Presence of the large aquatic snake Palaeophis africanus in the middle Eocene marine margin of the Congo Basin,Cabinda, Angola

Ten isolated snake vertebrae from Landana and Sassa-Zao, Cabinda Exclave, Angola, present a “primitive” grade morphology with a weak lateral compression and do not belong to Palaeophis aff. typhaeus as originally referred to. They well belong to a single taxon and are here attributed to Palaeophis africanus for which the intracolumnar variation is described and illustrated. This species is Lutetian (middle Eocene) in age and originates from a marine coastal environment confirming again the aquatic capabilities of palaeophiid snakes. It represents the third largest species of Palaeophis with P. colossaeus and P. maghrebianus to which it is closely related in our tentative phylogenetic analysis, indicating that these three taxa could belong to an African clade. This study also contributes to the debate on the existence of primitive and advanced grades among palaeophiid snakes. Palaeophis presents laterally compressed anterior trunk vertebrae that could have been often erroneously considered as representing advanced grade species and potential parataxonomy.     

Convergent evolution and character correlation in burrowing reptiles: towards a resolution of squamate relationships

The affinities of three problematic groups of elongate, burrowing reptiles (amphisbaenians, dibamids and snakes) are reassessed through a phylogenetic analysis of all the major groups of squamates, including the important fossil taxa Sineoamphisbaena, mosasauroids and Pachyrhachis; 230 phylogenetically informative osteological characters were evaluated in 22 taxa. Snakes (including Pachyrhachis) are anguimorphs, being related firstly to large marine mosasauroids, and secondly to monitor lizards (varanids). Scincids and cordylids are not related to lacertiforms as previously thought, but to anguimorphs. Amphisbaenians and dibamids are closely related, and Sineoamphisbaena is the sister group to this clade. The amphisbaenian-dibamid-Sineoamphisbaena clade, in turn, is related to gekkotans and xantusiids. When the fossil taxa are ignored, snakes, amphisbaenians and dibamids form an apparently well-corroborated clade nested within anguimorphs. However, nearly all of the characters supporting this arrangement are correlated with head-first burrowing (miniaturization, cranial consolidation, body elongation, limb reduction), and invariably co-occur in other tetrapods with similar habits. These characters are potentially very misleading because of their sheer number and because they largely represent reductions or losses. It takes very drastic downweighting of these linked characters to alter tree topology: if fossils are excluded from the analysis, a (probably spurious) clade consisting of elongate, fossorial taxa almost always results. These results underscore the importance of including all relevant taxa in phylogenetic analyses. Inferring squamate phylogeny depends critically on the inclusion of certain (fossil) taxa with combinations of character states that demonstrate convergent evolution of the elongate, fossorial ecomorph in amphisbaenians and dibamids, and in snakes. In the all-taxon analysis, the position of snakes within anguimorphs is more strongly-corroborated than the association of amphisbaenians and dibamids with gekkotans. When the critical fossil taxa are deleted, snakes ‘attract’ the amphisbaenian-dibamid clade on the basis of a suite of correlated characters. While snakes remain anchored in anguimorphs, the amphisbaenian-dibamid clade moves away from gekkotans to join them. Regardless of the varying positions of the three elongate burrowing taxa, the interrelationships between the remaining limbed squamates (‘lizards’) are constant; thus, the heterodox affinities of scincids, cordylids, and xantusiids identified in this analysis appear to be robust. Finally, the position of Pachyrhachis as a basal snake rather than (as recently suggested) a derived snake is supported on both phylogenetic and evolutionary grounds.     

Primary homologies of the circumorbital bones of snakes

Some snakes have two circumorbital ossifications that in the current literature are usually referred to as the postorbital and supraorbital. We review the arguments that have been proposed to justify this interpretation and provide counter‐arguments that reject those conjectures of primary homology based on the observation of 32 species of lizards and 81 species of snakes (both extant and fossil). We present similarity arguments, both topological and structural, for reinterpretation of the primary homologies of the dorsal and posterior orbital ossifications of snakes. Applying the test of similarity, we conclude that the posterior orbital ossification of snakes is topologically consistent as the homolog of the lacertilian jugal, and that the dorsal orbital ossification present in some snakes (e.g., pythons, Loxocemus, and Calabaria) is the homolog of the lacertilian postfrontal. We therefore propose that the terms postorbital and supraorbital should be abandoned as reference language for the circumorbital bones of snakes, and be replaced with the terms jugal and postfrontal, respectively. The primary homology claim for the snake “postorbital” fails the test of similarity, while the term “supraorbital” is an unnecessary and inaccurate application of the concept of a neomorphic ossification, for an element that passes the test of similarity as a postfrontal. This reinterpretation of the circumorbital bones of snakes is bound to have important repercussions for future phylogenetic analyses and consequently for our understanding of the origin and evolution of snakes. J. Morphol. 274:973–986, 2013. © 2013 Wiley Periodicals, Inc.     

The naso-frontal joint in snakes as revealed by high-resolution X-ray computed tomography of intact and complete skulls

The naso-frontal joint of snakes is described on the basis of high-resolution X-ray computed tomography scans of single individuals of spirit-preserved snake specimens. The suspension of the snout unit from the braincase at the naso-frontal joint shows some broad evolutionary trends among snakes with potential phylogenetic implications, such as sutured or fused medial frontal flanges formed by the medial frontal pillars and the frontal subolfactory processes (in alethinophidians), the restriction of the usually extended dorsoventral contact of the medial nasal flange with the medial frontal flanges to a dorsal or ventral contact (in macrostomatans), and the transfer of the main element of snout suspension from the nasal to the septomaxilla (in colubroids). Some phylogenetic implications of the morphological characters identified in this study are outlined and discussed.     

The emerging phylogenetic pattern of parthenogenesis in snakes

Parthenogenesis occurs across a variety of vertebrate taxa. Within squamate reptiles (lizards and snakes), a group for which the largest number of cases has been documented, both obligate and facultative types of parthenogenesis exists, although the obligate form in snakes appears to be restricted to a single basal species of blind snake, Indotyphlops braminus. By contrast, a number of snake species that otherwise reproduce sexually have been found capable of facultative parthenogenesis. Because the original documentation of this phenomenon was restricted to subjects held in captivity and isolated from males, facultative parthenogenesis was attributed as a captive syndrome. However, its recent discovery in nature shifts the paradigm and identifies this form of reproduction as a potentially important feature of vertebrate evolution. In light of the growing number of documented cases of parthenogenesis, it is now possible to review the phylogenetic distribution in snakes and thus identify subtle variations and commonalities that may exist through the characterization of its emerging properties. Based on our findings, we propose partitioning facultative parthenogenesis in snakes into two categories, type A and type B, based on the sex of the progeny produced, their viability, sex chromosome morphology, and ploidy, as well as their phylogenetic position. Furthermore, we introduce a hypothesis (directionality of heterogamety hypothesis) to explain the production of female‐only parthenogens in basal alethinophidian snakes and male‐only parthenogens in caenophidian (advanced) snakes.     

A new species of Lapparentophis from the mid-Cretaceous Kem Kem beds,Morocco, with remarks on the distribution of lapparentophiid snakes

Two isolated trunk vertebrae from the ?uppermost Albian–lower Cenomanian Kem Kem beds of Morocco are described and assigned to Lapparentophis, an early snake genus known from coeval deposits in Algeria. The Moroccan specimens represent a new species, Lapparentophis ragei, which can be distinguished from the type and only known species, Lapparentophis defrennei, by its smaller size, its more elongate vertebrae, the presence of parazygosphenal foramina, and paradiapophyses extending anteroventrally closer to the cotyle. The discovery of Lapparentophis in the Kem Kem beds adds to the relatively diverse snake assemblage previously reported from this formation and extends the geographical range of the genus. The distribution of Lapparentophis and lapparentophiid-grade (?lapparentophiid) snakes is discussed. This poorly known family of terrestrial snakes seems to be restricted to the latest Albian–early Cenomanian of North Africa, with the exception of Pouitella from the early–middle Cenomanian of France. As for many other vertebrate taxa of this period, this distribution is consistent with a dispersal event from Africa to the western part of the European archipelago.     

A workflow of massive identification and application of intron markers using snakes as a model

Relative to the commonly used mitochondrial and nuclear protein‐coding genes, the noncoding intron sequences are a promising source of informative markers that have the potential to resolve difficult phylogenetic nodes such as rapid radiations and recent divergences. Yet many issues exist in the use of intron markers, which prevent their extensive application as conventional markers. We used the diverse group of snakes as an example to try paving the way for massive identification and application of intron markers. We performed a series of bioinformatics screenings which identified appropriate introns between single‐copy and conserved exons from two snake genomes, adding particular constraints on sequence length variability and sequence variability. A total of 1,273 candidate intron loci were retrieved. Primers for nested polymerase chain reaction (PCR) were designed for over a hundred candidates and tested in 16 snake representatives. 96 intron markers were developed that could be amplified across a broad range of snake taxa with high PCR successful rates. The markers were then applied to 49 snake samples. The large number of amplicons was subjected to next‐generation sequencing (NGS). An analytic strategy was developed to accurately recover the amplicon sequences, and approximately, 76% of the marker sequences were recovered. The average p‐distances of the intron markers at interfamily, intergenus, interspecies, and intraspecies levels were .168, .052, .015, and .004, respectively, suggesting that they were useful to study snake relationships of different evolutionary depths. A snake phylogeny was constructed with the intron markers, which produced concordant results with robust support at both interfamily and intragenus levels. The intron markers provide a convenient way to explore the signals in the noncoding regions to address the controversies on the snake tree. Our improved strategy of genome screening is effective and can be applied to other animal groups. NGS coupled with appropriate sequence processing can greatly facilitate the extensive application of molecular markers.     

Additional vertebral material of Thaumastophis (Serpentes: Caenophidia) from the early Eocene of India provides new insights on the early diversification of colubroidean snakes

The Ypresian Cambay Shale Formation at Vastan, Mangrol, and Tadkeshwar lignite mines in Gujarat, western India, has yielded a rich vertebrate fauna including madtsoiid, palaeophiid, booid, and colubroidean-like snakes. The latter are particularly abundant, but their systematic affinities are difficult to resolve. Here we describe new specimens of the colubroidean-like snake Thaumastophis missiaeni, including anterior, middle, and posterior trunk vertebrae, as well as caudal vertebrae. The combination of primitive and derived caenophidian and colubroidean vertebral characters confirms Thaumastophis as the earliest known stem-colubriform snake while Procerophis, from the same beds, is more derived and considered to represent a crown-Colubriformes. Additionally, Thaumastophis shares with Renenutet enmerwer from the late Eocene of Egypt a unique combination of vertebral characters that suggests an exchange with North Africa was possible along the southern margin of the Neotethys. We erect the new family Thaumastophiidae for Thaumastophis and Renenutet on the basis of their shared derived vertebral morphology.     

High ecomorphological diversity among Early Cretaceous frogs from a large subtropical wetland of Iberia

Anurans are extremely diverse amphibians with a unique Bauplan, whose origin, early ecomorphological diversification, and adaptive significance remain elusive. Their early fossil record is improving at an accelerated pace worldwide, but its contribution to these issues is still wanting. Here we explore ecomorphological diversity among Early Cretaceous (Barremian) frogs that inhabited a large subtropical wetland from Iberia by inferring locomotor abilities with a phylogenetic flexible discriminant analysis on data from limb proportions, which strongly correlate with locomotion. The results show a remarkable diversity among these frogs when compared with the extant diversity from this region and from tropical and subtropical wetland assemblages worldwide, encompassing miniature to medium-size jumpers and dedicated swimmers with more extreme proportions than extant ‘archeobatrachians,’ but also more generalized jumping and/or swimming forms. This agrees with the inferred wetland paleoenvironment and the hypothesis regarding early frogs as small poor jumpers or swimmers that evolved their peculiar Bauplan in aquatic environments.     

Predation upon Hatchling Dinosaurs by a New Snake from the Late Cretaceous of India

Derived large-mouthed snakes (macrostomatans) possess numerous specializations in their skull and lower jaws that allow them to consume large vertebrate prey. In contrast, basal snakes lack these adaptations and feed primarily on small prey items. The sequence of osteological and behavioral modifications involved in the evolution of the macrostomatan condition has remained an open question because of disagreement about the origin and interrelationships of snakes, the paucity of well-preserved early snake fossils on many continental landmasses, and the lack of information about the feeding ecology of early snakes. We report on a partial skeleton of a new 3.5-m-long snake, Sanajeh indicus gen. et sp. nov., recovered from Upper Cretaceous rocks of western India. S. indicus was fossilized in association with a sauropod dinosaur egg clutch, coiled around an egg and adjacent to the remains of a ca. 0.5-m-long hatchling. Multiple snake-egg associations at the site strongly suggest that S. indicus frequented nesting grounds and preyed on hatchling sauropods. We interpret this pattern as “ethofossil” preservation of feeding behavior. S. indicus lacks specializations of modern egg-eaters and of macrostomatans, and skull and vertebral synapomorphies place it in an intermediate position in snake phylogeny. Sanajeh and its large-bodied madtsoiid sister taxa Yurlunggur camfieldensis and Wonambi naracoortensis from the Neogene of Australia show specializations for intraoral prey transport but lack the adaptations for wide gape that characterize living macrostomatan snakes. The Dholi Dungri fossils are the second definitive association between sauropod eggs and embryonic or hatchling remains. New fossils from western India provide direct evidence of feeding ecology in a Mesozoic snake and demonstrate predation risks for hatchling sauropod dinosaurs. Our results suggest that large body size and jaw mobility afforded some non-macrostomatan snakes a greater diversity of prey items than previously suspected on the basis of extant basal snakes.     

Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction

The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs as well as to long-term physiographic changes that created new biogeographic theaters and new habitats. Snakes underwent massive ecological diversification during this period, repeatedly evolving novel dietary adaptations and prey preferences. The evolutionary tempo and mode of these trophic ecological changes remain virtually unknown, especially compared with co-radiating lineages of birds and mammals that are simultaneously predators and prey of snakes. Here, we assemble a dataset on snake diets (34,060 observations on the diets of 882 species) to investigate the history and dynamics of the multidimensional trophic niche during the global radiation of snakes. Our results show that per-lineage dietary niche breadths remained remarkably constant even as snakes diversified to occupy disparate outposts of dietary ecospace. Rapid increases in dietary diversity and complexity occurred in the early Cenozoic, and the overall rate of ecospace expansion has slowed through time, suggesting a potential response to ecological opportunity in the wake of the end-Cretaceous mass extinction. Explosive bursts of trophic innovation followed colonization of the Nearctic and Neotropical realms by a group of snakes that today comprises a majority of living snake diversity. Our results indicate that repeated transformational shifts in dietary ecology are important drivers of adaptive radiation in snakes and provide a framework for analyzing and visualizing the evolution of complex ecological phenotypes on phylogenetic trees.

The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs and long-term physiographic changes. This phylogenetic natural history study offers new insights into the evolution of snake ecological diversity after the end-Cretaceous mass extinction, as they took advantage of these new opportunities.     

The phylogenetic distribution and morphological variation of the ‘pouch’ in female snakes

Siegel D.S., Miralles A, Trauth S.E. and Aldridge R.D. 2011. The phylogenetic distribution and morphological variation of the ‘pouch’ in female snakes. —Acta Zoologica (Stockholm) 93 : 400–408. The urodaeum of female snakes is a chamber that receives the oviducts, urinary ducts, and intestine. Previous studies have indicated that a derived region of unknown function persists between the urodaeum and oviducts in some snakes of the Colubroides. This structure was recently termed the ‘pouch’; however, it is also commonly referred to as the vaginal pouch. A broad sampling of female snakes revealed that the pouch evolved once on the branch leading to Colubroides. The presence of the pouch in Colubroides is not unambiguous, as this feature was lost in some members of the Atractaspididae and Lamprophiidae. Variation was also observed in pouch morphology between taxa of the Colubroides. Variation included the following: (1) whether the pouch was bifurcated and if so, were the arms of the pouch separated caudally, (2) whether separated pouch arms were split by a caudal bifurcation of the urodaeum or through medial septa of the pouch arms, and (3) the absence or presence of oviducal papillae invading the cranial/lateral extremity of the pouch. The variation in pouch morphology observed does not appear to be correlated with the evolutionary history of Colubroides and polymorphism within families is common.     

Phylogenetic correlation between male–male fighting and mode of prey subjugation in snakes

Male–male fighting (MMF) in snakes is a sexually dimorphic trait in adults that is expressed during breeding periods and confers reproductive advantages to winners. This trait, however, is not ubiquitous among the approximately 2,700 species of extant snakes, and past research shows evidence of taxonomic trends. We evaluated the phylogenetic distribution of MMF in extant snakes using two previously published estimates of snake evolutionary history. We clearly identified multiple independent gains and losses of MMF in snakes and phylogenetically important taxa for which information on MMF is lacking. We followed this with two tests of the association of MMF with mode of prey capture using the concentrated-changes test (CCT) of Maddison (1990), and a third test using the subtree decomposition method of Read and Nee (1995). In the CCT analyses, first we tested whether MMF was randomly distributed with respect to mode of prey subjugation in snake lineages. This hypothesis was rejected, with MMF being significantly more concentrated in taxa that subjugate prey by constriction and/or envenomation. Second, we tested a more temporally exact hypothesis: whether changes in state of MMF were randomly distributed with respect to occurrences of state changes in mode of prey subjugation. Results of this test depended on the exact test parameters used. In general, however, this hypothesis also was rejected, suggesting that loss of constriction and/or envenomation typically results in loss of MMF, or vice versa. Last, the subtree decomposition test indicated a significant correlation between evolution of MMF and evolution of constriction and/or envenomation as the primary mode of prey subjugation. We propose that the relationship between these states is not causal but results from both characters being independent adaptations to energy resource scarcity. Received in revised form: 20 March 2001 Electronic Publication     

Phylogeny of snake trypanosomes inferred by SSU rDNA sequences, their possible transmission by phlebotomines, and taxonomic appraisal by molecular, cross-infection and morphological analysis

Blood examination by microhaematocrit and haemoculture of 459 snakes belonging to 37 species revealed 2.4% trypanosome prevalence in species of Viperidae (Crotalus durissus and Bothrops jararaca) and Colubridae (Pseudoboa nigra). Trypanosome cultures from C. durissus and P. nigra were behaviourally and morphologically indistinguishable. In addition, the growth and morphological features of a trypanosome from the sand fly Viannamyia tuberculata were similar to those of snake isolates. Cross-infection experiments revealed a lack of host restriction, as snakes of 3 species were infected with the trypanosome from C. durissus. Phylogeny based on ribosomal sequences revealed that snake trypanosomes clustered together with the sand fly trypanosome, forming a new phylogenetic lineage within Trypanosoma closest to a clade of lizard trypanosomes transmitted by sand flies. The clade of trypanosomes from snakes and lizards suggests an association between the evolutionary histories of these trypanosomes and their squamate hosts. Moreover, data strongly indicated that these trypanosomes are transmitted by sand flies. The flaws of the current taxonomy of snake trypanosomes are discussed, and the need for molecular parameters to be adopted is emphasized. To our knowledge, this is the first molecular phylogenetic study of snake trypanosomes.     

The skull of the Upper Cretaceous snake Dinilysia patagonica Smith‐Woodward, 1901, and its phylogenetic position revisited

The cranial anatomy of Dinilysia patagonica, a terrestrial snake from the Upper Cretaceous of Argentina, is redescribed and illustrated, based on high‐resolution X‐ray computed tomography and better preparations made on previously known specimens, including the holotype. Previously unreported characters reinforce the intriguing mosaic nature of the skull of Dinilysia, with a suite of plesiomorphic and apomorphic characters with respect to extant snakes. Newly recognized plesiomorphies are the absence of the medial vertical flange of the nasal, lateral position of the prefrontal, lizard‐like contact between vomer and palatine, floor of the recessus scalae tympani formed by the basioccipital, posterolateral corners of the basisphenoid strongly ventrolaterally projected, and absence of a medial parietal pillar separating the telencephalon and mesencephalon, amongst others. We also reinterpreted the structures forming the otic region of Dinilysia, confirming the presence of a crista circumfenestralis, which represents an important derived ophidian synapomorphy. Both plesiomorphic and apomorphic traits of Dinilysia are treated in detail and illustrated accordingly. Results of a phylogenetic analysis support a basal position of Dinilysia, as the sister‐taxon to all extant snakes. The fossil taxa Yurlunggur, Haasiophis, Eupodophis, Pachyrhachis, and Wonambi appear as derived snakes nested within the extant clade Alethinophidia, as stem‐taxa to the crown‐clade Macrostomata. The hypothesis of a sister‐group relationship between Dinilysia and Najash rionegrina, as suggested by some authors, is rejected by the results of our analysis. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 194–238.     

The phylogenetic position of Anomochilidae (Reptilia: Serpentes): first evidence from DNA sequences

Previously, anilioids (Aniliidae, Anomochilidae, Cylindrophiidae and Uropeltidae) were considered the only extant, non‐macrostomatan alethinophidian snakes. Although their monophyly and intrarelationships remained poorly established, their fossoriality, small gape, and inferred phylogenetic position have been important evidence in orthodox scenarios about early snake evolution. Recent molecular studies including aniliids, cylindrophiids and uropeltids indicate anilioid polyphyly, with the latter two families comprising a clade nested within Macrostomata. We carried out the first molecular phylogenetic analysis to include the very poorly known and seemingly rare Anomochilidae. Only partial sequences of 12S and 16S rRNA mitochondrial genes could be amplified from tissue collected from a single dead specimen of Anomochilus leonardi. Amplification failed for nuclear and other mitochondrial genes, and for all the investigated genes for the holotype and paratype of A. leonardi. Analyses recovered a para‐ or polyphyletic Anilioidea. Anomochilus is recovered as most closely related to Cylindrophis maculatus (rendering Cylindrophiidae possibly paraphyletic). The relatively small amount of available data produces only moderate levels of support, but the stability of taxa and agreement across different analytical methods and with larger analyses of snake phylogeny support the abandonment of Anilioidea as a natural taxon, and the recognition of a higher category for a clade comprising Asian anilioids (Anomochilidae, Cylindrophiidae and Uropeltidae).     

Squamate reptiles from the middle Eocene of Lissieu (France). A landmark in the middle Eocene of Europe

In Europe, faunas of squamates (lizards and snakes) from the middle Eocene are very poorly known, with the exception of those from the level MP 16 (latest middle Eocene). From the MP 11-MP 15 interval, squamates were previously reported only from Messel (MP 11, earliest middle Eocene) and from the untere and obere Mittelkohle of Geiseltal (MP 12 and MP 13 respectively) in Germany. The present report describes the middle Eocene assemblage of squamates from Lissieu (France), the first fauna reported from the level MP 14. Whereas fossils from Messel and Geiseltal are mostly articulated skeletons, fossils from Lissieu are represented by disarticulated bones; such fossils may be more easily compared to those from other Cenozoic localities, in which bones are almost always disarticulated. The fauna from Lissieu is more diverse than those from the Geiseltal sites and approximately as diverse as that from Messel as they are presently known; it is comprised of 17 distinct taxa. These taxa cannot be all identified to the species or genus level. They belong to iguanids, gekkonids, lacertids, anguids, thecoglossan platynotans, ophidians incertaesedis, boids, ?tropidophiines, “tropidophiids” incertaesedis, booids incertaesedis, and perhaps russellophiids. The fauna includes several new taxa but only a presumed tropidophiine snake may be named on the basis of the available material. The fauna from Lissieu is a mixture of taxa restricted to the middle Eocene and taxa known from older or younger levels. Taxa shared by Lissieu and the few other localities from the middle Eocene of Europe are rare. This fauna from Lissieu represents a stratigraphical landmark for the middle Eocene.     

Hidden support from unpromising data sets strongly unites snakes with anguimorph ‘lizards’

A combined analysis of nuclear, mitochondrial and morphological data robustly resolves snakes as the sister taxon to anguimorph ‘lizards’. Analysed in isolation, nuclear DNA (nDNA) produces a trichotomy between snakes, iguanians and anguimorphs, mitochondrial DNA (mtDNA) is largely uninformative at deeper levels, and morphology tends to nest snakes deep within anguimorphs or with various legless squamate groups. When analysed simultaneously, the nuclear signal is sufficiently strong that mtDNA and morphology are constrained to choose between alternative resolutions of the iguanian–anguimorph–snake trichotomy (generated by the nDNA) – and both support the snake–anguimorph solution. Combined analyses of fast‐evolving or idiosyncratically evolving markers (mtNDA, morphology) with conservative traits (e.g. nuclear genes) might be the best way to resolve ancient, closely spaced divergences. Fast or idiosyncratic markers potentially provide the most information about short, ancient internodes, but can converge on spurious trees if analysed in isolation. However, if constrained to only choosing between plausible trees, such data can contribute unique and valuable phylogenetic signal that resolves such problematic divergences.     

A mitogenomic study on the phylogenetic position of snakes

Phylogenetic relationships of squamates (lizards, amphisbaenians and snakes) have received considerable attention, although no consensus has been reached concerning some basal divergences. This paper focuses on the Serpentes (snakes), whose phylogenetic position within the Squamata remains uncertain despite a number of morphological and molecular studies. Some mitogenomic studies have suggested a sister-group relationship between snakes and varanid lizards, while other studies have identified snakes and lizards as sister groups. However, recent studies using nuclear data have presented a different scenario, with snakes being more closely related to anguimorph and iguanian lizards. In this mitogenomic study we have examined the above hypotheses with the inclusion of amphisbaenians, one gekkotan and one acrodont lizard, taxa not represented in previous mitogenomic studies. To this end we have also extended the representation of snakes by sequencing five additional snake genomes: two scolecophidians ( Ramphotyphlops australis and Typhlops mirus ) two henophidians ( Eunectes notaeus and Boa constrictor ) and one caenophidian ( Elaphe guttata ). The phylogenetic analysis recovered snakes and amphisbaenians as sister groups, thereby differing from previous hypotheses. In addition to a discussion on previous morphological and molecular studies in light of the results presented here, the current study also provides some details regarding features of the new snake mitochondrial genomes described.