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Evolutionary relationships are defined in terms of descent from a common ancestor Traits evolving on a tree A A is more closely related to B than to C E B because F 03‐327/727 Lecture 3 C • E, the common ancestor of A and B is more recent than D Time • F, the common ancestor of A and C. 1 3 Traits evolving on a tree A character is a heritable trait or “well defined feature that … can assume one or more mutually exclusive states”* * Graur and Li, Molecular Evolution, 2000 • Introduction to characters, character state matrices, and ancestral state reconstruction Taxon 1 Taxon 2 Taxon 3 … • Properties of characters Character 1 Character 2 Character‐states –Ancestral (basal) and derived states Character 3 … – Monophyletic states • Cladistics Character States Examples: eye color blue, brown, green mammary glands present, absent number of legs 0, 2, 4, 6, 8, etc. 4 5 1 Evolutionary change on a tree Evolutionary change on a tree •Given •Given –a tree –a tree –a set of characters that are variable for these taxa, –a set of characters that are variable for these taxa, –a character state matrix for the leaf taxa –a character state matrix for the leaf taxa •infer •infer –the character states of each ancestral node and –the character states of each ancestral node and –the state changes along each branch –the state changes along each branch • such the number of changes required is minimal Parsimony * Graur and Li, Molecular Evolution,6 2000 * Graur and Li, Molecular Evolution,7 2000 No tool use Tool use Ancestral character states: gain: tool use loss: tool use tool use tool use Pattern Caudal Caudal Forehead Pattern Shape Bulge? Striped Spot Round No Barred None Forked No Gorilla Chimp Human Gorilla Chimp Human Tool Tool Barred None Forked No No Yes Yes No Yes Yes use use Barred Round Yes There may be more than one None most parsimonious solution. 9 10 2 Ancestral character states : Ancestral character states : Character: Pattern Caudal Caudal Forehead Character: Pattern Caudal Caudal Forehead Pattern Shape Bulge? Pattern Shape Bulge? Striped Spot Round No Striped Spot Round No Striped Striped Spot Barred None Forked No Barred None Forked No Barred None Forked No Barred None Forked No Barred None Round Yes Barred None Round Yes 11 12 Ancestral character states : Ancestral character states : Note this history is equally parsimonious: Character: Pattern Caudal Caudal Forehead Character: Pattern Caudal Caudal Forehead Pattern Shape Bulge? Pattern Shape Bulge? Striped Spot Round No Striped Spot Round No Barred Striped No spot Spot Barred Forked No Barred Forked No None None Round→Forked Round Barred None Forked No Barred None Forked No Barred None Round Yes Barred None Round Yes 13 14 3 Ancestral character states : Questions to ask with character state analysis •What were the properties of the ancestor? Character: Pattern Caudal Caudal Forehead Pattern Shape Bulge? •Which states are basal, which derived? Striped Spot Round No Striped •Did certain character states arise more than once, Spot Barred Forked No independently? None Round→Forked Round No bulge – Parallel losses Barred Forked No None –Convergent evolution, parallel gains Barred None Round Yes Gain bulge 15 16 Why is “basal” a loaded word? • Ancestral (basal) states: furry, light • Low body mass (~50kg) Monotremes are early • Fur branching species • Doesn’t use tools gain: tool use gain: furry, light Monotremes are basal in body mass tool use the sense that they diverge loss: fur from the base of the tree Character state transitions Monotremes are not primitive species Gorilla Chimp Human • Derived states Evolutionary change is occurring on this Fur Yes Yes No • High body mass (~175kg) branch, as well as other branches. • No fur Wt Heavy Light Light Tool • Tool use No Yes Yes Monotremes do not necessarily have the use properties of the ancestor of all mammals 17 18 4 Traits evolving on a tree Monotremes are not primitive species • Introduction to characters, character state matrices, and ancestral state reconstruction • Properties of characters Monotremes do not necessarily have the properties of the ancestor of all mammals – Ancestral (basal) and derived states Monophyletic states For example, the platypus has the unique • Cladistics ability to finding things in the dark using electroreception. 19 20 Monophyletic traits Monophyletic characters A two‐state character (trait) is monophyletic with respect to a tree, A trait is monophyletic if the taxa that possess the trait if it can be explained by a single state transition. • form a clade • constitute all the descendants of a common ancestor A B C D • The orange trait was gained once • Taxa with the orange trait form a clade • The orange trait is monophyletic • The blue trait is not monophyletic • The derived (orange) trait is monophyletic • The ancestral (blue) trait is not monophyletic 22 25 5 When is a trait not monophyletic? Which characters are monophyletic? A two‐state character (trait) is monophyletic with respect to a tree, if it is ancestral & and was subsequently lost. Pattern Caudal Caudal Forehead Pattern Shape Bulge? Striped Spot Round No • The red trait was lost once • Taxa lacking the red trait (i.e., blue taxa) Barred None Forked No form a clade • The blue trait (i.e, the absence of red) is Barred None Forked No monophyletic • The red trait is not monophyletic Barred None Round Yes • The derived trait (lack of red) is monophyletic • The ancestral red trait is not monophyletic 26 27 Pattern Caudal Caudal Forehead Pattern Caudal Caudal Forehead Pattern Shape Bulge? Pattern Shape Bulge? Striped Spot Round No Striped Spot Round No Barred None Forked No Barred None Forked No Barred None Forked No Barred None Forked No Barred None Round Yes Barred None Round Yes Gain bulge • The forehead bulge was gained once • The tail spot was lost once • The forehead bulge is monophyletic • The “spot free” tail is monophyletic • The “bulge free” profile is not monophyletic • The caudal spot is not monophyletic 28 29 6 When is a trait not monophyletic? Is blood‐squirting a monophyletic trait? No Independent gains or losses Hypothesis 1: Independent losses Reversal: A trait is gained and The species possessing the orange later lost (or vice versa). trait are not monophyletic, because Blood‐squirting? No Yes of two independent gains Loss of orange Gain of orange The species possessing the blue trait are not monophyletic, because of two independent losses 30 31 Data: A single character with two states: orange and blue. Is blood‐squirting a monophyletic trait? No Which of the following geographic Hypothesis 2: Blood‐squirting was gained twice traits are monophyletic? independently and lost once (a reversal). A Blood‐squirting? No Yes Highland Mexico Southwestern USA Eastern and Central USA Other South American Caribbean B 32 33 Matsuoka et al. (2002) 7 Traits evolving on a tree Is social behavior in sweat bees monophyletic? • Introduction to characters, character state matrices, and If not, why not? ancestral state reconstruction • Properties of characters – Ancestral (basal) and derived states – Monophyletic states • Cladistics Source: Brady, S.G., S. Sipes, A Pearson, B. Danforth. 2006. Proceedings of the Royal Society B. doi:10.1098/rspb.2006.3496 36 37 Phylogeny and classification Cladistic approach to evolutionary trees (Willi Hennig 1966) Monophyletic group Includes an ancestor and all of its descendants •Gather data on characters to be used • Establish the character states • Determine which states are ancestral (polarize the A B C D characters) • Select outgroup(s) with all ancestral states • Taxonomic groups are based on shared, derived characters •Apply the principle of parsimony to obtain a hierarchical organization of taxa that minimizes state transitions Only monophyletic groups (clades) are recognized in cladistic classification 38 40 8 Terminology not required for this course Cladistic approach to evolutionary trees (but that you may encounter in your reading) (Willi Hennig 1966) Plesiomorphy Character state found in ancestor of group •Gather data on characters to be used Apomorphy Derived character state in descendants of group • Establish the character states Symplesiomorphy Shared, ancestral character state Determine which states are ancestral (polarize the Synapomorphy Shared, derived character state characters) Select outgroup(s) with all ancestral states A B C D Taxonomic groups are based on shared, derived “Blue” and “square” are plesiomorphic monophyletic characters “Small size” is an apomorphy for A •Apply the principle of parsimony to obtain a hierarchical “Red” is a synapomorphy for A + B organization of taxa that minimizes state transitions “Circle” is a synapomorphy for A + B + C …but a symplesiomorphy for A + B 43 44 In this example, the outgroup has all the ancestral character states A vertebrate tree based on cladistic principles Character: Pattern Caudal Caudal Forehead Pattern Shape Bulge? Striped Spot Round No Striped Spot Barred Forked No None Round→Forked Round No bulge Barred None Forked No • Each clade is defined by a single derived trait Barred None Round Yes • No parallel gains, no reversals Gain bulge 45 46 9 A Deuterostome cladistic tree The traits mapped onto the phylogeny were Problems with the cladistics carefully chosen to be derived states that define these groups. Determine which states are ancestral (polarize the characters) – Difficult to know whether a trait is ancestral Select outgroup(s) with all ancestral states –How to find such an outgroup? Taxonomic groups are based on shared, derived monophyletic characters –Many traits are gained and lost or gained multiple times independently. 47 48 Examples of groups that do not fit the cladistic framework Examples of groups that do not fit the cladistic framework “Lizards” (Sauria) are not “Lizards” (Sauria) are not monophyletic monophyletic Snakes (Serpentes) are monophyletic within lizards Squamata (lizards + snakes) form a clade that is sister to sphenodontida (Snakes are derived, limbless lizards .) 51 52 Fry et al.
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  • Hemidactylium Scutatum): out of Appalachia and Into the Glacial Aftermath

    Hemidactylium Scutatum): out of Appalachia and Into the Glacial Aftermath

    RANGE-WIDE PHYLOGEOGRAPHY OF THE FOUR-TOED SALAMANDER (HEMIDACTYLIUM SCUTATUM): OUT OF APPALACHIA AND INTO THE GLACIAL AFTERMATH Timothy A. Herman A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2009 Committee: Juan Bouzat, Advisor Christopher Phillips Karen Root ii ABSTRACT Juan Bouzat, Advisor Due to its limited vagility, deep ancestry, and broad distribution, the four-toed salamander (Hemidactylium scutatum) is well suited to track biogeographic patterns across eastern North America. The range of the monotypic genus Hemidactylium is highly disjunct in its southern and western portions, and even within contiguous portions is highly localized around pockets of preferred nesting habitat. Over 330 Hemidactylium genetic samples from 79 field locations were collected and analyzed via mtDNA sequencing of the cytochrome oxidase 1 gene (co1). Phylogenetic analyses showed deep divergences at this marker (>10% between some haplotypes) and strong support for regional monophyletic clades with minimal overlap. Patterns of haplotype distribution suggest major river drainages, both ancient and modern, as boundaries to dispersal. Two distinct allopatric clades account for all sampling sites within glaciated areas of North America yet show differing patterns of recolonization. High levels of haplotype diversity were detected in the southern Appalachians, with several members of widely ranging clades represented in the region as well as other unique, endemic, and highly divergent lineages. Bayesian divergence time analyses estimated the common ancestor of all living Hemidactylium included in the study at roughly 8 million years ago, with the most basal splits in the species confined to the Blue Ridge Mountains.