Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira)

Pleurodires or side-necked turtles are today restricted to freshwater environments of South America, Africa– Madagascar and Australia, but in the past they were distributed much more broadly, being found also on Eurasia, India and North America, and marine environments. Two hypotheses were proposed to explain this distribution; in the first, vicariance would have shaped the current geographical distribution and, in the second, extinctions constrained a previously widespread distribution. Here, we aim to reconstruct pleurodiran biogeographic history and diversification patterns based on a new phylogenetic hypothesis recovered from the analysis of the largest morphological dataset yet compiled for the lineage, testing which biogeographical process prevailed during its evolutionary history. The resulting topology generally agrees with previous hypotheses of the group and shows that most diversification shifts were related to the exploration of new niches, e.g. littoral or marine radiations. In addition, as other turtles, pleurodires do not seem to have been much affected by either the Cretaceous– Palaeogene or the Eocene–Oligocene mass extinctions. The biogeographic analyses highlight the predominance of both anagenetic and cladogenetic dispersal events and support the importance of transoceanic dispersals as a more common driver of area changes than previously thought, agreeing with previous studies with other non-turtle lineages.Fil: Ferreira, Gabriel S.. Universidade de Sao Paulo; Brasil. Senckenberg Centre For Human Evolution And Palaeoenvironment; Alemania. Universität Tübingen; AlemaniaFil: Bronzati Filho, Mario. Bayerische Staatssammlung für Paläontologie und Geologie; AlemaniaFil: Langer, Max C.. Universidade de Sao Paulo; BrasilFil: Sterli, Juliana. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology

The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties of water and air. We investigate the shape and size of the air‐filled middle ear cavity of 56 extant turtles using 3D data and phylogenetic comparative analysis to test for correlations between habitat preferences and the shape and size of the middle ear cavity. Only weak correlations are found between middle ear cavity size and ecology, with aquatic taxa having proportionally smaller cavity volumes. The middle ear cavity of turtles exhibits high shape diversity among species, but we found no relationship between this shape variation and ecology. Surprisingly, the estimated acoustic transformer ratio, a key functional parameter of impedance‐matching ears in vertebrates, also shows no relation to habitat preferences (aquatic/terrestrial) in turtles. We suggest that middle ear cavity shape may be controlled by factors unrelated to hearing, such as the spatial demands of surrounding cranial structures. A review of the fossil record suggests that the modern turtle ear evolved during the Early to Middle Jurassic in stem turtles broadly adapted to freshwater and terrestrial settings. This, combined with our finding that evolutionary transitions between habitats caused only weak evolutionary changes in middle ear structure, suggests that tympanic hearing in turtles evolved as a compromise between subaerial and underwater hearing

A toothed turtle from the Late Jurassic of China and the global biogeographic history of turtles

Turtles (Testudinata) are a successful lineage of vertebrates with about 350 extant species that inhabit all major oceans and landmasses with tropical to temperate climates. The rich fossil record of turtles documents the adaptation of various sub- lineages to a broad range of habitat preferences, but a synthetic biogeographic model is still lacking for the group.Results: We herein describe a new species of fossil turtle from the Late Jurassic of Xinjiang, China, Sichuanchelys palatodentata sp. nov., that is highly unusual by plesiomorphically exhibiting palatal teeth. Phylogenetic analysis places the Late Jurassic Sichuanchelys palatodentata in a clade with the Late Cretaceous Mongolochelys efremovi outside crown group Testudines thereby establishing the prolonged presence of a previously unrecognized clade of turtles in Asia, herein named Sichuanchelyidae. In contrast to previous hypotheses, M. efremovi and Kallokibotion bajazidi are not found within Meiolaniformes, a clade that is here reinterpreted as being restricted to Gondwana.Conclusions: A revision of the global distribution of fossil and recent turtle reveals that the three primary lineages of derived, aquatic turtles, including the crown, Paracryptodira, Pan-Pleurodira, and Pan- Cryptodira can be traced back to the Middle Jurassic of Euramerica, Gondwana, and Asia, respectively, which resulted from the primary break up of Pangaea at that time. The two primary lineages of Pleurodira, Pan-Pelomedusoides and Pan-Chelidae, can similarly be traced back to the Cretaceous of northern and southern Gondwana, respectively, which were separated from one another by a large desert zone during that time. The primary divergence of crown turtles was therefore driven by vicariance to the primary freshwater aquatic habitat of these lineages. The temporally persistent lineages of basal turtles, Helochelydridae, Meiolaniformes, Sichuanchelyidae, can similarly be traced back to the Late Mesozoic of Euramerica, southern Gondwana, and Asia. Given the ambiguous phylogenetic relationships of these three lineages, it is unclear if their diversification was driven by vicariance as well, or if they display a vicariance-like pattern. The clean, primary signal apparent among early turtles is secondarily obliterated throughout the Late Cretaceous to Recent by extensive dispersal of continental turtles and by multiple invasions of marine habitats

Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites

Advancements in molecular science are continually improving our knowledge of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here, we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to approximately 2500 years old from the Caribbean and Florida's Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen despite deposition in the tropics. All samples can be identified to species-level with the exception of the Kemp's ridley (Lepidochelys kempii) and olive ridley (L. olivacea) turtles, which can be separated to genus level, having diverged from one another only approximately 5 Ma. Additionally, we identify a single homologous peptide that allows the separation of archaeological green turtle samples, Chelonia spp., into two distinct groups, which potentially signifies a difference in genetic stock. The majority of the archaeological samples are identified as green turtle (Chelonia spp.; 63%), with hawksbill (Eretmochelys imbricata; 17%) and ridley turtles (Lepidochelys spp.; 3%) making up smaller proportions of the assemblage. There were no molecular identifications of the loggerhead turtle (Caretta caretta) in the assemblage despite 9% of the samples being morphologically identified as such, highlighting the difficulties in relying on morphological identifications alone in archaeological remains. Finally, we present the first marine turtle molecular phylogeny using collagen (I) amino acid sequences and find our analyses match recent phylogenies based on nuclear and mitochondrial DNA. Our results highlight the advantage of using collagen fingerprinting to supplement morphological analyses of turtle bones and support the usefulness of this technique for assessing their past distributions across the Caribbean and Florida's Gulf Coast, especially in these tropical environments where DNA preservation may be poor

Climate-mediated diversification of turtles in the Cretaceous

The file attached is the published version of the article

A Selection Index for Gene Expression Evolution and Its Application to the Divergence between Humans and Chimpanzees

The importance of gene regulation in animal evolution is a matter of long-standing interest, but measuring the impact of selection on gene expression has proven a challenge. Here, we propose a selection index of gene expression as a straightforward method for assessing the mode and strength of selection operating on gene expression levels. The index is based on the widely used McDonald-Kreitman test and requires the estimation of four quantities: the within-species and between-species expression variances as well as the sequence heterozygosity and divergence of neutrally evolving sequences. We apply the method to data from human and chimpanzee lymphoblastoid cell lines and show that gene expression is in general under strong stabilizing selection. We also demonstrate how the same framework can be used to estimate the proportion of adaptive gene expression evolution

Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases

<p>Abstract</p> <p>Background</p> <p>Identifying quantitative trait loci (QTL) for both additive and epistatic effects raises the statistical issue of selecting variables from a large number of candidates using a small number of observations. Missing trait and/or marker values prevent one from directly applying the classical model selection criteria such as Akaike's information criterion (AIC) and Bayesian information criterion (BIC).</p> <p>Results</p> <p>We propose a two-step Bayesian variable selection method which deals with the sparse parameter space and the small sample size issues. The regression coefficient priors are flexible enough to incorporate the characteristic of "large <it>p </it>small <it>n</it>" data. Specifically, sparseness and possible asymmetry of the significant coefficients are dealt with by developing a Gibbs sampling algorithm to stochastically search through low-dimensional subspaces for significant variables. The superior performance of the approach is demonstrated via simulation study. We also applied it to real QTL mapping datasets.</p> <p>Conclusion</p> <p>The two-step procedure coupled with Bayesian classification offers flexibility in modeling "large p small n" data, especially for the sparse and asymmetric parameter space. This approach can be extended to other settings characterized by high dimension and low sample size.</p

Overexpression of IL-1ra gene up-regulates interleukin-1β converting enzyme (ICE) gene expression: possible mechanism underlying IL-1β-resistance of cancer cells

We investigated the interaction of endogenous interleukin (IL)-1β, IL-1ra, and interleukin-1β converting enzyme (ICE) in four human urological cancer cell lines, KU-19-19, KU-1, KU-2 and KU-19-20. Northern blot analysis showed that IL-1β gene was expressed in all cell lines. On the other hand, in KU-19-19 and KU-19-20, the gene expressions of both IL-1ra and ICE were suppressed. MTT assay revealed that IL-1β (10 ng ml−1) promoted cell growth in KU-19-19 and KU-19-20, while it inhibited in KU-1 and KU-2. An ICE inhibitor, Acetyl-Tyr-Val-Ala-Asp-CHO (YVAD-CHO) blocked IL-1β-induced growth inhibition in KU-1 and KU-2. Overexpression of the secretory type IL-1ra with adenovirus vector (AxIL-1ra) enhanced ICE gene expression, while exogenous IL-1ra (100 ng ml–1) did not enhance it. Furthermore, AxIL-1ra treatment promoted endogenous IL-1β secretion and induced significant growth inhibition and apoptotic cell death on KU-19-19 and KU-19-20. Treatment with either IL-1ra (100 ng ml−1), IL-1β antibody (100 μg ml−1), or YVAD-CHO blocked AxIL-1ra-induced cell death in KU-19-19 and KU-19-20. These results suggest that IL-1β-sensitivity depends on the level of ICE gene expression, which is regulated by the level of endogenous sIL-1ra expression. This is a first report on the intracellular function of sIL-1ra and these findings may provide key insights into the mechanism underlying the viability of cancer cells. © 1999 Cancer Research Campaig

Toward a quantitative understanding of the Wnt/beta-catenin pathway through simulation and experiment

Wnt signaling regulates cell survival, proliferation, and differentiation throughout development and is aberrantly regulated in cancer. The pathway is activated when Wnt ligands bind to specific receptors on the cell surface, resulting in the stabilization and nuclear accumulation of the transcriptional co‐activator β‐catenin. Mathematical and computational models have been used to study the spatial and temporal regulation of the Wnt/β‐catenin pathway and to investigate the functional impact of mutations in key components. Such models range in complexity, from time‐dependent, ordinary differential equations that describe the biochemical interactions between key pathway components within a single cell, to complex, multiscale models that incorporate the role of the Wnt/β‐catenin pathway target genes in tissue homeostasis and carcinogenesis. This review aims to summarize recent progress in mathematical modeling of the Wnt pathway and to highlight new biological results that could form the basis for future theoretical investigations designed to increase the utility of theoretical models of Wnt signaling in the biomedical arena