Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (<i>Acinonyx jubatus</i>)

Prost, Stefan; Machado, Ana Paula; Zumbroich, Julia; Preier, Lisa; Mahtani-Williams, Sarita; Meißner, René; Guschanski, Katerina; Brealey, Jaelle C.; Fernandes, Carlos; Vercammen, Paul; Hunter, Luke; Abramov, Alexei V.; Plášil, Martin; Hořín, Petr; Godsall-Bottriell, Lena; Bottriell, Paul; Dalton, Desiré L.; Kotzé, Antoinette; Burger, Pamela A.

doi:10.1111/mec.16577

Cited by 28 publications

(38 citation statements)

References 104 publications

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“…For example, A. j. raineyi and A. j. jubatus have recently been merged into a single subspecies, namely A. j. jubatus, based on mtDNA data (Kitchener et al, 2017). Yet, this nding does not t recent evidence obtained from genome-wide SNP data (Prost et al, 2022), raising questions about the validity of mtDNA markers for subspecies assignment in cheetahs. In their study, Prost et al (2022) suggest incomplete lineage sorting (ILS) or mitochondrial capture (MC) as possible reasons for the presence of two mitochondrial haplogroups in East African cheetahs, one of which is shared with the Southern African subspecies, A. j. jubatus.…”

Section: Introductioncontrasting

confidence: 71%

“…Yet, this nding does not t recent evidence obtained from genome-wide SNP data (Prost et al, 2022), raising questions about the validity of mtDNA markers for subspecies assignment in cheetahs. In their study, Prost et al (2022) suggest incomplete lineage sorting (ILS) or mitochondrial capture (MC) as possible reasons for the presence of two mitochondrial haplogroups in East African cheetahs, one of which is shared with the Southern African subspecies, A. j. jubatus. ILS is the retention of two or more alleles originating from an ancestral population in one or two populations after divergence/ speciation (Hahn, 2019).…”

Section: Introductioncontrasting

confidence: 71%

“…We included all ve traditionally recognized subspecies (assigned to subspecies based on geographical origin), more precisely, 75 A. j. jubatus, 39 A. j. raineyi, 51 A. j. soemmeringii, 51 A. j. venaticus, 31 A. j. hecki and 16 individuals of unknown origin. We also included samples previously used in Prost et al (2022). A complete list of all 263 individual samples with detailed information, including origin, age, and conducted analysis, can be found in Supplementary Table S1.…”

Section: Sample Collectionmentioning

confidence: 99%

“…The Cheetah Subspecies-speci c Amplicons (CSAs) are short mtDNA barcodes that contain speci c SNPs, which allow discrimination between the ve identi ed cheetah mitochondrial haplogroups. We designed six CSAs (Table 1) that include a total of 17 relevant SNPs and one 3-bp deletion (two were later excluded with CSA-6, see below), three of which were previously applied in Prost et al (2022). A combination of all six amplicons enables an unambiguous mitochondrial haplogroup assignment, and, depending on the haplogroup, a single SNP can already be diagnostic.…”

Section: Dna Extractionmentioning

confidence: 99%

“…To obtain better insights into the mitochondrial phylogeography of cheetahs and to investigate potential polymorphisms for subspecies identi cation, we used 15 mitochondrial SNPs and a 3-bp deletion in the NADH dehydrogenase subunit 5 (ND5; Charruau et al, 2011 andProst et al, 2022), ampli ed in ve short mtDNA mini-barcodes (cheetah subspecies speci c amplicons; CSAs), to infer the presence of mitochondrial haplotypes/haplogroups throughout the cheetah's current and former range. The CSAs, not exceeding 200 bp in length, were chosen to enable ampli cation even in highly degraded samples e.g., museum or con scated material.…”

Section: Introductionmentioning

confidence: 99%

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The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

Meißner

Winter

Westerhüs

et al. 2022

Preprint

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There are only about 7,100 adolescent and adult cheetahs remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah's phylogeography using a large-scale mtDNA data set to re ne subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah's whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show con icting mtDNA signals. Our analyses support previous ndings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identi cation and monitoring. However, the detection of the A. j. soemmeringii speci c haplogroup by a newly designed Ampli cation-Refractory Mutation System (ARMS) can already provide support for conservation measures.

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Section: Introductioncontrasting

confidence: 71%

Section: Introductioncontrasting

confidence: 71%

Section: Sample Collectionmentioning

confidence: 99%

Section: Dna Extractionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

Meißner

Winter

Westerhüs

et al. 2022

Preprint

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Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania

Lohay

Lee

Wu-Cavener

et al. 2023

Ecology and Evolution

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The Masai giraffe has experienced a population decline from 70,000 to 35,000 in the past three decades and was declared an endangered subspecies by the IUCN in 2019. The remaining number of Masai giraffe are geographically separated by the steep cliffs of the Gregory Rift escarpments (GRE) in Tanzania and Kenya dividing them into two populations, one west and one east of the GRE. The cliffs of the GRE are formidable barriers to east–west dispersal and gene flow and the few remaining natural corridors through the GRE are occupied by human settlements. To assess the impact of the GRE on Masai giraffe gene flow, we examined whole genome sequences of nuclear and mitochondrial DNA (mtDNA) variation in populations located east (Tarangire ecosystem) and west (Serengeti ecosystem) of the GRE in northern Tanzania. Evidence from mtDNA variation, which measures female‐mediated gene flow, suggests that females have not migrated across the GRE between populations in the Serengeti and Tarangire ecosystems in the past ~289,000 years. The analysis of nuclear DNA variation compared to mtDNA DNA variation suggests that male‐mediated gene flow across the GRE has occurred more recently but stopped a few thousand years ago. Our findings show that Masai giraffes are split into two populations and fulfill the criteria for designation as distinct evolutionary significant units (ESUs), which we denote as western Masai giraffe and eastern Masai giraffe. While establishing giraffe dispersal corridors across the GRE is impractical, conservation efforts should be focused on maintaining connectivity among populations within each of these two populations. The importance of these efforts is heightened by our finding that the inbreeding coefficients are high in some of these Masai giraffe populations, which could result in inbreeding depression in the small and fragmented populations.

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Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink

Balmori‐de la Puente,

Escoda,

Fernández‐González

et al. 2023

Ecology and Evolution

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The application of next‐generation sequencing (NGS) to non‐invasive samples is one of the most promising methods in conservation genomics, but these types of samples present significant challenges for NGS. The European mink (Mustela lutreola) is critically endangered throughout its range. However, important aspects such as census size and inbreeding remain still unknown in many populations, so it is crucial to develop new methods to monitor this species. In this work, we placed hair tubes along riverbanks in a border area of the Iberian population, which allowed the genetic identification of 76 European mink hair samples. We then applied a reduced representation genomic sequencing (ddRAD) technique to a subset of these samples to test whether we could extract sufficient genomic information from them. We show that several problems with the DNA, including contamination, fragmentation, oxidation, and possibly sample mixing, affected the samples. Using various bioinformatic techniques to reduce these problems, we were able to unambiguously genotype 19 hair samples belonging to six individuals. This small number of individuals showed that the demographic status of the species in this peripheral population is worse than expected. The data obtained also allowed us to perform preliminary analyses of relatedness and inbreeding. Although further improvements in sampling and analysis are needed, the application of the ddRAD technique to non‐invasively obtained hairs represents a significant advance in the genomic study of endangered species.

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Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)

Abstract: † We deeply regret the passing of our esteemed colleague Paul Botriell during the course of the project.

Cited by 28 publications

References 104 publications

The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania

Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink

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