James F. Parham

A phylogenomic analysis of turtles

Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography. Future studies of turtle phylogeny using fossil turtles should use this topology as a scaffold for their morphological phylogenetic analyses.

A Divergence Dating Analysis of Turtles Using Fossil Calibrations: An Example of Best Practices

Abstract Turtles have served as a model system for molecular divergence dating studies using fossil calibrations. However, because some parts of the fossil record of turtles are very well known, divergence age estimates from molecular phylogenies often do not differ greatly from those observed directly from the fossil record alone. Also, the phylogenetic position and age of turtle fossil calibrations used in previous studies have not been adequately justified. We provide the first explicitly justified minimum and soft maximum age constraints on 22 clades of turtles following best practice protocols. Using these data we undertook a Bayesian relaxed molecular clock analysis establishing a timescale for the evolution of crown Testudines that we exploit in attempting to address evolutionary questions that cannot be resolved with fossils alone. Some of these questions, such as whether the turtle crown originated in the Triassic or Jurassic, cannot be resolved by our analysis. However, our results generate novel age-of-origination estimates for clades within crown Testudines. Finally, we compare our fossil calibrations and posterior age estimates to those from other studies, revealing substantial differences in results and interpretation.

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.

The Fossil Calibration Database-A New Resource for Divergence Dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the database.

The dilemma of trade samples and the importance of museum vouchers— caveats from a study on the extinction of Steller's sea cow: a comment on Crerar et al. (2014)

Crerar et al. [[1][1]] recently argued that a population of Stellers sea cows ( Hydrodamalis gigas ) persisted on St Lawrence Island (SLI), Alaska, well into historical time. If true, then Stellers sea cows were hunted to extinction in multiple places at different times in the past millennium [[2

Isolation and characterization of microsatellite markers for identifying hybridization and genetic pollution associated with red-eared slider turtles (Trachemys scripta elegans)

Fourteen microsatellite markers were isolated and characterized from a microsatellite enriched genomic library obtained for the invasive red-eared slider turtle Trachemys scripta elegans (TSE). All but one locus conformed to Hardy–Weinberg equilibrium and none displayed linkage disequilibrium. The number of alleles ranged from 5 to 17 with observed heterozygosity values ranging from 0.26 to 0.96 for 23 individuals collected from its native range in the Mississippi River drainage. These markers will be useful in characterizing TSE populations and invaded populations of other Trachemys and could aid in the development of conservation management policies for invasive TSE.

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.

New Data on the Ontogeny and Senescence of Desmostylus (Desmostylia, Mammalia)

ABSTRACT n Ontogenetic sequence and life stage determination among the desmostylians are poorly understood and known mostly from the study of dental eruption. Advanced-age life stages are nearly unknown. New material of an individual Desmostylus from the late middle to late Miocene of Orange County, California, represents the most ontogenetically advanced described specimen of the genus and helps characterize a more complete ontogenetic sequence. The material consists of a partial mandible that exhibits bony swellings, indicative of Desmostylus, but also lacks postcanine teeth (dental senescence). Comparisons with known juvenile Desmostylus and adult-stage individuals with similar bony swellings, but that still exhibit postcanine teeth, provide evidence that the Orange County specimen is that of an elderly Desmostylus. By incorporating the characteristics of this specimen into the ontogenetic sequence of the genus, a complete eruption pattern of the lower jaw can be recreated. The development of the mandible and tooth eruption sequence in Desmostylus is similar to the characteristic ontogeny of Afrotheria. In Afrotheria, the eruption of the final set of molars is delayed until the mandible has grown to maximum length. Desmostylia has been placed in Afrotheria, suggesting that the similarities in ontogenetic sequences may derive from a shared ancestry. Recent studies that place Desmostylia as stem perissodactyls suggest that the Afrotheria-like dental ontogeny may be independently derived within Desmostylia, or Desmostylus.