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Molecular Ecology Resources

Courtney N Passow, Thomas J Y Kono, Bethany A Stahl, James B Jaggard, Alex C Keene, Suzanne E McGaugh
RNA-sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer-term storage as it rapidly permeates tissue to protect cellular RNA...
November 17, 2018: Molecular Ecology Resources
Christian Schmid-Egger, Jakub Straka, Toshko Ljubomirov, Gergin A Blagoev, Jérôme Morinière, Stefan Schmidt
The apoid wasps have traditionally been regarded as a paraphyletic assemblage of four families (Ampulicidae, Crabronidae, Heterogynaidae and Sphecidae) that are closely related to the bees (Anthophila). The present study covers the three families of apoid wasps known to occur in Europe, i.e., the Ampulicidae, Crabronidae, and Sphecidae. DNA barcode sequences of 3,695 specimens of apoid wasps were analyzed for the present study, including 21 specimens of Ampulicidae, 3,398 Crabronidae, and 276 Sphecidae. The sequences of the dataset represent 661 species of apoid wasps, including two species of Ampulicidae, 613 of Crabronidae, and 46 species of Sphecidae...
November 15, 2018: Molecular Ecology Resources
Matthew H Van Dam, Michelle Trautwein, Greg Spicer, Lauren Esposito
Mites (Acari) are one of the most diverse groups of life on Earth, yet their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in-silico by constructing a phylogeny using 13 existing Acari genomes, as well as 6 additional taxa from a variety of genomic sources...
November 9, 2018: Molecular Ecology Resources
Yanjun Shen, Nicolas Hubert, Yan Huang, Xuzheng Wang, Xiaoni Gan, Zuogang Peng, Shunping He
Intensification of inland fisheries and aquatic landscape conversion led to a drastic decline of fish populations in the Yangtze River (YR) during the last decades. This situation urges for the development of a large-scale molecular assessment of YR ichthyofauna to further develop standardized methods of molecular identification for conservation and fisheries management purposes. We present here the results of a large-scale campaign to DNA barcode YR freshwater fishes that succeeded in producing 1,424 new DNA barcodes for 123 species...
October 30, 2018: Molecular Ecology Resources
Jean-Paul Soularue, Armel Thöni, Léo Arnoux, Valérie Le Corre, Antoine Kremer
Metapop is a stochastic individual-based simulation program. It uses quantitative genetics theory to produce an explicit description of the typical life cycle of monoecious and hermaphroditic plant species. Genome structure, the relationship between genotype and phenotype, and the effects of landscape heterogeneity on each individual can be finely parameterized by the user. Unlike most existing simulation packages, Metapop can simulate phenotypic plasticity, which may have a genetic component, and assortative mating, two important features of tree species...
October 25, 2018: Molecular Ecology Resources
Rémi Tournebize, Valérie Poncet, Mattias Jakobsson, Yves Vigouroux, Stéphanie Manel
Inferring the mode and tempo of natural selection helps further our understanding of adaptation to past environmental changes. Here we introduce McSwan, a method to detect and date past and recent natural selection events in the case of a hard sweep. The method is based on the comparison of site frequency spectra obtained under various demographic models that include selection. McSwan demonstrated high power (high sensitivity and specificity) in capturing hard selective sweep events without requiring haplotype phasing...
October 24, 2018: Molecular Ecology Resources
Leho Tedersoo, Rein Drenkhan, Sten Anslan, Carmen Morales-Rodriguez, Michelle Cleary
High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: 1) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host-associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; 2) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and 3) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology...
October 24, 2018: Molecular Ecology Resources
Antton Alberdi, Ostaizka Aizpurua, Kristine Bohmann, Shyam Gopalakrishnan, Christina Lynggaard, Martin Nielsen, M Thomas P Gilbert
The application of DNA sequencing-based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits of animals. Due to the high resolution and prey detection capacity they provide, both metabarcoding and shotgun sequencing are increasingly used to address ecological questions grounded in dietary relationships. Despite their great promise in this context, recent research has unveiled how a wealth of biological (related to the study system) and technical (related to the methodology) factors can distort the signal of taxonomic diversity...
October 24, 2018: Molecular Ecology Resources
Andjin Siegenthaler, Owen S Wangensteen, Ana Z Soto, Chiara Benvenuto, Laura Corrigan, Stefano Mariani
Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services, and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time are one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity...
October 24, 2018: Molecular Ecology Resources
Siv Nam Khang Hoff, Helle T Baalsrud, Ave Tooming-Klunderud, Morten Skage, Todd Richmond, Gregor Obernosterer, Reza Shirzadi, Ole Kristian Tørresen, Kjetill S Jakobsen, Sissel Jentoft
Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years...
October 17, 2018: Molecular Ecology Resources
Praveen Nadukkalam Ravindran, Paul Bentzen, Ian R Bradbury, Robert G Beiko
Restriction-site associated DNA sequencing (RADseq) is a powerful tool for genotyping of individuals, but the identification of loci and assignment of sequence reads is a crucial and often challenging step. The optimal parameter settings for a given de novo RADseq assembly varies between datasets and can be difficult and computationally expensive to determine. Here we introduce RADProc, a software package that uses a graph data structure to represent all sequence reads and their similarity relationships. Storing sequence-comparison results in a graph eliminates unnecessary and redundant sequence-similarity calculations...
October 12, 2018: Molecular Ecology Resources
C S Stobie, M J Cunningham, C J Oosthuizen, P Bloomer
Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years, however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy Next-Generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many Single Nucleotide Polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses...
October 12, 2018: Molecular Ecology Resources
Castrense Savojardo, Andrea Luchetti, Pier Luigi Martelli, Rita Casadio, Barbara Mantovani
Crustaceans of the order Notostraca (Branchiopoda) are distributed worldwide and are known for the remarkable morphological stasis between their extant and Permian fossil species. Moreover, these crustaceans show relevant ecological traits and a wide range of reproductive strategies. However, genomic studies on notostracans are fairly limited. Here, we present the genome sequences of two notostracan taxa, Lepidurus arcticus and Lepidurus apus lubbocki. Taking advantage of the small genome sizes (~0.11 pg) of these taxa, genomes were sequenced for one individual per species with one run on the Illumina HiSeq X platform...
October 4, 2018: Molecular Ecology Resources
Michelle A Jusino, Mark T Banik, Jonathan M Palmer, Amy K Wray, Lei Xiao, Emma Pelton, Jesse R Barber, Akito Y Kawahara, Claudio Gratton, M Zachariah Peery, Daniel L Lindner
DNA analysis of predator feces using high-throughput amplicon sequencing (HTS) enhances our understanding of predator-prey interactions. However, conclusions drawn from this technique are constrained by biases that occur in multiple steps of the HTS workflow. To better characterize insectivorous animal diets, we used DNA from a diverse set of arthropods to assess PCR biases of commonly used and novel primer pairs for the mitochondrial gene, cytochrome oxidase C subunit 1 (COI). We compared diversity recovered from HTS of bat guano samples using a commonly used primer pair "ZBJ" to results using the novel primer pair "ANML"...
October 3, 2018: Molecular Ecology Resources
Wentao Chen, Gentile Francesco Ficetola
Site occupancy-detection models (SODMs) are statistical models widely used for biodiversity surveys where imperfect detection of species occurs. For instance, SODMs are increasingly used to analyse environmental DNA (eDNA) data, taking into account the occurrence of both false-positive and false-negative errors. However, species occurrence data are often characterized by spatial and temporal autocorrelation, which might challenge the use of standard SODMs. Here we reviewed the literature of eDNA biodiversity surveys and found that most of studies do not take into account spatial or temporal autocorrelation...
September 29, 2018: Molecular Ecology Resources
Samantha Hauser, Kristin Wakeland, Paul Leberg
Studies of genetic population structure often involve numerous tests of Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD) and genetic differentiation. Tests of HWE or LD are important precursors to population structure assessments. When conducting multiple related statistical tests, type I error increases, e.g., familywise error rate (FWER) inflation. FWER inflation can alter the results of statistical tests and thus the conclusions. We surveyed literature from 2011 to 2013 to determine if studies of population structure assess LD and HWE and if FWER corrections were applied consistently across different types of tests...
September 28, 2018: Molecular Ecology Resources
Tomasz Suchan, Gerard Talavera, Llorenç Sáez, Michał Ronikier, Roger Vila
Insects account for a large portion of Earth's biodiversity and are key players for ecosystems, notably as pollinators. While insect migration is suspected to represent a natural phenomenon of major importance, remarkably little is known about it, except for a few flagship species. The reason for this situation is mainly due to technical limitations in the study of insect movement. Here we propose using metabarcoding of pollen carried by insects as a method for tracking their migrations. We developed a flexible and simple protocol allowing efficient multiplexing and not requiring DNA extraction, one of the most time consuming part of metabarcoding protocols, and apply this method to the study of the long-distance migration of the butterfly Vanessa cardui, an emerging model for insect migration...
September 28, 2018: Molecular Ecology Resources
Christian Wurzbacher, Ellen Larsson, Johan Bengtsson-Palme, Silke Van den Wyngaert, Sten Svantesson, Erik Kristiansson, Maiko Kagami, R Henrik Nilsson
Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats...
September 21, 2018: Molecular Ecology Resources
Marylaure de La Harpe, Jaqueline Hess, Oriane Loiseau, Nicolas Salamin, Christian Lexer, Margot Paris
Understanding the genetics of biological diversification across micro- and macro-evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant family with high diversity in the tropics, studies of diversification at the population and species levels are still hampered by a lack of genomic markers suitable for the genotyping of large numbers of recently diverged taxa...
September 21, 2018: Molecular Ecology Resources
Laura M Bergner, Richard J Orton, Ana da Silva Filipe, Andrew E Shaw, Daniel J Becker, Carlos Tello, Roman Biek, Daniel G Streicker
Microbial communities play an important role in organismal and ecosystem health. While high throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses present and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities...
September 21, 2018: Molecular Ecology Resources
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