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:10.1101/2023.02.10.528067

Cited by 2 publications

(4 citation statements)

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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

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“…We used the protocol described for the implementation of the method (https://github.com/popgenmethods/smcpp) as is. We set the mutation rate to 5.3*10^-9/base/generation (Prado et al 2023) and a generation time of 31 years. The estimates from this method are reliable for estimating demographic events between a hundred generations ago to forty thousand generations ago.…”

Section: Methodsmentioning

confidence: 99%

“…Then performed PSMC with the default settings. We plotted the results assuming a mutation rate of 5.3*10^-9/base/generation (Prado et al 2023) and a generation time of 31 years. The time point where the effective population size estimated from the pseudo-diploid individual rises exponentially is the point where the two haplotypes do not coalesce and hence signify population divergence.…”

Section: Methodsmentioning

confidence: 99%

“…Overall, our results emphasise the antiquity of the Northern populations of elephants consistent with Vidya et al (2005b, 2009). Palkopoulou et al (2018) had suggested a more recent divergence which could be due to the differences in the mutation rates used for making inferences (4.06e-8 vs 5.3e-9; Prado et al 2023). Vidya et al (2009) made inferences on phylogeography based solely on mitochondrial DNA sequences, which are expected to provide older estimates of divergence times even up to an order of magnitude greater (Zheng et al 2011).…”

Section: Introductionmentioning

confidence: 99%

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Serial colonization shapes genetic variation and defines conservation units in Asian elephants

Khan,

Sil,

Thekaekara

et al. 2023

Preprint

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Megaherbivores are primary consumers who provide unique ecosystem services. Given their body size, they are disproportionately threatened in the Anthropocene. Asian elephants are the largest extant terrestrial megaherbivores native to Asia, with 60% of the population found in India. Despite their ecological and cultural importance, the management/conservation units, genetic history, diversity and threats remain understudied. We re-sequenced 31 whole genomes (between 11X - 32X) from all known elephant landscapes in India, and identified five management/conservation units corresponding to elephants in northern India, central India and three in southern India. The genetic data reveal signatures of serial colonisation, and a dilution of diversity from north to south of India. The northern populations diverged from other populations more than 70,000 years ago, and have the highest genetic diversity, with low inbreeding/high effective size (Pi = 0.39, SD:0.2; FROH> 1MB= 0.09, SD:0.03). Two of three populations in southern India have low diversity and are inbred with much lower effective sizes than current populations sizes (Pi = 0.25, SD:0.29 and 0.29, SD:0.23; FROH> 1MB= 0.25, SD:0.09 and 0.17, SD:0.02). Additionally, future generations are expected to be more inbred since pairs of extant elephants have large tracts of the genome that are already identical. Analyses of genetic load reveals purging of potentially high-effect deleterious alleles in the southern populations and potential dilution of all deleterious alleles from north to south in India. However, southern Indian elephants are highly homozygous for all the deleterious alleles that persist, despite dilution and purging. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity make them high priority for conservation and management attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to geographic signatures of serial founding events even in large mobile endangered species.

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Genomic Resources for Asian (Elephas maximus) and African Savannah Elephant (Loxodonta africana) Conservation and Health Research

Cited by 2 publications

References 71 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

Serial colonization shapes genetic variation and defines conservation units in Asian elephants

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