From writing to reading the encyclopedia of life

Hebert, Paul D. N.; Hollingsworth, Peter M.; Hajibabaei, Mehrdad

doi:10.1098/rstb.2015.0321

Cited by 55 publications

(49 citation statements)

References 134 publications

(160 reference statements)

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“…Because of features characteristic to mitochondrial genome, mtDNA‐based markers are expected to show rapid lineage sorting permitting efficient discrimination between species (Hebert et al., ). Rapid lineage sorting is expected to be further promoted by recurrent selective sweeps characteristic to mtDNA (Jiggins, ).…”

Section: Discussionmentioning

confidence: 99%

“…Resolving the extent of mitonuclear discordance is particularly relevant within the DNA barcoding framework of the animal kingdom that solely relies on mtDNA. While an average of 95% success in differentiating species is reported for the animal DNA barcoding region (Hebert, Hollingsworth, & Hajibabaei, 2016), DNA barcoding has frequently revealed obvious cases of mitonuclear discordance, which in lack of nuclear data is often referred to as "DNA barcode sharing" or "deep intraspecific DNA barcode divergences" (Hausmann et al, 2013;Mutanen et al, 2016).…”

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confidence: 99%

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Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression

2018

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Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression

2018

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“…Limited availability of aeDNA templates and differential amplification of particular DNA templates can cause false positives/negatives (Leonardi et al, 2017). Because these methods require high-quality databases for comparison, the lack of genetic information about the vast majority of coral reef organisms (Carugati, Corinaldesi, Dell'Anno, & Danovaro, 2015;Leray & Knowlton, 2016) presently limits our studies to well-known components of the reef, such as the macroalgae studied here. There are a number of procedures that could be used in the future to enhance recovery of taxa obtained from our aeDNA libraries, including selective enrichment of target DNA and shotgun metagenomics (Alberdi, Aizpurua, Gilbert, & Bohmann, 2018;Orlando & Cooper, 2014).…”

Section: Limitationsmentioning

confidence: 99%

Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

et al. 2019

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Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high‐throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft‐bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft‐bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.

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“…Beyond using the DNA barcode as an aid to taxonomy, the enormity of data now available make it appropriate to extend the applications of the "broad but not deep" vista that COI barcodes uniquely provide [20,22,23]. In a founding document of phylogeography, Avise and colleagues noted the long-standing divide in biology between the intellectual lineages of Linnaeus for whom species are discrete entities and those of Darwin who emphasize incremental change within species leading to new species [4].…”

Section: Incompletely Studied Groupsmentioning

confidence: 99%

Why should mitochondria define species?

Stoeckle

Thaler

2018

Preprint

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More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes—drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years.

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From writing to reading the encyclopedia of life

Abstract: One contribution of 16 to a theme issue 'From DNA barcodes to biomes'.

Cited by 55 publications

References 134 publications

Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression

Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression

Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

Why should mitochondria define species?

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