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Molecular Ecology Resources

Robert Lehmann, Damien J Lightfoot, Celia Schunter, Craig T Michell, Hajime Ohyanagi, Katsuhiko Mineta, Sylvain Foret, Michael L Berumen, David J Miller, Manuel Aranda, Takashi Gojobori, Philip L Munday, Timothy Ravasi
The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification...
September 10, 2018: Molecular Ecology Resources
D C Blower, C Riginos, J R Ovenden
Molecular genetic estimates of population effective size (Ne ) lose accuracy and precision when insufficient numbers of samples or loci are used. Ideally researchers would like to forecast the necessary power when planning their project. NeOGen (genetic Ne for Overlapping Generations) enables estimates of precision and accuracy in advance of empirical investigation and allows exploration of the power available in different user-specified age-structured sampling schemes. NeOGen provides a population simulation and genetic power analysis framework that simulates the demographics, genetic composition, and Ne , from species-specific life-history, mortality, population size, and genetic priors...
September 7, 2018: Molecular Ecology Resources
Miklós Bálint, Carsten Nowak, Orsolya Márton, Steffen U Pauls, Claudia Wittwer, José Luis Aramayo, Arne Schulze, Thierry Chambert, Berardino Cocchiararo, Martin Jansen
Rapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programmes. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g., the use of different microhabitats by different species and life stages)...
August 29, 2018: Molecular Ecology Resources
Jan-Niklas Macher, Aurelién Vivancos, Jeremy J Piggott, Fernanda C Centeno, Christoph D Matthaei, Florian Leese
Freshwater biodiversity provides important ecosystem services and is at the core of water quality monitoring worldwide. To assess freshwater biodiversity, genetic methods such as metabarcoding are increasingly used as they are faster and allow better taxonomic resolution than manual identification methods. Either sampled organisms are used directly for "bulk metabarcoding," or water is filtered and the extracted environmental DNA serves as a proxy for biodiversity via "eDNA metabarcoding." Despite the advantages of both methods, questions remain regarding their comparability and applicability for routine biomonitoring and stressor impact assessment...
August 21, 2018: Molecular Ecology Resources
Miriam Schalamun, Ramawatar Nagar, David Kainer, Eleanor Beavan, David Eccles, John P Rathjen, Robert Lanfear, Benjamin Schwessinger
Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realising their full potential is critically reliant on extracting high quality, high molecular weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time consuming and costly...
August 17, 2018: Molecular Ecology Resources
Felix Heeger, Elizabeth C Bourne, Christiane Baschien, Andrey Yurkov, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Camila J Mazzoni, Michael T Monaghan
DNA metabarcoding is widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints limit most studies to marker lengths below 600 base pairs (bp). Longer sequencing reads of several thousand bp are now possible with third-generation sequencing. Increased marker lengths provide greater taxonomic resolution and allow for phylogenetic methods of classification, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most bioinformatics tools for DNA metabarcoding were designed for short reads and are therefore unsuitable...
August 14, 2018: Molecular Ecology Resources
Shengchen Shan, Evgeny V Mavrodiev, Riqing Li, Zhengzhi Zhang, Bernard A Hauser, Pamela S Soltis, Douglas E Soltis, Bing Yang
Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing site-specific mutations in Tragopogon protoplasts...
August 7, 2018: Molecular Ecology Resources
Valentina Peona, Matthias H Weissensteiner, Alexander Suh
The genomics revolution has led to the sequencing of a large variety of nonmodel organisms often referred to as "whole" or "complete" genome assemblies. But how complete are these, really? Here, we use birds as an example for nonmodel vertebrates and find that, although suitable in principle for genomic studies, the current standard of short-read assemblies misses a significant proportion of the expected genome size (7% to 42%; mean 20 ± 9%). In particular, regions with strongly deviating nucleotide composition (e...
July 23, 2018: Molecular Ecology Resources
Marijke Autenrieth, Stefanie Hartmann, Ljerka Lah, Anna Roos, Alice B Dennis, Ralph Tiedemann
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2...
July 23, 2018: Molecular Ecology Resources
Carolyn A Wessinger, John K Kelly, Peng Jiang, Mark D Rausher, Lena C Hileman
Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to nonmodel species has been generating dense genome-wide markers that satisfy the key requirement that marker data are error-free. Here, we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. This "SNP-skimming" approach involves two steps: an initial genome-wide scan to identify putative targets followed by deep sequencing for confirmation of targeted loci...
July 23, 2018: Molecular Ecology Resources
Tristan Cordier, Dominik Forster, Yoann Dufresne, Catarina I M Martins, Thorsten Stoeck, Jan Pawlowski
Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations of the traditional morphotaxonomy-based bioassessment. Recently, we demonstrated that supervised machine learning (SML) can be used to predict accurate biotic indices values from eDNA metabarcoding data, regardless of the taxonomic affiliation of the sequences. However, it is unknown to which extent the accuracy of such models depends on taxonomic resolution of molecular markers or how SML compares with metabarcoding approaches targeting well-established bioindicator species...
July 17, 2018: Molecular Ecology Resources
Michal Drori, Anna Rice, Moshe Einhorn, Ofer Chay, Lior Glick, Itay Mayrose
Phylogeny reconstruction is a key instrument in numerous biological analyses, ranging from evolutionary and ecology research, to conservation and systems biology. The increasing accumulation of genomic data makes it possible to reconstruct phylogenies with both high accuracy and at increasingly finer resolution. Yet, taking advantage of the enormous amount of sequence data available requires the use of computational tools for efficient data retrieval and processing, or else the process could quickly become an error-prone endeavour...
July 16, 2018: Molecular Ecology Resources
Taylor M Wilcox, Katherine E Zarn, Maxine P Piggott, Michael K Young, Kevin S McKelvey, Michael K Schwartz
Environmental DNA (eDNA) sampling-the detection of genetic material in the environment to infer species presence-has rapidly grown as a tool for sampling aquatic animal communities. A potentially powerful feature of environmental sampling is that all taxa within the habitat shed DNA and so may be detectable, creating opportunity for whole-community assessments. However, animal DNA in the environment tends to be comparatively rare, making it necessary to enrich for genetic targets from focal taxa prior to sequencing...
July 16, 2018: Molecular Ecology Resources
Zhanshan Sam Ma, Lianwei Li
The first step of any metagenome sequencing project is to get the inventory of OTU abundances (operational taxonomic units) and/or metagenomic gene abundances. The former is generated with 16S-rRNA-tagged amplicon sequencing technology, and the latter can be generated from either gene-targeted or whole-sample shotgun metagenomics technologies. With 16S-rRNA data sets, measuring community diversity with diversity indexes such as species richness and Shannon's index has been a de facto standard analysis; nevertheless, similarly comprehensive approaches to metagenomic gene abundances are still largely missing, despite that both OTU and gene abundances are DNA reads...
July 9, 2018: Molecular Ecology Resources
Patrick G R Wright, Fiona Mathews, Henry Schofield, Colin Morris, Joe Burrage, Adam Smith, Emma L Dempster, Patrick B Hamilton
The age profile of populations fundamentally affects their conservation status. Yet, age is frequently difficult to assess in wild animals. Here, we assessed the use of DNA methylation of homologous genes to establish the age structure of a rare and elusive wild mammal: the Bechstein's bat (Myotis bechsteinii). We collected 62 wing punches from individuals whose ages were known as a result of a long-term banding study. DNA methylation was measured at seven CpG sites from three genes, which have previously shown age-associated changes in humans and laboratory mice...
July 7, 2018: Molecular Ecology Resources
Daniel W Förster, James K Bull, Dorina Lenz, Marijke Autenrieth, Johanna L A Paijmans, Robert H S Kraus, Carsten Nowak, Helmut Bayerl, Ralph Kuehn, Alexander P Saveljev, Magda Sindičić, Michael Hofreiter, Krzysztof Schmidt, Jörns Fickel
Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus)...
July 6, 2018: Molecular Ecology Resources
Wei Xiong, Aibin Zhan
The degradation of freshwater ecosystems has become a common ecological and environmental problem globally. Owing to the complexity of biological communities, there remain tremendous technical challenges for investigating influence of environmental stressors (e.g., chemical pollution) on biological communities. High-throughput sequencing-based metabarcoding provides a powerful tool to reveal complex interactions between environments and biological communities. Among many technical issues, the clustering strategies for operational taxonomic units (OTUs) which are crucial for assessing biodiversity of communities, may affect final conclusions...
July 6, 2018: Molecular Ecology Resources
Scott D Foster, Pierre Feutry, Peter M Grewe, Oliver Berry, Francis K C Hui, Campbell R Davies
Delineating naturally occurring and self-sustaining subpopulations (stocks) of a species is an important task, especially for species harvested from the wild. Despite its central importance to natural resource management, analytical methods used to delineate stocks are often, and increasingly, borrowed from superficially similar analytical tasks in human genetics even though models specifically for stock identification have been previously developed. Unfortunately, the analytical tasks in resource management and human genetics are not identical-questions about humans are typically aimed at inferring ancestry (often referred to as "admixture") rather than breeding stocks...
June 26, 2018: Molecular Ecology Resources
Huan Fan, Anthony R Ives, Yann Surget-Groba
Reduced-representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data...
June 25, 2018: Molecular Ecology Resources
Anna W Santure, Dany Garant
The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such "gene mapping" studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment...
July 2018: Molecular Ecology Resources
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