2,140 results match your criteria Molecular ecology resources[Journal]


A hierarchical Bayesian Beta regression approach to study the effects of geographic genetic structure and spatial autocorrelation on species distribution range shifts.

Mol Ecol Resour 2019 Apr 16. Epub 2019 Apr 16.

CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.

Global climate change (GCC) may be imposing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intra-specific genetic structure and spatial autocorrelation (SAC) of data in distribution range models. Read More

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http://dx.doi.org/10.1111/1755-0998.13024DOI Listing

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors.

Mol Ecol Resour 2019 Apr 15. Epub 2019 Apr 15.

Institute of Evolution, & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.

As a model organism for studies of cell and environmental biology, the free-living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e. separate germline and somatic nuclei in each cell/organism), "gene-sized" chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13
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http://dx.doi.org/10.1111/1755-0998.13023DOI Listing
April 2019
4 Reads

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring.

Mol Ecol Resour 2019 Apr 12. Epub 2019 Apr 12.

Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada.

This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 BINs, including 2,700 CO1 haplotype clusters without species level assignment, so called "dark taxa". Overall, 88 out of 117 families (75%) recorded from Germany were covered, more than 50% of the 9,544 known species of Diptera Germany. Read More

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http://dx.doi.org/10.1111/1755-0998.13022DOI Listing

The chromosome-level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high-altitude environment of the Tibetan plateau.

Mol Ecol Resour 2019 Apr 12. Epub 2019 Apr 12.

College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.

Triplophysa is one genus among the endemic fishes of the Tibetan Plateau in China. Triplophysa tibetana, which lives at a recorded altitude of ~4000 m and plays an important role in the highland aquatic ecosystem, serves as an excellent model for investigating high-altitude environmental adaptation. However, evolutionary and conservation studies of Triplophysa tibetana to date have been limited by scarce genomic resources for the Triplophysa genus. Read More

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http://dx.doi.org/10.1111/1755-0998.13021DOI Listing
April 2019
2 Reads

Testing for Hardy-Weinberg Equilibrium in Structured Populations using Genotype or Low-Depth NGS Data.

Mol Ecol Resour 2019 Apr 11. Epub 2019 Apr 11.

Section of Bioinformatics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

Testing for deviations from Hardy-Weinberg Equilibrium (HWE) is a common practice for quality control in genetic studies. Variable sites violating HWE may be identified as technical errors in the sequencing or genotyping process, or they may be of special evolutionary interest. Large-scale genetic studies based on next-generation sequencing (NGS) methods have become more prevalent as cost is decreasing but these methods are still associated with statistical uncertainty. Read More

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http://dx.doi.org/10.1111/1755-0998.13019DOI Listing

Improving Illumina assemblies with Hi-C and long reads: an example with the North African dromedary.

Mol Ecol Resour 2019 Apr 11. Epub 2019 Apr 11.

Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, Vetmeduni Vienna, Vienna, Austria.

Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome is the dromedary (Camelus dromedarius). Read More

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http://dx.doi.org/10.1111/1755-0998.13020DOI Listing

Assessing the influence of sample tagging and library preparation on DNA metabarcoding.

Mol Ecol Resour 2019 Apr 9. Epub 2019 Apr 9.

Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany.

Metabarcoding is increasingly used to assess species biodiversity by High-Throughput Sequencing where millions of sequences can be generated in parallel and multiple samples can be analysed in one sequencing run. Generating amplified fragments with a unique tag for each sample is crucial, as it allows assigning sequences to the original samples. The tagging through fusion primers is a fast and cheap alternative to commercially produced ligation-based kits. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13
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http://dx.doi.org/10.1111/1755-0998.13018DOI Listing
April 2019
2 Reads

A guide to the application of Hill numbers to DNA based diversity analyses.

Mol Ecol Resour 2019 Apr 4. Epub 2019 Apr 4.

Section for Evolutionary Genomics, University of Copenhagen, 1350, Copenhagen, Denmark.

With the advent of DNA sequencing-based techniques, the way we detect and measure biodiversity is undergoing a radical shift. There is also an increasing awareness of the need to employ intuitively meaningful diversity measures based on unified statistical frameworks, so that different results can be easily interpreted and compared. This article aims to serve as a guide to implementing biodiversity assessment using the general statistical framework developed around Hill numbers into the analysis of systems characterised using DNA sequencing-based techniques (e. Read More

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http://dx.doi.org/10.1111/1755-0998.13014DOI Listing

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes.

Mol Ecol Resour 2019 Apr 4. Epub 2019 Apr 4.

GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.

The Helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub-Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Read More

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http://dx.doi.org/10.1111/1755-0998.13017DOI Listing

Metapop2: re-implementation of software for the analysis and management of subdivided populations using gene and allelic diversity.

Mol Ecol Resour 2019 Apr 2. Epub 2019 Apr 2.

Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain.

Management programs often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity, however, can also provide complementary and useful information for conservation programs, as it is highly sensitive to population bottlenecks, and is more related to long-term selection response than heterozygosity. Read More

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http://dx.doi.org/10.1111/1755-0998.13015DOI Listing

Phylogenomics using low-depth whole genome sequencing: a case study with the olive tribe.

Mol Ecol Resour 2019 Apr 1. Epub 2019 Apr 1.

Laboratoire Évolution & Diversité Biologique (EDB, UMR5174), Université de Toulouse, CNRS, UPS, IRD, 118 route de Narbonne, F-31062, Toulouse, France.

Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historic species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these datasets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Read More

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http://dx.doi.org/10.1111/1755-0998.13016DOI Listing
April 2019
3 Reads

Evaluating NGS methods for routine monitoring of wild bees: metabarcoding, mitogenomics or NGS barcoding.

Mol Ecol Resour 2019 Mar 26. Epub 2019 Mar 26.

Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.

Implementing cost-effective monitoring programs for wild bees remains challenging due to the high costs of sampling and specimen identification. To reduce costs, next generation sequencing (NGS)-based methods have lately been suggested as alternatives to morphology-based identifications. To provide a comprehensive presentation of the advantages and weaknesses of different NGS-based identification methods, we assessed three of the most promising ones, namely metabarcoding, mitogenomics and NGS barcoding. Read More

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http://dx.doi.org/10.1111/1755-0998.13013DOI Listing

Have the cake and eat it: Optimising non-destructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring.

Mol Ecol Resour 2019 Mar 22. Epub 2019 Mar 22.

CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.

DNA metabarcoding can contribute to improving cost-effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardisation efforts are still required to mainstream its application into biomonitoring programs. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenised bulk samples, which is time consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimise and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples, and thus including potential PCR inhibitors and non-target organisms. Read More

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http://dx.doi.org/10.1111/1755-0998.13012DOI Listing
March 2019
1 Read

Laboratory contamination over time during low-biomass sample analysis.

Mol Ecol Resour 2019 Mar 19. Epub 2019 Mar 19.

Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.

Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g. Read More

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http://dx.doi.org/10.1111/1755-0998.13011DOI Listing

Phylin 2.0: Extending the phylogeographic interpolation method to include uncertainty and user-defined distance metrics.

Mol Ecol Resour 2019 Mar 14. Epub 2019 Mar 14.

CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade, do Porto, R. Padre Armando Quintas, 4485-661, Vairão, Portugal.

Estimating geographic ranges of intra-specific evolutionary lineages is crucial to the fields of biogeography, evolution, and biodiversity conser-vation. Models of isolation mechanisms often consider multiple distances in order to explain genetic divergence. Yet, the available methods to esti-mate the geographical ranges of lineages are based on direct geographical distances, neglecting other distance metrics that can better explain the spatial genetic structure. Read More

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https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13
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http://dx.doi.org/10.1111/1755-0998.13010DOI Listing
March 2019
2 Reads
3.712 Impact Factor

Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.

Mol Ecol Resour 2019 Mar 8. Epub 2019 Mar 8.

Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University Norbyvägen, 18D, 752 36, Uppsala, Sweden.

The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged a wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. Read More

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http://dx.doi.org/10.1111/1755-0998.13009DOI Listing
March 2019
1 Read

Making use of the social network in conservation genomics: Integrating kinship and network analyses to understand connectivity.

Mol Ecol Resour 2019 Mar;19(2):307-309

Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, UK.

Inferring and quantifying recent barriers to connectivity is increasingly important for conservation and management in a world undergoing rapid environmental change. Traditional measures of genetic differentiation can take many generations to reflect a new barrier to connectivity. Although methods that use the linkage disequilibrium signal in mixed genetic samples are able to reflect recent levels of gene flow, they are not suitable for use in situations with low levels of genetic differentiation. Read More

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http://dx.doi.org/10.1111/1755-0998.12950DOI Listing
March 2019
1 Read

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
3 Reads

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
2 Reads

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
1 Read

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
6 Reads
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
15 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
16 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
3 Reads

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

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
7 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
6 Reads

Ultralong 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, Groningen, The Netherlands.

Telomere length (TL) is increasingly being 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, while terminal telomeres have been divided in shorter (Class II) telomeres and ultralong (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
2 Reads

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, 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 demography to be taken 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
1 Read

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
1 Read

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, 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
1 Read

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
1 Read

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
28 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, China.

Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500 million/year. 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
25 Reads

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

Mol Ecol Resour 2019 Mar;19(2):426-438

Department of Anatomy, University of Otago, Dunedin, 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
March 2019
1 Read

A versatile Rapture (RAD-Capture) platform for genotyping marine turtles.

Mol Ecol Resour 2019 Mar;19(2):497-511

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

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

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.

OD Taxonomy and Phylogeny - JEMU, Royal Belgian Institute of Natural Sciences, 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
3 Reads

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

Mol Ecol Resour 2019 Mar 6;19(2):411-425. Epub 2019 Feb 6.

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
March 2019
1 Read

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

Mol Ecol Resour 2019 Mar 6;19(2):536-551. Epub 2019 Feb 6.

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
March 2019
2 Reads

Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea.

Mol Ecol Resour 2019 Mar;19(2):526-535

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
March 2019
20 Reads

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

Mol Ecol Resour 2019 Mar 6;19(2):512-525. Epub 2019 Feb 6.

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
March 2019
3 Reads

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

Mol Ecol Resour 2019 Mar 21;19(2):552-566. Epub 2019 Feb 21.

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393187PMC

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

Mol Ecol Resour 2019 Mar;19(2):439-455

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 submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. Read More

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