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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.

SUBMITTER: von Seth J

PROVIDER: S-EPMC8071806 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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

von Seth Johanna J Dussex Nicolas N Díez-Del-Molino David D van der Valk Tom T Kutschera Verena E VE Kierczak Marcin M Steiner Cynthia C CC Liu Shanlin S Gilbert M Thomas P MTP Sinding Mikkel-Holger S MS Prost Stefan S Guschanski Katerina K Nathan Senthilvel K S S SKSS Brace Selina S Chan Yvonne L YL Wheat Christopher W CW Skoglund Pontus P Ryder Oliver A OA Goossens Benoit B Götherström Anders A Dalén Love L

Nature communications 20210426 1

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 th ...[more]

PMID: 33896938

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Project description:In the 200 years since the Sumatran rhinoceros was first scientifically described (Fisher 1814), the range of the species has contracted from a broad region in Southeast Asia to three areas on the island of Sumatra and one in Kalimantan, Indonesia. Assessing population and spatial distribution of this very rare species is challenging because of their elusiveness and very low population number. Using an occupancy model with spatial dependency, we assessed the fraction of the total landscape occupied by Sumatran rhinos over a 30,345-km2 survey area and the effects of covariates in the areas where they are known to occur. In the Leuser Landscape (surveyed in 2007), the model averaging result of conditional occupancy estimate was ψ(SE[ψ]) = 0.151(0.109) or 2,371.47 km2, and the model averaging result of replicated level detection probability p(SE[p]) = 0.252(0.267); in Way Kambas National Park--2008: ψ(SE[ψ]) = 0.468(0.165) or 634.18 km2, and p(SE[p]) = 0.138(0.571); and in Bukit Barisan Selatan National Park--2010: ψ(SE[ψ]) = 0.322(0.049) or 819.67 km2, and p(SE[p]) = 0.365(0.42). In the Leuser Landscape, rhino occurrence was positively associated with primary dry land forest and rivers, and negatively associated with the presence of a road. In Way Kambas, occurrence was negatively associated with the presence of a road. In Bukit Barisan Selatan, occurrence was negatively associated with presence of primary dryland forest and rivers. Using the probabilities of site occupancy, we developed spatially explicit maps that can be used to outline intensive protection zones for in-situ conservation efforts, and provide a detailed assessment of conserving Sumatran rhinos in the wild. We summarize our core recommendation in four points: consolidate small population, strong protection, determine the percentage of breeding females, and recognize the cost of doing nothing. To reduce the probability of poaching, here we present only the randomized location of site level occupancy in our result while retaining the overall estimation of occupancy for a given area. ψ

Project description:An understanding of genetic diversity and the population genetic processes that impact future population viability is vital for the management and recovery of declining populations of threatened species. Styphelia longissima (Ericaceae) is a critically endangered shrub, restricted to a single fragmented population near Eneabba, 250 km north of Perth, Western Australia. For this population, we sought to characterize population genetic variation and its spatial structure, and aspects of the mating portfolio, from which strategies that optimize the conservation of this diversity are identified. A comprehensive survey was carried out and 220 adults, and 106 seedlings from 14 maternal plants, were genotyped using 13 microsatellite markers. Levels of genetic variation and its spatial structure were assessed, and mating system parameters were estimated. Paternity was assigned to the offspring of a subsection of plants, which allowed for the calculation of realized pollen dispersal. Allelic richness and levels of expected heterozygosity were higher than predicted for a small isolated population. Spatial autocorrelation analysis identified fine-scale genetic structure at a scale of 20 m, but no genetic structure was found at larger scales. Mean outcrossing rate (t m = 0.66) reflects self-compatibility and a mixed-mating system. Multiple paternity was low, where 61 % of maternal siblings shared the same sire. Realized pollen dispersal was highly restricted, with 95 % of outcrossing events occurring at 7 m or less, and a mean pollen dispersal distance of 3.8 m. Nearest-neighbour matings were common (55 % of all outcross events), and 97 % of mating events were between the three nearest-neighbours. This study has provided critical baseline data on genetic diversity, mating system and pollen dispersal for future monitoring of S. longissima. Broadly applicable conservation strategies such as implementing a genetic monitoring plan, diluting spatial genetic structure in the natural population, genetically optimizing ex situ collections and incorporating genetic knowledge into translocations will help to manage the future erosion of the high genetic variation detected.

Dataset Information

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

Publications

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

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