THOUSANDS OF SINGLE NUCLEOTIDE POLYMORPHISMS IN THE CRITICALLY EN- DANGERED KEMP’S RIDLEY SEA TURTLE (LEPIDOCHELYS KEMPII) REVEALED BY DOU- BLE-DIGEST RESTRICTION-ASSOCIATED DNA SEQUENCING: OPPORTUNITIES FOR PREVIOUSLY ELUSIVE CONSERVATION GE- NETICS RESEARCH.—Among sea turtles, the Kemp’s ridley is the most endangered and geographically restricted, with its distribution mostly confined to the Gulf of Mexico (NMFS and USFWS, 2015). After experiencing a severe and sustained bottleneck that put this species on the verge of extinction, it appeared to be rebounding successfully, as evidenced by an exponential growth in the number of nests observed per nesting season, following decades of Mexico–United States bi-national efforts aimed at its recovery (Heppell et al., 2007). Unfortunately, nesting was severely reduced by ~35% during 2010 (the year of the BP Deepwa- ter Horizon oil spill in the Gulf of Mexico), as compared to nesting rates in 2009 (NMFS and USFWS, 2015). Although nesting rebounded during 2011 and 2012 to levels similar to that of 2009, nesting declined drastically again during 2013 and experienced a further drop during 2014 (NMFS and USFWS, 2015; Shaver et al., 2016). The number of nests in 2014 represents a 46% decrease from 2012, which was the year with the highest recorded number of nests since 1965 (Sarti, 2014). Should nesting continue to de- cline, long-term species recovery efforts will be compromised. Therefore, there is deep concern about the future of the Kemp’s ridley, and data to inform and assess bi-national management and conservation measures are urgently needed (Plotkin and Bernardo, 2014). Population ge- netics information crucial to the long-term conservation of the Kemp’s ridley, including baseline data required for monitoring its future status, is lacking. This includes estimations of genomic diversity, effective population size, and number of breeders; assessment of levels of population differentiation; and detection of genomic signatures of bottlenecks.
A growing body of knowledge on the diversity and evolution of intertidal isopods across different regions worldwide has enhanced our understanding on biological diversification at the poorly studied, yet vast, sea–land interface. High genetic divergences among numerous allopatric lineages have been identified within presumed single broadly distributed species. Excirolana mayana is an intertidal isopod that is commonly found in sandy beaches throughout the Gulf of California. Its distribution in the Pacific extends from this basin to Colombia and in the Atlantic from Florida to Venezuela. Despite its broad distribution and ecological importance, its evolutionary history has been largely neglected. Herein, we examined phylogeographic patterns of E. mayana in the Gulf of California and the Caribbean, based on maximum-likelihood and Bayesian phylogenetic analyses of DNA sequences from four mitochondrial genes (16S rDNA, 12S rDNA, cytochrome oxidase I gene, and cytochrome b gene). We compared the phylogeographic patterns of E. mayana with those of the coastal isopods Ligia and Excirolana braziliensis (Gulf of California and Caribbean) and Tylos (Gulf of California). We found highly divergent lineages in both, the Gulf of California and Caribbean, suggesting the presence of multiple species. We identified two instances of Atlantic–Pacific divergences. Some geographical structuring among the major clades found in the Caribbean is observed. Haplotypes from the Gulf of California form a monophyletic group sister to a lineage found in Venezuela. Phylogeographic patterns of E. mayana in the Gulf of California differ from those observed in Ligia and Tylos in this region. Nonetheless, several clades of E. mayana have similar distributions to clades of these two other isopod taxa. The high levels of cryptic diversity detected in E. mayana also pose challenges for the conservation of this isopod and its fragile environment, the sandy shores.