Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth

Roca, Alfred L.; Ishida, Yasuko; Nikolaidis, Nikolas; Kolokotronis, Sergios‐Orestis; Fratpietro, Stephen; Stewardson, Kristin; Hensley, Shannon M.; Tisdale, Michele; Боескоров, Г. Г.; Greenwood, Alex D.

doi:10.1186/1471-2148-9-232

Cited by 20 publications

(13 citation statements)

References 71 publications

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“…Approximately 0.25 g of bone or coprolite powder was extracted using a silica-based extraction kit for aDNA (GENECLEAN Ancient DNA Extraction Kit; MP Biomedicals). The protocol followed the vendor’s instructions and has been successfully applied to a variety of ancient sample types ( Wyatt et al 2008 ; Roca et al 2009 ). Mock extractions were performed with each museum specimen as negative control for contamination during extraction.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary Relationships among Extinct and Extant Sloths: The Evidence of Mitogenomes and Retroviruses

et al. 2016

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Macroevolutionary trends exhibited by retroviruses are complex and not entirely understood. The sloth endogenized foamy-like retrovirus (SloEFV), which demonstrates incongruence in virus–host evolution among extant sloths (Order Folivora), has not been investigated heretofore in any extinct sloth lineages and its premodern history within folivorans is therefore unknown. Determining retroviral coevolutionary trends requires a robust phylogeny of the viral host, but the highly reduced modern sloth fauna (6 species in 2 genera) does not adequately represent what was once a highly diversified clade (∼100 genera) of placental mammals. At present, the amount of molecular data available for extinct sloth taxa is limited, and analytical results based on these data tend to conflict with phylogenetic inferences made on the basis of morphological studies. To augment the molecular data set, we applied hybridization capture and next-generation Illumina sequencing to two extinct and three extant sloth species to retrieve full mitochondrial genomes (mitogenomes) from the hosts and the polymerase gene of SloEFV. The results produced a fully resolved and well-supported phylogeny that supports dividing crown families into two major clades: 1) The three-toed sloth, Bradypus, and Nothrotheriidae and 2) Megalonychidae, including the two-toed sloth, Choloepus, and Mylodontidae. Our calibrated time tree indicates that the Miocene epoch (23.5 Ma), particularly its earlier part, was an important interval for folivoran diversification. Both extant and extinct sloths demonstrate multiple complex invasions of SloEFV into the ancestral sloth germline followed by subsequent introgressions across different sloth lineages. Thus, sloth mitogenome and SloEFV evolution occurred separately and in parallel among sloths.

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Section: Methodsmentioning

confidence: 99%

Evolutionary Relationships among Extinct and Extant Sloths: The Evidence of Mitogenomes and Retroviruses

et al. 2016

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“…Approximately 250 mg of skin tissue was extracted using the Geneclean Ancient DNA Extraction Kit from MP Biomedicals, USA. The protocol of the kit was followed according to the manufacturer’s instructions; the same kit had previously been used successfully for ancient DNA extraction from samples of rat skin and woolly mammoth bone [31,32]. Mock extractions were performed with each set of koala museum specimens as a control for contamination during the extraction procedure.…”

Section: Methodsmentioning

confidence: 99%

Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus)

et al. 2012

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BackgroundThe koala (Phascolarctos cinereus) is an arboreal marsupial that was historically widespread across eastern Australia until the end of the 19th century when it suffered a steep population decline. Hunting for the fur trade, habitat conversion, and disease contributed to a precipitous reduction in koala population size during the late 1800s and early 1900s. To examine the effects of these reductions in population size on koala genetic diversity, we sequenced part of the hypervariable region of mitochondrial DNA (mtDNA) in koala museum specimens collected in the 19th and 20th centuries, hypothesizing that the historical samples would exhibit greater genetic diversity.ResultsThe mtDNA haplotypes present in historical museum samples were identical to haplotypes found in modern koala populations, and no novel haplotypes were detected. Rarefaction analyses suggested that the mtDNA genetic diversity present in the museum samples was similar to that of modern koalas.ConclusionsLow mtDNA diversity may have been present in koala populations prior to recent population declines. When considering management strategies, low genetic diversity of the mtDNA hypervariable region may not indicate recent inbreeding or founder events but may reflect an older historical pattern for koalas.

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“…DNA from approximately 250 mg of koala skin tissue (7 mm × 7 mm) per museum specimen was obtained using a silica-based extraction kit for aDNA (GENECLEAN Ancient DNA Extraction Kit, MP Biomedicals, USA). The protocol followed the manufacturer’s instructions and has been successfully applied to a variety of ancient sample types ( Wyatt et al, 2008 ; Roca et al, 2009 ). Mock extractions were performed with each set of koala museum specimens as negative controls for extraction.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

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Ishida

et al. 2016

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Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized.Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized.Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

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Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth

Cited by 20 publications

References 71 publications

Evolutionary Relationships among Extinct and Extant Sloths: The Evidence of Mitogenomes and Retroviruses

Evolutionary Relationships among Extinct and Extant Sloths: The Evidence of Mitogenomes and Retroviruses

Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus)

Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

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