Phylogenetic analysis. Characters

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1 Typical steps: Phylogenetic analysis Selection of taxa. Selection of characters. Construction of data matrix: character coding. Estimating the best-fitting tree (model) from the data matrix: phylogenetic inference. Characters Taxon Sp A Sp B Sp C Sp D Sp E Sp F Sp G Sp H B F H D G E C A Character: Characters What are individuals? Compare for what purpose? Is a character a property of an individual, or of a set of individuals? How are characters comparable among individuals? Heritability? The problems associated with the biological character problem are so complex and multifaceted and this issue is so conceptually immature that any single author s account is doomed to be too narrow and lopsided to be of much use. Günter Wagner The Character Concept in Evolutionary Biology (2001) 1

2 Characters Most agree that characters must be observable, quantifiable, and variable features of organisms. Many ways of characterizing characters: Quasi-independent independent functional units in morphology or genetics. Heritable units in morphology or genetics. Natural subsystems of individual organisms characterized by constraints on their possible states. Abstractions based on the mental decomposition of organisms. Organisms having the same character are similar in some sense. How is similarity assessed? How similar is similar? Homology In phylogenetics, the term character is tightly associated with concept of homology: 2

3 Homology Homology implies similarity of characters due to common ancestry. Characters whose similarity is due to common ancestry are homologous. Characters whose similarity is not due to common ancestry are analogous. Hypothesis of homology is a proposition that shared similarity among organisms originated in a recent common ancestor. Some issues: Is homology strictly a presence/absence kind of property? Can two characters be 50% homologous? How is homology typically assessed? Positional topology. Common developmental patterns (e.g., tissue similarity). Underlying genetic structure. Continuity in fossil record. If evolution produces changes in characters, don t homology relationships change over time? Homologous characters Conventional definition: correspondence of features among taxa due to common ancestry. Evidence about homology comes from: Paleontology: sequences of fossils. Comparative biology: comparisons among living species. Developmental biology: common embryonic origin. In general, homologous structures are given the same name in different species. Homologous features may have different structures and functions in different groups. Homology is a hypothesis. 3

4 Homologous characters Homology Homologous structures might not be similar in position, structure, or function: E.g., homology of jaw bones of fish with auditory ossicles of mammal: Evidence from development and fossil record. Tympanum Malleus Incus Stapes Angular Articular Quadrate Hyomandibular 4

5 Homology Structures similar in position, structure, and function might not be homologous: E.g., development of alimentary canal from gastrocoel (archenteron) in vertebrates: t Sharks, most bony fishes: originates from roof. Agnathans, urodeles: originates from floor. Anurans: ua originates from roof and floor. Most amniotes: entire gastrocoel + other tissues. 5

6 Analogy Functional convergence. Often observed in organisms subject to convergent evolution. Similar selection regimes may produce similar characteristics. Analogous characters 6

7 Implications for phylogenetic inference Homology results in similarity that is consistent with the phylogenetic model. Mechanism: inheritance from common ancestor. Analogy results in similarity that is inconsistent with the phylogenetic model. Mechanism: evolutionary convergence. Homoplasy (residual variation) thus has two components: Similarity due to analogy. Dissimilarity. 7

8 Levels of homology Phylogenetic or taxic homology is special case of more general hierarchy of homology types: Iterative homology: correspondence between different characters (or repeated characters) in the same individual at the same time. Ontogenetic homology: correspondence between characters of the same individual at different times. Polymorphic homology: correspondence between characters of different individuals of the same taxon (e.g., species). Taxic homology: correspondence between characters found in different species or higher taxa. The conundrum of logical circularity: If homology is similarity due to common ancestry: Then we must know patterns of ancestry to correctly identify homologies. If evolution produces change in genetics and morphology, and homologies change over time: Then we must know patterns of change to correctly identify homologies. But if characters must be homologous (i.e., comparable) to be useful in phylogenetic inference: Then homologies must be identified in order to infer patterns of ancestry and change. 8

9 Homology recognition Leads to two fundamentally different concepts of homology recognition: (1) Prior homology recognition: Use evidence from structure, function, development, or fossil record to hypothesize homologies within monophyletic group. Use hypothetical homologies to infer phylogenetic relationships. (2) Posterior homology recognition: Use inferred phylogenetic relationships to infer homologies based on inferred monophyletic groups. Use other evidence to test homologies. Homology = synapomorphy. Prior homology recognition Characters H Taxon Sp A Sp B Sp C Sp D Sp E Sp F Sp G Sp H B F D G E C A 9

10 Posterior homology recognition A B C O A B C O Important distinction Character: a biological feature that varies among taxa. = Variable. Examples: Flower color Possession of scales Femur length Nucleotide at particular position within a DNA coding sequence. Character state: value of a character for a particular taxon. = Instantiation of the variable. Examples: {red, pink, white} {scales absent, scales present} {positive integer/10} {A, T, C, G} 10

11 Characters and states Prior homology recognition concepts associated with characters. Homologies hypothesized prior to phylogenetic analysis. Based on criteria of position, developmental pattern, genetic structure, fossil record. Assumptions of homology not testable at level of current phylogenetic analysis. Might be tested at higher (more inclusive) level. Posterior homology recognition concepts associated with character states. Synapomorphies inferred from results of a phylogenetic analysis. Can be tested independently by examining biological basis of character states. Homology in molecular biology Molecular biologists may have done more to confound the meaning of the term homology than have any other group of scientists. David Hillis, 1994 Common misuse of term: percent similarity. E.g., two gene sequences are 50% homologous. Typical meaning: share 50% of their aligned nucleotides in common. No implication of common ancestry, just similarity. 11

12 Homology in molecular biology Problem: Most genes are evolutionarily related. Et Extant tgenomes derived dby duplication, modification, and recombination of small number of original replicating sequences. Therefore most genes are homologous at some level. Necessary to constrain concept of homology to most recent relationship shared by two given genes. Homology in molecular biology Some processes that trace back to single genealogical precursor: Speciation: divergence of lineages of organisms. Gene duplication: divergence of lineages of genes within an organismal lineage. Horizontal (lateral) gene transfer: divergence of lineages of genes by transfer across different organismal lineages. Kinds of homology of whole genes, based on process: Orthologous genes (or products): homologues that diverged as result of speciation event. Paralogous genes (or products): homologues that diverged as result of gene duplication event. Xenologous genes (or products): homologues that diverged as result of lateral gene transfer. 12

13 Homology in molecular biology Positional homology: at level of single nucleotide site (or amino-acid site). In phylogenetic analysis of DNA sequences: Characters: nucleotide positions. Character states: different kinds of nucleotides. Homology in molecular biology Positional homology inferred from alignment procedure: Simplified, naïve form of phylogenetic analysis. Separate optimization i step: Many possible alignment models, based on differing assumptions about probabilities of substitution, insertion, and deletion. For low sequence similarity, results of subsequent phylogenetic analysis can be highly dependent on results of alignment. Recent multiple-alignment algorithms are very sophisticated: May iteratively combine alignment and phylogenetic-inference steps. 13

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