Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

Abstract

Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

“…ROH were estimated using the VCF file based on the Sumatran rhinoceros reference (see "ROH" and "Configuration" in Additional file 3 for parameter choices). Larger proportions of the reference were in ROH >= 2 Mb in modern samples than in historical samples (Figure 3C), suggesting stronger effects of inbreeding in the modern population, consistent with von Seth et al [43]. No variants of potentially high impact on the protein (which include LOF variants) were found in any of the samples in the snpEff analyses of the VCF files based on the White rhinoceros reference and 253 gene predictions.…”

“…Numbers of variants in the other impact categories were similar across historical and modern samples (Figure 3D). Unlike genome-wide estimates [43], relative mutational load estimated from the top 1% of GERP scores based on the White rhinoceros reference and 30 outgroup species (Additional file 1, table S2, figure S1) were similar between historical and modern samples for our test dataset (Figure 3E; see Additional file 1, figure S4 for a histogram of GERP scores).…”

New developments in the field of genomic technologies and their relevance to conservation management

“…Such bioinformatic identification of deleterious alleles rely on evolutionary conservation (Cooper et al 2005;Pollard et al 2010), physicochemical properties and their putative effect on the functionality of genes (Ng and Henikoff 2003) or combined approaches (Kircher et al 2014;Wang et al 2010). Although the deleteriousness of single variants remains notoriously difficult to predict from sequence data alone, when combined they can provide a reliable estimate of genetic load in a comparative framework (van der Valk et al 2019;von Seth et al 2021).…”

Genetic diversity loss in the Anthropocene

“…-von Seth et al (von Seth et al, 2021) studied the highly-threatened species Dicerorhinus sumatrensis. They used Illumina WGS of 16 individuals of the last remaining populations and shared the data directly with us.…”

“…They used Genotyping-by-Sequencing of 242 individuals of the last remaining populations and shared the data directly with us. From a total set of 166,564 SNPs with a genotyping rate of 0.964632, 10,000 were randomly selected for our analyses.-von Seth et al(von Seth et al, 2021) studied the highly-threatened species Dicerorhinus sumatrensis. They used Illumina WGS of 16 individuals of the last remaining populations and shared the data directly with us.…”