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Molecular Ecology Resources

Anders Bjørnsgaard Aas, Marie Louise Davey, Håvard Kauserud
The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance...
October 24, 2016: Molecular Ecology Resources
James Starrett, Shahan Derkarabetian, Marshal Hedin, Robert W Bryson, John E McCormack, Brant C Faircloth
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress...
October 21, 2016: Molecular Ecology Resources
Abdolbaset Ghorbani, Barbara Gravendeel, Sugirthini Selliah, Shahin Zarré, Hugo de Boer
Tubers of terrestrial orchids are harvested and traded from the eastern Mediterranean to the Caspian Sea for the traditional product Salep. Over-exploitation of wild populations and increased middle-class prosperity have escalated prices for Salep, causing overharvesting, depletion of native populations and providing an incentive to expand harvesting to untapped areas in Iran. Limited morphological distinctiveness among traded Salep tubers renders species identification impossible, making it difficult to establish which species are targeted and affected the most...
October 21, 2016: Molecular Ecology Resources
Stefan Schmidt, Andreas Taeger, Jérôme Morinière, Andrew Liston, Stephan M Blank, Katja Kramp, Manfred Kraus, Olga Schmidt, Erik Heibo, Marko Prous, Tommi Nyman, Tobias Malm, Julie Stahlhut
The 'Symphyta' is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8,750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5,360 specimens of 'Symphyta', mainly adults, and 4,362 sequences covering 1,037 species were deemed of suitable quality for inclusion in the analysis. All extant families are represented, except for the Anaxyelidae. The majority of species and specimens are from Europe, but approximately 38% of the species and 13% of the specimens are of non-European origin...
October 21, 2016: Molecular Ecology Resources
Jean-Rene Arseneau, Royce Steeves, Mark Laflamme
The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that co-precipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often co-precipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle...
October 21, 2016: Molecular Ecology Resources
Brent C Emerson, Juliane Casquet, Heriberto López, Pedro Cardoso, Paulo A V Borges, Noémy Mollaret, Pedro Oromí, Dominique Strasberg, Christophe Thébaud
Obtaining fundamental biodiversity metrics such as alpha, beta and gamma diversity for arthropods is often complicated by a lack of prior taxonomic information and/or taxonomic expertise, which can result in unreliable morphologically based estimates. We provide a set of standardized ecological and molecular sampling protocols that can be employed by researchers whose taxonomic skills may be limited, and where there may be a lack of robust a priori information regarding the regional pool of species. These protocols combine mass sampling of arthropods, classification of samples into parataxonomic units (PUs), and selective sampling of individuals for mtDNA sequencing to infer biological species...
October 21, 2016: Molecular Ecology Resources
Anna J MacDonald, Stephen D Sarre
Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates non-invasive ecological studies, but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity, and utility...
October 21, 2016: Molecular Ecology Resources
Lauren M Schiebelhut, Sarah S Abboud, Liza E Gómez Daglio, Holly F Swift, Michael N Dawson
The inclusion of next-generation sequencing technologies in population genetic and phylogenetic studies has elevated the need to balance time and cost of DNA extraction without compromising DNA quality. We tested eight extraction methods - ranging from low- to high-throughput techniques - and eight phyla: Annelida, Arthropoda, Cnidaria, Chordata, Echinodermata, Mollusca, Ochrophyta, and Porifera. We assessed DNA yield, purity, efficacy, and cost of each method. Extraction efficacy was quantified using the proportion of successful polymerase chain reaction (PCR) amplification of two molecular markers for metazoans (mitochondrial COI and nuclear Histone 3) and one for Ochrophyta (mitochondrial nad6) at four time points - 0...
October 21, 2016: Molecular Ecology Resources
Margaret E Hunter, Robert M Dorazio, John S S Butterfield, Gaia Meigs-Friend, Leo G Nico, Jason A Ferrante
A set of universal guidelines is needed to determine the limit of detection (LOD) in PCR-based analyses of low concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjective, possibly resulting in biased estimates of species' presence. Here, a conservative LOD analysis grounded in analytical chemistry is proposed to correct for overestimated DNA concentrations predominantly caused by the concentration plateau, a nonlinear relationship between expected and measured DNA concentrations...
October 21, 2016: Molecular Ecology Resources
Garrett J McKinney, Ryan K Waples, Lisa W Seeb, James E Seeb
Whole genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians, resulting in a pervasiveness of paralogous loci and the potential for both disomic and tetrasomic inheritance in the same genome. Paralogs can be difficult to reliably genotype and are often excluded from genotyping-by-sequencing (GBS) analyses; however, removal requires paralogs to be identified which is difficult without a reference genome. We present a method for identifying paralogs in natural populations by combining two properties of duplicated loci: 1) the expected frequency of heterozygotes exceeds that for singleton loci, and 2) within heterozygotes, observed read ratios for each allele in GBS data will deviate from the 1:1 expected for singleton (diploid) loci...
October 19, 2016: Molecular Ecology Resources
Fátima Sánchez Barreiro, Filipe G Vieira, Michael D Martin, James Haile, M Thomas P Gilbert, Nathan Wales
Population genetic studies of non-model organisms frequently employ reduced representation library (RRL) methodologies, many of which rely on protocols in which genomic DNA is digested by one or more restriction enzymes. However, because high molecular weight DNA is recommended for these protocols, samples with degraded DNA are generally unsuitable for RRL methods. Given that ancient and historic specimens can provide key temporal perspectives to evolutionary questions, we explored how custom-designed RNA probes could enrich for RRL loci (Restriction Enzyme-Associated Loci baits, or REALbaits)...
October 19, 2016: Molecular Ecology Resources
Aleksandra Biedrzycka, Alvaro Sebastian, Magdalena Migalska, Helena Westerdahl, Jacek Radwan
Characterisation of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated dataset, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches...
October 19, 2016: Molecular Ecology Resources
Jonathan Sandoval-Castillo, Catherine R M Attard, Shashikanth Marri, Chris J Brauer, Luciana M Möller, Luciano B Beheregaray
Captive breeding programs are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programs have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group-breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding...
October 18, 2016: Molecular Ecology Resources
Scott A Pavey, Martin Laporte, Eric Normandeau, Jérémy Gaudin, Louis Letourneau, Sébastien Boisvert, Jacques Corbeil, Céline Audet, Louis Bernatchez
Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American Eel. This genome contained 305,043 contigs (N50 = 7,397) and 79,209 scaffolds (N50 = 86,641) for a total size of 1...
October 18, 2016: Molecular Ecology Resources
Christian M Parobek, Frederick I Archer, Michelle E DePrenger-Levin, Sean M Hoban, Libby Liggins, Allan E Strand
Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier, and a steep conceptual learning curve...
October 13, 2016: Molecular Ecology Resources
Shenglin Liu, Michael M Hansen
The Pairwise Sequentially Markovian Coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole genome data, we here use simulations to investigate its applicability to reference genome aligned RAD (Restriction site Associated DNA) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of the genome that the RAD data covers...
October 8, 2016: Molecular Ecology Resources
Sanna Olsson, Pedro Seoane Zonjic, Rocío Bautista, M Gonzalo Claros, Santiago C González-Martínez, Ivan Scotti, Caroline Scotti-Saintagne, Olivier J Hardy, Myriam Heuertz
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L. f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1...
October 8, 2016: Molecular Ecology Resources
Roman V Briskine, Timothy Paape, Rie Shimizu-Inatsugi, Tomoaki Nishiyama, Satoru Akama, Jun Sese, Kentaro K Shimizu
The self-incompatible species Arabidopsis halleri is a close relative of the self-compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability makes A. halleri a useful model for ecological genomics studies.We used long-insert mate-pair libraries to improve the genome assembly of the A. halleri ssp.gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0...
September 27, 2016: Molecular Ecology Resources
Adrien Rieux, Camilo E Khatchikian
Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions...
September 26, 2016: Molecular Ecology Resources
Chia-Hao Chang, Kwang-Tsao Shao, Han-Yang Lin, Yung-Chieh Chiu, Mao-Ying Lee, Shih-Hui Liu, Pai-Lei Lin
Species identification based on the DNA sequence of a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome, DNA barcoding, is widely applied to assist in sustainable exploitation of fish resources and the protection of fish biodiversity. The aim of this study was to establish a reliable barcoding reference database of the native ray-finned fishes in Taiwan. A total of 2,993 individuals, belonging to 1,245 species within 637 genera, 184 families, and 29 orders of ray-finned fishes and representing approximately 40% of the recorded ray-finned fishes in Taiwan, were PCR amplified at the barcode region and bidirectionally sequenced...
September 26, 2016: Molecular Ecology Resources
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