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Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species.

ABSTRACT: Reconstructing past events of hybridization and population size changes are required to understand speciation mechanisms and current patterns of genetic diversity, and ultimately contribute to species' conservation. Sea turtles are ancient species currently facing anthropogenic threats including climate change, fisheries, and illegal hunting. Five of the seven extant sea turtle species are known to currently hybridize, especially along the Brazilian coast where some populations can have ~32%-42% of hybrids. Although frequently observed today, it is not clear what role hybridization plays in the evolutionary diversification of this group of reptiles. In this study, we generated whole genome resequencing data of the five globally distributed sea turtle species to estimate a calibrated phylogeny and the population size dynamics, and to understand the role of hybridization in shaping the genomes of these ancient species. Our results reveal discordant species divergence dates between mitochondrial and nuclear genomes, with a high frequency of conflicting trees throughout the nuclear genome suggesting that some sea turtle species frequently hybridized in the past. The reconstruction of the species' demography showed a general decline in effective population sizes with no signs of recovery, except for the leatherback sea turtle. Furthermore, we discuss the influence of reference bias in our estimates. We show long-lasting ancestral gene flow events within Chelonioidea that continued for millions of years after initial divergence. Speciation with gene flow is a common pattern in marine species, and it raises questions whether current hybridization events should be considered as a part of these species' evolutionary history or a conservation issue.

SUBMITTER: Vilaca ST

PROVIDER: S-EPMC9292604 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world's most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry & Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected Plutella from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and Wolbachia infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays. RESULTS:The two Plutella species coexisted on wild brassicas and canola crops, but only 10% of Plutella individuals were P. australiana. This species was not found on commercial Brassica vegetable crops, which are routinely sprayed with insecticides. Bioassays found that P. australiana was 19-306 fold more susceptible to four commonly-used insecticides than P. xylostella. Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in P. australiana, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5% of P. xylostella. CONCLUSIONS:Despite sympatric distributions and the capacity to hybridize, strong genomic and phenotypic divergence exists between these Plutella species that is consistent with contrasting colonization histories and reproductive isolation after secondary contact. Although P. australiana is a potential pest of brassicaceous crops, it is of secondary importance to P. xylostella.

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Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species.

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