Characterization of 10 novel microsatellite loci and cross-amplification of two loci in the snapping turtle (Chelydra serpentina)

Low coverage sequencing provides insights into the key features of the nuclear and mitochondrial genomes of the Alligator Snapping Turtle Macrochelys temminckii

The alligator snapping turtle Macrochelys temminckii is a culturally, ecologically, and evolutionary relevant species of conservation concern. In this study, we conducted a genome survey of M. temminckii. Using a low-coverage short read sequencing strategy, this study estimated the genome size, repetitive genome content, annotated and quantified repetitive elements, assembled the 45S rRNA DNA operon, and characterized in detail the mitochondrial genome of M. temminckii. Using a k-mer strategy, the estimated haploid genome size varied between 3.77 and 3.19 Gbp, which is within the range previously reported for other representatives of the family Chelydridae. Repetitive genome content estimates using different k-mers (21 to 51) indicated that more than 75% of the genome of M. temminckii comprised repetitive elements. Taking into account only annotated repetitive elements, the most common repetitive elements were classified as Class I - Long Interspersed Nuclear Element (LINE) which were more abundant than Class I - Penelope and Class I - Long Terminal Repeat (LTR) Ty3-gypsy mobile elements. Less abundant repeat element families in the nuclear genome of M. temminckii included Class I - DIRS mobile elements and Satellite DNA. The nuclear ribosomal operon was partially assembled into two contigs, one encoding the complete ssrDNA and a second comprising the full lsrDNA. The AT-rich complete mitochondrial genome was 16,570 bp long. These new genomic resources are of utmost importance to aid in the development of conservation plans for this freshwater turtle.

Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”

Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.