Population genetics and evolutionary history of the endangered Eld's deer (Rucervus eldii) with implications for planning species recovery.

Eld's deer (Rucervus eldii) with three recognised subspecies (R. e. eldii, R. e. thamin, and R. e. siamensis) represents one of the most threatened cervids found in Southeast Asia. The species has experienced considerable range contractions and local extinctions owing to habitat loss and fragmentation, hunting, and illegal trade across its distribution range over the last century. Understanding the patterns of genetic variation is crucial for planning effective conservation strategies. This study investigated the phylogeography, divergence events and systematics of Eld's deer subspecies using the largest mtDNA dataset compiled to date. We also analysed the genetic structure and demographic history of R. e. eldii using 19 microsatellite markers. Our results showed that R. e. siamensis exhibits two divergent mtDNA lineages (mainland and Hainan Island), which diverged around 0.2 Mya (95% HPD 0.1-0.2), possibly driven by the fluctuating sea levels of the Early Holocene period. The divergence between R. e. eldii and R. e. siamensis occurred around 0.4 Mya (95% HPD 0.3-0.5), potentially associated with the adaptations to warm and humid climate with open grassland vegetation that predominated the region. Furthermore, R. e. eldii exhibits low levels of genetic diversity and small contemporary effective population size (median = 7, 4.7-10.8 at 95% CI) with widespread historical genetic bottlenecks which accentuates its vulnerability to inbreeding and extinction. Based on the observed significant evolutionary and systematic distance between Eld's deer and other species of the genus Rucervus, we propose to classify Eld's deer (Cervus eldii) in the genus Cervus, which is in congruent with previous phylogenetic studies. This study provides important conservation implications required to direct the ongoing population recovery programs and planning future conservation strategies.

Demographic and genetic structure of a severely fragmented population of the endangered hog deer (Axis porcinus) in the Indo-Burma biodiversity hotspot.

The population of the globally endangered hog deer (Axis porcinus) has declined severely across its geographic range. Intensive monitoring of its demographic and genetic status is necessary. We examined the demographic and genetic structure of a small hog deer population in Keibul Lamjao National Park (KLNP), located on the western fringe of the Indo-Burma biodiversity hotspot for conservation planning. The distribution pattern of hog deer in the Park was derived based on the presence/absence of faecal pellets in 1 km × 1 km grids. We used double-observer distance sampling method to derive the hog deer abundance and population structure and compared with previous data to derive the population trend. We determined the genetic diversity of the population through microsatellite screening and bottleneck detection. The overall pellet density was 0.34 ± 0.02 pellets km-2 restricted to only 22.34 ± 0.20 km2 area of the park. The estimated density of the deer in the park was 1.82-4.32 individuals km-2. The population showed a declining trend from 2006-08 (p < 0.05, R2 = 0.916) with 8% annum-1 and an increasing trend from 2003-2018 (p < 0.05, R2 = 0.9304) with 10% annum-1. The adult male-to-female ratio and fawn-to-doe ratio were 36.2 ± 1.9 males per 100 females and 16.5 ± 0.4 fawns per 100 females, respectively. The molecular examination suggested that the mean number of alleles at 23 loci was 2.70 ± 0.18, the observed heterozygosity (Ho) ranged from 0.26 to 0.63 (mean 0.42 ± 0.02), the expected heterozygosity (He) ranged from 0.23 to 0.73 (χ = 0.51 ± 0.03), and the polymorphic information content (PIC) ranged from 0.2 to 0.67 (χ = 0.43 ± 0.03) indicating a moderate level of genetic diversity. Although no bottleneck in the population was observed, the loss of genetic diversity may affect the evolutionary potential of the species at the site by limiting the selection flexibility. Conservation planning coupled with scientific management regime will help in the long term persistence of the population in the region.

Genetic analysis of endangered hog deer (Axis porcinus) reveals two distinct lineages from the Indian subcontinent.

The hog deer (Axis porcinus) is threatened by habitat alteration, fragmentation, and poaching, which have led to a drastic decline of its wild population. Two subspecies of A. porcinus have been described from its distribution range. A. p. porcinus is reported to occur from Pakistan along the Himalayan foothills through Nepal, India and Myanmar, and A. p. annamiticus is found in Thailand, Indo-China, Laos, Cambodia, and Vietnam. However, the current distribution range of A. p. annamiticus is still unclear. We used the partial control region (CR) of mitochondrial DNA (mtDNA) and seven microsatellite loci to investigate the intra-species structure, differentiation, and demographic history of hog deer populations from three landscapes, the Terai Arc, Northeast, and Indo-Burma (Keibul Lamjao National Park (KLNP), Manipur, India) landscapes. We also carried out divergence time estimation using the complete mitogenome. The level of variation was ~4%, and the time of divergence of the KLNP population and the other Indian populations was about 0.22 Mya, i.e., during the last glaciation periods of the Late Pleistocene/Early Holocene. The KLNP haplotypes of the control region were shared with the Southeast Asian subspecies, A. p. annamiticus. The results of the investigations of the microsatellite loci supported the mtDNA results unambiguously. Two genetically distinct lineages are found in India: one is found from the Terai Arc to Assam (A. p. porcinus) and the other in Manipur (A. p. annamiticus). The genetic diversity in KLNP was low and exhibited a higher degree of genetic differentiation compared with major Indian populations. The Bayesian skyline plots indicated that after a long phase of historic demographic stability, the populations of both the lineages of hog deer suffered pronounced declines during the period from ~800 years BP to 5000 years BP. In summary, our finding provided evidence that the KLNP population is probably a prime, isolated and sustaining stock of A. p. annamiticus and should be managed as evolutionarily significant units (ESUs).