2,124 results match your criteria Molecular ecology resources[Journal]


Metabarcoding a Diverse Arthropod Mock Community.

Mol Ecol Resour 2019 Feb 18. Epub 2019 Feb 18.

Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada, N1G 2W1.

Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. Read More

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http://dx.doi.org/10.1111/1755-0998.13008DOI Listing
February 2019

Avian mitochondrial genomes retrieved from museum eggshell.

Mol Ecol Resour 2019 Feb 17. Epub 2019 Feb 17.

Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, ACT, 2601, Australia.

Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historic populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more-diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60 year-old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterise the yield and quality of such DNA. Read More

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http://dx.doi.org/10.1111/1755-0998.13007DOI Listing
February 2019

A new cost-effective and fast direct PCR protocol for insects based on PBS buffer.

Mol Ecol Resour 2019 Feb 13. Epub 2019 Feb 13.

Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.

Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. Read More

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http://dx.doi.org/10.1111/1755-0998.13005DOI Listing
February 2019

Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol.

Mol Ecol Resour 2019 Feb 13. Epub 2019 Feb 13.

CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.

Target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as micro-arthropods can be challenging. Read More

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http://dx.doi.org/10.1111/1755-0998.13006DOI Listing
February 2019

SymPortal: a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling.

Mol Ecol Resour 2019 Feb 11. Epub 2019 Feb 11.

Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next-generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterise taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium), the multi-copy nature of the marker complicates its use. Read More

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http://dx.doi.org/10.1111/1755-0998.13004DOI Listing
February 2019

The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution.

Mol Ecol Resour 2019 Feb 8. Epub 2019 Feb 8.

BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong Province, 266555, China.

Marine mammals are important models for studying convergent evolution and aquatic adaption, thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of sperm whale including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparison with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. Read More

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http://dx.doi.org/10.1111/1755-0998.13003DOI Listing
February 2019
1 Read
3.712 Impact Factor

Bioaerosol Biomonitoring: Sampling Optimisation for Molecular Microbial Ecology.

Mol Ecol Resour 2019 Feb 8. Epub 2019 Feb 8.

University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, CO4 3SQ, UK.

Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry, and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Read More

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http://doi.wiley.com/10.1111/1755-0998.13002
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http://dx.doi.org/10.1111/1755-0998.13002DOI Listing
February 2019
3 Reads
3.712 Impact Factor

Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna.

Mol Ecol Resour 2019 Jan 31. Epub 2019 Jan 31.

Institute for Environment and Society, Brown University, Providence, RI, USA.

Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA-barcode library for a savanna ecosystem in equatorial East Africa. Read More

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http://doi.wiley.com/10.1111/1755-0998.13001
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http://dx.doi.org/10.1111/1755-0998.13001DOI Listing
January 2019
10 Reads

Continued misuse of multiple testing correction methods in population genetics-A wake-up call?

Mol Ecol Resour 2019 Jan;19(1):23-26

Department of Biological Sciences, California State University San Marcos, San Marcos, California.

Population geneticists often use multiple independent hypothesis tests of Hardy-Weinberg Equilibrium (HWE), Linkage Disequilibrium (LD), and population differentiation, to make broad inferences about their systems of choice. However, correcting for Family-Wise Error Rates (FWER) that are inflated due to multiple comparisons, is sparingly reported in our current literature. In this issue of Molecular Ecology Resources, perform a meta-analysis of 215 population genetics studies published between 2011 and 2013 to show (i) scarce use of FWER corrections across all three classes of tests, and (ii) when used, inconsistent application of correction methods with a clear bias towards less-conservative corrections for tests of population differentiation, than for tests of HWE, and LD. Read More

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http://dx.doi.org/10.1111/1755-0998.12969DOI Listing
January 2019

Measuring global fish species richness with eDNA metabarcoding.

Mol Ecol Resour 2019 Jan;19(1):19-22

Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California.

Despite mounting threats to global freshwater and marine biodiversity, including climate change, habitat alteration, overharvesting and pollution, we struggle to know which species are present below the water's surface that are suffering from these stressors. However, the idea that a water sample containing environmental DNA (eDNA) can be screened using high-throughput sequencing and bioinformatics to reveal the identity of aquatic species is a revolutionary advance for studying the patterns of species extirpation, invasive species establishment and the dynamics of species richness. To date, many of the critical tests of fisheries diversity using this metabarcoding approach have been conducted in lower diversity systems (<40 fish species), but in this issue of Molecular Ecology Resources, Cilleros et al. Read More

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http://dx.doi.org/10.1111/1755-0998.12929DOI Listing
January 2019

Editorial 2019.

Mol Ecol Resour 2019 Jan;19(1):1-18

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http://dx.doi.org/10.1111/1755-0998.12976DOI Listing
January 2019

The future is now: amplicon sequencing and sequence capture usher in the conservation genomics era.

Mol Ecol Resour 2019 Jan 25. Epub 2019 Jan 25.

U.S. Geological Survey, Wisconsin Cooperative Fishery Researcfh Unit, College of Natural Resources, University of Wisconsin-Stevens Point.

The genomics revolution has initiated a new era of population genetics where genome-wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well-studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Read More

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http://dx.doi.org/10.1111/1755-0998.12998DOI Listing
January 2019
5 Reads

Developing non-invasive methodologies to assess koala population health through detecting Chlamydia from scats.

Mol Ecol Resour 2019 Jan 25. Epub 2019 Jan 25.

Global Change Ecology Research Group, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, 4556, Australia.

Wildlife diseases are a recognized driver of global biodiversity loss, have substantial economic impacts, and are increasingly becoming a threat to human health. Disease surveillance is critical but remains difficult in the wild due to the substantial costs and potential biases associated with most disease detection methods. Non-invasive scat surveys have been proposed as a health monitoring methodology to overcome some of these limitations. Read More

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http://doi.wiley.com/10.1111/1755-0998.12999
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http://dx.doi.org/10.1111/1755-0998.12999DOI Listing
January 2019
5 Reads

Too much of a good thing? Finding the most informative genetic dataset to answer conservation questions.

Mol Ecol Resour 2019 Jan 25. Epub 2019 Jan 25.

School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.

Molecular markers are a useful tool allowing conservation and population managers to shed light on genetic processes affecting threatened populations. However, as technological advancements in molecular techniques continue to evolve, conservationists are frequently faced with new genetic markers, each with nuanced variation in their characteristics as well as advantages and disadvantages for informing various questions. We used a well-studied population of Tasmanian devils from Maria Island to illustrate the issues associated with combining multiple genetic datasets and to help answer a question posed by many population managers: which dataset will provide the most precise and accurate estimates of the population processes we are trying to measure? We analysed individual heterozygosity (as internal relatedness, IR) of 96 individuals, calculated using four genetic marker types (putatively neutral microsatellites, MHC-linked microsatellites, reduced representation sequencing, and candidate region resequencing). Read More

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http://dx.doi.org/10.1111/1755-0998.12997DOI Listing
January 2019

A parsimony estimator of the number of populations from a STRUCTURE-like analysis.

Authors:
Jinliang Wang

Mol Ecol Resour 2019 Jan 25. Epub 2019 Jan 25.

Institute of Zoology, Zoological Society of London, London, NW1 4RY, United Kingdom.

Population genetics model based Bayesian methods have been proposed and widely applied to making unsupervised inference of population structure from a sample of multilocus genotypes. Usually they provide good estimates of the ancestry (or population membership) of sampled individuals by clustering them probabilistically or proportionally into (anonymous) populations. However, they have difficulties in accurately estimating the number of populations (K) represented by the sampled individuals. Read More

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http://doi.wiley.com/10.1111/1755-0998.13000
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http://dx.doi.org/10.1111/1755-0998.13000DOI Listing
January 2019
3 Reads

Ultra-long telomeres shorten with age in nestling great tits but are static in adults and mask attrition of short telomeres.

Mol Ecol Resour 2019 Jan 23. Epub 2019 Jan 23.

Groningen Institute of Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.

Telomere length (TL) is increasingly used as a biomarker of senescence, but measuring telomeres remains a challenge. Within tissue samples, TL varies between cells and chromosomes. Class I telomeres are (presumably static) interstitial telomeric sequences, and terminal telomeres have been divided in shorter (Class II) telomeres and ultra-long (Class III) telomeres, and the presence of the latter varies strongly between species. Read More

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http://dx.doi.org/10.1111/1755-0998.12996DOI Listing
January 2019

LDJump: Estimating Variable Recombination Rates from Population Genetic Data.

Mol Ecol Resour 2019 Jan 21. Epub 2019 Jan 21.

Department of Applied Statistics, Johannes Kepler University Linz, Austria.

As recombination plays an important role in evolution, its estimation and the identification of hotspot positions is of considerable interest. We propose a novel approach for estimating population recombination rates based on genotyping or sequence data that involves a sequential multiscale change point estimator. Our method also permits to take demography into account. Read More

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http://dx.doi.org/10.1111/1755-0998.12994DOI Listing
January 2019

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets.

Mol Ecol Resour 2019 Jan 19. Epub 2019 Jan 19.

University of Washington, Department of Biology, Seattle, WA, 98195.

One common method of minimizing errors in large DNA sequence datasets is to drop variable sites with a minor allele frequency below some specified threshold. Though widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical SNP dataset to demonstrate the impacts of minor allele frequency (MAF) thresholds on inference of population structure - often the first step in analysis of population genomic data. Read More

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http://dx.doi.org/10.1111/1755-0998.12995DOI Listing
January 2019
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A roadmap for high-throughput sequencing studies of wild animal populations using non-invasive samples and hybridization capture.

Mol Ecol Resour 2019 Jan 14. Epub 2019 Jan 14.

Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.

Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although non-invasive samples, such as feces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Read More

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http://dx.doi.org/10.1111/1755-0998.12993DOI Listing
January 2019

The Quetzal Coalescence template library: a C++ programmers resource for integrating distributional, demographic and coalescent models.

Mol Ecol Resour 2019 Jan 14. Epub 2019 Jan 14.

Laboratoire Evolution, Génomes, Comportement et Ecologie, UMR CNRS 9191, IRD 247 and Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France.

Background: Genetic samples can be used to understand and predict the behavior of species living in a fragmented and temporally changing environment. To this aim, models of coalescence conditioned to environment through an explicit modeling of population growth and migration have been developed in the past years, and simulators implementing these models have been developed, enabling biologists to estimate parameters of interest with Approximate Bayesian Computation techniques. However, model choice is still limited, and developing new coalescence simulators is extremely time consuming because code reuse is limited. Read More

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http://dx.doi.org/10.1111/1755-0998.12992DOI Listing
January 2019

Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae).

Mol Ecol Resour 2019 Jan 13. Epub 2019 Jan 13.

WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland.

Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Read More

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http://dx.doi.org/10.1111/1755-0998.12991DOI Listing
January 2019

Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data.

Mol Ecol Resour 2019 Jan 11. Epub 2019 Jan 11.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE, 75236, Uppsala, Sweden.

Restriction-site associated DNA sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods often lead to biased estimates of allele frequencies and thereby to erroneous population genetic inference. Estimating the distribution of sample allele frequencies without calling genotypes was shown to improve population inference from whole genome sequencing data, but the ability of this approach to account for RADSeq-specific biases remains unexplored. Here we assess in how far genotype-free methods of allele frequency estimation affect demographic inference from empirical RADSeq data. Read More

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http://dx.doi.org/10.1111/1755-0998.12990DOI Listing
January 2019

Detecting Wahlund effects together with amplification problems: cryptic species, null alleles and short allele dominance in Glossina pallidipes populations from Tanzania.

Mol Ecol Resour 2019 Jan 7. Epub 2019 Jan 7.

Intertryp, IRD, Cirad, Univ Montpellier, Montpellier, France.

Population genetics is a convenient tool to study the population biology of non-model and hard to sample species. This is particularly true for parasites and vectors. Heterozygote deficits and/or linkage disequilibrium often occur in such studies and detecting the origin of those (Wahlund effect, reproductive system or amplification problems) is uneasy. Read More

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http://dx.doi.org/10.1111/1755-0998.12989DOI Listing
January 2019
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Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs.

Mol Ecol Resour 2018 Dec 28. Epub 2018 Dec 28.

Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China.

Horseshoe crabs including Tachypleus tridentatus are a group of marine arthropods and living fossil species which have existed on the earth for ~500 million years. However, the genetic mechanisms underlying their unique adaptive ability are still unclear. Here, we assembled the first chromosome-level T. Read More

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http://doi.wiley.com/10.1111/1755-0998.12988
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http://dx.doi.org/10.1111/1755-0998.12988DOI Listing
December 2018
22 Reads
3.712 Impact Factor

Environmental DNA for the enumeration and management of Pacific salmon.

Mol Ecol Resour 2018 Dec 28. Epub 2018 Dec 28.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.

Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. Read More

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http://doi.wiley.com/10.1111/1755-0998.12987
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http://dx.doi.org/10.1111/1755-0998.12987DOI Listing
December 2018
20 Reads

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement.

Mol Ecol Resour 2018 Dec 21. Epub 2018 Dec 21.

Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand.

While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along-shore water flow. Read More

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http://dx.doi.org/10.1111/1755-0998.12982DOI Listing
December 2018
1 Read

A Versatile Rapture (RAD-Capture) Platform for Genotyping Marine Turtles.

Mol Ecol Resour 2018 Dec 21. Epub 2018 Dec 21.

Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, 92037, USA.

Advances in high-throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration are rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions, certain research goals necessitate tailoring methods to specific study organisms, such as high-throughput genotyping of the same loci that are comparable over large spatial and temporal scales. These needs are particularly common for studies of highly mobile species of conservation concern like marine turtles, where life history traits, limited financial resources and other constraints require affordable, adaptable methods for HTS genotyping to meet a variety of study goals. Read More

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http://dx.doi.org/10.1111/1755-0998.12980DOI Listing
December 2018

DNA barcoding fishes from the Congo and the Lower Guinean provinces: assembling a reference library for poorly inventoried fauna.

Mol Ecol Resour 2018 Dec 21. Epub 2018 Dec 21.

Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny - JEMU, Vautierstraat 29, B-1000, Brussels, Belgium.

The Congolese and Lower Guinean ichthyological provinces are understudied hotspots of the global fish diversity. Here, we barcoded 741 specimens from the Lower and Middle Congo River and from three major drainage basins of the Lower Guinean ichthyological province, Kouilou-Niari, Nyanga and Ogowe. We identified 194 morphospecies belonging to 82 genera and 25 families. Read More

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http://dx.doi.org/10.1111/1755-0998.12983DOI Listing
December 2018
2 Reads

Age estimation in a long-lived seabird (Ardenna tenuirostris) using DNA methylation-based biomarkers.

Mol Ecol Resour 2018 Dec 21. Epub 2018 Dec 21.

Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia.

Age structure is a fundamental aspect of animal population biology. Age is strongly related to individual physiological condition, reproductive potential and mortality rate. Currently, there are no robust molecular methods for age estimation in birds. Read More

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http://dx.doi.org/10.1111/1755-0998.12981DOI Listing
December 2018

Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra.

Mol Ecol Resour 2018 Dec 21. Epub 2018 Dec 21.

WSL Swiss Federal Research Institute, Birmensdorf, Switzerland.

Despite decreasing sequencing costs, whole-genome sequencing for population-based genome scans for selection is still prohibitively expensive for organisms with large genomes. Moreover, the repetitive nature of large genomes often represents a challenge in bioinformatic and downstream analyses. Here, we use in-depth transcriptome sequencing to design probes for exome capture in Swiss stone pine (Pinus cembra), a conifer with an estimated genome size of 29. Read More

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http://dx.doi.org/10.1111/1755-0998.12986DOI Listing
December 2018
2 Reads

Discovering Millions of Plankton Genomic Markers from the Atlantic Ocean and the Mediterranean Sea.

Mol Ecol Resour 2018 Dec 21. Epub 2018 Dec 21.

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.

Comparison of the molecular diversity in all plankton populations present in geographically distant water columns may allow for a holistic view of the connectivity, isolation and adaptation of organisms in the marine environment. In this context, a large-scale detection and analysis of genomic variants directly in metagenomic data appeared as a powerful strategy for the identification of genetic structures and genes under natural selection in plankton. Here, we used DiscoSnp++, a reference-free variant caller, to produce genetic variants from large-scale metagenomic data and assessed its accuracy on the copepod Oithona nana in terms of variant calling, allele frequency estimation and population genomic statistics by comparing it to the state-of-the-art method. Read More

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http://doi.wiley.com/10.1111/1755-0998.12985
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http://dx.doi.org/10.1111/1755-0998.12985DOI Listing
December 2018
14 Reads

MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements.

Mol Ecol Resour 2018 Dec 21. Epub 2018 Dec 21.

Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. Read More

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http://dx.doi.org/10.1111/1755-0998.12984DOI Listing
December 2018

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes.

Mol Ecol Resour 2018 Nov 22. Epub 2018 Nov 22.

Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon.

There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. Read More

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http://dx.doi.org/10.1111/1755-0998.12968DOI Listing
November 2018

A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes, and pure cultures.

Mol Ecol Resour 2018 Dec 19. Epub 2018 Dec 19.

Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.

The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the sub-millimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules i.e. Read More

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http://dx.doi.org/10.1111/1755-0998.12979DOI Listing
December 2018

Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus).

Mol Ecol Resour 2018 Nov 22. Epub 2018 Nov 22.

Moore Laboratory of Zoology, Occidental College, Los Angeles, California.

With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. Read More

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http://dx.doi.org/10.1111/1755-0998.12970DOI Listing
November 2018

Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics.

Mol Ecol Resour 2018 Dec 18. Epub 2018 Dec 18.

School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA, 98105, USA.

Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Read More

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http://doi.wiley.com/10.1111/1755-0998.12978
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http://dx.doi.org/10.1111/1755-0998.12978DOI Listing
December 2018
4 Reads

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 next generation sequencing 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, 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, Maryland.

Whole genome sequencing of bacterial isolates has become a daily task in many laboratories, 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
2 Reads

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, Western Australia, 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 are needed on how to best implement eDNA field sampling approaches to maximize 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, Barcelona, Spain.

Analysing 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 analyse 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
19 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, New York.

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
14 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, Saint Paul, Minnesota.

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
13 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://doi.wiley.com/10.1111/1755-0998.12963
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http://dx.doi.org/10.1111/1755-0998.12963DOI Listing
November 2018
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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://doi.wiley.com/10.1111/1755-0998.12961
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http://dx.doi.org/10.1111/1755-0998.12961DOI Listing
October 2018
4 Reads

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 2019 Jan 4;19(1):296-305. Epub 2018 Dec 4.

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
January 2019
8 Reads

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

Mol Ecol Resour 2019 Jan 22;19(1):283-295. Epub 2018 Nov 22.

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
January 2019
6 Reads