Nucleotide variation in the mitochondrial genome provides evidence for dual routes of postglacial recolonization and genetic recombination in the northeastern brook trout (Salvelinus fontinalis)

Pilgrim, Brettney L.; Perry, Robert; Barron, J L; Marshall, H. Dawn

doi:10.4238/2012.september.26.2

Cited by 7 publications

(7 citation statements)

References 36 publications

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“…These results are relevant concerning the DNA barcoding for fishes (and possibly other organisms where introgression may have happened). Interspecific mtDNA recombination such as detected in the ND3 and ND6 genes of H. taimen (the present data) and ND1 gene of Salmo [77] and Salvelinus [78] (see Discussion), may importantly limit the usefulness of mtDNA barcoding for species identification.…”

Section: Resultsmentioning

confidence: 59%

“…There are also multiple evidence of mtDNA recombination in plants, fungi, and animals, including humans (review in [81]–[82]). However, instances of interspecific mtDNA recombination have been rarely detected in hybridizing conifers [83], salmonids, Salmo and Salvelinus [77]–[78], and primates [84], which could probably be explained by fact that in most cases the data obtained involve relatively short DNA fragments or indirect genetic markers like allozymes, PCR-RFLP or microsatellites. The indirect approaches, albeit may yield correct conclusions about introgression, do not elucidate the precise architecture of the introgression events.…”

Section: Discussionmentioning

confidence: 99%

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Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

Balakirev

Романов

Mikheev³

et al. 2013

PLoS ONE

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Siberian taimen Hucho taimen is the largest representative of the family Salmonidae inhabiting rivers of northern Eurasia. The species is under intensive aquaculture activity. To monitor natural taimen populations we have sequenced a portion (8,141 bp) of the mitochondrial (mt) genome in 28 specimens of H. taimen from six localities in the Amur River basin. Nucleotide variability is low (π = 0.0010), but structured in two divergent haplotype groups. A comparison of the data with the GenBank H. taimen mt genome (HQ897271) reveals significant differences between them in spite of the fact that the fish specimens come from neighboring geographical areas. The distribution of divergence is non-uniform with two highly pronounced divergent regions centered on two genes, ND3 and ND6. To clarify the pattern of divergence we sequenced the corresponding portion of the mt genome of lenok Brachymystax tumensis and analyzed the GenBank complete mt genomes of related species. We have found that the first and second divergent regions are identical between the GenBank H. taimen and two lenok subspecies, B. lenok and B. lenok tsinlingensis, respectively. Consequently, both divergent regions represent introgressed mtDNA resulting from intergeneric hybridization between the two lenok subspecies and H. taimen. Introgression is, however, not detected in our specimens. This plus the precise identity of the introgressed fragments between the donor and the recipient GenBank sequence suggests that the introgression is local and very recent, probably due to artificial manipulations involving taimen – lenok intergeneric hybridization. Human-mediated hybridization may become a major threat to aquatic biodiversity. Consequently we suggest that due attention needs to be given to this threat by means of responsible breeding program management, so as to prevent a potential spread of hybrid fishes that could jeopardize the resilience of locally adapted gene pools of the native H. taimen populations.

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Section: Resultsmentioning

confidence: 59%

Section: Discussionmentioning

confidence: 99%

Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

Balakirev

Романов

Mikheev³

et al. 2013

PLoS ONE

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“…For some fish species like Arctogadus glacialis, Boreogadus saida complete genomes are available (Breines et al 2008). There is a high interest in postglacial colonization of fishes like Salvelinus fontinalis (Pilgrim et al 2012), Coregonus nasus (Harris and Taylor 2010) or Coregonu lavaretus (Østbye et al 2006). We can also find lots of studies about genetic diversity of different species (Kai et al 2011;Kovpak et al 2011), as in the future it might be crucial for adaptations to a changing environment.…”

Section: Nektonmentioning

confidence: 99%

Arctic Ocean Biodiversity and DNA Barcoding – A Climate Change Perspective

Walczyńska

Mańko

Weydmann

2018

YOUMARES 8 – Oceans Across Boundaries: Learning From Each Other

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Global changes are initiating a cascade of complex processes, which result, among other things, in global climate warming. Effects of global climate change are most pronounced in the Arctic, where the associate processes are progressing at a more rapid pace than in the rest of the world. Intensified transport of warmer water masses into the Arctic is causing shifts in species distributions and efforts to understand and track these change are currently intensified. However, Arctic marine fauna is the result of different recurring colonization events by Atlantic and Pacific Ocean populations, producing a very confounding evolutionary signal and making species identification by traditional morphological taxonomic analysis extremely challenging. In addition, many marine species are too small or too similar to identify reliably, even with profound taxonomic expertise. Nevertheless, the majority of current research focusing on artic marine communities still relies on the analysis of samples with traditional taxonomic methods, which tends to lack the necessary taxonomic, spatial and temporal resolution needed to understand the drastic ecosystem shifts underway. However, molecular methods are providing new opportunities to the field and their continuous development can accelerate and facilitate ecological research in the Arctic. Here, we discuss molecular methods currently available to study marine Arctic biodiversity, encouraging the DNA barcoding for improved descriptions, inventory and providing examples of DNA barcoding utilization in Arctic diversity research and investigations into ecosystem drivers.

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“…Instances of interspecific mtDNA recombination have been occasionally detected in hybridizing conifers, 38 salmonids, Salmo and Salvelinus , 39 , 40 and primates. 41 We, however, conjecture that the number of recombinant sequences persisting in GenBank could be higher if they are mostly indistinct with basic phylogenetic analysis.…”

Section: Resultsmentioning

confidence: 99%

“…A complete morphological description of C czerskii has been performed by one of the authors of this work (P.A.S.). 13 Cottus czerskii differs from all other Palearctic Cottinae by the following complex of features: the presence of teeth on the palatines, a long internal ray of the ventral fin (73.4%-96.0% of the length of the largest ray of the ventral fin), full body seismosensoric canal of 39 to 44 pores passing through the midline of the body, high total number of vertebrae (38)(39)(40), and large body size (up to 25 cm in total length).…”

Section: Methodsmentioning

confidence: 99%

Complete Mitochondrial Genomes of the Cherskii’s SculpinCottus czerskiiand Siberian TaimenHucho taimenReveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

Balakirev

Saveliev

Ayala

2017

Evol Bioinform Online

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The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii’s sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii. Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis, submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information.

show abstract

Nucleotide variation in the mitochondrial genome provides evidence for dual routes of postglacial recolonization and genetic recombination in the northeastern brook trout (Salvelinus fontinalis)

Cited by 7 publications

References 36 publications

Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

Arctic Ocean Biodiversity and DNA Barcoding – A Climate Change Perspective

Complete Mitochondrial Genomes of the Cherskii’s SculpinCottus czerskiiand Siberian TaimenHucho taimenReveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome

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