Colubroids or advanced snakes form a monophyletic group comprising four families: Atractaspididae (11 genera, 70 species), “Colubridae” (300 genera, 1850 species), Elapidae (65 genera, 270 species) and Viperidae (33 genera, 240 species). A preliminary classification of colubroids based both on morphological and molecular data is presented and all extant genera of “Colubridae” are listed accordingly. The front-fanged venom system (displayed by some Atractaspididae, all Elapidae and all Viperidae) evolved several times independently and appeared early within colubroids. The rear-fanged venom system (displayed by some Atractaspididae and many “Colubridae”) has been studied less than the front-fanged system, although it is clear that opisthoglyph “Colubridae” constitute a polyphyletic group. The other components of the venom apparatus, the glands and the secretions, also show great variability, rendering the reconstruction of the evolutionary history of the venom apparatus difficult. Nevertheless, the presenc...

Colubroid systematics: evidence for an early appearance of the venom apparatus followed by extensive evolutionary tinkering

By September 2009 an estimated 9084 species of extant reptiles have been described by a total of 4579 papers and books which are listed in a supplementary file. In this review I summarize the history of these species beginning with Linnaeus in 1758. While it took 80 years to reach the first 1000 species in 1838, species descriptions since then have been added roughly at the rate of 1000 new species every 20 years, with a significant acceleration only during the past two decades. The top 40 most productive herpetologists (in terms of “species output”) have described 4780 species, amounting to over half of all species. George Albert Boulenger leads this elite list with 573 species that are still recognized today. Historically, 18 classic works of the 18 th and 19 th century can be singled out, describing almost 1000 species still recognized, including the Erpetologie Generale, published between 1834 and 1854 in nine volumes. The top 25 journals have published more than 3600 species descriptions in the past 250 years (including 169 in Zootaxa, ranked sixth), corresponding to about 40% of all species.

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The original descriptions of reptiles

Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar’s serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species tree approaches. We also examined the individual gene trees in comparison to the 377-locus species tree using the program MetaTree. Using the full anchored dataset under a variety of methods gave us the same, well-supported phylogeny for pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a monophyletic radiation in Madagascar. In addition, within Madagascar, the two major clades inferred correspond largely to the aglyphous and opisthoglyphous genera, suggesting that feeding specializations associated with tooth venom delivery may have played a major role in the early diversification of this radiation. The comparison of tree topologies from the concatenated and species-tree methods using different datasets indicated the 5-locus dataset cannot beused to infer a correct phylogeny for the pseudoxyrhophiines under any method tested here and that summary statistics methods require 50 or more loci to consistently recover the species-tree inferred using the complete anchored dataset. However, as few as 15 loci may infer the correct topology when using the full coalescent species tree method *BEAST. MetaTree analyses of each gene tree from the Sanger and anchored datasets found that none of the individual gene trees matched the 377-locus species tree, and that no gene trees were identical with respect to topology. Our results suggest that ≥50 loci may be necessary to confidently infer phylogenies when using summaryspecies-tree methods, but that the coalescent-based method *BEAST consistently recovers the same topology using only 15 loci. These results reinforce that datasets with small numbers of markers may result in misleading topologies, and further, that the method of inference used to generate a phylogeny also has a major influence on the number of loci necessary to infer robust species trees.

http://anchoredphylogeny.com/download/other_publications/Ruane_et_al_BMC_Pseudoxyrhophiines_Ruane_et_al_2015.pdf

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

Species delimitation and species concepts have been a matter of debate among biodiversity researchers in the last decades, resulting in integrative taxonomy approaches and the use of modern species concepts, such as the phylogenetic, evolutionary or general lineage species concepts. The discussion of subspecies status and concepts has been addressed much less extensively, with some researchers completely refraining from recognizing subspecies. However, allopatric insular populations that are particularly differentiated have traditionally been assigned subspecies status. We studied the molecular phylogeny and morphology of endemic Comoran tree snakes of the genus Lycodryas. Taking an integrative taxonomic approach, we used the concept of independent lines of evidence to discriminate between evidence for specific and subspecific status. Molecular (mtDNA) and morphological data provided sufficient evidence to support four different taxa within Comoran Lycodryas. In a revision of this group, we propose two species, each with two subspecies. We present a discussion of the strong sexual dichromatism unique to Comoran Lycodryas within the genus and related genera that may be explained by sexual selection in combination with the absence of major predators. Then, we discuss the effects of insular evolution and the “island rule” on morphological traits in Comoran Lycodryas and in Liophidium mayottensis, another snake endemic to the Comoros. The absence of larger-bodied snakes may have promoted an increase in body size and the number of dorsal scale rows in these species. Finally, we discuss the subspecies concept, its applications and its significance for integrative taxonomy and for limiting taxonomic inflation. We emphasize that taxon descriptions should be based on an integrative approach using several lines of evidence, preferably in combination with statements on the underlying species concepts or operational criteria, to increase the objectivity and comparability of descriptions.

/pdf/island-evolution-and-systematic-revision-of-comoran-snakes-5akbl614rc.pdf

Island evolution and systematic revision of Comoran snakes: why and when subspecies still make sense.

Members of the Crotalus triseriatus species group of montane rattlesnakes are widely distributed across the highlands of Mexico and southwestern USA. Although five species are currently recognized within the group, species limits remain to be tested. Genetic studies suggest that species may be paraphyletic and that at least one cryptic species may be present. We generate 3,346 base pairs of DNA sequence data from seven nuclear loci to test competing models of species delimitation in the C. triseriatus group using Bayes factor delimitation. We also examine museum specimens from the Trans-Mexican Volcanic Belt for evidence of cryptic species. We find strong support for a nine-species model and genetic and morphological evidence for recognizing two new species within the group, which we formally describe here. Our results suggest that the current taxonomy of the C. triseriatus species group does not reflect evolutionary history. We suggest several conservative taxonomic changes to the group, but future studies are needed to better clarify relationships among species and examine genetic patterns and structure within wide-ranging lineages.

/pdf/multilocus-species-delimitation-in-the-crotalus-triseriatus-3242r0mw9t.pdf

Multilocus species delimitation in the Crotalus triseriatus species group (Serpentes: Viperidae: Crotalinae), with the description of two new species

IN the present volume Mr. Boulenger,the author of the Catalogues of Batrachia, and of the Lizards, Tortoises, Rhynchocephalians and Crocodiles, amongst the Reptilia, commences the description of the only order of living reptiles not hitherto treated by him in the octavo series of British Museum Catalogues. Catalogue of the Snakes in the British Museum (Natural History). Vol. I. By George Albert Boulenger. (London: 1893.)

W. T. Blanford

Papers

Catalogue of the Snakes in the British Museum (Natural History)