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Hybrid detection in a sea turtle hybridization hotspot in Brazil


About the author: Alexandra DeCandia is a postdoctoral fellow at Smithsonian’s National Zoo and Conservation Biology Institute. Her research applies diverse molecular techniques to wildlife conservation and disease management of North American mammals. Alexandra received her Ph.D. from Princeton University in 2020 and her B.A. from Columbia University in 2015. For her career, she strives to work along the intersection of scientific research, wildlife conservation, and science communication. For more information, please visit her website.



Sea turtles and their ancestors have roamed the world’s oceans for more than 100 million years. Over the course of millennia, these living dinosaurs developed an intricate life cycle containing mysteries we have yet to solve.

This cycle begins at beach rookeries. Guided by starlight, hatchlings race towards the sea as soon as they emerge from their sand-covered nests. They swim continuously for days and enter a period of life called “the lost years”, where they develop far from coastlines and predators. Years later and many pounds heavier, juvenile turtles migrate to near-shore foraging grounds until they reach sexual maturity, when they return to their natal beaches. After mating (often with multiple partners), females haul their heavy bodies to shore, bury their clutches, and return to sea – restarting this decades-long cycle (SWOT).

The migratory lifestyle of sea turtles, although stable for millennia, now exposes these ocean nomads to innumerable anthropogenic threats. These include climate change, fisheries bycatch, loss of coastal habitat, pollution, and exploitation for the illegal wildlife trade (WWF). As numbers fall, the additional threat of interspecific hybridization emerges within shared mating and nesting grounds. Sea turtle species diverged from one another between 20-100 million years ago; thus hybridization may lead to outbreeding depression, where hybrids and their offspring suffer from reduced fitness or reproductive success. As a result, it is critically important to identify hybridization hot spots and study the effects of these interspecific unions.

Loggerhead (Caretta caretta) sea turtle hatchlings.
Photo Credit: U.S. Fish and Wildlife Service Northeast Region (Wikimedia Commons)

The northeastern coast of Brazil is one such hot spot. Coastlines within the state of Bahia contain large-scale rookeries of vulnerable loggerhead (Caretta caretta) andcritically endangered hawksbill (Eretmochelys imbricata) turtles. Similar overlap is observed in the state of Sergipe between loggerhead and vulnerable olive ridley (Lepidochelys olivacea) turtles. In some locations, the frequency of hybrids has reached as high as 42% within the last few decades, rendering hybridization a serious cause for concern in this region.

The first step towards addressing this concern is hybrid detection. Traditional methods rely on a handful of mitochondrial or nuclear markers to identify F1 (e.g., loggerhead x hawksbill) and F2 (e.g., F1 hybrid x hawksbill) etc. hybrids. However, these methods possess high error rates and lack fine-scale resolution. To overcome these limitations, Arantes et al. (2020) developed a highly informative multilocus panel of genomic markers to identify sea turtle hybrids. Drawn from reduced representation ddRAD data, the panel consists of loci with high intra- and interspecific variation to enable surveys of population structure as well as hybrid detection. To minimize ascertainment bias, the authors used Sanger sequencing to analyze variation as phased haplotypes. The dataset contained samples from five species of sea turtles, including loggerhead, hawksbill, olive ridley, green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles.

Hawksbill (Eretmochelys imbricata) sea turtle.
Photo Credit: U.S. Fish and Wildlife Service Southeast Region (Wikimedia Commons)

The multilocus panel effectively differentiated between the five species included in this study and was even able to detect fine-scale population structure within species. It additionally identified 29 F1 hybrids through their intermediate genomic composition. These included 15 loggerhead x hawksbill hybrids, 12 loggerhead x olive ridley hybrids, and two hawksbill x olive ridley hybrids. Interestingly, only six >F1 hybrids were identified, with all six samples collected from hatchlings. Four were even sampled from the same nest, with two containing loggerhead and hawksbill ancestry, and two containing ancestry from loggerhead, hawksbill, and green sea turtles! Considered together, these results (and this clutch in particular) exemplify the complicated nature of sea turtle hybridization. They further highlight the utility of high-resolution genomic techniques for informing wildlife conservation.

The panel developed by Arantes et al. (2020) provides a valuable tool for the study and management of sea turtles – not only in Brazil, but around the world. Future work can identify other hybridization hotspots and assess the risk of outbreeding depression in F1 and >F1 hybrids. Analyses of hybrid diet, health, fitness, behavior, and genomics can all help ascertain that risk. This will become increasingly important as sea turtle populations continue to decline worldwide, leading to higher rates of hybridization. Ultimately, the best way to reduce hybridization is to halt these declines. But to do so, we’ll need to mitigate climate change, promote sustainable fisheries, save coastal habitat, minimize pollution, and end the illegal wildlife trade. The task is daunting, but the outcome is worthwhile: sea turtles roaming the oceans for millennia to come.


Larissa S Arantes, Sibelle T Vilaça, Camila J Mazzoni, Fabrício R Santos, New genetic insights about hybridization and population structure of hawksbill and loggerhead turtles from Brazil, Journal of Heredity, esaa024


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