Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World’s Rarest Hyena Species, the Brown Hyena

Westbury, Michael V.; Hartmann, Stefanie; Barlow, Axel; Wiesel, Ingrid; Leo, Viyanna; Welch, Rebecca J.; Parker, Daniel M.; Sicks, Florian; Ludwig, Arne; Dalén, Love; Hofreiter, Michael

doi:10.1093/molbev/msy037

Cited by 82 publications

(96 citation statements)

References 64 publications

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“…DNA was extracted from the Somalian C. crocuta sample, built into Illumina sequencing libraries, and sequenced on a HiSeq 2000 Illumina platform using 2 × 100 bp paired-end sequencing by the BGI (www.bgi.com). We additionally included previously published mitochondrial genomes from spotted hyena, cave hyena, striped hyena, brown hyena, and aardwolf (30)(31)(32) and the nuclear genomes of the brown and striped hyena (32). The Somalian hyena sample came from the Frozen Zoo (Frozen Zoo ID no.…”

Section: Modern Samplesmentioning

confidence: 99%

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

et al. 2020

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The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.

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Section: Modern Samplesmentioning

confidence: 99%

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

et al. 2020

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“…This is lower relative to the other two sub-species of lion, African lion and white lion and comparable with Eurasian lynx which is also facing the risk of extinction 20 The rate is also much lower than the average (0.00094) reported for Felidae genomic diversity. The low genomic diversity characterized by low rate of heterozygous SNPs per base pair can be attributed to the low effective population size of Asiatic lion in wild 21 as demonstrated for brown hyena 22 but a genetic investigation with multiple…”

Section: Genetic Diversity Of Asiatic Lionmentioning

confidence: 99%

De novo assembly and annotation of Asiatic lion (Panthera leo persica) genome

Ara

Sowpati

Kumar

et al. 2019

Preprint

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We report the first draft of the whole genome assembly of a male Asiatic lion, Atul and whole transcriptomes of five Asiatic lion individuals. Evaluation of genetic diversity placed the Asiatic lion in the lowest bracket of genomic diversity index highlighting the gravity of its conservation status. Comparative analysis with other felids and mammalian genomes unraveled the evolutionary history of Asiatic lion and its position among other felids. The genome is estimated to be 2.3 Gb (Gigabase) long with 62X sequence coverage and is found to have 20,543 protein-coding genes. About 2.66% of the genome is covered by simple sequence repeats (SSRs) and 0.4% is estimated to have segmental duplications. Comparison with seven well annotated genomes indicates the presence of 6,295 single copy orthologs, 4 co-orthologs, 21 paralogs uniquely present in Asiatic lion and 8,024 other orthologs. Assessment of male and female transcriptomes gave a list of genes specifically expressed in the male.

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“…Additional sources of error may include polymerase errors introduced during library preparation [19] as well as incorrect mapping of reads-both of which would result in transition-and transversion-based errors. A potentially useful method to account for these problems is to remove all singletons from the dataset prior to analysis (e.g., [20]). This can be effective if clades are reasonably and equally sampled.…”

Section: Introductionmentioning

confidence: 99%

Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates

Barlow

Hartmann

González

et al. 2020

Genes

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A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.

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Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World’s Rarest Hyena Species, the Brown Hyena

Cited by 82 publications

References 64 publications

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

De novo assembly and annotation of Asiatic lion (Panthera leo persica) genome

Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates

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