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Fig. 1 A-C. Trimeresurus sumatranus, ZFMK 76340 in On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae)
Fig. 1 A-C. Trimeresurus sumatranus, ZFMK 76340, neotype of Coluber sumatranus Raffles, 1822, southwest Sumatra, Bengkulu Province, Sumatra. A. dorsal view of the body, B. ventral view of the body, C. lateral view oft the head. Photo: G. Vogel.
Fig. 3A. MZB.Ophi.5452 in On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae)
Fig. 3A. MZB.Ophi.5452 live holotype of Trimeresurus gunaleni spec. nov. from Mt. Sibayak, ca. 1,800 m a.s.l., west of Brastagi, Sumatera Utara Province, Sumatra, adult female. Photo: G. Vogel.
Fig. 10 in On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae)
Fig. 10. Live female of Trimeresurus malcolmi from Mount Kinabalu, Sabah, Borneo. Photo: M. Dehling.
Figure 2 in Morphological and molecular evidence for phylogeny and classification of South American pitvipers, genera Bothrops, Bothriopsis, and Bothrocophias (Serpentes: Viperidae)
Figure 2. Bayesian Markov Chain Monte Carlo (MCMC) 50% majority-rule consensus phylogram, including taxa with morphological data only (analysis 8). The phylogram is derived from an analysis of 2343 bp mitochondrial and 85 gap-weighted or majority-coded morphological characters. The posterior probabilities are shown above nodes; bootstrap values from parsimony analysis of the same data set are shown below nodes (analysis 7). The parsimony analysis shows minor topological differences from the Bayesian analysis; refer to Figure S3 for the parsimony cladogram. Grey circles indicate posterior probabilities of 95 or greater, and bootstrap values of 70 or greater. Dashes indicate support values of less than 50. Letters correspond to the major lineages: A, Bothrocophias clade; B, Bothrops alternatus clade; C, Bothrops neuwiedi + Bothrops jararaca clade; D, Bothriopsis clade; E, Bothrops atrox clade.
Figure 1 in Morphological and molecular evidence for phylogeny and classification of South American pitvipers, genera Bothrops, Bothriopsis, and Bothrocophias (Serpentes: Viperidae)
Figure 1. Bayesian Markov Chain Monte Carlo (MCMC) 50% majority-rule consensus phylogram, excluding taxa with morphological data only (analysis 11). The phylogram is derived from an analysis of 2343 bp of mitochondrial DNA and 85 gap-weighted or majority-coded morphological characters. The posterior probabilities are shown above nodes; bootstrap values from parsimony analysis of the same data set are shown below nodes (analysis 10). The parsimony analysis shows minor topological differences from Bayesian analysis; refer to Figure S1 for parsimony cladogram. Grey circles indicate posterior probabilities of 95 or greater and bootstrap values of 70 or greater. Letters correspond to major lineages: A, Bothrocophias clade; B, Bothrops alternatus clade; C, Bothrops neuwiedi + Bothrops jararaca clade; D, Bothriopsis clade; E, Bothrops atrox clade.
Data from: Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)
Aim: A number of processes can lead to weak or conflicting phylogenetic signals, especially in geographically dynamic regions where unstable landscapes and climates promote complex evolutionary histories. The Middle American pitviper genus Bothriechis has a complex biogeographic distribution and previous phylogenetic analyses have recovered conflicting topologies based on the data type used. Here, we tested whether historic conflicts in the phylogeny were the result of reticulate evolution and whether the inferred biogeographic history of the group would enable contact among reticulate lineages. Location: Middle America Taxon: Palm-Pitvipers (genus Bothriechis) Methods: We generated a phylogenomic dataset using an anchored phylogenomics approach and inferred a genomics-based species tree and mitochondrial tree to assess incongruence among datasets. We then generated a dated phylogeny and conducted ancestral area reconstruction to examine the biogeographic history surrounding the diversification of these species. We additionally tested whether the discordance among trees is better explained by lineage sorting or reticulate evolution by testing models of reticulate evolution inferred through multiple methods. Results: We found strong support for discordance in the phylogeny of <i>Bothriechis</i> and corresponding evidence for reticulate evolution among lineages with incongruent placement. Ancestral area reconstruction placed these taxa in adjacent regions during the time period when reticulation was projected to take place and suggested a biogeographic history heavily influenced by vicariant processes. Main conclusions: Reticulation among geographically proximate lineages has driven apparent genomic discordance in Bothriechis and is responsible for historical incongruence in the phylogeny. Inference of the order of events suggests that reticulation in Nuclear Middle American occurred during a time of geologic upheaval, promoting lineage divergence and secondary contact. Reticulate evolution and similar processes can have substantial impacts on the evolutionary trajectory of taxa and are important to explicitly test for in biogeographically complex regions. Main conclusions: Reticulation among geographically proximate lineages has driven apparent genomic discordance in Bothriechis and is responsible for historical incongruence in the phylogeny. Inference of the order of events suggests that reticulation in Nuclear Middle American occurred during a time of geologic upheaval, promoting lineage divergence and secondary contact. Reticulate evolution and similar processes can have substantial impacts on the evolutionary trajectory of taxa and are important to explicitly test for in biogeographically complex regions.
Phylogenetically diverse diets favor more complex venoms in North American pitvipers
<p>The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are traits composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates considerably over evolutionary timescales, with apparent increases and decreases in complexity, yet the evolutionary causes of this variation is unclear. Here, we tested alternative hypotheses for the link between venom complexity and ecological sources of selection related to diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths <em>Crotalus, Sistrurus </em>and <em>Agkistrodon</em>. We generated independent transcriptomic and proteomic measures of venom complexity and then estimated prey diversity using the past century's extensive natural history studies on these snakes. We then conducted comparative tests relating different measures of predator venom complexity and prey community diversity using the first, genome-scale, dated phylogenies for this clade of snakes. Strikingly, phylogenetic diversity of prey was more strongly correlated to venom diversity than was species diversity, implicating prey species divergence, rather than the number of lineages alone, in the evolution of venom complexity. This positive relationship was observed within three of the four largest toxin gene families in viper venom. Given documented examples of taxonomic specificity of venoms spanning several levels of divergence, we suggest that the phylogenetic diversity of prey measures functionally-relevant divergence in the molecular targets of venom, a claim supported by diversity in the coagulation cascade targets of snake venom serine proteases. Our results support the general concept that the evolved diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.</p>
Fig. 13. MZB.Ophi.5452 in On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae)
Fig. 13. MZB.Ophi.5452 holotype of Trimeresurus gunaleni spec. nov., adult female. Photo: N. Maury.
Fig. 15 in On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae)
Fig. 15. Habitat of Trimeresurus gunaleni spec. nov. Photo: D. Gunalen.
Fig. 9 in On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae)
Fig. 9. Live female of Trimeresurus sumatranus from Bengkulu Province, Sumatra. Photo: G. Vogel.
Fig. 14 in On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae)
Fig. 14. Live female of Trimeresurus sumatranus from Bengkulu Province, Sumatra. Photo: N. Maury.
Fig. 16 in On Trimeresurus sumatranus (Raffles, 1822), with the designation of a neotype and the description of a new species of pitviper from Sumatra (Squamata: Viperidae: Crotalinae)
Fig. 16. Habitat of Trimeresurus gunaleni spec. nov. Photo: D. Gunalen.
Genetic variability, management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis
<p>Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as <i>Bothrops insularis</i>, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (i) characterize the genetic diversity of <i>ex-situ</i> and <i>in-situ</i> populations of <i>B. insularis</i> using heterologous microsatellites; (ii) investigate genetic structure among and within these populations; and (iii) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the <i>B. neuwiedi</i> group were used to access genetic diversity indexes of <i>ex-situ</i> and <i>in-situ</i> populations. Low-to-medium genetic diversity parameters were found. Both populations showed low — albeit significant — values of system of mating inbreeding coefficient, whereas only the <i>in-situ</i> population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the <i>in-situ</i> one, which is crucial for considering a reintroduction process into the island.</p>
Data from: Reticulate evolution in nuclear Middle America causes discordance in the phylogeny of palm‐pitvipers (Viperidae: Bothriechis)
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Genetic variability, management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis
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Phylogenetically diverse diets favor more complex venoms in North American pitvipers
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Data from: Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers
Using multiple markers and multiple analytical approaches is critical for establishing species boundaries reliably, especially so in the case of cryptic species. Despite development of new and powerful analytical methods, most studies continue to adopt a few, with the choice often being subjective. One such example is routine analysis of Amplified Fragment Length Polymorphism (AFLP) data using population genetic models despite disparity between method assumptions and data properties. The application of newly developed methods for analyzing this dominant marker may not be entirely clear in the context of species delimitation. In this study, we use AFLPs and mtDNA to investigate cryptic speciation in the Trimeresurus macrops complex that belongs to a taxonomically difficult lineage of Asian pitvipers. We analyze AFLPs using population genetic, phylogenetic, multivariate statistical, and Bayes Factor Delimitation methods. A gene tree from three mtDNA markers provided additional evidence. Our results show that the inferences about species boundaries that can be derived from population genetic analysis of AFLPs have certain limitations. In contrast, four multivariate statistical analyses produced clear clusters that are consistent with each other, as well as with Bayes Factor Delimitation results, and with mtDNA and total evidence phylogenies. Furthermore, our results concur with allopatric distributions and patterns of variation in individual morphological characters previously identified in the three proposed species: T. macrops sensu stricto, T. cardamomensis, and T. rubeus. Our study provides evidence for reproductive isolation and genetic distinctiveness that define these taxa as full species. In addition, we re-emphasize the importance of examining congruence of results from multiple methods of AFLP analysis for inferring species diversity.
Data from: Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon
Examining species diversity and mechanisms of speciation using coalescent models provides a framework for how regional diversity is accrued, even in well-studied areas such as the Nearctic. It is likely, that gene flow among closely-related species with adjacent distributions may be common. However, the absence of gene flow is a primary assumption of many phylogeographical methods that produce species trees and delimit species using Bayesian or likelihood functions in a coalescent framework. In the present study, we examine delimitation when gene flow between species is present using empirical datasets from two species of North American pitvipers of the genus Agkistrodon. We also use niche modelling to determine whether these young lineages occur in distinct environmental niches. To manage the problem of gene flow between species, we first identify admixed individuals, demonstrate that gene flow has occurred, and then identify the impact of alternative population assignments of admixed individuals on delimitation posterior probabilities. In addition, we examine the influence of mitochondrial genes relative to other loci combined in coalescent analyses that delimit species. Here, we find that the copperheads (Agkistrodon contortrix) and the cottonmouths (Agkistrodon piscivorus) are each composed of two distinct species, with each occupying different niches. Importantly, we find that species can be delimited when the amount of gene flow between lineages is low, although the methods are acutely sensitive to population assignment of individuals.
FIGURE 1 in A new species of pitviper of the genus Popeia (Squamata: Viperidae) from Pulau Tioman, Pahang, West Malaysia
FIGURE 1. The phylogenetic relationships of the southern clade of Sanders et al. (2006) using the taxonomy of Vogel et al. (2004). Sanders et al. (2006) consider the entire clade to be Popeia sabahi.
FIGURE 4 in A new species of pitviper of the genus Popeia (Squamata: Viperidae) from Pulau Tioman, Pahang, West Malaysia
FIGURE 4. Left: Male Popeia fucata (LSUHC 5098, SVL 585 mm) from Genting Highlands, Pahang, West Malaysia. Right: Male paratype P. buniana (ZRC 6118, SVL 604 mm) from the TekekJuara trail, Pulau Tioman, Pahang, West Malaysia. Note the longer P. buniana is much more gracile in body stature.
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