Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories.

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

Landscape limits gene flow and drives population structure in Agassiz's desert tortoise (Gopherus agassizii).

Distance, environmental heterogeneity and local adaptation can strongly influence population structure and connectivity. Understanding how these factors shape the genomic landscape of threatened species is a major goal in conservation genomics and wildlife management. Herein, we use thousands (6,859) of single nucleotide polymorphism markers and spatial data from hundreds of individuals (n = 646) to re-evaluate the population structure of Agassiz's desert tortoise (Gopherus agassizii). Analyses resolve from 4 to 8 spatially well-defined clusters across the range. Western, central, and southern populations within the Western Mojave recovery unit are consistent throughout, while analyses sometimes merge other recovery units depending on the level of clustering. Causal modeling consistently associates genetic connectivity with least-cost distance, based on multiple landscape features associated with tortoise habitat, better than geographic distance. Some features include elevation, soil depth, rock volume, precipitation, and vegetation coverage, suggesting that physical, climatic, and biotic landscape features have played a strong evolutionary role restricting gene flow between populations. Further, 12 highly differentiated outlier loci have associated functions that may be involved with neurogenesis, wound healing, lipid metabolism, and possibly vitellogenesis. Together, these findings have important implications for recovery programs, such as translocations, population augmentation, reproduction in captivity and the identification of ecologically important genes, opening new venues for conservation genomics in desert tortoises.

The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species.

Agassiz's desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

Living with the genetic signature of Miocene induced change: evidence from the phylogeographic structure of the endemic angulate tortoise Chersina angulata.

The phylogeographic structure of the monotypic endemic southern African angulate tortoise Chersina angulata was investigated throughout its distribution with the use of partial sequences from three mtDNA loci (COI, cyt b and ND4). Phylogeographic and phylogenetic structuring obtained for the three mtDNA markers were highly congruent and suggested the presence of two genetically distinct, reciprocally monophyletic evolutionary lineages. Group one contained two subclades with haplotypes from the north-western Cape and south-western Cape, respectively, while haplotypes from the southern Cape comprised group two. The two major clades were separated by nine and eight mutational steps for COI and ND4, respectively. Of the three mtDNA gene regions examined, the ND4 partial sequence contained the most phylogenetic signal. Haplotype diversity was generally low and we recovered 34 haplotypes for the 125 animals sequenced for the ND4 subunit. Nested clade analyses performed on the variable ND4 partial sequences suggested the presence of two major refugial areas for this species. The demographic history of the taxon was characterised by range expansion and prolonged historical fragmentation. Divergence time estimates suggest that the temporal and spatial distribution of the taxon was sculpted by changes in temperature and rainfall patterns since the late Miocene. Corroborative evidence from other reptiles is also suggestive of a late Miocene divergence, indicating that this was a major epoch for cladogenesis in southern Africa. Apart from the genetic differences between the two major clades, we also note morphometric and behavioural differences, alluding to the presence of two putative taxa nested within C. angulata.

Growing and shrinking in the smallest tortoise, Homopus signatus signatus: the importance of rain.

Climate change models predict that the range of the world's smallest tortoise, Homopus signatus signatus, will aridify and contract in the next decades. To evaluate the effects of annual variation in rainfall on the growth of H. s. signatus, we recorded annual growth rates of wild individuals from spring 2000 to spring 2004. Juveniles grew faster than did adults, and females grew faster than did males. Growth correlated strongly with the amount of rain that fell during the time just before and within the growth periods. Growth rates were lowest in 2002-2003, when almost no rain fell between September 2002 and August 2003. In this period, more than 54% of the tortoises had negative growth rates for their straight carapace length (SCL), shell height (SH), and shell volume (SV); maximum shrinking for SCL, SH, and SV was 4, 11, and 12%, respectively. The shell of H. s. signatus has some flexibility dorso-ventrally, so a reduction in internal matter due to starvation or dehydration may have caused SH to shrink. Because the length and width of the shell seem more rigid, reversible bone resorption may have contributed to shrinkage, particularly of the shell width and plastron length. Based on growth rates for all years, female H. s. signatus need 11-12 years to mature, approximately twice as long as would be expected allometrically for such a small species. However, if aridification lowers average growth rates to the level of 2002-2003, females would require 30 years to mature. Additionally, aridification would lower average and maximum female size, resulting in smaller eggs and hatchlings. These projected life history responses to aridification heighten the threat posed by the predicted range contraction of this red-listed species.

Viewing chelonian reproductive ecology through acoustic windows: cranial and inguinal perspectives.

Ultrasonography is a powerful new tool in reproductive physiology and ecology but quantitative evaluations of acoustic window efficacies are necessary to assess methodological accuracy. We evaluated the efficacy of the left inguinal, right inguinal and cranial acoustic windows for detecting ovarian follicles and oviducal eggs in three tortoise species. Incorporating cranial results improved upon inguinal efficacies for detecting follicles in the three species, and for detecting eggs in Chersina angulata, which had small inguinal apertures for its body size. The cranial window provided the best follicle results (highest numbers detected) but the left inguinal window provided the best egg results. This asymmetry was probably due to the primarily posterior position of the oviducts (eggs) and the pliable ovarian sheets allowing follicles to move cranially. The left-right asymmetry may result from intestinal asymmetry (i.e., between the cecum and descending colon) in obscuring ultrasound transmission or displacing follicles and eggs. Seasonal influences upon efficacies varied with species, partially due to species differences in a) reproductive cycles and b) size and number of follicles and eggs. We attributed other efficacy differences among species to differences in body size and shell morphology, especially the inguinal apertures. Correlation analyses revealed strong individual influences upon window efficacy, suggesting that individuals varied in the position of follicles and eggs and the degree of obfuscation by nonreproductive structures. The paucity of correlations between efficacies and body size reflects the complex interactions of body size, shell morphology, reproductive structures and reproductive cycles on efficacies.

Clinical disease and laboratory abnormalities in free-ranging desert tortoises in California (1990-1995).

Desert tortoise (Gopherus agassizii) populations have experienced precipitous declines resulting from the cumulative impact of habitat loss and human and disease-related mortality. Diagnosis of disease in live, free-ranging tortoises is facilitated by evaluation of clinical signs and laboratory test results but may be complicated by seasonal and environmental effects. The goals of this study were: 1) to describe and monitor clinical and laboratory signs of disease in adult, free-ranging desert tortoises at three sites in the Mojave Desert of California (USA) between October 1990 and October 1995; 2) to evaluate associations between clinical signs and hematologic, biochemical, serologic, and microbiologic test results; 3) to characterize disease patterns by site, season, and sex; and 4) to assess the utility of diagnostic tests in predicting morbidity and mortality. Venous blood samples were obtained four times per year from tortoises of both sexes at the Desert Tortoise Research Natural Area (DTNA), Goffs/Fenner Valley, and Ivanpah Valley. Tortoises were given a physical examination, and clinical abnormalities were graded by type and severity. Of 108 tortoises, 68.5% had clinical signs of upper respiratory tract disease consistent with mycoplasmosis at least once during the study period. In addition, 48.1% developed moderate to severe shell lesions consistent with cutaneous dyskeratosis. Ulcerated or plaque-like oral lesions were noted on single occasions in 23% of tortoises at Goffs and 6% of tortoises at Ivanpah. Tortoises with oral lesions were significantly more likely than tortoises without lesions to have positive nasal cultures for Mycoplasma agassizii (P = 0.001) and to be dehydrated (P = 0.0007). Nine tortoises had marked azotemia (blood urea nitrogen [BUN] > 100 mg/dl) or persistent azotemia (BUN 63-76 mg/dl); four of these died, three of which had necropsy confirmation of urinary tract disease. Laboratory tests had low sensitivity but high specificity in assessing morbidity and mortality; there was marked discrepancy between serologic and culture results for M. agassizii. Compared with tortoises at other sites, tortoises at DTNA were more likely to be seropositive for M. agassizii. Tortoises at Goffs were significantly more likely to have moderate to severe shell disease, oral lesions, positive nasal cultures for M. agassizii, and increased plasma aspartate aminotransferase activity. The severe disease prevalence in Goffs tortoises likely contributed to the population decline that occurred during and subsequent to this study.

Effects of climatic variation on field metabolism and water relations of desert tortoises.

We used the doubly labeled water method to measure the field metabolic rates (FMRs, in kJ kg-1 day-1) and water flux rates (WIRs, in ml H2O kg-1 day-1) of adult desert tortoises (Gopherus agassizii) in three parts of the Mojave Desert in California over a 3.5-year period, in order to develop insights into the physiological responses of this threatened species to climate variation among sites and years. FMR, WIR, and the water economy index (WEI, in ml H2O kJ-1, an indicator of drinking of free water) differed extensively among seasons, among study sites, between sexes, and among years. In high-rainfall years, males had higher FMRs than females. Average daily rates of energy and water use by desert tortoises were extraordinarily variable: 28-fold differences in FMR and 237-fold differences in WIR were measured. Some of this variation was due to seasonal conditions, with rates being low during cold winter months and higher in the warm seasons. However, much of the variation was due to responses to year-to-year variation in rainfall. Annual spring peaks in FMR and WIR were higher in wet years than in drought years. Site differences in seasonal patterns were apparently due to geographic differences in rainfall patterns (more summer rain at eastern Mojave sites). In spring 1992, during an El Niño (ENSO) event, the WEI was greater than the maximal value obtainable from consuming succulent vegetation, indicating copious drinking of rainwater at that time. The physiological and behavioral flexibility of desert tortoises, evident in individuals living at all three study sites, appears central to their ability to survive droughts and benefit from periods of resource abundance. The strong effects of the El Niño (ENSO) weather pattern on tortoise physiology, reproduction, and survival elucidated in this and other studies suggest that local manifestations of global climate events could have a long-term influence on the tortoise populations in the Mojave Desert.