Can mtDNA Barcodes Be Used to Delimit Species? A Response to Pons et al. (2006)

Lohse, Konrad

doi:10.1093/sysbio/syp039

Cited by 171 publications

(166 citation statements)

References 19 publications

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“…However, the Yule and coalescent models make several assumptions that are unrealistic for free-living species [15,[49][50][51][52], potentially limiting their value in this context. For instance, the Yule [38] model assumes a constant rate of speciation and no extinction.…”

Section: Discussion (A) Testing the General Mixed Yule -Coalescentmentioning

confidence: 99%

“…Whether this inflection point corresponds with the species-population boundary is debatable [15,16]. However, waiting times between ancient coalescent events are expected to be long, relative to waiting times of recent coalescent events [51,52].…”

Section: Discussion (A) Testing the General Mixed Yule -Coalescentmentioning

confidence: 99%

“…However, our simulations suggest that extinction is far less important than other factors, such as the magnitude and variance of N e . Nevertheless, Lohse [15] showed that incomplete sampling of demes could result in overestimates of diversity through the artificial construction of sequence clusters.…”

Section: Discussion (A) Testing the General Mixed Yule -Coalescentmentioning

confidence: 99%

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Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats

et al. 2012

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Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule -coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size (N e ) and speciation rate (SR; per lineage per million years) was less than or equal to 10 5 , while interspecific variation in N e was twofold or less. However, at higher but also biologically relevant values of N e Â SR and when N e varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N e , SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.

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Section: Discussion (A) Testing the General Mixed Yule -Coalescentmentioning

confidence: 99%

Section: Discussion (A) Testing the General Mixed Yule -Coalescentmentioning

confidence: 99%

Section: Discussion (A) Testing the General Mixed Yule -Coalescentmentioning

confidence: 99%

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Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats

et al. 2012

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“…Application of a general mixed Yule coalescent (GMYC) model-based approach to identifying discrete evolutionary clusters (47,48) yielded an additional 40 "entities" beyond the 74 identified by the bivariate barcode gap analysis. The restricted geographic sampling in our study, however, could be hampering the GMYC analysis (49,50), and we therefore prefer the more conservative estimate of 74 total species named and candidate.…”

Section: Sevenmentioning

confidence: 99%

Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama

Crawford

Lips²,

Bermingham³

2010

Proc. Natl. Acad. Sci. U.S.A.

315

310

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Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.amphibian decline | biodiversity | chytridiomycosis | DNA barcoding | phylogenetic diversity

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“…For the COX1 DNA barcode to work under neutral theory, there must be sufficient time for lineages to sort via random accumulation of neutral mutations (Hudson and Coyne 2002) and gene flow among species must be negligible (Lohse 2009). In birds, however, huge radiations of species with unique COX1 nucleotide sequences evolved within a time period significantly less than the time required for complete lineage sorting under neutral theory.…”

Section: Introductionmentioning

confidence: 99%

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

Hill

2016

Ecology and Evolution

149

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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Can mtDNA Barcodes Be Used to Delimit Species? A Response to Pons et al. (2006)

Cited by 171 publications

References 19 publications

Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats

Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats

Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama

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

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