Kevin de Queiroz

Smithsonian Institution · Department of Vertebrate Zoology

Achalinus, commonly known as odd-scaled snakes due to their unique scutellation, are a fascinating group of xenodermid snakes distributed throughout east Asia. Currently, northern Vietnam is known to host six species of Achalinus, three of which are considered endemic. During recent herpetofaunal surveys conducted in the Bac Me District of Ha Giang...

Adaptive radiation is a widely recognized pattern of evolution wherein substantial phenotypic change accompanies rapid speciation. Adaptive radiation may be triggered by environmental opportunities resulting from dispersal to new areas or via the evolution of traits, called key innovations, that allow for invasion of new niches. Species sampling is...

Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here we present a phylogenetic analysis of all 379 extant species of Anolis, with new...

The turtle shell is a complex structure that currently serves a largely protective function in this iconically slow-moving group. Developmental and fossil data indicate that one of the first steps toward the shelled body plan was broadening of the ribs (approximately 50 my before the completed shell). Broadened ribs alone provide little protection...

This annotated checklist of the world's iguanas (Iguanidae; Iguaninae) represents an update by the Iguana Taxonomy Working Group (ITWG) of its 2011 list. We recognize 44 extant species (19 subspecies across six species) in eight genera. Ctenosaura (as currently recognized) is the most diverse, with 18 species, and Amblyrhynchus is the least diverse...

Significance An unresolved question in ecology is whether the structure of ecological communities can be stable over very long timescales. Here we describe a wealth of new amber fossils for an ancient radiation of Hispaniolan lizards that, until now, has had a very poor fossil record. These fossils provide an important and previously unavailable pe...

Background. The turtle body plan differs markedly from that of other vertebrates and serves as a model system for studying structural and developmental evolution. Incorporation of the ribs into the iconic turtle shell negates the rib movements that effect lung ventilation in the majority of air-breathing amniotes (the clade encompassing mammals, li...

Background. The turtle body plan differs markedly from that of other vertebrates and serves as a model system for studying structural and developmental evolution. Incorporation of the ribs into the iconic turtle shell negates the rib movements that effect lung ventilation in the majority of air-breathing amniotes (the clade encompassing mammals, li...

The discovery of three new species of Enyalioides from the tropical Andes in Ecuador and northern Peru is reported. Enyalioides altotambo sp. n. occurs in northwestern Ecuador and differs from other species of Enyalioides in having dorsal scales that are both smooth and homogeneous in size, a brown iris, and in lacking enlarged, circular and keeled...

The turtle body plan differs markedly from that of other vertebrates and serves as a model system for studying structural and developmental evolution. Incorporation of the ribs into the turtle shell negates the costal movements that effect lung ventilation in other air-breathing amniotes. Instead, turtles have a unique abdominal-muscle-based ventil...

Starting with articles by Bock (1973) and Wiley (1975) in this journal, the field of systematic biology has a history, reviewed by Helfenbein and DeSalle (2005), of examining its methods in the context of the philosophy of science articulated by Karl R. Popper (e.g., 1959, 1962, 1983). Two main categories of debates have emerged in this literature....

New information is presented on old records of four species of snakes from four different islands in Micronesia. A record of Dendrelaphis caudolineatus from Saipan is reexamined and the specimen reidentified as D. philippinensis, and a snake from Pohnpei previously recorded only as an unidentified species of Dendrelaphis is identified as D. punctul...

The turtle shell represents a unique modification of the ancestral tetrapod body plan. The homologies of its approximately 50 bones have been the subject of debate for more than 200 years. Although most of those homologies are now firmly established, the evolutionary origin of the dorsal median nuchal bone of the carapace remains unresolved. We pro...

Adopting the perspective of graph theory, Martin et al. (2010) described two kinds of phylogenetic trees, which they termed node-based and stem- or branch-based, that differ with respect to the biological interpretations of their component nodes and branches. After establishing equivalency between the two different kinds of trees in terms of encode...

We report the discovery of two sympatric new species of Enyalioides from a montane rainforest of the Río Huallaga basin in northeastern Peru. Among other characters, the first new species is distinguishable from other Enyalioides by the combination of the following characters: strongly keeled ventral scales, more than 37 longitudinal rows of dorsal...

We present a phylogenetic analysis of the Dactyloa clade of Anolis lizards, based on morpholog- ical (66 characters of external morphology and osteology) and molecular (,4,700 bases of mitochon- drial and nuclear DNA) data. Our set of morphological characters includes some that exhibit continuous variation and others that exhibit polymorphism withi...

In a continuing debate about the usefulness of phylogenetic nomenclature, Platnick (2012) has apparently conceded the two main points of our previous paper (de Queiroz and Donoghue 2011) by providing no counter-arguments. First, contrary to Platnick's previous assertions, when appropriate comparisons are made (i.e., between taxonomies consisting of...

Abstract. Linnaeus and other 18th Century naturalists practiced nomenclature in a way that associated taxon names more strongly with taxa (groups) than with the categorical ranks of the taxonomic (“Linnaean”) hierarchy. For those early naturalists, ranks functioned merely as devices for indicating hierarchical position that did not affect the appli...

Although scientific names are the accepted means of referring to species in the scientific literature, common names continue to serve important functions in both scientific and popular communication. That fact is evident from the inclusion of both scientific and common names in checklists published by various taxonomically specialized scientific so...

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 geno...

The Dactyloa clade, one of two major subgroups of mainland Anolis lizards, is distributed from Costa Rica to Peru, including the Amazon region and the southern Lesser Antilles. We estimated the phylogenetic relationships within Dactyloa based on mitochondrial (ND2, five transfer-RNAs, COI) and nuclear (RAG1) gene regions using likelihood and Bayesi...

Charles Darwin introduced a novel idea into the concept of species, namely that species are branches in the lines of descent (segments of population lineages). In addition to this novel evolutionary component, Darwin's species concept also retained an older taxonomic component, namely the view that the species category is a taxonomic rank; moreover...

The clade Hoplocercinae includes 13 species assigned to three taxa traditionally ranked as genera-Enyalioides, Hoplocercus, and Morunasaurus-, and distributed on both sides of the Andes from Panama to Brazil. We provide a revised taxonomy of Hoplocercinae including synonymies, diagnoses, standardized descriptions, distributions, notes on color and...

Most lizard communities are characterized by having one or two dominant species and a handful of other species that occur at relatively low densities. However, Soroa, a site in the Sierra del Rosario of western Cuba, is home to 11 sympatric species of Anolis, of which nine are found in high abundance. In this study, we evaluate how interspecific di...

We describe a new species of Enyalioides from mid-elevation rainforests in southeastern Ecuador. This represents the fifth species of Enyalioides known to occur east of the Andes in South America; the other four species are E. cofanorum, E. laticeps, E. microlepis and E. praestabilis. Among other characters, the new species can be distinguished fro...

Hoplocercine lizards form a clade of 11 currently recognized species traditionally placed in three genera (Enyalioides, Hoplocercus, and Morunasaurus) that occur in the lowlands on both sides of the Andes between Panama and the Brazilian Cerrado. We analyze 11 mitochondrial and two nuclear loci using probabilistic methods and different partitioning...

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 d...

Phylogenetic analyses of DNA sequences were conducted to evaluate four alternative hypotheses of phrynosomatine sand lizard relationships. Sequences comprising 2871 aligned base pair positions representing the regions spanning ND1-COI and cyt b-tRNA(Thr) of the mitochondrial genome from all recognized sand lizard species were analyzed using unparti...

We used sequences of the mitochondria control region to assess the distribution of genetic variation within and among populations of the poeciliid fish species Xiphophorus birchmanni. We collected 122 X. birchmanni samples from 11 sites in three drainage systems comprising the distribution of the species. We found low levels of polymorphism among a...

Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, and apomorphies in between. An in...

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 metapopula...

Swordtail fish have been studied extensively in relation to diverse aspects of biology; however, little attention has been paid to the patterns of genetic variation within and among populations of swordtails. In this study, we sequenced the mtDNA control region from 65 individuals and 10 populations of Xiphophorus cortezi to investigate the genetic...

We determined the karyotype of Anolis desechensis and compared it with the known karyotypes of other members of the Anolis cristatellus series. The diploid (2N) number of chromosomes of two male A. desechensis was 27, with six pairs of large metacentric macrochromosomes, six pairs of microchromosomes of gradually decreasing size, and sex chromosome...

Laurin, M., de Queiroz, K. & Cantino, P. D. (2006). Sense and stability of taxon names. —Zoologica Scripta, 35, 113 –114.

A report from the First International Phylogenetic Nomenclature Meeting recently published in Cladistics conveys several misconceptions about the PhyloCode and presents an erroneous interpretation of discussions that took place at that meeting. Contrary to Pickett's assertions, the PhyloCode is designed to name clades, not paraphyletic groups; the...

At least three different issues are commonly referred to by the term "the species problem": one concerns the necessary properties of species, a second the processes responsible for the existence of species, and a third methods for inferring species limits. Solutions have recently been proposed to the first two problems, which are conceptual in natu...

Contemporary species concepts are diverse. Nonetheless, all share the fundamental idea that species are segments of Uneages at the population level of biological organ- ization. They differ in the secondary properties (e.g., intrinsic reproductive isolation, monophyly, diagnosability) that are treated as necessary for considering lineages to be spe...

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...

The philosopher Karl Popper described a concept termed degree of corroboration, C, for evaluating and comparing hypotheses according to the results of their tests. C is, fundamentally, a comparison of two likelihoods: p(e|hb), the likelihood of the hypothesis (h) in conjunction with the background knowledge (b), and p(e|b), the likelihood of b alon...

To determine the evolutionary relationships within the Anolis cristatellus series, we employed phylogenetic analyses of previously published karyotype and allozyme data as well as newly collected morphological data and mitochondrial DNA sequences (fragments of the 12S RNA and cytochrome b genes). The relationships inferred from continuous maximum l...

The snake allozyme data of Dowling et al. (1996) are highly ambiguous concerning the higher level phylogeny of snakes, though they maybe informative at lower hierarchical levels. The high degree of resolution in the original tree of Dowling et al. (1996:Figs. 1–6) is an analytical artifact that results from failure to consider alternative trees imp...

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...

Kluge's (2001, Syst. Biol. 50:322-330) continued arguments that phylogenetic methods based on the statistical principle of likelihood are incompatible with the philosophy of science described by Karl Popper are based on false premises related to Kluge's misrepresentations of Popper's philosophy. Contrary to Kluge's conjectures, likelihood methods a...

We report the results of phylogenetic analyses of 1447 bases of mitochondrial DNA sequence for 21 populations representing seven species of the Anolis grahami series (A. conspersus, A. garmani, A. grahami, A. lineatopus, A. opalinus, A. reconditus, and A. valencienni), six of which occur on Jamaica. These data include 705 characters that are phylog...

Forey's Part I (Goals and Mechanics of the PhyloCode) ' ' Part 1 of Forey's paper was intended to provide readers with an impartial description of the goals and mechanics of the PhyloCode. This section is largely accurate but omits some important issues, which we would like to describe, and contains some misleading statements, which we would like t...

We report a phylogenetic analysis of approximately 1330 bases of mitochondrial DNA sequence for eight species of the Anolis roquet series (Anolis aeneus, Anolis bonairensis, Anolis extremus, Anolis griseus, Anolis luciae, Anolis richardi, Anolis roquet, Anolis trinitatus). These data contain 410 characters that are parsimony informative for the A....

Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in parti...

•Lizards in Ihe Anolis bimaculatus group from the northern Lesser Antilles have played an important role in theoretical and empirical developments in ecology, behavior, and evolution over the last four decades. Despite intense interest, the lack of a formal phylogenetic analysis for the bimaculatus group has limited comparative,and historical evolu...

Twenty-nine populations of Xiphophorus fishes representing nine species of northern swordtails, one southern swordtail and a platyfish were assayed electrophoretically for allozyme variation. Phylogenetic relationships were inferred using parsimony and likelihood analysis of gene frequency characters, as well as Fitch-Margoliash, minimum evolution...

The taxon name "Aves" is currently used for several different clades, a situation that violates the fundamental nomenclatural principle that, to minimize ambiguity, each taxon name should refer to a single taxon. To clarify this situation, we explore some general issues concerning the properties of the three classes of phylogenetic definitions, inc...

Nucleotide sequences of the mitochondrial protein coding cytochrome b (cyt b; 650 bp) and small-subunit 12S ribosomal RNA (approximately 350 bp) genes were used in analyses of phylogenetic relationships among extant phrynosomatid sand lizards, including an examination of competing hypotheses regarding the evolution of "earlessness." Sequences were...

We reanalyzed data from a recently published study of higher-Ievel snake relationships 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 eq...

Nucleotide sequences of the mitochondrial protein coding cytochrome b (cyt b; 650 bp) and small-subunit 12S ribosomal RNA (� 350 bp) genes were used in analyses of phylogenetic relation- ships among extant phrynosomatid sand lizards, including an examination of competing hypotheses regarding the evolution of "earlessness." Sequences were obtained f...

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, i...

We examine phylogenetic relationships among anoles using mitochondrial DNA sequences from the NADH dehydrogenase subunit 2 gene (ND2) and five transfer-RNA genes representing 1,455 alignable base positions and 866 phylogenetically informative characters (parsimony criterion). We also present 16 morphological characters for phylogenetic analysis. Ou...

This fresh collection of essays, drawn from a broad range of disciplines, brings neglected cognitive, anthropological, and historical dimensions to philosophical debates over species. The concept of species has played a central role in both evolutionary biology and the philosophy of biology, and has been the focus of a number of books in recent yea...