Implications of Hybridization, NUMTs, and Overlooked Diversity for DNA Barcoding of Eurasian Ground Squirrels

Ermakov, Oleg A.; Simonov, Evgeniy; Surin, V. L.; Титов, С. В.; Брандлер, О. В.; Ivanova, Natalia V.; Borisenko, Alex

doi:10.1371/journal.pone.0117201

Cited by 41 publications

(35 citation statements)

References 57 publications

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“…This over‐representation increases the likelihood that uncharacterized sequences will be identified as Prickly Sculpin. Databases like NCBI are broadly comprehensive, and may contain haplotype–morphotype combinations (e.g., hybrids, introgressed haplotypes, or retained ancestral alleles; Collins and Cruickshank, ; Ermakov et al, ; Moritz and Cicero, ) that are relevant to specific geographic regions, but misleading outside of those regions. Similarly, taxonomic revisions and errors in classification and DNA sequencing can accumulate in NCBI, and these may affect classification accuracy.…”

Section: Discussionmentioning

confidence: 99%

Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets

et al. 2019

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Environmental DNA (eDNA) assays for single‐ and multi‐species detection show promise for providing standardized assessment methods for diverse taxa, but techniques for evaluating multiple taxonomically divergent assemblages are in their infancy. We evaluated whether microfluidic multiplex metabarcoding on the Fluidigm Access Array™ platform and high‐throughput sequencing could identify diverse stream and riparian assemblages from 48 taxon‐general and taxon‐specific metabarcode primers. eDNA screening was paired with electrofishing along a stream continuum to evaluate congruence between methods. A fish hatchery located midway along the stream continuum provided a dispersal barrier, and a point source for non‐native White Sturgeon (Acipencer transmontanus). Microfluidic metabarcoding had 87% accuracy with respect to electrofishing and detected all 13 species electrofishing observed. Taxon‐specific barcoding primers were more successful than taxon‐general universal metabarcoding primers at classifying sequences to species. Both types of markers detected a transition from downstream sites dominated by multiple fish species, to upstream sites dominated by a single species; however, we failed to detect a complementary transition in amphibian occupancy. White Sturgeon was only detected at the hatchery outflow, indicating eDNA transport was not detectable ~2.4 km from its source. Overall, we identified 878 predicted taxa. Most sequences (50.1%) derived from fish (Actinopteri, Petromyzontidae), oomycetes (21.3%), arthropoda (classes Insecta, Decapoda; 16.5%), and apicomplexan parasites (3.8%). Taxa accounting for ~1% or less of sequences included freshwater red algae, diatoms, amphibians, and beaver. Our work shows that microfluidic metabarcoding can survey multiple phyla per assay, providing fine discrimination required to resolve closely related species, and enable data‐driven prioritization for multiple forest health objectives.

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Section: Discussionmentioning

confidence: 99%

Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets

et al. 2019

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“…Recent works have highlighted the growing importance of DNA barcoding in clarifying the taxonomic status and provenance of sciurid populations (see e.g. Gabrielli et al 2014;Ermakov et al 2015;Stevenson-Holt & Sinclair 2015). These studies also provide evidence for the importance of molecular surveys in management and conservation actions on sciurid species.…”

Section: Introductionmentioning

confidence: 93%

“…These markers were chosen because of their growing relevance in the field of modern integrative taxonomy (see e.g. Galimberti et al 2012a;Ermakov et al 2015) and because a huge number of D-loop sequences are available for the species group treated in this study (Gabrielli et al 2014). Moreover, the 2 markers typically show high mutation rates, which is essential to better identify similarities and differences among different species (CoxI) and even populations (D-loop).…”

Section: Morphometric Analysismentioning

confidence: 99%

Preventing species invasion: A role for integrative taxonomy?

Mazzamuto

Galimberti

Cremonesi

et al. 2016

Integrative Zoology

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Integrative taxonomy, a multi-disciplinary approach adding modern techniques to traditional morphology-based methods (e.g. molecular and morphological criteria), can play an important role in bioinvasion research to identify introduced taxa, discover pathways of introduction and inform authorities to control and prevent future introductions. The present study is the first on introduced populations of Callosciurus, Asiatic tree squirrels, known as potentially invasive species in Europe (Italy, Belgium and France). We combined molecular (mitochondrial DNA markers: CoxI, D-loop) and morphometric analysis on skulls, comparing them to the widest morphological and molecular datasets ever assembled for Callosciurus. Squirrels collected in Italy and Belgium share the same haplotypes and skull characteristics, but are conspicuously different from the French population in Antibes. Genetic data revealed close similarity between French squirrels and Pallas's squirrels, Callosciurus erythraeus, from Taiwan, China. Italian and Belgian squirrels formed an independent taxonomic lineage in genetic analyses, whose taxonomic rank needs further investigation. The morphological and morphometric characteristics of these 2 populations are, however, similar to known specimens assigned to Callosciurus erythraeus. These results may indicate a common origin for the populations found in Belgium and Italy. In contrast, French specimens suggest an independent introduction event of squirrels originating from Asia.

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“…Numtlar, PZR tabanlı mitokondriyal araştırmalarda sıklıkla istenmeyen paraloglar olarak algılanır [51][52]. Du Buy ve Riley [53] tarafından ilk keşfedildikten sonra, bitkiler, maya, nematodlar, böcekler ve memeliler ve kuşlar gibi omurgalılar da dahil olmak üzere birçok organizma grubunda bulunmuştur [54][55][56].…”

Section: Ncbt: Yalancı Gen öZellikleriunclassified

Genetic structuring of Anatolian Bombus lapidarius L. (Apidae: Hymenoptera) populations

Altun

Korkmaz

Basibuyuk

2018

ANADOLU UNIVERSITY JOURNAL OF SCIENCE AND TECHNOLOGY –C Life Sciences and Biotechnology

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ÖZETAnadolu, Avrupa'nın günümüz biyoçeşitliliğine önemli derecede katkı sağlayan bölgelerden birisidir. Bazı günümüz orta ve kuzey Avrupa popülasyonlarının buzul dönemlerinde Anadolu'da barınmış popülasyonlardan giden öncülerce oluşturulduğu savunulmaktadır. Soğuk tercih eden hayvanlar yayılış örüntülerinde buzul dönemlerinde genişleme buzullar arası dönemlerde ise daralma sergiledikleri için model organizmalar olarak kabul edilmektedir. Bu kapsamda Anadolu'nun, tarihsel biyocoğrafyası ve genetik çeşitliliği konusunda bilgi edinmek amacıyla Karadeniz bölgesinde yayılış gösteren Bombus lapidarius'un 14 kadar popülasyonundan COI ve nCTB gen bölgeleri çalışılmıştır. Her iki belirteç açısından da haplotip çeşitliliği ve özgün haplotip sayısı yüksek olup, popülasyonlar arasında anlamlı bir genetik farklılaşma saptanmıştır. Özellikle Doğu-Batı farklılaşması Karadeniz boyunca desteklenmektedir. Tüm analizlerde Doğu4 ve Doğu5 popülasyonlarının diğer popülasyonlardan belirgin olarak farklı olduğu görülmektedir. Bu farklılaşma popülasyonların coğrafik yayılış örüntüleri ile doğrudan ilişkilidir. Aynı zamanda bu popülasyonlar ayrı bir soy hattı oluşturmaktadır. Ayrıca Batı popülasyonları son türemiş popülasyonlar olarak görülmektedir.Anahtar Kelimeler: mtDNA, NUMT, Anadolu, Filocoğrafya, Genetik yapı, Coğrafik genetik yapılanma GENETIC STRUCTURING OF ANATOLIAN BOMBUS LAPIDARIUS L. (APIDAE: HYMENOPTERA) POPULATIONS ABSTRACTAnatolia is one of the important regions which have contributed to current biodiversity of Europe. It is suggested that some of the current central and northern populations of Europe have been originated from populations took refuge during glacial ages. Cold preferring animals are accepted as model organisms because they exhibit range expansion and range contraction patterns during glacial and interglacial periods, respectively. In order to improve our knowledge on biogeography and genetic diversity of Anatolia, the distribution pattern of Bombus lapidarius were investigated in the Black Sea region using COI and nCTB genes from 14 populations. High numbers of unique and diverse haplotypes were observed in both markers, suggesting genetic differentiations among populations. East-West differentiation is particularly supported throughout the Black Sea region. All analyses indicate that the East4 and East5 populations exhibit significantly differentiation from other populations. This differentiation is directly related to the geographical distribution patterns of populations. These populations constitute a separate lineage at the same time. In addition, Western populations can be accepted as recently derived populations.

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Implications of Hybridization, NUMTs, and Overlooked Diversity for DNA Barcoding of Eurasian Ground Squirrels

Cited by 41 publications

References 57 publications

Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets

Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets

Preventing species invasion: A role for integrative taxonomy?

Genetic structuring of Anatolian Bombus lapidarius L. (Apidae: Hymenoptera) populations

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