2,088 results match your criteria Molecular ecology resources[Journal]


Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution.

Mol Ecol Resour 2018 Dec 16. Epub 2018 Dec 16.

Museum of Southwestern Biology and Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, New Mexico, 87131-0001, USA.

Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus, and Leucocytoozoon) represent an exciting multi-host, multi-parasite system in ecology and evolution. Global research in this field accelerated after 1) the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques. Read More

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http://dx.doi.org/10.1111/1755-0998.12977DOI Listing
December 2018
1 Read

When to use NGS or diagnostic PCR in diet analyses.

Mol Ecol Resour 2018 Dec 3. Epub 2018 Dec 3.

Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Austria.

Next Generation sequencing (NGS) is increasingly used for diet analyses; however, it may not always describe diet samples well. A reason for this is that diet samples contain mixtures of food-DNA in different amounts as well as consumer-DNA which can reduce the food-DNA characterized. Because of this, detections will depend on the relative amount and identity of each type of DNA. Read More

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http://dx.doi.org/10.1111/1755-0998.12974DOI Listing
December 2018

In-Depth Comparative Analysis of Illumina MiSeq Run Metrics: Development of a Wet-lab Quality Assessment Tool.

Mol Ecol Resour 2018 Dec 2. Epub 2018 Dec 2.

Department of Microbiology, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA, 20740.

Whole genome sequencing of bacterial isolates has become a daily task in many labs, generating incredible amounts of data. However, data acquisition is not an end in itself; the goal is to acquire high quality data useful for understanding genetic relationships. Having a method that could rapidly determine which of the many available run metrics are the most important indicators of overall run quality and having a way to monitor these during a given sequencing run would be extremely helpful to this effect. Read More

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http://dx.doi.org/10.1111/1755-0998.12973DOI Listing
December 2018

Inferring introgression using RADseq and D : power and pitfalls revealed in a case study of spiny lizards (Sceloporus).

Mol Ecol Resour 2018 Dec 1. Epub 2018 Dec 1.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.

Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with non-model species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simple approach for inferring introgression using RADseq data, and apply it to a case study involving spiny lizards (Sceloporus) from northeastern México. Read More

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http://dx.doi.org/10.1111/1755-0998.12972DOI Listing
December 2018
1 Read

Environmental DNA metabarcoding studies are critically affected by substrate selection.

Mol Ecol Resour 2018 Nov 28. Epub 2018 Nov 28.

Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.

Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data is needed on how to best implement eDNA field sampling approaches to maximise their utility for each specific application. Read More

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http://dx.doi.org/10.1111/1755-0998.12971DOI Listing
November 2018

Quantitative analysis of connectivity in populations of a semi-aquatic mammal using kinship categories and network assortativity.

Mol Ecol Resour 2018 Nov 20. Epub 2018 Nov 20.

Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra),, Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain.

Analyzing the impact of anthropogenic and natural river barriers on the dispersal of aquatic and semi-aquatic species may be critical for their conservation. Knowledge of kinship relationships between individuals and reconstructions of pedigrees obtained using genomic data can be extremely useful, not only for studying the social organization of animals, but also inferring contemporary dispersal and quantifying the effect of specific barriers on current connectivity. In this study, we used kinship data to analyze connectivity patterns in a small semi-aquatic mammal, the Pyrenean desman (Galemys pyrenaicus), in an area comprising two river systems with close headwaters and dams of various heights and types. Read More

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http://dx.doi.org/10.1111/1755-0998.12967DOI Listing
November 2018
7 Reads

A high-quality chromosome-level genome assembly of a generalist herbivore, Trichoplusia ni.

Mol Ecol Resour 2018 Nov 18. Epub 2018 Nov 18.

Department of Entomology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA.

The cabbage looper, Trichoplusia ni, is a globally distributed highly polyphagous herbivore and an important agricultural pest. T. ni has evolved resistance to various chemical insecticides, and is one of the only two insect species that have evolved resistance to the biopesticide Bacillus thuringiensis (Bt) in agricultural systems and has been selected for resistance to baculovirus infections. Read More

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http://doi.wiley.com/10.1111/1755-0998.12966
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http://dx.doi.org/10.1111/1755-0998.12966DOI Listing
November 2018
7 Reads

Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods.

Mol Ecol Resour 2018 Nov 17. Epub 2018 Nov 17.

Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN, 55108.

RNA-sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Read More

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http://doi.wiley.com/10.1111/1755-0998.12965
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http://dx.doi.org/10.1111/1755-0998.12965DOI Listing
November 2018
7 Reads

DNA barcodes identify 99 per cent of apoid wasp species (Hymenoptera: Ampulicidae, Crabronidae, Sphecidae) from the Western Palearctic.

Mol Ecol Resour 2018 Nov 15. Epub 2018 Nov 15.

SNSB-Zoologische Staatssammlung, Munich, Germany.

The apoid wasps have traditionally been regarded as a paraphyletic assemblage of four families (Ampulicidae, Crabronidae, Heterogynaidae and Sphecidae) that are closely related to the bees (Anthophila). The present study covers the three families of apoid wasps known to occur in Europe, that is, the Ampulicidae, Crabronidae and Sphecidae. DNA barcode sequences of 3,695 specimens of apoid wasps were analysed for the present study, including 21 specimens of Ampulicidae, 3,398 Crabronidae and 276 Sphecidae. Read More

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http://dx.doi.org/10.1111/1755-0998.12963DOI Listing
November 2018

Advancing mite phylogenomics: Designing ultraconserved elements for acari phylogeny.

Mol Ecol Resour 2018 Nov 9. Epub 2018 Nov 9.

Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr, San Francisco, CA, 94118, USA.

Mites (Acari) are one of the most diverse groups of life on Earth, yet their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. Read More

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http://dx.doi.org/10.1111/1755-0998.12962DOI Listing
November 2018

DNA barcoding the ichthyofauna of the Yangtze River: insights from the molecular inventory of a mega-diverse temperate fauna.

Mol Ecol Resour 2018 Oct 30. Epub 2018 Oct 30.

The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.

Intensification of inland fisheries and aquatic landscape conversion led to a drastic decline of fish populations in the Yangtze River (YR) during the last decades. This situation urges for the development of a large-scale molecular assessment of YR ichthyofauna to further develop standardized methods of molecular identification for conservation and fisheries management purposes. We present here the results of a large-scale campaign to DNA barcode YR freshwater fishes that succeeded in producing 1,424 new DNA barcodes for 123 species. Read More

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http://dx.doi.org/10.1111/1755-0998.12961DOI Listing
October 2018

Ancient DNA: The quest for the best.

Mol Ecol Resour 2018 Nov;18(6):1185-1187

Institut Jacques Monod, CNRS, University Paris Diderot, Paris, France.

It is the dream of all researchers working with ancient DNA to identify prior to DNA extraction from bone the specimens or specific zones within them that contain the highest proportion of endogenous DNA. As it impacts the sacrifice of precious ancient specimens and the financial support needed for the analyses, the question is of high importance to the scientific field of palaeogenomics. The "Holy Grail" of palaeogenomics was reached when Cristina Gamba et al. Read More

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http://dx.doi.org/10.1111/1755-0998.12931DOI Listing
November 2018

Metapop: An individual-based model for simulating the evolution of tree populations in spatially and temporally heterogeneous landscapes.

Mol Ecol Resour 2018 Oct 25. Epub 2018 Oct 25.

BIOGECO, INRA, Univ. Bordeaux, Cestas, France.

Metapop is a stochastic individual-based simulation program. It uses quantitative genetics theory to produce an explicit description of the typical life cycle of monoecious and hermaphroditic plant species. Genome structure, the relationship between genotype and phenotype, and the effects of landscape heterogeneity on each individual can be finely parameterized by the user. Read More

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http://doi.wiley.com/10.1111/1755-0998.12958
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http://dx.doi.org/10.1111/1755-0998.12958DOI Listing
October 2018
4 Reads

McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes.

Mol Ecol Resour 2018 Oct 24. Epub 2018 Oct 24.

EPHE, PSL Research University, CNRS, University of Montpellier, Montpellier SupAgro, IRD, INRA, UMR:5175 CEFE, Montpellier, France.

Inferring the mode and tempo of natural selection helps further our understanding of adaptation to past environmental changes. Here, we introduce McSwan, a method to detect and date past and recent natural selection events in the case of a hard sweep. The method is based on the comparison of site frequency spectra obtained under various demographic models that include selection. Read More

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http://doi.wiley.com/10.1111/1755-0998.12957
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http://dx.doi.org/10.1111/1755-0998.12957DOI Listing
October 2018
3 Reads

High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations.

Mol Ecol Resour 2018 Oct 24. Epub 2018 Oct 24.

Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden.

High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Read More

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http://doi.wiley.com/10.1111/1755-0998.12959
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http://dx.doi.org/10.1111/1755-0998.12959DOI Listing
October 2018
11 Reads

Promises and pitfalls of using high-throughput sequencing for diet analysis.

Mol Ecol Resour 2018 Oct 24. Epub 2018 Oct 24.

Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

The application of high-throughput sequencing-based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits of animals. Due to the high resolution and prey detection capacity they provide, both metabarcoding and shotgun sequencing are increasingly used to address ecological questions grounded in dietary relationships. Despite their great promise in this context, recent research has unveiled how a wealth of biological (related to the study system) and technical (related to the methodology) factors can distort the signal of taxonomic composition and diversity. Read More

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http://dx.doi.org/10.1111/1755-0998.12960DOI Listing
October 2018

Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring.

Mol Ecol Resour 2018 Oct 24. Epub 2018 Oct 24.

Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK.

Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Read More

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http://doi.wiley.com/10.1111/1755-0998.12956
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http://dx.doi.org/10.1111/1755-0998.12956DOI Listing
October 2018
3 Reads

Long-read sequence capture of the haemoglobin gene clusters across codfish species.

Mol Ecol Resour 2018 Oct 17. Epub 2018 Oct 17.

Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.

Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Read More

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http://dx.doi.org/10.1111/1755-0998.12955DOI Listing
October 2018

RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data.

Mol Ecol Resour 2018 Oct 12. Epub 2018 Oct 12.

Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, B3H 4R2, Canada.

Restriction-site associated DNA sequencing (RADseq) is a powerful tool for genotyping of individuals, but the identification of loci and assignment of sequence reads is a crucial and often challenging step. The optimal parameter settings for a given de novo RADseq assembly varies between datasets and can be difficult and computationally expensive to determine. Here we introduce RADProc, a software package that uses a graph data structure to represent all sequence reads and their similarity relationships. Read More

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http://doi.wiley.com/10.1111/1755-0998.12954
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http://dx.doi.org/10.1111/1755-0998.12954DOI Listing
October 2018
1 Read

Finding stories in noise: Mitochondrial portraits from RAD data.

Mol Ecol Resour 2018 Oct 12. Epub 2018 Oct 12.

Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, South Africa.

Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years; however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy next-generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many single nucleotide polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses. Read More

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http://dx.doi.org/10.1111/1755-0998.12953DOI Listing
October 2018

Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca).

Mol Ecol Resour 2018 Oct 4. Epub 2018 Oct 4.

Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.

Crustaceans of the order Notostraca (Branchiopoda) are distributed worldwide and are known for the remarkable morphological stasis between their extant and Permian fossil species. Moreover, these crustaceans show relevant ecological traits and a wide range of reproductive strategies. However, genomic studies on notostracans are fairly limited. Read More

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http://doi.wiley.com/10.1111/1755-0998.12952
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http://dx.doi.org/10.1111/1755-0998.12952DOI Listing
October 2018
5 Reads

An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals.

Mol Ecol Resour 2018 Oct 3. Epub 2018 Oct 3.

United States Department of Agriculture Forest Service, Northern Research Station, Center for Forest Mycology Research, One Gifford Pinchot Drive, Madison, Wisconsin, USA.

DNA analysis of predator feces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). Read More

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http://dx.doi.org/10.1111/1755-0998.12951DOI Listing
October 2018

Conditionally autoregressive models improve occupancy analyses of autocorrelated data: An example with environmental DNA.

Mol Ecol Resour 2018 Sep 29. Epub 2018 Sep 29.

Laboratoire d'Écologie Alpine (LECA), CNRS, Univ. Grenoble Alpes, Grenoble, France.

Site occupancy-detection models (SODMs) are statistical models widely used for biodiversity surveys where imperfect detection of species occurs. For instance, SODMs are increasingly used to analyse environmental DNA (eDNA) data, taking into account the occurrence of both false-positive and false-negative errors. However, species occurrence data are often characterized by spatial and temporal autocorrelation, which might challenge the use of standard SODMs. Read More

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http://dx.doi.org/10.1111/1755-0998.12949DOI Listing
September 2018

Inconsistent use of multiple comparison corrections in studies of population genetic structure: Are some type I errors more tolerable than others?

Mol Ecol Resour 2018 Sep 28. Epub 2018 Sep 28.

Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana.

Studies of genetic population structure often involve numerous tests of Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD) and genetic differentiation. Tests of HWE or LD are important precursors to population structure assessments. When conducting multiple related statistical tests, type I error increases, e. Read More

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http://dx.doi.org/10.1111/1755-0998.12947DOI Listing
September 2018

Pollen metabarcoding as a tool for tracking long-distance insect migrations.

Mol Ecol Resour 2018 Sep 28. Epub 2018 Sep 28.

Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.

Insects account for a large portion of Earth's biodiversity and are key players for ecosystems, notably as pollinators. While insect migration is suspected to represent a natural phenomenon of major importance, remarkably little is known about it, except for a few flagship species. The reason for this situation is mainly due to technical limitations in the study of insect movement. Read More

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http://doi.wiley.com/10.1111/1755-0998.12948
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http://dx.doi.org/10.1111/1755-0998.12948DOI Listing
September 2018
5 Reads

Unveiling the RNA virosphere associated with marine microorganisms.

Mol Ecol Resour 2018 Nov 6;18(6):1444-1455. Epub 2018 Sep 6.

Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.

The study of extracellular DNA viral particles in the ocean is currently one of the most advanced fields of research in viral metagenomic analysis. However, even though the intracellular viruses of marine microorganisms might be the major source of extracellular virus particles in the ocean, the diversity of these intracellular viruses is not well understood. Here, our newly developed method, referred to herein as fragmented and primer ligated dsRNA sequencing (flds) version 2, identified considerable genetic diversity of marine RNA viruses in cell fractions obtained from surface seawater. Read More

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http://dx.doi.org/10.1111/1755-0998.12936DOI Listing
November 2018
8 Reads

Introducing ribosomal tandem repeat barcoding for fungi.

Mol Ecol Resour 2018 Sep 21. Epub 2018 Sep 21.

Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.

Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. Read More

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http://doi.wiley.com/10.1111/1755-0998.12944
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http://dx.doi.org/10.1111/1755-0998.12944DOI Listing
September 2018
2 Reads

A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms.

Mol Ecol Resour 2018 Sep 21. Epub 2018 Sep 21.

Department of Biology, Unit Ecology and Evolution, University of Fribourg, Fribourg, Switzerland.

Understanding the genetics of biological diversification across micro- and macro-evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant family with high diversity in the tropics, studies of diversification at the population and species levels are still hampered by a lack of genomic markers suitable for the genotyping of large numbers of recently diverged taxa. To fill this gap, we used a whole genome sequencing approach to develop target sequencing for molecular markers in 4,184 genome regions, including 4,051 genes and 133 non-genic putatively neutral regions. Read More

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http://dx.doi.org/10.1111/1755-0998.12945DOI Listing
September 2018

Using noninvasive metagenomics to characterize viral communities from wildlife.

Mol Ecol Resour 2018 Sep 21. Epub 2018 Sep 21.

Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.

Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Read More

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http://doi.wiley.com/10.1111/1755-0998.12946
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http://dx.doi.org/10.1111/1755-0998.12946DOI Listing
September 2018
4 Reads

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods.

Mol Ecol Resour 2018 Sep 17. Epub 2018 Sep 17.

Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.

Insect metabarcoding has been mainly based on PCR amplification of short fragments within the "barcoding region" of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. Read More

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http://dx.doi.org/10.1111/1755-0998.12942DOI Listing
September 2018
1 Read

Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo.

Mol Ecol Resour 2018 Sep 17. Epub 2018 Sep 17.

School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.

The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. Read More

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http://dx.doi.org/10.1111/1755-0998.12943DOI Listing
September 2018

Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula.

Mol Ecol Resour 2018 Sep 10. Epub 2018 Sep 10.

KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Read More

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http://dx.doi.org/10.1111/1755-0998.12939DOI Listing
September 2018
7 Reads

neogen: A tool to predict genetic effective population size (N ) for species with generational overlap and to assist empirical N study design.

Mol Ecol Resour 2018 Sep 7. Epub 2018 Sep 7.

Molecular Fisheries Laboratory, The University of Queensland, St. Lucia, Queensland, Australia.

Molecular genetic estimates of population effective size (N ) lose accuracy and precision when insufficient numbers of samples or loci are used. Ideally, researchers would like to forecast the necessary power when planning their project. neogen (genetic N for Overlapping Generations) enables estimates of precision and accuracy in advance of empirical investigation and allows exploration of the power available in different user-specified age-structured sampling schemes. Read More

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http://dx.doi.org/10.1111/1755-0998.12941DOI Listing
September 2018

Accuracy, limitations and cost efficiency of eDNA-based community survey in tropical frogs.

Mol Ecol Resour 2018 Nov 29;18(6):1415-1426. Epub 2018 Aug 29.

Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany.

Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e. Read More

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http://dx.doi.org/10.1111/1755-0998.12934DOI Listing
November 2018
14 Reads

Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers.

Mol Ecol Resour 2018 Nov 9;18(6):1456-1468. Epub 2018 Sep 9.

Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.

Freshwater biodiversity provides important ecosystem services and is at the core of water quality monitoring worldwide. To assess freshwater biodiversity, genetic methods such as metabarcoding are increasingly used as they are faster and allow better taxonomic resolution than manual identification methods. Either sampled organisms are used directly for "bulk metabarcoding," or water is filtered and the extracted environmental DNA serves as a proxy for biodiversity via "eDNA metabarcoding. Read More

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http://dx.doi.org/10.1111/1755-0998.12940DOI Listing
November 2018

Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora.

Mol Ecol Resour 2018 Aug 17. Epub 2018 Aug 17.

Research School of Biology, The Australian National University, Acton, ACT, Australia.

Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high-quality, high-molecular-weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. Read More

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http://dx.doi.org/10.1111/1755-0998.12938DOI Listing
August 2018
1 Read

Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments.

Mol Ecol Resour 2018 Nov 23;18(6):1500-1514. Epub 2018 Sep 23.

Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.

DNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third-generation sequencing. Read More

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http://doi.wiley.com/10.1111/1755-0998.12937
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http://dx.doi.org/10.1111/1755-0998.12937DOI Listing
November 2018
11 Reads

Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy.

Mol Ecol Resour 2018 Nov 11;18(6):1427-1443. Epub 2018 Sep 11.

Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa.

Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. Read More

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http://dx.doi.org/10.1111/1755-0998.12935DOI Listing
November 2018
1 Read

How complete are "complete" genome assemblies?-An avian perspective.

Mol Ecol Resour 2018 Nov 16;18(6):1188-1195. Epub 2018 Aug 16.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

The genomics revolution has led to the sequencing of a large variety of nonmodel organisms often referred to as "whole" or "complete" genome assemblies. But how complete are these, really? Here, we use birds as an example for nonmodel vertebrates and find that, although suitable in principle for genomic studies, the current standard of short-read assemblies misses a significant proportion of the expected genome size (7% to 42%; mean 20 ± 9%). In particular, regions with strongly deviating nucleotide composition (e. Read More

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http://dx.doi.org/10.1111/1755-0998.12933DOI Listing
November 2018
5 Reads

High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena).

Mol Ecol Resour 2018 Nov 13;18(6):1469-1481. Epub 2018 Aug 13.

Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany.

The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Read More

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http://dx.doi.org/10.1111/1755-0998.12932DOI Listing
November 2018

SNP-skimming: A fast approach to map loci generating quantitative variation in natural populations.

Mol Ecol Resour 2018 Nov 8;18(6):1402-1414. Epub 2018 Aug 8.

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas.

Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to nonmodel species has been generating dense genome-wide markers that satisfy the key requirement that marker data are error-free. Here, we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. Read More

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http://dx.doi.org/10.1111/1755-0998.12930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207453PMC
November 2018
10 Reads

Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring.

Mol Ecol Resour 2018 Nov 3;18(6):1381-1391. Epub 2018 Aug 3.

Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.

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. Read More

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http://dx.doi.org/10.1111/1755-0998.12926DOI Listing
November 2018

OneTwoTree: An online tool for phylogeny reconstruction.

Mol Ecol Resour 2018 Nov 3;18(6):1492-1499. Epub 2018 Aug 3.

School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.

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. Read More

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http://dx.doi.org/10.1111/1755-0998.12927DOI Listing
November 2018

Capture enrichment of aquatic environmental DNA: A first proof of concept.

Mol Ecol Resour 2018 Nov 11;18(6):1392-1401. Epub 2018 Aug 11.

Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, U.S. Department of Agriculture, Forest Service, Missoula, Montana.

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. Read More

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http://dx.doi.org/10.1111/1755-0998.12928DOI Listing
November 2018
15 Reads

Measuring metagenome diversity and similarity with Hill numbers.

Mol Ecol Resour 2018 Nov 27;18(6):1339-1355. Epub 2018 Jul 27.

Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

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 data sets, measuring community diversity with diversity indexes such as species richness and Shannon's index has 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. Read More

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http://dx.doi.org/10.1111/1755-0998.12923DOI Listing
November 2018

Application of a novel molecular method to age free-living wild Bechstein's bats.

Mol Ecol Resour 2018 Nov 27;18(6):1374-1380. Epub 2018 Jul 27.

Bioscience, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.

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). Read More

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http://dx.doi.org/10.1111/1755-0998.12925DOI Listing
November 2018
3 Reads

Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species.

Mol Ecol Resour 2018 Nov 30;18(6):1356-1373. Epub 2018 Jul 30.

Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.

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 nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Read More

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http://dx.doi.org/10.1111/1755-0998.12924DOI Listing
November 2018
9 Reads

Testing clustering strategies for metabarcoding-based investigation of community-environment interactions.

Mol Ecol Resour 2018 Nov 25;18(6):1326-1338. Epub 2018 Jul 25.

Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China.

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. Read More

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http://dx.doi.org/10.1111/1755-0998.12922DOI Listing
November 2018

Reliably discriminating stock structure with genetic markers: Mixture models with robust and fast computation.

Mol Ecol Resour 2018 Nov 17;18(6):1310-1325. Epub 2018 Jul 17.

Oceans and Atmosphere, CSIRO, Hobart, Tasmania, Australia.

Delineating naturally occurring and self-sustaining subpopulations (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. Read More

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http://dx.doi.org/10.1111/1755-0998.12920DOI Listing
November 2018
1 Read

Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment.

Mol Ecol Resour 2018 Nov 20;18(6):1482-1491. Epub 2018 Jul 20.

Institut des Sciences de la Forêt Tempérée, Université du Québec en Outaouais, Ripon, Quebec, Canada.

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. Read More

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http://dx.doi.org/10.1111/1755-0998.12921DOI Listing
November 2018