Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.
<h4>Background</h4>Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequenc...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-05-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19461892/pdf/?tool=EBI |
| _version_ | 1818721462052192256 |
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| author | Oscar Ramírez Elena Gigli Pere Bover Josep Antoni Alcover Jaume Bertranpetit Jose Castresana Carles Lalueza-Fox |
| author_facet | Oscar Ramírez Elena Gigli Pere Bover Josep Antoni Alcover Jaume Bertranpetit Jose Castresana Carles Lalueza-Fox |
| author_sort | Oscar Ramírez |
| collection | DOAJ |
| description | <h4>Background</h4>Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. METHODOLOGY/PRINCIPALS FINDINGS: A DNA extraction of a approximately 6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.<h4>Conclusions</h4>A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions. |
| first_indexed | 2024-12-17T20:39:07Z |
| format | Article |
| id | doaj.art-5ab6c14d9a6543398ae70653707846fe |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-17T20:39:07Z |
| publishDate | 2009-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-5ab6c14d9a6543398ae70653707846fe2022-12-21T21:33:22ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-05-0145e567010.1371/journal.pone.0005670Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.Oscar RamírezElena GigliPere BoverJosep Antoni AlcoverJaume BertranpetitJose CastresanaCarles Lalueza-Fox<h4>Background</h4>Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. METHODOLOGY/PRINCIPALS FINDINGS: A DNA extraction of a approximately 6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.<h4>Conclusions</h4>A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19461892/pdf/?tool=EBI |
| spellingShingle | Oscar Ramírez Elena Gigli Pere Bover Josep Antoni Alcover Jaume Bertranpetit Jose Castresana Carles Lalueza-Fox Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. PLoS ONE |
| title | Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. |
| title_full | Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. |
| title_fullStr | Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. |
| title_full_unstemmed | Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. |
| title_short | Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. |
| title_sort | paleogenomics in a temperate environment shotgun sequencing from an extinct mediterranean caprine |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19461892/pdf/?tool=EBI |
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