A Genomic Perspective on the Shortcomings of Mitochondrial DNA for “Barcoding” Identification

Rubinoff, Daniel; Cameron, Stephen L.; Will, Kipling

doi:10.1093/jhered/esl036

Cited by 423 publications

(336 citation statements)

References 91 publications

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“…Because of a typically higher rate of sequence divergence, a lower threshold of 94% sequence identity, after a higher initial threshold, was used for the assembly of CO1 groups, resulting in lower sequence similarity in the final species groupings. 53,54 The CO1 group sequences that matched the same anopheline species reference sequence were collapsed into one group. This was reflected in the lower CO1 sequence similarity within a final species group when compared with that within the same species ITS2 sequence.…”

Section: Resultsmentioning

confidence: 99%

Molecular Characterization Reveals Diverse and Unknown Malaria Vectors in the Western Kenyan Highlands

Laurent¹,

Cooke²,

Krishnankutty³

et al. 2016

The American Society of Tropical Medicine and Hygiene

120

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Abstract. The success of mosquito-based malaria control is dependent upon susceptible bionomic traits in local malaria vectors. It is crucial to have accurate and reliable methods to determine mosquito species composition in areas subject to malaria. An unexpectedly diverse set of Anopheles species was collected in the western Kenyan highlands, including unidentified and potentially new species carrying the malaria parasite Plasmodium falciparum. This study identified 2,340 anopheline specimens using both ribosomal DNA internal transcribed spacer region 2 and mitochondrial DNA cytochrome oxidase subunit 1 loci. Seventeen distinct sequence groups were identified. Of these, only eight could be molecularly identified through comparison to published and voucher sequences. Of the unidentified species, four were found to carry P. falciparum by circumsporozoite enzyme-linked immunosorbent assay and polymerase chain reaction, the most abundant of which had infection rates comparable to a primary vector in the area, Anopheles funestus. High-quality adult specimens of these unidentified species could not be matched to museum voucher specimens or conclusively identified using multiple keys, suggesting that they may have not been previously described. These unidentified vectors were captured outdoors. Diverse and unknown species have been incriminated in malaria transmission in the western Kenya highlands using molecular identification of unusual morphological variants of field specimens. This study demonstrates the value of using molecular methods to compliment vector identifications and highlights the need for accurate characterization of mosquito species and their associated behaviors for effective malaria control.

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Section: Resultsmentioning

confidence: 99%

Molecular Characterization Reveals Diverse and Unknown Malaria Vectors in the Western Kenyan Highlands

Laurent¹,

Cooke²,

Krishnankutty³

et al. 2016

The American Society of Tropical Medicine and Hygiene

120

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“…There are many potential pitfalls in the interpretation of COI barcodes in terms of the evolution of taxa (Rubinoff et al 2006). Those most likely to confound our analysis are that patterns of evolution for mitochondrial genes do not always correspond precisely with those of their owner species.…”

Section: Discussionmentioning

confidence: 99%

Bombus cullumanus—an extinct European bumblebee species?

et al. 2012

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-Bombus cullumanus s. str. has attracted some of the greatest conservation concerns among bumblebees in Europe because it might now be extinct. However, there has been long-standing disagreement about whether it is conspecific with other eastern pale-banded bumblebees. We investigate these relationships using new data from DNA (COI) barcodes. The results support a Nearctic rufocinctus-group (Bombus rufocinctus) and a Palaearctic cullumanus-group, the latter with just three species: Bombus semenoviellus, Bombus unicus and B. cullumanus s. l. (including several differently coloured taxa). We conclude that, although any persisting B. cullumanus cullumanus s. str. might be a regional conservation priority within Europe, nevertheless, because the species remains common elsewhere within its range in Asia, globally a higher conservation priority should be given to B. unicus, which is genetically more distinct and appears to have a much smaller population in the Russian Far East.bumblebee / Bombus / barcode / taxonomy / conservation

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“…2006; Rubinoff et al. 2006). By classical Bateson–Dobzhansky–Muller models of allopatric speciation, cladogenesis begins when two or more populations are separated in space or time such that gene flow among the populations is disrupted (Coyne and Orr 2004; Price 2007).…”

Section: Introductionmentioning

confidence: 99%

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

Hill

2016

Ecology and Evolution

142

178

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Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population‐specific mitonuclear coadaptations create between‐population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.

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A Genomic Perspective on the Shortcomings of Mitochondrial DNA for “Barcoding” Identification

Cited by 423 publications

References 91 publications

Molecular Characterization Reveals Diverse and Unknown Malaria Vectors in the Western Kenyan Highlands

Molecular Characterization Reveals Diverse and Unknown Malaria Vectors in the Western Kenyan Highlands

Bombus cullumanus—an extinct European bumblebee species?

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

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