Phylogeography of the dugong (Dugong dugon) based on historical samples identifies vulnerable Indian Ocean populations

Abstract

We investigated the phylogeography of the dugong (Dugong dugon) across its original range using museum material from 14 natural history museum and university collections. The mitochondrial DNA control region was successfully amplified from samples of bone or tooth powder from 162 individuals. These samples range from 1827 to 1996 and span the historical distribution range of the dugong. We were able to successfully amplify overlapping fragments of the D-loop region of the mitochondrial DNA (mtDNA) resulting in sequences of a 355 bp fragment for 162 individuals for the final analyses. This included a new sequence (189 bp) from a previously unidentified piece of skin of the extinct Steller’s sea cow (Hydrodamalis gigas), as an outgroup. The resulting dugong sequences match those from previous studies of dugongs from Australia and Indonesia, but revealed several new and divergent mtDNA lineages in the Indian Ocean. One mtDNA lineage includes most specimens from the Western Indian Ocean, with another distinct lineage isolated to nearby Madagascar and Comores. There is little geographic structuring detectable among other populations in the Western Indian Ocean and all populations from that region appear to have historically contained comparatively low levels of genetic diversity. The genetic diversity of several Indian Ocean samples collected after 1950 was lower than that of the samples collected earlier from similar locations, a result coincident with the anecdotal reductions in population size. The new lineages and potential loss of diversity highlight the particular conservation importance and vulnerability of dugong populations in the Western Indian Ocean.

Mitochondrial phylogeography reveals high haplotype diversity and unique genetic lineage in Indian dugongs (Dugong dugon)

“… Global dugong alignment of 537 sequences (309 bp) consisting of Indian dugong sequences generated in this study ( n = 21) and sequences downloaded from GenBank ( n = 516) from previously published studies (Haile, 2008; Jayasankar et al, 2009; Bushell, 2013; Blair et al, 2014; Seddon et al, 2014; Plön et al, 2019). Only 88 sequences (out of 163) could be used from Plön et al (2019) due to the presence of a large number of gaps in the remaining sequences.…”

“… Global dugong alignment of 537 sequences (309 bp) consisting of Indian dugong sequences generated in this study ( n = 21) and sequences downloaded from GenBank ( n = 516) from previously published studies (Haile, 2008; Jayasankar et al, 2009; Bushell, 2013; Blair et al, 2014; Seddon et al, 2014; Plön et al, 2019). Only 88 sequences (out of 163) could be used from Plön et al (2019) due to the presence of a large number of gaps in the remaining sequences. The sequences were arranged into global dugong distribution representing Pacific (Australia: 383; Papua New Guinea: 5; New Caledonia and Palau: 1 each); South‐east Asia (Thailand 56; Indonesia: 7; Japan: 2; Philippines and Malaysia/Sabah: 1 each); South Asia (India: 24; Sri Lanka: 4; Mauritius: 2); North‐west Indian Ocean (Djibouti: 8; Bahrain and Red Sea: 6 each; Egypt: 5; United Arab Emirates: 4; Sudan: 2); and South‐west Indian Ocean (Tanzania: 7; Madagascar: 5; East Africa, Mozambique, and Kenya: 2 each; Comoros: 1) regions. Indian dugong alignment consisting of 21 sequences (789 bp) of mtDNA control region sequences generated in this study.…”

“…Lack of long‐term monitoring and systematic sampling have also resulted in a paucity of reliable information on their genetic lineage in comparison with other dugong populations. So far, genetic status of dugong populations is known from published studies in Australia (Tikel, 1997; McDonald, 2005; Blair et al, 2014; Seddon et al, 2014), Thailand (Palmer, 2004; Bushell, 2013), and the western Indian Ocean (Plön et al, 2019). These studies indicate three major dugong genetic lineages: Australian (restricted and widespread), South‐east Asian, and Western Indian Ocean (Blair, Marsh & Jones, 2013; Plön et al, 2019).…”

“…So far, genetic status of dugong populations is known from published studies in Australia (Tikel, 1997; McDonald, 2005; Blair et al, 2014; Seddon et al, 2014), Thailand (Palmer, 2004; Bushell, 2013), and the western Indian Ocean (Plön et al, 2019). These studies indicate three major dugong genetic lineages: Australian (restricted and widespread), South‐east Asian, and Western Indian Ocean (Blair, Marsh & Jones, 2013; Plön et al, 2019). Recent work by Plön et al (2019) suggests that the Sri Lankan dugongs are genetically divergent from other populations, based on very limited samples ( n = 4).…”

“…These studies indicate three major dugong genetic lineages: Australian (restricted and widespread), South‐east Asian, and Western Indian Ocean (Blair, Marsh & Jones, 2013; Plön et al, 2019). Recent work by Plön et al (2019) suggests that the Sri Lankan dugongs are genetically divergent from other populations, based on very limited samples ( n = 4). Given rapidly declining populations of dugongs in South Asia with recent local extinctions in Mauritius, Maldives, and parts of the Indian and Sri Lankan coasts (Marsh et al, 2002), adequate sampling to ascertain their position vis‐à‐vis global populations is of critical importance.…”