A phylogenomic analysis of turtles

Trophic convergence of marine vertebrate communities worldwide

Biogeographic regions arise due to constraints on species ranges, fostering lineage divergence as a result. Yet, convergent evolution means that evolutionary distinct lineages can share similar characteristics when subjected to similar environmental conditions. The ecological convergence of distinct regions has been demonstrated in terrestrial communities, but it remains uncertain if marine systems exhibit similar patterns, given the greater ease of dispersal in the ocean. Using information on the dietary preferences of marine vertebrates, we develop an ocean regionalization that groups regions with similar trophic communities, describing how species are organized into trophic guilds and how guilds overlap with one another. Six types of trophic communities emerge globally, largely explained by temperature, productivity, and depth. Regions with analogous environments support similar numbers of species with analogous feeding strategies, even if the species do not share the same evolutionary origins. These findings support the notion that independently evolving sets of marine species can converge into functionally analogous trophic communities when exposed to similar environmental conditions. They also provide a benchmark for studying the functional consequences of global environmental change.

Skin Appendage Proteins of Tetrapods: Building Blocks of Claws, Feathers, Hair and Other Cornified Epithelial Structures

Reptiles, birds, mammals and amphibians, together forming the clade tetrapods, have a large diversity of cornified skin appendages, such as scales, feathers, hair and claws. The skin appendages consist of dead epithelial cells that are tightly packed with specific structural proteins. Here, we review the molecular diversity and expression patterns of major types of skin appendage proteins, namely keratin intermediate filament proteins, keratin-associated proteins (KRTAPs) and proteins encoded by genes of the epidermal differentiation complex (EDC), including corneous beta-proteins, also known as beta-keratins. We summarize the current knowledge about the components of skin appendages with a focus on keratins and EDC proteins that have recently been identified in reptiles and birds. We discuss gaps of knowledge and suggest directions of future research.

Macro- and microscopic anatomy of the digestive tract in the red-eared slider (Emydidae: Trachemys scripta elegans)

The red-eared sliders (Emydidae: Trachemys scripta) is characterised by a high adaptability to a variety of environment and threatens the habitat of Japanese native species. The ability to digest a variety of diets may attribute to the high adaptive capacity of this species to various environments, however, the digestive morphology remains scarcely described in red-eared sliders. In this study, we investigated the macro- and microscopic anatomy of the esophagus, stomach, small intestine, and large intestine in red-eared sliders. All segments of the digestive tract had longitudinal mucosal folds, the height and width of which varied in each segment of the digestive tract. The stomach had the highest and widest mucosal folds. The mucosal folds in the proximal-to-middle small intestine exhibited a zigzag shape, whereas those in the distal small intestine were linear. The wall of the digestive tract regularly consisted of mucosa, submucosa, tunica muscularis, and tunica adventitia or serosa. In each segment of the digestive tract, the epithelial structure was different. The esophagus and small intestine were lined by the pseudostratified columnar epithelium. In both segments, the basal part of the pseudostratified epithelium included proliferating cell nuclear antigen (PCNA)-positive proliferating cells. The stomach and large intestine were lined by the simple columnar epithelium. In the stomach and large intestine, PCNA-positive proliferating cells were present in the neck of the proper gastric gland and crypt-like structures, respectively. The proper gastric gland was composed of oxynticopeptic and mucous cells. This study revealed the detailed macro- and microscopic anatomy of the digestive tract in red-eared sliders. Overall, our findings may provide an anatomical basis for understanding the relationship between morphology and function in the digestive tract of turtles.

Variations in humeral and femoral strains across body sizes and limb posture in American alligators

Bone loading is a crucial factor that constrains locomotor capacities of terrestrial tetrapods. To date, limb bone strains and stresses have been studied across various animals, with a primary emphasis on consistent bone loading in mammals of different sizes and variations in loading regimes across different clades and limb postures. However, the relationships between body size, limb posture and limb bone loading remain unclear in animals with non-parasagittally moving limbs, limiting our understanding of the evolution of limb functions in tetrapods. To address this, we investigated in vivo strains of the humerus and femur in juvenile to subadult American alligators as they walked with various limb postures. We found that principal strains on the ventromedial cortex of the femoral midshaft increased with larger sizes among the three individuals displaying similar limb postures. This indicates that larger individuals experience greater limb bone strains when maintaining similar limb postures to smaller individuals. Axial and shear strains in the humerus were generally reduced with a more erect limb posture, while trends in the femur varied among individuals. Given that larger alligators have been shown to adopt a more erect limb posture, the transition from sprawling to erect limb posture, particularly in the forelimb, might be linked to the evolution of larger body sizes in archosaurs, potentially as a means to mitigate limb bone loading. Moreover, both the humerus and femur experienced decreased shear loads compared with axial loads with a more erect limb posture, suggesting proportional changes in bone loading regimes throughout the evolution of limb posture.

De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes

Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq: Apalone spinifera (ZZ/ZW, 2n = 66) and Staurotypus triporcatus (XX/XY, 2n = 54). We detected differences in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear genomes. Namely, whole-genome comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of genome reshuffling in Apalone (Trionychidae) whose karyotype is highly conserved when compared to chicken (likely ancestral for turtles), and (2) a moderate rate of fusions/fissions in Staurotypus (Kinosternidae) and Trachemys scripta (Emydidae). Furthermore, we identified a chromosome folding pattern that enables "centromere-telomere interactions" previously undetected in turtles. The combined turtle pattern of "centromere-telomere interactions" (discovered here) plus "centromere clustering" (previously reported in sauropsids) is novel for amniotes and it counters previous hypotheses about amniote 3D chromatin structure. We hypothesize that the divergent pattern found in turtles originated from an amniote ancestral state defined by a nuclear configuration with extensive associations among microchromosomes that were preserved upon the reshuffling of the linear genome.

Chromosome-level genome of diamondback terrapin provides insight into the genetic basis of salinity adaptation

Diamondback terrapins (Malaclemys terrapin centrata) exhibit strong environmental adaptability and live in both freshwater and saltwater. However, the genetic basis of this adaptability has not been the focus of research. In this study, we successfully constructed a ∼2.21-Gb chromosome-level genome assembly for M. t. centrata using high-coverage and high-depth genomic sequencing data generated on multiple platforms. The M. t. centrata genome contains 25 chromosomes and the scaffold N50 of ∼143.75 Mb, demonstrating high continuity and accuracy. In total, 53.82% of the genome assembly was composed of repetitive sequences, and 22 435 protein-coding genes were predicted. Our phylogenetic analysis indicated that M. t. centrata was closely related to the red-eared slider turtle (Trachemys scripta elegans), with divergence approximately ∼23.6 million years ago (Mya) during the early Neogene period of the Cenozoic era. The population size of M. t. centrata decreased significantly over the past ∼14 Mya during the Cenozoic era. Comparative genomic analysis indicated that 36 gene families related to ion transport were expanded and several genes (AQP3, solute carrier subfamily, and potassium channel genes) underwent specific amino acid site mutations in the M. t. centrata genome. Changes to these ion transport-related genes may have contributed to the remarkable salinity adaptability of diamondback terrapin. The results of this study not only provide a high-quality reference genome for M. t. centrata but also elucidate the possible genetic basis for salinity adaptation in this species.

Effect of egg incubator temperature on sex differentiation in Korat chickens

The effect of incubator temperature on sex differentiation in Korat chickens was investigated. The experiments were divided into two sets: temperature applied throughout the entire incubation period and temperature applied during certain periods (days 3-6 of incubation) by either increasing above the standard or decreasing below the standard temperature. In each experiment, 300 Korat chicken eggs were separated into three groups of 5 repetitions, with 20 eggs in each group. This was done using a completely randomized design for each experiment: a group using a temperature below the standard for incubation (36.0 °C), a group using the standard incubation temperature (37.7 °C), and a group using a temperature above the standard for incubation (38.0 °C). W chromosomes were detected at hatch; histology examined reproductive structures after 35 days. Increasing the temperature to 38.0 °C throughout the entire incubation period resulted in no significant difference in hatching rates compared to the standard temperature (P > 0.05). Raising the temperature to 38.0 °C throughout the entire incubation and during certain periods resulted in changes in the reproductive structure of chickens, leading to a mismatch between chromosomal and gonadal sex, observed at 9.7% and 5.9% of individuals with W chromosomes possessed testes, indicating a mismatch between chromosomal and gonadal sex. However, decreasing the temperature to 36.0 °C throughout the incubation period resulted in lower hatching rates compared to the standard temperature (P < 0.05). Incubating eggs at 36.0 °C for specific periods resulted in 19.4% of genetic males developing ovaries instead of testes. The presence of ovaries in individuals without W chromosomes indicated this mismatch. The results of this study provide evidence that temperature plays a role in sex differentiation in Korat chickens, as demonstrated by the detection of W chromosomes and histological studies of testes and ovaries. Moreover, this study presents the first evidence in broilers that temperature can affect sex differentiation.

Skull osteology, neuroanatomy, and jaw-related myology of the pig-nosed turtle Carettochelys insculpta (Cryptodira, Trionychia)

The osteology, neuroanatomy, and musculature are known for most primary clades of turtles (i.e., "families"), but knowledge is still lacking for one particular clade, the Carettochelyidae. Carettochelyids are represented by only one living taxon, the pig-nosed turtle Carettochelys insculpta. Here, we use micro-computed tomography of osteological and contrast-enhanced stained specimens to describe the cranial osteology, neuroanatomy, circulatory system, and jaw musculature of Carettochelys insculpta. The jaw-related myology is described in detail for the first time for this taxon, including m. zygomaticomandibularis, a muscular unit only found in trionychians. We also document a unique arterial pattern for the internal carotid artery and its subordinate branches and provide an extensive list of osteological ontogenetic differences. The present work provides new insights into the craniomandibular anatomy of turtles and will allow a better understanding of the evolutionary history of the circulatory system of trionychians and intraspecific variation among turtles.

The topological organization of the turtle cranium is constrained and conserved over long evolutionary timescales

The cranium of turtles (Testudines) is characterized by the secondary reduction of temporal fenestrae and loss of cranial joints (i.e., characteristics of anapsid, akinetic skulls). Evolution and ontogeny of the turtle cranium are associated with shape changes. Cranial shape variation among Testudines can partially be explained by dietary and functional adaptations (neck retraction), but it is unclear if cranial topology shows similar ecomorphological signal, or if it is decoupled from shape evolution. We assess the topological arrangement of cranial bones (i.e., number, relative positioning, connections), using anatomical network analysis. Non-shelled stem turtles have similar cranial arrangements to archosauromorph outgroups. Shelled turtles (Testudinata) evolve a unique cranial organization that is associated with bone losses (e.g., supratemporal, lacrimal, ectopterygoid) and an increase in complexity (i.e., densely and highly interconnected skulls with low path lengths between bones), resulting from the closure of skull openings and establishment of unusual connections such as a parietal-pterygoid contact in the secondary braincase. Topological changes evolutionarily predate many shape changes. Topological variation and taxonomic morphospace discrimination among crown turtles are low, indicating that cranial topology may be constrained. Observed variation results from repeated losses of nonintegral bones (i.e., premaxilla, nasal, epipterygoid, quadratojugal), and changes in temporal emarginations and palate construction. We observe only minor ontogenetic changes. Topology is not influenced by diet and habitat, contrasting cranial shape. Our results indicate that turtles have a unique cranial topology among reptiles that is conserved after its initial establishment, and shows that cranial topology and shape have different evolutionary histories.

PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era

The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, prior to core analyses, traditional methods typically involve intricate and time-consuming procedures, including assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple sequence alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive data sets. In this study, we develop PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as a reference for phylogenetic and evolutionary analyses. Through testing with simulated data sets of species spanning the tree of life, PhyloAln demonstrates consistently robust performance compared with other reference-based tools across different data types, sequencing technologies, coverages, and species, with percent completeness and identity at least 50 percentage points higher in the alignments. Additionally, we validate the efficacy of PhyloAln in removing a minimum of 90% foreign and 70% cross-contamination issues, which are prevalent in sequencing data but often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments (completeness mostly larger than 80%, identity larger than 90%) and reconstructing robust phylogenies using real data sets of transcriptomes of ladybird beetles, plastid genes of peppers, or ultraconserved elements of turtles. With these advantages, PhyloAln is expected to facilitate phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.

Developmental energetics in the oviparous corn snake, Pantherophis guttatus, confirms a conservative evolutionary pattern in snakes

Eggs of oviparous reptiles are ideal models for studying evolutionary patterns of embryonic metabolism since they allow tracking of energy allocation during development. Analyzing oxygen consumption of whole eggs throughout development indicates three patterns among reptiles. Embryos initially grow and consume oxygen exponentially, but oxygen consumption slows, or drops before hatching in some species. Turtles, crocodilians, and most lizards follow curves with initial exponential increases followed by declines, whereas embryonic snakes that have been studied exhibit a consistently exponential pattern. This study measured oxygen consumption of corn snake, Pantherophis guttatus, embryos to determine if this species also exhibits an exponential increase in oxygen consumption. Individual eggs, sampled weekly from oviposition to hatching, were placed in respirometry chambers for 24-h during which oxygen consumption was recorded. Embryos were staged and carcasses and yolk were weighed separately. Results indicate steady inclines in oxygen consumption during early stages of development, with a rapid increase prior to hatching. The findings support the hypothesis that embryonic oxygen consumption of snakes differs from most other non-avian reptiles. Total energy required for development was determined based on calorimetry of initial yolk compared to hatchlings and residual yolk and by integration of the area under the curve plotting oxygen consumption versus age of embryos. The cost of development estimates based on these two methods were 6.4 and 10.0 kJ, respectively. Our results emphasize the unique physiological aspects of snake embryogenesis and illustrate how the study of physiological characteristics can contribute to the broader understanding of reptilian evolution.

The Role of Locomotory Ancestry on Secondarily Aquatic Transitions

Land-to-sea evolutionary transitions are great transformations where terrestrial amniote clades returned to aquatic environments. These secondarily aquatic amniote clades include charismatic marine mammal and marine reptile groups, as well as countless semi-aquatic forms that modified their terrestrial locomotor anatomy to varying degrees to be suited for swimming via axial and/or appendicular propulsion. The terrestrial ancestors of secondarily aquatic groups would have started off swimming strikingly differently from one another given their evolutionary histories, as inferred by the way modern terrestrial amniotes swim. With such stark locomotor functional differences between reptiles and mammals, we ask if this impacted these transitions. Axial propulsion appears favored by aquatic descendants of terrestrially sprawling quadrupedal reptiles, with exceptions. Appendicular propulsion is more prevalent across the aquatic descendants of ancestrally parasagittal-postured mammals, particularly early transitioning forms. Ancestral terrestrial anatomical differences that precede secondarily aquatic invasions between mammals and reptiles, as well as the distribution of axial and appendicular swimming in secondarily aquatic clades, may indicate that ancestral terrestrial locomotor anatomy played a role, potentially in both constraint and facilitation, in certain aquatic locomotion styles. This perspective of the land-to-sea transition can lead to new avenues of functional, biomechanical, and developmental study of secondarily aquatic transitions.

Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences

The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021-2040 and 2061-2080 compared with the current distribution. The present study indicates that proper conservation management requires greater attention to the causes and solutions to the fragmented distribution and safeguarding of this endangered species in the Indus, Ganges, and Brahmaputra (IGB) river basins.

Description of trunk neural crest migration and peripheral nervous system formation in the Egyptian cobra Naja haje haje

The neural crest is a stem cell population that forms in the neurectoderm of all vertebrates and gives rise to a diverse set of cells such as sensory neurons, Schwann cells and melanocytes. Neural crest development in snakes is still poorly understood. From the point of view of evolutionary and comparative anatomy is an interesting topic given the unique anatomy of snakes. The aim of the study was to characterize how trunk neural crest cells (TNCC) migrate in the developing elapid snake Naja haje haje and consequently, look at the beginnings of development of neural crest derived sensory ganglia (DRG) and spinal nerves. We found that trunk neural crest and DRG development in Naja haje haje is like what has been described in other vertebrates and the colubrid snake strengthening our knowledge on the conserved mechanisms of neural crest development across species. Here we use the marker HNK1 to follow the migratory behavior of TNCC in the elapid snake Naja haje haje through stages 1-6 (1-9 days postoviposition). We observed that the TNCC of both snake species migrate through the rostral portion of the somite, a pattern also conserved in birds and mammals. The development of cobra peripheral nervous system, using neuronal and glial markers, showed the presence of spectrin in Schwann cell precursors and of axonal plexus along the length of the cobra embryos. In conclusion, cobra embryos show strong conserved patterns in TNCC and PNS development among vertebrates.

An armoured marine reptile from the Early Triassic of South China and its phylogenetic and evolutionary implications

Sauropterygia was a taxonomically and ecomorphologically diverse clade of Mesozoic marine reptiles spanning the Early Triassic to the Late Cretaceous. Sauropterygians are traditionally divided into two groups representing two markedly different body plans - the short-necked, durophagous Placodontia and the long-necked Eosauropterygia - whereas Saurosphargidae, a small clade of armoured marine reptiles, is generally considered as the sauropterygian sister-group. However, the early evolutionary history of sauropterygians and their phylogenetic relationships with other groups within Diapsida are still incompletely understood. Here, we report a new saurosphargid from the Early Triassic (Olenekian) of South China - Prosaurosphargis yingzishanensis gen. et sp. nov. - representing the earliest known occurrence of the clade. An updated phylogenetic analysis focussing on the interrelationships among diapsid reptiles recovers saurosphargids as nested within sauropterygians, forming a clade with eosauropterygians to the exclusion of placodonts. Furthermore, a clade comprising Eusaurosphargis and Palatodonta is recovered as the sauropterygian sister-group within Sauropterygomorpha tax. nov. The phylogenetic position of several Early and Middle Triassic sauropterygians of previously uncertain phylogenetic affinity, such as Atopodentatus, Hanosaurus, Majiashanosaurus, and Corosaurus, is also clarified, elucidating the early evolutionary assembly of the sauropterygian body plan. Finally, our phylogenetic analysis supports the placement of Testudines and Archosauromorpha within Archelosauria, a result strongly corroborated by molecular data, but only recently recovered in a phylogenetic analysis using a morphology-only dataset. Our study provides evidence for the rapid diversification of sauropterygians in the aftermath of the Permo-Triassic mass extinction event and emphasises the importance of broad taxonomic sampling in reconstructing phylogenetic relationships among extinct taxa.

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.

Phylogenomics, evolution of trophic traits and divergence times of hemiodontid fishes (Ostariophysi: Characiformes)

The South American characiform family Hemiodontidae comprises five genera and 34 species. The family lacks comprehensive phylogenetic hypotheses resolving its species relationships. The studies that addressed these questions exhibited a narrow taxon sampling or used single-locus markers. Herein we surveyed hundreds of ultraconserved elements (UCEs) loci to provide the first molecular phylogenetic hypothesis and divergence time estimates for hemiodontids encompassing all its genera and most species (27 of the 34 valid species). We also tracked the history of the protractile upper jaw in the genera Argonectes and Bivibranchia across the recovered phylogenies through ancestral state reconstruction. Our results corroborate the monophyly of Hemiodontidae and the genera Argonectes and Bivibranchia in all phylogenetic methods with maximum clade support. The genera Anodus and Hemiodus were not monophyletic because Anodus elongatus was sister to the monotypic Micromischodus instead of A. orinocensis, and H. immaculatus did not form a clade with its other congeners, but instead was sister to the clade including Anodus and Micromischodus. All remaining species of Hemiodus were placed together into a monophyletic group, where they were arranged into four major subclades. The relationship in the family is summarised as: (Bivibranchia, (Argonectes, ((H. immaculatus, (Anodus, Micromischodus)), Hemiodus clade))), in discordance with the morphological phylogeny that placed all genera monophyletic and resolved the family as: ((Anodus, Micromischodus), (Hemiodus, (Argonectes, Bivibranchia))). The origin of Hemiodontidae was estimated from the Late Cretaceous to the Middle Paleogene, with the mean age in the Paleocene, while the origin of most hemiodontid genera except Bivibranchia occurred in the Miocene. Unordered parsimony and likelihood reconstruction indicates that Argonectes and Bivibranchia developed their protractile upper jaw independently.

The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini)

North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.

Topological analysis of vertebrate phylogenetic trees utilizing Horton's first law

Phylogenetic trees visually represent evolution and diversification. While many studies have focused on the number and length of edges (branches), topological properties, such as edge connection patterns, are also important. In this study, the topological properties of phylogenetic trees were quantified, focusing on edge connection patterns. Horton's first law was applied to quantify the overall, rather than local, topological properties of phylogenetic trees. The topological properties of vertebrate phylogenetic trees for spiny-rayed fishes, Amphibians, turtles, Squamata, Aves, and placental mammals were analyzed. The topological features discussed herein include the number of first-order edges, maximum order, and bifurcation ratio. The average bifurcation ratio of all trees was approximately 3, suggesting that phylogenetic trees for different taxa have a common mechanism of evolution. Vertebrate phylogenetic trees were compared with artificial branching objects created from neutral stochastic branching model simulations. The topological properties of the actual vertebrate phylogenetic trees agreed with those of the artificial branching objects. Our study suggests that evolutionary events do not change the overall topological properties of actual phylogenetic trees, even if the number and length of the edges change. Specifically, non-neutral events (e.g., environmental changes and mass extinction) are not main factors associated with topological properties. The results instead demonstrate a relationship between the bifurcation ratio and symmetricity in the context of temporal changes of topological properties. When the number of first-order edges increased and the maximum order remained constant, the bifurcation ratio increased and symmetricity decreased. When the number of first-order edges increased and the maximum order increased by one, the bifurcation ratio decreased and symmetricity increased.

A quantum leap in the evolution of platyhelminths: host-switching from turtles to hippopotamuses illustrated from a phylogenetic meta-analysis of polystomes (Monogenea, Polystomatidae)

While monogenean worms are mainly parasites of the gills and skin of fish, and to a lesser extent parasites of the oral cavity, urinary bladder, and/or conjunctival sacs of amphibians and freshwater turtles, Oculotrema hippopotami Stunkard, 1924 is the single monogenean polystome reported from a mammal, the common hippopotamus (Hippopotamus amphibius Linnaeus). Several hypotheses have been suggested in the last decade to explain the origin of this enigmatic parasite which infects the conjunctival sacs of H. amphibius. Based on a molecular phylogeny inferred from nuclear (28S and 18S) and mitochondrial (12S and COI) sequences of O. hippopotami and chelonian polystomes, we found a sister group relationship between O. hippopotami and Apaloneotrema moleri (Du Preez & Morrison, 2012). This result suggests lateral parasite transfer between freshwater turtles and hippopotamuses, thus likely reflecting one of the most exceptional known examples of host-switching in the course of vertebrate evolution. It also demonstrates that the proximity in the ecological habitat of parasites within host species is an important feature for their speciation and diversification. Because A. moleri and its host, the Florida softshell turtle (Apalone ferox (Schneider)), are restricted to the USA, we suggest that an ancestral stock of parasites may have been isolated on primitive African trionychids after they diverged from their American relatives, and then switched to hippopotamuses or anthracotheres in Africa.

Phylogenomics reconciles molecular data with the rich fossil record on the origin of living turtles

Although a consensus exists that all living turtles fall within either Pleurodira or Cryptodira clades, estimating when these lineages split is still under debate. Most molecular studies date the split in the Triassic Period, whereas a Jurassic age is unanimous among morphological studies. Each hypothesis implies different paleobiogeographical scenarios to explain early turtle evolution. Here we explored the rich turtle fossil record with the Fossilized Birth-Death (FBD) and the traditional node dating (ND) methods using complete mitochondrial genomes (147 taxa) and a set of nuclear orthologs with over 10 million bp (25 taxa) to date the major splits in Testudines. Our results support an Early Jurassic split (191-182 Ma) for the crown Testudines with great consistency across different dating methods and datasets, with a narrow confidence interval. This result is independently supported by the oldest fossils of Testudines that postdate the Middle Jurassic (174 Ma), which were not used for calibration in this study. This age coincides with the Pangaea fragmentation and the formation of saltwater barriers such as the Atlantic Ocean and the Turgai Strait, supporting that diversification in Testudines was triggered by vicariance. Our ages of the splits in Pleurodira coincide with the geologic events of the Late Jurassic and Early Cretaceous. Conversely, the early Cryptodira radiation remained in Laurasia, and its diversification ensued as all its major lineages expanded their distribution into every continent during the Cenozoic. We provide the first detailed hypothesis of the evolution of Cryptodira in the Southern Hemisphere, in which our time estimates are correlated with each contact between landmasses derived from Gondwana and Laurasia. Although most South American Cryptodira arrived through the Great American Biotic Interchange, our results indicate that the Chelonoidis ancestor probably arrived from Africa through the chain islands of the South Atlantic during the Paleogene. Together, the presence of ancient turtle diversity and the vital role that turtles occupy in marine and terrestrial ecosystems underline South America as a chief area for conservation.

The Story of the Finest Armor: Developmental Aspects of Reptile Skin

The reptile skin is a barrier against water loss and pathogens and an armor for mechanical damages. The integument of reptiles consists of two main layers: the epidermis and the dermis. The epidermis, the hard cover of the body which has an armor-like role, varies among extant reptiles in terms of structural aspects such as thickness, hardness or the kinds of appendages it constitutes. The reptile epithelial cells of the epidermis (keratinocytes) are composed of two main proteins: intermediate filament keratins (IFKs) and corneous beta proteins (CBPs). The outer horny layer of the epidermis, stratum corneum, is constituted of keratinocytes by means of terminal differentiation or cornification which is a result of the protein interactions where CBPs associate with and coat the initial scaffold of IFKs. Reptiles were able to colonize the terrestrial environment due to the changes in these epidermal structures, which led to various cornified epidermal appendages such as scales and scutes, a beak, claws or setae. Developmental and structural aspects of the epidermal CBPs as well as their shared chromosomal locus (EDC) indicate an ancestral origin that gave rise to the finest armor of reptilians.

100 million years of turtle paleoniche dynamics enable the prediction of latitudinal range shifts in a warming world

Past responses to environmental change provide vital baseline data for estimating the potential resilience of extant taxa to future change. Here, we investigate the latitudinal range contraction that terrestrial and freshwater turtles (Testudinata) experienced from the Late Cretaceous to the Paleogene (100.5-23.03 mya) in response to major climatic changes. We apply ecological niche modeling (ENM) to reconstruct turtle niches, using ancient and modern distribution data, paleogeographic reconstructions, and the HadCM3L climate model to quantify their range shifts in the Cretaceous and late Eocene. We then use the insights provided by these models to infer their probable ecological responses to future climate scenarios at different representative concentration pathways (RCPs 4.5 and 8.5 for 2100), which project globally increased temperatures and spreading arid biomes at lower to mid-latitudes. We show that turtle ranges are predicted to expand poleward in the Northern Hemisphere, with decreased habitat suitability at lower latitudes, inverting a trend of latitudinal range contraction that has been prevalent since the Eocene. Trionychids and freshwater turtles can more easily track their niches than Testudinidae and other terrestrial groups. However, habitat destruction and fragmentation at higher latitudes will probably reduce the capability of turtles and tortoises to cope with future climate changes.

Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation

The group Anguimorpha represents one of the most unified squamate clades in terms of body plan, ecomorphology, ecophysiology and evolution. On the other hand, the anguimorphs vary between different habitats and ecological niches. Therefore, we focused on the group Anguimorpha to test a possible correlation between heart morphology and ecological niche with respect to phylogenetic position in Squamata with Sphenodon, Salvator, and Pogona as the outgroups. The chosen lepidosaurian species were investigated by microCT. Generally, all lepidosaurs had two well-developed atria with complete interatrial septum and one ventricle divided by ventricular septa to three different areas. The ventricles of all lepidosaurians had a compact layer and abundant trabeculae. The compact layer and trabeculae were developed in accordance with particular ecological niche of the species, the trabeculae in nocturnal animals with low metabolism, such as Sphenodon, Heloderma or Lanthanotus were more massive. On the other hand athletic animals, such as varanids or Salvator, had ventricle compartmentalization divided by three incomplete septa. A difference between varanids and Salvator was found in compact layer thickness: thicker in monitor lizards and possibly linked to their mammalian-like high blood pressure, and the level of ventricular septation. In summary: heart morphology varied among clades in connection with the ecological niche of particular species and it reflects the phylogenetic position in model clade Anguimorpha. In the absence of fossil evidence, this is the closest approach how to understand heart evolution and septation in clade with different cardiac compartmentalization levels.

Functional complexity in the chorioallantoic membrane of an oviparous snake: Specializations for calcium uptake from the eggshell

The chorioallantoic membrane of oviparous reptiles forms a vascular interface with the eggshell. The eggshell contains calcium, primarily as calcium carbonate. Extraction and mobilization of this calcium by the chorioallantoic membrane contributes importantly to embryonic nutrition. Development of the chorioallantoic membrane is primarily known from studies of squamates and birds. Although there are pronounced differences in eggshell structure, squamate and bird embryos each mobilize calcium from eggshells. Specialized cells in the chicken chorionic epithelium transport calcium from the eggshell aided by a second population of cells that secrete protons generated by the enzyme carbonic anhydrase. Calcium transporting cells also are present in the chorioallantoic membrane of corn snakes, although these cells function differently than those of chickens. We used histology and immunohistology to characterize the morphology and functional attributes of the chorioallantoic membrane of corn snakes. We identified two populations of cells in the outer layer of the chorionic epithelium. Calbindin-D_28K , a cellular marker for calcium transport expressed in squamate chorioallantoic membranes, is localized in large, flattened cells that predominate in the chorionic epithelium. Smaller cells, interspersed among the large cells, express carbonic anhydrase 2, an enzyme not previously localized in the chorionic epithelium of an oviparous squamate. These findings indicate that differentiation of chorionic epithelial cells contributes to extraction and transport of calcium from the eggshell. The presence of specializations of chorioallantoic membranes for calcium uptake from eggshells in chickens and corn snakes suggests that eggshell calcium was a source of embryonic nutrition early in the evolution of Sauropsida.

The appendicular myology of Stegoceras validum (Ornithischia: Pachycephalosauridae) and implications for the head-butting hypothesis

In this study, we use an exceptional skeleton of the pachycephalosaur Stegoceras validum (UALVP 2) to inform a comprehensive appendicular muscle reconstruction of the animal, with the goal of better understanding the functional morphology of the pachycephalosaur postcranial skeleton. We find that S. validum possessed a conservative forelimb musculature, particularly in comparison to early saurischian bipeds. By contrast, the pelvic and hind limb musculature are more derived, reflecting peculiarities of the underlying skeletal anatomy. The iliotibialis, ischiocaudalis, and caudofemoralis muscles have enlarged attachment sites and the caudofemoralis has greater leverage owing to the distal displacement of the fourth trochanter along the femur. These larger muscles, in combination with the wide pelvis and stout hind limbs, produced a stronger, more stable pelvic structure that would have proved advantageous during hypothesized intraspecific head-butting contests. The pelvis may have been further stabilized by enlarged sacroiliac ligaments, which stemmed from the unique medial iliac flange of the pachycephalosaurs. Although the pubis of UALVP 2 is not preserved, the pubes of other pachycephalosaurs are highly reduced. The puboischiofemoralis musculature was likely also reduced accordingly, and compensated for by the aforementioned improved pelvic musculature.

The diverse terminology of reptile eggshell microstructure and its effect on phylogenetic comparative analyses

Reptile eggshell ensures water and gas exchange during incubation and plays a key role in reproductive success. The diversity of reptilian incubation and life history strategies has led to many clade-specific structural adaptations of their eggshell, which have been studied in extant taxa (i.e. birds, crocodilians, turtles, and lepidosaurs). Most studies on non-avian eggshells were performed over 30 years ago and categorized reptile eggshells into two main types: "hard" and "soft" - sometimes with a third intermediate category, "semi-rigid." In recent years, however, debate over the evolution of eggshell structure of major reptile clades has revealed how definitions of hard and soft eggshells influence inferred deep-time evolutionary patterns. Here, we review the diversity of extant and fossil eggshell with a focus on major reptile clades, and the criteria that have been used to define hard, soft, and semi-rigid eggshells. We show that all scoring approaches that retain these categories discretize continuous quantitative traits (e.g. eggshell thickness) and do not consider independent variation of other functionally important microstructural traits (e.g. degree of calcification, shell unit inner structure). We demonstrate the effect of three published approaches to discretizing eggshell type into hard, semi-rigid, and soft on ancestral state reconstructions using 200+ species representing all major extant and extinct reptile clades. These approaches result in different ancestral states for all major clades including Archosauria and Dinosauria, despite a difference in scoring for only 1-4% of the sample. Proposed scenarios of reptile eggshell evolution are highly conditioned by sampling, tree calibration, and lack of congruence between definitions of eggshell type. We conclude that the traditional "soft/hard/semi-rigid" classification of reptilian eggshells should be abandoned and provide guidelines for future descriptions focusing on specific functionally relevant characteristics (e.g. inner structures of shell units, pores, and membrane elements), analyses of these traits in a phylogenetic context, and sampling of previously undescribed taxa, including fossil eggs.

Successive climate crises in the deep past drove the early evolution and radiation of reptiles

Climate change-induced mass extinctions provide unique opportunities to explore the impacts of global environmental disturbances on organismal evolution. However, their influence on terrestrial ecosystems remains poorly understood. Here, we provide a new time tree for the early evolution of reptiles and their closest relatives to reconstruct how the Permian-Triassic climatic crises shaped their long-term evolutionary trajectory. By combining rates of phenotypic evolution, mode of selection, body size, and global temperature data, we reveal an intimate association between reptile evolutionary dynamics and climate change in the deep past. We show that the origin and phenotypic radiation of reptiles was not solely driven by ecological opportunity following the end-Permian extinction as previously thought but also the result of multiple adaptive responses to climatic shifts spanning 57 million years.

A systematic compendium of turtle mandibular anatomy using digital dissections of soft tissue and osteology

Turtles are a charismatic reptile group with a peculiar body plan, which most notably includes the shell. Anatomists have often focused descriptive efforts on the shell and other strongly derived body parts, such as the akinetic skull, or the cervical vertebrae. Other parts of turtle osteology, like the girdles, limbs, and mandibles, are documented with less rigor and detail. The mandible is the primary skeletal element involved in food acquisition and initial food processing of turtles, and its features are thus likely linked to feeding ecology. In addition, the mandible of turtles is composed of up to seven bones (sometimes fused to as little as three) and has thus anatomical complexity that may be insightful for systematic purposes and phylogenetic research. Despite apparent complexity and diversity to the mandible of turtles, this anatomical system has not been systematically studied, not even in search of characters that might improve phylogenetic resolution. Here, we describe the mandibular osteology for all major subclades of extant turtles with the help of digitally dissected 3D models derived from high-resolution computed tomography (μCT) scans of 70 extant species. We provide 31 fully segmented mandibles, as well as 3D models of the mandibular musculature, innervation, and arterial circulation of the cryptodire Dermatemys mawii. We synthesize observed variation into 51 morphological characters, which we optimize onto a molecular phylogeny. This analysis shows some mandibular characters to have high systematic value, whereas others are highly homoplastic and may underlie ecological influences or other factors invoking variation.

Skull Sutures and Cranial Mechanics in the Permian Reptile Captorhinus aguti and the Evolution of the Temporal Region in Early Amniotes

While most early limbed vertebrates possessed a fully-roofed dermatocranium in their temporal skull region, temporal fenestrae and excavations evolved independently at least twice in the earliest amniotes, with several different variations in shape and position of the openings. Yet, the specific drivers behind this evolution have been only barely understood. It has been mostly explained by adaptations of the feeding apparatus as a response to new functional demands in the terrestrial realm, including a rearrangement of the jaw musculature as well as changes in strain distribution. Temporal fenestrae have been retained in most extant amniotes but have also been lost again, notably in turtles. However, even turtles do not represent an optimal analog for the condition in the ancestral amniote, highlighting the necessity to examine Paleozoic fossil material. Here, we describe in detail the sutures in the dermatocranium of the Permian reptile Captorhinus aguti (Amniota, Captorhinidae) to illustrate bone integrity in an early non-fenestrated amniote skull. We reconstruct the jaw adductor musculature and discuss its relation to intracranial articulations and bone flexibility within the temporal region. Lastly, we examine whether the reconstructed cranial mechanics in C. aguti could be treated as a model for the ancestor of fenestrated amniotes. We show that C. aguti likely exhibited a reduced loading in the areas at the intersection of jugal, squamosal, and postorbital, as well as at the contact between parietal and postorbital. We argue that these “weak” areas are prone for the development of temporal openings and may be treated as the possible precursors for infratemporal and supratemporal fenestrae in early amniotes. These findings provide a good basis for future studies on other non-fenestrated taxa close to the amniote base, for example diadectomorphs or other non-diapsid reptiles.

A Genomic Perspective on the Evolutionary Diversification of Turtles

To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa. Our results suggest that gene tree-species tree discordance in these datasets is likely driven by population-level processes such as incomplete lineage sorting. We found very little effect of substitutional saturation on species tree topologies, and no clear phylogenetic patterns in codon usage bias and compositional heterogeneity. There was no correlation between gene and site concordance, node age, and DNA substitution rate across most annotated genomic regions. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible in order to obtain accurate phylogenies for assessing conservation priorities in turtles.

The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade

The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing Gavialis basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian Portugalosuchus azenhae was recently described as the oldest crown crocodilian, with affinities to Gavialis, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration. Here, we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians, including Portugalosuchus. Our analyses incorporating DNA data robustly recovered Portugalosuchus outside Crocodylia (as well as thoracosaurs, planocraniids and Borealosuchus spp.), questioning the status of Portugalosuchus as crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss the impact of ambiguous fossil calibration and how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.

Foreflipper and hindflipper muscle reconstructions of Cryptoclidus eurymerus in comparison to functional analogues: introduction of a myological mechanism for flipper twisting

BACKGROUND

Plesiosaurs, diapsid crown-group Sauropterygia, inhabited the oceans from the Late Triassic to the Late Cretaceous. Their most exceptional characteristic are four hydrofoil-like flippers. The question whether plesiosaurs employed their four flippers in underwater flight, rowing flight, or rowing has not been settled yet. Plesiosaur locomotory muscles have been reconstructed in the past, but neither the pelvic muscles nor the distal fore- and hindflipper musculature have been reconstructed entirely.

METHODS

All plesiosaur locomotory muscles were reconstructed in order to find out whether it is possible to identify muscles that are necessary for underwater flight including those that enable flipper rotation and twisting. Flipper twisting has been proven by hydrodynamic studies to be necessary for efficient underwater flight. So, Cryptoclidus eurymerus fore- and hindflipper muscles and ligaments were reconstructed using the extant phylogenetic bracket (Testudines, Crocodylia, and Lepidosauria) and correlated with osteological features and checked for their functionality. Muscle functions were geometrically derived in relation to the glenoid and acetabulum position. Additionally, myology of functionally analogous Chelonioidea, Spheniscidae, Otariinae, and Cetacea is used to extract general myological adaptations of secondary aquatic tetrapods to inform the phylogenetically inferred muscle reconstructions.

RESULTS

A total of 52 plesiosaur fore- and hindflipper muscles were reconstructed. Amongst these are flipper depressors, elevators, retractors, protractors, and rotators. These muscles enable a fore- and hindflipper downstroke and upstroke, the two sequences that represent an underwater flight flipper beat cycle. Additionally, other muscles were capable of twisting fore- and hindflippers along their length axis during down- and upstroke accordingly. A combination of these muscles that actively aid in flipper twisting and intermetacarpal/intermetatarsal and metacarpodigital/metatarsodigital ligament systems, that passively engage the successive digits, could have accomplished fore-and hindflipper length axis twisting in plesiosaurs that is essential for underwater flight. Furthermore, five muscles that could possibly actively adjust the flipper profiles for efficient underwater flight were found, too.

Phylogenomic analyses resolve relationships among garter snakes (Thamnophis: Natricinae: Colubridae) and elucidate biogeographic history and morphological evolution

Garter snakes (Thamnophis) are a successful group of natricines endemic to North America. They have become important natural models for ecological and evolutionary research, yet prior efforts to resolve phylogenetic relationships have resulted in conflicting topologies and weak support for certain relationships. Here, we use genomic data generated with a reduced representation double-digest RADseq approach to reassess evolutionary relationships across Thamnophis. We then use the resulting phylogeny to better understand how biogeography and feeding ecology have influenced lineage diversification and morphological evolution. We recovered highly congruent and strongly supported topologies from maximum likelihood and Bayesian analyses, but some discordance with a multispecies coalescent approach. All phylogenomic estimates split Thamnophis into two clades largely defined by northern and southern North American species. Divergence time estimates and biogeographic analyses indicate a mid-Miocene origin of Thamnophis in Mexico. In addition, historic vicariant events thought to explain biogeographic patterns in other lineages (e.g., Isthmus of Tehuantepec, Rocky Mountain Range, and Trans-Mexican Volcanic Belt) appear to have influenced patterns of diversification in Thamnophis as well. Analyses of morphological traits associated with feeding ecology showed moderate to strong phylogenetic signal. Nevertheless, phylogenetic ANOVA suggested significant differences in certain cranial morphologies between aquatic specialists and garter snakes that are terrestrial-aquatic generalists, independent of evolutionary history. Our new estimate of Thamnophis phylogeny yields an improved understanding of the biogeographic history and morphological evolution of garter snakes, and provides a robust framework for future research on these snakes.

A new model of forelimb ecomorphology for predicting the ancient habitats of fossil turtles

Various morphological proxies have been used to infer habitat preferences among fossil turtles and their early ancestors, but most are tightly linked to phylogeny, thereby minimizing their predictive power. One particularly widely used model incorporates linear measurements of the forelimb (humerus + ulna + manus), but in addition to the issue of phylogenetic correlation, it does not estimate the likelihood of habitat assignment. Here, we introduce a new model that uses intramanual measurements (digit III metacarpal + non-ungual phalanges + ungual) to statistically estimate habitat likelihood and that has greater predictive strength than prior estimators. Application of the model supports the hypothesis that stem-turtles were primarily terrestrial in nature and recovers the nanhsiungchelyid Basilemys (a fossil crown-group turtle) as having lived primarily on land, despite some prior claims to the contrary.

Chromosome-level genome assembly of the Chinese three-keeled pond turtle (Mauremys reevesii) provides insights into freshwater adaptation

Mauremys reevesii is an endangered freshwater turtle that symbolizes longevity in Chinese culture. Despite its importance, genetic studies of this species remain limited, with no genomic sequence reported to date. Here, we report a high-quality, chromosome-level genomic sequence of M. reevesii obtained using a combination of Nanopore and Hi-C sequencing technologies. The 2.37 Gb M. reevesii genome was assembled from a total of ~226.80 Gb of Nanopore sequencing data. The M. reevesii genome contig N50 is 34.73 Mb, the highest value in published turtle genomes. In total, 18,238 genes were functionally annotated. The contigs were clustered and ordered onto 27 pseudochromosomes covering ~96.55% of the genome assembled with Hi-C data. To explore genome evolution, synteny analysis was performed between M. reevesii (freshwater turtle) and Gopherus evgoodei (terrestrial turtle) genomes. In general, each chromosome of M. reevesii corresponded to one chromosome of Gopherus evgoodei, but some interchromosomal rearrangements occurred between the two species based on the assembled genomes. These interchromosomal rearrangements were further confirmed by mapping of the long-read nanopore data to the assembly. The reconstructed demographic history showed varied effective population size among freshwater, marine and terrestrial turtles. We also discovered expansion of genes related to the innate immune system in M. reevesii that may provide defence against freshwater pathogens. The high-quality genomic sequence provides a valuable genetic resource for further studies of genetics and genome evolution in turtles.

Phylogenomics of alligator lizards elucidate diversification patterns across the Mexican Transition Zone and support the recognition of a new genus

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity.

45S rDNA Repeats of Turtles and Crocodiles Harbor a Functional 5S rRNA Gene Specifically Expressed in Oocytes

In most eukaryotic genomes, tandemly repeated copies of 5S rRNA genes are clustered outside the nucleolus organizer region (NOR), which normally encodes three other major rRNAs: 18S, 5.8S, and 28S. Our analysis of turtle rDNA sequences has revealed a 5S rDNA insertion into the NOR intergenic spacer in antisense orientation. The insertion (hereafter called NOR-5S rRNA gene) has a length of 119 bp and coexists with the canonical 5S rDNA clusters outside the NOR. Despite the ∼20% nucleotide difference between the two 5S gene sequences, their internal control regions for RNA polymerase III are similar. Using the turtle Trachemys scripta as a model species, we showed the NOR-5S rDNA specific expression in oocytes. This expression is concurrent with the NOR rDNA amplification during oocyte growth. We show that in vitellogenic oocytes, the NOR-5S rRNA prevails over the canonical 5S rRNA in the ribosomes, suggesting a role of modified ribosomes in oocyte-specific translation. The orders Testudines and Crocodilia seem to be the only taxa of vertebrates with such a peculiar rDNA organization. We speculate that the amplification of the 5S rRNA genes as a part of the NOR DNA during oogenesis provides a dosage balance between transcription of all the four ribosomal RNAs while producing a maternal pool of extra ribosomes. We further hypothesize that the NOR-5S rDNA insertion appeared in the Archelosauria clade during the Permian period and was lost later in the ancestors of Aves.

Sex Chromosomes and Master Sex-Determining Genes in Turtles and Other Reptiles

Among tetrapods, the well differentiated heteromorphic sex chromosomes of birds and mammals have been highly investigated and their master sex-determining (MSD) gene, Dmrt1 and SRY, respectively, have been identified. The homomorphic sex chromosomes of reptiles have been the least studied, but the gap with birds and mammals has begun to fill. This review describes our current knowledge of reptilian sex chromosomes at the cytogenetic and molecular level. Most of it arose recently from various studies comparing male to female gene content. This includes restriction site-associated DNA sequencing (RAD-Seq) experiments in several male and female samples, RNA sequencing and identification of Z- or X-linked genes by male/female comparative transcriptome coverage, and male/female transcriptomic or transcriptome/genome substraction approaches allowing the identification of Y- or W-linked transcripts. A few putative master sex-determining (MSD) genes have been proposed, but none has been demonstrated yet. Lastly, future directions in the field of reptilian sex chromosomes and their MSD gene studies are considered.

Dispersal, not vicariance, explains the biogeographic origin of iguanas on Madagascar

Lizards of the clade Iguanidae (sensu lato) are primarily a New World group. Thus, the remarkable presence of an endemic lineage of iguanas (family Opluridae) on the isolated Indian Ocean island of Madagascar has long been considered a biogeographic anomaly. Previous work attributed this disjunct extant distribution to: (1) vicariance at about 140-165 Ma, caused by the breakup of Gondwana and the separation of South America, Africa, and Madagascar (with subsequent extinction of iguanas on Africa, and potentially other Gondwanan landmasses), (2) vicariance at about 80-90 Ma, caused by the sundering of hypothesized land-bridge connections between South America, Antarctica, India, and Madagascar, or (3) long-distance overwater dispersal from South America to Madagascar. Each hypothesis has been supported with molecular divergence dating analyses, and thus the biogeographic origin of the Opluridae is not yet well resolved. Here we utilize genetic sequences of ultraconserved elements for all Iguania families and the majority of Iguanidae (s.l.) genera, and morphological data for extant and fossil taxa (used for divergence dating analyses), to produce the most comprehensive dataset applied to date to test these origin hypotheses. We find strong support for a sister relationship between the Opluridae (Madagascar) and Leiosauridae (South America). Divergence of the Opluridae from Leiosauridae is dated to between the late Cretaceous and mid-Paleogene, at a time when Madagascar was already an island and was isolated from all other Gondwanan landmasses. Consequently, our results support a hypothesis of long-distance overwater dispersal of the Opluridae lineage, either directly from South America to Madagascar or potentially via Antarctica or Africa, leading to this radiation of iguanas in the Indian Ocean.

The locomotion of extinct secondarily aquatic tetrapods

The colonisation of freshwater and marine ecosystems by land vertebrates has repeatedly occurred in amphibians, reptiles, birds and mammals over the course of 300 million years. Functional interpretations of the fossil record are crucial to understanding the forces shaping these evolutionary transitions. Secondarily aquatic tetrapods have acquired a suite of anatomical, physiological and behavioural adaptations to locomotion in water. However, much of this information is lost for extinct clades, with fossil evidence often restricted to osteological data and a few extraordinary specimens with soft tissue preservation. Traditionally, functional morphology in fossil secondarily aquatic tetrapods was investigated through comparative anatomy and correlation with living functional analogues. However, in the last two decades, biomechanics in palaeobiology has experienced a remarkable methodological shift. Anatomy-based approaches are increasingly rigorous, informed by quantitative techniques for analysing shape. Moreover, the incorporation of physics-based methods has enabled objective tests of functional hypotheses, revealing the importance of hydrodynamic forces as drivers of evolutionary innovation and adaptation. Here, we present an overview of the latest research on the locomotion of extinct secondarily aquatic tetrapods, with a focus on amniotes, highlighting the state-of-the-art experimental approaches used in this field. We discuss the suitability of these techniques for exploring different aspects of locomotory adaptation, analysing their advantages and limitations and laying out recommendations for their application, with the aim to inform future experimental strategies. Furthermore, we outline some unexplored research avenues that have been successfully deployed in other areas of palaeobiomechanical research, such as the use of dynamic models in feeding mechanics and terrestrial locomotion, thus providing a new methodological synthesis for the field of locomotory biomechanics in extinct secondarily aquatic vertebrates. Advances in imaging technology and three-dimensional modelling software, new developments in robotics, and increased availability and awareness of numerical methods like computational fluid dynamics make this an exciting time for analysing form and function in ancient vertebrates.

A review of the osteoderms of lizards (Reptilia: Squamata)

Osteoderms are mineralised structures consisting mainly of calcium phosphate and collagen. They form directly within the skin, with or without physical contact with the skeleton. Osteoderms, in some form, may be primitive for tetrapods as a whole, and are found in representatives of most major living lineages including turtles, crocodilians, lizards, armadillos, and some frogs, as well as extinct taxa ranging from early tetrapods to dinosaurs. However, their distribution in time and space raises questions about their evolution and homology in individual groups. Among lizards and their relatives, osteoderms may be completely absent; present only on the head or dorsum; or present all over the body in one of several arrangements, including non-overlapping mineralised clusters, a continuous covering of overlapping plates, or as spicular mineralisations that thicken with age. This diversity makes lizards an excellent focal group in which to study osteoderm structure, function, development and evolution. In the past, the focus of researchers was primarily on the histological structure and/or the gross anatomy of individual osteoderms in a limited sample of taxa. Those studies demonstrated that lizard osteoderms are sometimes two-layered structures, with a vitreous, avascular layer just below the epidermis and a deeper internal layer with abundant collagen within the deep dermis. However, there is considerable variation on this model, in terms of the arrangement of collagen fibres, presence of extra tissues, and/or a cancellous bone core bordered by cortices. Moreover, there is a lack of consensus on the contribution, if any, of osteoblasts in osteoderm development, despite research describing patterns of resorption and replacement that would suggest both osteoclast and osteoblast involvement. Key to this is information on development, but our understanding of the genetic and skeletogenic processes involved in osteoderm development and patterning remains minimal. The most common proposition for the presence of osteoderms is that they provide a protective armour. However, the large morphological and distributional diversity in lizard osteoderms raises the possibility that they may have other roles such as biomechanical reinforcement in response to ecological or functional constraints. If lizard osteoderms are primarily for defence, whether against predators or conspecifics, then this 'bony armour' might be predicted to have different structural and/or mechanical properties compared to other hard tissues (generally intended for support and locomotion). The cellular and biomineralisation mechanisms by which osteoderms are formed could also be different from those of other hard tissues, as reflected in their material composition and nanostructure. Material properties, especially the combination of malleability and resistance to impact, are of interest to the biomimetics and bioinspired material communities in the development of protective clothing and body armour. Currently, the literature on osteoderms is patchy and is distributed across a wide range of journals. Herein we present a synthesis of current knowledge on lizard osteoderm evolution and distribution, micro- and macrostructure, development, and function, with a view to stimulating further work.

A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins

Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.

Independent pseudogenizations and losses of sox15 during amniote diversification following asymmetric ohnolog evolution

Background

Four ohnologous genes (sox1, sox2, sox3, and sox15) were generated by two rounds of whole-genome duplication in a vertebrate ancestor. In eutherian mammals, Sox1, Sox2, and Sox3 participate in central nervous system (CNS) development. Sox15 has a function in skeletal muscle regeneration and has little functional overlap with the other three ohnologs. In contrast, the frog Xenopus laevis and zebrafish orthologs of sox15 as well as sox1-3 function in CNS development. We previously reported that Sox15 is involved in mouse placental development as neofunctionalization, but is pseudogenized in the marsupial opossum. These findings suggest that sox15 might have evolved with divergent gene fates during vertebrate evolution. However, knowledge concerning sox15 in other vertebrate lineages than therian mammals, anuran amphibians, and teleost fish is scarce. Our purpose in this study was to clarify the fate and molecular evolution of sox15 during vertebrate evolution.

Results

We searched for sox15 orthologs in all vertebrate classes from agnathans to mammals by significant sequence similarity and synteny analyses using vertebrate genome databases. Interestingly, sox15 was independently pseudogenized at least twice during diversification of the marsupial mammals. Moreover, we observed independent gene loss of sox15 at least twice during reptile evolution in squamates and crocodile-bird diversification. Codon-based phylogenetic tree and selective analyses revealed an increased d_N/d_S ratio for sox15 compared to the other three ohnologs during jawed vertebrate evolution.

Conclusions

The findings revealed an asymmetric evolution of sox15 among the four ohnologs during vertebrate evolution, which was supported by the increased d_N/d_S values in cartilaginous fishes, anuran amphibians, and amniotes. The increased d_N/d_S value of sox15 may have been caused mainly by relaxed selection. Notably, independent pseudogenizations and losses of sox15 were observed during marsupial and reptile evolution, respectively. Both might have been caused by strong relaxed selection. The drastic gene fates of sox15, including neofunctionalization and pseudogenizations/losses during amniote diversification, might be caused by a release from evolutionary constraints.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01864-z.

The evolutionary biomechanics of locomotor function in giant land animals

Giant land vertebrates have evolved more than 30 times, notably in dinosaurs and mammals. The evolutionary and biomechanical perspectives considered here unify data from extant and extinct species, assessing current theory regarding how the locomotor biomechanics of giants has evolved. In terrestrial tetrapods, isometric and allometric scaling patterns of bones are evident throughout evolutionary history, reflecting general trends and lineage-specific divergences as animals evolve giant size. Added to data on the scaling of other supportive tissues and neuromuscular control, these patterns illuminate how lineages of giant tetrapods each evolved into robust forms adapted to the constraints of gigantism, but with some morphological variation. Insights from scaling of the leverage of limbs and trends in maximal speed reinforce the idea that, beyond 100-300 kg of body mass, tetrapods reduce their locomotor abilities, and eventually may lose entire behaviours such as galloping or even running. Compared with prehistory, extant megafaunas are depauperate in diversity and morphological disparity; therefore, turning to the fossil record can tell us more about the evolutionary biomechanics of giant tetrapods. Interspecific variation and uncertainty about unknown aspects of form and function in living and extinct taxa still render it impossible to use first principles of theoretical biomechanics to tightly bound the limits of gigantism. Yet sauropod dinosaurs demonstrate that >50 tonne masses repeatedly evolved, with body plans quite different from those of mammalian giants. Considering the largest bipedal dinosaurs, and the disparity in locomotor function of modern megafauna, this shows that even in terrestrial giants there is flexibility allowing divergent locomotor specialisations.