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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/30014577/supervised-machine-learning-outperforms-taxonomy-based-environmental-dna-metabarcoding-applied-to-biomonitoring
#1
Tristan Cordier, Dominik Forster, Yoann Dufresne, Catarina Im Martins, Thorsten Stoeck, Jan Pawlowski
Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations of the traditional morphotaxonomy-based bioassessment. Recently, we demonstrated that supervised machine learning (SML) can be used to predict accurate biotic indices values from eDNA metabarcoding data, regardless of the taxonomic affiliation of the sequences. However, it is unknown to which extent the accuracy of such models depends on taxonomic resolution of molecular markers or how SML compares with metabarcoding approaches targeting well-established bioindicator species...
July 17, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/30010236/onetwotree-an-online-tool-for-phylogeny-reconstruction
#2
Michal Drori, Anna Rice, Moshe Einhorn, Ofer Chay, Lior Glick, Itay Mayrose
Phylogeny reconstruction is a key instrument in numerous biological analyses, ranging from evolutionary and ecology research, to conservation and systems biology. The increasing accumulation of genomic data makes it possible to reconstruct phylogenies with both high accuracy and at increasingly finer resolution. Yet, taking advantage of the enormous amount of sequence data available requires the use of computational tools for efficient data retrieval and processing, or else the process could quickly become an error-prone endeavour...
July 16, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/30009542/capture-enrichment-of-aquatic-environmental-dna-a-first-proof-of-concept
#3
Taylor M Wilcox, Katherine E Zarn, Maxine P Piggott, Michael K Young, Kevin S McKelvey, Michael K Schwartz
Environmental DNA (eDNA) sampling - the detection of genetic material in the environment to infer species presence - has rapidly grown as a tool for sampling aquatic animal communities. A potentially powerful feature of environmental sampling is that all taxa within the habitat shed DNA and so may be detectable, creating opportunity for whole-community assessments. However, animal DNA in the environment tends to be comparatively rare, making it necessary to enrich for genetic targets from focal taxa prior to sequencing...
July 16, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29985552/measuring-metagenome-diversity-and-similarity-with-hill-numbers
#4
Zhanshan Sam Ma, Lianwei Li
The first step of any metagenome sequencing project is to get the inventory of OTU abundances (operational taxonomic units) and/or metagenomic gene abundances. The former is generated with 16S-rRNA-tagged amplicon sequencing technology, and the latter can be generated from either gene-targeted or whole-sample shotgun metagenomics technologies. With 16S-rRNA datasets, measuring community diversity with diversity indexes such as species richness and Shannon index have been a de facto standard analysis; nevertheless, similarly comprehensive approaches to metagenomic gene abundances are still largely missing, despite that both OTU and gene abundances are DNA reads...
July 9, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29981199/application-of-a-novel-molecular-method-to-age-free-living-wild-bechstein-s-bats
#5
Patrick G R Wright, Fiona Mathews, Henry Schofield, Colin Morris, Joe Burrage, Adam Smith, Emma L Dempster, Patrick B Hamilton
The age profile of populations fundamentally affects their conservation status. Yet age is frequently difficult to assess in wild animals. Here, we assessed the use of DNA methylation of homologous genes to establish the age structure of a rare and elusive wild mammal: the Bechstein's bat (Myotis bechsteinii). We collected 62 wing punches from individuals whose ages were known as a result of a long-term banding study. DNA methylation was measured at seven CpG sites from three genes which have previously shown age-associated changes in humans and laboratory mice...
July 7, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29978939/targeted-re-sequencing-of-coding-dna-sequences-for-snp-discovery-in-non-model-species
#6
Daniel W Förster, James K Bull, Dorina Lenz, Marijke Autenrieth, Johanna L A Paijmans, Robert H S Kraus, Carsten Nowak, Helmut Bayerl, Ralph Kuehn, Alexander P Saveljev, Magda Sindičić, Michael Hofreiter, Krzysztof Schmidt, Jörns Fickel
Targeted capture coupled with high throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for non-model organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a non-model organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus)...
July 6, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29978606/testing-clustering-strategies-for-metabarcoding-based-investigation-of-community-environment-interactions
#7
Wei Xiong, Aibin Zhan
The degradation of freshwater ecosystems has become a common ecological and environmental problem globally. Owing to the complexity of biological communities, there remain tremendous technical challenges for investigating influence of environmental stressors (e.g. chemical pollution) on biological communities. High-throughput sequencing-based metabarcoding provides a powerful tool to reveal complex interactions between environments and biological communities. Among many technical issues, the clustering strategies for Operational Taxonomic Units (OTUs) which are crucial for assessing biodiversity of communities, may affect final conclusions...
July 6, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29943898/reliably-discriminating-stock-structure-with-genetic-markers-mixture-models-with-robust-and-fast-computation
#8
Scott D Foster, Pierre Feutry, Peter M Grewe, Oliver Berry, Francis K C Hui, Campbell R Davies
Delineating naturally occurring and self-sustaining sub-populations (stocks) of a species is an important task, especially for species harvested from the wild. Despite its central importance to natural resource management, analytical methods used to delineate stocks are often, and increasingly, borrowed from superficially similar analytical tasks in human genetics even though models specifically for stock identification have been previously developed. Unfortunately, the analytical tasks in resource management and human genetics are not identical { questions about humans are typically aimed at inferring ancestry (often referred to as 'admixture') rather than breeding stocks...
June 26, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29939475/reconstructing-phylogeny-from-reduced-representation-genome-sequencing-data-without-assembly-or-alignment
#9
Huan Fan, Anthony R Ives, Yann Surget-Groba
Reduced-representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data...
June 25, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29923321/boosting-dna-metabarcoding-for-biomonitoring-with-phylogenetic-estimation-of-otus-ecological-profiles
#10
F Keck, V Vasselon, F Rimet, A Bouchez, M Kahlert
DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices which are based on the estimated abundances of species in a community and their ecological profiles can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of OTUs' ecological profiles (OTU-PITI approach)...
June 19, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29877042/debugging-diversity-a-pan-continental-exploration-of-the-potential-of-terrestrial-blood-feeding-leeches-as-a-vertebrate-monitoring-tool
#11
Ida Baerholm Schnell, Kristine Bohmann, Sebastian E Schultze, Stine R Richter, Dáithí C Murray, Mikkel-Holger S Sinding, David Bass, John E Cadle, Mason J Campbell, Rainer Dolch, David P Edwards, Thomas N E Gray, Teis Hansen, Anh Nguyen Quang Hoa, Christina Lehmkuhl Noer, Sigrid Heise-Pavlov, Adam F Sander Pedersen, Juliot Carl Ramamonjisoa, Mark E Siddall, Andrew Tilker, Carl Traeholt, Nicholas Wilkinson, Paul Woodcock, Douglas W Yu, Mads Frost Bertelsen, Michael Bunce, M Thomas P Gilbert
The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents...
June 7, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29877032/optimized-dna-sampling-of-ancient-bones-using-computed-tomography-scans
#12
Federica Alberti, Javier Gonzalez, Johanna L A Paijmans, Nikolas Basler, Michaela Preick, Kirstin Henneberger, Alexandra Trinks, Gernot Rabeder, Nicholas J Conard, Susanne C Münzel, Ulrich Joger, Guido Fritsch, Thomas Hildebrandt, Michael Hofreiter, Axel Barlow
The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling...
June 7, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29870119/a-bioinformatic-pipeline-for-identifying-informative-single-nucleotide-polymorphism-panels-for-parentage-assignment-from-radseq-data
#13
Kimberly R Andrews, Jennifer R Adams, E Frances Cassirer, Raina K Plowright, Colby Gardner, Maggie Dwire, Paul A Hohenlohe, Lisette P Waits
The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power...
June 5, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29858523/rpase-individual-based-allele-specific-expression-detection-without-prior-knowledge-of-haplotype-phase
#14
Mi Wang, Severin Uebbing, Yudi Pawitan, Douglas G Scofield
Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele-specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel method called RPASE (Read-backed Phasing-based ASE detection) to test for genes that show ASE. With mapped RNA-seq data from a single individual and a list of SNPs from the same individual as the only input, RPASE is capable of aggregating information across multiple dependent SNPs and producing individual-based gene-level tests for ASE...
June 2, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29856123/evaluating-sample-size-to-estimate-genetic-management-metrics-in-the-genomics-era
#15
Elizabeth P Flesch, Jay J Rotella, Jennifer M Thomson, Tabitha A Graves, Robert A Garrott
Inbreeding and relationship metrics among and within populations are useful measures for genetic management of wild populations, but accuracy and precision of estimates can be influenced by the number of individual genotypes analysed. Biologists are confronted with varied advice regarding the sample size necessary for reliable estimates when using genomic tools. We developed a simulation framework to identify the optimal sample size for three widely used metrics to enable quantification of expected variance and relative bias of estimates and a comparison of results among populations...
June 1, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29847023/the-hitchhiker-s-guide-to-single-locus-species-delimitation
#16
Simon Dellicour, Jean-François Flot
Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single-gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species-poor samples and/or tree-based approaches: as a result, travellers in the land of single-locus species delimitation lack a comprehensive "hitchhiker's guide" highlighting the sweet spots and dangers on their road...
May 30, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29802793/towards-robust-and-repeatable-sampling-methods-in-edna-based-studies
#17
REVIEW
Ian A Dickie, Stephane Boyer, Hannah L Buckley, Richard P Duncan, Paul P Gardner, Ian D Hogg, Robert J Holdaway, Gavin Lear, Andreas Makiola, Sergio E Morales, Jeff R Powell, Louise Weaver
DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75)...
May 26, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29802785/evaluation-of-redundancy-analysis-to-identify-signatures-of-local-adaptation
#18
Thibaut Capblancq, Keurcien Luu, Michael G B Blum, Eric Bazin
Ordination is a common tool in ecology that aims at representing complex biological information in a reduced space. In landscape genetics, ordination methods such as principal component analysis (PCA) have been used to detect adaptive variation based on genomic data. Taking advantage of environmental data in addition to genotype data, redundancy analysis (RDA) is another ordination approach that is useful to detect adaptive variation. This study aims at proposing a test statistic based on RDA to search for loci under selection...
May 26, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29797549/minimizing-polymerase-biases-in-metabarcoding
#19
Ruth V Nichols, Christopher Vollmers, Lee A Newsom, Yue Wang, Peter D Heintzman, McKenna Leighton, Richard E Green, Beth Shapiro
DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or "barcode," from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of each taxon to the overall composition of amplified product...
May 24, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29791787/dna-barcoding-of-microgastrine-parasitoid-wasps-hymenoptera-braconidae-using-high-throughput-methods-more-than-doubles-the-number-of-species-known-for-australia
#20
Erinn P Fagan-Jeffries, Steven J B Cooper, Terry Bertozzi, Tessa M Bradford, Andrew D Austin
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 99 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this...
May 23, 2018: Molecular Ecology Resources
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