The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes

Squamate reptiles number approximately 8000 living species and are a major component of the world's terrestrial vertebrate diversity. However, the established relationships of the higher-level groups have been questioned in recent molecular analyses. Here we expand the molecular data to include DNA sequences, totaling 6192 base pairs (bp), from nine nuclear protein-coding genes (C-mos, RAG1, RAG2, R35, HOXA13, JUN, alpha-enolase, amelogenin and MAFB) for 19 taxa representing all major lineages. Our phylogenetic analyses yield a largely resolved phylogeny that challenges previous morphological analyses and requires a new classification. The limbless dibamids are the most basal squamates. Of the remaining taxa (Bifurcata), the gekkonids form a basal lineage. The Unidentata, squamates that are neither dibamids nor gekkonids, are divided into the Scinciformata (scincids, xantusiids, and cordylids) and the Episquamata (remaining taxa). Episquamata includes Laterata (Teiformata, Lacertiformata, and Amphisbaenia, with the latter two joined in Lacertibaenia) and Toxicofera (iguanians, anguimorphs and snakes). Our results reject several previous hypotheses that identified either the varanids, or a burrowing lineage such as amphisbaenians or dibamids, as the closest relative of snakes. Our study also rejects the monophyly of both Scleroglossa and Autarchoglossa, because Iguania, a species-rich lineage (ca. 1440 sp.), is in a highly nested position rather than being basal among Squamata. Thus iguanians should not be viewed as representing a primitive state of squamate evolution but rather a specialized and successful clade combining lingual prehension, dependence on visual cues, and ambush foraging mode, and which feeds mainly on prey avoided by other squamates. Molecular time estimates show that the Triassic and Jurassic (from 250 to 150 Myr) were important times for squamate evolution and diversification.     

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.     

A family of short retroposons (Squam1) from squamate reptiles (Reptilia: Squamata): Structure,evolution, and correlation with phylogeny

Sequences of the SINE family specific to squamate reptiles have been isolated from the genomes of lacertid lizards and sequenced. These retroposons, which we called Squam1, are 360–390 bp long and contain a region similar to the tRNA gene sequence at the 5’ end. This family has also been detected in representatives of other reptile families (varanids, iguanids (Anolis), gekkonids, and snakes), being absent from the genomes of crocodiles as well as amphibians, birds, and mammals. The primary structures of Squam1 copies have been comprehensively analyzed and compared with GenBank sequences. The genomes of most taxa contain two to three SINE subfamilies with specific diagnostic features in their primary structures. Individual similarity between the copies within each taxon is about 85%, with intrageneric similarity being only slightly higher. A comparison of consensus sequences between different lizard families has shown that Squam1 may be a convenient phylogenetic marker for this group of reptiles, having a number of both apomorphic and more or less pronounced synapomorphic features. By this criterion, snakes slightly differ from lizards but obviously belong to the same clade. However, they show no special affinity to varanids as the putative closest relatives of snakes, compared to other lizards.     

Evolutionary diversification of clades of squamate reptiles

We analysed the diversification of squamate reptiles (7488 species) based on a new molecular phylogeny, and compared the results to similar estimates for passerine birds (5712 species). The number of species in each of 36 squamate lineages showed no evidence of phylogenetic conservatism. Compared with a random speciation-extinction process with parameters estimated from the size distribution of clades, the alethinophidian snakes (2600 species) were larger than expected and 13 clades, each having fewer than 20 species, were smaller than expected, indicating rate heterogeneity. From a lineage-through-time plot, we estimated that a provisional rate of lineage extinction (0.66 per Myr) was 94% of the rate of lineage splitting (0.70 per Myr). Diversification in squamate lineages was independent of their stem age, but strongly related to the area of the region within which they occur. Tropical vs. temperate latitude exerted a marginally significant influence on species richness. In comparison with passerine birds, squamates share several clade features, including: (1) independence of species richness and age; (2) lack of phylogenetic signal with respect to clade size; (3) general absence of exceptionally large clades; (4) over-representation of small clades; (5) influence of region size on clade size; and (6) similar rates of speciation and extinction. The evidence for both groups suggests that clade size has achieved long-term equilibrium, suggesting negative feedback of species richness on the rate of diversification.     

Bergmann's rule in nonavian reptiles: turtles follow it,lizards and snakes reverse it

Abstract Bergmann's rule is currently defined as a within-species tendency for increasing body size with increasing latitude or decreasing environmental temperature. This well-known ecogeographic pattern has been considered a general trend for all animals, yet support for Bergmann's rule has only been demonstrated for mammals and birds. Here we evaluate Bergmann's rule in two groups of reptiles: chelonians (turtles) and squamates (lizards and snakes). We perform both nonphylogenetic and phylogenetic analyses and show that chelonians follow Bergmann's rule (19 of 23 species increase in size with latitude; 14 of 15 species decrease in size with temperature), whereas squamates follow the converse to Bergmann's rule (61 of 83 species decrease in size with latitude; 40 of 56 species increase in size with temperature). Size patterns of chelonians are significant using both nonphylogenetic and phylogenetic methods, whereas only the nonphylogenetic analyses are significant for squamates. These trends are consistent among major groups of chelonians and squamates for which data are available. This is the first study to document the converse to Bergmann's rule in any major animal group as well as the first to show Bergmann's rule in a major group of ectotherms. The traditional explanation for Bergmann's rule is that larger endothermic individuals conserve heat better in cooler areas. However, our finding that at least one ectothermic group also follows Bergmann's rule suggests that additional factors may be important. Several alternative processes, such as selection for rapid heat gain in cooler areas, may be responsible for the converse to Bergmann's rule in squamates.     

Egg teeth of squamate reptiles and their phylogenetic significance

Original and published data on the structure of egg teeth in squamate reptiles and the phylogenetic significance of corresponding characters are reviewed, elaborating A.M. Sergeev’s ideas on the subject. Problems are discussed concerning the use of this character in modern phylogenetic constructions and the necessity of new embryological investigations to resolve the issue concerning the formation of an unpaired egg tooth rudiment in all Squamata except the Dibamidae and Gekkota.     

Comparative myology of the forelimb of Liolaemus sand lizards (Liolaemidae)

The lizard genus Liolaemus includes numerous constituent clusters of putatively related taxa, one of which is the Liolaemus boulengeri group, which in turn includes the sand lizards (of the Liolaemus wiegmannii subgroup). Members of the sand lizard group exhibit three different modes of burying into sand. The general morphology of the forelimb muscles of those Liolaemus species is analysed. Herein, we present a study of the forelimb musculature of all species considered by Halloy et al. (1998). This study has three principal goals. First, we are seeking myological characters that will be useful in formulating phylogenetic hypothesis about the species of Liolaemus. With these characters, we also wish to compile morphological data that represent the morphological space implied in the diverse locomotor behaviours of these animals. Second, we are looking for derived features that reflect functional changes in the use of forelimb. Third, we wish to provide a cladistic analysis that can be used to test phylogenetic hypothesis derived from other sources of data. We present 48 characters in a data set and analyse it cladistically. We obtained a hypothesis of relationships of the Liolaemus species and compared this with previous hypotheses based on other characters. The trees obtained are not congruent with previously proposed phylogenies. We were unable to identify in our trees nodes that are based on structures reflecting functional changes in the use of the forelimb. The morphological similarities in the forelimb musculature of all species analysed seems to conform a very conservative general anatomical pattern with which Liolaemus sand lizards perform most of their locomotor behaviours.     

The loss of the lower temporal arcade in diapsid reptiles

The fossil record of diapsid reptiles does not provide conclusive evidence that the loss of the lower temporal arcade is correlated with the development of streptostyly. Analysis of the structure of the external jaw adductor in extant lizards results in the formulation of an alternative hypothesis to explain the loss of the lower temporal arcade in lepidosaurs. Extant lizards show the development of a posteroventral portion of the superficialis layer (lb) of the external adductor, which invades the lateral surface of the lower jaw, thus escaping the original confines of the external adductor. The development and expansion of a posteroventral lb muscle would have to be correlated with the loss of at least the posterior portion of the lower temporal arcade. Fossil lepidosaurs such as Clevosaurus, Prolacerta and Macrocnemus show the reduction of the lower temporal arcade from back to front, which is consistent with the hypothesis of the development of a posteroventral lb muscle.     

Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): structure and phylogenetic significance

Short interspersed elements (SINEs) are important nuclear molecular markers of the evolution of many eukaryotes. However, the SINEs of squamate reptile genomes have been little studied. We first identified two families of SINEs, termed Squam1 and Squam2, in the DNA of meadow lizard Darevskia praticola (Lacertidae) by performing DNA hybridization and PCR. Later, the same families of retrotransposons were found using the same methods in members of another 25 lizard families (from Iguania, Scincomorpha, Gekkota, Varanoidea, and Diploglossa infraorders) and two snake families, but their abundances in these taxa varied greatly. Both SINEs were Squamata-specific and were absent from mammals, birds, crocodiles, turtles, amphibians, and fish. Squam1 possessed some characteristics common to tRNA-related SINEs from fish and mammals, while Squam2 belonged to the tRNA(Ala) group of SINEs and had a more unusual and divergent structure. Squam2-related sequences were found in several unannotated GenBank sequences of squamate reptiles. Squam1 abundance in the Polychrotidae, Agamidae, Leiolepididae, Chamaeleonidae, Scincidae, Lacertidae, Gekkonidae, Varanidae, Helodermatidae, and two snake families were 10(2) -10(4) times higher than those in other taxa (Corytophanidae, Iguanidae, Anguidae, Cordylidae, Gerrhosauridae, Pygopodidae, and Eublepharidae). A less dramatic degree of copy number variation was observed for Squam2 in different taxa. Several Squam1 copies from Lacertidae, Chamaeleonidae, Gekkonidae, Varanidae, and Colubridae were sequenced and found to have evident orthologous features, as well as taxa-specific autapomorphies. Squam1 from Lacertidae and Chamaeleonidae could be divided into several subgroups based on sequence differences. Possible applications of these SINEs as Squamata phylogeny markers are discussed.     

Buccal swabbing as a source of DNA from squamate reptiles

Buccal swabbing was compared with other tissues as a source of DNA for microsatellite genotyping from two squamate reptiles. For both species, the lizard Lacerta agilis and the snake Coronella austriaca, buccal swabbing proved more reliable than tissues including tail tips, toe clips and ventral scale clips.     

Evolution of placentation among squamate reptiles: recent research and future directions

Squamate reptiles are uniquely suited to study of evolution of reproductive mode and pattern of embryonic nutrition. Viviparous species have evolved from oviparous ancestors on numerous occasions, patterns of nutritional provision to embryos range widely from lecithotrophy, at one end of a continuum, to placentotrophy at the other, and structure and function of the maternal-embryonic relationship is highly constrained resulting in parallel evolutionary trajectories among taxa. Embryos of oviparous species primarily receive nourishment from yolk, but also mobilize a significant quantity of calcium from the eggshell. Most viviparous species also are predominantly lecithotrophic, yet all viviparous species are placentotrophic to some degree. Similarities in embryonic development and nutritional pattern between oviparous species and most viviparous species suggest that the pattern of nutrition of oviparous squamates is an exaptation for the evolution of viviparity and that placentotrophy and viviparity evolve concomitantly. The few species of squamates that rely substantially on placentotrophy have structural modifications of the interface between the embryo and mother that are interpreted as adaptations to enhance nutritional exchange. Recent studies have extended understanding of the diversity of embryonic nutrition and placental structure and have resulted in hypotheses for transitions in the evolution of placentotrophy, yet data are available for few species. Indirect tests of these hypotheses, by comparison of structural-functional relationships among clades in which viviparity has evolved, awaits further study of the reproductive biology of squamates.     

Aspects of vertebral development in lizards and snakes

The embryonic and postnatal development of vertebrae of the mid-trunk and mid-tail in Lacerta vivipara, Anguis fragilis and Natrix natrix have been studied. Centra and neural arches develop independently after the perichordal tube has been formed, the neurocentral suture representing a consistent boundary between them. The condyle and cup of each centrum are formed by differential growth of cartilage; in Anguis and Natrix the joints between centra are synovial. The zygosphenial joints of Lacerta are continuous with the zygapophysial joints and not separate from them as in snakes. The autotomy splits in the tail vertebrae of Lacerta are derived from four distinct components which become continuous in postnatal life. The chordal cartilage is not involved in the split formation.     

The phylogeny of varanoid lizards and the affinities of snakes

Evidence that platynotan squamates (living varanoid lizards, snakes and their fossil relatives) are monophyletic is presented. Evolutionary relationships within this group are then ascertained through a cladistic analysis of 144 osteological characters. Mosasauroids (aigialosaurs and mosasaurs), a group of large marine lizards, are identified as the nearest relatives of snakes, thus resolving the long-standing problem of snake affinities. The mosasauroid–snake clade (Pythonomorpha) is corroborated by 40 derived characters, including recumbent replacement teeth, thecodonty, four or fewer premaxillary teeth, supratemporal–prootic contact, free mandibular tips, crista circumfenestralis, straight vertical splenio-angular joint, loss of posterior ramus of the coronoid, reduced basipterygoid processes, reduced interpterygoid vacuity, zygosphene–zygantral articulations, and absence of epiphyses on the axial skeleton and skull. After mosasauroids, the next closest relatives of snakes are varanids (Varanus, Saniwa and Saniwides) and lanthanotids (Lanthanotus and Cherminotus). Derived features uniting varanids and lanthanotids include nine cervical vertebrae and three or fewer pairs of sternal ribs. The varanid–lanthanotid–pythonomorph clade, here termed Thecoglossa, is supported by features such as the anteriorly positioned basal tubera, and the loss of the second epibranchial. Successive outgroups to thecoglossans are Telmasaurus, an unresolved polytomy (Estesia, Gobidermatidae and Helodermatidae), Paravaranus and Proplatynota. The ''necrosaurs'' are demonstrated to be an artificial (polyphyletic) assemblage of primitive platynotans that are not particularly closely related to each other.Snakes are presumed to have evolved from small, limbless, burrowing lizards and the inability of previous analyses to resolve the affinities of snakes has been attributed to extensive convergence among the numerous lineages of such lizards. The present study contradicts this claim, demonstrating that the problem is due instead to omission of critical fossil taxa. No modern phylogenetic analysis of squamate relationships has simultaneously included both mosasauroids and snakes: previous studies have therefore failed to identify the mosasauroid–snake association and the suite of derived characters supporting it. Mosasauroids are large aquatic animals with well-developed appendages, and none of the derived characters uniting mosasauroids and snakes is obviously correlated with miniaturization, limb reduction or fossoriality. Recognition that mosasauroids, followed by varanids and lanthanotids, are the nearest relatives of snakes will also facilitate studies of relationships within snakes, which until now have been hampered by uncertainty over the most appropriate (closely-related) lizard outgroups.     

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.     

Promiscuity in sand lizards (Lacerta agilis) and adder snakes (Vipera berus): causes and consequences

We review postcopulatory phenomena in the Swedish sand lizard (Lacerta agilis) and adder (Vipera berus), and in particular, links between female promiscuity, determinants of paternity, and offspring viability. In both species, females mate multiply and exhibit a positive relationship between the number of partners and offspring viability. We conclude that this relationship is most likely the result of variable genetic compatibility between mates arising from postcopulatory phenomena, predominantly assortative fertilization with respect to parental genotypes. However, males who were more successful at mate acquisition were also more successful in situations of sperm competition, suggesting a possible link between male (diploid and haploid) genetic quality per se and probability of fertilization. Neither the number of partners nor the number of matings influenced the risk of infertility in sand lizards, suggesting that selection for reduced risk of infertility is not a sufficient explanation for maintaining female promiscuity in this population. Finally, we conclude that the relatively low genetic variability exhibited by our study populations may have facilitated detection of genetic benefits compared to more outbred ones. However, recent work derived from outbred populations in other taxa suggest a greater generality of the principles we discuss than previously may have been appreciated.     

Phylogenetic implications and diagenetic stability of macromolecules from pleistocene and recent shells of Mercenaria mercenaria (mollusca,bivalvia)

The phylogeny and diagenesis of Pleistocene and Recent bivalves were studied immunologically by use of a conventional antiserum elicited against an EDTA‐soluble macromolecular extract from shells of the modern bivalve mollusc Mercenaria mercenaria. ELISA tests of the antiserum with shell fragments of a wide range of modern bivalves gave taxonomically significant results. The antiserum reacted with palaeoheterodonts and heterodonts but not with representatives of other bivalve subclasses. This phylogenetic reactivity was also apparent in tests with fossil shells, although the specificity and overall strength of the reaction were both reduced. Absorption of the antiserum with etched shell powders of various (palaeo)heterodonts yielded more specific antibody preparations.

Investigations of shell matrix diagenesis, using the anti‐Mercenaria serum, demonstrated that small amounts of original determinants could be detected even in fossils over one million years old. The reactivity of the serum with extracts of fossil Mercenaria decreased with sample age. The relationship between serum reactivity and the degree of amino acid racemization was almost linear. Clearly, the various determinants to which antibodies were elicited were being destroyed at different rates.     

Morphology, development, and evolution of fetal membranes and placentation in squamate reptiles

Current studies on fetal membranes of reptiles are providing insight into three major historical transformations: evolution of the amniote egg, evolution of viviparity, and evolution of placentotrophy. Squamates (lizards and snakes) are ideal for such studies because their fetal membranes sustain embryos in oviparous species and contribute to placentas in viviparous species. Ultrastructure of the fetal membranes in oviparous corn snakes (Pituophis guttatus) shows that the chorioallantois is specialized for gas exchange and the omphalopleure, for water absorption. Transmission and scanning electron microscopic studies of viviparous thamnophine snakes (Thamnophis, Storeria) have revealed morphological specializations for gas exchange and absorption in the intra-uterine environment that represent modifications of features found in oviparous species. Thus, fetal membranes in oviparous species show morphological differentiation for distinct functions that have been recruited and enhanced under viviparous conditions. The ultimate in specialization of fetal membranes is found in viviparous skinks of South America (Mabuya) and Africa (Trachylepis, Eumecia), in which placentotrophy accounts for nearly all of the nutrients for development. Ongoing research on these lizards has revealed morphological specializations of the chorioallantoic placenta through which nutrient transfer is accomplished. In addition, African Trachylepis show an invasive form of implantation, in which uterine epithelium is replaced by invading chorionic cells. Ongoing analysis of these lizards shows how integration of multiple lines of evidence can provide insight into the evolution of developmental and reproductive specializations once thought to be confined to eutherian mammals.     

Functional and evolutionary morphology of lingual feeding in squamate reptiles: phylogenetics and kinematics

Use of the tongue as a prehensile organ during the ingestion stage of feeding in lizards was studied cinegraphically in seven species. Within Squamata, lingual prehension is limited to a single clade, the Iguania (Iguanidae, Agamidae and Chamaeleontidae), which includes all 'fleshy-tongued' lizards. All remaining squamates (Scleroglossa) use the jaws alone for prey prehension. Lingual prehension and a 'fleshy' tongue are primitive squamate characteristics. Kinematically, lingual ingestion cycles are similar to previously described transport cycles in having slow open, fast open, fast close and slow close-power stroke phases. Tongue movements are sequentially correlated with jaw movements as they are in transport. However, during ingestion, anterior movement of the tongue includes an extra-oral, as well as intra-oral component. Tongue protrusion results in a pronounced slow open-II phase at a large gape distance. A high degree of variability in quantitative aspects of ingestion and transport cycles suggests that modulation through sensory feedback is an important aspect of lizard feeding. Preliminary evidence indicates an important role for hyoid movement in tongue protrusion. Our results are consistent with the Bramble & Wake (1985) model generalized feeding cycle and support their contention that specialized feeding mechanisms often represent modifications of a basic pattern, particularly modification of the slow open phase.