Morphological Species Delimitation in The Western Pond Turtle (Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification?

As the discovery of cryptic species has increased in frequency, there has been an interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods (MLMs) to investigate whether plastron shape can differentiate two putative cryptic turtle species, Actinemys marmorata and Actinemys pallida. Actinemys has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, the other consisting of two subspecies of Trachemys (T. scripta scripta, T. scripta elegans). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via MLMs. In contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in Actinemys. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for Actinemys. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between A. marmorata and A. pallida specimens, lending tentative morphological support to the hypothesis of two Actinemys species. However, the machine learning results also underscore that Actinemys as a whole has lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.

A large non‐marine turtle from the Upper Cretaceous of Alabama and a review of North American “Macrobaenids”

The abundant record of marine turtles from the Late Cretaceous of Appalachia contrasts with the relatively poor record of contemporaneous terrestrial and freshwater species. A new taxon from the Santonian-Campanian of Alabama, Appalachemys ebersolei gen. et sp. nov., is described here and assigned to a grade of freshwater turtles known as "macrobaenids." Appalachemys can be differentiated from other "macrobaenids" by the presence of a nearly round carapace, deep nuchal emargination, and nine pairs of costals. With a carapace more than 80 cm in length, Appalachemys is among the largest freshwater turtles to ever inhabit North America. The absence of pre-Campanian "macrobaenids" from Laramidia indicates that the North American distribution of this grade may have been restricted to Appalachia prior to the recession of the Western Interior Seaway. Phylogenetic analysis places Appalachemys as the sister taxon to all post-Santonian "macrobaenids." Although the phylogeny lacks statistical support, it demonstrates morphological similarities between the K/Pg boundary species Osteopygis emarginatus and Maastrichtian-Danian species referred to Judithemys. We, therefore, refer all but the Campanian type species of Judithemys to the genus Osteopygis. A review of all North American "macrobaenid" occurrences reveals that despite originating in Asia, the record of the grade (as defined here) is predominantly North American. Future studies can test whether late Paleocene records in Asia and Europe resulted from dispersal from North America.

Integrating and updating wildlife conservation in China

China has about 11% of the world’s total wildlife species, so strengthening China’s wildlife conservation is of great significance to global biodiversity. Despite some successful cases and conservation efforts, 21.4% of China’s vertebrate species are threatened by human activities. The booming wildlife trade in China has posed serious threat to wildlife in China and throughout the world, while leading to a high risk of transmission of infectious zoonotic diseases. China’s wildlife conservation has faced a series of challenges, two of which are an impractical, separated management of wildlife and outdated protected species lists. Although the Wildlife Protection Law of China was revised in 2016, the issues of separated management remain, and the protected species lists are still not adequately revised. These issues have led to inefficient and overlapping management, waste of administrative resources, and serious obstacles to wildlife protection. In this article, we analyze the negative effects of current separated management of wildlife species and outdated protected species lists, and provide some suggestions for amendment of the laws and reform of wildlife management system.

Sea turtle demand in China threatens the survival of wild populations

Sea turtles are an important umbrella species in marine ecosystems. The populations of all five species of sea turtles in China have dropped sharply due to massive illegal trade and habitat loss. The fast-growing demand for sea turtle displays from Chinese aquariums and private individuals has led to a large-scale illegal trade domestically and internationally. Captive sea turtles are also frequently kept in harsh environments with severe injuries and high mortality rates. Sea turtles have only recently been upgraded from level II to level I on the “List of Wildlife under Special State Protection”, this protection level has therefore not matched the real status of sea turtles over the past three decades. The additional collusion between the government and business corporations encourages illegal trade. We argue that the commercial use of sea turtles must be completely prohibited to guarantee their future survival in Chinese waters.

An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)

Among vertebrates, turtles have many unique characteristics providing biologists with opportunities to study novel evolutionary innovations and processes. We present here a high-quality, partially phased, and chromosome-level Red-Eared Slider (Trachemys scripta elegans, TSE) genome as a reference for future research on turtle and tetrapod evolution. This TSE assembly is 2.269 Gb in length, has one of the highest scaffold N50 and N90 values of any published turtle genome to date (N50 = 129.68 Mb and N90 = 19 Mb), and has a total of 28,415 annotated genes. We introduce synteny analyses using BUSCO single-copy orthologs, which reveal two chromosome fusion events accounting for differences in chromosome counts between emydids and other cryptodire turtles and reveal many fission/fusion events for birds, crocodiles, and snakes relative to TSE. This annotated chromosome-level genome will provide an important reference genome for future studies on turtle, vertebrate, and chromosome evolution.

Genetic variation and admixture of red-eared sliders (Trachemys scripta elegans) in the USA

The most ubiquitous, abundant, and invasive turtle on Earth, Trachemys scripta elegans (TSE, "red-eared slider"), is one of four taxa in a clade that is native to the USA and adjacent Mexico (three subspecies of Trachemys scripta plus Trachemys gaigeae). The present range-wide study of this clade is based on 173 known-locality mtDNA sequences combined with ddRAD libraries for 43 samples emphasizing the western part of the range of TSE, its contact with that of T. gaigeae, and anthropogenic hybrids between TSE and T. s. scripta. The data presented here are the first to sample the TSE × T. s. scripta intergrade zone or TSE × T. s. scripta crosses from introduced turtles. In the western part of its range (New Mexico and Texas), most samples of TSE from the Pecos River have mtDNA haplotypes matching T. gaigeae. Structure analysis of SNPs from the ddRAD show evidence of genetic admixture between T. gaigeae and TSE in all included samples from the Rio Grande and Pecos River. These populations also exhibit T. gaigeae-like head stripes, i.e., a postorbital marking that does not reach the eye. The genetic and morphological data are thereby reconciled, as both suggest that these TSE are intergrades. We recommend that these populations continue to be considered TSE, despite the admixture with T. gaigeae. In the Eastern United States, some samples of the morphologically intermediate subspecies T. s. troostii are not genetically distinct from TSE and some samples share morphological characters and genetic affinities with T. s. scripta. Based on these observations we conclude that the taxon T. s. troostii represents intergrades between TSE and T. s. scripta and should not be considered a valid taxon. Near the already established part of the intergrade zone between TSE and T. s. scripta, TSE mtDNA haplotypes have naturally introgressed into typical-looking samples of T. s. scripta in Georgia. Hybrids between introduced TSE and T. s. scripta are also confirmed deeper within the natural range of T. s. scripta in South Carolina and Virginia. Given the examples of feral hybrids deep within its range shown here and elsewhere, the threat of genetic pollution of T. s. scripta by feral TSE is established.

A new tuskless walrus from the Miocene of Orange County, California, with comments on the diversity and taxonomy of odobenids

We describe Titanotaria orangensis (gen. et. sp. nov.), a new species of walrus (odobenid) from the upper Miocene Oso Member of the Capistrano Formation of Orange County, California. This species is important because: (1) It is one of the best-known and latest-surviving tuskless walruses; (2) It raises the number of reported odobenid taxa from the Oso Member to four species making it one of the richest walrus assemblages known (along with the basal Purisima of Northern California); (3) It is just the second record of a tuskless walrus from the same unit as a tusked taxon. Our phylogenetic analysis places T. orangensis as sister to a clade that includes Imagotaria downsi, Pontolis magnus, Dusignathus spp., Gomphotaria pugnax, and Odobeninae. We propose new branch-based phylogenetic definitions for Odobenidae, Odobeninae, and a new node-based name (Neodobenia) for the clade that includes Dusignathus spp., G. pugnax, and Odobeninae. A richness analysis at the 0.1 Ma level that incorporates stratigraphic uncertainty and ghost lineages demonstrates maximum peaks of richness (up to eight or nine coeval lineages) near the base of Odobenidae, Neodobenia, and Odobenini. A more conservative minimum curve demonstrates that standing richness may have been much lower than the maximum lineage richness estimates that are biased by stratigraphic uncertainty. Overall the odobenid fossil record is uneven, with large time slices of the record missing on either side of the Pacific Ocean at some times and biases from the preserved depositional environments at other times. We recognize a provisional timescale for the transition of East Pacific odobenid assemblages that include "basal odobenids" (stem neodobenians) from the Empire and older formations (>7 Ma), to a mixture of basal odobenids and neodobenians from the Capistrano and basal Purisima (7-5 Ma), and then just neodobenians from all younger units (<5 Ma). The large amount of undescribed material will add new taxa and range extensions for existing taxa, which will likely change some of the patterns we describe.

A new species of Peritresius Leidy, 1856 (Testudines: Pan-Cheloniidae) from the Late Cretaceous (Campanian) of Alabama, USA, and the occurrence of the genus within the Mississippi Embayment of North America

Late Cretaceous members of Peritresius belong to a diverse clade of marine adapted turtles currently thought to be some of the earliest representatives of the lineage leading to modern hard-shelled sea turtles (Pan-Cheloniidae). Prior studies have suggested that Peritresius was monospecific, with a distribution restricted to Maastrichtian deposits in North America. However, new Peritresius specimens identified from Alabama and Mississippi, USA, show that the genus contains two taxa, Peritresius ornatus, and a new species Peritresius martini sp. nov. These two taxa are characterized by the presence of a generally cordiform carapace with moderately serrated peripherals, well-developed ventral flanges beginning at the third peripheral, squarish umbilical and lateral plastral fontanelles, and a narrow bridge formed by the contact between the hyoplastron and hypoplastron. Peritresius martini sp. nov. can be distinguished by its lack of dermal ornamentation and the presence of a 'rib-free' 10th peripheral. These new specimens represent the first occurrences of Peritresius from the Late Cretaceous Mississippi Embayment and extend the temporal range of this genus back to the early Campanian. When tested within a global phylogenetic context, Peritresius is placed on the stem of Cheloniidae (Pan-Cheloniidae) along with Ctenochelys and Allopleuron hofmanni. The heavily vascularized and uniquely sculptured dermal elements of P. ornatus are interpreted here as potentially relating to thermoregulation and therefore may have been one of the key factors contributing to the survival of Peritresius into the Maastrichtian, a period of cooling when other lineages of Campanian marine turtles (e.g., Protostegids, Toxochelys, and Ctenochelys) went extinct.

Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.

Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea

Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities.

Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers

Determining whether a conflict between gene trees and species trees represents incomplete lineage sorting (ILS) or hybridization involving native and/or invasive species has implications for reconstructing evolutionary relationships and guiding conservation decisions. Among vertebrates, turtles represent an exceptional case for exploring these issues because of the propensity for even distantly related lineages to hybridize. In this study we investigate a group of freshwater turtles (Trachemys) from a part of its range (the Greater Antilles) where it is purported to have undergone reticulation events from both natural and anthropogenic processes. We sequenced mtDNA for 83 samples, sequenced three nuDNA markers for 45 samples, and cloned 29 polymorphic sequences, to identify species boundaries, hybridization, and intergrade zones for Antillean Trachemys and nearby mainland populations. Initial coalescent analyses of phased nuclear alleles (using (*)BEAST) recovered a Bayesian species tree that strongly conflicted with the mtDNA phylogeny and traditional taxonomy, and appeared to be confounded by hybridization. Therefore, we undertook exploratory phylogenetic analyses of mismatched alleles from the "coestimated" gene trees (Heled and Drummond, 2010) in order to identify potential hybrid origins. The geography, morphology, and sampling context of most samples with potential introgressed alleles suggest hybridization over ILS. We identify contact zones between different species on Jamaica (T. decussata × T. terrapen), on Hispaniola (T. decorata × T. stejnegeri), and in Central America (T. emolli × T. venusta). We are unable to determine whether the distribution of T. decussata on Jamaica is natural or the result of prehistoric introduction by Native Americans. This uncertainty means that the conservation status of the Jamaican T. decussata populations and contact zone with T. terrapen are unresolved. Human-mediated dispersal events were more conclusively implicated for the prehistoric translocation of T. stejnegeri between Puerto Rico and Hispaniola, as well as the more recent genetic pollution of native species by an invasive pet turtle native to the USA (T. scripta elegans). Finally, we test the impact of introgressed alleles using the multispecies coalescent in a Bayesian framework and show that studies that do not phase heterozygote sequences of hybrid individuals may recover the correct species tree, but overall support for clades that include hybrid individuals may be reduced.

Synthesizing and databasing fossil calibrations: divergence dating and beyond

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3-6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.

Introduced delicacy or native species? A natural origin of Bermudian terrapins supported by fossil and genetic data

Humans have greatly altered the natural distribution of species, making it difficult to distinguish between natural and introduced populations. This is a problem for conservation efforts because native or introduced status can determine whether a species is afforded protection or persecuted as an invasive pest. Holocene colonization events are especially difficult to discern, particularly when the species in question is a naturally good disperser and widely transported by people. In this study, we test the origin of such a species, the diamondback terrapin (Malaclemys terrapin), on Bermuda using a combination of palaeontologic (fossil, radiometric and palaeoenvironmental) and genetic data. These lines of evidence support the hypothesis that terrapins are relatively recent (between 3000 and 400 years ago) natural colonizers of Bermuda. The tiny population of Bermudian terrapins represents the second naturally occurring non-marine reptile that still survives on one of the most densely populated and heavily developed oceanic islands in the world. We recommend that they should be given protection as a native species.

Assembly of the eastern North American herpetofauna: new evidence from lizards and frogs

Darwin first recognized the importance of episodic intercontinental dispersal in the establishment of worldwide biotic diversity. Faunal exchange across the Bering Land Bridge is a major example of such dispersal. Here, we demonstrate with mitochondrial DNA evidence that three independent dispersal events from Asia to North America are the source for almost all lizard taxa found in continental eastern North America. Two other dispersal events across Beringia account for observed diversity among North American ranid frogs, one of the most species-rich groups of frogs in eastern North America. The contribution of faunal elements from Asia via dispersal across Beringia is a dominant theme in the historical assembly of the eastern North American herpetofauna.

The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA

BACKGROUND

The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis.

RESULTS

We sequenced the complete mt genome of Platysternon and the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement of Platysternon with Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered that Platysternon mtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles.

CONCLUSION

Our study robustly determines the phylogenetic placement of Platysternon and provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placing Platysternon with chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of the Platysternon mtDNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded, examples of this are rare. So far, duplicated control regions have been reported for mt genomes from just 12 clades of metazoans, including Platysternon.

The phylogeny of Mediterranean tortoises and their close relatives based on complete mitochondrial genome sequences from museum specimens

As part of an ongoing project to generate a mitochondrial database for terrestrial tortoises based on museum specimens, the complete mitochondrial genome sequences of 10 species and a approximately 14kb sequence from an eleventh species are reported. The sampling of the present study emphasizes Mediterranean tortoises (genus Testudo and their close relatives). Our new sequences are aligned, along with those of two testudinoid turtles from GenBank, Chrysemys picta and Mauremys reevesii, yielding an alignment of 14,858 positions, of which 3238 are parsimony informative. We develop a phylogenetic taxonomy for Testudo and related species based on well-supported, diagnosable clades. Several well-supported nodes are recovered, including the monophyly of a restricted Testudo, T. kleinmanni+T. marginata (the Chersus clade), and the placement of the enigmatic African pancake tortoise (Malacochersus tornieri) within the predominantly Palearctic greater Testudo group (Testudona tax. nov.). Despite the large amount of sequence reported, there is low statistical support for some nodes within Testudona and so we do not propose names for those groups. A preliminary and conservative estimation of divergence times implies a late Miocene diversification for the testudonan clade (6-10 million years ago), matching their first appearance in the fossil record. The multi-continental distribution of testudonan turtles can be explained by the establishment of permanent connections between Europe, Africa, and Asia at this time. The arrival of testudonan turtles to Africa occurred after one or more initial tortoise invasions gave rise to the diverse (>25 species) 'Geochelone complex.' Two unusual genomic features are reported for the mtDNA of one tortoise, M. tornieri: (1) nad4 has a shift of reading frame that we suggest is resolved by translational frameshifting of the mRNA on the ribosome during protein synthesis and (2) there are two copies of the control region and trnF, with the latter having experienced multiple-nucleotide substitutions in a pattern suggesting that each is being maintained by selection.

Evolutionary distinctiveness of the extinct Yunnan box turtle (Cuora yunnanensis) revealed by DNA from an old museum specimen

Cuora yunnanensis is an extinct turtle known from 12 specimens collected from Yunnan, China, before 1908. We used ancient DNA methods to sequence 1723 base pairs of mitochondrial DNA from a museum specimen of C. yunnanensis. Unlike some rare 'species' recently described from the pet trade, C. yunnanensis represents a lineage that is distinct from other known turtles. Besides C. yunnanensis, two other valid species (C. mccordi, C. zhoui) are unknown in the wild but are supposedly from Yunnan. Intensive field surveys for surviving wild populations of these critically endangered species are urgently needed.