Mitogenomic sequences better resolve stock structure of southern Greater Caribbean green turtle rookeries

Abstract

Analyses of mitochondrial control region polymorphisms have supported the presence of several demographically independent green turtle (Chelonia mydas) rookeries in the Greater Caribbean region. However, extensive sharing of common haplotypes based on 490-bp control region sequences confounds assessment of the scale of natal homing and population structure among regional rookeries. We screened the majority of the mitochondrial genomes of 20 green turtles carrying the common haplotype CM-A5 and representing the rookeries of Buck Island, St. Croix, United States Virgin Islands (USVI); Aves Island, Venezuela; Galibi, Suriname; and Tortuguero, Costa Rica. Five single-nucleotide polymorphisms (SNPs) were identified that subdivided CM-A5 among regions. Mitogenomic pairwise φ(ST) values of eastern Caribbean rookery comparisons were markedly lower than the respective pairwise F(ST) values. This discrepancy results from the presence of haplotypes representing two divergent lineages in each rookery, highlighting the importance of choosing the appropriate test statistic for addressing the study question. Haplotype frequency differentiation supports demographic independence of Aves Island and Suriname, emphasizing the need to recognize the smaller Aves rookery as a distinct management unit. Aves Island and Buck Island rookeries shared mitogenomic haplotypes; however, frequency divergence suggests that the Buck Island rookery is sufficiently demographically isolated to warrant management unit status for the USVI rookeries. Given that haplotype sharing among rookeries is common in marine turtles with cosmopolitan distributions, mitogenomic sequencing may enhance inferences of population structure and phylogeography, as well as improve the resolution of mixed stock analyses aimed at estimating natal origins of foraging turtles.

Connectivity, population structure, and conservation of Ecuadorian green sea turtles

“…Alternatively, the use of mitochondrial short tandem repeats (Tiko chinski et al 2012) or mitogenomic sequencing could help reveal cryptic differentiation among Ecuadorian populations, as found in Caribbean rookeries (Shamblin et al 2012). Despite the limitations, these are robust results which suggest close genetic links be tween the Ecuadorian stocks in spite of their geographic separation that could be used as the first step in redefining MUs for these populations.…”

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

“…However, the landlocked population had mitogenomes shared among multiple individuals and unique to that population. In contrast, Atlantic wolffish ( Anarhichas lupus ; Lait, 2016; Lait & Carr, under review), green turtle ( Chelonia mydas ; Shamblin et al., 2012), and speartooth shark ( Glyphis glyphis ; Feutry et al., 2014) all include mitogenomes shared among individuals that are widely dispersed. The latter suggests recent origin of these lineages followed by dispersal, whereas the limitation of identical cod to a confined space is suggestive of founder effect and/or local drift on a scale of a few thousand years.…”

Advances in the Application of Genetics in Marine Turtle Biology and Conservation

“…In cases where there is not extensive haplotype sharing among rookeries, the extended control region sequence can effectively identify natal origin of foraging turtles (LeRoux et al, 2012). However, when overlaps in control region haplotypes among rookeries are prevalent, the addition of other mtDNA markers or complete mitogenomic sequencing can help resolve uncertainties (Shamblin et al, 2012a). Informative nuclear markers have also now been developed for all marine turtle species, offering finer-scale resolution in some biological contexts, and applicability to research questions about the male component of populations.…”

“…For mtDNA, this began with the development of primers that target an extended control region sequence (i.e., 766 vs. 490 bp; Shamblin et al, 2012b), and recently extended to identification of diagnostic variants in other mtDNA regions (Shamblin et al, 2012a;Tikochinski et al, 2012) and whole mitogenome sequencing (Duchêne et al, 2012). In cases where there is not extensive haplotype sharing among rookeries, the extended control region sequence can effectively identify natal origin of foraging turtles (LeRoux et al, 2012).…”

“…These patterns made it unclear if there is mixing among females nesting at these rookeries, or if there is population structure undetected by this particular marker. To resolve this question, Shamblin et al (2012a) sequenced nearly the entire 16,000 bp mitogenome from 20 individuals from these rookeries as well as Buck Island, US Virgin Islands (USVI) to detect informative variable positions outside of the standard control region sequence. They found four variants in other regions of the mitogenome that divided CM-A5 into three haplotypes that were regionally structured.…”