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Background: Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations., Results: We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance., Conclusions: Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.

Within Southern California, east Pacific green sea turtles (Chelonia mydas) forage year-round, taking advantage of diverse food resources, including seagrass, marine algae, and invertebrates. Assessing persistent organic pollutants (POP) in green turtle aggregations in the Seal Beach National Wildlife Refuge (SBNWR, n = 17) and San Diego Bay (SDB, n = 25) can help quantify contamination risks for these populations. Blood plasma was analyzed for polychlorinated biphenyls (PCBs), organochlorinated pesticides (OCPs), and polybrominated diphenyl ethers (PBDEs). PCBs and body size explained much of the separation of turtles by foraging aggregation in a principal component analysis. Turtles from SDB had significantly (p < 0.001) higher total PCBs than SBNWR turtles. Most PCBs detected in turtles were non-dioxin-like PCB congeners (153, 138, 99) that are associated with neurotoxicity. Recaptured turtles' POP levels changed significantly over time indicating significant variation in POP levels through time and space, even among adjacent foraging locations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Foraging aggregations of east Pacific green sea turtles (Chelonia mydas) inhabit the Seal Beach National Wildlife Refuge (SBNWR) and San Diego Bay (SDB), two habitats in southern California, USA, located near urbanized areas. Both juvenile and adult green turtles forage in these areas and exhibit high site fidelity, which potentially exposes green turtles to anthropogenic contaminants. We assessed 21 trace metals (TM) bioaccumulated in green turtle scute and red blood cell (RBC) samples collected from SBNWR (n = 16 turtles) and SDB (n = 20 turtles) using acid digestion and inductively coupled plasma mass spectrometry. Principal component analyses of TM composition indicate that SBNWR and SDB turtles have location-specific contaminant signatures, characterized by differences in cadmium and selenium concentrations: SBNWR turtles had significantly more cadmium and selenium in RBC and more selenium in scute samples, than SDB turtles. Cadmium and selenium concentrations in RBC had a strong positive relationship, regardless of location. SBNWR turtles had higher selenium in RBCs than previously measured in other green turtle populations globally. Due to different retention times in blood vs. scute, these results suggest that SBNWR turtles have high long- and short-term selenium exposure. Turtles from SBNWR and SDB had higher trace metal concentrations than documented in green turtle populations that inhabit non-urbanized areas, supporting the hypothesis that coastal cities can increase trace metal exposure to local green turtles. Our study finds evidence that green turtle TM concentrations can differ between urbanized habitats and that long-term monitoring of these green turtles may be necessary., (Copyright © 2019. Published by Elsevier Ltd.)

Climate change affects species and ecosystems around the globe [1]. The impacts of rising temperature are particularly pertinent in species with temperature-dependent sex determination (TSD), where the sex of an individual is determined by incubation temperature during embryonic development [2]. In sea turtles, the proportion of female hatchlings increases with the incubation temperature. With average global temperature predicted to increase 2.6°C by 2100 [3], many sea turtle populations are in danger of high egg mortality and female-only offspring production. Unfortunately, determining the sex ratios of hatchlings at nesting beaches carries both logistical and ethical complications. However, sex ratio data obtained at foraging grounds provides information on the amalgamation of immature and adult turtles hatched from different nesting beaches over many years. Here, for the first time, we use genetic markers and a mixed-stock analysis (MSA), combined with sex determination through laparoscopy and endocrinology, to link male and female green turtles foraging in the Great Barrier Reef (GBR) to the nesting beach from which they hatched. Our results show a moderate female sex bias (65%-69% female) in turtles originating from the cooler southern GBR nesting beaches, while turtles originating from warmer northern GBR nesting beaches were extremely female-biased (99.1% of juvenile, 99.8% of subadult, and 86.8% of adult-sized turtles). Combining our results with temperature data show that the northern GBR green turtle rookeries have been producing primarily females for more than two decades and that the complete feminization of this population is possible in the near future., (Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Determining sex ratios of endangered populations is important for wildlife management, particularly species subject to sex-specific threats or that exhibit temperature-dependent sex determination. Sea turtle sex is determined by incubation temperature and individuals lack external sex-based traits until sexual maturity. Previous research utilized serum/plasma testosterone radioimmunoassays (RIA) to determine sex in immature/juvenile sea turtles. However, there has been a growing application of enzyme-linked immunosorbent assay (ELISA) for wildlife endocrinology studies, but no study on sea turtles has compared the results of ELISA and RIA. This study provides the first sex ratio for a threatened East Pacific green sea turtle (Chelonia mydas) foraging aggregation, a critical step for future management of this species. Here, we validate a testosterone ELISA and compare results between RIA and ELISA of duplicate samples. The ELISA demonstrated excellent correspondence with the RIA for providing testosterone concentrations for sex determination. Neither assay proved reliable for predicting the sex of reproductively active females with increased testosterone production. We then applied ELISA to examine the sex ratio of 69 green turtles foraging in San Diego Bay, California. Of 45 immature turtles sampled, sex could not be determined for three turtles because testosterone concentrations fell between the ranges for either sex (females: 4.1-113.1 pg/mL, males: 198.4-2,613.0 pg/mL) and these turtles were not subsequently recaptured to enable sex determination; using a Bayesian model to predict probabilities of turtle sex we predicted all three 'unknowns' were female (> 0.86). Additionally, the model assigned all turtles with their correct sex (if determined at recapture) with 100% accuracy. Results indicated a female bias (2.83F:1M) among all turtles in the aggregation; when focusing only on putative immature turtles the sex ratio was 3.5F:1M. With appropriate validation, ELISA sexing could be applied to other sea turtle species, and serve as a crucial conservation tool.

Although holistic conservation addressing all sources of mortality for endangered species or stocks is the preferred conservation strategy, limited budgets require a criterion to prioritize conservation investments. We compared the cost-effectiveness of nesting site and at-sea conservation strategies for Pacific leatherback turtles (Dermochelys coriacea). We sought to determine which conservation strategy or mix of strategies would produce the largest increase in population growth rate per dollar. Alternative strategies included protection of nesters and their eggs at nesting beaches in Indonesia, gear changes, effort restrictions, and caps on turtle takes in the Hawaiian (U.S.A.) longline swordfish fishery, and temporal and area closures in the California (U.S.A.) drift gill net fishery. We used a population model with a biological metric to measure the effects of conservation alternatives. We normalized all effects by cost to prioritize those strategies with the greatest biological effect relative to its economic cost. We used Monte Carlo simulation to address uncertainty in the main variables and to calculate probability distributions for cost-effectiveness measures. Nesting beach protection was the most cost-effective means of achieving increases in leatherback populations. This result creates the possibility of noncompensatory bycatch mitigation, where high-bycatch fisheries invest in protecting nesting beaches. An example of this practice is U.S. processors of longline tuna and California drift gill net fishers that tax themselves to finance low-cost nesting site protection. Under certain conditions, fisheries interventions, such as technologies that reduce leatherback bycatch without substantially decreasing target species catch, can be cost-effective. Reducing bycatch in coastal areas where bycatch is high, particularly adjacent to nesting beaches, may be cost-effective, particularly, if fisheries in the area are small and of little commercial value., (© 2014 Society for Conservation Biology.)

Fisheries bycatch is a critical source of mortality for rapidly declining populations of leatherback turtles, Dermochelys coriacea. We integrated use-intensity distributions for 135 satellite-tracked adult turtles with longline fishing effort to estimate predicted bycatch risk over space and time in the Pacific Ocean. Areas of predicted bycatch risk did not overlap for eastern and western Pacific nesting populations, warranting their consideration as distinct management units with respect to fisheries bycatch. For western Pacific nesting populations, we identified several areas of high risk in the north and central Pacific, but greatest risk was adjacent to primary nesting beaches in tropical seas of Indo-Pacific islands, largely confined to several exclusive economic zones under the jurisdiction of national authorities. For eastern Pacific nesting populations, we identified moderate risk associated with migrations to nesting beaches, but the greatest risk was in the South Pacific Gyre, a broad pelagic zone outside national waters where management is currently lacking and may prove difficult to implement. Efforts should focus on these predicted hotspots to develop more targeted management approaches to alleviate leatherback bycatch.

Strandings of marine megafauna can provide valuable information on cause of death at sea. However, as stranding probabilities are usually very low and highly variable in space and time, interpreting the results can be challenging. We evaluated the magnitude and distribution of at-sea mortality of marine turtles along the Pacific coast of Baja California Sur, México during 2010-11, using a combination of counting stranded animals and drifter experiments. A total of 594 carcasses were found during the study period, with loggerhead (62%) and green turtles (31%) being the most common species. 87% of the strandings occurred in the southern Gulf of Ulloa, a known hotspot of loggerhead distribution in the Eastern Pacific. While only 1.8% of the deaths could be definitively attributed to bycatch (net marks, hooks), seasonal variation in stranding frequencies closely corresponded to the main fishing seasons. Estimated stranding probabilities from drifter experiments varied among sites and trials (0.05-0.8), implying that only a fraction of dead sea turtles can be observed at beaches. Total mortality estimates for 15-day periods around the floater trials were highest for PSL, a beach in the southern Gulf of Ulloa, ranging between 11 sea turtles in October 2011 to 107 in August 2010. Loggerhead turtles were the most numerous, followed by green and olive ridley turtles. Our study showed that drifter trials combined with beach monitoring can provide estimates for death at sea to measure the impact of small-scale fisheries that are notoriously difficult to monitor for by-catch. We also provided recommendations to improve the precision of the mortality estimates for future studies and highlight the importance of estimating impacts of small-scale fisheries on marine megafauna.

Interactions with fisheries are believed to be a major cause of mortality for adult leatherback turtles (Dermochelys coriacea), which is of particular concern in the Pacific Ocean, where they have been rapidly declining. In order to identify where these interactions are occurring and how they may be reduced, it is essential first to understand the movements and behavior of leatherback turtles. There are two regional nesting populations in the East Pacific (EP) and West Pacific (WP), comprising multiple nesting sites. We synthesized tracking data from the two populations and compared their movement patterns. A switching state-space model was applied to 135 Argos satellite tracks to account for observation error, and to distinguish between migratory and area-restricted search behaviors. The tracking data, from the largest leatherback data set ever assembled, indicated that there was a high degree of spatial segregation between EP and WP leatherbacks. Area-restricted search behavior mainly occurred in the southeast Pacific for the EP leatherbacks, whereas the WP leatherbacks had several different search areas in the California Current, central North Pacific, South China Sea, off eastern Indonesia, and off southeastern Australia. We also extracted remotely sensed oceanographic data and applied a generalized linear mixed model to determine if leatherbacks exhibited different behavior in relation to environmental variables. For the WP population, the probability of area-restricted search behavior was positively correlated with chlorophyll-a concentration. This response was less strong in the EP population, but these turtles had a higher probability of search behavior where there was greater Ekman upwelling, which may increase the transport of nutrients and consequently prey availability. These divergent responses to oceanographic conditions have implications for leatherback vulnerability to fisheries interactions and to the effects of climate change. The occurrence of leatherback turtles within both coastal and pelagic areas means they have a high risk of exposure to many different fisheries, which may be very distant from their nesting sites. The EP leatherbacks have more limited foraging grounds than the WP leatherbacks, which could make them more susceptible to any temperature or prey changes that occur in response to climate change.

Longitudinal capture-mark-recapture data were used to estimate abundance and survival rates for green turtles ( Chelonia mydas) in San Diego Bay, California, USA. These turtles were closely associated with warm effluent from a power plant during winter months. The life stage distribution of green turtles in the bay ranged from post-pelagic juveniles to adults (44.0–110.4 cm straight carapace length). During 99 capture sessions between December 2, 1990, and March 25, 2009, 96 individual green turtles were caught. To estimate abundance and survival rates, robust-design mark-recapture models were fitted to capture-recapture histories using software MARK. The estimated annual survival rate was 0.861 (SE = 0.147, 95% CI = 0.356–0.986), whereas annual abundance ranged from 16 (SE = 6.3, 95% CI = 4–29) to 61 (SE = 13.2, 95% CI = 36–88). This study provides the first survival rate and abundance estimates for a green turtle foraging population in the highly industrialized San Diego Bay. [ABSTRACT FROM AUTHOR]

Protection of endangered species requires an understanding of their spatial ecology in relation to human activities. Recent improvements in monitoring technologies, such as automated acoustic telemetry, have enabled the collection of these data for mobile marine organisms such as sea turtles. The east Pacific green sea turtle Chelonia mydas uses San Diego Bay, CA, a heavily developed ecosystem, as a year-round foraging ground. We used a combination of manual and automated acoustic telemetry from 2009 to 2011 to elucidate the distribution of green turtles throughout South San Diego Bay and to understand their diel behavior. Tracked turtles (n=20) ranged in size from 54.9 to 102.5cm straight carapace length and had fidelity to two sites: the warm-water effluent channel of a waterfront power plant and an eelgrass meadow. Turtles tracked manually during the night were more sedentary (mean swimming speed±SE: 0.38±0.03kmh−1) and generally restricted their activity to waters near the power plant. During the day, turtles swam at higher speeds (0.67±0.07kmh−1) and were mainly found in eelgrass meadows where they are known to forage. Turtles were occasionally found near a shipping terminal, which occurred almost exclusively during the daytime. Turtles in areas of increased boat traffic are at risk of vessel strikes, and future monitoring should investigate the potential for turtle–human interactions in other heavily-used areas of San Diego Bay. Future monitoring should also characterize how turtle behavior may change following the decommissioning of the power plant, which occurred six months before the end of this study. [ABSTRACT FROM AUTHOR]