Population genetics of the critically endangered three-striped turtle, Batagur dhongoka, from the Ganga river system using mitochondrial DNA and microsatellite analysis

Abstract

The three-striped roofed (Batagur dhongoka) is a semi-aquatic turtle that belongs to family Geoemydidae. Due to anthropogenic pressure, it has been facing an intense decline of over 80% in its distribution range in the past 50 years. It is considered as 'Critically Endangered' so effective conservation strategies are needed to protect the species by determining their genetic diversity and population genetic structure. This study investigates the genetic diversity, population structure and demographic pattern of B. dhongoka from two Turtle Rescue and Rehabilitation Centre established near Ganga river using mitochondrial cytochrome b (Cyt b: 1140 bp) ; control region (CR: 451 bp) and ten nuclear microsatellite loci. mtDNA results show low levels of nucleotide diversity (π = 0.0022) in B. dhongoka haplotypes and provide evidence for a low substitution rate. The demographic pattern estimated by the Bayesian skyline plot (BSP) analysis indicates historical stability followed by growth in the effective population size, with a recent reduction in population size from ~ 2 thousand years ago. The microsatellite findings show a moderate level of observed heterozygosity (Ho: 0.49). Bayesian-based clustering analysis revealed weak genetic structures in B. dhongoka and presence of admixed assignations suggesting close genetic relationships. These findings shed light on B. dhongoka's genetic status and underline the necessity of comprehensive rehabilitation and relocation programs and conservation and management techniques to ensure the species' long-term survival. In order to ensure the effective protection and conservation of B. dhongoka, the Government of India has taken a proactive measure by incorporating it into Schedule I of the Wildlife (Protection) Act, 1972, as amended in 2022.

Keywords: Genetic diversity; Heterozygosity; Microsatellite; Population structure; mtDNA.

Figure 1

Median-joining network inferred from Batagur dhongoka mitochondrial DNA haplotypes. The size of each circle indicates the relative frequency of the corresponding haplotype in the whole dataset. Short tick lines between haplotypes show the number of mutations.

Figure 2

Factorial correspondence analysis (FCA), computed using GENETIX 4.02, shows relationships among the multilocus genotypes of two Batagur dhongoka populations (TRRC: Turtle Rescue and Rehabilitation Centre, Sarnath; GARRC: Ganga Aqualife Rescue and Rehabilitation Centre, Narora). Axis 1, Axis 2 and Axis 3 are the first, second and third principal factors of variability.

Figure 3

CLUMPK genetic structure plot derived from Bayesian-based cluster analysis in STRUCTURE. The proportion of color in each bar represents the assignment probability of an individual, corresponding to different groups of TRRC: Turtle Rescue and Rehabilitation Centre, Sarnath and GARRC: Ganga Aqualife Rescue and Rehabilitation Centre, Narora.

Figure 4

The mismatch distributions graph dashed line showing observed distribution; solid line showing the theoretical expected distribution under a growth-decline model.

Figure 5

Bayesian skyline plots representing historical demographic trends of Batagur dhongoka. X-axis shows time before present in million years ago (MYA). Y-axis indicates effective population size on a logarithmic scale. The thick solid lines represent mean estimates for effective population size, and differentially colored areas reflect the 95% highest posterior density intervals.

Figure 6

Map of the study area showing sampling sites of Batagur dhongoka, which was created using ArcGIS Desktop: Release 10.6.1 Redlands, CA: Environmental systems Research Institute.