Kevin de Queiroz

Species Concepts and Species Delimitation

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.

Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names

Defining the names of taxa in terms of common ancestry, that is, using phylogenetic definitions of taxon names, departs from a tradition of character-based definitions by granting the concept of evolution a central role in taxonomy. Phylogenetic definitions bear on other taxonomic principles and practices, including the following: (1) Names cannot be applied to nonmonophyletic taxa as the result of mistaken ideas about relationships or characters. Such mistakes do not affect conclusions about the monophyly of taxa but about their content and/or diagnoses. Because nonmonophyletic taxa can only be named deliberately, they are easily avoid- ed. (2) Definitions are clearly distinguished from descriptions and diagnoses. Definitions are ontological statements about the existence of entities that result from the relationships of common ancestry among their parts; descriptions and diagnoses are epistemological statements about how we recognize the parts of those entities. (3) By precisely specifying the clade (ancestor) with which a name is associated, phylogenetic definitions clarify the limits of taxa, and this in turn clarifies related phenomena such as time of origin and duration. (4) Unlike the case for character-based intensional definitions and enumerative extensional definitions, phylogenetic definitions provide an unambiguous criterion for synonymy of taxon names: names are syn- onymous if they refer to clades stemming from the same ancestor. (5) Because of their relevance to synonymy, phylogenetic definitions also are relevant to priority, of both names and authorship. In phylogenetic taxonomy, priority is based not on first use of a name at a particular rank or rank-group but on first use of a name in association with a particular ancestor. (Definition; diagnosis; nomenclature; phylogeny; priority; synonymy; taxonomy.)

Ernst Mayr and the modern concept of species

Ernst Mayr played a central role in the establishment of the general concept of species as metapopulation lineages, and he is the author of one of the most popular of the numerous alternative definitions of the species category. Reconciliation of incompatible species definitions and the development of a unified species concept require rejecting the interpretation of various contingent properties of metapopulation lineages, including intrinsic reproductive isolation in Mayrs definition, as necessary properties of species. On the other hand, the general concept of species as metapopulation lineages advocated by Mayr forms the foundation of this reconciliation, which follows from a corollary of that concept also advocated by Mayr: the proposition that the species is a fundamental category of biological organization. Although the general metapopulation lineage species concept and Mayrs popular species definition are commonly confused under the name “the biological species concept,” they are more or less clearly distinguished in Mayrs early writings on the subject. Virtually all modern concepts and definitions of the species category, not only those that require intrinsic reproductive isolation, are to be considered biological according to the criterion proposed by Mayr. Definitions of the species category that identify a particular contingent property of metapopulation lineages (including intrinsic reproductive isolation) as a necessary property of species reduce the number of metapopulation lineages that are to be recognized taxonomically as species, but they cause conflicts among alternative species definitions and compromise the status of the species as a basic category of biological organization.

The genome of the green anole lizard and a comparative analysis with birds and mammals

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse—more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

Toward a phylogenetic system of biological nomenclature

Despite the widely held belief that modem biological taxonomy is evolutionary, some of the most fundamental concepts and principles in the current system of biological nomenclature are based on a nonevolutionary convention that pre-dates widespread acceptance of an evolutionary world view by more than a century. The development of a phylogenetic system of nomenclature requires reformulating these concepts and principles so that they are no longer based on the Linnean categories but on the tenet of common descent.

PHYLOGENETIC SYSTEMATICS AND THE SPECIES PROBLEM

Abstract— A tension has arisen over the primacy of interbreeding versus monophyly in defining the species category. Manifestations of this tension include unnecessary restriction of the concept of monophyly as well as inappropriate attribution of “species” properties, to “higher taxa”, and vice versa. Distinctions between systems (wholes) deriving their existence from different underlying. processes have been obscured by failure to acknowledge different interpretations of the concept of individuality. We identify interbreeding (resulting in populations) and evolutionary descent (resulting in monophyletic groups) as two processes of interest to phylogenetic systematists, and explore the relations between the systems resulting from these processes. In the case of sexual reproduction, populations of interbreeding organisms (regardless of whether they are monophyletic) exist as cohesive wholes and play a special role in phylogenetic systematics, being the least inclusive entities appropriate for use as terminal units in phylogenetic analysis of organismal relationships. Both sexual and asexual organisms form monophyletic groups. Accepting the reality and significance of both interbreeding and monophyly emphasizes that a conscious decision must be made regarding which phenomenon should be used to define the species category. Examination of species concepts that focus either on interbreeding or on common descent leads us to conclude that several alternatives are acceptable from the standpoint of phylogenetic systematics but that no one species concept can meet the needs of all comparative biologists.

Niche lability in the evolution of a Caribbean lizard community

Niche conservatism—the tendency for closely related species to be ecologically similar—is widespread. However, most studies compare closely related taxa that occur in allopatry; in sympatry, the stabilizing forces that promote niche conservatism, and thus inhibit niche shifts, may be countered by natural selection favouring ecological divergence to minimize the intensity of interspecific interactions. Consequently, the relative importance of niche conservatism versus niche divergence in determining community structure has received little attention. Here, we examine a tropical lizard community in which species have a long evolutionary history of ecological interaction. We find that evolutionary divergence overcomes niche conservatism: closely related species are no more ecologically similar than expected by random divergence and some distantly related species are ecologically similar, leading to a community in which the relationship between ecological similarity and phylogenetic relatedness is very weak. Despite this lack of niche conservatism, the ecological structuring of the community has a phylogenetic component: niche complementarity only occurs among distantly related species, which suggests that the strength of ecological interactions among species may be related to phylogeny, but it is not necessarily the most closely related species that interact most strongly.

Phylogenetic Relationships and Tempo of Early Diversification in Anolis Lizards

We examine phylogenetic relationships among anoles using mitochondrial DNA se- quences from the NADH dehydrogenase subunit 2 gene (ND2) andve transfer-RNA genes repre- senting 1,455 alignable base positions and 866 phylogenetically informative characters (parsimony criterion). We also present 16 morphological characters for phylogenetic analysis. Our analyses yielded poorly-supported nodes deep in the anole tree but many well-supported nodes for more recent phylogenetic divergences. We test the hypothesis that the major clades of anoles form a hard polytomy and present a general statistical framework for testing hypotheses of simultaneous branching of lineages by using molecular sequence data. Our results suggest that rapid diversi- �cation early in the evolutionary history of anoles explains why numerous researchers have had difculty reconstructing well-supported dichotomous phylogenetic trees for anoles. ( Anolis; mito- chondrial DNA; parametric bootstrap; permutation test; phylogeny; polytomy.)

Systematics and the Darwinian Revolution

Taxonomies of living things and the methods used to produce them changed little with the institutionalization of evolutionary thinking in biology. Instead, the relationships expressed in existing taxonomies were merely reinterpreted as the result of evolution, and evolutionary concepts were developed to justify existing methods. I argue that the delay of the Darwinian Revolution in biological taxonomy has resulted partly from a failure to distinguish between two fundamentally different ways of ordering identified by Griffiths (1974): classification and systematization. Classification consists of ordering entities into classes, groups defined by the attributes of their members; in contrast, systematization consists of ordering entities into systems, more inclusive entities whose existence depends on some natural process through which their parts are related. Evolutionary, or phylogenetic, systematics takes evolutionary descent to be the natural process of interest in biological taxonomy. I outline a genera...Taxonomies of living things and the methods used to produce them changed little with the institutionalization of evolutionary thinking in biology. Instead, the relationships expressed in existing taxonomies were merely reinterpreted as the result of evolution, and evolutionary concepts were developed to justify existing methods. I argue that the delay of the Darwinian Revolution in biological taxonomy has resulted partly from a failure to distinguish between two fundamentally different ways of ordering identified by Griffiths (1974): classification and systematization. Classification consists of ordering entities into classes, groups defined by the attributes of their members; in contrast, systematization consists of ordering entities into systems, more inclusive entities whose existence depends on some natural process through which their parts are related. Evolutionary, or phylogenetic, systematics takes evolutionary descent to be the natural process of interest in biological taxonomy. I outline a general framework for a truly phylogenetic systematics and examine some of its consequences.

Admixture determines genetic diversity and population differentiation in the biological invasion of a lizard species

Molecular genetic analyses show that introduced populations undergoing biological invasions often bring together individuals from genetically disparate native-range source populations, which can elevate genotypic variation if these individuals interbreed. Differential admixture among multiple native-range sources explains mitochondrial haplotypic diversity within and differentiation among invasive populations of the lizard Anolis sagrei. Our examination of microsatellite variation supports the hypothesis that lizards from disparate native-range sources, identified using mtDNA haplotypes, form genetically admixed introduced populations. Furthermore, within-population genotypic diversity increases with the number of sources and among-population genotypic differentiation reflects disparity in their native-range sources. If adaptive genetic variation is similarly restructured, then the ability of invasive species to adapt to new conditions may be enhanced.