Molecular phylogeny of elapid snakes and a consideration of their biogeographic history

Evolutionary relationships among the major elapid clades, particularly the taxonomic position of the partially aquatic sea kraits (Latkauda) and the fully aquatic true sea snakes have been the subject of much debate. To discriminate among existing phylogenetic and biogeographic hypotheses, portions of both the 16S rRNA and cytochrome b mitochondrial DNA genes were sequenced from 16 genera and 17 species representing all major elapid snake clades from throughout the world and two non-elapid outgroups. This sequence data yielded 181 informative sites under parsimony. Parsimony analyses of the separate data sets produced trees of broad agreement although less well supported than the single most parsimonious tree resulting from the combined analyses. These results support the following hypotheses: (1) the Afro-Asian cobra radiation forms one or more sister groups to other elapids, (2) American and Asian coral snakes form a clade, corroborating morphological studies, (3) Bungarus forms a sister group to the hydrophiines comprised of Latkauda, terrestrial Australo-Papuan elapids and true sea snakes, (4) Latkauda and true sea snakes do not form a monophyletic group but instead each group shares an independent history with terrestrial Australo-Papuan elapids, corroborating previous studies, (5) a lineage of Melanesian elapids forms the sister group to Latkauda, terrestrial Australian species and true sea snakes. In agreement with previous morphologically based studies, the sequence data suggests that Bungarus and Latkauda represent transitional clades between the elapine 'palatine erectors' and hydrophiine 'palatine draggers'. Both intra and inter-clade genetic distances are considerable, implying that each of the major radiations have had long independent histories. I suggest an African, Asian, or Afro-Asian origin for elapids as a group, with independent Asian origins for American coral snakes and the hydrophiines.     

Phylogeny of Australasian venomous snakes (Colubroidea, Elapidae, Hydrophiinae) based on phenotypic and molecular evidence

Scanlon, John D. & Lee, Michael S. Y. (2004). Phylogeny of Australasian venomous snakes (Colubroidea, Elapidae, Hydrophiinae) based on phenotypic and molecular evidence. — Zoologica Scripta , 33 , 335–366.
Phylogenetic relationships among Hydrophiinae (Australasian and marine elapid snakes) are inferred using 87 characters from external, skeletal, hemipenial and internal anatomy, ecology, and chromosomes as well as available sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Parsimony analysis of the combined data retrieves many widely accepted clades; while observed bootstrap or branch (Bremer) support for these is often weak, most have never been corroborated previously by a rigorous numerical analysis. Sea kraits ( Laticauda ) and Solomon Islands elapids are basal to the remaining hydrophiines (Australian terrestrial forms and hydrophiin sea snakes). The latter clade includes three main lineages: a large-bodied oviparous lineage, a small-bodied oviparous lineage, and a viviparous lineage (which also includes the hydrophiin sea snakes, strongly reaffirmed as monophyletic). While the Solomons retain a relictual fauna, New Guinea has less endemism and has been invaded multiple times by Australian lineages, so there is no clear 'stepping stone' pattern supporting a northern (Asian, rather than Gondwanan) biogeographical origin.     

Ecological and historical legacies on global diversity gradients in marine elapid snakes

Global diversity gradients have been extensively investigated for several biological groups. However, little is known whether the diversity drivers of clades that underwent major environmental transition (e.g., from land to sea) are equivalent across these different environmental settings. Here, we ask if the pattern of diversity of marine elapid snakes is determined by factors analogous to those previously found for terrestrial lineages. Through a model selection framework, we compare the effect of factors that represent five ecological and historical hypotheses. We found that both ecological and historical factors play significant roles, but habitat structure, which can be linked to historical climatic changes, was better supported. This result agrees with that previously found for terrestrial elapids, despite the different environmental pressures in terrestrial and marine contexts. Our findings suggest an equivalence of the underlying process of diversity gradient within the same lineage from land and sea, irrespective of the different physiological, spatial and historical constraints.     

Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences

Published molecular phylogenetic studies of elapid snakes agree that the marine and Australo-Melanesian forms are collectively monophyletic. Recent studies, however, disagree on the relationships of the African, American, and Asian forms. To resolve the relationships of the African, American, and Asian species to each other and to the marine/Australo-Melanesian clade, we sequenced the entire cytochrome b gene for 28 elapids; 2 additional elapid sequences from GenBank were also included. This sample includes all African, American, and Asian genera (except for the rare African Pseudohaje), as well as a representative sample of marine/Australo-Melanesian genera. The data were analyzed by the methods of maximum-parsimony and maximum-likelihood. Both types of analyses yielded similar trees, from which the following conclusions can be drawn: (1) Homoroselaps falls outside a clade formed by the remaining elapids; (2) the remaining elapids are divisible into two broad sister clades, the marine/Australo-Melanesian species vs the African, American, and Asian species; (3) American coral snakes cluster with Asian coral snakes; and (4) the "true" cobra genus Naja is probably not monophyletic as the result of excluding such genera as Boulengerina and Paranaja.     

Venom glands and some associated muscles in sea snakes

The venom glands and related muscles of sea snakes conform in their general structure to those of the terrestrial elapids. The venom gland, however, is smaller in size and the accessory gland is considerably reduced. A similar pattern is found in the Australian elapid Notechis. The musculus compressor glandulae is well developed in the sea snakes and in some species its posterior-medial portion runs uninterruptedly from the origin to the insertion of the muscle. This might be considered as a primitive condition suggesting an early divergence of the sea snakes from an ancestral elapid stock. Three species of sea snakes, Aipysurus eydouxi, Emydocephalus annulatus, and E. ijimae, feed on fish eggs and have very small, but still functioning, venom glands. The reduced accessory gland of the sea snakes is apparently connected with their aquatic environment, as a similar condition is found also in the elapine Boulengerina annulata which lives in large lakes of Central Africa. The similarity in structure of the venom gland between sea snakes and Notechis scutatus may point to a possible phylogenetic relationship between this group of Australian elapids and hydrophiine snakes.     

Fingerprint correspondence of hemoglobins and the relationships of sea snakes.

1. Peptide fingerprints of tryptic digests of the globins of sea snake species of Hydrophis, Pelamis, Aipysurus, Laticauda and the terrestrial elapid Naja were compared. 2. Globin divergence, as estimated from peptide fingerprints, paralleled closely transferrin divergence, as measured immunologically. 3. Taxonomic affinities, suggested by the fingerprint data, are concordant with McDowell's taxonomic system for sea snakes with the following exceptions: (a) Laticauda shows a closer affinity to the true sea snakes than to the terrestrial elapid Naja. (b) Sea snakes appear to be more widely divergent from terrestrial elapids than his scheme suggests.     

Influence of the venom delivery system on intraoral prey transport in snakes

We compared intraoral prey transport in venomous snake species from four families (two atractaspidids, nine elapids, three colubrids, 44 viperids) with that in eight non-venomous colubrid species, most feeding on similar mammalian prey. The morphology of the venom delivery system suggests that intraoral prey transport performance should be slightly decreased in atractaspidids, unmodified in most elapids and venomous colubrids, and increased or unmodified in vipers, as compared to that in non-venomous colubrid snakes. Our measurements of relative intraoral prey transport performance show that differences among families do not match expectations based on morphology or past studies. Decreased performance in Atractaspis results from reduction and loss of teeth on the medial palatal elements and dentaries, but affects only early phases of ingestion. Although joint and bone features of elapids and colubrids are similar, intraoral prey transport performance is significantly lower in elapids than in colubrids. Predicted enhancement of intraoral prey transport performance in vipers as compared to colubrids was not borne out by measurements, presumably because palatopterygoid movement during intraoral prey transport is reduced in many viper species to limit fang erection. Absence of significant performance differences between colubrids and viperids might suggest that evolution of the viperid venom delivery system was subject to little selection pressure from intraoral prey transport. Another possibility is that there are trade-offs between intraoral prey transport and strike performance in vipers related to relative skull mass and jaw fragility. Immobilizing prey prior to intraoral transport places less demand on transport performance in vipers. In this model, the conservative kinesis and greater robustness of the colubrid palate has greater potential for transporting live prey with less risk of injury.     

Monophyly of elapid snakes (Serpentes: Elapidae). An assessment of the evidence

The defining morphological characters of the family Elapidae are analysed in an attempt to evaluate whether the front-fanged, proteroglyphous, snakes constitute a natural (monophyletic) group or whether proteroglyphy is more likely to be a condition achieved independently by a number of higher snake lineages. The evidence relating to presumed elapids whose affinities have been questioned, namely a South African genus Homoroselaps and New World proteroglyphs (Micrurus and Micruroides) , is examined. It concluded that Homoroselaps is a genuinely equivocal case, the evidence for its inclusion in the Elapidae is balanced by features which suggest that it is more closely related to the Aparallactinae. However, Micrurus and Micruroides seem clearly to be more closely related to undisputed elapids than to any other caenophidians. It is suggested that, at least for the present, the family Elapidae be retained in its broad sense to include all proteroglyphous snakes.     

Multiple colonization of Madagascar and Socotra by colubrid snakes: evidence from nuclear and mitochondrial gene phylogenies

Colubrid snakes form a speciose group of unclarified phylogeny. Their almost cosmopolitan distribution could be interpreted as a product of plate-tectonic vicariance. We used sequences of the nuclear c-mos, the mitochondrial cytochrome b and the 16S rRNA genes in 41 taxa to elucidate the relationships between the endemic colubrid genera found in Madagascar and in the Socotra archipelago. The well-resolved trees indicate multiple origins of both the Malagasy and the Socotran taxa. The Malagasy genus Mimophis was nested within the Psammophiinae, and the Socotran Hemerophis was closely related to Old World representatives of the former genus Coluber. The remaining 14 genera of Malagasy colubrids formed a monophyletic sister group of the Socotran Ditypophis (together forming the Pseudoxyrhophiinae). Molecular-clock estimates place the divergence of Malagasy and Socotran colubrids from their non-insular sister groups into a time-frame between the Eocene and Miocene. Over-seas rafting is the most likely hypothesis for the origin of at least the Malagasy taxa. The discovery of a large monophyletic clade of colubrids endemic to Madagascar indicates a need for taxonomic changes. The relationship of this radiation to the Socotran Ditypophis highlights the potential of the Indian Ocean islands to act as an evolutionary reservoir for lineages that have become extinct in Africa and Asia.     

Mid-Tertiary elapid snakes (Squamata, Colubroidea) from Riversleigh, northern Australia: early steps in a continent-wide adaptive radiation

Vertebral and cranial remains of elapid snakes have been collected from fossil assemblages at Riversleigh, north-west Queensland, Australia; most are Miocene but one may be late Oligocene and another as young as Pliocene. The oldest specimen (probably the oldest elapid yet known anywhere) is a vertebra that can be referred provisionally to the extant taxon Laticauda (Hydrophiinae, sensu Slowinski and Keogh, 2000), implying that the basal divergences among Australasian hydrophiine lineages had occurred by the early Miocene, in contrast to most previous estimates for the age of this geographically isolated adaptive radiation. Associated vertebrae and jaw elements from a Late Miocene deposit are described as Incongruelaps iteratus nov. gen. et sp., which has a unique combination of unusual derived characters otherwise found separately in several extant hydrophiine taxa that are only distantly related. Associated vertebrae from other sites, and two parietals from a possibly Pliocene deposit, suggest the presence of several other taxa distinct from extant forms, but the amount of material (and knowledge of variation in extant taxa) is currently insufficient to diagnose these forms. The Tertiary elapids of Riversleigh thus appear to be relatively diverse taxonomically, but low in abundance and, with one exception, not referable to extant taxa below the level of Hydrophiinae. This implies that the present diversity of hydrophiine elapids (31 recognized terrestrial genera, and approximately 16 marine) represents the result of substantial extinction as well as the “cone of increasing diversity” that could be inferred from phylogenetic studies on extant forms.     

Tribal delimitation and phylogenetic relationships of Loteae and Coronilleae (Faboideae: Fabaceae) with special reference to Lotus: evidence from nuclear ribosomal ITS sequences

The temperate herbaceous tribes Loteae and Coronilleae have traditionally been regarded as taxonomically distinct entities. More recent morphological assessments, however, have challenged this view and suggest combining the two tribes under Loteae. Two key features used to distinguish the Coronilleae from Loteae include jointed fruits and branched root nodules. We evaluate the taxonomic utility of these characters using information derived from phylogenetic analyses of the internal transcribed spacers ITS1 + 2, and the intervening 5.8S region of nuclear ribosomal DNA. Results from this study show that neither the Loteae nor Coronilleae form individual monophyletic groups, and that key fruit and root nodule characters used to distinguish the Coronilleae are homoplastic. Given these data, we support the recognition of a single tribe, Loteae. We also find that Lotus, the largest and most morphologically complex genus in either tribe, is not monophyletic. Rather, it consists of two geographically distinct lineages, Old and New World, each of which are more closely related to other Loteae genera: Old World Lotus are more closely related to Old World Anthyllis, while New World Lotus show closer affinities to Old World Coronilla. These data also have important implications for the biogeography of New World Lotus: equally most parsimonious reconstructions suggest a complex scenario of intercontinental dispersals that involve not only Old World Lotus but Coronilla as well.     

DID EGG‐LAYING BOAS BREAK DOLLO'S LAW? PHYLOGENETIC EVIDENCE FOR REVERSAL TO OVIPARITY IN SAND BOAS (ERYX: BOIDAE)

Re-evolution of lost complex morphological characters has been proposed for several characters, including insect wings, limbs, eyes in snakes, and digits in lizards, among others. There has also been much interest in whether the transition from oviparity to viviparity is reversible, particularly in squamate reptiles where the transition to viviparity has occurred more times than in any other lineage. Here, we present a phylogenetic analysis of boid snakes based on a concatenated multigene study of all genera of erycines, New and Old World boines, plus other groups thought to be closely related with boines such as monotypic species Calabaria and Casarea . We reconstruct ancestral parity mode on this phylogeny and present statistical evidence that oviparity reevolved in a species of Old World sand boa in the genus Eryx nearly 60 million years after the initial boid transition to viviparity. Remarkably, like other viviparous boas hatchlings of oviparous Eryx lack an egg-tooth providing independent evidence that oviparity is a derived state in these species.     

Molecular phylogeny and divergence dates for Australasian elapids and sea snakes (hydrophiinae): evidence from seven genes for rapid evolutionary radiations

One of the most prolific radiations of venomous snakes, the Australo-Melanesian Hydrophiinae includes approximately 100 species of Australasian terrestrial elapids plus all approximately 60 species of viviparous sea snakes. Here, we estimate hydrophiine relationships based on a large data set comprising 5800 bp drawn from seven genes (mitochondrial: ND4, cytb, 12S, 16S; nuclear: rag1, cmos, myh). These data were analysed using parsimony, likelihood and Bayesian methods to better resolve hydrophiine phylogeny and provide a timescale for the terrestrial and marine radiations. Among oviparous forms, Cacophis, Furina and Demansia are basal to other Australian elapids (core oxyuranines). The Melanesian Toxicocalamus and Aspidomorphus group with Demansia, indicating multiple dispersal events between New Guinea and Australia. Oxyuranus and Pseudonaja form a robust clade. The small burrowing taxa form two separate clades, one consisting of Vermicella and Neelaps calanotus, and the other including Simoselaps, Brachyurophis and Neelaps bimaculatus. The viviparous terrestrial elapids form three separate groups: Acanthophis, the Rhinoplocephalus group and the Notechis-Hemiaspis group. True sea snakes (Hydrophiini) are robustly united with the Notechis-Hemiaspis group. Many of the retrieved groupings are consistent with previous molecular and morphological analyses, but the polyphyly of the viviparous and burrowing groups, and of Neelaps, are novel results. Bayesian relaxed clock analyses indicate very recent divergences: the approximately 160 species of the core Australian radiation (including sea snakes) arose within the last 10 Myr, with most inter-generic splits dating to between 10 and 6 Ma. The Hydrophis sea snake lineage is an exceptionally rapid radiation, with > 40 species evolving within the last 5 Myr.     

Functional plasticity of the venom delivery system in snakes with a focus on the poststrike prey release behavior

We explored variations in the morphology and function of the envenomation system in the four families of snakes comprising the Colubroidea (Viperidae, Elapidae, Atractaspididae, and Colubridae) using our own prey capture records and those from the literature. We first described the current knowledge of the morphology and function of venom delivery systems and then explored the functional plasticity found in those systems, focusing on how the propensity of snakes to release prey after the strike is influenced by various ecological parameters. Front-fanged families (Viperidae, Elapidae, and Atractaspididae) differ in the morphology and topographical relationships of the maxilla as well as in the lengths of their dorsal constrictor muscles (retractor vomeris; protractor, retractor, and levator pterygoidei; protractor quadrati), which move the bones comprising the upper jaw, giving some viperids relatively greater maxillary mobility compared to that of other colubroids. Rear-fanged colubrids vary in maxillary rotation capabilities, but most have a relatively unmodified palatal morphology compared to non-venomous colubrids. Viperids launch rapid strikes at prey, whereas elapids and colubrids use a variety of behaviors to grab prey. Viperids and elapids envenomate prey by opening their mouth and rotating both maxillae to erect their fangs. Both fangs are embedded in the prey by a bite that often results in some retraction of the maxilla. In contrast, Atractaspis (Atractaspididae) envenomates prey by extruding a fang unilaterally from its closed mouth and stabbing it into the prey by a downward-backwards jerk of its head. Rear-fanged colubrids envenomate prey by repeated unilateral or bilateral raking motions of one or both maxillae, some aspects of which are kinematically similar to the envenomation behavior in Atractaspis. The envenomation behavior, including the strike and prey release behaviors, varies within families as a function of prey size and habitat preference. Rear-fanged colubrids, arboreal viperids, and elapids tend to hold on to their prey after striking it, whereas atractaspidids and many terrestrial viperids release their prey after striking it. Larger prey are more frequently released than smaller prey by terrestrial front-fanged species. Venom delivery systems demonstrate a range of kinematic patterns that are correlated to sometimes only minor modifications of a common morphology of the jaw apparatus. The kinematics of the jaw apparatus are correlated with phylogeny, but also show functional plasticity relating to habitat and prey.     

Sapayoa aenigma: a New World representative of 'Old World suboscines'

Passerine birds are very plastic in their adaptations, which has made it difficult to define phylogenetic lineages and correctly allocate all species to these. Sapayoa aenigma, a member of the large group of New World flycatchers, has been difficult to place, and DNA-DNA hybridization experiments have indicated that it may have been misplaced. This is confirmed here, as base sequencing of two nuclear genes places it as a deep branch in the group of broadbills and pittas of the Old World tropics. The peculiar distribution of this lineage may be best explained in terms of a Gondwanic and Late Cretaceous origin of the passerine birds, as this particular lineage dispersed from the Antarctic landmass, reaching the Old World tropics via the drifting Indian plate, and South America via the West Antarctic Peninsula.     

Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes)

The subfamily Crotalinae (pitvipers) contains over 190 species of venomous snakes distributed in both the Old and New World. We incorporated an extensive sampling of taxa (including 28 of 29 genera), and sequences of four mitochondrial gene fragments (2.3kb) per individual, to estimate the phylogeny of pitvipers based on maximum parsimony and Bayesian phylogenetic methods. Our Bayesian analyses incorporated complex mixed models of nucleotide evolution that allocated independent models to various partitions of the dataset within combined analyses. We compared results of unpartitioned versus partitioned Bayesian analyses to investigate how much unpartitioned (versus partitioned) models were forced to compromise estimates of model parameters, and whether complex models substantially alter phylogenetic conclusions to the extent that they appear to extract more phylogenetic signal than simple models. Our results indicate that complex models do extract more phylogenetic signal from the data. We also address how differences in phylogenetic results (e.g., bipartition posterior probabilities) obtained from simple versus complex models may be interpreted in terms of relative credibility. Our estimates of pitviper phylogeny suggest that nearly all recently proposed generic reallocations appear valid, although certain Old and New World genera (Ovophis, Trimeresurus, and Bothrops) remain poly- or paraphyletic and require further taxonomic revision. While a majority of nodes were resolved, we could not confidently estimate the basal relationships among New World genera and which lineage of Old World species is most closely related to this New World group.     

Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes

Portions of two mitochondrial genes (12S and 16S ribosomal RNA) were sequenced to determine the phylogenetic relationships among the major clades of snakes. Thirty-six species, representing nearly all extant families, were examined and compared with sequences of a tuatara and three families of lizards. Snakes were found to constitute a monophyletic group (confidence probability [CP] = 96%), with the scolecophidians (blind snakes) as the most basal lineages (CP = 99%). This finding supports the hypothesis that snakes underwent a subterranean period early in their evolution. Caenophidians (advanced snakes), excluding Acrochordus, were found to be monophyletic (CP = 99%). Among the caenophidians, viperids were monophyletic (CP = 98%) and formed the sister group to the elapids plus colubrids (CP = 94%). Within the viperids, two monophyletic groups were identified: true vipers (CP = 98%) and pit vipers plus Azemiops (CP = 99%). The elapids plus Atractaspis formed a monophyletic clade (CP = 99%). Within the paraphyletic Colubridae, the largely Holarctic Colubrinae was found to be a monophyletic assemblage (CP = 98%), and the Xenodontinae was found to be polyphyletic (CP = 91%). Monophyly of the henophidians (primitive snakes) was neither supported nor rejected because of the weak resolution of relationships among those taxa, except for the clustering of Calabaria with a uropeltid, Rhinophis (CP = 94%).      

Chloroplast DNA restriction site variation in theVernonieae (Asteraceae), an initial appraisal of the relationship of New and Old World taxa and the monophyly ofVernonia

Chloroplast DNA restriction site variation was examined for 35 taxa in theVernonieae and four outgroup tribes, using 17 restriction enzymes mapped for ca. 900 restriction sites per species; 139 mutations were found to be phylogenetically informative. Phylogenetic trees were constructed using Wagner and weighted parsimony, and evaluated by bootstrap and decay analyses. Relationships of Old and New World taxa indicate complex geographical relationships; there was no clear geographic separation by hemisphere. The relationships between Old and New World Vernonias found here support prior morphological analyses. The sister group to all New and most Old World taxa was composed of a small group of Old World species including yellow-flowered, trinervate-leaved species previously postulated to be basal in the tribe. The majority of both New and Old World taxa are derived from a lineage beginning with the monotypic genusStokesia, an endemic of the southeastern United States. The genusVernonia was also found to be paraphyletic within both the New and Old World. Available data do not support either the separation ofVernonia or the tribeVernonieae into geographically distinct lineages. The pattern of relationships within theVernonieae for taxa from North America, Asia, Africa, Central and South America is most similar to that of several other groups of both plants and animals with a boreotropical origin, rather than an origin in Gondwanaland. Such a pattern of distribution suggests more ancient vicariant events than are routinely postulated for theAsteraceae.     

Inferring Species Trees from Gene Trees: A Phylogenetic Analysis of the Elapidae (Serpentes) Based on the Amino Acid Sequences of Venom Proteins

Toward the goal of recovering the phylogenetic relationships among elapid snakes, we separately found the shortest trees from the amino acid sequences for the venom proteins phospholipase A₂and the short neurotoxin, collectively representing 32 species in 16 genera. We then applied a method we term gene tree parsimony for inferring species trees from gene trees that works by finding the species tree which minimizes the number of deep coalescences or gene duplications plus unsampled sequences necessary to fit each gene tree to the species tree. This procedure, which is both logical and generally applicable, avoids many of the problems of previous approaches for inferring species trees from gene trees. The results support a division of the elapids examined into sister groups of the Australian and marine (laticaudines and hydrophiines) species, and the African and Asian species. Within the former clade, the sea snakes are shown to be diphyletic, with the laticaudines and hydrophiines having separate origins. This finding is corroborated by previous studies, which provide support for the usefulness of gene tree parsimony.