Explore the vast range of titles available.

To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

A phylogeny of birds is presented from targeted genomic sequencing of 198 species of living birds representing all major avian lineages; the results find five major clades forming successive sister taxa to the rest of Neoaves and do not support the recently proposed Neoavian clades of Columbea and Passerea. A new look at the bird lineage The evolutionary relationships of bird species remain a contentious issue. Richard Prum et al . used targeted genomic sequencing to compare more than 259 nuclear loci from each of 198 living bird species, representing all major avian lineages and two crocodilian outgroups. The results favour a phylogeny consisting of five major clades forming successive sister taxa to the rest of Neoaves, and do not support two recently proposed Neoavian clades — Columbea and Passerea — as natural groups. Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10 7 bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin ( Opisthocomus hoazin ) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades—Columbea and Passerea 1 —were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.

Zooarchaeologists have long relied on linear traces and pits found on the surfaces of ancient bones to infer ancient hominid behaviors such as slicing, chopping, and percussive actions during butchery of mammal carcasses. However, such claims about Plio–Pleistocene hominids rely mostly on very small assemblages of bony remains. Furthermore, recent experiments on trampling animals and biting crocodiles have shown each to be capable of producing mimics of such marks. This equifinality—the creation of similar products by different processes—makes deciphering early archaeological bone assemblages difficult. Bone modifications among Ethiopian Plio–Pleistocene hominid and faunal remains at Asa Issie, Maka, Hadar, and Bouri were reassessed in light of these findings. The results show that crocodiles were important modifiers of these bone assemblages. The relative roles of hominids, mammalian carnivores, and crocodiles in the formation of Oldowan zooarchaeological assemblages will only be accurately revealed by better bounding equifinality. Critical analysis within a consilience-based approach is identified as the pathway forward. More experimental studies and increased archaeological fieldwork aimed at generating adequate samples are now required.

Background The American alligator ( Alligator mississippiensis ) displays temperature-dependent sex determination (TSD), in which incubation temperature during embryonic development determines the sexual fate of the individual. However, the molecular mechanisms governing this process remain a mystery, including the influence of initial environmental temperature on the comprehensive gonadal gene expression patterns occurring during TSD. Results Our characterization of transcriptomes during alligator TSD allowed us to identify novel candidate genes involved in TSD initiation. High-throughput RNA sequencing (RNA-seq) was performed on gonads collected from A. mississippiensis embryos incubated at both a male and a female producing temperature (33.5 °C and 30 °C, respectively) in a time series during sexual development. RNA-seq yielded 375.2 million paired-end reads, which were mapped and assembled, and used to characterize differential gene expression. Changes in the transcriptome occurring as a function of both development and sexual differentiation were extensively profiled. Forty-one differentially expressed genes were detected in response to incubation at male producing temperature, and included genes such as Wnt signaling factor WNT11, histone demethylase KDM6B , and transcription factor C/EBPA . Furthermore, comparative analysis of development- and sex-dependent differential gene expression revealed 230 candidate genes involved in alligator sex determination and differentiation, and early details of the suspected male-fate commitment were profiled. We also discovered sexually dimorphic expression of uncharacterized ncRNAs and other novel elements, such as unique expression patterns of HEMGN and ARX . Twenty-five of the differentially expressed genes identified in our analysis were putative transcriptional regulators, among which were MYBL2, MYCL, and HOXC10, in addition to conventional sex differentiation genes such as SOX9 , and FOXL2. Inferred gene regulatory network was constructed, and the gene-gene and temperature-gene interactions were predicted. Conclusions Gonadal global gene expression kinetics during sex determination has been extensively profiled for the first time in a TSD species. These findings provide insights into the genetic framework underlying TSD, and expand our current understanding of the developmental fate pathways during vertebrate sex determination.

True crocodiles (Crocodylus) are the most broadly distributed, ecologically diverse, and species-rich crocodylian genus, comprising about half of extant crocodylian diversity and exhibiting a circumtropical distribution. Crocodylus traditionally has been viewed as an ancient group of morphologically conserved species that originated in Africa prior to continental breakup. In this study, these long-held notions about the temporal and geographic origin of Crocodylus are tested using DNA sequence data of 10 loci from 76 individuals representing all 23 crocodylian species. I infer a time-calibrated species tree of all Crocodylia and estimate the spatial pattern of diversification within Crocodylus. For the first time, a fully resolved phylogenetic estimate of all Crocodylia is well-supported. The results overturn traditional views of the evolution of Crocodylus by demonstrating that the true crocodiles are not \"living-fossils\" that originated in Africa. Rather, Crocodylus originated from an ancestor in the tropics of the Late Miocene Indo-Pacific, and rapidly radiated and dispersed around the globe during a period marked by mass extinctions of fellow crocodylians. The findings also reveal more diversity within the genus than is recognized by current taxonomy.

Reptiles are the most morphologically and physiologically diverse tetrapods, and have undergone 300 million years of adaptive evolution. Within the reptilian tetrapods, geckos possess several interesting features, including the ability to regenerate autotomized tails and to climb on smooth surfaces. Here we sequence the genome of Gekko japonicus (Schlegel’s Japanese Gecko) and investigate genetic elements related to its physiology. We obtain a draft G. japonicus genome sequence of 2.55 Gb and annotated 22,487 genes. Comparative genomic analysis reveals specific gene family expansions or reductions that are associated with the formation of adhesive setae, nocturnal vision and tail regeneration, as well as the diversification of olfactory sensation. The obtained genomic data provide robust genetic evidence of adaptive evolution in reptiles. Geckos are small, agile reptiles with nocturnal habits. Here, the authors sequence the genome of the Schlegel’s Japanese Gecko and reveal gene family expansions and reductions associated with formation of adhesive setae, nocturnal vision, tail regeneration, and diversification of olfactory sensation.

Challenges in freshwater organism conservation in West Africa are worsened by significant knowledge gaps, even for charismatic species like crocodiles. This study addresses these gaps by assessing crocodile diversity, distribution, and conservation threats in Guinea-Bissau, where existing data is outdated. We used visual surveys, inquiries, molecular barcoding, camera trapping, and bibliographic reviews to investigate crocodile populations. Notably, we found evidence suggesting the Nile crocodile ( Crocodylus niloticus ), previously thought extinct in West Africa since about 200 years, may persist in Guinea-Bissau’s Cacheu region. We also confirmed the presence of the West African crocodile ( Crocodylus suchus ) in major river basins and coastal lagoons, including the Bijagós Archipelago, and the West African dwarf crocodile ( Osteolaemus cf. tetraspis ) in the southern mainland and the Bijagós Archipelago. Habitat loss and deliberate killings were identified as major threats. Standardized surveys and genetic sampling are essential to assess population size, connectivity, and genetic diversity, informing evolutionary studies and conservation planning. Conservation efforts should prioritize habitat protection through community-managed reserves and restoration initiatives. Additionally, engaging local communities to raise awareness and develop conflict mitigation strategies is crucial, particularly in areas with human-crocodile interactions.

Background The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes. Results In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation. Conclusions These results provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.

Skulls are a critical part of the crocodile through which we can distinguish between the different genera and species. Most of the crocodiles which previously studied from the Eocene–Oligocene to the Miocene times in Egypt were concerned with the identification of the genus and sometimes on the species without a detailed focusing on the evolution, comparing between them and trying to determine the ancestor or the closest species of them to the living crocodile in Egypt. The only known living species of Crocodylus in Egypt is Crocodylus niloticus which inhabits Lake Nasser in Aswan, southern of Egypt. From the Cenozoic era, broad snouted crocodiles diversity had been reported in Egypt. About 35 million years ago, through the Eocene epoch, the crocodilian fossils from Fayum provided evidence of the diversity of crocodile species including Crocodylus articeps and Crocodylus megarhinus . In addition to that, throughout the Early Miocene epoch, from about 18 million years ago, in Wadi Moghra Egypt crocodilian fossils demonstrate another diversity, extended to the first appearance of Rimasuchus lloydi which placed inside the Osteolaeminae later. By various measurements and carefully morphological examination of the different species recorded from Egypt, it was found that there are high levels of variation in morphology of the skulls including their dimensions, and the sutures shapes especially between premaxilla and maxilla ventrally and also between maxilla and palatine, as well as the extension of the maxillary ramus of the ectopterygoid. Using cluster analysis, it is proven that Eocene Crocodylus is the ancestor to all known broad snouted species recorded from Egypt since the Eocene time. The closest species to the Eocene specimen is the living Crocodylus niloticus . That in fact make that most of the broad snouted crocodiles in Egypt are endemic.

The crocodyliform Shamosuchus is known from numerous Late Cretaceous localities in southern and eastern Mongolia and fragmentary remains from Uzbekistan. Seven species of Shamosuchus have been named from six localities in Mongolia and three in Uzbekistan. Six species originally described as Paralligator were later referred to Shamosuchus. Only the type species, Shamosuchus djadochtaensis has been examined in detail. Many of the named species of Shamosuchus show striking similarity in size and cranial morphology but most are based on partial remains suggesting that the true species diversity is overestimated. A review of all species referred to Shamosuchus recognizes three valid taxa: Shamosuchus djadochtaensis, S. gradilifrons, and S. major. Shamosuchus sungaricus, S. borealis, and S. karakalpakensis are nomena dubia, whereas S. ancestralis, S. ulgicus, S. tersus, and S. ulanicus are junior subjective synonyms of S. gradilifrons. Phylogenetic analysis of 318 phenotypic characters recovers a Paralligatoridae clade consisting of Shamosuchus, Rugosuchus, Batrachomimus, Glen Rose Form, and Wannchampsus. Shamosuchus is non-monophyletic: S. djadochtaensis is near the base of Paralligatoridae whereas S. gradilifrons + S. major are the most deeply nested. The name Paralligator is resurrected for this clade. Rugosuchus and Batrachomimus are sister taxa to Paralligator. Paralligatoridae is closely related to Theriosuchus, hylaeochampsids and a speciose Allodaposuchus clade, which together are the sister group of Borealosuchus plus Crocodylia. These results support the presence of a diverse clade in eastern Asia and western North America throughout the Cretaceous with origins in the Late Jurassic.