Naoki Irie and colleagues report the draft genomes of the soft-shell and green sea turtles. Their genome-wide phylogenetic analysis supports the hypothesis that turtles are a sister group of crocodilians and birds.

/pdf/the-draft-genomes-of-soft-shell-turtle-and-green-sea-turtle-fd4tl2b1nm.pdf

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species’ physiological capacities to withstand extreme anoxia and tissue freezing. Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle’s extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

/pdf/the-western-painted-turtle-genome-a-model-for-the-evolution-2jw0fdw5vi.pdf

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

There are currently ca. 317 recognized species of turtles and tortoises in the world. Of those that have been assessed on the IUCN Red List, 63% are considered threatened, and 10% are critically endangered, with ca. 42% of all known turtle species threatened. Without directed strategic conservation planning, a significant portion of turtle diversity could be lost over the next century. Toward that conservation effort, we compiled museum and literature occurrence records for all of the world's tortoises and freshwater turtle species to determine their distributions and identify priority regions for conservation. We constructed projected range maps for each species by selecting geographic information system–defined hydrologic unit compartments (HUCs) with verified locality points, and then added HUCs that connected known point localities in the same watershed or physiographic region and that had similar habitats and elevations as the verified HUCs. We analyzed a total of 305 turtle species and assi...

https://bioone.org/journals/Chelonian-Conservation-and-Biology/volume-8/issue-2/CCB-0774.1/A-Global-Analysis-of-Tortoise-and-Freshwater-Turtle-Distributions-with/10.2744/CCB-0774.1.pdf

A Global Analysis of Tortoise and Freshwater Turtle Distributions with Identification of Priority Conservation Areas

The early evolution of archosauromorphs during the Permo-Triassic constitutes an excellent empirical case study to shed light on evolutionary radiations in deep time and the timing and processes of recovery of terrestrial faunas after a mass extinction. However, macroevolutionary studies of early archosauromorphs are currently limited by poor knowledge of their phylogenetic relationships. In particular, one of the main early archosauromorph groups that need an exhaustive phylogenetic study is "Proterosuchia," which as historically conceived includes members of both Proterosuchidae and Erythrosuchidae. A new data matrix composed of 96 separate taxa (several of them not included in a quantitative phylogenetic analysis before) and 600 osteological characters was assembled and analysed to generate a comprehensive higher-level phylogenetic hypothesis of basal archosauromorphs and shed light on the species-level interrelationships of taxa historically identified as proterosuchian archosauriforms. The results of the analysis using maximum parsimony include a polyphyletic "Prolacertiformes" and "Protorosauria," in which the Permian Aenigmastropheus and Protorosaurus are the most basal archosauromorphs. The enigmatic choristoderans are either found as the sister-taxa of all other lepidosauromorphs or archosauromorphs, but consistently placed within Sauria. Prolacertids, rhynchosaurs, allokotosaurians and tanystropheids are the major successive sister clades of Archosauriformes. The Early Triassic Tasmaniosaurus is recovered as the sister-taxon of Archosauriformes. Proterosuchidae is unambiguosly restricted to five species that occur immediately after and before the Permo-Triassic boundary, thus implying that they are a short-lived "disaster" clade. Erythrosuchidae is composed of eight nominal species that occur during the Early and Middle Triassic. "Proterosuchia" is polyphyletic, in which erythrosuchids are more closely related to Euparkeria and more crownward archosauriforms than to proterosuchids, and several species are found widespread along the archosauromorph tree, some being nested within Archosauria (e.g., "Chasmatosaurus ultimus," Youngosuchus). Doswelliids and proterochampsids are recovered as more closely related to each other than to other archosauromorphs, forming a large clade (Proterochampsia) of semi-aquatic to aquatic forms that includes the bizarre genus Vancleavea. Euparkeria is one of the sister-taxa of the clade composed of proterochampsians and archosaurs. The putative Indian archosaur Yarasuchus is recovered in a polytomy with Euparkeria and more crownward archosauriforms, and as more closely related to the Russian Dongusuchus than to other species. Phytosaurs are recovered as the sister-taxa of all other pseudosuchians, thus being nested within Archosauria.

The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriforms

Although often overlooked, the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes but most details of their evolution and development remain confused and uncertain. Herein we re-evaluate the tetrapod integumentary skeleton by integrating comparative developmental and tissue structure data. Three types of tetrapod integumentary elements are recognized: (1) osteoderms, common to representatives of most major taxonomic lineages; (2) dermal scales, unique to gymnophionans; and (3) the lamina calcarea, an enigmatic tissue found only in some anurans. As presently understood, all are derivatives of the ancestral cosmoid scale and all originate from scleroblastic neural crest cells. Osteoderms are plesiomorphic for tetrapods but demonstrate considerable lineage-specific variability in size, shape, and tissue structure and composition. While metaplastic ossification often plays a role in osteoderm development, it is not the exclusive mode of skeletogenesis. All osteoderms share a common origin within the dermis (at or adjacent to the stratum superficiale) and are composed primarily (but not exclusively) of osseous tissue. These data support the notion that all osteoderms are derivatives of a neural crest-derived osteogenic cell population (with possible matrix contributions from the overlying epidermis) and share a deep homology associated with the skeletogenic competence of the dermis. Gymnophionan dermal scales are structurally similar to the elasmoid scales of most teleosts and are not comparable with osteoderms. Whereas details of development are lacking, it is hypothesized that dermal scales are derivatives of an odontogenic neural crest cell population and that skeletogenesis is comparable with the formation of elasmoid scales. Little is known about the lamina calcarea. It is proposed that this tissue layer is also odontogenic in origin, but clearly further study is necessary. Although not homologous as organs, all elements of the integumentary skeleton share a basic and essential relationship with the integument, connecting them with the ancestral rhombic scale.

/pdf/the-integumentary-skeleton-of-tetrapods-origin-evolution-and-3bg5k9m18s.pdf

The integumentary skeleton of tetrapods: origin, evolution, and development

A well preserved 220-million-year-old fossil from marine deposits of the Late Triassic of Guizhou in southwest China sheds light on the intermediate steps in the acquisition of the unique turtle body-plan. Transitional forms are scarce in this lineage, making this transition one of the mysteries of reptile evolution. The find is the most primitive turtle known. It has a fully developed plastron, the ventral dermal armour, evolved before the carapace, the dorsal (upper) part of the shell structure. In this fossil the carapace consists of neural plates only. This suggest that the carapace developed via ossification of the neural plates and broadening of the ribs — a sequence that echoes the developmental pattern in young turtles today. 220-million-year-old fossils from southwestern China represent the most primitive turtle known, and shed light on intermediate steps in the acquisition of the unique and highly specialized turtle body-plan. The origin of the turtle body plan remains one of the great mysteries of reptile evolution. The anatomy of turtles is highly derived, which renders it difficult to establish the relationships of turtles with other groups of reptiles. The oldest known turtle, Proganochelys from the Late Triassic period of Germany1, has a fully formed shell and offers no clue as to its origin. Here we describe a new 220-million-year-old turtle from China, somewhat older than Proganochelys, that documents an intermediate step in the evolution of the shell and associated structures. A ventral plastron is fully developed, but the dorsal carapace consists of neural plates only. The dorsal ribs are expanded, and osteoderms are absent. The new species shows that the plastron evolved before the carapace and that the first step of carapace formation is the ossification of the neural plates coupled with a broadening of the ribs. This corresponds to early embryonic stages of carapace formation in extant turtles, and shows that the turtle shell is not derived from a fusion of osteoderms. Phylogenetic analysis places the new species basal to all known turtles, fossil and extant. The marine deposits that yielded the fossils indicate that this primitive turtle inhabited marginal areas of the sea or river deltas.

An ancestral turtle from the Late Triassic of southwestern China

Scientific Reports 7: Article number: 46028; published online: 10 April 2017; updated: 20 October 2017. The Supplementary Information file originally published with this Article, contained errors in the Supplementary Figure S6. The taxon ‘Parasuchus hislopi’ was accidentally inserted twice and ‘Smilosuchus lithodendrorum’ was inadvertently transposed with Smilosuchus adamanensis’.

/pdf/correction-corrigendum-a-short-snouted-middle-triassic-4m3bqm3bnq.pdf

Correction: Corrigendum: A Short-Snouted, Middle Triassic Phytosaur and its Implications for the Morphological Evolution and Biogeography of Phytosauria

A new genus and species of marine reptile is described from the Pelsonian (Anisian, Middle Triassic) of Luoping County, Yunnan Province, southwestern China. This diapsid reptile with a secondarily closed upper temporal fossa is the sister taxon to Saurosphargis from the lower Muschelkalk (Anisian, Middle Triassic) of central Europe. It further emphasizes the close faunal affinities between the Eastern and Western Tethyan realm. The new taxon is convergent on cyamodontoid placodonts in having developed a dorsal body armor composed of small osteoderms. The underlying ribs are transversely broadened so as to establish contact along their length, thus forming a closed dorsal ‘rib basket,’ a unique morphology shared with Saurosphargis.

https://bioone.org/journals/journal-of-vertebrate-paleontology/volume-31/issue-2/02724634.2011.550368/A-New-Triassic-Marine-Reptile-from-Southwestern-China/10.1080/02724634.2011.550368.pdf

A New Triassic Marine Reptile from Southwestern China

Wumengosaurus delicatomandibularis Jiang et al., 2008, is restudied on the basis of three new specimens. Many elements of the skeleton that were either briefly or not described at all in the original study are detailed. With the additional information derived from the new specimens, we have revised the diagnosis of W. delicatomandibularis. A phylogenetic analysis further demonstrates that the Pachypleurosauria is not a monophyletic group and questions that W. delicatomandibularis is closely related to the Pachypleurosauria. W. delicatomandibularis might represent the basal-most member of a monophyletic clade that includes the Nothosauroidea and those taxa assigned to the ‘Pachypleurosauria.’ The five known specimens show morphological variation in W. delicatomandibularis, as in Keichousaurus and in pachypleurosaurs such as Neusticosaurus and Serpianosaurus.

https://bioone.org/journals/journal-of-vertebrate-paleontology/volume-31/issue-1/02724634.2011.546724/New-Information-on-Wumengosaurus-delicatomandibularis-Jiang-et-al-2008-Diapsida/10.1080/02724634.2011.546724.pdf

New Information on Wumengosaurus delicatomandibularis Jiang et al., 2008 (Diapsida: Sauropterygia), with a Revision of the Osteology and Phylogeny of the Taxon

A new species of the terrestrial protorosaur Macrocnemus is briefly described and named Macrocne-mus fuyuanensis sp. nov. The specimen was found from the marine Triassic of Yunnan Province, southwestern China. It differs from the type species M. bassanii in having the following characters: (1) 17 or 18 dorsal vertebrae; (2) relatively long humerus; and (3) femur longer than tibia. M. fuyuanensis is the only record of the genus outside Monte San Giorgio area and the first definite terrestrial reptile found from the marine Triassic of China. The age of the fossil-bearing Zhuganpo Member of the Falang Formation is believed to be the Ladinian based on associated vertebrate fauna. The existence of Mac-rocnemus in the limestone suggests the presence of a terrestrial ecosystem which probably originated from the Anisian and well developed in the Ladinian in this region. The island system along the north-coast of Tethyan during the Triassic was probably an important route for the exchanges of rep-tiles, especially the terrestrial reptiles between the west and east.

Li-Jun Zhao

Papers

An ancestral turtle from the Late Triassic of southwestern China

Correction: Corrigendum: A Short-Snouted, Middle Triassic Phytosaur and its Implications for the Morphological Evolution and Biogeography of Phytosauria

A New Triassic Marine Reptile from Southwestern China

New Information on Wumengosaurus delicatomandibularis Jiang et al., 2008 (Diapsida: Sauropterygia), with a Revision of the Osteology and Phylogeny of the Taxon

A new species of Macrocnemus (Reptilia: Protorosauria) from the Middle Triassic of southwestern China and its palaeogeographical implication