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  The importance of DNA barcode choice in biogeographic analyses — a case study on marine midges of the genus Clunio

Fuhrmann, N., & Kaiser, T. S. (2020). The importance of DNA barcode choice in biogeographic analyses — a case study on marine midges of the genus Clunio. Genome, 00(00), 1-11. doi:10.1139/gen-2019-0191.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-B3E8-A Version Permalink: http://hdl.handle.net/21.11116/0000-0006-B3E9-9
Genre: Journal Article

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 Creators:
Fuhrmann, Nico1, Author              
Kaiser, Tobias S.1, 2, Author              
Affiliations:
1Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2355691              
2IMPRS on Ecological Interactions, MPI for Chemical Ecology, Max Planck Society, ou_421900              

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Free keywords: DNA barcoding, mitochondrial genome, cytochrome oxidase I, haplotype network, diversity, ecotype
 Abstract: DNA barcodes are widely used for species identification and biogeographic studies. Here, we compare the use of full mitochondrial genomes versus DNA barcodes and other mitochondrial DNA fragments for biogeographic and ecological analyses. Our dataset comprised 120 mitochondrial genomes from the genus Clunio (Diptera: Chironomidae), comprising five populations from two closely related species (Clunio marinus and Clunio balticus) and three ecotypes. We extracted cytochrome oxidase c subunit I (COI) barcodes and partitioned the mitochondrial genomes into non-overlapping windows of 750 or 1500 bp. Haplotype networks and diversity indices were compared for these windows and full mitochondrial genomes (15.4 kb). Full mitochondrial genomes indicate complete geographic isolation between populations, but do not allow for conclusions on the separation of ecotypes or species. COI barcodes have comparatively few polymorphisms, ideal for species identification, but do not resolve geographic isolation. Many of the similarly sized 750 bp windows have higher nucleotide and haplotype diversity than COI barcodes, but still do not resolve biogeography. Only when increasing the window size to 1500 bp, two windows resolve biogeography reasonably well. Our results suggest that the design and use of DNA barcodes in biogeographic studies must be carefully evaluated for each investigated species.

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Language(s): eng - English
 Dates: 2019-11-122020-03-262020-06-082020-06
 Publication Status: Published in print
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 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1139/gen-2019-0191
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Title: Genome
Source Genre: Journal
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Publ. Info: Ottawa : NRC Research Press
Pages: - Volume / Issue: 00 (00) Sequence Number: - Start / End Page: 1 - 11 Identifier: ISSN: 0831-2796
CoNE: https://pure.mpg.de/cone/journals/resource/954927527784