Genetic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) in the Gulf of Thailand

Abstract

The Irrawaddy dolphin ( Orcaella brevirostris ) is an endangered, small cetacean species which is widely distributed in rivers, estuaries, and coastal waters throughout the tropical and subtropical Indo-Pacific. Despite the extensive distribution of this species, little is known of individual movements or genetic exchange among regions in Thailand. Here, we evaluate the genetic diversity and genetic structure of O. brevirostris in the eastern, northern and western Gulf of Thailand, and Andaman Sea. Although phylogenetic relationships and network analysis based on 15 haplotypes obtained from 32 individuals reveal no obvious divergence, significant genetic differentiation in mitochondrial DNA (overall F ST = 0.226, P < 0.001; Φ ST = 0.252, P < 0.001) is apparent among regions. Of 18 tested microsatellite loci, 10 are polymorphic and successfully characterized in 28 individuals, revealing significant genetic differentiation (overall F ST = 0.077, P < 0.05) among the four sampling sites. Structure analysis reveals two inferred genetic clusters. Additionally, Mantel analysis demonstrates individual-by-individual genetic distances and geographic distances follow an isolation-by-distance model. We speculate that the significant genetic structure of O. brevirostris in Thailand is associated with a combination of geographical distribution patterns, environmental and anthropogenic factors, and local adaptations.

Mitogenomes provide insight into complex evolutionary history of freshwater and coastal Irrawaddy dolphin (Orcaella brevirostris Gray, 1866) in Thailand and Indonesia

“…Compared to their conspecifics, there is a closer genetic affinity between the haplotype OBID03 from PPU, Indonesia and OBTH04 in both SKL and LGT, and Hap7 from SKL, Thailand (Beasley et al, 2005). Similarly, the haplotype Obr13 from the Andaman coast in western Thailand (Dai et al, 2021) was clustered within the strongly supported MHK clade, The Obr4 haplotype (Dai et al, 2021) from LGT, Thailand was also more closely related to the Chilika population in India compared to their Thailand conspecifics. Overall, the current results do not support reciprocal monophyly of both the Thailand and Indonesian haplotypes in relation to those from other populations.…”

“…The control region and mitogenome sequences from this study were combined with those derived from other populations (Beasley et al, 2005;Jayasankar et al, 2011;Caballero et al, 2019;Dai et al, 2021) and deposited in the NCBI database (https://www.ncbi.nlm.nih.gov/). The best fitted nucleotide substitution model was estimated using ModelFinder (Kalyaanamoorthy et al, 2017) and a phylogenetic tree was reconstructed based on maximum likelihood with ultrafast 10,000 bootstrap replicates (Hoang et al, 2018) on the IQ-TREE web server (http://iqtree.cibiv.…”

“…Compared to a single-gene phylogeny, a larger number of single nucleotide polymorphisms (SNPs) in the mitogenome phylogeny provide a more reliable estimation of population-level genetic diversity, inference of divergence time, species origins and subsequent colonization events (Arnason et al, 2004;Galtier et al, 2009;Palmer et al, 2011;Bayas-Rea et al, 2018). The population-level genetic diversity and structure of Irrawaddy dolphins based on the control region of the mitogenome are available only for those in the Mekong River and the Gulf of Thailand (Krützen et al, 2018;Caballero et al, 2019;Dai et al, 2021). Control regionbased phylogeographic studies support a close genetic affinity between Thailand and Indonesian populations; however, statistical support for such phylogenetic relationships is low (Krützen et al, 2018;Caballero et al, 2019).…”

The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation

“…Cetacean stranding provides a unique opportunity to gain biological and ecological knowledge of cetaceans [62]. Previous studies have obtained microsatellites loci from stranded S. chinensis and identified them via PCR amplification [18,24]. We aligned the previous identified microsatellite markers to our genome.…”

“…In addition, microsatellites were also applied to understand the genetic differentiation and speciation processes in Chilean dolphins [21]. However, currently, few SSR markers have been reported for S. chinensis [18,23,24]. Genome-wide characterization of microsatellites is imperative for better species identification and conservation research, particularly for the endangered S. chinensis.…”