Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output

Abstract

Hybridization between sea turtle species occurs with particularly high frequency at two adjacent nesting areas in northeastern Brazil. To understand the outcomes of hybridization and their consequences for sea turtle conservation, we need to evaluate the extent of hybridization occurrence and possible deleterious effects in the hybrid progeny. Thus, we investigated the hypothesis of the existence of a new hybrid spot offshore of Brazil's northeastern coast. The Abrolhos Archipelago is surrounded by the largest and richest coral reefs in the South Atlantic and is known to be a nesting site for loggerhead turtles (Caretta caretta). In this study, we performed a multidisciplinary investigation into levels of hybridization in sea turtles and their reproductive output in the Abrolhos beaches. Genetic data from mitochondrial DNA (mtDNA) and six autosomal markers showed that there are first-generation hybrid females nesting in Abrolhos, resulting from crossings between hawksbill males (Eretmochelys imbricata) and loggerhead females, and backcrossed hatchlings from both parental species. The type and extent of hybridization were characterized using genomic data obtained with the 3RAD method, which confirmed backcrossing between F1 hybrids and loggerhead turtles. The reproductive output data of Abrolhos nests suggests a disadvantage of hybrids when compared to loggerheads. For the first time, we have shown the association between hybridization and low reproductive success, which may represent a threat to sea turtle conservation.

Figure 1

The Abrolhos Archipelago. It is located along the Brazilian coast (a), in the Abrolhos bank in south Bahia state (b) and encompasses five small islands (c). The nesting sites of sea turtles include short sand stretches in Redonda (d) and Santa Bárbara (e) islands.

Figure 2

Bayesian estimates of the hybrid index (HI) for each individual analyzed in Abrolhos Archipelago. Blue and red points represent the parental reference sets of loggerhead and hawksbill turtles, respectively. Cyan points represent nesting females and grey points are hatchlings from 20 nests from Abrolhos. The HI was estimated with gghybrid. HI estimated values equal to 0.0 denote pure loggerhead turtles and 1.0 denote pure hawksbill individuals; lines represent 95% confidence intervals.

Figure 3

Genetic structure of parental species and their hybrids based on 3RAD data. Admixture proportions based on two clusters (K = 2) estimated by STRUCTURE (a) and assignment of hybrid class by NewHybrids (b). The plots include the five hawksbill and five loggerhead turtles and 14 hatchlings from six different nests from Abrolhos. The order of the individuals within the different groups is the same in both plots.

Figure 4

Graphical summary of morphological and reproductive parameters comparing loggerhead turtles and hybrids from the Abrolhos Archipelago. The hatching success (a), clutch size (b), incubation period (c), curved carapace width—CCW (d) and curved carapace length—CCL (e) are shown for both groups. Error bars show standard error. Statistical analysis was performed by nonparametric t test (Mann–Whitney U test). **P < 0.05; *P < 0.01.

Figure 5

Temporal nesting distribution of hybrids (N = 16) and loggerhead turtles (N = 31) analyzed in this study.