Papers by Jack W. Sites, Jr.
Evolution, Jul 1, 1990
Chromosomes and allozymes were studied from chromosomally distinct unisexual (races Band C) and b... more Chromosomes and allozymes were studied from chromosomally distinct unisexual (races Band C) and bisexual (races D and E) populations of the teiid lizard Cnemidophorus lemniscatus, and from selected outgroup taxa (c. murinus, C. nigricolor, Ameiva ameiva, and A. auberi). Karyotyping confirmed the racial identity of individuals and showed that the chromosomal composition of populations at specific localities has remained the same for 20 years. All individuals of both unisexual populations were heterozygous for a pericentric inversion that distinguishes D and E bisexuals. Also, the unisexuals were all heterozygous for 8 of II protein loci for which D and E were fixed or nearly fixed for different alleles. Most of these alleles represent derived states relative to the other Cnemidophorus and Ameiva analyzed, and the fixed heterozygote condition at these nine markers provides unequivocal support for the hypothesis that the unisexual C. lemniscatus arose by hybridization between ancestors genetically similar to extant D and E populations. At the remaining three loci for which D and E show fixed differences, the unisexuals were homozygous rather than heterozygous. This suggests that either (I) allozymes have been lost by mutations to null, silent, or convergent mobility states, (2) ancestral genotypes were similar to but not identical with the extant D and E races, and/or (3) limited recombination may occur between unisexual genomes. Allozyme-based genetic distances between D and E were large, suggesting that bisexual races D and E are genetically isolated; each race should be accorded full species status. This conclusion is supported by the absence of any clear biochemical evidence for their monophyly with respect to the other Cnemidophorus examined. Cladistic analyses of 17 phylogenetically informative loci revealed two equally parsimonious shortest trees, one supporting monophyly and the other paraphy-Iy of the C. lemniscatus complex. Further testing of the monophyly of C. lemniscatus requires additional data. With the present study, the evidence that all parthenogenetic Cnemidophorus are of hybrid origin is complete.
Systematic Biology
In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus king... more In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the “gray zone” of speciation, phylogeographic patterns in the Patagonian region,...
Diversity, 2019
Three new species of Liolaemus belonging to the L. montanus group are described from Perú. Two ne... more Three new species of Liolaemus belonging to the L. montanus group are described from Perú. Two new species are restricted to the Ica and Moquegua departments on the Pacific coast, and one new species is only known from an isolated highland in Ayacucho department. These three new species differ from closely related species in their coloration patterns and head shape. We comment on the conservation issues of the new species and other Peruvian species of the L. montanus group.
Journal of Biogeography, 2018
Aim: To assess the effects of historical events on the tempo and mode of diversification of the l... more Aim: To assess the effects of historical events on the tempo and mode of diversification of the lizard Polychrus acutirostris along the South American diagonal of open formations (DOF). Location: Caatinga and Cerrado biomes in Brazil. We sequenced fragments of one mtDNA and three nuDNA genes of 68 individuals from 33 localities. We used population assignment methods to access genetic structure and estimate lineage boundaries. Next, we estimated lineage relationships, intraspecific diversity, environmental niche similarity and demographic history. Finally, we tested 12 diversification scenarios using an approximate Bayesian computation (ABC) approach. We recovered three non-overlapping, geographically structured lineages corresponding to Caatinga, north-east Cerrado and south-west Cerrado, with the major divergence event dating to the Late Neogene. We also recovered a complex scenario of divergence associated with gene flow and niche divergence. We show a complex history of diversification along the South American DOF. Our findings support the role of environmental features as the likely drivers of P. acutirostris intraspecific diversification during the Late Neogene.
Molecular phylogenetics and evolution, 2018
The Pleistocenic Arc Hypothesis (PAH) posits that South American Seasonally Dry Tropical Forests ... more The Pleistocenic Arc Hypothesis (PAH) posits that South American Seasonally Dry Tropical Forests (SDTF) were interconnected during Pleistocene glacial periods, enabling the expansion of species ranges that were subsequently fragmented in interglacial periods, promoting speciation. The lizard genus Lygodactylus occurs in Africa, Madagascar, and South America. Compared to the high diversity of African Lygodactylus, only two species are known to occur in South America, L. klugei and L. wetzeli, distributed in SDTFs and the Chaco, respectively. We use a phylogenetic approach based on mitochondrial (ND2) and nuclear (RAG-1) markers covering the known range of South American Lygodactylus to investigate (i) if they are monophyletic relative to their African congeners, (ii) if their divergence is congruent with the fragmentation of the PAH, and (iii) if cryptic diversity exists within currently recognized species. Maximum likelihood and Bayesian phylogenetic analyses recovered a well-suppor...
Ecology and Evolution, 2017
Sexes can differ in features associated with differential reproduction, which can be used during ... more Sexes can differ in features associated with differential reproduction, which can be used during courtship or aggressive encounters. Some traits tend to evolve independently between sexes and emerge as sexually dimorphic within the organismal phenotype. We characterize such a relationship by estimating the phenotypic integration of the head morphology and modularity of the crest in the casque-headed lizards (Corytophanidae). In this clade, some species show extreme sexual dimorphism (e.g., head crests in the genus Basiliscus) while in others, both sexes are monomorphic. To characterize these patterns, we define phenotypic integration at the interspecific level as a pattern or network of traits evidenced by phylogenetically adjusted correlations that persist among species. At this level, modularity is an increased connectedness (e.g., higher correlation) among sections of these networks that persist in a lineage during the evolution of complex phenotypes. To test both concepts, we used phylogenetic geomorphometrics to characterize the head structure of corytophanid lizards, based on a time-calibrated phylogeny that includes candidate fossil ancestors. We found evidence of an older diversification of corytophanids than previously reported (~67 vs. ~23.5 MYA) and show that this clade includes two morphological head architectures: (1) Sexually dimorphic crests present in males that are evolving independently from the rest of the head structure, and (2) full integration of the head morphology in monomorphic species. We propose that both architectures are optimal evolutionary trajectories of the parietal crest bones in the head of these lizards. In sexually dimorphic species, these bones are elongated and thinner, and gave rise to the extended crest used in male courtship displays. In monomorphic species, the parietal crest grew thicker in both sexes to allow for a better insertion of muscles associated with a stronger bite.
Ecology and Evolution, 2017
The phylogenetic relationships and biogeographic history of Caribbean island ameivas (Pholidoscel... more The phylogenetic relationships and biogeographic history of Caribbean island ameivas (Pholidoscelis) are not well-known because of incomplete sampling, conflicting datasets, and poor support for many clades. Here, we use phylogenomic and mitochondrial DNA datasets to reconstruct a well-supported phylogeny and assess historical colonization patterns in the group. We obtained sequence data from 316 nuclear loci and one mitochondrial marker for 16 of 19 extant species of the Caribbean endemic genus Pholidoscelis. Phylogenetic analyses were carried out using both concatenation and species tree approaches. To estimate divergence times, we used fossil teiids to calibrate a timetree which was used to elucidate the historical biogeography of these lizards. All phylogenetic analyses recovered four well-supported species groups (clades) recognized previously and supported novel relationships of those groups, including a (P. auberi + P. lineolatus) clade (western + central Caribbean), and a (P. exsul + P. plei) clade (eastern Caribbean). Divergence between Pholidoscelis and its sister clade was estimated to have occurred ~25 Ma, with subsequent diversification on Caribbean islands occurring over the last 11 Myr. Of the six models compared in the biogeographic analyses, the scenario which considered the distance among islands and allowed dispersal in all directions best fit the data. These reconstructions suggest that the ancestor of this group colonized either Hispaniola or Puerto Rico from Middle America. We provide a well-supported phylogeny of Pholidoscelis with novel relationships not reported in previous studies that were based on significantly smaller datasets. We propose that Pholidoscelis colonized the eastern Greater Antilles from Middle America based on our biogeographic analysis, phylogeny, and divergence time estimates. The closing of the Central American Seaway and subsequent formation of the modern Atlantic meridional overturning circulation may have promoted dispersal in this group.
Biological Journal of the Linnean Society, 2016
We utilize robust geographical genetic sampling, and phylogenetic analysis of a new multilocus da... more We utilize robust geographical genetic sampling, and phylogenetic analysis of a new multilocus dataset to provide the first inference of relationships among Philippine Gonocephalus, combined with estimates of putative species diversity, in this almost unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographical levels across the archipelago. We present the first survey of genetic lineage diversity, coupled with an archipelago-wide clarification of geographical structure in a unique archipelago-endemic radiation. Philippine Gonocephalus have previously escaped the attention of biogeographers as a result of the taxonomic confusion associated with low numbers of preserved specimens in museum collections. With new vouchered material and genetic sampling from a comprehensive, archipelago-wide vertebrate biodiversity inventory, our findings join many recent studies in highlighting the unprecedented faunal diversity in one of the world's most unique biodiversity conservation hotspots.
Molecular Phylogenetics and Evolution, 2016
A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, a... more A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "nextgeneration" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656 bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena).
Annual Review of Ecology, Evolution, and Systematics, 2011
Squamate reptiles (lizards and snakes) are a diverse clade in which there appear to have been mul... more Squamate reptiles (lizards and snakes) are a diverse clade in which there appear to have been multiple origins of many remarkable traits, including (a) parthenogenetic reproduction, (b) viviparity, (c) snake-like, limb-reduced body form, (d) herbivory, and (e) venom. These repeated transitions make squamates an outstanding/excellent system for addressing many fundamental questions in evolutionary biology. For example, they are the only vertebrate group with true parthenogenesis (with at least 40 separate origins), they have more origins of viviparity than any other group of vertebrates, and they have undergone dramatic changes in body form (lizard-like to snake-like) dozens of times. New molecular phylogenies for squamates have overturned many traditional hypotheses and taxonomies based on morphology and are now revealing exciting new insights into the evolution of many of these traits at both higher and lower taxonomic levels. In this review, we summarize many of these new insights...
Zoological Journal of the Linnean Society, 2005
A new genus and species of a short limbed and slightly elongate gymnophthalmid lizard is describe... more A new genus and species of a short limbed and slightly elongate gymnophthalmid lizard is described from the Atlantic rain forests of north-eastern Brazil. The new genus is also characterized by short and stout pentadactyl limbs, presence of prefrontals, absence of frontoparietals, distinctive ear opening and eyelid, two pairs of genials, a distinct collar, smooth, quadrangular, dorsal scales, quadrangular ventrals, fused postfrontal and postorbital bones, and two pairs of sternal ribs. The geographical distribution of the new taxon extends from the state of Rio Grande do Norte to the northern bank of the Rio São Francisco in the state of Alagoas. All specimens were obtained in leaf litter, an observation which agrees with the fossorial habits suggested by the body shape and massive aspect of the head of this species. A phylogenetic analysis based on external morphology, osteology, and molecular data recovered the new lizard as the sister genus to Anotosaura , and Colobosauroides as the sister group to these two.
Systematic Biology, 2000
Several data partitions, including nuclear and mitochondrial gene sequences, chromosomes, isoenzy... more Several data partitions, including nuclear and mitochondrial gene sequences, chromosomes, isoenzymes, and morphological characters, were used to propose a new phylogeny and to test previously published hypotheses about the phylogenetic positions of basal clades of the lizard genus Sceloporus and the relationship of Sceloporus to the former genus "Sator". In accord with earlier studies, our results grouped "Sator" as internal to Sceloporus, and both support a hypothesis of transgul an vicariance for the origin of the former genus "Sator" on islands in the Sea of Cortez. Robustness of support for internal nodes in our best tree was established though widely used indices (bootstrap proportions, decay values) but also through congruence among independent data partitions. Several deep nodes in the tree recovered by several methods, including equally weighted and differentially weighted parsimony and maximum likelihood models, are only weakly supported by the traditional indices. This methodological concordance is taken as evidence for insensitivity of the deep structure of the topology to alternative assumptions.
Systematic Biology, 2007
We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test phylo... more We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test phylogenetic relationships in the South American "lava lizards" (genus Microlophus) and describe a strategy for aligning noncoding sequences that accounts for differences in tempo and class of mutational events. We focus on seven nuclear introns that vary in size and frequency of multibase length mutations (i.e., indels) and present a manual alignment strategy that incorporates insertions and deletions (indels) for each intron. Our method is based on mechanistic explanations of intron evolution that does not require a guide tree. We also use a progressive alignment algorithm (Probabilistic Alignment Kit; PRANK) and distinguishes insertions from deletions and avoids the "gapcost" conundrum. We describe an approach to selecting a guide tree purged of ambiguously aligned regions and use this to refine PRANK performance. We show that although manual alignment is successful in finding repeat motifs and the most obvious indels, some regions can only be subjectively aligned, and there are limits to the size and complexity of a data matrix for which this approach can be taken. PRANK alignments identified more parsimony-informative indels while simultaneously increasing nucleotide identity in conserved sequence blocks flanking the indel regions. When comparing manual and PRANK with two widely used methods (CLUSTAL, MUSCLE) for the alignment of the most length-variable intron, only PRANK recovered a tree congruent at deeper nodes with the combined data tree inferred from all nuclear gene regions. We take this concordance as an objective function of alignment quality and present a strongly supported phylogenetic hypothesis for Microlophus relationships. From this hypothesis we show that (1) a coded indel data partition derived from the PRANK alignment contributed significantly to nodal support and (2) the indel data set permitted detection of significant conflict between mitochondrial and nuclear data partitions, which we hypothesize arose from secondary contact of distantly related taxa, followed by hybridization and mtDNA introgression.
Science, 2010
Demise of the Lizards Despite pessimistic forecasts from recent studies examining the effects of ... more Demise of the Lizards Despite pessimistic forecasts from recent studies examining the effects of global climate change on species, and observed extinctions in local geographic areas, there is little evidence so far of global-scale extinctions. Sinervo et al. (p. 894 ; see the Perspective by Huey et al. ) find that extinctions resulting from climate change are currently reducing global lizard diversity. Climate records during the past century were synthesized with detailed surveys of Mexican species at 200 sites over the past 30 years. Temperature change has been so rapid in this region that rates of adaptation have not kept pace with climate change. The models were then extended to all families of lizards at >1000 sites across the globe, and suggest that climate change-induced extinctions are currently affecting worldwide lizard assemblages.
Molecular Phylogenetics and Evolution, 2006
The rapid increase in the ability to generate molecular data, and the focus on model-based method... more The rapid increase in the ability to generate molecular data, and the focus on model-based methods for tree reconstruction have greatly advanced the use of phylogenetics in many Welds. The recent Xurry of new analytical techniques has focused almost solely on tree reconstruction, whereas alignment issues have received far less attention. In this paper, we use a diverse sampling of gene regions from lizards of the genus Mabuya to compare the impact, on phylogeny estimation, of new maximum likelihood alignment algorithms with more widely used methods. Sequences aligned under diVerent optimality criteria are analyzed using partitioned Bayesian analysis with independent models and parameter settings for each gene region, and the most strongly supported phylogenetic hypothesis is then used to test the hypothesis of two colonizations of the New World by African scincid lizards. Our results show that the consistent use of model-based methods in both alignment and tree reconstruction leads to trees with more optimal likelihood scores than the use of independent criteria in alignment and tree reconstruction. We corroborate and extend earlier evidence for two independent colonizations of South America by scincid lizards. Relationships within South American Mabuya are found to be in need of taxonomic revision, speciWcally complexes under the names M. heathi, M. agilis, and M. bistriata (sensu, M.T. Rodrigues, Papeis Avulsos de Zoologia 41 (2000) 313).
Molecular Phylogenetics and Evolution, 2011
We investigated the evolutionary relationships among populations of two threatened Red Data Book ... more We investigated the evolutionary relationships among populations of two threatened Red Data Book fossorial skinks, Scelotes gronovii and Scelotes kasneri, along the Western Cape Coast of South Africa. The genus Scelotes shows considerable variation in limb and digit reduction. We sampled four localities purported to contain S. gronovii and seven of S. kasneri, encompassing all of each species' limited distribution. Each of these species lack forelimbs, and differ by the number of digits on the hind limbs, among other morphological characters; S. gronovii bears a single digit and S. kasneri bears two digits on the hind limbs. Sequence data obtained from three mtDNA (16S ribosomal RNA, cytochrome b, and nicotinamide adenine dinucleotide dehydrogenase 1 unit; 2035 bp ttl.) and two nuclear (dynein axonemal heavy chain 3 and the natural killer tumor recognition; 1848 bp ttl.) gene regions were used to reconstruct the evolutionary relationships among the two focal species and several other co-distributed species ( Scelotes bipes, Scelotes montispectus, and Scelotes sexlineatus). Phylogenetic results (Bayesian and parsimony) revealed that several populations previously considered S. kasneri actually belong to other species, and others are paraphyletic with respect to one another. Additionally, populations of S. gronovii were also found to be paraphyletic, with populations south of the Berg River supported as sister to S. bipes, and populations north of the Berg River sister the remaining sampled species. Our results require a redefinition of S. sexlineatus to encompass populations morphologically convergent with S. kasneri and restrict the ranges of the already threatened S. kasneri and S. gronovii even further. The paraphyly of S. gronovii and the placement of each clade as sister to clades of species bearing two digits on the hind limbs suggests that digit loss has occurred at least twice in this group.
Molecular Phylogenetics and Evolution, 2012
Recently, phylogenetics has expanded to routinely include estimation of clade ages in addition to... more Recently, phylogenetics has expanded to routinely include estimation of clade ages in addition to their relationships. Various dating methods have been used, but their relative performance remains understudied. Here, we generate and assemble an extensive phylogenomic data set for squamate reptiles (lizards and snakes) and evaluate two widely used dating methods, penalized likelihood in r8s (r8s-PL) and Bayesian estimation with uncorrelated relaxed rates among lineages (BEAST). We obtained sequence data from 25 nuclear loci ($500-1000 bp per gene; 19,020 bp total) for 64 squamate species and nine outgroup taxa, estimated the phylogeny, and estimated divergence dates using 14 fossil calibrations. We then evaluated how well each method approximated these dates using random subsets of the nuclear loci (2, 5, 10, 15, and 20; replicated 10 times each), and using $1 kb of the mitochondrial ND2 gene. We find that estimates from r8s-PL based on 2, 5, or 10 loci can differ considerably from those based on 25 loci (mean absolute value of differences between 2-locus and 25-locus estimates were 9.0 Myr). Estimates from BEAST are somewhat more consistent given limited sampling of loci (mean absolute value of differences between 2 and 25-locus estimates were 5.0 Myr). Most strikingly, age estimates using r8s-PL for ND2 were $68-82 Myr older (mean = 73.1) than those using 25 nuclear loci with r8s-PL. These results show that dates from r8s-PL with a limited number of loci (and especially mitochondrial data) can differ considerably from estimates derived from a large number of nuclear loci, whereas estimates from BEAST derived from fewer nuclear loci or mitochondrial data alone can be surprisingly similar to those from many nuclear loci. However, estimates from BEAST using relatively few loci and mitochondrial data could still show substantial deviations from the full data set (>50 Myr), suggesting the benefits of sampling many nuclear loci. Finally, we found that confidence intervals on ages from BEAST were not significantly different when sampling 2 vs. 25 loci, suggesting that adding loci decreased errors but did not increase confidence in those estimates.
Molecular Biology and Evolution, 1996
A New Species of Liolaemus (Squamata: Iguania: Liolaemidae) from Northwestern Patagonia (Neuquén, Argentina)
Herpetologica, 2003
... Lobo, F. and RE Espinoza . 1999. Two new cryptic species of Liolaemus (Iguania: Tropiduridae)... more ... Lobo, F. and RE Espinoza . 1999. Two new cryptic species of Liolaemus (Iguania: Tropiduridae) from northwestern Argentina: resolution of the purported reproductive bimodality of Liolaemus alticolor. Copeia 1999:122140. Lobo, F. and S. Kretzschmar . 1996. ...
Cytogenetic and Genome Research, 2009
The genus Sceloporus is a diverse clade of lizards that exhibits substantial variation in chromos... more The genus Sceloporus is a diverse clade of lizards that exhibits substantial variation in chromosome numbers and sex chromosome heteromorphisms, 2 features of the genome that are static among most other pleurodont iguanian lizards. Evolutionary changes to the fundamental number of chromosomes are hypothesized to be a primary factor responsible for driving the diversification of Sceloporus. We explore the patterns of chromosome evolution in Sceloporus using a combination of ancestral state estimations and species diversification tests. Phylogenetic relationships and divergence times within Sceloporus (53 species representing all 19 species groups) are estimated using 4 nuclear genes (>3.3 kb) and relaxed-clock analyses that incorporate a fossil calibration on the root of the tree. We test the hypothesis that chromosome evolution is correlated with shifts in species diversification using cross-validation predictive densities, a new Bayesian approach for modeling the number of speci...
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Papers by Jack W. Sites, Jr.