Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding

Laforest, Brandon J.; Winegardner, Amanda K.; Zaheer, Omar A.; Jeffery, Nicholas W.; Boyle, Elizabeth E.; Adamowicz, Sarah J.

doi:10.1186/1472-6785-13-13

Cited by 21 publications

(20 citation statements)

References 41 publications

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“…The 561 PCR reactions yielded 486 NGS barcodes, i.e. the overall barcoding success rate was 86%, which is similar or higher than what was found in other studies of freshwater (Laforest et al, 2013;Jackson et al, 2014) or other insects (Hajibabaei et al, 2006a;Gibson et al, 2014). Overall, NGS success rates were high (97.2%: 486/500; larvae: 245/250: 98%; adults: 241/250: 96%) because secondary signals due to heteroplasmy and/or pseudogenes rarely lead to sequencing failure in NGS Shokralla et al, 2014).…”

Section: Methodssupporting

confidence: 79%

$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen‐rich samples

et al. 2015

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Several of the biggest challenges in taxonomy and systematics are related to a toxic mixture of small size, abundance, and rarity. There are too many species in groups with too few taxonomists and many of these species are very rare and hard to find because they are hidden in mass samples. To make matters worse, these species often have life‐history stages that are morphologically so different that it is difficult to identify them as semaphoronts of the same species. We demonstrate that these biodiversity challenges can be addressed with cost‐effective molecular markers. Here, we describe a next‐generation‐sequencing protocol that can yield barcodes at a chemical cost of < 0.40 USD per specimen. We use this protocol to generate molecular markers for 1015 specimens of tropical midges (Diptera: Chironomidae). The barcodes cluster into 52–61 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering (OC), Generalized Mixed Yule Coalescent (GMYC), or Poisson Tree Process (PTP) is used. More than half of the putative species are rare (< 10 specimens) and we are able to match larvae and adults for 24 of these OTUs. We argue that the proposed protocol will help with processing specimen‐rich biodiversity samples at low cost.

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Section: Methodssupporting

confidence: 79%

$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen‐rich samples

et al. 2015

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“…This indicates that eDNA could be used as a new tool for rapid network‐level richness analyses and biodiversity assessments. Such systematic BioBlitz sampling (Laforest et al, ; Lundmark, ) across hitherto understudied complete river catchments may be a promising avenue, since minimally trained people without any taxonomic expertise can collect great parts of regional or even landscape richness in a rapid time frame with this method.…”

Section: Discussionmentioning

confidence: 99%

Assessing different components of diversity across a river network using eDNA

et al. 2019

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Assessing individual components of biodiversity, such as local or regional taxon richness, and differences in community composition is a long‐standing challenge in ecology. It is especially relevant in spatially structured and diverse ecosystems. Environmental DNA (eDNA) has been suggested as a novel technique to detect taxa and therefore may allow to accurately measure biodiversity. However, we do not yet fully understand the comparability of eDNA‐based assessments to classical morphological approaches. We assessed may‐, stone‐, and caddisfly genera with two contemporary methods, namely eDNA sampling followed by molecular identification and kicknet sampling followed by morphological identification. We sampled 61 sites distributed over a large river network, allowing a comparison of various diversity measures from the catchment to site levels and providing insights into how these measures relate to network properties. We extended our data with historical morphological records of total diversity at the catchment level. At the catchment scale, identification based on eDNA and kicknet samples detected similar proportions of the overall and cumulative historically documented richness (gamma diversity), 42% and 46%, respectively. We detected a good overlap (62%) between genera identified from eDNA and kicknet samples at the regional scale. At the local scale, we found highly congruent values of local taxon richness (alpha diversity) between eDNA and kicknet samples. Richness of eDNA was positively related to discharge, a descriptor of network position, while kicknet was not. Beta diversity, a measure of dissimilarity between sites, was comparable for the two contemporary methods and is driven by species replacement and not by nestedness. Although eDNA approaches are still in their infancy and optimization regarding sampling design and laboratory work is still needed, our results indicate that it can capture different components of diversity, proving its potential utility as a new tool for large sampling campaigns across hitherto understudied complete river catchments.

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“…Even this concerted effort is not likely to have recorded the cryptic species that would have been exposed only by molecular means. To overcome the limitations imposed by solely morphology-based identification, DNA barcodes (2) are now used in many biodiversity and taxonomic studies (3)(4)(5)(6)(7)(8). Sorting and tissue sampling of individual specimens from bulk samples before single-specimen sequencing, however, is slow and labor-intensive.…”

mentioning

confidence: 99%

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

Gibson

Shokralla

Porter

et al. 2014

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

274

296

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Conventional assessments of ecosystem sample composition are based on morphology-based or DNA barcode identification of individuals. Both approaches are costly and time-consuming, especially when applied to the large number of specimens and taxa commonly included in ecological investigations. Next-generation sequencing approaches can overcome the bottleneck of individual specimen isolation and identification by simultaneously sequencing specimens of all taxa in a bulk mixture. Here we apply multiple parallel amplification primers, multiple DNA barcode markers, 454-pyrosequencing, and Illumina MiSeq sequencing to the same sample to maximize recovery of the arthropod macrobiome and the bacterial and other microbial microbiome of a bulk arthropod sample. We validate this method with a complex sample containing 1,066 morphologically distinguishable arthropods from a tropical terrestrial ecosystem with high taxonomic diversity. Multiamplicon next-generation DNA barcoding was able to recover sequences corresponding to 91% of the distinguishable individuals in a bulk environmental sample, as well as many species present as undistinguishable tissue. 454-pyrosequencing was able to recover 10 more families of arthropods and 30 more species than did conventional Sanger sequencing of each individual specimen. The use of other loci (16S and 18S ribosomal DNA gene regions) also added the detection of species of microbes associated with these terrestrial arthropods. This method greatly decreases the time and money necessary to perform DNA-based comparisons of biodiversity among ecosystem samples. This methodology opens the door to much cheaper and increased capacity for ecological and evolutionary studies applicable to a wide range of socio-economic issues, as well as a basic understanding of how the world works.cytochrome c oxidase subunit I | Costa Rica | insect | Malaise trap | NGS

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Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding

Cited by 21 publications

References 41 publications

$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen‐rich samples

$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen‐rich samples

Assessing different components of diversity across a river network using eDNA

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

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