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Classification

Classification. Taxonomic categories: Kingdom, Phylum, Class, Order, Family, Genus, Species (these are taxa, higher taxa > genus). Kingdom Animalia MULTICELLULAR & CAPABLE OF LOCOMOTION Phylum Chordata NOTOCHORD Class: Mammalia HAIR & MILK Order: Primates FINGERNAILS

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Classification

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  1. Classification Taxonomic categories: Kingdom, Phylum, Class, Order, Family, Genus, Species (these are taxa, higher taxa > genus) Kingdom AnimaliaMULTICELLULAR & CAPABLE OF LOCOMOTION Phylum ChordataNOTOCHORD Class: MammaliaHAIR & MILK Order: PrimatesFINGERNAILS Family: CercopithecidaeNON-PREHENSILE TAIL Genus: MacacaMACAQUE MONKEYS Species: mulattaRHESUS MACAQUE Rhesus Monkey

  2. Taxonomy & Nomenclature Binomical nomenclature: Homo sapiens (above genus not italicized) Holotype: “type” specimen, deposited in a museum Paratype: reference specimen, usually from same locality Principal of priority: oldest name (synonym) is valid Breviceps gibbosus (Linnaeus, 1758) Rana gibbosa: Linnaeus, 1758 Breviceps genus: Merrem, 1820

  3. Cryptic Speciation: Gray Tree Frog Hyla versicolor LeConte, 1825 4N: POLYPLOID 2N: DIPLOID Hyla chrysoscelis Cope, 1880 Hyla versicolor LeConte, 1825

  4. Synonymy (“Lumping”) Dendrobates tinctorius (Cuvier, 1797) Dendrobates azureus Hoogmoed, 1969 DNA identical Dendrobates tinctorius (Cuvier, 1797)

  5. Anagenesis & Cladogenesis Anagenesis: aka phyletic change, over time enough mutations become fixed so that the new population is distinguishable from the ancestral population (microevolution) Cladogenesis: one population becomes separated from another, and over time, both become different species (macroevolution)

  6. Macroevolution is not a linear progression… THERE IS NO MISSING LINK!!!! …but a branching tree over time

  7. Anatomy of a phylogenetic tree TAXA BRANCH (Lineage) NODE (Common ancestor) Ingroup Outgroup Key terms: Clade (monophyletic group) Sister taxa ROOT

  8. Monophyletic, paraphyletic, & polyphyletic groups MONOPHYLETIC PARAPHYLETIC POLYPHYLETIC

  9. Characters Characters can be morphological (shape of wing, number of bones), behavioral, biochemical, or involve DNA sequence data. Different forms of a character are character states. Autapomorphy: derived character state present in a single lineage Plesiomophy: ancestral character state Homology: a character state shared by taxa without modification from a common ancestor Synapomorphy: a homologous character state that supports the monophyly of a group through common ancestry Homoplasy: a character state that has independently evolved two or more times, or similarity that is NOT from common ancestry (convergent evolution)

  10. Example 1

  11. 1 1 1 Example 2

  12. Synapomorphies & Natural Classifications

  13. Maximum Parsimony Principle of Parsimony, or Occam’s Razor: the simplest explanation is preferred If Tuna and Whale are closest relatives, characters 2-9 must evolve independently in the whale (evolve twice!)

  14. Characters 2-9 evolve only once in this phylogeny. Parsimony says this is the simplest and thus preferred explanation- we want the fewest character changes

  15. The problem with parsimony… Long-branch attraction: Species with many autapomorphies will be chosen as sister groups, when in reality they are not With DNA sequence data, Maximum Parsimony weights all character state changes (mutations) as equal, but in reality they are biased

  16. Maximum Likelihood Transition mutations occur at a higher frequency than transversions Maximum likelihood assigns probabilities of character change to each state and then calculates the likelihood of any potential phylogenetic tree, using complex models Likelihood asks: what is the probability of the data, given the preferred model?

  17. Bayesian Inference Closely related to Maximum Likelihood- this method also uses complex models of mutation to avoid the pitfalls of parsimony. Bayesian Inference asks: does the chosen model fit the data? What is the probability of the model, given the data? Bayesian and Likelihood trees are often very similar Euglenoid ML tree:

  18. How do we know this really works? Mutagen used to mimic speciation in viruses, scientists could document mutation changes and “cladogenesis” events, phylogenetic analysis produced one true tree

  19. Molecular clocks Idea is: DNA sequences mutate at a constant rate, and so it is possible to correlate number of mutational changes to a node in a phylogenetic tree, thus estimating the date of speciation Molecular clock estimates can be calibrated with fossils (if they are available for a given group) by providing a minimal estimate of time since divergence Problems: distantly related taxa rarely have similar mutation rates, creating problems for molecular clocks. Fossils used in calibrations have inexact ages, making clock estimates inexact also. Recent trends: scientists are combining fossils calibrations with well-dated geological events (e.g., splitting of Africa and South America 100 mya) to created rough estimates of speciation events

  20. Challenges to Phylogeny Reconstruction Scoring characters How to score morphological characters: Bird foot: four digits Lizard foot: five digits WHICH DIGIT HAS BEEN LOST IN BIRDS?

  21. Challenges to Phylogeny Reconstruction 2 Homoplasy is common! Three equally parsimonious reconstructions of life history evolution on a simplified mitochondrial genome cladogram. Larvae represent transitions from direct development to a biphasic life history (larval stage). "dd" represents transitions from a biphasic life history (larvae) to direct development. (a) The ancestral plethodontid evolves direct development. Larvae reevolve three times in clades A-C. (b) The ancestral plethodontid has a biphasic life history. Direct development evolves in Clades B, Pl. and C. Larvae reevolve in Clades B and C. (c) The ancestral plethodontid has a biphasic life history. Direct development evolves twice within Clade B, and once in C and Pl. Larvae reevolve in D. fuscus (Clade C).

  22. Challenges to Phylogeny Reconstruction 3 Over time, DNA mutations at the same base position can erase evidence of common ancestry Adaptive radiations can occur so quickly that distinctive synapomorphies don’t have time to develop; e.g. gecko speciation Hard polytomy: multiple lineages evolved from one ancestor (rare) Soft polytomy: relationships of lineages uncertain

  23. Challenges to Phylogeny Reconstruction 4 Orthologous (derived from speciation event) vs. Paralogous (derived from duplication event) Genes- analagous to homology vs. homoplasy Polymorphism problems: Haplotypes (variant DNA sequences of a gene) from Genes 1 & 2 form a monophyletic group, suggesting that species A & B are sister taxa- this is wrong 2 shared bp substitutions (thick tick marks)

  24. Speciation via hybridization Common pattern in ferns

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