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.     

Uncoupling ecological innovation and speciation in sea snakes (Elapidae, Hydrophiinae, Hydrophiini)

The viviparous sea snakes (Hydrophiini) are by far the most successful living marine reptiles, with ～ 60 species that comprise a prominent component of shallow-water marine ecosystems throughout the Indo-West Pacific. Phylogenetically nested within the ～ 100 species of terrestrial Australo-Melanesian elapids (Hydrophiinae), molecular timescales suggest that the Hydrophiini are also very young, perhaps only ～ 8-13 Myr old. Here, we use likelihood-based analyses of combined phylogenetic and taxonomic data for Hydrophiinae to show that the initial invasion of marine habitats was not accompanied by elevated diversification rates. Rather, a dramatic three to six-fold increase in diversification rates occurred at least 3-5 Myr after this transition, in a single nested clade: the Hydrophis group accounts for ～ 80% of species richness in Hydrophiini and ～ 35% of species richness in (terrestrial and marine) Hydrophiinae. Furthermore, other co-distributed lineages of viviparous sea snakes (and marine Laticauda, Acrochordus and homalopsid snakes) are not especially species rich. Invasion of the oceans has not (by itself) accelerated diversification in Hydrophiini; novelties characterizing the Hydrophis group alone must have contributed to its evolutionary and ecological success.     

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.     

Notes on the Australian sea-snake Ephalophis greyi M. Smith (Serpentes:Elapidae, Hydrophiinae) and the origin and classification of sea-snakes

The type and two other specimens of Ephalophis greyi are described. The venom gland musculature is of the Demansia type, with an isolated muscle running from the quadrate to the rear of the venom gland. The only other hydrophiine with the Demansia pattern of venom gland musculature, Hydrophis mertoni Roux, is referred, for this and other reasons, to the genus Ephalophis as E. mertoni (Roux). Some notes on a skull of E. mertoni are presented, along with a revised diagnosis of Ephalophis. The Demansia pattern of venom gland muscles seen in Ephalophis is primitive for the Hydrophiinae and other members of that subfamily have secondarily taken on a Glyphodon type of musculature of the venom gland by loss of the muscle slip from quadrate to gland. The Demansia group of terrestrial elapids, particularly the genus Drepanodontis Worrell, stand close to the origin of the Hydrophiinae. A classification of the Hydrophiinae into three generic groups is presented, with Ephalophis, Aipysurus , and Emydocephalus referred to an Aipysurus group.     

Trophic divergence despite morphological convergence in a continental radiation of snakes

Ecological and phenotypic convergence is a potential outcome of adaptive radiation in response to ecological opportunity. However, a number of factors may limit convergence during evolutionary radiations, including interregional differences in biogeographic history and clade-specific constraints on form and function. Here, we demonstrate that a single clade of terrestrial snakes from Australia—the oxyuranine elapids—exhibits widespread morphological convergence with a phylogenetically diverse and distantly related assemblage of snakes from North America. Australian elapids have evolved nearly the full spectrum of phenotypic modalities that occurs among North American snakes. Much of the convergence appears to involve the recurrent evolution of stereotyped morphologies associated with foraging mode, locomotion and habitat use. By contrast, analysis of snake diets indicates striking divergence in feeding ecology between these faunas, partially reflecting regional differences in ecological allometry between Australia and North America. Widespread phenotypic convergence with the North American snake fauna coupled with divergence in feeding ecology are clear examples of how independent continental radiations may converge along some ecological axes yet differ profoundly along others.     

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.     

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.     

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.     

The molecular evolutionary tree of lizards,snakes, and amphisbaenians

Squamate reptiles (lizards, snakes, amphisbaenians) number approximately 8200 living species and are a major component of the world's terrestrial vertebrate diversity. Recent molecular phylogenies based on protein-coding nuclear genes have challenged the classical, morphology-based concept of squamate relationships, requiring new classifications, and drawing new evolutionary and biogeographic hypotheses. Even the key and long-held concept of a dichotomy between iguanians (～1470 sp.) and scleroglossans (all other squamates) has been refuted because molecular trees place iguanians in a highly nested position. Together with snakes and anguimorphs, iguanians form a clade – Toxicofera – characterized by the presence of toxin secreting oral glands and demonstrating a single early origin of venom in squamates. Consequently, neither the varanid lizards nor burrowing lineages such as amphisbaenians or dibamid lizards are the closest relative of snakes. The squamate timetree shows that most major groups diversified in the Jurassic and Cretaceous, 200–66 million years (Myr) ago. In contrast, five of the six families of amphisbaenians arose during the early Cenozoic, ～60–40 Myr ago, and oceanic dispersal on floating islands apparently played a significant role in their distribution on both sides of the Atlantic Ocean. Among snakes, molecular data support the basic division between the small fossorial scolecophidians (～370 sp.) and the alethinophidians (all other snakes, ～2700 sp.). They show that the alethinophidians were primitively macrostomatan and that this condition was secondarily lost by burrowing lineages. The diversification of alethinophidians resulted from a mid-Cretaceous vicariant event, the separation of South America from Africa, giving rise to Amerophidia (aniliids and tropidophiids) and Afrophidia (all other alethinophidians). Finally, molecular phylogenies have made it possible to draw a detailed evolutionary history of venom among advanced snakes (Caenophidia), a key functional innovation underlying their radiation (～2500 sp.). To cite this article: N. Vidal, S.B. Hedges, C. R. Biologies 332 (2009).     

Aspidomorphus, a genus of New Guinea snakes of the Family Elapidae, with notes on related genera

The Australian snakes that have been included in Aspidomorphus differ markedly from that genus, particularly in hemipenial morphology and in the absence of a muscular slip from the quadrate bone to the venom gland; the genus Aspidomorphus is therefore restricted to the New Guniea species. Aspidomorphus (as here restricted) is closely related to Demansia (in the restricted sense of Worrell, essentially D. psammophis, D. torquata , and D. olivacea ), but the Australian species generally referred to Aspidomorphus seem to be related to Glyphodon . The genera Aspidomorphus, Demansia, Rhinhoplocephalus and Drepanodontis form a natural group. Aspidomorphus contains three species, each identifiable by hemipenial features as well as by details of colouration: A. muelleri (= A. mülleri mülleri and A. m. interruptus of Brongersma's revision); A. lineaticollis (= A. mülleri lineaticollis and A. m. lineatus of Brongersma); and A. schlegeli. The last species differs from the others in the form of the maxillary bone and the anterior mandibular dentition; it seems to be confined to northwestern New Guinea and adjacent islands, since specimens from the eastern end of New Guinea that had been referred to schlegeli are actually A. lineaticollis. In all three species some geographical variation can be demonstrated, at least in ventral count, but it is not considered necessary to use trinomials to indicate that geographical variation exists. Pseudonaja textilis is recorded from New Guinea for the first time. (McDowell.)
Examination reveals Demansia ornaticeps is properly referred to Demansia. (Cogger.)     

Moving in two worlds: aquatic and terrestrial locomotion in sea snakes (Laticauda colubrina,Laticaudidae)

Yellow‐lipped sea kraits (Laticauda colubrina) are amphibious in their habits. We measured their locomotor speeds in water and on land to investigate two topics: (1) to what degree have adaptations to increase swimming speed (paddle‐like tail etc.) reduced terrestrial locomotor ability in sea kraits?; and (2) do a sea krait’s sex and body size influence its locomotor ability in these two habitats, as might be expected from the fact that different age and sex classes of sea kraits use the marine and terrestrial environments in different ways? To estimate ancestral states for locomotor performance, we measured speeds of three species of Australian terrestrial elapids that spend part of their time foraging in water. The evolutionary modifications of Laticauda for marine life have enhanced their swimming speeds by about 60%, but decreased their terrestrial locomotor speed by about 80%. Larger snakes moved faster than smaller individuals in absolute terms but were slower in terms of body lengths travelled per second, especially on land. Male sea kraits were faster than females (independent of the body‐size effect), especially on land. Prey items in the gut reduced locomotor speeds both on land and in water. Proteroglyphous snakes may offer exceptional opportunities to study phylogenetic shifts in locomotor ability, because (1) they display multiple independent evolutionary shifts from terrestrial to aquatic habits, and (2) one proteroglyph lineage (the laticaudids) displays considerable intraspecific and interspecific diversity in terms of the degree to which they use terrestrial vs. aquatic habitats.     

Dehydration and drinking responses in a pelagic sea snake

Recent investigations of water balance in sea snakes demonstrated that amphibious sea kraits (Laticauda spp.) dehydrate in seawater and require fresh water to restore deficits in body water. Here, we report similar findings for Pelamis platurus, a viviparous, pelagic, entirely marine species of hydrophiine ("true") sea snake. We sampled snakes at Golfo de Papagayo, Guanacaste, Costa Rica and demonstrated they do not drink seawater but fresh water at variable deficits of body water incurred by dehydration. The threshold dehydration at which snakes first drink fresh water is -18.3 ± 1.1 % (mean ± SE) loss of body mass, which is roughly twice the magnitude of mass deficit at which sea kraits drink fresh water. Compared to sea kraits, Pelamis drink relatively larger volumes of water and make up a larger percentage of the dehydration deficit. Some dehydrated Pelamis also were shown to drink brackish water up to 50% seawater, but most drank at lower brackish values and 20% of the snakes tested did not drink at all. Like sea kraits, Pelamis dehydrate when kept in seawater in the laboratory. Moreover, some individuals drank fresh water immediately following capture, providing preliminary evidence that Pelamis dehydrate at sea. Thus, this widely distributed pelagic species remains subject to dehydration in marine environments where it retains a capacity to sense and to drink fresh water. In comparison with sea kraits, however, Pelamis represents a more advanced stage in the evolutionary transition to a fully marine life and appears to be less dependent on fresh water.     

Physical properties of some snake plasma albumins

The albumin-like proteins were purified from the plasma of three terrestrial elapids and two sea snakes. The albumin-like fraction averaged 25% (range: 21-30%) in concentration of the total plasma proteins as determined by densitometer. The physical properties of the albumin-like proteins purified from these snakes were compared. These properties, e.g. electrophoretic mobility, isoelectric point, extinction coefficient, and molecular weight, were shown to be strikingly similar to those of human plasma albumin. The physical properties of the plasma albumins of the snakes studied are similar to one another. This similarity does not explain our previous observation that Naja albumin is considerably remote immunologically from those of other elapids (Mao et al., 1983).     

An immunological assessment of the phylogenetic position of New World coral snakes

The New World coral snakes (micrurines), genera Micrurus and Micruroides have recently been seen as derived from a lineage of South American colubrids, rather than from a common lineage with Old World elapids and sea snakes as traditionally accepted. We compared serum albumins of representative coral snakes, Old World elapids, sea snakes, and neotropical colubrids immunologically. Phylogenetic analysis of the biochemical data unambiguously allies the micrurines with the family Elapidae as it is currently understood. Using the albumin molecular clock calibration derived from other terrestrial vertebrates. we suggest a late Oligocene-early Miocene separation between the New and Old World elapid lineages. This requires a movement of elapid stocks from Asia into North America, and supporting evidence for this model is derived from several paleontological sources. We suggest that a number of extant micrurine lineages have had long independent histories.     

Phylogenetic relationships within laticaudine sea snakes (Elapidae)

The sea snake subfamily Laticaudinae consists of a single genus with eight named species, based on morphological characters. We used microsatellite and mitochondrial DNA (mtDNA) data to clarify the adaptive radiation of these oviparous sea snakes in the South Pacific, with special reference to New Caledonia and Vanuatu. A mitochondrial DNA data set (ND4 gene 793 bp) was obtained from 345 individuals of the five species of Laticauda sp. sea snakes endemic to the region. Maximum likelihood and Bayesian approaches yielded the same optimal tree topology, identifying two major clades (yellow-banded and blue-banded sea snakes). Although all laticaudine sea snakes rely on small islands as oviposition sites, the two lineages differ in their use of marine vs. terrestrial habitats. A highly aquatic species (Laticauda laticaudata) shows a strong pattern of genetic isolation by distance, implying that the patchy distribution of terrestrial habitats has had little impact on gene flow. The more terrestrial clade (Laticauda colubrina, Laticauda frontalis, Laticauda guineai, Laticauda saintgironsi) shows stronger geographic differentiation in allelic frequencies, associated with island groups rather than with geographic distance. Microsatellites and mtDNA suggest that L. frontalis (restricted to Vanuatu) represents a recent founder-induced speciation event, from allopatric migrants of the New Caledonian taxon L. saintgironsi. A major divergence in speciation patterns between the two major clades of laticaudine snakes thus correlates with (and perhaps, is driven by) differences in the importance of terrestrial habitats in the species' ecology.     

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.     

Independent innovation in the evolution of paddle-shaped tails in viviparous sea snakes (Elapidae: Hydrophiinae)

The viviparous sea snakes (Hydrophiinae) comprise ~90% of living marine reptiles and display many physical and behavioral adaptations for breathing, diving, and achieving osmotic balance in marine habitats. Among the most important innovations found in marine snakes are their paddle-shaped (dorsoventrally expanded) tails, which provide propulsive thrust in the dense aquatic medium. Here, we reconstruct the evolution of caudal paddles in viviparous sea snakes using a dated molecular phylogeny for all major lineages and computed tomography of internal osteological structures. Bayesian ancestral state reconstructions show that extremely large caudal paddles supported by elongated vertebral processes are unlikely to have been present in the most recent common ancestor of extant sea snakes. Instead, these characters appear to have been acquired independently in two highly marine lineages of relatively recent origin. Both the Aipysurus and Hydrophis lineages have elongated neural spines that support the dorsal edge of their large paddles. However, whereas in the Aipysurus lineage the ventral edge of the paddle is supported by elongated haemapophyses, this support is provided by elongated and ventrally directed pleurapophyses in the Hydrophis lineage. Three semi-marine lineages (Hydrelaps, Ephalophis, and Parahydrophis) form the sister group to the Hydrophis clade and have small paddles with poorly developed dorsal and ventral supports, consistent with their amphibious lifestyle. Overall, our results suggest that not only are the viviparous hydrophiines the only lineage of marine snakes to have acquired extremely large, skeletally supported caudal paddles but also that this innovation has occurred twice in the group in the past ~2-6 million years.     

Degeneration patterns of the olfactory receptor genes in sea snakes

The sense of smell relies on the diversity of olfactory receptor (OR) repertoires in vertebrates. It has been hypothesized that different types of ORs are required in terrestrial and marine environments. Here we show that viviparous sea snakes, which do not rely on a terrestrial environment, have significantly lost ORs compared with their terrestrial relatives, supporting the hypothesis. On the other hand, oviparous sea snakes, which rely on a terrestrial environment for laying eggs, still maintain their ORs, reflecting the importance of the terrestrial environment for them. Furthermore, we found one Colubroidea snake (including sea snakes and their terrestrial relatives)‐specific OR subfamily which had diverged widely during snake evolution after the blind snake–Colubroidea snake split. Interestingly, no pseudogenes are included in this subfamily in sea snakes, and this subfamily seems to have been expanding rapidly even in an underwater environment. These findings suggest that the Colubroidea‐specific ORs detect nonvolatile odorants.     

Molecular evidence for Gondwanan origins of multiple lineages within a diverse Australasian gecko radiation

Aim Gondwanan lineages are a prominent component of the Australian terrestrial biota. However, most squamate (lizard and snake) lineages in Australia appear to be derived from relatively recent dispersal from Asia (< 30 Ma) and in situ diversification, subsequent to the isolation of Australia from other Gondwanan landmasses. We test the hypothesis that the Australian radiation of diplodactyloid geckos (families Carphodactylidae, Diplodactylidae and Pygopodidae), in contrast to other endemic squamate groups, has a Gondwanan origin and comprises multiple lineages that originated before the separation of Australia from Antarctica. Location Australasia. Methods Bayesian (beast ) and penalized likelihood rate smoothing (PLRS) (r 8s ) molecular dating methods and two long nuclear DNA sequences (RAG‐1 and c‐mos) were used to estimate a timeframe for divergence events among 18 genera and 30 species of Australian diplodactyloids. Results At least five lineages of Australian diplodactyloid geckos are estimated to have originated > 34 Ma (pre‐Oligocene) and basal splits among the Australian diplodactyloids occurred c. 70 Ma. However, most extant generic and intergeneric diversity within diplodactyloid lineages appears to post‐date the late Oligocene (< 30 Ma). Main conclusions Basal divergences within the diplodactyloids significantly pre‐date the final break‐up of East Gondwana, indicating that the group is one of the most ancient extant endemic vertebrate radiations east of Wallace’s Line. At least five Australian lineages of diplodactyloid gecko are each as old or older than other well‐dated Australian squamate radiations (e.g. elapid snakes and agamids). The limbless Pygopodidae (morphologically the most aberrant living geckos) appears to have radiated before Australia was occupied by potential ecological analogues. However, in spite of the great age of the diplodactyloid radiation, most extant diversity appears to be of relatively recent origin, a pattern that is shared with other Australian squamate lineages.