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ABSTRACT: Numerous taxa show ancient intertropical disjunct distributions. Many can be explained by well-known processes of historical vicariance, such as the breakup of Gondwanaland. Others, such as Asian-Neotropical divergences are not as well understood. To clarify the phylogenetic position and understand biogeographic and temporal origins the geographically disjunct and morphologically unique genera of hinged-teeth snakes, Scaphiodontophis (n=1) and Sibynophis (n=9; Colubridae), we inferred a time-calibrated phylogeny with additional 107 taxa representing the superfamily Colubroidea using four genes (c-mos, cyt-b, ND2, RAG-1; 3085bp). We used this tree to estimate ancestral areas for the group. The results show that Scaphiodontophis is sister to Sibynophis, which both originated in the late Eocene/Oligocene in Asia and likely dispersed through Beringia to the New World, but unlike other snake groups left no extant species in temperate North America. Current recognition of Scaphiodontophiinae renders Colubrinae paraphyletic, and we resurrect the previously named subfamily Sibynophiinae to encompass both genera and use the tribes Sibynophiini (Sibynophis) and Scaphiodontophiini (Scaphiodontophis) to highlight the geographically distinct areas occupied by these taxa. These results suggest that intercontinental dispersal with extinction in intermediate areas can explain puzzling patterns of ancient intertropical disjunct distributions.
Molecular Phylogenetics and Evolution 10/2012; · 3.61 Impact Factor
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ABSTRACT: Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.
Proceedings of the Royal Society B: Biological Sciences 10/2012; · 5.41 Impact Factor
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ABSTRACT: Aim We examine diversification in Caribbean alsophiine snakes and hypothesize that, given the ecological opportunity presented by colonization of the West Indies, alsophiines should show the signature of an early burst of diversification and associated low within-clade ecological and morphological disparification. We also test whether changes in morphology and ecology are associated with changes in diversification rate, as trait-dependent diversification is hypothesized to affect historical inferences of diversification and disparification. Finally, as replicated radiations are found across the West Indies in the anoles, we test for significant differences in ecological and morphological assemblages and rates among the major island groups.Location The West Indies.Methods A time-calibrated phylogeny produced from six genes using relaxed clock methods in beast was constructed to estimate ancestral areas using Lagrange. Maximum body size and ecological niche were scored for all species in the phylogeny, and comparative phylogenetic methods in R using geiger, laser, ape and our own code were used to examine diversification through time, disparification and trait-dependent diversification from this dated phylogeny.Results The pattern of species diversification did not differ significantly from the Yule model of diversification. Morphology and ecology fitted a Brownian and white noise model of diversification, respectively. Although not significantly different, morphological disparification was lower than the Brownian null model, whereas ecological disparification was significantly greater than the null. Trait-dependent diversification analyses suggested that the constant null models provided the best fit to these data. There was no significant signal of rate variation among the major island groups for size, but moderate evidence for niche.Main conclusions Although ecological opportunity was similarly present for alsophiines as it was for anoles, the snakes fail to show an early burst of speciation. Potential reasons for this include the young age of the group, and staggered diversification due to waiting times between island colonization. In turn, ecological and morphological disparities do not necessarily follow predictable patterns related to species diversification. Thus, the presence of ecological opportunity alone is not necessarily sufficient to trigger replicated adaptive radiations in areas.
Journal of Biogeography 02/2012; 39(3):465 - 475. · 4.54 Impact Factor
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ABSTRACT: Snake diversity varies by at least two orders of magnitude among extant lineages, with numerous groups containing only one or two species, and several young clades exhibiting exceptional richness (>700 taxa). With a phylogeny containing all known families and subfamilies, we find that these patterns cannot be explained by background rates of speciation and extinction. The majority of diversity appears to derive from a radiation within the superfamily Colubroidea, potentially stemming from the colonization of new areas and the evolution of advanced venom-delivery systems. In contrast, negative relationships between clade age, clade size, and diversification rate suggest the potential for possible bias in estimated diversification rates, interpreted by some recent authors as support for ecologically mediated limits on diversity. However, evidence from the fossil record indicates that numerous lineages were far more diverse in the past, and that extinction has had an important impact on extant diversity patterns. Thus, failure to adequately account for extinction appears to prevent both rate- and diversity-limited models from fully characterizing richness dynamics in snakes. We suggest that clade-level extinction may provide a key mechanism for explaining negative or hump-shaped relationships between clade age and diversity, and the prevalence of ancient, species-poor lineages in numerous groups.
Evolution 01/2012; 66(1):163-78. · 5.15 Impact Factor
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R Alexander Pyron
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ABSTRACT: Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.
Systematic Biology 07/2011; 60(4):466-81. · 10.23 Impact Factor
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ABSTRACT: What explains the striking variation in local species richness across the globe and the remarkable diversity of rainforest sites in Amazonia? Here, we apply a novel phylogenetic approach to these questions, using treefrogs (Hylidae) as a model system. Hylids show dramatic variation in local richness globally and incredible local diversity in Amazonia. We find that variation in local richness is not explained primarily by climatic factors, rates of diversification (speciation and extinction) nor morphological variation. Instead, local richness patterns are explained predominantly by the timing of colonization of each region, and Amazonian megadiversity is linked to the long-term sympatry of multiple clades in that region. Our results also suggest intriguing interactions between clade diversification, trait evolution and the accumulation of local richness. Specifically, sympatry between clades seems to slow diversification and trait evolution, but prevents neither the accumulation of local richness over time nor the co-occurrence of similar species.
Ecology Letters 07/2011; 14(7):643-52. · 17.56 Impact Factor
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ABSTRACT: Molecular phylogenies are often used to test hypotheses about the tempo and mode of speciation and extinction. One commonly used statistic is Pybus and Harvey's γ, which measures the density of ordered internode distances on an ultrametric tree to infer earlier (negative γ) or later (positive γ) bursts of diversification. However, coalescent theory predicts that γ might be biased toward negative values (inferring early bursts of diversification) when using gene trees rather than species trees. Gene divergences predate species divergences, increasingly so at higher effective population sizes (N(e)), and proportionally more so toward the tips of the tree. Thus, gene trees will have a higher density of older nodes in many cases (particularly at higher N(e)), due to the disproportionate lengthening of terminal branches. This will yield an artifactual signature of early bursts of diversification when estimating γ from gene trees. We simulate gene trees within species trees under both Yule (pure-birth) and birth-death processes, and demonstrate support for these predictions. However, for most realistic estimates of θ in natural populations, gene trees provide relatively good estimates of γ, despite the disproportionate overestimation of younger node ages. This is corroborated with an empirical dataset of North American fence lizards (Sceloporus).
Evolution 07/2011; 65(7):1851-61. · 5.15 Impact Factor
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ABSTRACT: The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>6800 species). Despite much recent focus on their conservation, diversification, and systematics, no previous phylogeny for the group has contained more than 522 species. However, numerous studies with limited taxon sampling have generated large amounts of partially overlapping sequence data for many species. Here, we combine these data and produce a novel estimate of extant amphibian phylogeny, containing 2871 species (∼40% of the known extant species) from 432 genera (∼85% of the ∼500 currently recognized extant genera). Each sampled species contains up to 12,712 bp from 12 genes (three mitochondrial, nine nuclear), with an average of 2563 bp per species. This data set provides strong support for many groups recognized in previous studies, but it also suggests non-monophyly for several currently recognized families, particularly in hyloid frogs (e.g., Ceratophryidae, Cycloramphidae, Leptodactylidae, Strabomantidae). To correct these and other problems, we provide a revised classification of extant amphibians for taxa traditionally delimited at the family and subfamily levels. This new taxonomy includes several families not recognized in current classifications (e.g., Alsodidae, Batrachylidae, Rhinodermatidae, Odontophrynidae, Telmatobiidae), but which are strongly supported and important for avoiding non-monophyly of current families. Finally, this study provides further evidence that the supermatrix approach provides an effective strategy for inferring large-scale phylogenies using the combined results of previous studies, despite many taxa having extensive missing data.
Molecular Phylogenetics and Evolution 06/2011; 61(2):543-83. · 3.61 Impact Factor
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ABSTRACT: The impact of barriers to dispersal and gene flow is often inferred to be the primary cause of lineage divergence and phylogeographic structure in terrestrial organisms. In particular, the Mississippi River has been implicated as a barrier to gene flow in many species, including aquatic taxa. However, if barriers are permeable to organisms, then phylogeographic structure may be difficult to detect due to gene flow between lineages. Using time-calibrated Bayesian phylogenetic analyses of mtDNA, and phylogeographic coalescent simulations, we determine if the Mississippi River operates as a barrier to gene flow in the aquatic diamond-backed watersnake (Nerodia rhombifer). The phylogenetic analyses support a basal division within N. rhombifer mtDNA lineages that coincides with populations generally east and west of the Mississippi River. These results, and that of the divergence dating analyses, therefore suggest that the river was a significant barrier to gene flow in the Pleistocene ∼ 1.4 million years ago, presumably during an interglacial period when the river was much wider. However, we also detect western haplotypes in the eastern clade, and vice versa, thereby indicating that this barrier has not been complete. Nonetheless, the coalescent simulations that account for limited migration suggest that the Mississippi River was an important feature that shaped the phylogeographic history of this aquatic snake in the USA despite limited gene flow.
Molecular Phylogenetics and Evolution 11/2010; 57(2):552-60. · 3.61 Impact Factor
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ABSTRACT: The superfamily Colubroidea (> 2500 species) includes the majority of snake species and is one of the most conspicuous and well-known radiations of terrestrial vertebrates. However, many aspects of the phylogeny of the group remain contentious, and dozens of genera have yet to be included in molecular phylogenetic analyses. We present a new, large-scale, likelihood-based phylogeny for the colubroids, including 761 species sampled for up to five genes: cytochrome b (93% of 761 species sampled), ND4 (69%), ND2 (28%), c-mos (54%), and RAG-1 (13%), totaling up to 5814bp per species. We also compare likelihood bootstrapping and a recently proposed ultra-fast measure of branch support (Shimodaira-Hasegawa-like [SHL] approximate likelihood ratio), and find that the SHL test shows strong support for several clades that were weakly-supported by bootstrapping in this or previous analyses (e.g., Dipsadinae, Lamprophiidae). We find that SHL values are positively related to branch lengths, but show stronger support for shorter branches than bootstrapping. Despite extensive missing data for many taxa (mean=67% per species), neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that most highly incomplete taxa are placed in the expected families from previous taxonomy, typically with very strong support. The phylogeny indicates that the Neotropical colubrine genus Scaphiodontophis represents an unexpectedly ancient lineage within Colubridae. We present a revised higher-level classification of Colubroidea, which includes a new subfamily for Scaphiodontophis (Scaphiodontophiinae). Our study provides the most comprehensive phylogeny of Colubroidea to date, and suggests that SHL values may provide a useful complement to bootstrapping for estimating support on likelihood-based trees.
Molecular Phylogenetics and Evolution 11/2010; 58(2):329-42. · 3.61 Impact Factor
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ABSTRACT: Aim Three common patterns have emerged in comparative phylogeographic analyses at many barriers: (1) a potential geographic pseudocongruence of lineage divergences; (2) a disconnect between the inference of temporally clustered, relatively recent timing for observed speciation events, and dates spanning a broader, apparently random time-scale; and (3) an apparent prevalence of speciation with recent or continuing gene flow. It is unclear if there is a unifying explanation for these phenomena. We argue that the interaction between geographic barriers to dispersal and ecological limits on the distribution of species can explain these patterns. We suggest that these patterns can be explained by the presence of a continuum between two underlying processes, here termed ‘hard’ and ‘soft’ allopatric divergence, which result from the interplay between organismal ecology and the physioecological nature of geographic barriers.Location Examples from North America.Methods We examine comparative phylogeographic divergences in 18 groups of terrestrial vertebrates at two major biogeographic features in North America – the Mississippi River Embayment and the Cochise Filter Barrier – to test predictions made by this hypothesis.Results We find support for the two distinct processes of hard and soft allopatry, and note several examples exhibiting characteristics of both. Hard allopatry is caused by physical barriers promoting divergence as a function of consistent geographic isolation. Soft allopatry is caused by ecological processes that isolate populations geographically in allopatric refugia through niche conservatism, or across ecological transition zones through niche divergence, but which may be periodic or inconsistent through time.Main conclusions Viewing geographic speciation as a continuum between hard and soft allopatry can explain all three patterns as a consequence of the physical and ecological mechanisms that isolate populations, and provides an alternative perspective on the impact of ecological factors and physical barriers on lineage formation.
Journal of Biogeography 09/2010; 37(10):2005 - 2015. · 4.54 Impact Factor
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R Alexander Pyron
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ABSTRACT: Estimating divergence times using molecular sequence data has become a common application of statistical phylogenetics. However, disparities between estimated ages for clades produced in different studies have become equally commonplace. Here, I propose a method for the objective assessment of the likelihood of inferred divergence times to evaluate the placement of fossil constraints using information from the broader fossil record. The inclusion of nodes from the Tree of Life for which credible age ranges are known, in addition to the fossil constraints used in the ingroup, will allow for the comparison of alternate fossil placements when the phylogenetic affinity of a fossil is ambiguous as well as provide a heuristic assessment of the global likelihood of estimated divergence times. The use of these "likelihood checkpoints" will allow for the comparison of inferred dates across data sets and across taxonomic groups to place divergence time estimates into a broader evolutionary timescale. The method is illustrated with an example using an expanded phylogenetic estimate of the Gnathostomata, inferred with relaxed-clock molecular dating methods.
Systematic Biology 03/2010; 59(2):185-94. · 10.23 Impact Factor
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ABSTRACT: Ecological adaptive radiation theory predicts an increase in both morphological and specific diversification when organisms colonize new environments. Accordingly, bursts of morphological diversification, characterized by low within-subclade morphological disparity, may be associated with these increases in speciation rates. Conversely, increasing species density, reduction in available habitat, or increasing extinction rates are expected to cause rates of diversification to decline. We test these hypotheses by examining the tempo and mode of speciation in the lampropeltinine snakes, a morphologically variable group that colonized the New World approximately 24 million years ago and radiated throughout the Miocene. We show that specific diversification increased early in the history of the group, and that most morphological variation is partitioned among, rather than within subclades. These patterns provide further evidence for the hypothesis that morphological variation tends to be strongly partitioned among lineages when clades undergo early bursts of species diversification. A reduction in speciation rates may be indicative of density dependent effects due to a saturation of available ecological opportunity, rather than increases in extinction rates at the onset of the Pleistocene/Pliocene glacial cycles. This evidence runs counter to the general Pleistocene species pump model.
Evolution 11/2009; 64(4):934-43. · 5.15 Impact Factor
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ABSTRACT: Evolutionary correlations between functionally related character suites are expected as a consequence of coadaptation due to physiological relationships between traits. However, significant correlations may also exist between putatively unrelated characters due to shared relationships between those traits and underlying variables, such as body size. Although such patterns are often dismissed as simple body size scaling, this presumption may overlook important evolutionary patterns of diversification. If body size is the primary determinant of potential diversity in multiple unrelated characters, the observed differentiation of species may be governed by variability in body size, and any biotic or abiotic constraints on the diversification thereof. Here, we demonstrate that traits related to both predatory specialization (gape and diet preference) and predatory avoidance (the development of Batesian mimicry) are phylogenetically correlated in the North American snake tribe Lampropeltini. This is apparently due to shared relationships between those traits and adult body size, suggesting that size is the primary determinant of ecomorphological differentiation in the lampropeltinines. Diversification in body size is apparently not linked to climatic or environmental factors, and may have been driven by interspecific interactions such as competition. Additionally, we find the presence of a 'key zone' for the development of both rattle- and coral snake mimicry; only small snakes feeding primarily on ectothermic prey develop mimetic colour patterns, in or near the range of venomous model species.
Journal of Evolutionary Biology 09/2009; 22(10):2057-67. · 3.28 Impact Factor
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ABSTRACT: Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographical barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographical barriers are possible: (i) niche conservatism at a physical barrier; (ii) niche divergence at a physical barrier; and (iii) niche divergence in the absence of a physical barrier. We test for the presence of these patterns in a transcontinentally distributed snake species, the common kingsnake (Lampropeltis getula), to determine the relative frequency of niche conservatism or divergence in a single species complex inhabiting multiple distinct ecoregions. We infer the phylogeographic structure of the kingsnake using a range-wide data set sampled for the mitochondrial gene cytochrome b. We use coalescent simulation methods to test for the presence of structured lineage formation vs. fragmentation of a widespread ancestor. Finally, we use statistical techniques for creating and evaluating ecological niche models to test for conservatism of ecological niche preferences. Significant geographical structure is present in the kingsnake, for which coalescent tests indicate structured population division. Surprisingly, we find evidence for all three patterns of conservatism and divergence. This suggests that ecological niche preferences may be labile on recent phylogenetic timescales, and that lineage formation in widespread species can result from an interaction between inertial tendencies of niche conservatism and natural selection on populations in ecologically divergent habitats.
Molecular Ecology 08/2009; 18(16):3443-57. · 5.52 Impact Factor
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ABSTRACT: Aim A latitudinal gradient in species richness, defined as a decrease in biodiversity away from the equator, is one of the oldest known patterns in ecology and evolutionary biology. However, there are also many known cases of increasing poleward diversity, forming inverse latitudinal biodiversity gradients. As only three processes (speciation, extinction and dispersal) can directly affect species richness in areas, similar factors may be responsible for both classical (high tropical diversity) and inverse (high temperate diversity) gradients. Thus, a modified explanation for differential species richness which accounts for both patterns would be preferable to one which only explains high tropical biodiversity.Location The New World.Methods We test several proposed ecological, temporal, evolutionary and spatial explanations for latitudinal diversity gradients in the New World snake tribe Lampropeltini, which exhibits its highest biodiversity in temperate regions.Results We find that an extratropical peak in species richness is not explained by latitudinal variation in diversification rate, the mid-domain effect, or Rapoport's rule. Rather, earlier colonization and longer duration in the temperate zones allowing more time for speciation to increase biodiversity, phylogenetic niche conservatism limiting tropical dispersal and the expansion of the temperate zones in the Tertiary better explain inverse diversity gradients in this group.Main conclusions Our conclusions are the inverse of the predictions made by the tropical conservatism hypothesis to explain higher biodiversity near the equator. Therefore, we suggest that the processes invoked are not intrinsic to the tropics but are dependent on historical biogeography to determine the distribution of species richness, which we refer to as the ‘biogeographical conservatism hypothesis’.
Global Ecology and Biogeography. 06/2009; 18(4):406 - 415.
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ABSTRACT: The snake tribe Lampropeltini (the king, milk, pine, rat, short-tailed, long-nosed, scarlet, and glossy snakes) comprises a well-known group of common colubrids distributed throughout North America and northern South America. However, a robust phylogeny has thus far proven elusive. We infer a new phylogeny for the group including all known extant species based on multiple nuclear and mitochondrial genes, and present a revised taxonomy. We test the hypothesis of a Pleistocene 'species pump' being responsible for diversity in the group. We find that diversification of the lampropeltinines took place in the Neogene, rejecting the common model of a Pleistocene radiation.
Molecular Phylogenetics and Evolution 03/2009; 52(2):524-9. · 3.61 Impact Factor
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ABSTRACT: Differences in species richness between regions are ultimately explained by patterns of speciation, extinction, and biogeographic dispersal. Yet, few studies have considered the role of all three processes in generating the high biodiversity of tropical regions. A recent study of a speciose group of predominately New World frogs (Hylidae) showed that their low diversity in temperate regions was associated with relatively recent colonization of these regions, rather than latitudinal differences in diversification rates (rates of speciation-extinction). Here, we perform parallel analyses on the most species-rich group of Old World frogs (Ranidae; approximately 1300 species) to determine if similar processes drive the latitudinal diversity gradient. We estimate a time-calibrated phylogeny for 390 ranid species and use this phylogeny to analyze patterns of biogeography and diversification rates. As in hylids, we find a strong relationship between the timing of colonization of each region and its current diversity, with recent colonization of temperate regions from tropical regions. Diversification rates are similar in tropical and temperate clades, suggesting that neither accelerated tropical speciation rates nor greater temperate extinction rates explain high tropical diversity in this group. Instead, these results show the importance of historical biogeography in explaining high species richness in both the New World and Old World tropics.
Evolution 02/2009; 63(5):1217-31. · 5.15 Impact Factor
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ABSTRACT: We present a systematic revision of the Lampropeltis getula group, based on a recent range-wide phylogeographic analysis. We define our theoretical and operational concepts of species delimitation, and provide diagnoses based on mitochondrial DNA evidence, ecological niche modeling, morphology, and historical precedence. We find support for the recognition of five distinct species, which bear the name of the nominate subspecies found primarily within the range of each phylogeographic lineage: the Eastern lineage (Lampropeltis getula, Eastern Kingsnake), the Mississippi lineage (L. nigra, Black Kingsnake), the Central lineage (L. holbrooki, Speckled Kingsnake), the Desert lineage (L. splendida, Desert Kingsnake), and the Western lineage (L. californiae, California Kingsnake). Interestingly, all of these taxa had originally been described as distinct species and recognized as such for up to 101 years (in the case of L. californiae) before being demoted to subspecies. We discuss the impact that increasingly detailed genetic information from phylogeographic analyses may have on traditional taxonomy.
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Systematic Biology 05/2008; 57(2):317-28. · 10.23 Impact Factor
