Mitochondrial genomes and genetic structure of the Kemp's ridley sea turtle (Lepidochelys kempii)

Abstract

The Kemp's ridley (Lepidochelys kempii) is the world's most endangered sea turtle species and is primarily distributed in the Gulf of Mexico. In the United States, South Padre Island, Texas serves as a key nesting ground for the species. Genetic studies of the Kemp's ridley have been used to aid in conservation and management practices, with the mitochondrial control region as the most commonly used marker due to its perceived hypervariability and ease of sequencing. However, with the advent of next generation sequencing technology, targeting complete mitochondrial genomes is now feasible. Here, we describe a more complete mitochondrial genome for the Kemp's ridley than has been previously published in literature and demonstrate a cost-effective and efficient method for obtaining complete mitochondrial genomes from sea turtles. We compare the genetic diversity and taxonomic resolution obtained from whole mitochondrial genomes to that obtained from the mitochondrial control region alone. We compare current genetic diversity with previous records. Furthermore, we evaluate the genetic structure between the breeding stock in South Padre Island and that of deceased Kemp's ridleys recovered on the Northern coast of the Gulf of Mexico after the 2010 BP Deepwater Horizon oil spill, and of Kemp's ridleys stranded on the East Coast of the United States. Our results show that complete mitochondrial genomes provide greater resolution than the control region alone.They also show that the genetic diversity of the Kemp's ridley has remained stable, despite large population declines, and that the genetic makeup of deceased turtles stranded after the Deepwater Horizon oil spill is indistinguishable from the breeding stock in South Padre Island, Texas. K E Y W O R D Sconservation, control region, genetic diversity, next generation sequencing, phylogeny, phylogeography

Genetic diversity of immature Kemp's ridley (Lepidochelys kempii) sea turtles from the northern Gulf of Mexico

“…Although this population went through a significant bottleneck, genetic diversity for the species in both nesting females (Frey et al, 2014;Frandsen, Figueroa & George, 2020) and immature individuals (this study) appears stable. Kemp's ridleys continue to face multiple threats, however, including increased mortality as by-catch in commercial fishing activities in the past two decades (Putman, Hawkins & Gallaway, 2020) and environmental disasters such as the Deepwater Horizon oil spill that disproportionately affected Kemp's ridleys (Shaver et al, 2021).…”

Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)

“…Analysis of mitochondrial DNA from Lk15 (mitochondrial sequence obtained from non-enriched whole genome sequencing data from this sample) along with other published Kemp’s ridley mitochondrial D-loop control regions showed that Lk15 grouped within the haplotype 1 sub-group ( Figure 4 ). Since previous research shows that Kemp’s ridley turtles along the east coast of the United States are 80% likely to be haplotypes 1 and 2 (predominantly haplotype 1), and that 79% of haplotypes 1 and 2 originate from rookeries along the Texas coast [ 43 ], we can infer that Lk15 likely originated from Texas. These conclusions are based on currently available literature and may be subject to change, since Kemp’s ridley haplotype data are currently limited for regions other than Texas [ 43 , 44 , 45 ].…”

“…Since previous research shows that Kemp’s ridley turtles along the east coast of the United States are 80% likely to be haplotypes 1 and 2 (predominantly haplotype 1), and that 79% of haplotypes 1 and 2 originate from rookeries along the Texas coast [ 43 ], we can infer that Lk15 likely originated from Texas. These conclusions are based on currently available literature and may be subject to change, since Kemp’s ridley haplotype data are currently limited for regions other than Texas [ 43 , 44 , 45 ]. Phylogenetic analysis of ChHV5 UL30 and HP32 gene segments (described in detail in Section 3.4 ) suggests that this turtle harbored a Florida variant of ChHV5.…”

“…Phylogenetic analysis of ChHV5 UL30 and HP32 gene segments (described in detail in Section 3.4) suggests that this turtle harbored a Florida variant of ChHV5. Kemp's ridley turtles along the east coast of the United States are 80% likely to be haplotypes 1 and 2 (predominantly haplotype 1), and that 79% of haplotypes 1 and 2 originate from rookeries along the Texas coast [43], we can infer that Lk15 likely originated from Texas. These conclusions are based on currently available literature and may be subject to change, since Kemp's ridley haplotype data are currently limited for regions other than Texas [43][44][45].…”

Mitochondrial DNA Evaluation and Species Identification of Kemp’s Ridley Sea Turtle (Lepidochelys kempii) Bones After a 3-Year Exposure to Submerged Marine and Terrestrial Environments

“…Both species migrate internationally, and conservation biologists have been able to identify and track subpopulations through sequence differences in mitochondrial DNA (mtDNA). Due to female philopatry, in which pregnant females usually return to the beaches where they hatched, and because mtDNA is maternally inherited, individual haplotypes can be associated with specific beaches of origin (Allard et al, 1994;Duchene et al, 2012;Patricio et al, 2017;Frandsen et al, 2020). Combining the genetic data with GPS and satellite tracking reveals migratory pathways for sea turtles (Dutton et al, 2019;Gredzens and Shaver, 2020).…”