Genomic resources for Asian (<i>Elephas maximus</i>) and African savannah elephant (<i>Loxodonta africana</i>) conservation and health research

Prado, Natalia A.; Armstrong, Ellie E.; Brown, Janine L.; Goldenberg, Shifra Z.; Leimgruber, Peter; Pearson, Virginia R.; Maldonado, Jesús E.; Campana, Michael G.

doi:10.1093/jhered/esad034

Cited by 3 publications

(1 citation statement)

References 68 publications

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“…We therefore strongly encourage the sequencing of multiple trios per lineage to better infer rate variation. In many cases, a single sequenced trio per species may be all that is available (Bergeron et al 2023;Prado et al 2023). In these cases, an averaged rate across multiple closely related species may be preferable to avoid inferred extreme rates arising simply by chance.…”

Section: Discussionmentioning

confidence: 99%

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

Armstrong,

Carey,

Harkess

et al. 2024

Preprint

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Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error rates in sequence data and uncertainty in the fossil record. Here, we directly estimate de novo germline mutation rates for all extant members of Panthera, as well as the closely related outgroup Neofelis nebulosa, using pedigrees. We use a previously validated pipeline (RatesTools) to calculate mutation rate for each species and subsequently explore the impacts of the novel rates on historic effective population size estimates in each of these charismatic felids of conservation concern. Importantly, we find that the choice of reference genome, the data type and coverage, and the individual all impact estimates of the mutation rate. Despite these stochastic effects, we inferred that base pair mutation rates for all species fell between 0.5 and 1.4e-08 per generation per base pair (mean 0.81e-08 +/- 0.35-08 across Pantherinae). Our results provide a cautionary view on inter-species mutation rate comparisons, given the error associated with the reference genome choice and sequencing depth of coverage of the individuals.

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Section: Discussionmentioning

confidence: 99%

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

Armstrong,

Carey,

Harkess

et al. 2024

Preprint

Self Cite

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Genetic structure and diversity of semi-captive populations: the anomalous case of the Asian elephant

Maurer,

Dubois,

et al. 2024

Conserv Genet

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Wild species living in captivity are subject to loss of genetic diversity, inbreeding depression, and differentiation among populations. Only very few species have been under human care for centuries but have not been selectively bred, have free-ranging movements most of the time, and retain porous barriers to gene flow between wild and captive populations. Such captive populations are expected to retain high levels of genetic diversity and anthropogenic factors should result in a limited genetic differentiation from wild populations. Asian elephants have been trained and used by humans for at least 4000 years as war animals, mounts of kings and draught animals. In Myanmar and Laos, elephants are still being used for hauling timber in the forest while retaining traditional management practices including seasonal release, free mating and movement. However, habitat fragmentation, isolation and reduced gene flows are threatening both semi-captive and wild pools. We genotyped 167 semi-captive elephants from Laos and Myanmar using a panel of 11 microsatellite loci to estimate the genetic diversity and population structure. We found that elephants of both countries presented high levels of genetic diversity and a low degree of inbreeding, if any. This agrees with the expected high level of genetic diversity in semi-captive populations. We found a weak differentiation along a geographical gradient from southern Laos to northern Myanmar but no differentiation between wild-caught and captive-born pools. The potential value for conservation of a large population of semi-captive elephants has been recognized but the conservation community has yet to fully explore the potential role semi-captive elephants could play in maintaining gene flows.

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

Khan,

Sil,

Thekaekara

et al. 2024

Current Biology

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Genomic resources for Asian (Elephas maximus) and African savannah elephant (Loxodonta africana) conservation and health research

Cited by 3 publications

References 68 publications

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

Genetic structure and diversity of semi-captive populations: the anomalous case of the Asian elephant

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

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