds are crocodiles. Do they have features in common? Features in common: ‐ 4‐chambered heart ‐ Build nests & “sing ” ‐ Care for eggs by “brooding” ‐ Feathers are modified scales Can reason that their common ancestor & all descendants should have the same features; predict that dinosaurs have these too. Fossil Evidence to Support Prediction Fossil evidence for nesting & brooding behavior; internal organs (heart) rarely fossilize, thus the number of chambers cannot be determined. Molecular Homologies • Determine phylogenies based on comparison of nucleotide sequences and/or amino acid sequences of proteins: – Allows one to examine the phylogeny of very dissimilar species – Examine genetic diversity within a species – Determine evolution of specific genes Identical, homologous DNA segments of species 1 & 2; begin to diverge from common ancestor. Deletions & insertions occur Homologous regions (red letters) do not align because of mutations Homologous regions aligned via computer analysis Phylogenetic Trees Based on Molecular Data Comparison of DNA sequences of a homo‐ logous developmental gene; branch lengths proportional to amount of genetic change. What does this say about the gene in mouse v. Drosophila? Relationships here based on data above; branch lengths are proportional to time. Timing of branch points determined from fossil evidence Summary • Phylogenies examine evolutionary relationships – Relies on morphological, molecular, genetic, & fossil data – Taxonomy is a tool to aid in determining phylogenies • Cladistics emphasizes common ancestry to determine taxonomic groupings – Monophyletic taxa • Reconstructing phylogenies – Distinguish homologous v. homoplastic traits – Separate shared ancestral & shared derived characters – Phylogenetic trees: outgroup analysis • Molecular systematics – Analyze DNA, RNA, or protein sequences ...
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