Mitochondrial genetic diversity, phylogeny and population structure of <i>Hydropotes inermis</i> in South Korea

Abstract

The water deer (Hydropotes inermis) is one of the rarest species of deer in the family Cervidae. Only two subspecies exist in East Asia, and few studies have examined the genetic characteristics of the species. Here, we investigated the genetic diversity, phylogeny and population differentiation of the Korean subspecies (H. inermis argyropus). Seventeen mitochondrial D-loop haplotypes (822 bp) were detected and analyzed from 107 individual samples, together with a Chinese subspecies (H. inermis inermis) haplotype. The genetic diversity of the Korean subspecies is lower (π = 0.756%, h = 0.867) than that of the Chinese subspecies estimated in a previous study. This low genetic diversity may result from historical anthropogenic disturbances and/or a founder effect during the glacial period. The phylogenetic tree and median-joining network showed no location-specific distribution of D-loop haplotypes, but revealed two major lineages, A and B, of water deer. The A and B lineages were separated from each other at the beginning of the Pleistocene era (2.1-1.3 million years ago), with a genetic divergence of 1.332 ± 0.340%. The genetic divergence within lineages A and B was 0.525 ± 0.167% and 0.264 ± 0.113%, respectively. This suggests that climate change affected the division of the two lineages. Water deer sampled from the three Korean regions (26 locations) were slightly distinct in their genetic structure (AMOVA: F ST = 0.28416, P < 0.00001; Φ ST = 0.19239, P < 0.00001). Such slight population differentiation may be derived from differential dispersal ability in males and females. The use of genetic markers, such as nuclear microsatellite and Y-linked DNA markers, and samples collected from various localities in East Asia should improve our understanding of the water deer's genetic characteristics.

Northward Range Expansion of Water Deer in Northeast Asia: Direct Evidence and Management Implications

“…DNA was extracted using the Qiagen Blood and Tissue DNA extraction kit following the recommended protocols and precautions. We amplified a partial fragment of the mitochondrial cytochrome b gene [ 19 ] and D-loop sequences [ 20 ]. Positive amplifications were sequenced (in both directions) using the Bigdye terminator v3.1 cycle sequencing kit (Applied Biosystems, Waltham, MA, USA) and 3730 genetic analyzer (Applied Biosystems, USA).…”

“…The species identity of each of the analyzed samples was reconfirmed using NCBI BLAST. The phylogenetic position of water deer samples collected from the newly expanded range in Northeast China and the Russian Far East was verified in two steps: (1) among other deer species [ 21 ] using the cytochrome b gene and (2) within water deer subspecies using D-loop sequences [ 10 , 20 , 22 ].…”