Genetic features of Sri Lankan elephant, Elephas maximus maximus Linnaeus revealed by high throughput sequencing of mitogenome and ddRAD-seq.

Elephas maximus maximus Linnaeus, the Sri Lankan subspecies is the largest and the darkest among Asian elephants. Patches of depigmented areas with no skin color on the 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. Despite its ecological and evolutionary importance, the relationship between Sri Lankan elephants and their phylogenetic position among Asian elephants remains controversial. While identifying genetic diversity is the key to any conservation and management strategies, limited data is currently available. To address such issues, we analyzed 24 elephants with known parental lineages with high throughput ddRAD-seq. The mitogenome suggested the coalescence time of the Sri Lankan elephant at ~0.2 million years, and sister to Myanmar elephants supporting the hypothesis of the movement of elephants in Eurasia. 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 main clusters; north-eastern, mid-latitude, and southern regions. Interestingly, though it was believed that elephants from the Sinharaja rainforest are of an isolated population, the ddRAD-based genetic analysis clustered it with the north-eastern elephants. The effect of habitat fragmentation on genetic diversity could be further assessed with more samples with specific SNPs identified in the current study.

Revisiting traditional SSR based methodologies available for elephant genetic studies.

Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants' dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.

Reproductive performance of the largest captive Asian elephant (Elephas maximus) population in Sri Lanka.

The Pinnawela Elephant Orphanage (PEO) in Sri Lanka maintains one of the largest captive Asian elephant (Elephas maximus maximus) populations in the world, with a total of 79 animals (45 females and 34 males) at present. It was established in 1975 as an orphanage for rescued wild calves, and commenced natural breeding under controlled conditions when they reached breeding age. This study summarizes reproductive data of 65 live births from 38 years of records at PEO. The age at first calving (n=31) was 14.6±0.7years, and the numbers of females giving birth two, three, four and five times were 21, 8, 4 and 2, with corresponding inter-birth intervals (IBI) of 4.9±0.3, 4.8±0.5, 7.9±1.9 and 5.7±0.5years, respectively. Females giving birth to males (5.7±2.2years) had longer IBIs compared to birthing female calves (4.7±1.1years). The average gestation for 18 pregnancies with known conception dates was 667±11days. The average birth weight was similar for male (83.1±4.6kg; n=14) and female (82.8±8.4kg; n=6) calves. Sex ratio for live births was 36 male:29 female and not different from 1:1; however, more males (10/14) were born after a second parity. Calf mortality and stillbirth rates were low: 7.6% and 4.4%, respectively. This study highlights the successful breeding program at the PEO, providing baseline reproductive data that can aid in improving breeding of other elephants managed under captive conditions.

Molecular taxonomic position of the elephant schistosome, Bivitellobilharzia nairi, newly discovered in Sri Lanka.

Bivitellobilharzia nairi (Mudaliar and Ramanujachar, 1945) Dutt and Srivastava, 1955 was first recorded in India. A number of adult worm specimens of this schistosome species were recovered from a domestic elephant, which died in 1999 in Sri Lanka. This is the first report of this schistosome from Sri Lanka. In the present study, in order to clarify the phylogenetic relationship with other species of schistosomes, sequences from the second internal transcribed spacer (ITS2) of the ribosomal gene repeat, part of the 28S ribosomal RNA gene (28S), and part of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene from B. nairi were analyzed. Two intraspecific variations were seen within 13 individuals in the ITS2 region. In the CO1 region of the mitochondrial DNA, there were four haplotypes in the nucleotide sequences and two haplotypes in the amino acid sequences. Phylogenetic analysis using the nuclear DNA showed that B. nairi was basal to all of species of the genus Schistosoma. The 28S tree also showed that the mammalian lineage was monophyletic. However, phylogenetic analysis using the mitochondrial DNA showed that B. nairi was nested within the genus Schistosoma. The taxonomical position for this species as well as the contradiction between the results from the nuclear and mitochondrial genes were discussed.