Article

Phylogeny, biogeography and classification of the snake superfamily Elapoidea: A rapid radiation in the late Eocene

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Abstract

The snake superfamily Elapoidea presents one of the most intransigent problems in systematics of the Caenophidia. Its monophyly is undisputed and several cohesive constituent lineages have been identified (including the diverse and clinically important family Elapidae), but its basal phylogenetic structure is obscure. We investigate phylogenetic relationships and spatial and temporal history of the Elapoidea using 94 caenophidian species and approximately 2300–4300 bases of DNA sequence from one nuclear and four mitochondrial genes. Phylogenetic reconstruction was conducted in a parametric framework using complex models of sequence evolution. We employed Bayesian relaxed clocks and Penalized Likelihood with rate smoothing to date the phylogeny, in conjunction with seven fossil calibration constraints. Elapoid biogeography was investigated using maximum likelihood and maximum parsimony methods. Resolution was poor for early relationships in the Elapoidea and in Elapidae and our results imply rapid basal diversification in both clades, in the late Eocene of Africa (Elapoidea) and the mid-Oligocene of the Oriental region (Elapidae). We identify the major elapoid and elapid lineages, present a phylogenetic classification system for the superfamily (excluding Elapidae), and combine our phylogenetic, temporal and biogeographic results to provide an account of elapoid evolution in light of current palaeontological data and palaeogeographic models.© The Willi Hennig Society 2009.

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... Recently, several studies generated phylogenies of advanced African snakes, including colubrids, lamprophiids, elapids, and viperids [1][2][3][4][5][6][7][8][9]. In contrast, there has been only one morphology-based, phylogenetic study that focused on atractaspidines [10]. ...
... This grouping was supported by jaw musculature studies of Heymans [14][15], who transferred Atractaspis to the Subfamily Atractaspidinae (Atractaspininae, sensu Kelly et al. [16]). Several recent molecular [7][8][9] and morphological studies [17][18] recovered a monophyletic group containing both aparallactines and atractaspidines, and with few exceptions [19][20][21], current classification recognizes Aparallactinae and Atractaspidinae as sister taxa in the Family Lamprophiidae [2,[7][8][9][22][23][24][25]. Phylogenetic relationships within atractaspidines are not well known, because many phylogenetic studies that included atractaspidines were limited by low sample sizes [2, 8-10, 21-23, 26-27]. ...
... This grouping was supported by jaw musculature studies of Heymans [14][15], who transferred Atractaspis to the Subfamily Atractaspidinae (Atractaspininae, sensu Kelly et al. [16]). Several recent molecular [7][8][9] and morphological studies [17][18] recovered a monophyletic group containing both aparallactines and atractaspidines, and with few exceptions [19][20][21], current classification recognizes Aparallactinae and Atractaspidinae as sister taxa in the Family Lamprophiidae [2,[7][8][9][22][23][24][25]. Phylogenetic relationships within atractaspidines are not well known, because many phylogenetic studies that included atractaspidines were limited by low sample sizes [2, 8-10, 21-23, 26-27]. ...
Article
Full-text available
Atractaspidines are poorly studied, fossorial snakes that are found throughout Africa and western Asia, including the Middle East. We employed concatenated gene-tree analyses and divergence dating approaches to investigate evolutionary relationships and biogeographic patterns of atractaspidines with a multi-locus data set consisting of three mitochondrial (16S, cyt b, and ND4) and two nuclear genes (c-mos and RAG1). We sampled 91 individuals from both atractaspidine genera (Atractaspis and Homoroselaps). Additionally, we used ancestral-state reconstructions to investigate fang and diet evolution within Atractaspidinae and its sister lineage (Aparallactinae). Our results indicated that current classification of atractaspidines underestimates diversity within the group. Diversification occurred predominantly between the Miocene and Pliocene. Ancestral-state reconstructions suggest that snake dentition in these taxa might be highly plastic within relatively short periods of time to facilitate adaptations to dynamic foraging and life-history strategies.
... As is the case with many colubriform snakes, psammophiid taxa were once lumped into Colubridae (e.g., Bogert, 1940;Boulenger, 1896;Bourgeois, 1967Bourgeois, , 1968Broadley, 1977aBroadley, , 1977bDowling, 1975;Dowling & Duellman, 1978;Loveridge, 1940;Marx, 1988;Underwood, 1967); this is especially true in the palaeontological literature, where they were traditionally placed into Colubridae or the paraphyletic assemblage of "Colubrinae", as they (usually, but not always) share with "true" colubrids the absence of hypapophyses in mid-and posterior trunk vertebrae (e.g., Bailon, 1989Bailon, , 1991aBailon, , 1991bBailon & Aouraghe, 2002;Bailon et al., 2011;Barroso Ruíz & Bailon, 2006;Blain, 2012;Delfino, 2004;Holman, 1998;Meylan, 1987;Rage, 1984;Szyndlar, 1984Szyndlar, , 1988Szyndlar, , 1991aSzyndlar, , 2012. However, based on recent phylogenies, they are now generally recognized as part of the Elapoidea radiation (e.g., Burbrink et al., 2020;Figueroa et al., 2016;Kelly et al., 2008Kelly et al., , 2009McCartney et al., 2021;Pyron & Burbrink, 2012;Pyron et al., 2013;Vidal et al., 2008;Weinell & Brown, 2018;Zaher et al., 2009Zaher et al., , 2019Zheng & Wiens, 2016). Within elapoids, they are either treated as their own distinct family (Psammophiidae; e.g., Böhme & de Pury, 2011;Burbrink et al., 2020;Chen et al., 2021;Kelly et al., 2008Kelly et al., , 2009Speybroeck et al., 2020;Wallach et al., 2014;Zaher et al., 2009Zaher et al., , 2019 or either as a distinct subfamily within Lamprophiidae (Psammophiinae; e.g., Branch et al., 2019;Chippaux & Jackson, 2019;Figueroa et al., 2016;Keates et al., 2019;McCartney et al., 2014, 2021Pyron & Burbrink, 2012Pyron et al., 2013;Vidal et al., 2008;Weinell & Brown, 2018;Zheng & Wiens, 2016). ...
... However, based on recent phylogenies, they are now generally recognized as part of the Elapoidea radiation (e.g., Burbrink et al., 2020;Figueroa et al., 2016;Kelly et al., 2008Kelly et al., , 2009McCartney et al., 2021;Pyron & Burbrink, 2012;Pyron et al., 2013;Vidal et al., 2008;Weinell & Brown, 2018;Zaher et al., 2009Zaher et al., , 2019Zheng & Wiens, 2016). Within elapoids, they are either treated as their own distinct family (Psammophiidae; e.g., Böhme & de Pury, 2011;Burbrink et al., 2020;Chen et al., 2021;Kelly et al., 2008Kelly et al., , 2009Speybroeck et al., 2020;Wallach et al., 2014;Zaher et al., 2009Zaher et al., , 2019 or either as a distinct subfamily within Lamprophiidae (Psammophiinae; e.g., Branch et al., 2019;Chippaux & Jackson, 2019;Figueroa et al., 2016;Keates et al., 2019;McCartney et al., 2014, 2021Pyron & Burbrink, 2012Pyron et al., 2013;Vidal et al., 2008;Weinell & Brown, 2018;Zheng & Wiens, 2016). Indeed, the distinctive cranial anatomy of psammophiid genera compared with other colubriforms has been already highlighted since several decades (Bogert, 1940;Boulenger, 1896;Bourgeois, 1967Bourgeois, , 1968Szunyoghy, 1932;Szyndlar, 1988;Zaher et al., 2009). ...
... Anatomical terminology and measurements of snake vertebrae follow Szyndlar (1984) and Georgalis et al. (2021). Taxonomy follows Kelly et al. (2009) and Zaher et al. (2009. ...
Article
We here describe abundant new snake material from the late Miocene (MN 13) of Salobreña, Spain. Vertebral morphology suggests a referral of the specimens to the extant psammophiid Psammophis, documenting the first occurrence of this genus in Europe. The diversity and disparity across the vertebral morphology of different psammophiid genera is discussed. We identify vertebral features that could diagnose Psammophis and therefore enable the recognition of the genus in the fossil record. A comparison of the new Spanish form with other taxa is conducted. We provide a detailed review of the psammophiid fossil record. Material previously described from the middle Miocene of Beni Mellal, Morocco is here tentatively referred to as ?Psammophis sp., an action that renders that occurrence as the oldest (probable) record of the genus and Psammophiidae as a whole, providing thus a potential calibration point. On the other hand, Eastern European Pliocene material that had been previously supposedly referred to Psammophis is here discarded as being rather fragmentary, not affording any more precise determination. The two psammophiid genera Psammophis and Malpolon appear almost simultaneously in the European fossil record (MN 13), with the former achieving only a short-lived and apparently geographically limited distribution in the continent, while the latter still exists in its modern herpetofauna. We assess biogeographic implications of the new find, suggesting a direct dispersal event from northwestern Africa to the Iberian Peninsula during the late Miocene, facilitated by the Messinian Salinity Crisis. This article is protected by copyright. All rights reserved.
... Of these, Elapotinus picteti was recently shown to be related to Malagasy pseudoxyrhophines, and not the Aparallactinae (Kucharzewski et al., 2014). The East African and Middle Eastern genus Micrelaps, considered to be an aparallactine until recently, is currently classified as incertae sedis, because recent phylogenetic evidence suggests the genus shows no affinities with aparallactines (Rasmussen, 2002;Underwood and Kochva, 1993;Kelly et al., 2009;Pyron et al., 2013;Figueroa et al., 2016). Inclusion of the rarer genera (e.g. ...
... Many phylogenetic studies that included aparallactines have been limited by factors that are inherent to rare species, including low sample sizes and limited taxon sampling (Nagy et al., 2005;Kelly et al., 2011;Moyer and Jackson, 2011;Pyron et al., 2011Pyron et al., , 2013Figueroa et al., 2016). Kelly et al. (2009) provided a dating and biogeographic analysis of the superfamily Elapoidea, including aparallactines, but detailed biogeographic information (e.g. dating estimates) within the subfamily was not provided. ...
... Our study included sequences from six of the eight (not including Brachyophis and Hypoptophis) aparallactine genera (6/9 species of Amblyodipsas; 7/11 species of Aparallactus; 1/2 species of Chilorhinophis; 1/1 species of Macrelaps; 6/12 species of Polemon; 4/5 species of Xenocalamus) (Wallach et al., 2014;Uetz et al., 2017). Sequences from some of these individuals have been published previously (Kelly et al., 2009(Kelly et al., , 2011; new sequences were deposited in GenBank (Table 1). Concatenated trees were rooted with Acrochordus granulatus (Acrochordidae; Caenophidia) (not shown on Fig. 2). ...
... Numerous molecular phylogenetic studies of caenophidians have subsequently been conducted. Research foci associated with these analyses include molecular divergence timing estimates, biogeographic histories, diversification patterns, and the evolution of toxic venoms, making them the most intensely studied squamate clade with respect to molecular phylogenetics (e.g., Keogh, 1998;Burbrink et al., 2000;Gravlund et al., 2001;Burbrink, 2002;Vidal, 2002;Fry et al., 2003;Kelly et al., 2003;Keogh et al., 2003;Nagy et al., 2003;Pinou et al., 2004;Lawson et al., 2005;Lukoschek and Keogh, 2006;Burbrink and Lawson, 2007;Vidal et al., 2007;Fry et al., 2008;Hedges et al., 2009;Kelly et al., 2009;Pyron and Burbrink, 2009a,b,c;Zaher et al., 2009;Burbrink and Pyron, 2010;Sanders et al., 2010;Vidal et al., 2010;Murphy et al., 2011;Pyron et al., 2013a,b). The majority of studies have recovered the same sister-taxon relationship between Acrochordus and taxa traditionally included in Colubroidea (but see Pyron et al., 2013a for an alternate hypothesis of sister-taxon relationships of Acrochordus). ...
... The caenophidian fossil record has been more thoroughly documented than for any other squamate clade, with a few Late Cretaceous to early Paleogene records primarily, but not exclusively, from southern continental landmasses (e.g., Rage, 1975;Rage, 2008;Rage et al., 1992;Rage and Werner, 1999;Rage et al., 2013;Parmley and Holman, 2003;Head et al., 2005) and hundreds of records from the late Paleogene to Holocene of mainly North America and Europe (e.g., Rage, 1984[and references therein]; Szyndlar, 1984Szyndlar, , 1985Szyndlar, , 1987Szyndlar, , 1991aSzyndlar, , 1991bSzyndlar, , 2012Szyndlar and Schleich, 1993;Szyndlar and Rage, 1999;Holman, 2000 [and references therein]; Ivanov, 2000Ivanov, , 2002Ivanov and Böhme, 2011), as well as records from South America, Africa, and Asia (e.g., Albino, 1996;Albino and Montalvo, 2006;Rage, 1973Rage, , 1976Rage, , 2003Rage and Ginsburg, 1997;Rage and Danilov, 2008;Head, 2005, Head et al., 2006Head et al., 2007;Head and Bell, 2008). The published record has been used to calibrate multiple caenophidian molecular phylogenies (e.g., Noonan and Chippindale, 2006;Burbrink and Lawson, 2007;Wüster et al., 2007Wüster et al., , 2008Alfaro et al., 2008;Sanders et al., 2010;Kelly et al., 2009;Lukoschek et al. 2012;Pyron and Burbrink, 2012), with different fossils employed to produce highly disparate divergence estimates (Lukoschek et al., 2012). ...
... Wüster et al. (2008) employed similar records to those described here to minimally calibrate the divergence of Eurasian viperines, but used a reported record of late Miocene Sistrurus (Parmley and Holman, 2007) that we do not recognize due to absence of character support for assignment beyond Viperidae. Wüster et al. (2007Wüster et al. ( , 2008, and Kelly et al. (2009) followed the interpretation of Naja romani as a member of the Asian Naja clade (Szyndlar and Rage, 1990) to calibrate the divergence of Asian and African species. Conversely this analysis restricts calibrations of N. romani to only the Naja total clade (see also Lukoschek et al., 2012). ...
... Molecular phylogenies ultimately provided strong support for the monophyly of Caenophidia, and further corroborated more controversial morphological hypotheses, such as the polyphyly of solenoglyphous [11] and proteroglyphous snakes [12]. On the other hand, analyses of molecular evidence also obtained conflicting results for the positions of acrochordids and xenodermids at the base of the Caenophidian tree and highlighted the need of substantial taxonomic changes in order to obtain monophyletic familial level taxa [13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28]. Thus, despite notable advances, many questions regarding the higher-level phylogeny and taxonomy of Caenophidia remain unanswered, and a period of taxonomic instability has seen a number of different, and sometimes contradictory, classification schemes, with none of them being entirely satisfactory (S1 Table). ...
... However, Uetz et al. [33] taxonomic list seems to integrate more accurately the massive contribution of the Herpetological community in recent years and we use that as a framework to describe our results with respect to valid genera and species. However, we consider both taxonomic schemes at the family level to be problematic in several respects and follow instead the supra-familial and familial taxonomic scheme proposed by Zaher et al. [23,25], expanded here to include recently erected or recognized Pseudoxyrhophiinae, Grayiinae, Prosymnidae, and Pseudaspididae [22,26]. We also followed Savage [35] in the use of the family names Pareidae and Xenodermidae instead of Pareatidae and Xenodermatidae. ...
... Recently, Weinell and Brown [36] resolved a long-standing debate regarding the phylogenetic affinities of poorly known Cyclocorus, Oxyrhabdium, Hologerrhum, and Myersophis. Oxyrhabdium was first sequenced by Lawson et al. [18], and its affinities remained uncertain [22,23,26]. Cyclocorus was independently sequenced by us (this study) and Weinell and Brown [36]. ...
Article
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Caenophidian snakes include the file snake genus Acrochordus and advanced colubroidean snakes that radiated mainly during the Neogene. Although caenophidian snakes are a well-supported clade, their inferred affinities, based either on molecular or morphological data, remain poorly known or controversial. Here, we provide an expanded molecular phyloge-netic analysis of Caenophidia and use three non-parametric measures of support-Shimo-daira-Hasegawa-Like test (SHL), Felsentein (FBP) and transfer (TBE) bootstrap measures-to evaluate the robustness of each clade in the molecular tree. That very different alternative support values are common suggests that results based on only one support value should be viewed with caution. Using a scheme to combine support values, we find 20.9% of the 1265 clades comprising the inferred caenophidian tree are unambiguously supported by both SHL and FBP values, while almost 37% are unsupported or ambiguously supported, revealing the substantial extent of phylogenetic problems within Caenophidia. Combined FBP/TBE support values show similar results, while SHL/TBE result in slightly higher combined values. We consider key morphological attributes of colubroidean cranial, vertebral and hemipenial anatomy and provide additional morphological evidence supporting the clades Colubroides, Colubriformes, and Endoglyptodonta. We review and revise the relevant caenophidian fossil record and provide a time-calibrated tree derived from our molecular data to discuss the main cladogenetic events that resulted in present-day patterns of caenophidian diversification. Our results suggest that all extant families of Colubroidea and Elapoidea composing the present-day endoglyptodont fauna originated rapidly within the PLOS ONE | https://doi.
... All rights reserved. Molecular evidence suggests that the colubroid radiation had been under way by the time these forms came to dominate the fossil record, with most estimates suggesting an early Paleogene origin in Asia (Kelly et al., 2009;Vidal et al., 2009;Pyron and Burbrink, 2012). The fossil record is congruent with this early origin, given the occasional occurrence of colubroid snakes in the early Paleogene (Rage, 1974;Holman, 1993;Augé et al., 1997;Parmley and Holman, 2003;Head et al., 2005;Rage et al., 2008Rage et al., , 1992Smith, 2013), and possibly even the Late Cretaceous of Sudan (Rage and Werner, 1999). ...
... The fossil record is congruent with this early origin, given the occasional occurrence of colubroid snakes in the early Paleogene (Rage, 1974;Holman, 1993;Augé et al., 1997;Parmley and Holman, 2003;Head et al., 2005;Rage et al., 2008Rage et al., , 1992Smith, 2013), and possibly even the Late Cretaceous of Sudan (Rage and Werner, 1999). Molecular evidence also suggests a rapid radiation with most extant subfamilies appearing prior to the Neogene (Kelly et al., 2009;Vidal et al., 2009;Pyron and Burbrink, 2012). Unfortunately, the fact that the snake fossil record is largely composed of vertebrae means that many colubroid clades cannot be recognized in the fossil record; there has thus been no confirmation of the presence of these subclades, nor means of providing calibration points for refining molecular clock estimates. ...
... Unfortunately, the fact that the snake fossil record is largely composed of vertebrae means that many colubroid clades cannot be recognized in the fossil record; there has thus been no confirmation of the presence of these subclades, nor means of providing calibration points for refining molecular clock estimates. In particular, the large Afro-Eurasian clade Lamprophiidae, a group estimated to have originated in Africa during the Eocene (Kelly et al., 2009;Pyron and Burbrink, 2012), is unidentified in the fossil record outside of vertebrae referred to the psammophiine Malpolon from the Pliocene and Pleistocene of Europe and North Africa (Szyndlar, 1991(Szyndlar, , 1988Holman, 1998;Bailon, 2000). ...
Article
Extant snake faunas have their origins in the mid-Cenozoic, when colubroids replaced booid-grade snakes as the dominant species. Based on fossils from North America and Europe, the timing of this faunal changeover is thought to have occurred in the early Neogene, after a period of global cooling opened environments suitable for more active predators. However, new fossils from the late Oligocene of Tanzania have revealed an early colubroid-dominated fauna in Africa suggesting a different pattern of faunal turnover there. Additionally, molecular divergence times suggest colubroid diversification began sometime in the Paleogene, although the exact timing and driving forces behind the diversification are not clear. Here we present the first fossil snake referred to the African clade Lamprophiinae, and the oldest fossil known of Lamprophiidae. As such, this specimen provides the only potential fossil calibration point for the African snake radiation represented by Lamprophiidae, and is the oldest snake referred to Elapoidea. A molecular clock analysis using this and other previously reported fossils as calibration points reveals colubroid diversification minimally occurred in the earliest Paleogene, although a Cretaceous origin cannot be excluded. The elapoid and colubrid lineages diverged during the period of global warming near the Paleocene-Eocene boundary, with both clades diversifying beginning in the early Eocene (proximate to the Early Eocene Climate Optimum) and continuing into the cooler Miocene. The majority of subclades diverge well before the appearance of colubroid dominance in the fossil record. These results suggest an earlier diversification of colubroids than generally previously thought, with hypothesized origins of these clades in Asia and Africa where the fossil record is relatively poorly known. Further work in these regions may provide new insights into the timing of, and environmental influences contributing to the rise of colubroid snakes.
... The venomous coralsnakes of the family Elapidae comprise a diverse radiation of more than 170 taxa distributed in Southeast Asia and the New World (Campbell and Lamar, 2004;Castoe et al., 2007). Coralsnakes likely invaded the New World from Asia via a Beringian land bridge connecting Asia and North America during the late Oligocene (Kelly et al., 2009), similar to other major lineages of New World snakes (Castoe et al., 2007;Guo et al., 2012;Holman, 2000). Since their colonization of the New World, coralsnakes have diversified extensively across the Americas, into approximately 85 species in three genera (Micruroides, Micrurus and Leptomicrurus) that are now distributed from the US to Argentina (Campbell and Lamar, 2004). ...
... Although the phylogenetic relationships among the major coralsnake lineages and other elapid snakes are relatively well understood (Castoe et al., 2007;Kelly et al., 2009;Keogh, 1998;Slowinski and Keogh, 2000a), little is currently known about the species-level relationships within the genus Micrurus. Despite the high diversity and broad distribution of Micrurus, external morphology is highly conserved across species (Campbell and Lamar, 2004). ...
Article
New world coralsnakes of the genus Micrurus are a diverse radiation of highly venomous and brightly colored snakes that range from North Carolina to Argentina. Species in this group have played central roles in developing and testing hypotheses about the evolution of mimicry and aposematism. Despite their diversity and prominence as model systems, surprisingly little is known about species boundaries and phylogenetic relationships within Micrurus, which has substantially hindered meaningful analyses of their evolutionary history. Here we use mitochondrial genes together with thousands of nuclear genomic loci obtained via ddRADseq to study the phylogenetic relationships and population genomics of a subclade of the genus Micrurus: The M. diastema species complex. Our results indicate that prior species and species-group inferences based on morphology and color pattern have grossly misguided taxonomy, and that the M. diastema complex is not monophyletic. Based on our analyses of molecular data, we infer the phylogenetic relationships among species and populations, and provide a revised taxonomy for the group. Two non-sister species-complexes with similar color patterns are recognized, the M. distans and the M. diastema complexes, the first being basal to the monadal Micrurus and the second encompassing most North American monadal taxa. We examined all 13 species, and their respective subspecies, for a total of 24 recognized taxa in the M. diastema species complex. Our analyses suggest a reduction to 10 species, with no subspecific designations warranted, to be a more likely estimate of species diversity, namely, M. apiatus, M. browni, M. diastema, M. distans, M. ephippifer, M. fulvius, M. michoacanensis, M. oliveri, M. tener, and one undescribed species.
... The phylogenetic placement of Hemibungarus (False Coral Snakes) as a member of Elapidae is well-supported, but very little is known about the evolutionary history and biogeography of Cyclocorus (two species, each possessing two named subspecies), Hologerrhum (two species), Oxyrhabdium (two species, one of which contains two subspecies), and Myersophis (monotypic) (Fig. 1) (Brown et al., 2000;Castoe et al., 2007;Leviton, 1983Leviton, , 1964Leviton, , 1965Phenix et al., 2011). Genetic data support Oxyrhabdium as a member of Elapoidea, but the position of this lineage, now considered a member of the family Lamprophiidae (Uetz et al., 2017), relative to the other elapoids has remained tenuous Lawson et al., 2005;Kelly et al., 2009;Pyron et al., 2013;Figueroa et al., 2016). DNA sequence data have never been collected for Cyclocorus, Myersophis, and Hologerrhum, leading earlier authors to treat them as members of the family Colubridae, Lamprophiidae, or designated incertae sedis, with unresolved systematic affinities (Pyron et al., 2013;Leviton, 1965Leviton, , 1983Brown et al., 2000). ...
... We obtained additional Cytb sequences from GenBank for 135 individuals (128 species, 104 genera) spanning Colubridae, Elapoidea sensu Kelly et al. (2009), Homalopsidae, and Pareidae. All individuals are represented by homologous Cytb sequences and at least one individual from each sub-familial or equivalent major lineage (Figueroa et al., 2016) is represented by the nuclear gene cmos. ...
Article
The extraordinarily rich land vertebrate biodiversity of the Philippines includes at least 112 species of terrestrial snakes (74% of which are endemic to the archipelago) in 41 genera (12% endemic). Endemic Philippine snake genera include Cyclocorus (two species), Hemibungarus (three species), Hologerrhum (two species), Oxyrhabdium (two species), and Myersophis (monotypic). Although Hemibungarus and Oxyrhabdium have been included in previous species-level phylogenies, the affinities of the other three Philippine endemic genera are completely unknown. We generated novel DNA sequences for six species from four genera and analyzed these in conjunction with data from earlier studies to infer a phylogeny for the group containing Colubridae, Elapoidea (Elapidae + Lamprophiidae), and Homalopsidae. We present a novel phylogenetic result that strongly supports the existence of an entirely endemic Philippine radiation of elapoid snakes that originated 35-25 million years ago. We provide a revised, phylogeny-based classification to accommodate the new clade, transfer Cyclocorus, Hologerrhum, and Myersophis to Lamprophiidae, and provide the first estimate of the evolutionary relationships among these genera and the related Oxyrhabdium, setting the stage for future investigation of this entirely endemic, novel Philippine elapoid radiation.
... This family of snakes is very diverse, not only in southern Africa, but throughout the continent. This illustrates the scarcity of information on the evolution of African Elapidae, known mainly through molecular research (Kelly et al. 2009). In South Africa, XC 09-03µ9 fossil can only be described to family level, which could be either of the two groups of African spitting elapids: the genus Hemachatus or subgenus Afronaja. ...
Article
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There are about 151 snake species in southern Africa, but little is known about their diversity and evolution during the past 23 million years. Snakes are poorly represented, even in the richly fossiliferous Plio-Pleistocene deposits in the Cradle of Humankind. This is especially true for the venomous snakes of the family Elapidae which comprises the cobras, rinkhals, mambas, and African garter snakes. The Locus X Cave in the Bolt’s Farm Cave System in the Sterkfontein Valley yielded part of a snake maxilla carrying a complete fang, which was extracted from the cemented matrix (breccia) mainly by acid preparation in the Plio-Pleistocene Palaeontology section of the Ditsong National Museum of Natural History (DNMNH). The present study shows that this fossil belongs to a spitting snake in the family Elapidae. It is not possible at present to suggest a specific species as only fragmentary maxilla remains were discovered and there are no vertebrae associated with it. That noted, the fragmentary maxilla could either belong to rinkhals represented in southern Africa today by an endemic species Hemachatus haemachatus, or to Afronaja species. Unlike in southern Africa, a well-established methodology for comparing fossil and extant osteological material of snakes in palaeontology as well as in archaeology exists in Europe. Through analysing the snake maxilla from Locus X Cave in the Bolt’s Farm Cave System, this article presents a preliminary methodology to develop an approach that can be used for palaeo-herpetology and herpetology in general. This will assist in studying more of the herpetological remains from hominid-bearing sites, and give us an understanding of the palaeoenvironments of these sites.
... Both Vidal et al. (2008) and Kelly et al. (2009) demonstrated that the two snake species Amplorhinus multimaculatus and Ditypophis vivax are sister to Duberria. Hence the former two species were used as outgroups. ...
Article
Full-text available
We examined the impact of climatic fluctuations on the phylogeographic structure of the common slug eating snake (Duberria lutrix lutrix) throughout its distribution in South Africa. The evolutionary history within the taxon was examined using partial DNA sequence data for two mitochondrial genes (ND4 + cyt b) in combination with a nuclear locus (SPTBN1). Phylogenetic relationships were investigated for both the combined mtDNA and total evidence DNA sequence data. In addition, population and demographic analyses together with divergence time estimations were conducted on the combined mtDNA data. Topologies derived from the combined mtDNA analyses and the total evidence analyses were congruent and retrieved five statistically well-supported clades, suggesting that Duberria l. lutrix represents a species complex. The five clades were generally allopatric, separated by altitudinal barriers and characterised by the absence of shared mtDNA haplotypes suggesting long term isolation. Divergence time estimations indicate that the diversification within the D. l. lutrix species complex occurred during the Plio/Pleistocene as a result of climatic fluctuations and habitat shifts for the species. A taxonomic revision of the D. l. lutrix species complex may be required to delineate possible species boundaries.
... Within Elapidae, the Asian coral snake genus Calliophis also represents a monophyletic clade and the sister group to all other Asian and American coral snakes [8]. The common ancestor of the American coral snakes migrated into North America in the late Eocene to early Oligocene, roughly 30-25 Mya [9], across the 40 Km Bering land bridge of deciduous and coniferous forests, which connected Eastern Eurasia and Western North America from the early Tertiary until the end of the Miocene [10]. Extant New World coral snakes, the only elapids found in the Americas, constitute a taxonomic complex represented by the genera Leptomicrurus, Micruroides, and Micrurus [8,9,11,12], although Leptomicrurus is not unanimously recognized as a distinct genus from Micrurus [2,13]. ...
Article
Micrurus is a monophyletic genus of venomous coral snakes of the family Elapidae. The ~80 recognized species within this genus are endemic to the Americas, and are distributed from southeastern United States to northern Argentina. Although relatively few bites are recorded due to their reclusive nature, semi-fossorial habits, and their occurrence in sparsely populated areas, coral snakes possess powerful venoms that target the cholinergic system and, if early treatment is missed, can cause neuromuscular paralysis, respiratory failure, and death by asphyxiation within hours of envenoming. The to-date proteomically characterized 18 micrurine venoms exhibit a puzzling phenotypic dichotomy, characterized by the toxin arsenal being dominated either by pre-synaptically acting PLA2s or post-synaptic 3FTxs, and a general, but imperfect, distributional pattern of these venom phenotypes along the North-South axis of the American continent. The lack of perfect phylogenetic clustering suggests that phylogeny may not be the sole factor driving the evolution of the divergent venom phenotypes across Micrurus venoms. To shed new light on the origin and expression pattern of the 3FTx/PLA2 venom dichotomy, we have conducted a comparative proteomics analysis of venoms from the Brazilian ribbon coral snake, Micrurus lemniscatus carvalhoi, sourced from different localities in the Brazilian states of São Paulo; the Caatinga coral snake, M. ibiboboca, from central Bahia state (Brazil); two Micrurus specimens of uncertain taxonomy collected in the Brazilian states of Alagoas and Rio de Janeiro; and the Western ribbon coral snake, M. l. helleri, from Leticia, the southernmost town of the Colombian Department of Amazonas. Venoms from São Paulo and Rio de Janeiro showed 3FTx-predominant phenotypes, while in venoms from Leticia, Alagoas and Bahia PLA2s represented the major toxin family. Comparative venom proteomics suggests that both Micrurus venom phenotypes exhibit a high degree of toxin evolvability. Mapping the 3FTx/PLA2 dichotomy across the Americas points to a phylogeographic pattern for venom phenotypes consistent with, but more complex than, the North-South distribution hypothesis anticipated in previous investigations. Biological significance New World coral snakes (Micrurus: Elapidae) produce potent venoms that target pre- and post-synaptically cholinergic nerve terminals resulting in neuromuscular paralysis, and in severe envenomings, may lead to death from asphyxiation by respiratory arrest. Presynaptic β-neurotoxins of group IA PLA2 protein subfamily and postsynaptic α-neurotoxins with 3FTx fold are the major components (>80%) of coral snake venoms. Micrurine venoms exhibit a puzzling phenotypic venom dichotomy, characterized by the dominant expression of either α- or β-neurotoxins. The distribution of these alternative compositional profiles has been fragmentarily studied both across Micrurus phylogeny and along the North-South axis of the genus radiation in the American continent, from southern United States to Northern Argentina. The unpredictability of the neurotoxin profile across the distribution range of the coral snakes represents a difficulty for applying the most appropriate treatment upon a coral snakebite. A deep knowledge of the phylogeographic distribution and the evolution of dichotomic Micrurus venoms would be useful for tracing the evolutionary path to their present day phenotypes, rationalizing the patchy cross-reactivity of current Micrurus antivenoms, and improving the efficacy of antivenoms to neutralize coral snake envenomings.
... 'Out of Africa' dispersal is often followed by diversification in Asia and subsequent 'Out of Asia' dispersal back into Africa (Folinsbee & Brooks, 2007;Kodandaramaiah & Wahlberg, 2007). It is postulated that the connection of Africa and the Arabian peninsula to Eurasia from the mid-Oligocene (30-25 Ma; Jolivet & Faccenna, 2000;Willis & McElwain, 2002;Bosworth et al., 2005;Gheerbrant & Rage, 2006) facilitated the 'geo-dispersal' (sensu Lieberman & Eldredge, 1996) of many vertebrate and invertebrate taxa (Mey, 2005;Bossuyt et al., 2006;Folinsbee & Brooks, 2007;Kodandaramaiah & Wahlberg, 2007;Schaefer & Renner, 2008;Aduse-Poku et al., 2009;Kelly et al., 2009;Rasmussen & Cameron, 2010). Furthermore, the connection of Africa to Eurasia resulted in the closing of the Tethys Sea in the mid-Miocene (20-10 Ma), reorganizing oceanic currents (Hessami et al., 2001). ...
Article
The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four‐gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa. The tribe appears to have diversified during the Cenozoic, beginning c. 50–32 Ma, with most extant African lineages originating in the Miocene or later, well after the breakup of the Gondwanan landmass. Biogeographical analysis suggests an African origin for the tribe and a single dispersal event founding the Asian platypleurines, although additional taxon sampling and genetic data will be needed to confirm this pattern because key nodes in the tree are still weakly supported. Two Platypleurini genera from Madagascar (Pycna Amyot & Audinet‐Serville, Yanga Distant) are found to have originated by late Miocene dispersal of a single lineage from Africa. The genus Platypleura is recovered as polyphyletic, with Platypleura signifera Walker from South Africa and many Asian/Indian species apparently requiring assignment to different genera, and a new Platypleura concept is proposed with the synonymization of Azanicada Villet syn.n. The genera Orapa Distant and Hamza Distant, currently listed within separate tribes but suspected of platypleurine affinity, are nested deeply within the Platypleurini radiation. The tribe Orapini syn.n. is here synonymized while the tribe Hamzini is pending a decision of the ICZN to preserve nomenclatorial stability. The first molecular assessment of the African and Asian cicada tribes Hamzini, Orapini and Platypleurini shows Orapa and Hamza nested deeply within the Platypleurini radiation. The tribe Orapini syn.n. is a junior synonym of the tribe Platypleurini, while Azanicada syn.n. is synonymized with Platypleura and Platypleura zuluensis stat. rev. reassigned. The tribe has an African origin with subsequent dispersal in the Miocene to Asia following the collision of Africa and Asia, and with oceanic dispersal to Madagascar.
... We acknowledge the fact that this scheme promotes taxonomic stability for the long-standing name Colubroidea. However, such traditional taxonomic hierarchy no longer accommodates new knowledge of phylogenetic affinities within the group appropriately (Vidal et al., 2007;Kelly et al., 2009;Zaher et al., 2009). ...
... A number of studies indicated the paraphyly of the family Colubridae, as traditionally understood, in relation to the Elapidae and the Atractaspididae (Vidal and Hedges 2002;Nagy et al. 2003). As adopted by Kelly et al. (2008Kelly et al. ( , 2009, this resulted into relocating Malpolon (Montpellier snakes) to the family Psammophiidae. In addition, the clade containing the water snakes (Natrix) is now generally treated as the family Natricidae (see also Vidal et al. 2007, Zaher et al. 2009). ...
Article
Full-text available
Research on the taxonomy of European amphibians and reptiles has increased noticeably over the last few decades, indicating the need for recognition of new species and the cancellation of others. This paper provides a critical review of recent changes and draws up a tentative species list.
... We chose to begin with the dominant neurotoxin of the elapid family of snakes [16][17][18] . The elapid family of snakes account for ~60% of venomous snake species and includes over 50 genera, 300 species, and over 170 subspecies 19 . The α-neurotoxin three-finger toxins (3FTXs) are amongst the deadliest toxins in elapid venom 20 . ...
Preprint
Snake envenomation is a neglected tropical disease, causing over 100,000 deaths and 300,000 permanent disabilities in humans annually. Here we recover broadly neutralizing antivenom antibody lineages from the B-cell memory of a human subject with extensive history of snake venom exposure. Centi-3FTX-D09, an antibody from these lineages, recognized a conserved neutralizing epitope on 3-finger toxins (3FTXs), a dominant snake neurotoxin. Crystal structures of Centi-3FTX-D09 in complex with 3FTXs from mamba, taipan, krait, and cobra revealed epitope mimicry of the interface between these neurotoxins and their host target, the nicotinic acetylcholine receptor. Centi-3FTX-D09 provided in-vivo protection against diverse 3FTXs, whole venom challenge from cobras, black mamba, and king cobra, and, when combined with the phospholipase inhibitor varespladib, protection against tiger snake, krait, eastern brown, and taipans.
... The probable Asian origin of the common ancestor of extant elapids is suggested by the distribution of the basal lineages within this family (Keogh, 1998;Vidal et al., 2007;Castoe et al., 2007;Lee et al., 2016). Coral snakes presumably entered the Americas across the Bering land bridge, which connected Eastern Eurasia and Western North America from the early Tertiary until the end of the Miocene (Kelly et al., 2009). Phylogenetic and morphological data clearly position Sinomicrurus and Calliophis as the Asian coral snake representatives of the clade that includes all New World coral snakes, i.e. ...
... The Elapidae family (elapids), which has approximately 300 venomous snakes in 61 genera, is a monophyletic group among advanced snakes (Vonk et al., 2008). Several broad radiated lineages (diverged rapidly between around 31 and 26 mya), supported by fossil records and molecular evidence (Kelly et al., 2009) have been identified within the Elapidae, including the Afro-Asian cobras, Oriental kraits, Asian-American corals, and Australian and marine snakes, which are well known to be the most toxic snakes in the world. So far, the gene expression profiles of venom glands from four species (Pahari et al., 2007) have been reported using EST sequencing. ...
Article
Codon bias study in an organism gains significance in understanding the molecular mechanism as well as the functional conservation of gene expression during the course of evolution. The prime focus in this study is to compare the codon usage patterns among the four species belonging to the genus Bungarus (B. multicinctus, B. fasciatus, B. candidus and B. flaviceps) using several codon bias parameters. Our results suggested that relatively low codon bias exists in the coding sequences of the selected species. The compositional constraints together with gene expression level might influence the patterns of codon usage among the genes of Bungarus species. Both natural selection and mutation pressure affect the codon usage pattern in Bungarus species as evident from correspondence analysis. Neutrality plot indicates that natural selection played a major role while mutation pressure played a minor role in codon usage pattern of the genes in Bungarus species.
... As mentioned already the body of evidence relied upon to resolve the current taxonomy of the Colubroidea is immense. However some of the key published studies and relevant papers include the following: Alfaro et al. (2008), Cadle (1984Cadle ( , 1985, Chen et al. (2013), Collins (2006), Cope (1893), De Queiroz (2006, Dowling (1978), Dowling and Deullman (1978), Günther (1858), Huang et al. (2009), Jan (1863), Keller et al. (2003), Kelly et al. (2003Kelly et al. ( , 2009, Keogh (1998), Laurenti (1768), Lawson et al. (2005), Leviton (1968), Liem et al. (1971), Nixon et al. (2003), Pinau et al. (2004), Burbrink (2009, 2012), Pyron et al. (2011Pyron et al. ( , 2013, Rannala et al. (1998), Romer (1956), Vidal et al. (2007Vidal et al. ( , 2008Vidal et al. ( , 2009Vidal et al. ( , 2010, Caldwell (2009), Wiens (2003), Wiens and Moen (2008), Zaher (1999), Zaher et al. (2009Zaher et al. ( , 2012, Zhao and Adler (1993), Zug et al. (2001), Zwickl and Hillis (2002), and the sources cited therein, which includes relevant papers not necessarily themselves about snake taxonomy or phylogenetics, but yet deal with other vertebrates in relevant matters. I have no doubt that in the immediate term, there will be howls of protest from the usual quarters in terms of this new classification for the Colubroidea. ...
Article
Recent molecular studies have effectively resolved the phylogeny of most of the modern snakes. Notwithstanding this, the taxonomy at the family level is seen to be inconsistent between major clades, with family level groups of similar divergence times being classified by single authors variously as genera, subfamilies and families within single given papers. To correct the inconsistencies, some of the lower ranked groups are elevated to match the others already accorded family status. This also brings the taxonomy and nomenclature of the snakes more into line with other vertebrate groups, including most notably the birds and placental mammals. For the majority of affected clades there are already available names and each simply converts from subfamily to family. However, four well-established groups until now have not been formally named. Instead they have been shunted between other family-level groups, sometimes in placements that do not match the evidence. In view of recently published phylogenies which clearly show that these taxa should be placed separately, regardless of their very ancient affinities, they are named herein according to the Zoological Code (Ride et al. 1999). A further two groups, until now classified as being within the Pseudoxenodontinae and Colubrinae, both of which are now elevated to family status are removed from these and placed within their own families due to their early divergence. One of these in turn is divided into two newly named tribes. INTRODUCTION The currently recognized taxonomy of the extant snakes is a synthesis of countless studies over the past two centuries. Studies of morphology and habits have been complimented by the magnificent new technology of gene sequencing and the like. With all this information at hand, there have been numerous taxonomies proposed and more recently ever more detailed phylogenies produced using supermatrix generating computer progams. Over the past decade numerous phylogenies have been produced that have established the relationships of the lesser-known snake genera to other better known genera and computer-generated applications calibrated with known events have been able to accurately establish common ancestry time-lines and the like.
... ; Melville et al. 2001 (Ctenophorus ), 2008 (Ctenophorus/Rankinia ), 2011 (Amphibolurus/Lophognathus ); Shoo et al. 2008 (Tympanocryptis ); Edwards and Melville 2011 (Diporiphora ); Smith et al. 2011 (Diporiphora ); Ng et al. 2013 (Rankinia ); (Amphibolurus ) Gekkota Donnellan et al. 1999;Han et al. 2004;Gamble et al. 2008 Australia Gekkonidae 7 47 Southeast Asia Strasburg and Kearney 2005;Jackman et al. 2008;Heinicke et al. 2010Heinicke et al. , 2011Wood et al. 2012Kearney et al. 2003; Heinicke et al. 2010 (Nactus ); Fujita et al. 2010 (Heteronotia ); Pepper et al. 2011b; Sistrom et al. 2013Sistrom et al. , 2014 (Gehyra ) Australia Diplodactylidae 17 105 Gondwana Melville et al. 2004;Oliver et al. 2007Oliver et al. , 2012aOliver and Sanders 2009;Bauer 2011 Hoskin et al. 2003 (Orraya/Phyllurus/Saltuarius ); Melville et al. 2004 (Strophurus ); Pepper et al. 2006; Oliver et al. 2007 (Diplodactylus ) Fuller et al. 1998;Ast 2001;Schulte et al. 2003;Jennings and Pianka 2004;Fitch et al. 2006;Schuett et al. 2009;Vidal et al. 2012Fitch et al. 2006; Smissen et al. 2013 (Varanus ) Slowinski et al. 1997;Keogh 1998;Keogh et al. 1998;Scanlon and Lee 2004;Kuch et al. 2005;Wuster et al. 2005;Williams et al. 2008;Kelly et al. 2009Keogh et al. 2003; Skinner et al. 2005 (Pseudonaja ); Kuch et al. 2005 (Pseudechis ); Dubey et al. 2010 (Drysdalia ) Australia Elapidae; Hydrophiinae (true sea snakes) 12 33 Southeast Asia Sanders et al. , 2013Rasmussen et al. 2014 Lukoschek and Keogh 2006 (sea snakes); Lukoschek et al. ...
... After the genus Calliophis, the coral snakes are the second-most basal branch of the elapid family (Pyron et al. 2013;Lee et al. 2016). The clade originated in Asia and are currently represented there by the genus Sinomicrurus (5 species), but migrated across the Bering land bridge to the Americas roughly 30 million years ago (Uetz et al. 2016;Kelly et al. 2009;Lee et al. 2016). Once in the Americas coral snakes divided into the genera Micruroides (1 species) and Micrurus (79 species, including the 4 species often placed in the genus Leptomicrurus) which rapidly diversified and can be found from the southern United States to central Argentina (Uetz et al. 2016;Roze 1996;Wallach et al. 2014). ...
Article
Full-text available
Coral snakes, most notably the genus Micrurus, are the only terrestrial elapid snakes in the Americas. Elapid venoms are generally known for their potent neurotoxicity which is usually caused by Three-Finger Toxin (3FTx) proteins. These toxins can have a wide array of functions that have been characterized from the venom of other elapids. We examined publicly available sequences from Micrurus 3FTx to show that they belong to 8 monophyletic clades that diverged as deep in the 3FTx phylogenetic tree as the other clades with characterized functions. Functional residues from previously characterized clades of 3FTx are not well conserved in most of the Micrurus toxin clades. We also analyzed the patterns of selection on these toxins and find that they have been diversifying at different rates, with some having undergone extreme diversifying selection. This suggests that Micrurus 3FTx may contain a previously underappreciated functional diversity that has implications for the clinical outcomes of bite victims, the evolution and ecology of the genus, as well as the potential for biodiscovery efforts focusing on these toxins.
... The origin of Passeriformes had previously been is dated as approximately 82 MYA with the split into oscines/suboscines 62-78 MYA (Barker et al., 2004;Ericson et al., 2006); however, according to the most recent analyses, passerines originated 40-50 MYA and split 35-48 MYA (Jarvis et al., 2014;Prum et al., 2015). Colubroid snakes originated 43-58 MYA (Kelly et al., 2009); therefore, if we believe these dates this host switch could have happened on the direct ancestor of colubroids. ...
Article
The mite family Harpirhynchidae (Acariformes: Cheyletoidea) comprises 154 named species from 15 genera, all of which are permanent parasites of birds or snakes. We inferred the phylogeny of the family with maximum parsimony (MP) and Bayesian analyses for 67 ingroup and 3 outgroup species from the families Cheyletidae, Demodecidae, and Psorergatidae based on 177 morphological characters. The analyses revealed uncertainty of monophyly of the subfamily Harpirhynchinae. The subfamilies Harpypalpinae and Ophioptinae constitute a monophyletic group which is either sister to Demodecidae + Psorergatidae (supported by Bayesian analysis and by 59% of MP trees) or Harpirhynchinae (41% of MP trees). Harpirhynchids were shown to be highly host specific, with 69.5% being monoxenous species and 23% species are associated with several closely related hosts. Results of multinomial logistic regression showed that the microhabitat on the host and type of cysts produced by mites do not significantly influence at level of their host specificity. Ancestral host reconstruction shows that mites of the clade Harpypalpinae + Ophioptinae evolved to parasitism on Passeriformes independently from the Harpirhynchinae. Ancestor of ophioptines switched to an ancestor of colubroid snakes from passerines. In contrast, harpirhynchines colonized a common ancestor of neognathous birds. In the subfamily Harpirhynchinae, the ancestral microhabitat was probably the surface of the host's skin, with intracutaneous parasitism being a more derived lifestyle. According to reconstructed phylogenetic pattern, parasitism at the feather bases of passerine hosts arose independently in two genera (Neharpyrhynchus and Trichorhynchiella) from intracutaneous parasitism.
... Previous studies (e.g. Slowinski & Keogh 2000, Nagy et al. 2005, Kelly et al. 2009) demonstrated that African elapids of the genus Naja were non-monophyletic with respect to Boulengerina and Paranaja. The latter two genera were therefore, consolidated in Naja, with 26 extant species, 11 in Asia and 15 in Africa (Wallach et al. 2009). ...
Article
Full-text available
The Cobra-Preta (black snake in Portuguese) of Sao Tomé Island in the Gulf of Guinea has historically been referred to as Naja (Boulengerina) melanoleuca (Squamata: Elapidae). Its presence on the island has been traditionally explained as an introduction from the mainland by Portuguese settlers, supposedly to control the rat population. This explanation has been widely accepted by local authorities and even international conservation agencies. The taxonomic identity of this snake has remained undisputed by all taxonomists who have published about it, with the exception of L. Capocaccia in 1961. Arguments supporting the human introduction hypothesis are weak and are contradicted by historical, morphological and molecular data. Further, the biogeographic history of the Gulf of Guinea oceanic islands and recent insights on the taxonomic identity and evolutionary history of other taxonomic groups occurring there suggest that the Cobra-Preta, in fact, represents a distinct lineage of the melanoleuca group, endemic to São Tomé. We here describe the Cobra Preta as a new species. The new species differs from N. (B.) melanoleuca, its sister species, by a distinct coloration ventral pattern and the type of contact of the sublingual scales. Data on the toxicology, distribution, ecology, folklore and conservation status of the new species are presented.
... Therefore, to obtain estimates of the divergence times among P. schokari lineages, the dataset was expanded to span the superfamily Colubroidea plus Achrochordus, and thus make use of the calibration scheme used byWüster et al. (2008) andPook et al. (2009). Other authors have used a slightly different prior set (Sanders and Lee, 2008;Kelly et al., 2009), so we also dated the phylogeny according to the revised version bySanders et al. (2010). RAG2 was excluded given that it was not available for most of the dataset. ...
Article
Highlands, hydrographic systems and coastal areas have been hypothesised to form corridors across the hyperarid Sahara desert in North Africa, allowing dispersal and gene flow for non-xeric species. Here we aim to provide a genetic test for the trans-Saharan corridor model, and predict the location and stability of ecological-corridors, by combining phylogeography and palaeoclimatic modelling. The model was the Psammophis schokari (Schokari sand racer) group, fast-moving and widely distributed generalist colubrids occurring mostly in arid and semiarid scrublands. We combined dated phylogenies of mitochondrial and nuclear markers with palaeoclimatic modelling. For the phylogeographic analysis, we used 75 samples of P. schokari and P. aegyptius, and Bayesian and Maximum-Likelihood methods. For the ecological models, we used Maxent over the distribution of P. schokari and West African lineages. Models were projected to past conditions (mid Holocene, Last Glacial Maximum and Last Inter-Glacial) to infer climatic stable areas. Climatic stability was predicted to be mostly restricted to coastal areas and not spatially continuous. A putative temporary trans-Saharan corridor was identified in Eastern Sahara, with a more stable one along the Atlantic coast. Six parapatric lineages were identified within P. schokari, four occurring in North Africa. These likely diverged during the Pliocene. The Tamanraset River might have been a vicariant agent. African lineages may have experienced further subsequent diversification during the late Pleistocene. The main P.schokari refugia were probably located along the northern margins of the Sahara, allowing its North-to-South colonisation. Trans-Saharan corridors seem to have played a role in P. schokari biogeography, allowing colonization of central Saharan mountains and Sahel. Some might have worked as refugia, and even the most stable corridors may have sections working as filters, depending on each climatic phase. We expect the use of trans-Saharan corridors to decrease for more mesic species or with less dispersal capabilities.
... (2012), Brown et al. (2012aBrown et al. ( , 2012b, Burbrink and Pyron (2008), Burbrink et al. (2008), Cadle (1988), Daltry and Wüster (2002), Das (1994Das ( , 2003Das ( , 2010, David and Vogel (1996), David et al. (2008aDavid et al. ( , 2008b, de Queiroz and Gatesy (2007), Deuve (1970), Diamond and Gilpin (1983), Driskell et al. (2004), Dowling (1951), Drummond and Rambaut (2007), Drummond et al. (2006), Duméril, (1853), Edgar (2004), , Esselstyn et al. (2009, Evans et al. (2003), Ferner et al. (2000), Fritz (1993), Gamble et al. (2012), Gaulke (2002), Goris and Maeda (2004), Gravlund (2001), Greene (1997), Grismer et al. (2007Grismer et al. ( , 2008Grismer et al. ( , 2011Grismer et al. ( , 2014, Tillack (2001a, 2001b), Günther (1858Günther ( , 1868, Guo et al. (2013), Heaney (1985Heaney ( , 1986, Heaney et al. (1998Heaney et al. ( , 2005, Heise et al. (1995), Hikida et al. (1989), Hoser (2000, IUCN (2014), Jackson and Fritts (2004), Jansa et al. (2006), Jones and Kennedy (2008), Kelly et al. (2003Kelly et al. ( , 2009), Kraus and Brown (1998), Kuntz (1963), Lanza (1999), Lawson et al. (2005), Lee (2005), Lee and Scanlon (2002), Lei et al. (2014), Leviton (1955Leviton ( , 1965, Linnaeus (1758), Lue et al. (1999), Maki (1931Maki ( , 1933, Malhorta et al. (2011), Marshall (2010, McLeod et al. (2011), Mell (1922, Mori (1984), Mukherjee and Bhupathy (2007), Murphy et al. (2012), Neang et al. (2012Neang et al. ( , 2014, Nutphand (1986), Orlov et al. (2000Orlov et al. ( , 2003, Ota (1998Ota ( , 1991Ota ( , 2000, Ota and Ross (1994), Pauwels and Sumontha (2007), Pauwels et al. (2000aPauwels et al. ( , 2000bPauwels et al. ( , 2002Pauwels et al. ( , 2003Pauwels et al. ( , 2004Pauwels et al. ( , 2005Pauwels et al. ( , 2006, Pfenninger and Schwenk (2007), Philippe et al. (2004), Pope ( , 1929Pope ( , 1935, Posada (2008), Pyron and Burbrink (2009), Pyron et al. (2011, Rambaut and Drummond (2007), Reza (2010), Rieppel (1988), Ronquist and Huelsenbeck (2003), Saint Girons (1972), Sanderson et al. (2003), Siler et al. (2010Siler et al. ( , 2011Siler et al. ( , 2012aSiler et al. ( , 2012bSiler et al. ( , 2012cSiler et al. ( , 2013, Slowinski and Lawson (2005), Slowinski et al. (2001), Smith (1943), Stamatakis (2006), Stamatakis et al. (2008), Stejneger (1907), Stuart et al. (2006), Stuart and Chuaynkern (2007), Stuebing and Inger (1999), Swofford (1999), Szyndlar and Nguyen (1996), Taylor (1965), Thomson and Shaffer (2010), Toda (1987), Toriba (1982), Toriba and Hikida (1999), Toyama (1985), Tu (2004), Uchiyama et al. (2002), Vandewege et al. (2012), Vidal et al. (2007Vidal et al. ( , 2009), Vogel and Brachtel (2008), Vogel and David (2010), Vogel and Luo (2011, Wall (1921) Zhao (2002Zhao ( , 2006, Zhao and Adler (1993), Zhao and Jiang (1981), Zhao and Yang (1997), Zhao et al. (1998), Ziegler (2002, Ziegler et al. (2004Ziegler et al. ( , 2007 and sources cited therein. ...
Article
The Asiatic Wolf Snakes genus Lycodon Boie, 1826 as currently recognized, consists of about 48 species of which 15 have been formally described in the last 15 years (Neang et al. 2014). These snakes have for most of the last 188 years been treated as being within a single genus, namely Lycodon Boie, 1826. Other authors have proposed generic names for given species or species groups, with most if not all invariably being synonymised with Lycodon. By way of example, the most recent phylogenetic revisions by Siler et al. (2013) and Guo et al. (2013) merged the long recognized and used genus Dinodon Duméril, 1853 within a greater Lycodon. This is a position maintained by most other authors including for example Neang et al. (2014). However a comparison of where the line of divergence is drawn to define a genus between snakes within Lycodon sensu lato and other snake genera as currently recognized shows that by any reasonable interpretation Lycodon should be split to be consistent with the majority of other genera. This view is supported by molecular studies of Siler et al. (2013), Guo et al. (2013) and Grismer et al. (2014) if lined up against the comparative order-wide supermatrix constructed by Pyron et al. (2013), which clearly shows Lycodon as paraphyletic. As a result of the evidence within these and other studies, including numerous taxonomic ones based on morphology, Lycodon as currently recognized is split into seven genera, for which names are available for five. The other two genus groups, Snakebustersus gen. nov. and Apollopierson gen. nov. are formally named and defined according to the rules of the Zoological Code (Ride et al. 1999). Within various genera five new subgenera are also formally named for the first time and another genus Cercaspis Wagler, 1830 is resurrected and treated as being a monotypic subgenus within Lycodon. Also recognized are the following associated genera: Lepturophis Boulenger, 1900, Dryocalamus Günther, 1858 and Hydrophobus Günther, 1862, making a grand total of 10 genera within Lycodon sensu-lato. In order to best identify the relationships between all the associated genera a new tribe Snakebustersini tribe nov. is erected to accommodate the genera. Keywords: Taxonomy; Nomenclature; Lycodon; Dinodon; Tytleria; Ophites; Cercaspis; Tetragonosoma; Leptorhytaon; Dryocalamus; Hydrophobus; Sphecodes; Dannyelfakharikukri; new tribe; Snakebustersusini; new genera; Snakebustersus; Apollopierson; new subgenera; Mindanaosnakebustersus; Myanmarelfakhari; Sinoelfakhari; Paralycodon; Kotabilycodon.
... Madagascar was colonized twice by lamprophiids, first in the early-to-mid Miocene resulting in the core gemsnake radiation (Supplementary data available on Dryad) and second in the mid-to-late Miocene, resulting in the two species within the genus Mimophis. This agrees with previous studies attempting to date and number these colonization events, relying on mainly mtDNA data and reduced sampling of gemsnake taxa (Nagy et al. 2003;Vidal et al. 2008;Kelly et al. 2009). However, our result conflicts with other studies that found support for paraphyletic gemsnakes in Madagascar. ...
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Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world's mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr. [Gemsnakes; in situ diversification; island biogeography; Neogene; Pseudoxyrhophiinae; speciation.].
... Due to this unusual skull compression, snout shape and modified maxillary teeth, the higher taxonomical level of these snakes has been in flux. However, modern phylogenetic analyses have allowed them to be assigned to their own family, Prosymnidae (superfamily Elapoidea), sister to the family Psammophiidae (Vidal et al. 2008;Kelly et al. 2009;Pyron et al. 2013;Figueroa et al. 2016;Zaher et al. 2019). Currently, Prosymna is represented by 16 species Uetz et al. 2022), and recent phylogenetic work has shown that cryptic diversity may exist in the genus, especially within P. ambigua, P. frontalis, and P. stuhlmanni ). ...
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African Shovel-snout snakes ( Prosymna Gray, 1849) are small, semi-fossorial snakes with a unique compressed and beak-like snout. Prosymna occur mainly in the savanna of sub-Saharan Africa. Of the 16 currently recognised species, four occur in Angola: Prosymna ambigua Bocage, 1873, P. angolensis Boulenger, 1915, P. frontalis (Peters, 1867), and P. visseri FitzSimons, 1959. The taxonomical status and evolutionary relationships of P. angolensis have never been assessed due to the lack of genetic material. This species is known to occur from western Angola southwards to Namibia, and eastwards to Zambia, Botswana and Zimbabwe. The species shows considerable variation in dorsal colouration across its range, and with the lower ventral scales count, an ‘eastern race’ was suggested. In recent years, Prosymna material from different parts of Angola has been collected, and with phylogenetic analysis and High Resolution X-ray Computed Tomography, the taxonomic status of these populations can be reviewed. Strong phylogenetic evidence was found to include the angolensis subgroup as part of the larger sundevalli group, and the existence of three phylogenetic lineages within the angolensis subgroup were identified, which each exhibit clear morphological and colouration differences. One of these lineages is assigned to the nominotypical P. angolensis and the other two described as new species, one of which corroborates the distinct eastern population previously detected. These results reinforce that a considerable part of Angolan herpetological diversity is still to be described and the need for further studies.
... In order to evaluate the genetic variability of Micrelaps in Israel and assess the validity of M. tchernovi, we conducted phylogenetic analyses using 16 Micrelaps specimens from across its distribution range in Israel: 11 specimens were sequenced in this study and sequences of additional five specimens, all from Israel, from the collections of the Steinhardt Museum of Natural History, were retrieved from GenBank (from Portillo et al. 2018). One specimen of M. bicoloratus was used as an outgroup (from Kelly et al. 2009). The sequences include a specimen, TAU.R19142, that fits the diagnostic characters of M. tchernovi (Y. ...
Article
The enigmatic snake genus Micrelaps has uncertain phylogenetic affinities. The type species of the genus, Micrelaps muelleri, inhabits the Southern Levant. Snakes inhabiting the Jordan River Valley just south of the Sea of Galilee have been described as a new species, Micrelaps tchernovi, based on their distinct colour patterns, despite M. muelleri being well known to be variable in colour-pattern traits. Here we use morphological and molecular data to examine the taxonomic status and phylogenetic affinity of Levantine Micrelaps. We show that all scalation, colour, and pattern-related traits are extremely variable across the range of these snakes. Some morphological features show clinal variation related to temperature and precipitation, and snakes with a 'tchernovi' morph are merely at one end of a continuum of morphological variation. Both 'classical muelleri' and 'tchernovi' morphs occur in syntopy in the Jordan Valley and elsewhere in Israel. Against this background of high morphological variation, neutral genetic markers show almost no differentiation between snakes, no genetic structure is evident across populations, and no differences are to be found between the two putative species. We conclude that Levantine Micrelaps belongs to a single, morphologically variable, and genetically uniform species, Micrelaps muelleri, of which M. tchernovi is a junior synonym.
... Of the three families of front-fanged snakes occurring worldwide [1,2], only Elapidae occurs on the Australian continent. The Australasian region is home to the most diverse elapid snake radiation on the planet (Hydrophiinae). ...
Article
The Australasian region is home to the most diverse elapid snake radiation on the planet (Hydrophiinae). Many of these snakes have evolved into unique ecomorphs compared to elapids on other continents; however, their venom compositions are poorly known. The Australian elapid Hoplocephalus stephensii (Stephen’s banded snake) is an arboreal snake with a unique morphology. Human envenoming results in venom-induced consumption coagulopathy, without neurotoxicity. Using transcriptomics and a multi-step fractionation method involving reverse-phase high-performance liquid chromatography, sodium dodecyl sulfate polyacrylamide gel electrophoresis and bottom-up proteomics, we characterized the venom proteome of H. stephensii. 92% of the total protein component of the venom by weight was characterized, and included all dominant protein families and 4 secondary protein families. Eighteen toxins made up 76% of the venom, four previously characterized and 14 new toxins. The four dominant protein families made up 77% of the venom, including snake venom metalloprotease (SVMP; 36.7%; three identified toxins), phospholipase A2 (PLA2; 24.0%; five identified toxins), three-finger toxin (3FTx; 10.2%; two toxins) and snake venom serine protease (SVSP; 5.9%; one toxin; Hopsarin). Secondary protein families included L-amino acid oxidase (LAAO; 10.8%; one toxin), natriuretic peptide (NP; 0.8%; two toxins), cysteine-rich secretory protein (CRiSP; 1.7%; two toxins), c-type lectin (CTL; 1.1%; one toxin), and one minor protein family, nerve growth factor (NGF; 0.8%; one toxin). The venom composition of H. stephensii differs to other elapids, with a large proportion of SVMP and LAAO, and a relatively small amount of 3FTx. H. stephensii venom appeared to have less toxin diversity than other elapids, with only 18 toxins making up three-quarters of the venom.
... The lognormal distribution can take on various skewed shapes, which has merely a single unbounded tail of declining probability. It is usually the most suitable distribution for summarizing paleontological information as it can assign the highest point probability for the nodal age to be somewhat older than the oldest fossil (Ho and Phillips, 2009;Kelly et al., 2009). Whereas the exponential distribution shares some features with the lognormal distribution, one parameter is missing. ...
Article
Although the East Asian monsoon is believed to be an important driver for the origin and evolution of the biotas in this region, the association has rarely been rigorously tested. Here, using phylogenetic comparative methods and analyses of key innovations of adaptive traits, we investigated evolutionary patterns of the East Asian cyprinid opsariichthyin-xenocyprinin-cultrin clade; the dominant species in lakes and rivers, which are the typical productions of monsoon climate. Our molecular phylogenetic analyses revealed the relationships as (Opsariichthys-tribe + (((Oxygaster-tribe + Aphyocypris-tribe) + Metzia-tribe) + (Paralaubuca-tribe + (Squaliobarbus-tribe + (Hypophthalmichthys-tribe + (xenocyprinins + cultrins)))))). Based on Bayesian relaxed-clock methods, we found that origins of the Squaliobarbus- and Hypophthalmichthys-tribes bearing the key adaptation of riverine spawning with drifting eggs occurred 22.5 and 21.1 Mya, respectively. These times are consistent with the Early Miocene origin of major rivers (e.g., Yangtze River) and the appearance of the East Asian monsoon climate. Diversification of the cultrins, characterized by spawning of adhesive eggs as well as swimming and feeding in lentic waters, were estimated to have evolved 16.6 to 0.2 Mya. This period covers three phases of enhancement of the East Asian monsoon from the Middle Miocene to the Pliocene (around 15-13, 10-7, and 3.5 Mya). The habitats of these cultrins and their evolution also suggest the appearance and development of a lake-river environment during those periods. Therefore, our results suggest close relationships between the evolution of these fishes and geological events in East Asia. Further, they provide knowledge that may help facilitate future conservation strategies such as the maintenance of high river flows during dam construction and operation.
... The deeper level of phylogeny and systematics of the superfamily Elapoidea remains unstable (e.g., Figueroa et al., 2016;Kelly et al., 2009;Pyron et al., 2013;Zaher et al., 2019). However, the monophyly of families Atractaspididae and Lamprophiidae are well corroborated. ...
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Fossoriality evolved early in snakes, and has left its signature on the cranial morphology of many extinct Mesozoic and early Caenozoic forms. Knowledge of the cranial osteology of extant snakes is indispensable for associating the crania of extinct lineages with a particular mode of life; this applies to fossorial taxa as well. In the present work, we provide a detailed description of the cranium of Hypoptophis wilsonii, a member of the subfamily Aparallactinae, using micro‐computed tomography (CT). This is also the first thorough micro‐CT‐based description of any snake assigned to this African subfamily of predominantly mildly venomous, fossorial and elusive snakes. The cranium of Hypoptophis is adapted for a fossorial lifestyle, with increased consolidation of skull bones. Aparallactines show a tendency towards reduction of maxillary length by bringing the rear fangs forward. This development attains its pinnacle in the sister subfamily Atractaspidinae, in which the rear fang has become the ‘front fang’ by a loss of the part of the maxilla lying ahead of the fang. These dentitional changes likely reflect adaptation to subdue prey in snug burrows. An endocast of the inner ear of Hypoptophis shows that this genus has the inner ear typical of fossorial snakes, with a large, globular sacculus. A phylogenetic analysis based on morphology recovers Hypoptophis as a sister taxon to Aparallactus. We also discuss the implications of our observations on the burrowing origin hypothesis of snakes. This article is protected by copyright. All rights reserved.
... The family Elapidae (Reptilia: Squamata) comprises ~380 species of ecologically and morphologically diverse snakes (Greene, 1997;Uetz et al., 2020). The clade has a large global geographic distribution characterised by (1) an Asian origin and rapid diversification during the Oligocene, (2) colonization of the Americas and subsequent diversification by New World coral snakes, (3) repeated faunal exchanges between Africa and Asia, (4) colonization of Australia and subsequent spectacular diversification and (5) two independent transitions to marine lifestyles [see Kelly et al. (2009) for biogeographic review]. Elapids range in body size by more than an order of magnitude, from diminutive species with a maximum recorded total length ~300 mm to black mambas (Dendroaspis polylepis), coastal typans (Oxyuranus scutellatus) and king cobras (Ophiophagus hannah) that each regularly exceed 3 m in length Maritz et al., 2016). ...
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Identifying the traits of ancestral organisms can reveal patterns and drivers of organismal diversification. Unfortunately, reconstructing complex multistate traits (such as diet) remains challenging. Adopting a 'reconstruct, then aggregate' approach in a maximum likelihood framework, we reconstructed ancestral diets for 298 species of elapid snakes. We tested whether different prey types were correlated with one another, tested for one-way contingency between prey type pairs, and examined the relationship between snake body size and dietary composition. We demonstrate that the evolution of diet was characterized by niche conservation punctuated by repeated dietary shifts. The ancestor of elapids most likely fed on reptiles and possibly amphibians, with deviations from this ancestral diet occurring repeatedly due to shifts into marine environments and changes in body size. Moreover, we demonstrate important patterns of prey use, including one-way dependency-most obviously the inclusion of eggs being dependent on a diet that already included the producers of those eggs. Despite imperfect dietary data, our approach produced a robust overview of dietary evolution. Given the paucity of natural history information for many organisms, our approach has the potential to increase the number of lineages to which ancestral state reconstructions of multistate traits can be robustly applied.
... The family Elapidae (Reptilia: Squamata) comprises ~380 species of ecologically and morphologically diverse snakes (Greene, 1997;Uetz et al., 2020). The clade has a large global geographic distribution characterised by (1) an Asian origin and rapid diversification during the Oligocene, (2) colonization of the Americas and subsequent diversification by New World coral snakes, (3) repeated faunal exchanges between Africa and Asia, (4) colonization of Australia and subsequent spectacular diversification and (5) two independent transitions to marine lifestyles [see Kelly et al. (2009) for biogeographic review]. Elapids range in body size by more than an order of magnitude, from diminutive species with a maximum recorded total length ~300 mm to black mambas (Dendroaspis polylepis), coastal typans (Oxyuranus scutellatus) and king cobras (Ophiophagus hannah) that each regularly exceed 3 m in length Maritz et al., 2016). ...
Article
Identifying the traits of ancestral organisms can reveal patterns and drivers of organismal diversification. Unfortunately, reconstructing complex multistate traits (such as diet) remains challenging. Adopting a ‘reconstruct, then aggregate’ approach in a maximum likelihood framework, we reconstructed ancestral diets for 298 species of elapid snakes. We tested whether different prey types were correlated with one another, tested for one-way contingency between prey type pairs, and examined the relationship between snake body size and dietary composition. We demonstrate that the evolution of diet was characterized by niche conservation punctuated by repeated dietary shifts. The ancestor of elapids most likely fed on reptiles and possibly amphibians, with deviations from this ancestral diet occurring repeatedly due to shifts into marine environments and changes in body size. Moreover, we demonstrate important patterns of prey use, including one-way dependency—most obviously the inclusion of eggs being dependent on a diet that already included the producers of those eggs. Despite imperfect dietary data, our approach produced a robust overview of dietary evolution. Given the paucity of natural history information for many organisms, our approach has the potential to increase the number of lineages to which ancestral state reconstructions of multistate traits can be robustly applied.
... The taxonomic status of sea kraits traditionally has been interpreted variously as a separate family (Laticaudidae), a subfamily (Laticaudinae) of either the Hydrophiidae or Elapidae, or a Tribe (Hydrophiini) of the Hydrophiidae (reviewed by Heatwole 2010). Only in recent years has a combination of morphological analysis and molecular techniques begun to dispel the confusion surrounding the evolutionary relationships of these snakes to reveal an entirely different, and surprising, scenario (Slowinski et al. 1997;Keogh 1998;Lee and Scanlon 2002;Scanlon and Lee 2004;Sanders et al. 2008;Kelly et al. 2009;Pyron et al. 2013;Lee et al. 2016) in which the sea kraits and the sea snakes were found to be independent marine radiations nested within the terrestrial Elapidae. Sea kraits are now considered merely as a genus (Laticauda) within the family Elapidae (Pyron et al. 2013;Lee et al. 2016;Fig. ...
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The geographic range of sea kraits encompasses one of the geologically most-complex regions of the world. At its center lies Wallacea (the transition between the terrestrial biotas of the Asian and Australian tectonic plates) and the Indonesian Throughflow (nexus of the equatorial marine biotas of the Indian and Pacific oceans). The aim of this study was to elucidate the role of paleogeography, paleoclimatology, and oceanic currents in the evolution and distribution of sea kraits across these major biogeographic crossroads and beyond. A recent assessment of times of taxonomic divergence was projected against paleogeographic reconstructions to produce a parsimonious, hypothetical model of events critical for the origin, dispersal, and differentiation of this taxon. Times and degree of divergence of taxa suggested by recent morphological and molecular studies are in accord with various climatological and geologic events. The model postulates that the distribution of sea kraits was neither greatly affected by tectonics, other than the approach of the Australian Plate to the Asian one, nor dominated by the historic barriers to dispersal of terrestrial fauna across Wallacea, or by the Indonesian Throughflow. Rather, the model suggests that two major factors—paleogeographic alteration of the configuration of land and sea, and the directions of sea currents, past and present—provide an explanation of how these amphibious snakes (1) originated from a terrestrial Asian elapid ancestor, (2) subsequently generated the venomous Australian land snakes and their derivatives the true sea snakes, and (3) differentiated into the species complexes, species, and infraspecific entities of the genus Laticauda.
... Natricine snakes are a subfamily (Natricinae) within the family Colubridae (Vidal et al. 2008;Kelly et al. 2009;Zaher et al. 2009;Pyron et al. 2011;Figueroa et al. 2016), although considered a family-level taxon in their own right by Zaher et al. (2019), and comprise a large group of genera from Africa, Asia, Europe, North America, Central America and Australia. Most species are semi-aquatic and feed mostly on fish and amphibians (Broadley et al. 2003;Chippaux and Jackson 2019). ...
Article
The African natricine genus Limnophis is represented by two species: Limnophis bicolor Günther, 1865 and Limnophis bangweolicus (Mertens, 1936). They are stout-bodied, semi-aquatic snakes that mostly feed on fish and amphibians, and occur from Botswana and Namibia in the south throughout most of Zambia and Angola to the Democratic Republic of the Congo in the north. We gathered new material from the ranges of both species in Angola and Zambia in order to examine their taxonomic status and identify any overlooked diversity. We constructed a phylogenetic tree, based on three mitochondrial genes (16S, cytb, ND4) and one nuclear gene (cmos), which includes the first DNA sequence data for Limnophis. Three well-supported lineages were identified, each representing separate species. The taxonomic status of the two currently recognised species is validated, and we describe a new species of Limnophis from north-eastern Angola. The new species is distinguished from the others by the combination of distinct ventral and lateral head colouration and patterning, differences in head and ventral scalation, and uncorrected pairwise genetic distances to both L. bicolor and L. bangweolicus of 5.4–8.1% in cytb, 6.1–8.4% in ND4 and 2.7–8.3% in 16S.
... The remaining genera form two clades: the sea snakes (Laticauda and Hydrophis) uniting with Bungarus as the sister group to a well-supported clade including Ophiophagus and Naja (Fig. 2c). This result is consistent with previous phylogenetic studies (Kelly et al., 2009;Pyron et al., 2013;Zheng and Wiens, 2015). ...
... Using anchored phylogenomics , we generated a genomic data set for 289 species representing 75 families of squamates and one Rhynchocephalian (see Supplemental material available on Dryad at http://dx.doi.org/10.5061/dryad.6392n3s). Our taxonomic arrangement followed Hedges (2005, 2009), Conrad (2008), and Vidal et al. (2010) for higher-level squamatan clades; Pyron et al. (2013) and Barker et al. (2015) for Booidea and Pythonoidea familial and generic levels; Zaher et al. (2009) and Kelly et al. (2009), including nomenclatural suggestions of Savage (2015) and Rhodin et al. (2015) for higher and familial caenophidian clades. Whole genomic DNA was extracted from tissue using the Qiagen DNeasy kit following manufacturer's protocols at the Center for Anchored Phylogenomics at Florida State University and data were assembled using Anchored Phylogenomics (www.anchoredphylogeny.com). ...
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Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards and snakes, amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. Here, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites, phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of parsimony informative sites), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; and between the three toxiferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).
... might be referred to "Colubrinae" on the basis of its lightly built vertebrae and the absence of continuous hypapophyses throughout the vertebral column (Rage, 1984;Szyndlar, 1984Szyndlar, , 1991aSzyndlar, , b, 2012. However, recent advances in molecular phylogenetics of snakes, supported also by morphological data, have demonstrated that certain groups, such as psammophiids, lamprophiids, dipsadids, and certain atractaspidids, that have an overall similar vertebral anatomy, in fact lie outside colubrids and pertain instead to much distantly related clades (Lawson et al., 2005;Vidal et al., 2007Vidal et al., , 2008Kelly et al., 2008Kelly et al., , 2009Zaher et al., 2019). ...
Article
We herein describe Sardophis elaphoides Georgalis & Delfino n. gen. n. sp., a new snake taxon from the early Pleistocene of Monte Tuttavista VI, Sardinia, Italy. Sardophis elaphoides Georgalis & Delfino n. gen. n. sp. possesses a distinct vertebral anatomy and is diagnosed by a unique combination of features. The new Sardinian taxon is further compared in detail and differentiated from all extant European and North African snake species. Although the affinities of Sardophis elaphoides Georgalis & Delfino n. gen. n. sp. with colubroids are clear, its more inclusive relationships within that clade cannot be resolved with certainty. Being an insular form, Sardophis elaphoides Georgalis & Delfino n. gen. n. sp. adds significantly to our so far poor knowledge of island endemic snakes. An overview of the fossil record of snakes from the Mediterranean islands is provided. The new species increases the number of reptile taxa that went extinct in Sardinia during the late Neogene and Quaternary.
... O. hannah has been frequently found to group separately from the remaining cobra-like species, often as a sister lineage to mambas, Dendroaspis sp. (Kelly et al. 2009;Pyron et al. 2013;Lee et al. 2016). The results from this study don't however resolve the position of O. hannah, with poor support values placing the species as a sister species to the Asian coral snake, Hemibungarus calligaster, whereas Figueroa et al. (2016) placed O. Hannah adjacent to the mambas, Dendroaspis. ...
Thesis
The extant medically and socially important cobras have been the subject to several comparative taxonomic studies since the 1940s, but still lack an inclusive and thorough phylogenetic tree. With recent major advancements in phylogenetic analysis, it is now common to use multiple independent loci for studying the phylogenetic relationships within groups. For the first time, 27 from the 29 identified Naja species, alongside 5 putative new or elevated species had 4426 base pairs across 1701 sequences of mitochondrial and nuclear DNA sequence data analysed. The results continue to support the monophyletic core cobra clade encompassing the genera Walterinnesia, Aspidelaps, Hemachatus, Pseudohaje and Naja (1.0 Bayesian posterior probability (BPP)), in addition to the grouping of four monophyletic subgenera within Naja. The group of African spitting cobras, Afronaja, is positioned as the sister group to the rest of the genus. Moderate support (0.8 BPP) is found for the grouping of the Asian cobras, Naja, with the African non-spitting cobras, Ureaus. The closest relative to the genus Naja is Pseudohaje goldii, a genus and species never before included in phylogenetic analysis, followed by the sister taxa Hemachatus haemachatus. The king cobra continues to be positioned outside the core cobra group, sister to Hemibungarus calligaster. The results support the hypothesis of three independent origins of spitting, once in the monotypic Hemachatus haemachatus, once within the subgenus Afronaja, and the final origin within the Asian cobras, subgenus Naja. The relationships found were broadly consistent with previous studies, with the additional inclusion of more species creating the most comprehensive cobra phylogeny to date. Further molecular analysis, specifically species delimitation, must be undertaken to ascertain the position of the 5 putative new species included in this study.
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The genus Calliophis is the most basal branch of the family Elapidae and several species in it have developed highly elongated venom glands. Recent research has shown that C. bivirgatus has evolved a seemingly unique toxin (calliotoxin) that produces spastic paralysis in their prey by acting on the voltage-gated sodium (NaV) channels. We assembled a transcriptome from C. bivirgatus to investigate the molecular characteristics of these toxins and the venom as a whole. We find strong confirmation that this genus produces the classic elapid eight-cysteine three-finger toxins, that δδ-elapitoxins (toxins that resemble calliotoxin) are responsible for a substantial portion of the venom composition, and that these toxins form a distinct clade within a larger, more diverse clade of C. bivirgatus three-finger toxins. This broader clade of C. bivirgatus toxins also contains the previously named maticotoxins and is somewhat closely related to cytotoxins from other elapids. However, the toxins from this clade that have been characterized are not themselves cytotoxic. No other toxins show clear relationships to toxins of known function from other species.
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Pan‐trionychids (soft‐shelled turtles) are known from the Neogene and Quaternary fossil record of Africa. They have so far been totally absent in Palaeogene localities of the continent although they are commonly found in Palaeogene localities across Europe, North America, and Australasia; as such, their absence from the Palaeogene of Africa has been envisaged to be genuine. Here, I describe a large costal from the Eocene of Mali, which documents for the first time the presence of pan‐trionychid turtles in the Palaeogene of the then isolated Afro‐Arabia. The affinities of the new Malian pan‐trionychid with Neogene and Quaternary forms from Africa are discussed, as well as its biogeographic origins and potential dispersal scenarios from other landmasses to Afro‐Arabia during the Palaeogene.
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Prosymna is a specialized African snake genus lacking close relatives. The evolutionary relationships and history within Prosymna are poorly understood. Here we assembled a multi-gene data set including representatives for 11 of 16 species to investigate the phylogenetic relationships of this group. Our analyses support the monophyly of Prosymna and are congruent with species groups previously recognized on the basis of external morphology. Divergences among extant Prosymna began in the mid-Cenozoic, with the earliest divergence splitting northern from southern lineages. High-resolution computed tomography scans confirm that a specialized skull morphology is found across the genus and was probably present in the common ancestor of Prosymna. This specialization is exemplified by dentition featuring reduced anterior but greatly enlarged, blade-like posterior maxillary teeth and an unusually high degree of fusion of cranial bones. One species, P. visseri, has a hammer-like maxilla unlike that of any other known snake. Evidence for oophagy in Prosymna and the possible roles of morphological specializations in egg-slitting or egg-crushing feeding mechanisms are discussed.
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en While species boundaries between conspicuously divergent populations of the medically important snake genus Sinomicrurus are well established, instances of erratic chromatic and meristic variation continue to confound taxonomists, since the mid-1800s. This predicament can be attributed to an inadequate molecular phylogenetic framework and the lack of a comprehensive taxonomic representation of geographic variants. Here, we revisit lineage delineation in this genus, drawing cohesive evidence from a plurality of data and analysis types, including a promising, yet taxonomically under-utilized, supervised machine learning algorithm (random forest). Overall, this study incorporates data generated by molecular analyses as well as morphometrics and comparative anatomy based on 236 specimens from 28 different natural history collections examined by us, and an additional 161 records from 47 other sources. Our results indicate several very divergent evolutionary lineages concealed as subspecies. Thus, to better reflect this phylogenetic diversity, we raise S. macclellandi iwasakii from the southern Ryukyus and S. m. swinhoei from Taiwan to full species, and resurrect S. annularis. We highlight the need to distinguish at species level the current subspecies of S. japonicus, namely as, S. japonicus and S. boettgeri, and provide diagnostic characters to that end. On the other hand, given unpersuasive support of lineage independence, we sink Taiwanese S. hatori into S. sauteri and S. nigriventer into S. macclellandi. We also meticulously redescribe S. peinani from mainland China and Vietnam based on a substantial number of additional specimens, while synonymizing the recently described S. houi under S. kelloggi. We conclude with a discussion on the role of regional biogeography as a primary driver of cladogenesis in the genus. 摘要 zh 雖然醫學上廣受重視的Sinomicrurus屬蛇類群其物種之間的界限已因其明顯不同的外形而確立, 但自 1800 年代中期以來, 這類群所表現出的不穩定體色和測量形質上的變異持續困惑著分類學者。這種困境可歸因於不夠完整的分子親緣譜系框架和缺乏全面性的地理變異分類學表徵資訊。本研究重新審視該屬的親緣譜系劃分, 並從多項數據和分析類型進行聚類分析, 包括一種具有研究應用潛力但在分類學應用上卻被低估的机器学习演算法(random forest)。我們總共檢視了來自28 個自然史博物館所收藏的 236件標本, 以及其他來源的161件樣本, 結合分子遺傳變異、形態測量和比較解剖學所取得的資料並進行分析, 結果顯示Sinomicrurus屬的物種多樣性被嚴重低估, 幾個具有明顯分化的演化親緣譜系被評估為亞種。為了妥切反映這類群在系統發育上的多樣性, 我們將琉球南部的S. macclellandi iwasakii 和台灣的S. m. swinhoei兩個亞種提升到種的階層, 並再確認S. annularis的種的有效性。我們也認為S. japonicus當前的亞種需要在種的階層上進行区别,即應提升為S. japonicus和S. boettgeri, 並提供此兩個物種的檢索資訊。另一方面, 由於缺乏種的階層上的足夠證據支持, 我們將台灣的S. hatori併入S. sauteri,也將S. nigriventer併入了S. macclellandi。本研究也依據大量的標本測量資訊重新描述了中國大陸和越南的S. peinani,並認定最近發表的S. houi應為S. kelloggi的同物異名。本研究结语歸納并讨论了區域性生物地理分化運作為Sinomicrurus屬蛇類物種分化的主要驅動因素。
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Up to now, the oldest known colubrid snakes were fossils from the early Oligocene of Western Europe and from the Arabian Peninsula. An indeterminate colubrid has been recently recovered in the late Eocene of Thailand. The presence, in Asia, of the oldest known colubrid snake is consistent with an origin of this family in this continent. -Authors
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Phylogenetic relationships among genera of African colubrids were evaluated using estimates of divergence among serum albumins compared by microcomplement fixation. Representatives of about half of the extant genera of African colubrids, as well as the Elapidae, Atractaspis and the Madagascan colubrid Leioheterodon, were analysed. The tree of best fit to the data has an unresolved basal polychotomy comprising at least five lineages of colubrids, as well as Elapidae and Atractaspis; thus, colubrids were not demonstrably monophyletic with these data. Two cosmopolitan clades, colubrines and natricines, are represented in Africa by series of closely related genera, but divergence among other genera is relatively great. Rate tests show that this is apparently not due to higher rates of albumin evolution in these, relative to other colubrids. Among the other associations supported by the immunological data are: (1) Psammophis -(Rhamphiophis-Dipsina)-Malpolon-Psammophylax; (2) Amblyodipsas-Macrelaps; (3) (Lycodonomorphus-Lamprophis)-Mehelya; and (4) Colubrinae-Natricinae. Grayia is questionably associated with the colubrine-natricine lineage. Prosymna and Lycodon are clearly members of the colubrine clade, and Amplorhinus possibly associates with Leioheterodon . Gonionotophis, Duberria, Lycophidion and Pseudaspis show no strong association with any other genera, and represent other basal or near-basal clades within the colubrid/elapid radiation. The immunological data do not support a clade comprising the Elapidae, Atractaspis and some 'aparallactines' relative to Viperidae and other colubrids. The basal colubrid-elapid-Atractaspis divergence occurred more than 30 Myr ago, and the fossil record of colubrids in Africa greatly underestimates both the age and clade diversity of this group. In contrast to the pattern of radiation in the neotropics, where most colubrids belong to one of three major clades, in Africa only the colubrine lineage comprises a substantial portion of the extant generic diversity; most other genera stem from relatively ancient cladogenetic events and have few living representatives.
Article
Likelihood-based statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately a decade. By far the most commonly used is the Kishino-Hasegawa test. However, the assumptions that have to be made to ensure the validity of the Kishino–Hasegawa test place important restrictions on its applicability. In particular, it is only valid when the topologies being compared are specified a priori. Unfortunately, this means that the Kishino-Hasegawa test may be severely biased in many cases in which it is now commonly used: for example, in any case in which one of the competing topologies has been selected for testing because it is the maximum likelihood topology for the data set at hand. We review the theory of the Kishino-Hasegawa test and contend that for the majority of popular applications this test should not be used. Previously published results from invalid applications of the Kishino–Hasegawa test should be treated extremely cautiously, and future applications should use appropriate alternative tests instead. We review such alternative tests, both nonparametric and parametric, and give two examples which illustrate the importance of our contentions.
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— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Article
In a 1935 paper and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P-values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this article we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology, and psychology. We emphasize the following points:
Article
Middle and late Hemphillian (late Miocene) snakes from Nebraska were identified and interpreted. The mid-Hemphillian (ca. 7 Ma) Lemoyne Quarry of Keith Co., SW Nebraska yielded at least two boid, thirteen colubrid and two viperid snakes. The late Hemphillian (ca. 5 Ma) Devils Nest (Knox Co.), Santee (Knox Co.), and Mailbox Prospect (Antelope Co.) sites of NE Nebraska together yielded at least nine colubrids and one viperid snake. Twenty-four percent of the 16 mid-Hemphillian snake genera and 67% of the 12 species are extinct. Of the 9 genera and 7 species of late Hemphillian snakes, only Paleoheterodon tiheni is extinct. A snake from Lemoyne Quarry is described as new (Arizona voorhiesi).With this new information, the fossil record of Arikareean through Blancan (Miocene through Pliocene) snake genera from midcontinental North America suggests erycinine boids became extinct across the region by late Hemphillian time, and colubrid snakes became generically modern by early Blancan time. These events likely occurred because of major environmental and vegetational changes that took place during the late Miocene.
Article
The French Miocene (Orleanian and Astaracian) yielded five new species of snakes referable to four genera from the Neogene or Recent of North America: Texasophis meini nov. sp., Paleoheterodon arcuatus nov. sp., Neonatrix europaea nov. sp., Neonatrix crassa nov. sp. (Colibridae) and Micrurus gallicus nov. sp. («Elapidae). It is suggested that Micrurus and the previously described boid snake Albaneryx from the French Miocene probably represent lineages that originated in North America and reached Europe by way of Asia. Paleoheterodon and Neonatrix could have originated in Asia and subsequently reached Europe on one hand and North America on the other. Texasophis may have originated in North America and followed the same route as Micrurus and Albaneryx, but an alternative hypothesis is that it originated in Asia and spread toward Europe and North America in the same manner as Paleoheterodon and Neonatrix.