Molecular phylogenetics of squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree

Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos

Satellite DNA (satDNA) consists of sequences of DNA that form tandem repetitions across the genome, and it is notorious for its diversity and fast evolutionary rate. Despite its importance, satDNA has been only sporadically studied in reptile lineages. Here, we sequenced genomic DNA and PCR-amplified microdissected W chromosomes on the Illumina platform in order to characterize the monomers of satDNA from the Henkel's leaf-tailed gecko U. henkeli and to compare their topology by in situ hybridization in the karyotypes of the closely related Günther's flat-tail gecko U. guentheri and gold dust day gecko P. laticauda. We identified seventeen different satDNAs; twelve of them seem to accumulate in centromeres, telomeres and/or the W chromosome. Notably, centromeric and telomeric regions seem to share similar types of satDNAs, and we found two that seem to accumulate at both edges of all chromosomes in all three species. We speculate that the long-term stability of all-acrocentric karyotypes in geckos might be explained from the presence of specific satDNAs at the centromeric regions that are strong meiotic drivers, a hypothesis that should be further tested.

The macroevolutionary singularity of snakes

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.

Exceptionally rapid tooth development and ontogenetic changes in the feeding apparatus of the Komodo dragon

Dental developmental and replacement patterns in extinct amniotes have attracted a lot of attention. Notable among these are Paleozoic predatory synapsids, but also Mesozoic theropod dinosaurs, well known for having true ziphodonty, strongly serrated carinae with dentine cores within an enamel cap. The Komodo dragon, Varanus komodoensis, is the only extant terrestrial vertebrate to exhibit true ziphodonty, making it an ideal model organism for gaining new insights into the life history and feeding behaviours of theropod dinosaurs and early synapsids. We undertook a comparative dental histological analysis of this extant apex predator in combination with computed tomography of intact skulls. This study allowed us to reconstruct the dental morphology, ontogeny, and replacement patterns in the largest living lizard with known feeding behaviour, and apply our findings to extinct taxa where the behaviour is largely unknown. We discovered through computed tomography that V. komodoensis maintains up to five replacement teeth per tooth position, while histological analysis showed an exceptionally rapid formation of new teeth, every 40 days. Additionally, a dramatic ontogenetic shift in the dental morphology of V. komodoensis was also discovered, likely related to changes in feeding preferences and habitat. The juveniles have fewer dental specializations, lack true ziphodonty, are arboreal and feed mostly on insects, whereas the adults have strongly developed ziphodonty and are terrestrial apex predators with defleshing feeding behaviour. In addition, we found evidence that the ziphodont teeth of V. komodoensis have true ampullae (interdental folds for strengthening the serrations), similar to those found only in theropod dinosaurs. Comparisons with other species of Varanus and successive outgroup taxa reveal a complex pattern of dental features and adaptations, including the evolution of snake-like tongue flicking used for foraging for prey. However, only the Komodo dragon exhibits this remarkable set of dental innovations and specializations among squamates.

Embryonic development of the skull in a parthenogenetic lizard, the mourning gecko (Lepidodactylus lugubris)

Gekkotans are one of the major clades of squamate reptiles. As one of the earliest-diverging lineages, they are crucial in studying deep-level squamate phylogeny and evolution. Developmental studies can shed light on the origin of many important morphological characters, yet our knowledge of cranial development in gekkotans is very incomplete. Here, we describe the embryonic development of the skull in a parthenogenetic gekkonid, the mourning gecko (Lepidodactylus lugubris), studied using non-acidic double staining and histological sectioning. Our analysis indicates that the pterygoid is the first ossifying bone in the skull, as in almost all other studied squamates, followed closely by the surangular and prearticular. The next to appear are the dentary, frontal, parietal and squamosal. The tooth-bearing upper jaw bones, the premaxilla and maxilla, develop relatively late. In contrast to previous reports, the premaxilla starts ossifying from two distinct centres, reminiscent of the condition observed in diplodactylids and eublepharids. Only a single ossification centre of the postorbitofrontal is observed. Some of the endochondral bones of the braincase (prootic, opisthotic, supraoccipital) and the dermal parasphenoid are the last bones to appear. The skull roof is relatively poorly ossified near the time of hatching, with a large frontoparietal fontanelle still present. Many bones begin ossifying relatively later in L. lugubris than in the phyllodactylid Tarentola annularis, which suggests that its ossification sequence is heterochronic with respect to T. annularis.

The affinities of the Late Triassic Cryptovaranoides and the age of crown squamates

Most living reptile diversity is concentrated in Squamata (lizards, including snakes), which have poorly known origins in space and time. Recently, †Cryptovaranoides microlanius from the Late Triassic of the United Kingdom was described as the oldest crown squamate. If true, this result would push back the origin of all major lizard clades by 30-65 Myr and suggest that divergence times for reptile clades estimated using genomic and morphological data are grossly inaccurate. Here, we use computed tomography scans and expanded phylogenetic datasets to re-evaluate the phylogenetic affinities of †Cryptovaranoides and other putative early squamates. We robustly reject the crown squamate affinities of †Cryptovaranoides, and instead resolve †Cryptovaranoides as a potential member of the bird and crocodylian total clade, Archosauromorpha. Bayesian total evidence dating supports a Jurassic origin of crown squamates, not Triassic as recently suggested. We highlight how features traditionally linked to lepidosaurs are in fact widespread across Triassic reptiles. Our study reaffirms the importance of critically choosing and constructing morphological datasets and appropriate taxon sampling to test the phylogenetic affinities of problematic fossils and calibrate the Tree of Life.

The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly

Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest-quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified 9 of the 19 chromosomal scaffolds were assembled as a near-single contig, whereas the other 10 chromosomes were each scaffolded together from multiple contigs. We qualitatively identified that the percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction of previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000.

The Adrenal Gland of Squamata (Reptilia): A Comparative Overview

The adrenal gland is a complex endocrine organ composed of two components: a steroidogenic tissue, which produces steroid hormones, and a chromaffin tissue, which mainly produces norepinephrine and epinephrine. Through evolution, their relationships with each other changed. They begin as isolated chromaffin and steroidogenic cell aggregates, typical of fish, and end with the advanced compact gland, typical of mammals, which consists of an external steroidogenic cortical zone and an internal chromaffin medullary zone. The adrenal gland of reptiles is unique because, with few exceptions, it is near the gonads and genital ducts, and the chromaffin and steroidogenic tissues are closely associated. However, the degree of mixing is variable. For example, in Squamata, the mixing degree of chromaffin and steroidogenic tissues, their reciprocal position in the gland, and the relative quantities of norepinephrine and epinephrine secreted by the chromaffin cells are extremely variable. This variability could be related to the phylogenetic history of the species. After a brief discussion of the adrenal gland and its main functions in vertebrates, this overview will examine the general characteristics of the adrenal gland of squamates, the differences in morphology of the gland, and the possible relationships with the phylogeny of the different species.

The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order

Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.

Proteomic analysis of the mandibular glands from the Chinese crocodile lizard, Shinisaurus crocodilurus - Another venomous lizard?

Based on its phylogenetic relationship to monitor lizards (Varanidae), Gila monsters (Heloderma spp.), and the earless monitor Lanthanotus borneesis, the Chinese crocodile lizard, Shinisaurus crocodilurus, has been assigned to the Toxicofera clade, which comprises venomous reptiles. However, no data about composition and biological activities of its oral secretion have been reported. In the present study, a proteomic analysis of the mandibular gland of S. crocodilurus and, for comparison, of the herbivorous Solomon Island skink Corucia zebrata, was performed. Scanning electron microscopy (SEM) of the teeth from S. crocodilurus revealed a sharp ridge on the anterior surface, but no grooves, whereas those of C. zebrata possess a flattened crown with a pointed cusp. Proteomic analysis of their gland extracts provided no evidence of venom-derived peptides or proteins, strongly supporting the non-venomous character of these lizards. Data are available via ProteomeXchange with identifier PXD039424.

The revised reference genome of the leopard gecko ( Eublepharis macularius ) provides insight into the considerations of genome phasing and assembly

Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified that 9 of the 19 chromosomes were assembled as single contigs, while the other 10 chromosomes were each scaffolded together from two or more contigs. We qualitatively identified that percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000. The genome version and its associated annotations are also available via this Figshare repository https://doi.org/10.6084/m9.figshare.20069273 .

Cytogenetic Analysis of Seven Species of Gekkonid and Phyllodactylid Geckos

Geckos (Gekkota), the species-rich clade of reptiles with more than 2200 currently recognized species, demonstrate a remarkable variability in diploid chromosome numbers (2n = 16-48) and mode of sex determination. However, only a small fraction of gekkotan species have been studied with cytogenetic methods. Here, we applied both conventional (karyotype reconstruction and C-banding) and molecular (fluorescence in situ hybridization with probes for rDNA loci and telomeric repeats) cytogenetic analyses in seven species of geckos, namely Blaesodactylus boivini, Chondrodactylus laevigatus, Gekko badenii, Gekko cf. lionotum, Hemidactylus sahgali, Homopholis wahlbergii (Gekkonidae) and Ptyodactylus togoensis (Phyllodactylidae), in order to provide further insights into the evolution of karyotypes in geckos. Our analysis revealed the presence of interstitial telomeric repeats in four species, but we were not able to conclude if they are remnants of previous chromosome rearrangements or were formed by an accumulation of telomeric-like satellite motifs. Even though sex chromosomes were previously identified in several species from the genera Hemidactylus and Gekko by cytogenetic and/or genomic methods, they were not detected by us in any examined species. Our examined species either have poorly differentiated sex chromosomes or, possibly, environmental sex determination. Future studies should explore the effect of temperature and conduct genome-wide analyses in order to identify the mode of sex determination in these species.

Evolutionary origins of the prolonged extant squamate radiation

Squamata is the most diverse clade of terrestrial vertebrates. Although the origin of pan-squamates lies in the Triassic, the oldest undisputed members of extant clades known from nearly complete, uncrushed material come from the Cretaceous. Here, we describe three-dimensionally preserved partial skulls of two new crown lizards from the Late Jurassic of North America. Both species are placed at the base of the skink, girdled, and night lizard clade Pan-Scincoidea, which consistently occupies a position deep inside the squamate crown in both morphological and molecular phylogenies. The new lizards show that several features uniting pan-scincoids with another major lizard clade, the pan-lacertoids, in trees using morphology were convergently acquired as predicted by molecular analyses. Further, the palate of one new lizard bears a handful of ancestral saurian characteristics lost in nearly all extant squamates, revealing an underappreciated degree of complex morphological evolution in the early squamate crown. We find strong evidence for close relationships between the two new species and Cretaceous taxa from Eurasia. Together, these results suggest that early crown squamates had a wide geographic distribution and experienced complicated morphological evolution even while the Rhynchocephalia, now solely represented by the tuatara, was the dominant clade of lepidosaurs.

A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA

Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.

Convergence, divergence, and macroevolutionary constraint as revealed by anatomical network analysis of the squamate skull, with an emphasis on snakes

Traditionally considered the earliest-diverging group of snakes, scolecophidians are central to major evolutionary paradigms regarding squamate feeding mechanisms and the ecological origins of snakes. However, quantitative analyses of these phenomena remain scarce. Herein, we therefore assess skull modularity in squamates via anatomical network analysis, focusing on the interplay between ‘microstomy’ (small-gaped feeding), fossoriality, and miniaturization in scolecophidians. Our analyses reveal distinctive patterns of jaw connectivity across purported ‘microstomatans’, thus supporting a more complex scenario of jaw evolution than traditionally portrayed. We also find that fossoriality and miniaturization each define a similar region of topospace (i.e., connectivity-based morphospace), with their combined influence imposing further evolutionary constraint on skull architecture. These results ultimately indicate convergence among scolecophidians, refuting widespread perspectives of these snakes as fundamentally plesiomorphic and morphologically homogeneous. This network-based examination of skull modularity—the first of its kind for snakes, and one of the first to analyze squamates—thus provides key insights into macroevolutionary trends among squamates, with particular implications for snake origins and evolution.

Phylogenetic value of jaw elements of lacertid lizards (Squamata: Lacertoidea): a case study with Oligocene material from France

Several extinct species are known from the family Lacertidae, but due to poor preservation, many of them are based on single bones. Here, we compare phylogenetic signals of disarticulated premaxillae, maxillae and dentaries of lacertids from four French Oligocene localities (Coderet, La Colombière, Roqueprune 2, Mas de Got B). We identified five morphotypes among the premaxillae, six among the maxillae, and ten among the dentaries. These morphotypes were scored as individual taxa per locality into three separate character matrices with the same 246 characters, one matrix for each jaw element. Subsequently, the phylogenetic position of the morphotypes was tested using maximum parsimony. The consensus trees with the dentaries and the maxillae found a large polytomy including all taxa except the outgroup taxon Gekko gecko. The consensus tree with the premaxillae showed a considerably more resolved topology but found all morphotype taxa outside Lacertidae. In a second step, we compared the constitution of our three datasets and the morphotype taxa. Our results suggest that a combination of convergent characters and missing data led to the outgroup position of the premaxilla morphotype taxa. The poor resolution of the maxillae strict consensus is likely a consequence of their fragmentary preservation. For the dentaries, a high amount of missing data due to the high number of morphotype taxa most likely caused the poor tree resolution. Indeed, tests with fewer morphotypes found tree resolutions comparable to the premaxilla data. When linking the morphotypes, five possible lacertid "species" were found. Comparison with already known French Oligocene lacertid species points to a slightly higher species richness of Lacertidae at that time than known before. Reliable species classification based on phylogeny only seems possible when combining the jaw elements or in association with other cranial and postcranial material, putting some doubt on species identifications based on single bones.

The Review of the Autotomy of Agamid Lizards with Considerations about the Types of Autotomy and Regeneration

We present a review of the data on the intervertebral autotomy and regeneration of agamid lizards based on an analysis of information obtained over a 35-year period after the publication of thorough reviews (Arnold, 1984, 1988 and Bellairs, Bryant, 1985). It is supplemented by our own studies of 869 specimens of agamid lizards (Sauria, Agamidae) stored in the herpetological collections of the Zoological Institute of the Russian Academy of Sciences (St. Petersburg, Russia) and the Zoological Museum of the Moscow State University (Moscow, Russia), represented by 31 species of 16 genera. The manifestations of the ability for autotomy and regeneration in phylogenetic lineages within the family—Leiolepidinae, Amphibolurinae, Agaminae, Draconinae—are considered. A comparative morphological analysis of the structure of the caudal vertebrae was carried out using the Computer Microtomography Methods (micro-CT) in the following ecomorphological types of agama: (1) with developed abilities to caudal autotomy and regeneration, (2) with the ability to caudal autotomy but without regeneration and (3) without the ability to autotomy. The phenomenon of intervertebral autotomy (urotomy) in snakes is considered too. Possible ways of evolution of the ability to caudal autotomy as a defense strategy against predators are discussed in the phylogenetic context.

Ultrastructure of eggshell and embryological development of Salvator merianae (Squamata: Teiidae)

The objective of this study was to characterize the external morphology of Salvator meriane embryos in different stages of embryonic development and establish a relationship with the ultrastructure of the shell from oviductal transit to hatching. A total of 120 embryos were analyzed to describe their external morphology, and 78 eggs were used for the analysis of the shell. For embryonic development, the series was established according to the total length of the body. We established 40 embryonic stages from the primitive streak. In the early stages, the external morphological features are the C-shaped body, the maxillary, and mandibular fusion processes with the frontal process and the fusion of the forelimb with the digital plate. In the middle stages, the eyelid appears, and there are claws on the toes, cornification of fingers, and the onset of pigmentation. The last stage of embryonic development is characterized by the beginning of the formation of the scales, appear the toenails, and finalize the entire pigmentation. Regarding the relationship that exists with the ultrastructure of the egg during development, it was possible to observe a marked change in the composition of the shell and well-marked compaction during embryonic development, which may be related to the transport of calcium during embryonic ossification. Our results allowed us to show the complete sequence of embryonic development, determining the laying stage for this species. It was possible to establish a relationship with the ultrastructure of the eggshell from the oviductal transit to the moment of hatching.

Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).].

Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?

Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these data sets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data ($\sim $5000 loci) and subsampled data sets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic data sets (e.g., length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several "best practices" for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the phylogenetic results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses. [Alignment; concatenated analysis; phylogenomics; sequence length heterogeneity; species-tree analysis; trimming].

Embryonic skull development in the gecko, Tarentola annularis (Squamata: Gekkota: Phyllodactylidae)

Tarentola annularis is a climbing gecko with a wide distribution in Africa north of the equator. In the present paper, we describe the development of the osteocranium of this lizard, from the first appearance of the cranial elements up to the point of hatching. This is based on a combination of histology and cleared and stained specimens. This is the first comprehensive account of gekkotan pre-hatching skull development based on a comprehensive series of embryos, rather than a few selected stages. Given that Gekkota is now widely regarded as representing the sister group to other squamates, this account helps to fill a significant gap in the literature. Moreover, as many authors have considered features of the gekkotan skull and skeleton to be indicative of paedomorphosis, it is important to know whether this hypothesis is supported by delays in the onset of cranial ossification. In fact, we found the sequence of cranial bone ossification to be broadly comparable to that of other squamates studied to date, with no significant lags in development.

Squamate egg tooth development revisited using three-dimensional reconstructions of brown anole (Anolis sagrei, Squamata, Dactyloidae) dentition

The egg tooth is a hatching adaptation, characteristic of all squamates. In brown anole embryos, the first tooth that starts differentiating is the egg tooth. It develops from a single tooth germ and, similar to the regular dentition of all the other vertebrates, the differentiating egg tooth of the brown anole passes through classic morphological and developmental stages named according to the shape of the dental epithelium: epithelial thickening, dental lamina, tooth bud, cap and bell stages. The differentiating egg tooth consists of three parts: the enamel organ, hard tissues and dental pulp. Shortly before hatching, the egg tooth connects with the premaxilla. Attachment tissue of the egg tooth does not undergo mineralization, which makes it different from the other teeth of most squamates. After hatching, odontoclasts are involved in resorption of the egg tooth's remains. This study shows that the brown anole egg tooth does not completely conform to previous reports describing iguanomorph egg teeth and reveals a need to investigate its development in the context of squamate phylogeny.

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.

The atlas-axis complex in Dibamidae (Reptilia: Squamata) and their potential relatives: The effect of a fossorial lifestyle on the morphology of this skeletal bridge

We report on the first detailed study of the atlas-axis complex in the lizard clade Dibamidae, a family of poorly known fossorial squamates distributed in tropical or subtropical climates. This skeletal bridge is characterized by several features, such as the complete absence of the first intercentrum or the appearance of the first free cervical rib on the axis (usually less developed in Dibamus relative to that in Anelytropsis). Our study shows morphological differences of the atlas-axis complex in the Mexican blind lizard Anelytropsis relative to those of Asian Dibamus, the only two known extant genera of this clade. With regard to taxonomy and phylogenetic topology of the Dibamidae within Squamata, a huge conflict exists between morphology versus molecules. The morphology of the atlas-axis complex is therefore compared with several potential sister clades + Sphenodon. Dibamids share several features with limbless Gekkota, Scincoidea, and Amphisbaenia. The complete absence of the first intercentrum is observed in Rhineura floridana and in Ateuchosaurus chinensis as well, and the free rib associated with the synapophyses of the axis is also present in Acontias meleagris. However, some of these features may result from a limbless, burrowing ecology and thus could represent homoplastic characters. In any case, the morphology of the atlas-axis shows that dibamids share most character states with skinks. Although the atlas-axis complex forms only an additional source of information, this conclusion is consistent with most morphological rather than molecular tree topologies.

Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

The first potential fossil record of a dibamid reptile (Squamata: Dibamidae): a new taxon from the early Oligocene of Central Mongolia

Dibamid reptiles have a known current distribution on two continents (Asia and North America). Although this clade represents an early-diverging group in the Squamata and thus should have a long evolutionary history, no fossil record of these peculiar burrowing squamate reptiles has been documented so far. The fossil material described here comes from the early Oligocene of the Valley of Lakes in Central Mongolia. This material consists of jaws and is placed in the clade Dibamidae on the basis of its morphology, which is further confirmed by phylogenetic analyses. In spite of the fragmentary nature of this material, it thus forms the first, but putative, fossil evidence of this clade. If correctly interpreted, this material demonstrates the occurrence of Dibamidae in East Asia in the Palaeogene, indicating its distribution in higher latitudes than today. The preserved elements possess a unique combination of character states, and a new taxon name is therefore erected: Hoeckosaurus mongoliensis sp. nov. The dentary of Hoeckosaurus exhibits some characters of the two extant dibamid taxa. However, the open Meckel’s groove, together with other characters, show that this group was morphologically much more diverse in the past.

Discovery of a deeply divergent new lineage of vine snake (Colubridae: Ahaetuliinae: Proahaetulla gen. nov.) from the southern Western Ghats of Peninsular India with a revised key for Ahaetuliinae

The Western Ghats are well known as a biodiversity hotspot, but the full extent of its snake diversity is yet to be uncovered. Here, we describe a new genus and species of vine snake Proahaetulla antiqua gen. et sp. nov., from the Agasthyamalai hills in the southern Western Ghats. It was found to be a member of the Ahaetuliinae clade, which currently comprises the arboreal snake genera Ahaetulla, Dryophiops, Dendrelaphis and Chrysopelea, distributed in South and Southeast Asia. Proahaetulla shows a sister relationship with all currently known taxa belonging to the genus Ahaetulla, and shares ancestry with Dryophiops. In addition to its phylogenetic position and significant genetic divergence, this new taxon is also different in morphology from members of Ahaetuliinae in a combination of characters, having 12-13 partially serrated keels on the dorsal scale rows, 20 maxillary teeth and 3 postocular scales. Divergence dating reveals that the new genus is ancient, dating back to the Mid-Oligocene, and is one of the oldest persisting monotypic lineages of snakes in the Western Ghats. This discovery adds to the growing list of ancient lineages endemic to the Agasthyamalai hills and underscores the biogeographic significance of this isolated massif in the southern Western Ghats.

Gecko Adhesion in Space and Time: A Phylogenetic Perspective on the Scansorial Success Story

An evolutionary perspective on gecko adhesion was previously hampered by a lack of an explicit phylogeny for the group and of robust comparative methods to study trait evolution, an underappreciation for the taxonomic and structural diversity of geckos, and a dearth of fossil evidence bearing directly on the origin of the scansorial apparatus. With a multigene dataset as the basis for a comprehensive gekkotan phylogeny, model-based methods have recently been employed to estimate the number of unique derivations of the adhesive system and its role in lineage diversification. Evidence points to a single basal origin of the spinulate oberhautchen layer of the epidermis, which is a necessary precursor for the subsequent elaboration of a functional adhesive mechanism in geckos. However, multiple gains and losses are implicated for the elaborated setae that are necessary for adhesion via van der Waals forces. The well-supported phylogeny of gekkotans has demonstrated that convergence and parallelism in digital design are even more prevalent than previously believed. It also permits the reexamination of previously collected morphological data in an explicitly evolutionary context. Both time-calibrated trees and recently discovered amber fossils that preserve gecko toepads suggest that a fully-functional adhesive apparatus was not only present, but also represented by diverse architectures, by the mid-Cretaceous. Further characterization and phylogenetically-informed analyses of the other components of the adhesive system (muscles, tendons, blood sinuses, etc.) will permit a more comprehensive reconstruction of the evolutionary pathway(s) by which geckos have achieved their structural and taxonomic diversity. A phylogenetic perspective can meaningfully inform functional and performance studies of gecko adhesion and locomotion and can contribute to advances in bioinspired materials.

Duplications in Corneous Beta Protein Genes and the Evolution of Gecko Adhesion

Corneous proteins are an important component of the tetrapod integument. Duplication and diversification of keratins and associated proteins are linked with the origin of most novel integumentary structures like mammalian hair, avian feathers, and scutes covering turtle shells. Accordingly, the loss of integumentary structures often coincides with the loss of genes encoding keratin and associated proteins. For example, many hair keratins in dolphins and whales have become pseudogenes. The adhesive setae of geckos and anoles are composed of both intermediate filament keratins (IF-keratins, formerly known as alpha-keratins) and corneous beta-proteins (CBPs, formerly known as beta-keratins) and recent whole genome assemblies of two gecko species and an anole uncovered duplications in seta-specific CBPs in each of these lineages. While anoles evolved adhesive toepads just once, there are two competing hypotheses about the origin(s) of digital adhesion in geckos involving either a single origin or multiple origins. Using data from three published gecko genomes, I examine CBP gene evolution in geckos and find support for a hypothesis where CBP gene duplications are associated with the repeated evolution of digital adhesion. Although these results are preliminary, I discuss how additional gecko genome assemblies, combined with phylogenies of keratin and associated protein genes and gene duplication models, can provide rigorous tests of several hypotheses related to gecko CBP evolution. This includes a taxon sampling strategy for sequencing and assembly of gecko genomes that could help resolve competing hypotheses surrounding the origin(s) of digital adhesion.

Pectoral myology of limb-reduced worm lizards (Squamata, Amphisbaenia) suggests decoupling of the musculoskeletal system during the evolution of body elongation

Background

The evolution of elongated body forms in tetrapods has a strong influence on the musculoskeletal system, including the reduction of pelvic and pectoral girdles, as well as the limbs. However, despite extensive research in this area it still remains unknown how muscles within and around bony girdles are affected by these reductions. Here we investigate this issue using fossorial amphisbaenian reptiles, or worm lizards, as a model system, which show substantial variation in the degree of reductions of girdles and limbs. Using iodine-based contrast-enhanced computed tomography (diceCT), we analyze the composition of the shoulder muscles of the main clades of Amphisbaenia and their outgroups relative to the pectoral skeleton.

Results

All investigated amphisbaenian taxa retain the full set of 17 shoulder muscles, independent of the degree of limb and girdle reductions, whereas in some cases muscles are fused to complexes or changed in morphology relative to the ancestral condition. Bipes is the only taxon that retains forelimbs and an almost complete pectoral girdle. All other amphisbaenian families show more variation concerning the completeness of the pectoral girdle having reduced or absent girdle elements. Rhineura, which undergoes the most severe bone reductions, differs from all other taxa in possessing elongated muscle strands instead of discrete shoulder muscles. In all investigated amphisbaenians, the shoulder muscle agglomerate is shortened and shifted anteriorly relative to the ancestral position as seen in the outgroups.

Conclusions

Our results show that pectoral muscle anatomy does not necessarily correspond to the loss or reduction of bones, indicating a decoupling of the musculoskeletal system. Muscle attachment sites change from bones to non-skeletal areas, such as surrounding muscles, skin or connective tissue, whereas muscle origins themselves remain in the same region where the pectoral bones were ancestrally located. Our findings indicate a high degree of developmental autonomy within the musculoskeletal system, we predict that the observed evolutionary rearrangements of amphisbaenian shoulder muscles were driven by functional demands rather than by developmental constraints. Nevertheless, worm lizards display a spatial offset of both pectoral bones and muscles relative to the ancestral position, indicating severe developmental modifications of the amphisbaenian body axis.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1303-1) contains supplementary material, which is available to authorized users.

Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata

Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.

Novel Approaches for Phylogenetic Inference from Morphological Data and Total-Evidence Dating in Squamate Reptiles (Lizards, Snakes, and Amphisbaenians)

Here, I combine previously underutilized models and priors to perform more biologically realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backward transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for “asymmetric.” The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical data sets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend toward recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across data sets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological data sets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.

Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates.

Enter the Dragon: The Dynamic and Multifunctional Evolution of Anguimorpha Lizard Venoms

While snake venoms have been the subject of intense study, comparatively little work has been done on lizard venoms. In this study, we have examined the structural and functional diversification of anguimorph lizard venoms and associated toxins, and related these results to dentition and predatory ecology. Venom composition was shown to be highly variable across the 20 species of Heloderma, Lanthanotus, and Varanus included in our study. While kallikrein enzymes were ubiquitous, they were also a particularly multifunctional toxin type, with differential activities on enzyme substrates and also ability to degrade alpha or beta chains of fibrinogen that reflects structural variability. Examination of other toxin types also revealed similar variability in their presence and activity levels. The high level of venom chemistry variation in varanid lizards compared to that of helodermatid lizards suggests that venom may be subject to different selection pressures in these two families. These results not only contribute to our understanding of venom evolution but also reveal anguimorph lizard venoms to be rich sources of novel bioactive molecules with potential as drug design and development lead compounds.

Phylotranscriptomic consolidation of the jawed vertebrate timetree

Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large curated nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.

Evolution of developmental sequences in lepidosaurs

BACKGROUND

Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny.

METHODS

We used developmental sequences of 20 events in 29 species of lepidosaurs. These sequences were analysed using event-pairing and continuous analysis. They were transformed into cladistic characters and analysed in TNT. Ancestral state reconstructions were performed on two main phylogenetic hypotheses of squamates (morphological and molecular).

RESULTS

Cladistic analyses conducted using characters generated by these methods do not resemble any previously published phylogeny. Ancestral state reconstructions are equally consistent with both morphological and molecular hypotheses of squamate phylogeny. Only several inferred heterochronic events are common to all methods and phylogenies.

DISCUSSION

Results of the cladistic analyses, and the fact that reconstructions of heterochronic events show more similarities between certain methods rather than phylogenetic hypotheses, suggest that phylogenetic signal is at best weak in the studied developmental events. Possibly the developmental sequences analysed here evolve too quickly to recover deep divergences within Squamata.