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Molecular Ecology Resources

Roberto Arrigoni, Benoît Vacherie, Francesca Benzoni, Fabrizio Stefani, Eric Karsenti, Olivier Jaillon, Fabrice Not, Flavia Nunes, Claude Payri, Patrick Wincker, Valérie Barbe
Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly-used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are largely adopted as barcode marker to investigate marine plankton community structure worldwide...
November 27, 2016: Molecular Ecology Resources
Lindsay V Clark, Andrea Drauch Schreier
A major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci...
November 21, 2016: Molecular Ecology Resources
Irene Muñoz, Dora Henriques, Laura Jara, J Spencer Johnston, Julio Chávez-Galarza, Pilar De La Rúa, M Alice Pinto
The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A. m. mellifera colonies...
November 14, 2016: Molecular Ecology Resources
O Hawlitschek, J Morinière, G U C Lehmann, A W Lehmann, M Kropf, A Dunz, F Glaw, M Detcharoen, S Schmidt, A Hausmann, N U Szucsich, S A Caetano-Wyler, G Haszprunar
We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life, and Swiss Barcode of Life. Our dataset includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. 93 of these 122 species (76.2%, including all Ensifera), can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes...
November 14, 2016: Molecular Ecology Resources
Emmanuel Paradis, Thierry Gosselin, Niklaus J Grünwald, Thibaut Jombart, Stéphanie Manel, Hilmar Lapp
As a scientific field, population genetics, despite its relatively young age, occupies a central place in biology. It was considered early on, well before the foundation of molecular genetics, as the way forward to solve the forces behind the evolution of species (Fisher 1930). Today, many pressing issues in understanding or predicting biological responses are investigated through population genetics approaches, for example the adaptation of populations of animals or plants facing human-mediated global changes such as habitat destruction or climate warming (Fordham et al...
November 14, 2016: Molecular Ecology Resources
David B Lowry, Sean Hoban, Joanna L Kelley, Katie E Lotterhos, Laura K Reed, Michael F Antolin, Andrew Storfer
Understanding how and why populations evolve is of fundamental importance to molecular ecology. RADseq (Restriction site-Associated DNA sequencing), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography, and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation...
November 12, 2016: Molecular Ecology Resources
Mathieu Gautier, Alexander Klassmann, Renaud Vitalis
Identifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding to natural or artificial positive selection. To that end, statistics measuring the extent of haplotype homozygosity within (e.g., EHH, iHS) and between (Rsb or XP-EHH) populations have been proposed in the literature. The REHH package for R was previously developed to facilitate genome-wide scans of selection, based on the analysis of long-range haplotypes. However, its performance was not sufficient to cope with the growing size of available data sets...
November 11, 2016: Molecular Ecology Resources
Jason G Bragg, Sally Potter, Ke Bi, Renee Catullo, Stephen C Donnellan, Mark D B Eldridge, Leo Joseph, J Scott Keogh, Paul Oliver, Kevin C Rowe, Craig Moritz
High throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci and we now know that many lineages also exhibit substantial cryptic diversity. Here, we present a set of phylogenetically diverse transcriptome resources to enable exon-based sequence capture studies of Australian vertebrates, including transcriptome sequences for 4 species of birds, 4 frogs, 7 lizards and 7 mammals...
November 8, 2016: Molecular Ecology Resources
Petri Kemppainen, Bernt Rønning, Thomas Kvalnes, Ingerid J Hagen, Thor-Harald Ringsby, Anna M Billing, Henrik Pärn, Sigbjørn Lien, Arild Husby, Bernt-Erik Saether, Henrik Jensen
Experimental evolution studies can be used to explore genomic response to artificial and natural selection. In such studies, loci that display larger allele frequency change than expected by genetic drift alone are assumed to be directly or indirectly associated with traits under selection. However, such studies report surprisingly many loci under selection, suggesting that current tests for allele frequency change may be subject to p-value inflation and hence be anti-conservative. One factor known from genome wide association (GWA) studies to cause p-value inflation is population stratification, such as relatedness among individuals...
November 4, 2016: Molecular Ecology Resources
Michael D Karcher, Julia A Palacios, Shiwei Lan, Vladimir N Minin
We introduce phylodyn, an r package for phylodynamic analysis based on gene genealogies. The package's main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes several Markov chain Monte Carlo-based methods and an integrated nested Laplace approximation-based approach for phylodynamic inference that have been developed in recent years. Genealogical data describe the timed ancestral relationships of individuals sampled from a population of interest...
November 1, 2016: Molecular Ecology Resources
S Stucki, P Orozco-terWengel, B R Forester, S Duruz, L Colli, C Masembe, R Negrini, E Landguth, M R Jones, M W Bruford, P Taberlet, S Joost
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics-i.e. the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present Samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental datasets...
November 1, 2016: Molecular Ecology Resources
Rodney T Richardson, Johan Bengtsson-Palme, Reed M Johnson
The taxonomic classification of DNA sequences has become a critical component of numerous ecological research applications; however, few studies have evaluated the strengths and weaknesses of commonly used sequence classification approaches. Further, the methods and software available for sequence classification are diverse, creating an environment in which it may be difficult to determine the best course of action and the trade-offs made using different classification approaches. Here, we provide an in silico evaluation of three DNA sequence classifiers, the rdp Naïve Bayesian Classifier, rtax and utax...
October 31, 2016: Molecular Ecology Resources
François Rousset, Alexandre Gouy, Camille Martinez-Almoyna, Alexandre Courtiol
In recent years, simulation methods such as approximate Bayesian computation have extensively been used to infer parameters of population genetic models where the likelihood is intractable. We describe an alternative approach, summary likelihood, that provides a likelihood-based analysis of the information retained in the summary statistics whose distribution is simulated. We provide an automated implementation as a standard R package, Infusion, and we test the method, in particular for a scenario of inference of population-size change from genetic data...
October 31, 2016: Molecular Ecology Resources
Akiko Sato Yashima, Hideki Innan
Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates...
October 31, 2016: Molecular Ecology Resources
Alan Brelsford, Guillaume Lavanchy, Roberto Sermier, Anna Rausch, Nicolas Perrin
We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on non-invasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered dataset (411,446 RADtags) was more successful than searches from a filtered dataset (33,073 RADtags) for markers showing sex differences in heterozygosity or in allele frequencies...
October 28, 2016: Molecular Ecology Resources
Sanne Boessenkool, Kristian Hanghøj, Heidi M Nistelberger, Clio Der Sarkissian, Agata Gondek, Ludovic Orlando, James H Barrett, Bastiaan Star
The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few percent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a pre-digestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal...
October 28, 2016: Molecular Ecology Resources
Alex D Twyford, Rob W Ness
Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly...
October 28, 2016: 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
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