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Painted turtles are remarkable for their freeze tolerance and supercooling ability along with their associated resilience to hypoxia/anoxia and oxidative stress, rendering them an ideal biomedical model for hypoxia-induced injuries (including strokes), tissue cooling during surgeries, and organ cryopreservation. Yet, such research is hindered by their seasonal reproduction and slow maturation. Here we developed and characterized adult stem cell-derived turtle liver organoids (3D self-assembled in vitro structures) from painted, snapping, and spiny softshell turtles spanning ~175My of evolution, with a subset cryopreserved. This development is, to the best of our knowledge, a first for this vertebrate Order, and complements the only other non-avian reptile organoids from snake venom glands. Preliminary characterization, including morphological, transcriptomic, and proteomic analyses, revealed organoids enriched in cholangiocytes. Deriving organoids from distant turtles and life stages demonstrates that our techniques are broadly applicable to chelonians, permitting the development of functional genomic tools currently lacking in herpetological research. Such platform could potentially support studies including genome-to-phenome mapping, gene function, genome architecture, and adaptive responses to climate change, with implications for ecological, evolutionary, and biomedical research.Multi-omic profiling on 3D liver organoids derived from multiple species may help foster future research on unique turtle adaptations, along with their evolutionary and biomedical implications. [ABSTRACT FROM AUTHOR]

Endothelial cells (EC) coordinate vascular homeostasis and inflammation. In organ transplantation, EC are a direct alloimmune target. We posited that tissue specific heterogeneity of vascular EC may partly underlie the disparate organ-specific alloimmune risk. We examined the vascular endothelial response to inflammation across six primary endothelial beds from four major transplanted organs: the heart, lung, kidney and liver. First, we reanalyzed a public dataset of cardiac allograft rejection and found that endothelial inflammatory response genes were elevated in human cardiac allograft biopsies undergoing rejection compared with stable grafts. Next, the inducible inflammatory phenotypes of EC from heart, lung, kidney, and liver were characterized in vitro, focused on expression of adhesion molecules and chemokines, and recruitment of allogeneic peripheral blood mononuclear immune cells. Large vessel cardiac EC most highly upregulated VCAM-1, particularly compared with hepatic EC, supported greater leukocyte adhesion and had distinct chemokine profiles after stimulation with cytokines and complement. Differentially expressed gene candidates that are known regulators of cytokine signaling and inflammatory programming were verified in publicly available datasets of organ-specific endothelial transcriptomes. In summary, differential baseline expression of immune regulating genes may contribute to differential vascular inflammatory responses depending on organ. [ABSTRACT FROM AUTHOR]

Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical 'avian-like' karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur-theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning. [ABSTRACT FROM AUTHOR]

In oviparous vertebrates lacking parental care, resource allocation during reproduction is a major maternal effect that may enhance female fitness. In general, resource allocation strategies are expected to follow optimality models to solve the energy trade-offs between egg size and number. Such models predict that natural selection should optimize egg size while egg number is expected to vary with female size, thus maximizing offspring fitness and consequently, maternal fitness. Deviations from optimality predictions are commonly attributed to morphological constraints imposed by female size, such as reported for small-bodied turtle species. However, whether such anatomical constraints exist in smaller-bodied females within large-bodied clades remains unstudied. Here we tested whether resource allocation of the river turtle Podocnemis unifilis (a relatively smaller member of the large-bodied Podocnemididae) follows optimality theory, and found a pattern of egg elongation in smaller females that provides evidence of morphological constraints and of a reproductive trade-off with clutch size, whereas egg width supports the existence of an optimal egg size and no trade-off. Moreover, larger females laid larger clutches composed of rounder eggs, while smaller females laid fewer and relatively more elongated eggs. Elongated eggs from smaller females have larger volume relative to female size and to round eggs of equal width. We propose that elongated eggs represent a solution to a potential morphological constraint suffered by small females. Our results suggest that larger females may optimize fitness by increasing the number of eggs, while smaller females do so by producing larger eggs. Our data supports the notion that morphological constraints are likely more widespread than previously anticipated, such that they may not be exclusive of small-bodied lineages but may also exist in large-bodied lineages. [ABSTRACT FROM AUTHOR]

The evolutionary lability of sex-determining mechanisms across the tree of life is well recognized, yet the extent of molecular changes that accompany these repeated transitions remain obscure. Most turtles retain the ancestral temperature-dependent sex determination (TSD) from which multiple transitions to genotypic sex determination (GSD) occurred independently, and two contrasting hypotheses posit the existence or absence of reversals back to TSD. Here we examined the molecular evolution of the coding regions of a set of gene regulators involved in gonadal development in turtles and several other vertebrates. We found slower molecular evolution in turtles and crocodilians compared to other vertebrates, but an acceleration in Trionychia turtles and at some phylogenetic branches demarcating major taxonomic diversification events. Of all gene classes examined, hormone signaling genes, and Srd5a1 in particular, evolve faster in many lineages and especially in turtles. Our data show that sex-linked genes do not follow a ubiquitous nor uniform pattern of molecular evolution. We then evaluated turtle nucleotide and protein evolution under two evolutionary hypotheses with or without GSD-to-TSD reversals, and found that when GSD-to-TSD reversals are considered, all transitional branches irrespective of direction, exhibit accelerated molecular evolution of nucleotide sequences, while GSD-to-TSD transitional branches also show acceleration in protein evolution. Significant changes in predicted secondary structure that may affect protein function were identified in three genes that exhibited hastened evolution in turtles compared to other vertebrates or in transitional versus non-transitional branches within turtles, rendering them candidates for a key role during SDM evolution in turtles. [ABSTRACT FROM AUTHOR]

In species or developmental stages where the sex of an individual cannot be reliably identified through external morphology, molecular markers can provide a critical tool to study sex-specific traits that are elusive otherwise. Here we generated two sets of sex-diagnostic PCR primers for each of two focal turtle species with contrasting genotypic sex determination (GSD) systems: the wood turtle, Glyptemys insculpta (XX/XY), and the spiny softshell turtle, Apalone spinifera (ZZ/ZW). These markers identified males and females with 100% accuracy as validated with numerous individuals of known sex. Notably, one of the markers developed for G. insculpta permitted the successful diagnosis of individual sex in the critically-endangered bog turtle, Glyptemys muhlenbergii, also with 100% accuracy. This cross-species application provided the first evidence that G. muhlenbergii shares an XX/XY sex-determining mechanism with G. insculpta, a finding with important evolutionary and conservation implications. Similarly, the markers from A. spinifera were successful in identifying the sex of two individuals (one male and one female) of the Chinese softshell turtle, Pelodiscus sinensis (ZZ/ZW). These cross-species observations highlight the potential applicability of these types of markers on closely related taxa that share a sex-determining mechanism, which should be tested in a case-by-case basis. [ABSTRACT FROM AUTHOR]

Sex-specific plasticity can profoundly affect sexual size dimorphism (SSD), but its influence in female-larger-SSD vertebrates remains obscure. Theory predicts that sex-specific plasticity may drive SSD evolution if the larger sex benefits from optimal-growth conditions when available ( condition- dependent hypothesis), or if attaining a suboptimal size is penalized by selection ( adaptive canalization hypothesis). Sex-specific plasticity enhances the size of the larger sex in male-larger-SSD turtles but whether the same occurs in female-larger species is unknown. Sexual shape dimorphism (SShD) is also widespread in nature but is understudied, and whether SShD derives from sex-specific responses to identical selective pressures or from sex-specific selection remains unclear. Here we tested whether sex-specific growth plasticity underlies the development of sexual size and shape dimorphism in the female-larger-SSD turtle, Podocnemis expansa. Individuals hatched from several incubation temperatures and were raised under common-garden conditions with varying temperature and resources. Body size and shape were plastic and sexually dimorphic, but plasticity did not differ between the sexes, opposite to the male-larger turtle Chelydra serpentina. Maternal effects (egg size) were significant on size and shape, suggesting that females increase their fitness by allocating greater energy to enhance offspring growth. Results ruled out the sex-specific plasticity hypotheses in P. expansa, indicating that SSD and SShD do not derive form differential responses to identical drivers but from sex-specific selective pressures. Our results indicate that differential plasticity does not favor males inherently, nor the larger sex, as would be expected if it was a pervasive driver of macroevolutionary patterns of sexual dimorphism across turtle lineages. [ABSTRACT FROM AUTHOR]

DNA methylation plays an important role in the epigenetic control of developmental and behavioral plasticity, with connections to the generation of striking phenotypic differences between castes (larger, reproductive queens and smaller, non-reproductive workers) in honeybees and ants. Here, we provide the first comparative investigation of caste- and life stage-associated DNA methylation in several species of bees and vespid wasps displaying different levels of social organization. Our results reveal moderate levels of DNA methylation in most bees and wasps, with no clear relationship to the level of sociality. Strikingly, primitively social Polistes dominula paper wasps show unusually high overall DNA methylation and caste-related differences in site-specific methylation. These results suggest DNA methylation may play a role in the regulation of behavioral and physiological differences in primitively social species with more flexible caste differences. [ABSTRACT FROM AUTHOR]

Sexual size dimorphism (SSD) is widespread in nature and may result from selection operating differentially on males and females. Rensch's rule, the increase of SSD with body size in male-biased-SSD species (or decrease in female-biased-SSD species), is documented in invertebrates and vertebrates. In turtles, evidence for Rensch's rule is inconclusive and thus the forces underlying body size evolution remain obscure. Using a phylogenetic approach on 138 turtle species from 9 families, we found that turtles overall and three families follow Rensch's rule, five families display isometry of SSD with body size, while Podocnemididae potentially follows a pattern opposite to Rensch's rule. Furthermore, male size evolves at faster rates than female size. Female-biased-SSD appears ancestral in turtles while male-biased-SSD evolved in every polytypic family at least once. Body size follows an Ornstein-Uhlenbeck evolutionary model in both sexes and SSD types, ruling out drift as a driving process. We explored whether habitat type or sex determination might be general drivers of turtle body size evolution using a phylogenetic context. We found that males are proportionally larger in terrestrial habitats and smaller in more aquatic habitats, while the sex-determining mechanism had no influence on body size evolution. Together, our data indicate that Rensch's rule is not ubiquitous across vertebrates, but rather is prevalent in some lineages and not driven by a single force. Instead, our findings are consistent with the hypotheses that fecundity-selection might operate on females and ecological-selection on males; and that SSD and sex-determining mechanism evolve independently in these long-lived vertebrates. [ABSTRACT FROM AUTHOR]

Reptiles display a wide diversity of sex-determining mechanisms ranging from temperature-dependent sex determination (TSD) to genotypic sex determination (GSD) with either male (XY) or female (ZW) heterogamety. Despite this astounding variability, the origin, structure, and evolution of sex chromosomes remain poorly understood. In turtles, TSD is purportedly ancestral while GSD arose multiple times independently. Here we test whether independent (XY or ZW) or morphologically divergent heterogametic sex chromosome systems evolved in tryonichids (Cryptodira) using the GSD spiny softshell turtle, Apalone spinifera, a species with previously unidentified sex chromosomes. A female-specific signal from comparative genomic hybridization (CGH) was detected in a Giemsa/4′,6-diamidino-2-phenylindole faint portion of a microchromosome, indicating the presence of a ZZ/ZW system in A. spinifera. In situ hybridization of a fluorescently labeled 18S rRNA probe identified a large nucleolar organizer region block in the female-specific region of the W (co-localizing with the female-specific CGH signal) and a smaller block on the Z. The heteromorphic ZZ/ZW micro-sex chromosome system detected here is identical to that found in another tryonichid, the Chinese softshell turtle Pelodiscus sinensis, from which A. spinifera diverged ∼95 million years ago. These results reveal a striking sex chromosome conservation in tryonichids, compared to the divergent sex chromosome morphology observed among younger XX/XY systems in pleurodiran turtles. Our findings highlight the need to understand the drivers behind sex chromosome lability and conservation in different lineages and contribute to our knowledge of sex chromosome evolution in reptiles and vertebrates. [ABSTRACT FROM AUTHOR]

Sex-specific plasticity, the differential response that the genome of males and females may have to different environments, is a mechanism that can affect the degree of sexual dimorphism. Two adaptive hypotheses have been proposed to explain how sex-specific plasticity affects the evolution of sexual size dimorphism. The adaptive canalization hypothesis states that the larger sex exhibits lesser plasticity compared to the smaller sex due to strong directional selection for a large body size, which penalizes individuals attaining sub-optimal body sizes. The condition-dependence hypothesis states that the larger sex exhibits greater plasticity than the smaller sex due to strong directional selection for a large body size favoring a greater sensitivity as an opportunistic mechanism for growth enhancement under favorable conditions. While the relationship between sex-specific plasticity and sexual dimorphism has been studied mainly in invertebrates, its role in long-lived vertebrates has received little attention. In this study we tested the predictions derived from these two hypotheses by comparing the plastic responses of body size and shape of males and females of the snapping turtle ( Chelydra serpentina) raised under common garden conditions. Body size was plastic, sexually dimorphic, and the plasticity was also sex-specific, with males exhibiting greater body size plasticity relative to females. Because snapping turtle males are larger than females, sexual size dimorphism in this species appears to be driven by an increased plasticity of the larger sex over the smaller sex as predicted by the condition-dependent hypothesis. However, male body size was enhanced under relatively limited resources, in contrast to expectations from this model. Body shape was also plastic and sexually dimorphic, however no sex by environment interaction was found in this case. Instead, plasticity of sexual shape dimorphism seems to evolve in parallel for males and females as both sexes responded similarly to different environments. [ABSTRACT FROM AUTHOR]

We studied the population genetics of Podocnemis unifilis turtles within and among basins in the Orinoco and Amazon drainages using microsatellites. We detected high levels of genetic diversity in all sampled localities. However, 'M-ratio' tests revealed a substantial recent population decline in ten localities, in accord with current widespread exploitation. Our results reveal a consistent pattern across multiple analyses, showing a clear subdivision between the populations inhabiting the Amazon and Orinoco drainages despite a direct connection via the Casiquiare corridor, and suggesting the existence of two biogeographically independent and widely divergent lineages. Genetic differentiation followed an isolationby- distance model concordant with hypotheses about migration. It appears that migration occurs via the flooded forest in some drainages, and via river channels in those where geographic barriers preclude dispersal between basins or even among nearby tributaries of the same basin. These observations caution against making generalizations based on geographically restricted data, and indicate that geographically proximate populations may be demographically separate units requiring independent management. [ABSTRACT FROM AUTHOR]

Although the role of aromatase in many estrogen-dependent reproductive and metabolic functions is well documented in vertebrates, its involvement in the ovarian development of species exhibiting temperature-dependent sex determination (TSD) is incompletely understood. This is partly due to the conflicting temporal and spatial pattern of aromatase expression and activity across taxa. To help resolve this ongoing debate, we compared for the first time the embryological ontogeny of aromatase expression in turtles possessing genotypic sex determination (GSD) ( Apalone mutica) and TSD ( Chrysemys picta) incubated under identical conditions. As anticipated, we found no significant thermal differences in aromatase expression at any stage examined (prior to until the end of the thermosensitive period) in A. mutica. Surprisingly, the same was true for C. picta. When placed in a phylogenetic context, our results suggest that aromatase expression is evolutionarily plastic with respect to sex determination in reptiles, and that differences between reptilian TSD and GSD are not aromatase-driven. Further research across TSD and GSD species is warranted to fully decipher the evolution of functional differences among sex-determining mechanisms. [ABSTRACT FROM AUTHOR]