Dataset Information

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

ABSTRACT: Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.

SUBMITTER: Vernot B

PROVIDER: S-EPMC6743480 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Publications

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

Vernot Benjamin B Tucci Serena S Kelso Janet J Schraiber Joshua G JG Wolf Aaron B AB Gittelman Rachel M RM Dannemann Michael M Grote Steffi S McCoy Rajiv C RC Norton Heather H Scheinfeldt Laura B LB Merriwether David A DA Koki George G Friedlaender Jonathan S JS Wakefield Jon J Pääbo Svante S Akey Joshua M JM

Science (New York, N.Y.) 20160317 6282

Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 3 ...[more]

PMID: 26989198

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Project description:BACKGROUND: Trigonopterus weevils are widely distributed throughout Melanesia and hyperdiverse in New Guinea. They are a dominant feature in natural forests, with narrow altitudinal zonation. Their use in community ecology has been precluded by the "taxonomic impediment". METHODOLOGY/PRINCIPAL FINDINGS: We sampled >6,500 specimens from seven areas across New Guinea; 1,002 specimens assigned to 270 morphospecies were DNA sequenced. Objective clustering of a refined dataset (excluding nine cryptic species) at 3% threshold revealed 324 genetic clusters (DNA group count relative to number of morphospecies?=?20.0% overestimation of species diversity, or 120.0% agreement) and 85.6% taxonomic accuracy (the proportion of DNA groups that "perfectly" agree with morphology-based species hypotheses). Agreement and accuracy were best at an 8% threshold. GMYC analysis revealed 328 entities (21.5% overestimation) with 227 perfect GMYC entities (84.1% taxonomic accuracy). Both methods outperform the parataxonomist (19% underestimation; 31.6% taxonomic accuracy). The number of species found in more than one sampling area was highest in the Eastern Highlands and Huon (Sørensen similarity index 0.07, 4 shared species); ? of all areas had no species overlap. Success rates of DNA barcoding methods were lowest when species showed a pronounced geographical structure. In general, Trigonopterus show high ? and ?-diversity across New Guinea. CONCLUSIONS/SIGNIFICANCE: DNA barcoding is an excellent tool for biodiversity surveys but success rates might drop when closer localities are included. Hyperdiverse Trigonopterus are a useful taxon for evaluating forest remnants in Melanesia, allowing finer-grained analyses than would be possible with vertebrate taxa commonly used to date. Our protocol should help establish other groups of hyperdiverse fauna as target taxa for community ecology. Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species.

Dataset Information

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

Publications

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.

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