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Hippotragus leucophaeus

ABSTRACT: Identification of blue antelope museum specimens using mtDNA

PROVIDER: PRJNA776136 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20324700.fastq.gz	Fastqsanger.gz
	SRR20324701.fastq.gz	Fastqsanger.gz
	SRR20324702.fastq.gz	Fastqsanger.gz
	SRR20324703.fastq.gz	Fastqsanger.gz
	SRR20324681.fastq.gz	Fastqsanger.gz

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Hippotragus leucophaeus

Project description:Blue antelope nuclear genomes

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Project description:Identification of blue antelope museum specimens using mtDNA at NHMUK and NMS

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Hippotragus leucophaeus isolate:NRM590107

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Hippotragus leucophaeus

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Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus).

Project description:Native to southern Africa, the blue antelope (Hippotragus leucophaeus) is the only large African mammal species known to have become extinct in historical times. However, it was poorly documented prior to its extinction ~ 1800 AD, and many of the small number of museum specimens attributed to it are taxonomically contentious. This places limitations on our understanding of its morphology, ecology, and the mechanisms responsible for its demise. We retrieved genetic information from ten of the sixteen putative blue antelope museum specimens using both shotgun sequencing and mitochondrial genome target capture in an attempt to resolve the uncertainty surrounding the identification of these specimens. We found that only four of the ten investigated specimens, and not a single skull, represent the blue antelope. This indicates that the true number of historical museum specimens of the blue antelope is even smaller than previously thought, and therefore hardly any reference material is available for morphometric, comparative and genetic studies. Our study highlights how genetics can be used to identify rare species in natural history collections where other methods may fail or when records are scarce. Additionally, we present an improved mitochondrial reference genome for the blue antelope as well as one complete and two partial mitochondrial genomes. A first analysis of these mitochondrial genomes indicates low levels of maternal genetic diversity in the 'museum population', possibly confirming previous results that blue antelope population size was already low at the time of the European colonization of South Africa.

| S-EPMC7822880 | biostudies-literature

Hippotragus niger

Project description:Whole-genome re-sequencing of five sable antelope

| PRJNA403774 | ENA

Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).

Project description:The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.

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The molecular characterisation of mitochondrial DNA deficient oocytes using a pig model

Project description:Pig oocytes were stained with Brilliant cresyl blue to identify mtDNA deficient oocytes.

2018-04-11 | GSE108900 | GEO

Archival chromatin sequencing in eastern water dragon museum specimens

Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are sex-specific and environmental condition dependent.

2024-03-01 | GSE256157 | GEO

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