Abstract：
:Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequencing to uncover different taxonomic groups of organisms from complex diet samples. We validated this approach on 91 faeces of a large omnivorous mammal, the brown bear, using DNA metabarcoding markers targeting the plant, vertebrate and invertebrate components of the diet. We included internal controls in the experiments and performed PCR replication for accuracy validation in postsequencing data analysis. Using our multiplexing strategy, we significantly simplified the experimental procedure and accurately and concurrently identified different prey DNA corresponding to the targeted taxonomic groups, with ≥ 60% of taxa of all diet components identified to genus/species level. The systematic application of internal controls and replication was a useful and simple way to evaluate the performance of our experimental procedure, standardize the selection of sequence filtering parameters for each marker data and validate the accuracy of the results. Our general approach can be adapted to the analysis of dietary samples of various predator species in different ecosystems, for a number of conservation and ecological applications entailing large-scale population level diet assessment through cost-effective screening of multiple DNA metabarcodes, and the detection of fine dietary variation among samples or individuals and of rare food items.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
De Barba M,Miquel C,Boyer F,Mercier C,Rioux D,Coissac E,Taberlet Pdoi
10.1111/1755-0998.12188subject
Has Abstractpub_date
2014-03-01 00:00:00pages
306-23issue
2eissn
1755-098Xissn
1755-0998journal_volume
14pub_type
杂志文章abstract：:Camelids are characterized by their unique adaptive immune system that exhibits the generation of homodimeric heavy-chain immunoglobulins, somatic hypermutation of T-cell receptors, and low genetic diversity of major histocompatibility complex (MHC) genes. However, short-read assemblies are typically highly fragmented...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13141
更新日期：2020-05-01 00:00:00
abstract：:This study reports the isolation and characterization of 11 polymorphic microsatellites from a sand smelt (Atherina boyeri) genomic library. Enrichment was performed with di-, tri- and tetranucleotide motifs following the FIASCO procedure (fast isolation by AFLP of sequences containing repeats). All loci were found to...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02366.x
更新日期：2009-05-01 00:00:00
abstract：:Collectively called zooxanthellae, photosynthetic dinoflagellates in the family Symbiodiniaceae are typical endosymbionts that unequivocally mediate coral responses to environmental changes. Symbiodiniaceae are genetically diverse, encompassing at least nine phylogenetically distinct genera (clades A-I). The ribosomal...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13250
更新日期：2021-01-01 00:00:00
abstract：:DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located ins...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13212
更新日期：2020-11-01 00:00:00
abstract：:Amplified fragment length polymorphism (AFLP) fingerprint data are now commonly collected using DNA sequencers. AFLP genotypes are still often scored by eye from such data - a time-consuming, error-prone and subjective process. We present a semi-automated method of genotyping sequencer-collected AFLPs at predefined fr...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2007.02073.x
更新日期：2008-07-01 00:00:00
abstract：:We developed four multiplex panels comprising 19 microsatellite loci and tested their amplification in 21 rodent species important for agricultural and conservation management (Microtus, Arvicola, Chionomys). On average, 17.6 loci amplified per species. Number of alleles ranged from 1 to 19 per locus. We report an add...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02521.x
更新日期：2009-05-01 00:00:00
abstract：:Metabarcoding is increasingly used to assess species diversity by high-throughput sequencing where millions of sequences can be generated in parallel and multiple samples can be analysed in one sequencing run. Generating amplified fragments with a unique sequence identifier ('tag') for each sample is crucial, as it al...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13018
更新日期：2019-07-01 00:00:00
abstract：:The three-toed sloths (Bradypus) are slow-moving arboreal neotropical mammals. Understanding demographic variables (such as sex ratio) of populations is a key for conservation purposes. Nevertheless, gender assignment of Bradypus is particularly challenging because of the lack of sexual dimorphism in infants and in ad...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02820.x
更新日期：2010-07-01 00:00:00
abstract：:The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how the computer program Geneland ...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2010.02864.x
更新日期：2010-11-01 00:00:00
abstract：:This article documents the public availability of raw transcriptome sequence data and 63,020 SNPs for the polar bear (Ursus maritimus). ...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12190
更新日期：2014-01-01 00:00:00
abstract：:Thirty-four novel microsatellite markers developed for wood cricket (Nemobius sylvestris) were tested and optimized. Twenty-five microsatellite loci were polymorphic, exhibiting between two and nine alleles. Observed heterozygosities ranged from 0.038 to 0.925. The microsatellites were also tested in a species belongi...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02269.x
更新日期：2008-11-01 00:00:00
abstract：:Two recent articles were written in response to our paper "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." While we agree with some of the comments made by the authors of these two response papers, we still believe caution should be employed in RADseq stud...
journal_title：Molecular ecology resources
pub_type： 评论,信件
doi：10.1111/1755-0998.12677
更新日期：2017-05-01 00:00:00
abstract：:The emu (Dromaius novaehollandiae), a member of ratite family, is native to Australia and has been introduced to other countries worldwide. In this work, 10 polymorphic microsatellite loci were isolated and characterized for emu from public sequences. Polymorphism was surveyed in 22 individuals from two different popu...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02315.x
更新日期：2008-11-01 00:00:00
abstract：:Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been ...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2010.02965.x
更新日期：2011-03-01 00:00:00
abstract：:The Chilean isopod Excirolana hirsuticauda is a marine benthic brooder with wide distributional range and low potential for long-distance dispersal. Eleven microsatellite markers were developed for E. hirsuticauda using enriched libraries. Characterization of those loci in 35 individuals from Playa Blanca beach showed...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02186.x
更新日期：2008-09-01 00:00:00
abstract：:Our understanding of Glossina fuscipes fuscipes, a major vector of sleeping sickness, has been severely constrained by a lack of genetic markers for mapping and population genetic studies. Here we present 10 newly developed microsatellite loci for this tsetse species. Heterozygosity levels in Moyo, an Ugandan populati...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2008.02328.x
更新日期：2008-11-01 00:00:00
abstract：:We introduce phylodyn, an r package for phylodynamic analysis based on gene genealogies. The package's main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes several Markov chain Monte Carlo-based methods and an integrated nested Laplace...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12630
更新日期：2017-01-01 00:00:00
abstract：:We describe 15 polymorphic microsatellite loci from the white-ruffed manakin Corapipo altera, a common understory bird of Neotropical lowland and montane evergreen forests from eastern Honduras to northwestern Colombia. These markers were developed in order to assess population structure and genetic diversity in a fra...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1471-8286.2007.01929.x
更新日期：2008-01-01 00:00:00
abstract：:Eight polymorphic microsatellite loci were isolated and characterized from a microsatellite DNA-enriched DNA library for the leopard coralgrouper (Plectropomus leopardus Lacepède, 1802), a popular food fish in the East Indies. These loci showed polymorphism information content ranging from 0.493 to 0.854, allele numbe...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02690.x
更新日期：2009-11-01 00:00:00
abstract：:Nematodes play an important role in ecosystem processes, yet the relevance of nematode species diversity to ecology is unknown. Because nematode identification of all individuals at the species level using standard techniques is difficult and time-consuming, nematode communities are not resolved down to the species le...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02611.x
更新日期：2009-11-01 00:00:00
abstract：:We tested for cross-species amplification of microsatellite loci located throughout the domestic sheep (Ovis aries) genome in two north American mountain ungulates (bighorn sheep, Ovis canadensis, and mountain goats, Oreamnos americanus). We identified 247 new polymorphic markers in bighorn sheep (≥ 3 alleles in one o...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02575.x
更新日期：2009-07-01 00:00:00
abstract：:Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenc...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13160
更新日期：2020-07-01 00:00:00
abstract：:New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.12466
更新日期：2016-09-01 00:00:00
abstract：:Thirty-eight microsatellite loci were developed for the bird pollinated, autohexaploid, Eremophila glabra ssp. glabra. A genomic library was screened with dinucleotide and trinucleotide sequence repeats. Polymorphism ranged from one to 21 alleles per locus. Twenty-four loci exhibited null alleles, based on patterns of...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02618.x
更新日期：2009-07-01 00:00:00
abstract：:Luffa spp. (sponge gourd or ridge gourd) is an economically important vegetable crop widely cultivated in China, India and Southeast Asia. Here, we employed PacBio long-read single-molecule real-time (SMRT) sequencing to perform de novo genome assemblies of two commonly cultivated Luffa species, L. acutangula and L. c...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13240
更新日期：2021-01-01 00:00:00
abstract：:Microsatellite genotyping of hair and faeces using standard polymerase chain reaction (PCR) resulted in low success rates and high error rates in a 2003-2004 pilot study using noninvasive genetic sampling for the brown bear (Ursus arctos) in the Italian Alps. Thus, we evaluated the performance of multiplex pre-amplifi...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02818.x
更新日期：2010-07-01 00:00:00
abstract：:With the advent of next generation sequencing technologies, transcriptome level sequence collections are arising as prominent resources for the discovery of gene-based molecular markers. In a previous study more than 15,000 simple sequence repeats (SSRs) in expressed sequence tag (EST) sequences resulting from 454 pyr...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2011.03102.x
更新日期：2012-05-01 00:00:00
abstract：:Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intraspecific genetic structure and spatial autocorrelation ...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/1755-0998.13024
更新日期：2019-07-01 00:00:00
abstract：:Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic an...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02750.x
更新日期：2010-03-01 00:00:00
abstract：:The longheaded eagle ray, Aetobatus flagellum feeds mainly on bivalves, and there have been some indications that the current reduction in the bivalve population in southern Japan may be due to an increase in the number of longheaded eagle rays. Consequently, the 'predator control programme' for reducing the longheade...
journal_title：Molecular ecology resources
pub_type： 杂志文章
doi：10.1111/j.1755-0998.2009.02568.x
更新日期：2009-05-01 00:00:00
