Genetic features of Sri Lankan elephant, Elephas maximus maximus Linnaeus revealed by high throughput sequencing of Mitogenome, Nuclear Genome and ddRADseq. Elephas maximus maximus

Elephas maximus maximus Linnaeus, the Sri Lankan subspecies is the largest and the darkest among the Asian elephants. Patches of depigmentation areas with no skin color on ears, face, trunk, and belly morphologically differentiate it from the others. The elephant population in Sri Lanka is now limited to smaller areas and protected under Sri Lankan law. Identification of existing genetic diversity is the key to any conservation and management strategies. Despite its ecological and evolutionary importance, the inter-relationships within the Sri Lankan elephants and its phylogenetic position within Asian elephants remain controversial. To address such issues, we assembled the nuclear genome of a typical Sri Lankan elephant using the Asian elephant genome as a reference, while denovo assembled the mitogenome. Further, 24 elephants with known parental lineages were analyzed with high throughput ddRAD-seq. The mitogenome and nuclear coding sequences suggest coalescence time of the Sri Lanka elephant at ~0.2 million years, sisters to Myanmar elephants supporting the hypothesis of historical trade of elephants between two countries. Mainland elephants are phylogeographically diverse, and both mitochondrial and nuclear genomic data triangulate the provenance of Asian elephants. The highly polymorphic mitochondrial genes; CYTB and ND1 were identified as possible markers for future phylogeographic studies. The ddRAD-seq approach identified 50,490 genome-wide SNPs among Sri Lankan elephants. The genetic diversity within Sri Lankan elephants assessed with identified SNPs suggests a geographical differentiation resulting in three significant clusters; north-eastern, mid-latitude, and southern regions. The effect of habitat fragmentation on genetic diversity could be further assessed with more samples with specific SNPs identified in the current study.