Improving environmental and biodiversity monitoring in the Baltic Sea using <scp>DNA</scp> barcoding of Chironomidae (Diptera)

Brodin, Yngve; Ejdung, Gunilla; Strandberg, Jonas; Lyrholm, Thomas

doi:10.1111/1755-0998.12053

Cited by 53 publications

(56 citation statements)

References 36 publications

(35 reference statements)

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“…In the past, most aquatic biomonitoring studies assessed the incidence of indicator species (e.g., just chironomids, as Odume, Palmer, Arimoro, & Mensah, suggested), but not the whole community. Chironomids, like mites, are good indicators of water quality (Odume et al., ), and DNA barcoding has greatly improved their identification in the Baltic Sea (Brodin, Ejdung, Strandberg, & Lyrholm, ). However, the use of DNA barcodes in combination with light traps and improved specimen preservation makes it possible also to assess the entire zooplankton community.…”

Section: Discussionmentioning

confidence: 99%

Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton

Elías‐Gutiérrez

Valdéz-Moreno

Topan

et al. 2018

Ecology and Evolution

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Currently, freshwater zooplankton sampling and identification methodologies have remained virtually unchanged since they were first established in the beginning of the XX century. One major contributing factor to this slow progress is the limited success of modern genetic methodologies, such as DNA barcoding, in several of the main groups. This study demonstrates improved protocols which enable the rapid assessment of most animal taxa inhabiting any freshwater system by combining the use of light traps, careful fixation at low temperatures using ethanol, and zooplankton‐specific primers. We DNA‐barcoded 2,136 specimens from a diverse array of taxonomic assemblages (rotifers, mollusks, mites, crustaceans, insects, and fishes) from several Canadian and Mexican lakes with an average sequence success rate of 85.3%. In total, 325 Barcode Index Numbers (BINs) were detected with only three BINs (two cladocerans and one copepod) shared between Canada and Mexico, suggesting a much narrower distribution range of freshwater zooplankton than previously thought. This study is the first to broadly explore the metazoan biodiversity of freshwater systems with DNA barcodes to construct a reference library that represents the first step for future programs which aim to monitor ecosystem health, track invasive species, or improve knowledge of the ecology and distribution of freshwater zooplankton.

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Section: Discussionmentioning

confidence: 99%

Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton

Elías‐Gutiérrez

Valdéz-Moreno

Topan

et al. 2018

Ecology and Evolution

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“…; Brodin et al. ; Pyšek et al. ), and with the skills, methods and databases required to ensure that these approaches deliver their full potential (Yoccoz ).…”

Section: The Initial Stages – Entrainment Risk and Transportmentioning

confidence: 99%

Biological invasions, climate change and genomics

Chown

Hodgins

Griffin

et al. 2014

Evolutionary Applications

223

214

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The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species’ geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.

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“…, ; Brodin et al . ). In these studies, the commonly used sequences were of the mitochondrial genes cytochrome c oxidase subunit I ( COI ) and cytochrome b oxidase ( cytb ) and the nuclear genes globin 2β ( gb2β ), rudimentary ( CAD ) and ribosomal RNA ( 18S and 28S rRNA).…”

Section: Introductionmentioning

confidence: 97%

DNA barcoding supports reclassification of JapaneseChironomusspecies (Diptera: Chironomidae)

Kondo

Ueno

Ohbayashi

et al. 2016

Entomological Science

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Non‐biting midges (Diptera: Chironomidae) adapt to species‐specific environmental conditions and hence are promising bioindicators for aquatic and ecotoxicological monitoring. Although their utility for these purposes was historically limited by difficulties in their morphological identification, DNA barcoding offers a possible solution. Here, eight Japanese species of the genus Chironomus, which is characterized by its worldwide distribution and abundance among Chironomidae, were subjected to DNA barcoding using cytochromec oxidase subunit I (COI). To examine whether this DNA barcode is a useful indicator for Japanese species of Chironomus, we calculated genetic distances within and between the COI sequences of Chironomus species both from this study and worldwide and constructed phylogenetic trees. Based on 415 bp COI sequences and the Kimura two‐parameter model, the average genetic distances within 37 species and between 72 species were 2.6% and 17.2%, respectively. Although the ranges of genetic distances within and between species overlapped from 0.8% to 17.3%, 99.7% of average genetic distances between species were >3.0%. Some of this overlap is attributable to distances within species that were “too large” as well as those between species that were “too small”. Of eight Japanese species examined, two showed genetic distances between species that were below a 3.0% threshold, and four had distances within species that were greater than 3.0%. These results suggest a possible reclassification of these species and the need for further sampling to unveil biogeographic variations among different countries and regions.

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Improving environmental and biodiversity monitoring in the Baltic Sea using DNA barcoding of Chironomidae (Diptera)

Cited by 53 publications

References 36 publications

Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton

Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton

Biological invasions, climate change and genomics

DNA barcoding supports reclassification of JapaneseChironomusspecies (Diptera: Chironomidae)

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