Adrián Nieto-Montes de Oca

The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees

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.

Accommodating Heterogenous Rates of Evolution in Molecular Divergence Dating Methods: An Example Using Intercontinental Dispersal of Plestiodon (Eumeces) Lizards

Identifying and dating historical biological events is a fundamental goal of evolutionary biology, and recent analytical advances permit the modeling of factors known to affect both the accuracy and the precision of molecular date estimates. As the use of multilocus data sets becomes increasingly routine, it becomes more important to evaluate the potentially confounding effects of rate heterogeneity both within (e.g., codon positions) and among loci when estimating divergence times. Here, using Plestiodon lizards as a test case, we examine the effects of accommodating rate heterogeneity among data partitions on divergence time estimation. Plestiodon inhabits both East Asia and North America, yet both the geographic origin of the genus and timing of dispersal between the continents have been debated. For each of the eight independently evolving loci and a combined data set, we conduct single model and partitioned analyses. We found that extreme saturation has obscured the underlying rate of evolution in the mitochondrial DNA (mtDNA), resulting in severe underestimation of the rate in this locus. As a result, the age of the crown Plestiodon clade was overestimated by 15-17 Myr by the unpartitioned analysis of the combined loci data. However, the application of partition-specific models to the combined data resulted in ages that were fully congruent with those inferred by the individual nuclear loci. Although partitioning improved divergence date estimates of the mtDNA-only analysis, the ages were nonetheless overestimated, thus indicating an inadequacy of our current models to capture the complex nature of mtDNA evolution in over large time scales. Finally, the statistically incongruent age distributions inferred by the partitioned and unpartitioned analyses of the combined data support mutually exclusive hypotheses of the timing of intercontinental dispersal of Plestiodon from Asia to North America. Analyses that best capture the rate of evolution in the combined data set infer that this exchange occurred via Beringia ∼18.0-30 Ma.

MOLECULAR PHYLOGENETICS AND EVOLUTION OF SEXUAL DICHROMATISM AMONG POPULATIONS OF THE YARROW'S SPINY LIZARD (SCELOPORUS JARROVII )

Understanding evolution of geographic variation in sexually dimorphic traits is critical for understanding the role that sexual selection may play in speciation. We performed a phylogenetic analysis of geographic variation in sexual dichromatism in the Yarrows spiny lizard (Sceloporus jarrovii), a taxon that exhibits remarkable diversity in male coloration among populations (e.g., black, red, green, yellow, blue, brown). An mtDNA phylogeny based on approximately 880 bp from the 12S ribosomal RNA gene and 890 bp from the ND4 gene was reconstructed for 30 populations of S. jarrovii and eight other species of the torquatus species group using maximum‐likelihood and parsimony methods. The phylogeny suggests that S. jarrovii consists of at least five evolutionary species, none of which are sister taxa. Although intraspecific diversity in male coloration is less than indicated by previous taxonomy, two species formerly referred to as S. jarrovii exhibit impressive geographic variation in sexual dichromatism. In one of these species, the phylogeny shows the independent evolution of a distinctive blue color morph in different parts of the species range. This pattern suggests that sexual selection may lead to striking phenotypic divergence among conspecific populations and striking convergence. Results also demonstrate the importance of a phylogenetic perspective in studies of evolutionary processes within nominal species and the problematic nature of “polytypic” species recognized under the biological species concept.

A PHYLOGENETIC PERSPECTIVE ON ELEVATIONAL SPECIES RICHNESS PATTERNS IN MIDDLE AMERICAN TREEFROGS: WHY SO FEW SPECIES IN LOWLAND TROPICAL RAINFORESTS?

Abstract Differences in species richness at different elevations are widespread and important for conservation, but the causes of these patterns remain poorly understood. Here, we use a phylogenetic perspective to address the evolutionary and biogeographic processes that underlie elevational diversity patterns within a region. We focus on a diverse but well-studied fauna of tropical amphibians, the hylid frogs of Middle America. Middle American treefrogs show a “hump-shaped” pattern of species richness (common in many organisms and regions), with the highest regional diversity at intermediate elevations. We reconstructed phylogenetic relationships among 138 species by combining new and published sequence data from 10 genes and then used this phylogeny to infer evolutionary rates and patterns. The high species richness of intermediate elevations seems to result from two factors. First, a tendency for montane clades to have higher rates of diversification. Second, the early colonization of montane regions, leaving less time for speciation to build up species richness in lowland regions (including tropical rainforests) that have been colonized more recently. This “time-for-speciation” effect may explain many diversity patterns and has important implications for conservation. The results also imply that local-scale environmental factors alone may be insufficient to explain the high species richness of lowland tropical rainforests, and that diversification rates are lower in earths most species-rich biome.

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.

ELUCIDATION OF CRYPTIC DIVERSITY IN A WIDESPREAD NEARCTIC TREEFROG REVEALS EPISODES OF MITOCHONDRIAL GENE CAPTURE AS FROGS DIVERSIFIED ACROSS A DYNAMIC LANDSCAPE

We investigate the evolutionary history of the wide‐ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range‐wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well‐supported clades, five of which correspond to well‐defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate‐driven range shifts, have all played a role in the historical diversification of H. arenicolor.

Diet and reproductive biology of the viviparous lizard Sceloporus torquatus torquatus (Squamata : Phrynosomatidae)

The reproductive cycle and diet of a population of the viviparous lizard Sceloporus torquatus torquatus from the Pedregal de San Angel, Distrito Federal, Mexico, were studied. Ovarian activity began in June, and by October, one to five preovulatory follicles per ovary were present Ovulation took place in November and December, and parturition occurred in late April or early May. Relative litter and egg masses were higher at the end of development than at the beginning. Testes increased in size from June through September, when they reached their maximum volume and weight Testicular regression began at this point and was particularly accentuated in October and November. The diet of both sexes was composed primarily of insects; however, plant material (small flowers and fruits), spiders, isopods, and occasionally earthworms were also consumed. Both sexes consumed plant material throughout the year. In the dry season, males ingested twice as much food as females.

A revised phylogeny of holarctic treefrogs (Genus Hyla) based on nuclear and mitochondrial DNA sequences

Abstract The treefrog genus Hyla (Anura: Hylidae) consists of at least 31 species found in North America, Central America, Europe, and Asia and is the only genus of hylids that occurs outside the New World. Despite intensive work on the phylogeny of the genus in the past few years, several problems still exist regarding relationships within Hyla. These problems include the unusual placements of H. gratiosa and H. walkeri in some recent studies and the relatively limited taxon sampling of Asian species. In the present study, we revisit the phylogeny of Hyla to address some of these problems. First, we tested the unexpected placements of H. gratiosa and H. walkeri by sampling additional individuals of these species. Our results show that the unusual placements of H. gratiosa and H. walkeri in previous studies were most likely due to a mislabelled tissue sample and a misidentified specimen, respectively. Second, we included two species of Asian Hyla not included in previous phylogenies. Our study provides additional evidence for two separate colonizations of Hyla from the New World into Asia, and suggests an unusual biogeographic pattern in the Asian Hyla clades.

REPRODUCTIVE CYCLE OF SCELOPORUS GRAMMICUS (SQUAMATA: PHRYNOSOMATIDAE) FROM TEOTIHUACAN, MEXICO

Abstract Reproductive and fat body cycles were studied in a population of viviparous lizards (Sceloporus grammicus) from the Teotihuacán area, state of Mexico between October 1984 and September 1985. Males reached sexual maturity at a snout-vent length (SVL) of 44.5 mm and at an age of 6 to 7 mo; females reached sexual maturity at 44.1 mm SVL and at an age of 8 to 9 mo. Testicular mass of adult males began to increase in size in May and peaked during July, August, and September. Maximum testicular growth was associated with precipitation, but not with temperature and photoperiod. Enlarged vitellogenic follicles appeared during October, and females contained embryos in stages 1 through 8 during November. Females had embryos in later embryonic stages 29 through 40 from January to April. Vitellogenesis and embryonic development were associated with increasing photoperiod, temperature, and precipitation. Mean litter size was 5.09 ± 0.24 (2 to 9). Mean RCM was 0.338 ± 0.024 (0.015 to 0.80). Litter size and RCM were positively correlated with female SVL.

variation in reproductive traits within the lizard genus xenosaurus

Abstract We document variation among 13 populations of distinct species of the lizard genus Xenosaurus in four key reproductive traits: minimum size at maturity, litter size, size at birth, and relative clutch mass (RCM). Despite a common flattened morphology, considerable variation occurs in the examined traits. Minimum size at maturity varied between 92 and 110 mm snout–vent length (SVL), average litter size ranged between 2.1 and 5.7 newborns per female, mean size at birth varied between 40.6 and 51.6 mm SVL, and average RCM ranged between 0.16 and 0.35. We also found considerable interpopulational variation in mean size of reproductive females (from 102.9–119.2 mm SVL) and in the length of the birth season (from about one month to four months distributed between early May and late September). Litter size and RCM were the most variable traits with coefficients of variation above 20, whereas the other traits showed coefficients of variation between 4 and 7.4. Only the minimum size at maturity showed an ...—We document variation among 13 populations of distinct species of the lizard genus Xenosaurus in four key reproductive traits: minimum size at maturity, litter size, size at birth, and relative clutch mass (RCM). Despite a common flattened morphology, considerable variation occurs in the examined traits. Minimum size at maturity varied between 92 and 110 mm snout–vent length (SVL), average litter size ranged between 2.1 and 5.7 newborns per female, mean size at birth varied between 40.6 and 51.6 mm SVL, and average RCM ranged between 0.16 and 0.35. We also found considerable interpopulational variation in mean size of reproductive females (from 102.9–119.2 mm SVL) and in the length of the birth season (from about one month to four months distributed between early May and late September). Litter size and RCM were the most variable traits with coefficients of variation above 20, whereas the other traits showed coefficients of variation between 4 and 7.4. Only the minimum size at maturity showed an allometric effect. Litter size and size at birth were negatively correlated, which we interpret as evidence of a trade-off between these two traits. Cluster analyses revealed the existence of two main life-history strategies: populations with relatively large litters of small young and populations with small litters of large young. We suggest further ecological and phylogenetic analyses to explain the patterns of variation and covariation observed in the