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.     

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.     

Molecular evidence that the deadliest sea snake Enhydrina schistosa (Elapidae: Hydrophiinae) consists of two convergent species

We present a striking case of phenotypic convergence within the speciose and taxonomically unstable Hydrophis group of viviparous sea snakes. Enhydrina schistosa, the ‘beaked sea snake’, is abundant in coastal and inshore habitats throughout the Asian and Australian regions, where it is responsible for the large majority of recorded deaths and injuries from sea snake bites. Analyses of five independent mitochondrial and nuclear loci for populations spanning Australia, Indonesia and Sri Lanka indicate that this ‘species’ actually consists of two distinct lineages in Asia and Australia that are not closest relatives. As a result, Australian “E. schistosa” are elevated to species status and provisionally referred to Enhydrina zweifeli. Convergence in the characteristic ‘beaked’ morphology of these species is probably associated with the wide gape required to accommodate their spiny prey. Our findings have important implications for snake bite management in light of the medical importance of beaked sea snakes and the fact that the only sea snake anti-venom available is raised against Malaysian E. schistosa.     

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.     

Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae)

Species complexes undergoing rapid radiation present a challenge in molecular systematics because of the possibility that ancestral polymorphism is retained in component gene trees. Coalescent theory has demonstrated that gene trees often fail to match lineage trees when taxon divergence times are less than the ancestral effective population sizes. Suggestions to increase the number of loci and the number of individuals per taxon have been proposed; however, phylogenetic methods to adequately analyze these data in a coalescent framework are scarce. We compare two approaches to estimating lineage (species) trees using multiple individuals and multiple loci: the commonly used partitioned Bayesian analysis of concatenated sequences and a modification of a newly developed hierarchical Bayesian method (BEST) that simultaneously estimates gene trees and species trees from multilocus data. We test these approaches on a phylogeny of rapidly radiating species wherein divergence times are likely to be smaller than effective population sizes, and incomplete lineage sorting is known, in the rodent genus, Thomomys. We use seven independent noncoding nuclear sequence loci (total approximately 4300 bp) and between 1 and 12 individuals per taxon to construct a phylogenetic hypothesis for eight Thomomys species. The majority-rule consensus tree from the partitioned concatenated analysis included 14 strongly supported bipartitions, corroborating monophyletic species status of five of the eight named species. The BEST tree strongly supported only the split between the two subgenera and showed very low support for any other clade. Comparison of both lineage trees to individual gene trees revealed that the concatenation method appears to ignore conflicting signals among gene trees, whereas the BEST tree considers conflicting signals and downweights support for those nodes. Bayes factor analysis of posterior tree distributions from both analyses strongly favor the model underlying the BEST analysis. This comparison underscores the risks of overreliance on results from concatenation, and ignoring the properties of coalescence, especially in cases of recent, rapid radiations.     

A phylogenetic analysis of Pseudonaja (Hydrophiinae, Elapidae, Serpentes) based on mitochondrial DNA sequences

A phylogenetic analysis of mitochondrial ND4 and adjacent tRNA sequences for a geographically extensive series of specimens reveals nine major clades within Pseudonaja, of which six are largely coincident with nominal taxa (P. affinis, P. guttata, P. inframacula, P. ingrami, P. modesta, and P. textilis). The remaining three clades are composed of specimens presently referred to P. nuchalis. Two of these clades correspond with the "Darwin" and "Southern" morphs of previous authors, while the third clade incorporates the "Orange with black head" and "Pale head, grey nape" morphs. We are unable to confirm the presence of consistent karyotypic differences between "Orange with black head" and "Pale head, grey nape" specimens, however, P. inframacula, P. textilis, and P. nuchalis "Darwin" are found to exhibit distinctive karyotypes, as previously reported. These results, in conjunction with additional observations of karyotpic and morphological variation, are consistent with nine historically-independent lineages (i.e., species) within Pseudonaja. There is strong support for a clade composed of P. affinis, P. inframacula, P. ingrami, P. textilis, and the three P. nuchalis lineages, and for the relationships (P. inframacula, P. nuchalis "Southern") and (P. nuchalis "Darwin", P. nuchalis "Orange with black head"--"Pale head, grey nape" ).     

Molecular phylogeny of the genus Tibicina (Hemiptera, Cicadidae): rapid radiation and acoustic behaviour

To estimate the potential contribution of ethological and ecological parameters to the mechanisms of species formation and species isolation in the Palearctic cicada genus Tibicina , we constructed a molecular phylogenetic hypothesis of extant Tibicina species. Seven mitochondrial genes and a fragment of a nuclear gene were sequenced (3046 bp). Mitochondrial genes included 547 informative sites but the nuclear gene was too conserved to be included in the analysis. The tree was characterized by a basal polytomy indicating that Tibicina species arose rapidly. Such rapid radiation might explain the low divergence in the acoustic communication observed between species. Parameters describing habitat selection and acoustic communication were mapped onto the tree. A shift in habitat selection accompanied by acoustic changes might have contributed to one speciation event. The stochastic distribution of the same acoustic characters on the other branches of the tree implies, however, that the subtle acoustic differences between species could be the result of previous speciation events and independent evolutionary histories, rather than having contributed themselves in the speciation and isolation processes.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 611–626.     

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.     

The colouration of the venomous coral snakes (family Elapidae) and their mimics (families Aniliidae and Golubridae)

The bright coloured, highly venomous coral snakes, Leptomicrurus, Micrurus and Micruroides (family Elapidae) and a series of harmless or mildly toxic mimics form an important component of the snake fauna of the Americas. Coral snake patterns are defined as any dorsal pattern found in any species of venomous coral snake and/or any dorsal pattern containing a substantial amount of red, pink or orange distributed so as to resemble that of some species of venomous coral snake. The components of coral snake colouration are described and four principal dorsal patterns are recognized: unicolour, bicolour, tricolour and quadricolour. The tricolour patterns may be further clustered based on the number of black bands or rings separating the red ones as: monads, dyads, triads, tetrads or pentads. A detailed classification of all coral snake colour patterns is presented and each pattern is illustrated. The taxonomic distribution of these patterns is surveyed for mimics and the 56 species of highly venomous coral snakes. Among the latter, the most frequent encountered patterns are tricolour monads, tricolour triads and bicolour rings, in that order. No venomous coral snakes have a tricolour dyad, tricolour tetrad or quadricolour pattern. As many as 115 species of harmless or mildly toxic species, c. 18% of all American snakes, are regarded as coral snake mimics. The colouration and behavioural traits of venomous coral snakes combine to form a significant antipredator defence of an aposematic type. The mimics in turn receive protection from predators that innately or through learning avoid coral snake colour patterns. The precise resemblances in colouration between sympatric non-coral snakes and venomous coral snakes and the concordant geographic variation between the two strongly support this view. Batesian mimicry with the highly venomous coral snakes as the models and the other forms as the mimics is the favoured explanation for this situation. It is further concluded that a number of species in the genera Elaphe, Farancia, Nerodia and Thamnophis, although having red in their colouration, should not be included in the coral snake mimic guild.     

Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers

Evolutionary theory has gained tremendous insight from studies of adaptive radiations. High rates of speciation, morphological divergence, and hybridization, combined with low sequence variability, however, have prevented phylogenetic reconstruction for many radiations. The Hawaiian honeycreepers are an exceptional adaptive radiation, with high phenotypic diversity and speciation that occurred within the geologically constrained setting of the Hawaiian Islands. Here we analyze a new data set of 13 nuclear loci and pyrosequencing of mitochondrial genomes that resolves the Hawaiian honeycreeper phylogeny. We show that they are a sister taxon to Eurasian rosefinches (Carpodacus) and probably came to Hawaii from Asia. We use island ages to calibrate DNA substitution rates, which vary substantially among gene regions, and calculate divergence times, showing that the radiation began roughly when the oldest of the current large Hawaiian Islands (Kauai and Niihau) formed, ~5.7 million years ago (mya). We show that most of the lineages that gave rise to distinctive morphologies diverged after Oahu emerged (4.0-3.7 mya) but before the formation of Maui and adjacent islands (2.4-1.9 mya). Thus, the formation of Oahu, and subsequent cycles of colonization and speciation between Kauai and Oahu, played key roles in generating the morphological diversity of the extant honeycreepers.     

Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves)

Background  

The phylogeny of shorebirds (Aves: Charadriiformes) and their putative sister groups was reconstructed using approximately 5 kilobases of data from three nuclear loci and two mitochondrial genes, and compared to that based on two other nuclear loci.     

Feeding preferences in 2 disjunct populations of tiger snakes, Notechis scutatus (Elapidae)

Variations at both the genetic and phenotypic levels play animportant role in responses to food and food-related stimuli.Knowledge of such variations is crucial to understanding howpopulations adapt to changing environments. We investigatedthe dietary preferences of 2 tiger snake populations and comparedthe responses of diet-naive animals (laboratory-born neonates),diet-controlled animals (laboratory-reared juveniles), and naturaldiet–experienced animals (wild-caught adults) to visualand chemical cues from 6 prey types (mouse, skink, silver gull,chicken, shearwater, and frog). The mainland population inhabitsa swamp, feeds mostly on frogs, and suffers heavy predation.The second population inhabits a small nearby offshore islandwith no standing water (no frogs); feeds mostly on skinks, mice,and, as adults, silver gull chicks; and suffers no known predation.Although different prey are eaten in the 2 populations, adultwild-caught snakes from both populations showed a significantpreference for 3 types of prey (frog, mouse, and chick), irrespectiveof their natural diet. Neonates responded to all prey cues morethan they did to control stimuli in both populations. However,the island neonates showed significantly higher interest insilver gull chick stimuli (the main prey of the island adultsnakes) than did their mainland conspecifics. Laboratory-bredjuveniles displayed behavioral plasticity by significantly increasingtheir response to mice after being fed baby mice for 7 months.We conclude that genetic-based differences in food-related cuesare important in tiger snakes but that they are also capableof behavioral plasticity. Island adult and neonate snakes exhibitedresponses to prey types no longer consumed naturally (frog),suggesting that behavioral characters may have been retainedfor long periods under relaxed selection. Island neonates showeda strong interest in a novel prey item (silver gull). This resultcomplements previous work describing how island snakes havedeveloped the ability to swallow larger prey than usual, aswell as seemingly developing a taste for them.     

Morphometries of the ectopterygoid in advanced snakes (Colubroidea): a concordance of shape and phylogeny

A principal components analysis was performed on 20 measurements of the ectopterygoids of 85 colubroid snakes. This sample encompassed all the shape variation previously recognized in the ectopterygoid of colubroids. Simple proportions which correlate with the first two principal component axes are: relative ectopterygoid length with the first and five measures of absolute or relative head shape with the second. Using these simple proportions colubroid ectopterygoids can be sorted into four shape classes each concordant with a taxonomic grouping: relatively long with broad notched head—Crotalinac; relatively long with narrow, flat head—Viperinae; relatively short with broad, notched head—Colubridae; and relatively short with narrow, flat head—Elapidae. This concordance has an error of about 10⁰₀. We propose that these shape classes reflect phylogenetically old and conservative functional differences in the palatomaxillary complexes of the four taxonomic groupings. Other aspects of ectopterygoid shape are described and provisional character state phylogenies for some aspects of the ectopterygoid are presented. Finally, the bearing of our data on the systematics of aparallactines, micrurines, sea snakes, Azemiops and certain other genera are discussed.     

Toxicocalamus, a New Guinea genus of snakes of the family Elapidae

Toxicocalamus is expanded to include Apistocalamus and Ultrocalamus as subgenera. Pseudapistocalamus nymani, Apistocalamus pratti, A. loennbergi, and A. lamingtoni are considered geographic variations of Toxicocalamus ( Apistocalamus ) loriae. Toxicocalamus ( Ultrocalamus ) buergersi, synonymized with T. ( U. ) preussi by previous workers, is recognized as a distinct species because of many structural peculiarities (most notably, extension of the venom gland back within the body cavity nearly to the heart, as in Maticora ). Three species are described as new: T. ( Apistocalamus ) spiblepidotus, characterized by large size and peculiar colouration; T. ( A. ) holopelturus, characterized by entire subcaudals and hemi-penial structure; and T. ( Toxicocalamus ) misimae, differing from the related T. longissimus in much lower ventral count and in having only 15 scale rows. A population from Garaina (Morobe Division) is believed to be of recent origin from hybridization between T. ( A. ) loriae and T. ( T. ) stanleyanus. Toxicocalamus is most closely related to the Australian genera called Brachyurophis, Melwardia, Narophis, Rhinelaps, and Rhynchoelaps by Worrell, but here all grouped in the genus Rhynchoelaps. This Australian genus and Toxicocalamus make up the Rhynchoelaps group, which does not include the genera Vermicella (for V. annulata only), Ogmodon, or Parapistocalamus. The lack of a diastema behind the fang in the elapid genera Kerilia, Ogmodon, and Toxicocalamus is not a primitive, but a specialized, feature, probably developed independently in each of these genera as a mechanism for coordinating the replacement rhythm of the fangs with that of solid teeth behind. It is suggested that the solid maxillary teeth of Toxicocalamus are neomorphs, formed by backward extension of the fang-forming portion of the dental lamina.     

Snakes across the Strait: trans-Torresian phylogeographic relationships in three genera of Australasian snakes (Serpentes: Elapidae: Acanthophis, Oxyuranus, and Pseudechis)

We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis-death adders; Oxyuranus-taipans; Pseudechis-blacksnakes), using parsimony, maximum likelihood, and Bayesian analysis of sequences of the mitochondrial cytochrome b and ND4 genes. In Acanthophis and Pseudechis, we find evidence of multiple trans-Torresian sister-group relationships. Analyses of the timing of cladogenic events suggest crossings of the Torres Strait on several occasions between the late Miocene and the Pleistocene. These results support a hypothesis of repeated land connections between Australia and New Guinea in the late Cenozoic. Additionally, our results reveal undocumented genetic diversity in Acanthophis and Pseudechis, supporting the existence of more species than previously believed, and provide a phylogenetic framework for a reinterpretation of the systematics of these genera. In contrast, our Oxyuranus scutellatus samples from Queensland and two localities in New Guinea share a single haplotype, suggesting very recent (late Pleistocene) genetic exchange between New Guinean and Australian populations.     

Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci

Among vertebrates, cichlid fishes are the paradigmatic example of adaptive radiation and ecological specialization. In turn, molecular genetic studies of cichlids have focused primarily on more recently diverged groups. Here, we present an evolutionary hypothesis of the major lineages of cichlid fishes based on DNA sequence data from two nuclear loci. One marker, Tmo-4C4, is a single-copy locus containing a region of amino acid similarity to the muscle protein TITIN. Flanking sequence from a second, microsatellite, locus Tmo-M27, shows similarity to mammalian RAS guanine nucleotide-releasing factor. We compare and combine data from these loci to evaluate phylogenetic performance. In separate and combined analyses, the sequence data support and clarify previous morphological hypotheses of cichlid major-group relationships. Indian and Malagasy cichlids form a basal, paraphyletic group. Neotropical cichlids are the sister clade to an African assemblage composed of the paraphyletic west and Pan-African lineages and a group of east African rift lake taxa. We use a consensus phylogeny of the Cichlidae to trace evolutionary changes in the microsatellite repeat motif at Tmo-M27. Analysis reveals that the repeat region was nearly lost in the ancestor to cichlids and then amplified extensively in African taxa. Results demonstrate that the two new DNA markers could be widely applied in perciform systematics. Furthermore, the comparative approach can unveil mutational dynamics of simple-sequence repeat loci over long periods of fish evolution. Simple-sequence repeat regions are increasingly being found in introns of important regulatory genes. We address issues involving their function and suggest caution in making assumptions of strict neutrality.     

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.