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Shovel-nosed Salamanders, Desmognathus marmoratus (Moore, 1899), were long thought to represent a single species from the southern Appalachian Mountains of the eastern United States, ranging from northeastern Georgia to extreme southwestern Virginia. These populations have a highly derived ecomorphology, being fully aquatic with a specialized flattened and elongated phenotype adapted to rocky riffle zones in fast-flowing, high-gradient mountain streams. Because of this, they were originally described in a separate genus, Leurognathus Moore, 1899. Four additional species or subspecies were described from 1928–1956 based on regional geographic variation in phenotype before being synonymized with L. marmoratus in 1962, which was reassigned to Desmognathus in 1996. Molecular analyses subsequently revealed four distinct candidate lineages in two distantly related clades, which were recently re-delimited into three species. These are D. aureatus (Martof, 1956) from northeastern Georgia, D. intermedius (Pope, 1928) from western North Carolina, and D. marmoratus from northwestern North Carolina. We provide a systematic revision of these taxa, which do not represent a natural group but instead exhibit convergent phenotypes across multiple species, potentially driven by ancient episodes of adaptive introgression between ancestral lineages. Our recent fieldwork revealed an astonishingly disjunct and morphologically distinct population of D. marmoratus in the New River Gorge of West Virginia, which were previously confused with D. kanawha Pyron and Beamer, 2022. This locality is ~120 airline km away from the nearest populations of D. marmoratus in Virginia. No Shovel-nosed Salamanders have ever been found in the New River drainage during our extensive previous explorations or credibly reported in museum specimens or the literature. Additional cryptic populations of these taxa may remain.

Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large data sets. Integrative taxonomy can, therefore, reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We discover 2 geographic genetic clusters, for which demographic and spatial models of ecology and gene flow provide robust support for ecogeographic speciation despite limited phenotypic divergence. These data are integrated under evolutionary mechanisms (e.g., spatially localized gene flow with reduced migration) and reflected in emergent properties expected under models of reinforcement (e.g., ethological isolation and selection against hybrids). Their genetic divergence is prima facie evidence for species-level distinctiveness, supported by speciation models and divergence along axes such as behavior, geography, and climate that suggest an ecological basis with subsequent reinforcement through prezygotic isolation. As data sets grow more comprehensive, species-delimitation models can be tested, rejected, or corroborated as explicit speciation hypotheses, providing for reciprocal illumination of evolutionary processes and integrative taxonomies. [Desmognathus; integrative taxonomy; machine learning; species delimitation.]

Most swamp-dwelling dusky salamanders of the genus Desmognathus from the Coastal Plain were long treated as a single species (Desmognathus auriculatus) ranging from east Texas to southeastern Virginia. This taxon concept was based on the name Salamandra auriculata Holbrook, 1838 with type locality Riceboro, Liberty County, Georgia and a type series that could not be located by later authors. Recent workers have been unable to locate or verify swamp-dwelling populations from east Texas and western Louisiana, which appear to be extirpated and may not have represented a distinct taxon from co-occurring lineages of D. conanti. Recent molecular phylogenies have supported at least four distinct species-level taxa within D. auriculatus. Populations from the Gulf Coastal Plain in eastern Louisiana, Mississippi, and southwestern Alabama were recently described as D. valentinei Means, Lamb, and Bernardo, 2017 and D. pascagoula Pyron, O’Connell, Lamb, and Beamer, 2022. This leaves two remaining species-level lineages with uncertain taxonomy and nomenclature: D. auriculatus A (Alabama, Florida, and Georgia), and D. auriculatus B/C (Georgia, South Carolina, and North Carolina), both of which occur near the type locality. We recently located a specimen at the Muséum national d’Histoire naturelle in Paris (MNHN 0.4675) that we concluded is one of Holbrook’s syntypes and designated it as the lectotype, but without allocation. Here, we use linear morphometrics to confidently allocate it to D. auriculatus A, bolstered by examination of three historical topotypic collections. This requires a new name for D. auriculatus B/C, which we describe as D. valtos sp. nov. (suggested common name: Carolina Swamp Dusky Salamander) from Otter Creek, Craven County, North Carolina. Other related and sympatric species of Desmognathus remain to be described from the Atlantic Coastal Plain and adjacent Piedmont of the southeastern United States.

Tetrapods (amphibian, reptiles, birds and mammals) have become a central model system for global ecology, conservation, and biodiversity science at large. But continuing data gaps, limited data standardisation, and ongoing flux in taxonomic nomenclature constrain integrative research on this group and potentially cause biased inference. We combined and harmonised taxonomic, spatial, phylogenetic, and attribute data with phylogeny-based imputation to provide a comprehensive data resource (TetrapodTraits) that includes values, predictions, and sources for 75 attributes. These attributes include body size, activity time, micro- and macrohabitat, geography, environmental preferences, human influence and threat status, for all 33,281 tetrapod species covered in recent fully sampled phylogenies. We assess gaps and biases across taxa and space, finding that shared data missing in attribute values increased with taxon-level completeness and richness across clades. Prediction of missing attribute values using multiple assessment methods revealed substantial changes in estimated macroecological patterns. These results highlight particular biases incurred by non-random missingness and mechanisms to best address it. While there is an obvious need for further data collection and updates, our phylogeny- -informed database of tetrapod traits can support a better representation of undersampled species and their attributes in ecology, evolution, and conservation.

The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns – but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.

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

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]

Here, we provide updates to our recent paper reviewing the taxonomy and nomenclature of the Eastern ratsnakes (Pantherophis obsoletus complex, Colubridae, Serpentes). Specifically, we clarify that Coluber alleghaniensis Holbrook, 1836 is a subjective, rather than objective, senior synonym of Elaphis holbrookii Duméril, Bibron & Duméril, 1854. Contrary to our statement that USNM 1733–4 were syntypes of Scotophis lindheimerii Baird & Girard, 1853, the former is the holotype and the latter is the paratype. The holotype is lost and the paratype is in poor condition, but no neotype designation is warranted at present. We note that USNM 248870, which we designated as the lectotype of Coluber obsoletus lemniscatus Cope, 1888, was originally cataloged as USNM 4710. This catalog number was shared with the type of the salamander Amblystoma tenebrosum Baird & Girard, 1852, and the snake was re-cataloged as USNM 248870 in 1985. Finally, we originally treated C. reticulatus La Cépède, 1789 and C. reticularis Daudin, 1803 as senior subjective synonyms of C. corais Boie, 1827, but here corroborate recent authors in designating it a senior subjective synonym of C. obsoletus Say in James, 1823. As the Commission suppressed C. reticulatus La Cépède, 1789 (an exoplonym), this subsequently rendered C. reticularis Daudin, 1803 (an exoploneonym) unavailable as well.

Continental mountain areas cover15% of global land surface, yet these regions concentrate80% of global terrestrial diversity. One prominent hypothesis to explain this pattern proposes that high mountain diversities could be explained by higher diversification rates in regions of high topographic complexity (HTC). While high speciation in mountains has been detected for particular clades and regions, the global extent to which lineages experience faster speciation in mountains remains unknown. Here we addressed this issue using amphibians as a model system (7,000 species), and we found that families showing high speciation rates contain a high proportion of species distributed in mountains. Moreover, we found that lineages inhabiting areas of HTC speciate faster than lineages occupying areas that are topographically less complex. When comparing across regions, we identified the same pattern in five biogeographical realms where higher speciation rates are associated with higher levels of complex topography. Low-magnitude differences in speciation rates between some low and high complex topographies suggest that high mountain diversity is also affected by low extinction and/or high colonization rates. Nevertheless, our results bolster the importance of mountains as engines of speciation at different geographical scales and highlight their importance for the conservation of global biodiversity.

Squamates (lizards, snakes, and their kin such as amphisbaenians, or “worm lizards”) represent the world's most diverse clade of terrestrial vertebrates with ∼11,000 described extant species, representing key components in many of the world's most diverse ecosystems. With an evolutionary history dating back at least to the Middle Triassic at 242 Ma, the squamate Tree of Life also features numerous diverse but extinct branches, with hundreds of fossil species found all over the world. Despite their biological relevance both today and in the geological past, there remains a centuries-old controversy on how the major lineages of squamates are related to each other, with a direct impact on studies in ecology, evolution, paleontology, toxinology, and other fields. Here, we provide a historical overview of this long research tradition, from 19th century naturalists to 21st century phylogenomics, with special emphasis on several recent advances over the last two decades. These insights have had a dramatic effect on our understanding of the squamate Tree of Life and clarify several possible future research agendas. We provide an integrative perspective derived from genomics, morphology, and the fossil record and propose several points of synthesis in our current knowledge of broadscale squamate evolution and systematics. Key topics of interest include dating the origin and early evolution of lizards, the phylogenetic origin of snakes, the evolution of venom, recent agreements between morphological and molecular squamate evolutionary trees, genomic patterns of evolution, and the integration of morphological and molecular data sets. We conclude by providing perspectives on possible advancements in the field, directing researchers to promising future lines of investigation that are necessary to further expand our synthetic knowledge of squamate evolution.

Although currently most taxonomists claim to adhere to the concept of ‘phylogenetic taxonomy’, in fact most of the zoological classifications currently published are only in part ‘phylogenetic’ but include also phenetic or gradist approaches, in their arbitrary choices of the nodes formally recognised as taxa and in their attribution of ranks to these taxa. We here propose a new approach to ‘phylogenetic taxonomy and nomenclature’, exemplified by a phylogenetic classification or cladonomy of the extant amphibians (subclass Lissamphibia of the class Amphibia) derived from a supermatrix-based phylogenetic analysis using 4060 amphibian species, i.e. about half of the 8235 species recognised on 31 October 2020. These taxa were represented by a mean of 3029 bp (range: 197–13849 bp) of DNA sequence data from a mean of 4 genes (range: 1‒15). The cladistic tree thus generated was transferred into a classification according to a new taxonomic and nomenclatural methodology presented here, which allows a bijective or isomorphic relationship between the phylogenetic hypothesis and the classification through a rigorous use of suprageneric ranks, in which their hierarchy mirrors the structure of the tree. Our methodology differs from all previous ones in several particulars: [1] whereas the current International Code of Zoological Nomenclature uses only three ‘groups of names’ (species, genus and family), we recognise four nominal-series (species, genus, family and class); [2] we strictly follow the Code for the establishment of the valid nomen (scientific name) of taxa in the three lower nominal-series (however, in a few situations, we suggest improvements to the current Rules of the Code); [3] we provide precise and unambiguous Criteria for the assignment of suprageneric nomina to either the family- or the class-series, excluding nomina proposed expressly under unranked or pseudoranked nomenclatural systems; [4] in the class-series, for which the Code provides only incomplete Rules concerning availability, we provide precise, complete and unambiguous Criteria for the nomenclatural availability, taxonomic allocation and nomenclatural validity and correctness of nomina; [5] we stress the fact that nomenclatural ranks do not have biological definitions or meanings and that they should never be used in an ‘absolute’ way (e.g., to express degrees of genetic or phenetic divergence between taxa or hypothesised ages of cladogeneses) but in a ‘relative’ way: two taxa which are considered phylogenetically as sister-taxa should always be attributed to the same nomenclatural rank, but taxa bearing the same rank in different ‘clades’ are by no means ‘equivalent’, as the number of ranks depends largely on the number of terminal taxa (species) and on the degree of phylogenetic resolution of the tree; [6] because of this lack of ‘equivalence’, some arbitrary criteria are necessary to fix a starting point for assigning a given suprageneric rank to some taxa, from which the ranks of all other taxa will automatically derive through a simple implementation of the hierarchy of ranks: for this purpose we chose the rank family and we propose a ‘Ten Criteria Procedure’ allowing to fix the position of this rank in any zoological classification. As a result of the implementation of this set of Criteria, we obtained a new ranked classification of extant lissamphibians using 25 suprageneric ranks below the rank class (11 class-series and 14 family-series ranks), and including 34 class-series and 573 family-series taxa, and where the 575 genera we recognise are referred to 69 families and 87 subfamilies. We provide new nomina and diagnoses for 10 class-series taxa, 171 family-series taxa, 14 genus-series taxa and 1 species. As many new species of amphibians are permanently described, this classification and its nomenclature will certainly have to change many times in the future but, using the clear, explicit, complete, automatic and unambiguous methodology presented here, these changes will be easy to implement, and will not depend on subjective and arbitrary choices as it has too often been the case in the last decades. We suggest that applying this methodology in other zoological groups would improve considerably the homogeneity, clarity and usefulness of zoological taxonomy and nomenclature.

Jacob Green was born in 1790 to a prominent New Jersey family of scholars and theologians. He taught at the College of New Jersey (now Princeton University) from 1818 to 1822 before co-founding Jefferson Medical College (now Thomas Jefferson University) in 1825, where he taught Chemistry until his death in 1841. Between 1818 and 1831, he published a series of nine papers on lizards, salamanders, and snakes, authoring the original description of several well-known species of salamanders from the eastern United States. Many of his names are ambiguous; some have been adjudicated by the ICZN, while others are currently treated as nomina dubia. Here, we review all of Green’s publications, report on newly re-discovered or re-interpreted material from several major natural history collections, and resolve most if not all remaining issues through a series of taxonomic actions. In particular, we first designate a neotype for Salamandra nigra Green, 1818. We then place S. sinciput-albida Green, 1818 and S. frontalis Gray in Cuvier, 1831 in synonymy with S. scutata Temminck in Temminck & Schlegel, 1838 and invoke Reversal of Precedence under Article 23.9 to designate them nomina oblita. We also designate a lectotype for S. bislineata Green, 1818. Finally, we resurrect the name S. fusca Green, 1818 as the valid name for the species Desmognathus fuscus, assuming priority over Triturus fuscus Rafinesque, 1820, designating S. fusca Laurenti, 1768 a nomen oblitum, and placing S. nigra Green, 1818 in synonymy. While Green’s herpetological legacy is not as expansive as that of some of his successors such as Holbrook, he is nonetheless a foundational early worker in salamanders, having described some of the most-studied species in the world.

Frogs of the genus Ptychadena (Boulenger, 1917) have long been identified as harboring cryptic diversity and comprising numerous species-complexes (Largen 1997; Zimkus et al. 2017), and many authors have recognized the particularly high hidden richness in the Ethiopian highlands (Largen 1997; see Largen & Spawls 2010 and refs. within). This cryptic diversity was confirmed by recent molecular studies (Freilich et al. 2014; Smith et al. 2017a, Reyes-Velasco et al. 2018). Those authors identified a congruent set of evolutionarily distinct candidate species using both mitochondrial and nuclear DNA, and described the geographic and ecological isolation of these species in detail (Freilich et al. 2014; Smith et al. 2017a).

A recent molecular phylogenetic revision of the snake-eyed skinks (genus Panaspis Cope, 1868) uncovered extensive cryptic diversity, including several new species from throughout sub-Saharan Africa. Here, we describe one of these from Ethiopia as Panaspis annettesabinae sp. nov. This description is based on a previous molecular phylogeny and morphological, scalation, and coloration data collected from the type specimen. Phylogenetic analyses place the species alone in what we term the P. annettesabinae species group from Ethiopia. This group forms the sister lineage to a large southern African radiation and suggests a potential northern origin for much of the extant diversity of Panaspis. Many new taxa have recently been discovered in the genus and region, and there are several historical records of Panaspis from elsewhere in Ethiopia. Thus, we suggest that the range of this new species (known only from a single specimen at present) may be much larger, and that additional undescribed species may exist in northern sub-Saharan Africa.

Many animals breed exclusively in plants that accumulate rainwater (phytotelma; e.g., bromeliad, bamboo, fruit husk, and tree hole), to which they are either physiologically or behaviorally specialized for this microhabitat. Of the numerous life-history modes observed in frogs, few are as striking or potentially consequential as the transition from pond- or stream-breeding to the deposition of eggs or larvae in phytotelmata. Such specialization can increase offspring survivorship due to reduced competition and predation, representing potential ecological opportunity for adaptive radiation, yet few lineages of phytotelma-breeding frogs appear to have diversified extensively after such a transition, at least in the New World. We use a phylogeny of Neotropical frogs and data on breeding microhabitat to understand the evolutionary transitions involved with specialized phytotelma-breeding. First, we find that phytotelma-breeding is present in at least 168 species in 10 families of frogs. Across the phylogeny, we estimate 14 origins of phytotelma-breeding and 115 reversals, showing that phytotelma-breeding is a highly labile character. Second, phytotelma-breeding lineages overall have higher net diversification than nonphytotelma-breeding ones. This specialization represents an ecological opportunity resulting in increased diversification in most families with phytotelma-breeding lineages, whereas phytotelma-breeding toads have restricted diversification histories.

Additional file 2. Supplementary methods and information.

Global change imperils a large swath of the planet’s biodiversity, portending a future with decreasing species richness and functioning of natural ecosystems (1). However, the effects of global change are highly variable across scales (2). For example, while the data are contentious, patterns of local stability or increases in species richness have been reported globally in plants and animals (3). However, richness alone may not be the best indicator of global change (4), as the species composition of sites and the broader pool may vary significantly in response to anthropogenic pressures. In PNAS, Nowakowski et al. (5) tackle part of this conundrum empirically, surveying worldwide the impact that habitat conversion has on abundance and community assembly in amphibians. Interestingly, habitat conversion also creates not only the expected class of “losers,” species quickly reduced in abundance or driven extinct by human activities, but also a sizeable class of “winners,” species experiencing drastic ecological gains and increasing abundance in modified landscapes. Correspondingly, winners are overrepresented in modified communities, and drive communities overall to be more similar to each other than they were in the past. Across all sites, Nowakowski et al. (5) find that 81% of species declined in abundance in converted habitats, while 19% increased. The authors find that species’ responses to habitat conversion are phylogenetically conserved, likely related to traits that affect microhabitat use. Closely related species exhibit similar responses to disturbance, even in different sites in different areas. This results in nonrandom shifts in phylogenetic community structure, homogenizing communities and decreasing overall species-richness in the global pool of biodiversity. Species with specialized life histories or narrow microhabitat requirements related to vegetation and climate decreased drastically, such as Neotropical plethodontid salamanders like Bolitoglossa (4× decrease), Old World rhacophorid treefrogs like Pseudophilautus (28×), and New World direct-developing frogs like Pristimantis (6×). … [↵][1]1Email: rpyron{at}colubroid.org. [1]: #xref-corresp-1-1

Background The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic and Jurassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~ 25 crocodilian and ~ 360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with statistical and machine learning algorithms to present a phylogenetically informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species. Results In contrast to other terrestrial vertebrates and their own diversity in the fossil record, the recent extant lineages of turtles and crocodilians have not experienced any global mass extinctions or lineage-wide shifts in diversification rate or body-size evolution over time. We predict threat statuses for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened turtles and crocodilians in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies. Conclusions Extant turtles and crocodilians maintain unique, conserved morphologies which make them globally recognizable. Many species are threatened due to exploitation and global change. We use taxonomically complete, dated molecular phylogenies and various approaches to produce a comprehensive assessment of threat status and evolutionary distinctiveness of both groups. Neither group exhibits significant overall shifts in diversification rate or body-size evolution, or any signature of global mass extinctions in recent, extant lineages. However, the most evolutionarily distinct species tend to be the most threatened, and species richness and extinction risk are centered in areas of high anthropogenic disturbance, particularly South and Southeast Asia. Range size is the strongest predictor of threat, and a disproportionate amount of evolutionary diversity is at risk of imminent extinction.

The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~25 crocodilian and ~360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with machine learning algorithms to present a phylogenetically-informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species. In contrast to other terrestrial vertebrates and their own diversity in the fossil record, extant turtles and crocodilians have not experienced any mass extinctions or shifts in diversification rate, or any significant jumps in rates of body-size evolution over time. We predict threat for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened crocodile and turtle species in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies.

The Late Cretaceous saw distinctly endemic dinosaur faunas evolve in the northern and southern hemispheres. The Laurasian continents of North America and Asia were dominated by hadrosaurid and ceratopsian ornithischians, with tyrannosaurs as apex predators. In Gondwanan communities, including Africa, South America, India and Madagascar, titanosaurian sauropods dominated as herbivores and abelisaurids as predators. These patterns are thought to be driven by the breakup of Pangaea and formation of seaways limiting dispersal. Here, we report a new lambeosaurine hadrosaurid, Ajnabia odysseus gen. et sp. nov., from the upper Maastrichtian of Morocco, North Africa, the first Gondwanan representative of a clade formerly thought to be restricted to Laurasia. The new animal shows features unique to Hadrosauridae and specifically Lambeosaurinae. Phylogenetic analysis recovers it within Arenysaurini, a clade of lambeosaurines previously known only in Europe. Biogeographic modelling shows that lambeosaurines dispersed from Asia to Europe, then to Africa. Given the existence of large, persistent seaways isolating Africa and Europe from other continents, and the absence of the extensive, bidirectional interchange characterizing land bridges, these patterns suggest dispersals across marine barriers, similar to those seen in Cenozoic mammals, reptiles, and amphibians. Dispersal across marine barriers also occurs in other hadrosaurid lineages and titanosaurian sauropods, suggesting oceanic dispersal played a key role in structuring Mesozoic terrestrial dinosaur faunas.

Macroevolutionary rates of diversification and anthropogenic extinction risk differ vastly throughout the Tree of Life. This results in a highly heterogeneous distribution of Evolutionary distinctiveness (ED) and threat status among species. We examine the phylogenetic distribution of ED and threat status for squamates (amphisbaenians, lizards, and snakes) using fully-sampled phylogenies containing 9574 species and expert-based estimates of threat status for ~ 4000 species. We ask whether threatened species are more closely related than would be expected by chance and whether high-risk species represent a disproportionate amount of total evolutionary history. We found currently-assessed threat status to be phylogenetically clustered at broad level in Squamata, suggesting it is critical to assess extinction risks for close relatives of threatened lineages. Our findings show no association between threat status and ED, suggesting that future extinctions may not result in a disproportionate loss of evolutionary history. Lizards in degraded tropical regions (e.g., Madagascar, India, Australia, and the West Indies) seem to be at particular risk. A low number of threatened high-ED species in areas like the Amazon, Borneo, and Papua New Guinea may be due to a dearth of adequate risk assessments. It seems we have not yet reached a tipping point of extinction risk affecting a majority of species; 63% of the assessed species are not threatened and 56% are Least Concern. Nonetheless, our results show that immediate efforts should focus on geckos, iguanas, and chameleons, representing 67% of high-ED threatened species and 57% of Unassessed high-ED lineages.

The squamates occur in a variety of climates from tropical to Arctic regions. Being poikilotherms, snakes and lizards in temperate regions, and high elevation tropical environments, must adjust their reproductive biology to reproduce at a time that optimizes offspring survival. The two major components of the reproductive cycle in both males and females are gametogenesis and mating. The reproductive cycle of males is the focus of this study. In snakes in temperate climates, sperm production (spermatogenesis) may occur immediately prior to mating (prenuptial spermatogenesis) or following mating (postnuptial spermatogenesis). In postnuptial spermatogenesis, sperm are produced following the mating season and stored in the efferent testicular ducts (primarily the ductus deferens) until the following spring mating season. Given that most recent phylogenetic reconstructions resolve snakes as a monophyletic group of highly specialized lizards, it is generally assumed that lizards have spermatogenic cycles similar to snakes. Lizard spermatogenic cycles are often described as prenuptial or postnuptial. We propose that the major difference between snake and lizard spermatogenic cycles is the presence of postnuptial spermatogenesis in snakes and the absence of true postnuptial spermatogenesis in lizards. Our interpretation of lizard spermatogenic cycles suggests that all lizards have prenuptial spermatogenesis (i.e., sperm are produced immediately prior to mating). If fertilization occurs months after mating, the female, and not the male, stores the sperm until spring ovulation and fertilization. Using a variety of analytical tools, we analyzed the reproductive strategies of snakes and lizards, and we have concluded that they differ in fundamental ways. Most notably, prenuptial spermatogenesis is the ancestral condition for Squamata with continuous spermatogenesis evolving multiple times independently within lizards and snakes. We also found that postnuptial spermatogenesis evolved early in the evolutionary history of snakes but, we argue, has never evolved in lizards. We suggest that the evolutionary origin of snakes may account for the differences observed in snake versus lizard reproductive cycles, and we present a scenario for the evolution of snake reproductive cycles.

Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described, 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 “candidate species” and multiple paraphyletic taxa presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods do not estimate fully resolved relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in Desmognathus may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.

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

Summary Amphibians are among the most highly threatened lineages, with at least 2,000 species estimated to be in danger of extinction [ 1 , 2 ]. Alarmingly, another ∼2,200 species (∼25% of all ∼7,900 known species) are data deficient or not evaluated (hereinafter termed data deficient) by the International Union for Conservation of Nature (IUCN) [ 1 ]. Without an estimate of their status, data-deficient species are usually overlooked in conservation planning and resource allocation [ 3 ]. Amphibians have the highest proportion of data-deficient species of any vertebrate group [ 1 , 4 ], which highlights the need to estimate their threat status considering potentially imminent extinctions. We apply a trait-based spatio-phylogenetic statistical framework [ 5 ] to predict threat status for data-deficient species. Because ecological, geographical, and evolutionary attributes increase extinction risk [ 6 , 7 ], we used geographic distribution data [ 1 , 8 ], phylogenetically imputed ecological traits, and an amphibian phylogeny [ 9 ] to provide initial baseline predictions. We estimate that half of the ∼2,200 data-deficient species are threatened with extinction (vulnerable, endangered, or critically endangered), primarily in the Neotropics and Southeast Asia. This increases the number of amphibian species estimated to be threatened with extinction by ∼50%. Of these, we predict that ∼500 species are endangered or critically endangered, and three may be extinct already. We highlight families that are most at risk and suggest where urgent conservation is needed to avert their loss. We show that some of the most vulnerable species may also be the most poorly known and offer an analytical framework for preliminary analysis of their threat status in the face of deficient empirical data.

Systematics at the species level is still marked by theoretical and empirical tensions amongst the desires to identify geographical lineages, delimit species, and estimate their relationships. These goals are often confounded because each relies, at least to some extent, on the others being known. However, recently developed methods can simultaneously address all three. Furthermore, next-generation genomic sequencing allows us to generate large-scale molecular data sets to examine variation within species at a fine scale. Finally, a renaissance in morphological species validation allows us to integrate historical species definitions with coalescent models for species delimitation. Here, we investigate the applicability of these methods in an empirical case, in the Nearctic snake genus Storeria. Integrating trait data into species delimitation reduces the number of species delimited from molecular data alone. Whereas molecular data support eight distinct species-level lineages, including morphological data reduces this to four. The taxa Storeria dekayi, Storeria occipitomaculata, Storeria storerioides, and Storeria victa are considered distinct, monotypic species, with no subspecies recognized. We highlight the need for careful assessment of species delimitation, combining both computational genetic methods as well as traditional character-based descriptions. It is now possible to identify phylogeographical lineages, delimit species using molecular and morphological data, and estimate their relationships in a single coherent set of analyses. Moving forward, this will allow for more rapid and objective assessments of cryptic diversity at the species level.

Aim Size is one of the most important and obvious traits of an organism. Both small and large sizes have adaptive advantages and disadvantages. Body size–frequency distributions of most large clades are unimodal and right skewed. Species larger than the mean or range midpoint of body sizes are relatively scarce. Theoretical models suggest evolutionary rates are higher in small organisms with short generation times. Therefore diversification rates are usually thought to be maximal at relatively small body sizes. Empirical studies of the rates of molecular evolution and clade diversification, however, have usually indicated that both are unrelated to body size. Furthermore, it has been claimed that because snakes are longer than lizards, the size–frequency distribution of all squamate species is bimodal overall. We examined the shape of the size–frequency distribution of nearly all Squamata and Rhynchocephalia species, and investigated how size affected diversification rates. Location Global. Methods We collected data on maximum body length for 9805 lepidosaur (squamates and the tuatara) species (99.7% of all species) and converted them to mass using clade-specific allometric equations. Using methods that test for relationships between continuous traits and speciation and extinction rates on a large, dated phylogeny (4155 species), we investigated the relationship between diversification rates and body size. Results Living squamates span six orders of magnitude in body size, eight when giant extinct snakes and mosasaurs are included. The body size–frequency distributions of snakes and lizards separately, and of all lepidosaur species combined, are unimodal and right skewed. Nonetheless, we find neither linear nor hump-shaped relationships between size and diversification rates, except in snakes, where speciation and diversification are hump shaped. Main conclusions Despite a clear modality and skew in the body sizes of lepidosaurs, we find little evidence for faster diversification of modal-sized taxa, perhaps implying that larger-sized clades are relatively young.

We present a new molecular phylogeny of the stream treefrog genus Hyloscirtus, with an improved taxon sampling in the Hyloscirtus bogotensis group. The tree supports the existence of three clades within the genus (Hyloscirtus armatus group, H. bogotensis group and Hyloscirtus larinopygion group) in congruence with previous studies, and suggests the presence of at least three new species in the H. bogotensis group. Herein, we describe one of these species, Hyloscirtus mashpi n. sp. from the Pacific slope of the Ecuadorian Andes. The validity of the latter is supported by molecular, morphological and acoustic data. We also tested individuals of the new species for the chytrid fungus Batrachochytrium dendrobatidis, finding a prevalence of 17.6% (6 positives and 28 negatives). However, at sampled streams, frog densities were high, suggesting that H. mashpi n. sp. may be tolerant to the infection.

The time is past when a research program in systematics should be based on only a few genes, extant taxa, and ultrametric trees. Cheap genome sequencing, powerful statistical methods, and new fossil discoveries promise to reinvigorate research programs in evolutionary biology. Population genetics, phylogeography, and species delimitation all benefit from genomic data, not just tree building alone. Null-hypothesis testing and power analysis via simulation can increase the confidence and robustness of phylogenetic comparative methods. Merging morphological and molecular datasets for fossil and extant taxa gives a more complete view of the Tree of Life. Combined, these developments can foster a post-molecular systematics, integrating phylogenetic signal from the population up based on DNA and through time based on direct observation rather than inference.

A molecular phylogeny of the Neotropical snail-eating snakes (tribe Dipsadini) is presented including 43 (24 for the first time) of the 77 species, sampled for both nuclear and mitochondrial genes. Morphological and phylogenetic support was found for four new species of Dipsas and one of Sibon, which are described here based on their unique combination of molecular, meristic, and color pattern characteristics. Sibynomorphus is designated as a junior subjective synonym of Dipsas. Dipsaslatifrontalis and D.palmeri are resurrected from the synonymy of D.peruana. Dipsaslatifasciata is transferred from the synonymy of D.peruana to the synonymy of D.palmeri. A new name, D.jamespetersi, is erected for the taxon currently known as Sibynomorphuspetersi. Re-descriptions of D.latifrontalis and D.peruana are presented, as well as the first photographic voucher of an adult specimen of D.latifrontalis, along with photographs of all known Ecuadorian Dipsadini species. The first country record of D.variegata in Ecuador is provided and D.oligozonata removed from the list of Peruvian herpetofauna. With these changes, the number of Dipsadini reported in Ecuador increases to 22, 18 species of Dipsas and four of Sibon.