Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Evolution of Protein Molecules

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...

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Phylogenies and Community Ecology

I. the origin of species by means of natural selection

The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.

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Species Concepts and Species Delimitation

IVe reanalyzed data from a recently published study of higher-level snake relation- ships based on four slowly-evolving protein loci. The original study used phenetic clustering of genetic similarities and presented a single, highly resolved tree. Our reanalyses of these data reveal that the single published phenogram is only one of at least 10,000 equivalent UPGMA phenograms, the consensus of which is largely unresolved. Additive distance analysis and character-based parsi- mony analysis of the data also yield little resolution, indicating that these data are highly ambiguous regarding higher-level snake phylogeny. The high degree of resolution in the published phenogram is an analytical artifact resulting from the failure to consider alternative trees implied by tied distance values, which are numerous in the distance matrix derived from this particular data set. Although the published phenogram exhibits general agreement with traditional hypotheses about snake re- lationships, the same appears to be tnie for the thousands of equivalent phenograms, discrepancies among which sum to a substantial loss of resolution. Although the four loci sampled are evolving slowly relative to other commonly sunreyed protein loci, they are nevertheless evolving too rapidly to be informative about the higher level phylogeny of snakes.

Slowly-evolving protein loci and higher-level snake phylogeny: a reanalysis

In a recent review of early amniote evolution, Carroll (1982) criticized the methods of phylogenetic (cladistic, Hennigian) systematics. Specifically, he concluded that several of the most important assumptions of this methodology were contradicted by the evidence from early amniotes and that these contradictions resulted from the evolutionary process of adaptive radiation in this group. Our opinions concerning the utility of the phylogenetic method contrast strongly with those of Dr. Carroll. We feel that the problems he encountered result from his misunderstanding of the phylogenetic method rather than from inadequacies of this method itself Dr. Carroll is one of the most knowledgable students of early amniote evolution; here we present neither a detailed reanalysis of his characters nor a precise alternative to his phylogeny of this group. Instead, we argue that Carroll's own procedure was formulated such that his negative conclusions about the assumptions of the phylogenetic method were inevitable. We contend that many of Carroll's objections to the phylogenetic method rest on faulty reasoning. Carroll's most severe criticism of the phylogenetic method seems to be its ". . . assumption that the majority of derived features possessed in common by related groups are the result of inheritance from a common ancestor, rather than from convergence" (Carroll, 1982:104; but see Farris, 1983). For the early amniotes, Carroll (1982:102) finds that the distribution of derived features forms "an almost random mosaic" among his basic taxa. This leads him to conclude (Carroll, 1982:104) that "most of the derived character states recognized in two or more of the derived groups must be attributed to convergence." Thus, an important assumption of the phylogenetic method seems to be violated. We certainly agree that rampant convergence can lead the systematist to incorrect phylogenetic conclusions. However, if Carroll's scenario about early amniote evolution is correct and his prior assumptions about basic taxa are accepted, then he has chosen to discuss only those characters that must be convergent (see Fig. 1). In Carroll's scenario (p. 106), the time span from the Early Pennsylvanian to the Early Permian saw the appearance of "a succession of derived groups that may all be traced to the protorothyrid stock." Therefore, any true synapomorphies evidencing a close relationship among two or more of these "derived" groups must have arisen within Carroll's "Protorothyridae" (= Protorothyrididae). Carroll, however, is concerned with entirely different characters, specifically, those "in which the most primitive known members of each of the derived groups are more advanced than the protowthyrids" (Carroll, 1982:100, italics added). But if all the other groups of early amniotes are derived independently from "protorothyrids," then any such derived characters shared by two or more of these groups must by definition be convergent. Therefore, we do not find it suprising that Carroll (1982:102) finds no obvious congruence among these characters. Critics of the phylogenetic method (Mayr, 1981; Carroll, 1982) argue that evolutionary parallelism and convergence pose particular problems for this method. Platnick (1977) demonstrates clearly that the opposite is true, namely that analysis of shared apomorphies provides an unambiguous method of identifying cases involving convergence. Such a determination is made by considering the distribution of the feature in question in relation to those of other derived features among the taxa concerned. For a given character distribution, parallelism/convergence can be shown to be either necessary or unnecessary to account for the distribution of particular derived characters among the terminal taxa (Platnick, 1977). Convergence and parallelism refer to similarities derived independently rather than those inherited from a common ancestor. By definition then, an hypothesis of relationship must be established in order to support a claim of convergence. As Gaffney (1979) aptly states the case, "An argument for parallelism or convergence is simply an argument (often unstated) in favor of one phylogeny over an alternative one." Carroll (1982) provides no support for his alternative hypothesis of relationships. He presents no characters indicating that any particular "protorothyrid" shared a more recent common ancestor with one of his "derived" groups than with other "protorothyrids." Such evidence would be necessary to support his claim that 1) these "derived" groups were actually "derived from protorothyrids," and 2) that any particular derived characters shared by two or more of these "derived" groups (but not by "protorothyrids") are therefore convergent. Given that Carroll's hypothesis about early amniote phylogeny is true, then all of the derived characters shared by two or more of his derivative (non-proto-

Phylogenetic methods and the early history of amniotes: a comment on Carroll (1982)

de QueiroK, K. 2005. Linnaean, rank-based, and phylogenetic nomenclature: Restoring primacy to the link between names and taxa. Acta Univ. Lips. Symb. Bor. Upa. 33:3, 127-140. Uppsala, ISBN 91-554-6192-1. Linnaeus and other 18"" Century naturaii.sts practiced nomenclature in a way that associated laxon names more strongly with taxa (group.s) than with the categorical ranks of the taxonomic ("Linnaean") hierarchy. For IS'"* century naturalists, ranks functioned merely as devices for indicating hierarchical position that did not alTccl I he application of taxon names. Consequently, taxa did not change their names simply because of changes in rank. For example, the name RepiiUa did not change when the rank of the taxon designated by that name was changed from order to division or class. During the 19''' Century, a different approach to nomenclature emerged that made rank assignment centra! to the application of taxon names. Under this rankbased approach, which forms the ba.sis of the current botanical and zoological ctxlcs, names are implicitly defined in tenns of ranks and types and are therefore more strongly associated with ranks than with the taxa to which they refer. Consequently, taxa change their names simply because of changes in rank. Forexample, if the rank of die taxon/Icícacrae is changed from family to .subfamily, its name must change to Aceroklnae. Phylogenetic nomenclature is a new approach that ties taxon names to explicitly evolutionary concepts of taxa through definitions that describe taxa in terms of ancesu-y and descent. This approach once again associates ia.\on names more strongly with taxa than with ranks and thus represents a return, updated with evolutionary principles, to an approach similar to that practiced by Linnaeus and other 18'''Century naturalists,

Linneaen, rank-based, and phylogenetic nomenclature: Restoring primacy to the link between names and taxa

Principles of Systematic Zoology, 2nd Edition (Review)

The understanding of phylogenetic relationships within Anolis has seen great advances in the past ten years due to a significant number of phylogenetic studies based primarily on molecular data. Despite this large effort, there is still a large void of information regarding mainland species. According to recent phylogenies (Poe, 2004; Nicholson et al., 2005) mainland species belong to two non-nested clades: an unnamed clade (designated the M2 clade by Pinto et al. [2008]), which includes the deeply nested Central and South American species derived from Greater Antillean ancestors and Dactyloa (same as the latifrons series of Etheridge [1959] and the M1 clade of Pinto et al. [2008]), which represents one of the early branches in Anolis and includes species from Central and South America and the Lesser Antilles.

Kevin de Queiroz

Papers

Slowly-evolving protein loci and higher-level snake phylogeny: a reanalysis

Phylogenetic methods and the early history of amniotes: a comment on Carroll (1982)

Linneaen, rank-based, and phylogenetic nomenclature: Restoring primacy to the link between names and taxa

Principles of Systematic Zoology, 2nd Edition (Review)

Phylogenetic relationships of the Dactyloa clade, based on molecular and morphological data