Divergence and serial colonization shape genetic variation and define conservation units in Asian elephants

Area of Science:

• Genomics
• Conservation Biology
• Population Genetics

Background:

• Asian elephants (Elephas maximus) are ecologically and culturally significant megaherbivores in Asia.
• Their population genetic structure, diversity, and demographic history in India are understudied.
• Understanding these factors is crucial for effective management and conservation strategies.

Purpose of the Study:

• To analyze the population genetic structure and diversity of Asian elephants across India using whole-genome data.
• To investigate demographic history and identify distinct management/conservation units.
• To assess genetic load and its implications for conservation in different elephant populations.

Main Methods:

• Whole-genome sequencing of 34 Asian elephants from diverse Indian landscapes.
• Analysis of genetic diversity, inbreeding (FROH), effective population sizes, and genetic load.
• Identification of population structure and management/conservation units.

Main Results:

• Five management/conservation units were identified: Northern, Central, and three Southern India populations.
• Genetic diversity decreases from north to south, with northern populations showing higher diversity and lower inbreeding.
• Southern populations exhibit low diversity, high inbreeding, and evidence of deleterious allele purging, with remaining load being homozygous.

Conclusions:

• Northern elephant populations are genetically more diverse and less inbred than southern ones.
• Southernmost populations face high conservation priority due to low genetic diversity and high homozygosity of deleterious alleles.
• Genomic signatures of serial founding events correlate with patterns of genetic diversity and load in this endangered species.