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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/28695665/analysis-of-large-16s-rrna-illumina-datasets-impact-of-singleton-read-filtering-on-microbial-community-description
#1
Lucas Auer, Mahendra Mariadassou, Michael O'Donohue, Christophe Klopp, Guillermina Hernandez-Raquet
Next generation sequencing technologies give access to large sets of data which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large datasets is not only marred by technical biases and sequencing noise but also increases computation time and disk space use. To improve the accuracy of OTUs predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise...
July 11, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28681534/generalization-of-the-qst-framework-in-hierarchically-structured-populations-impacts-of-inbreeding-and-dominance
#2
Philippe Cubry, Ivan Scotti, Sylvie Oddou-Muratorio, François Lefèvre
QST is a differentiation parameter based on the decomposition of the genetic variance of a trait. In the case of additive inheritance and absence of selection, it is analogous to the genic differentiation measured on individual loci, FST . Thus, QST  - FST comparison is used to infer selection: selective divergence when QST  > FST , or convergence when QST  < FST. The definition of Q-statistics was extended to two-levels hierarchical population structures with Hardy-Weinberg equilibrium. Here, we generalize the Q-statistics framework to any hierarchical population structure...
July 6, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28675688/whole-mitochondrial-genome-capture-from-fecal-samples-and-museum-preserved-specimens
#3
Tom van der Valk, Frida Lona Durazo, Love Dalén, Katerina Guschanski
Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of non-invasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 non-invasively collected fecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee...
July 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28662317/clonestimate-a-bayesian-method-for-quantifying-rates-of-clonality-of-populations-genotyped-at-two-time-steps
#4
Ronan Becheler, Jean-Pierre Masson, Sophie Arnaud-Haond, Fabien Halkett, Stéphanie Mariette, Marie-Laure Guillemin, Myriam Valero, Christophe Destombe, Solenn Stoeckel
Partial clonality is commonly used in Eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal versus sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent populations, using an extended Wright-Fisher model explicitly integrating reproductive modes...
June 29, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28654208/inferring-past-demographic-changes-from-contemporary-genetic-data-a-simulation-based-evaluation-of-the-abc-methods-implemented-in-diyabc
#5
Andrea A Cabrera, Per J Palsbøll
Inferring the demographic history of species and their populations is crucial to understand their contemporary distribution, abundance, and adaptations. The high computational overhead of likelihood-based inference approaches severely restricts their applicability to large data sets or complex models. In response to these restrictions, Approximate Bayesian Computation (ABC) methods have been developed to infer the demographic past of populations and species. Here we present the results of an evaluation of the ABC-based approach implemented in the popular software package DIYABC using simulated data sets (mitochondrial DNA sequences, microsatellite genotypes and single nucleotide polymorphisms)...
June 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28654194/ecogenetics-an-r-package-for-the-management-and-exploratory-analysis-of-spatial-data-in-landscape-genetics
#6
Leandro G Roser, Laura I Ferreyra, Beatriz O Saidman, Juan César Vilardi
The integration of ecology and genetics has become established in recent decades, in hand with the development of new technologies, whose implementation is allowing an improvement of the tools used for data analysis. In a landscape genetics context, integrative management of population information from different sources can make spatial studies involving phenotypic, genotypic and environmental data simpler, more accessible and faster. Tools for exploratory analysis of autocorrelation can help to uncover the spatial genetic structure of populations and generate appropriate hypotheses in searching for possible causes and consequences of their spatial processes...
June 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28649779/an-integrated-framework-to-identify-wildlife-populations-under-threat-from-climate-change
#7
Orly Razgour, John B Taggart, Stephanie Manel, Javier Juste, Carlos Ibáñez, Hugo Rebelo, Antton Alberdi, Gareth Jones, Kirsty Park
Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential. We consider intraspecific vulnerability and population-level responses, an important but often neglected conservation research priority...
June 26, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28649712/cross-platform-compatibility-of-de-novo-aligned-snps-in-a-non-model-butterfly-genus
#8
Erin O Campbell, Corey S Davis, Julian R Dupuis, Kevin Muirhead, Felix A H Sperling
High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in non-model systems. Using double-digest restriction site associated DNA sequencing, we sequenced a common set of 22 specimens from the butterfly genus Speyeria on two different Illumina platforms, using two variations of library preparation...
June 26, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28603873/environmental-dna-enables-detection-of-terrestrial-mammals-from-forest-pond-water
#9
Masayuki Ushio, Hisato Fukuda, Toshiki Inoue, Kobayashi Makoto, Osamu Kishida, Keiichi Sato, Koichi Murata, Masato Nikaido, Tetsuya Sado, Yukuto Sato, Masamichi Takeshita, Wataru Iwasaki, Hiroki Yamanaka, Michio Kondoh, Masaki Miya
Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues...
June 11, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28544559/pipecraft-flexible-open-source-toolkit-for-bioinformatics-analysis-of-custom-high-throughput-amplicon-sequencing-data
#10
Sten Anslan, Mohammad Bahram, Indrek Hiiesalu, Leho Tedersoo
High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analyzed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user friendly graphical interface that links several public tools for analyzing amplicon sequencing data...
May 25, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28503747/friends-and-family-a-software-program-for-identification-of-unrelated-individuals-from-molecular-marker-data
#11
Deon de Jager, Petrus Swarts, Cindy Harper, Paulette Bloomer
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations...
May 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28488798/a-comparison-of-sedimentary-dna-and-pollen-from-lake-sediments-in-recording-vegetation-composition-at-the-siberian-treeline
#12
Bastian Niemeyer, Laura S Epp, Kathleen R Stoof-Leichsenring, Luidmila A Pestryakova, Ulrike Herzschuh
Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes...
May 10, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28477337/comparative-analysis-of-dna-extraction-methods-to-study-the-body-surface-microbiota-of-insects-a-case-study-with%C3%A2-ant-cuticular-bacteria
#13
Caroline Birer, Niklas Tysklind, Lucie Zinger, Christophe Duplais
High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behavior of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties to working with low bacterial DNA quantities as in individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm)...
May 6, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449359/transcriptomic-responses-of-solanum-dulcamara-to-natural-and-simulated-herbivory
#14
Tobias Lortzing, Vivien Firtzlaff, Duy Nguyen, Ivo Rieu, Sandra Stelzer, Martina Schad, Jim Kallarackal, Anke Steppuhn
Plants are attacked by diverse herbivores and respond with manifold defense responses. To study transcriptional and other early regulation events of these plant responses, herbivory is often simulated to standardize the temporal and spatial dynamics that vary tremendously for natural herbivory. Yet to what extent such simulations of herbivory are able to elicit the same plant response as real herbivory remains largely undetermined. We examined the transcriptional response of a wild model plant to herbivory by lepidopteran larvae and to a commonly used herbivory simulation by applying the larvae's oral secretions to standardized wounds...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449317/a-comparison-of-individual-based-genetic-distance-metrics-for-landscape-genetics
#15
A J Shirk, E L Landguth, S A Cushman
A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between pairwise genetic distances and landscape distances among sampled individuals in a population...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449274/a-dna-barcode-library-for-germany-s-mayflies-stoneflies-and-caddisflies-ephemeroptera-plecoptera-trichoptera
#16
Jérôme Morinière, Lars Hendrich, Michael Balke, Arne J Beermann, Tobias König, Monika Hess, Stefan Koch, Reinhard Müller, Florian Leese, Paul D N Hebert, Axel Hausmann, Christoph F Schubart, Gerhard Haszprunar
Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. However, a comprehensive DNA barcode library based upon taxonomically well-curated specimens can overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient, and reliable DNA-based identifications and assessments of ecological status...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449263/multi-dice-r-package-for-comparative-population-genomic-inference-under-hierarchical-co-demographic-models-of-independent-single-population-size-changes
#17
Alexander T Xue, Michael J Hickerson
Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis while benefiting in statistical power from aggregating datasets. This approach has been applied to classical phylogeographic datasets such as mitochondrial barcodes as well as reduced-genome polymorphism datasets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449215/rapid-degradation-of-longer-dna-fragments-enables-the-improved-estimation-of-distribution-and-biomass-using-environmental-dna
#18
Toshiaki Jo, Hiroaki Murakami, Reiji Masuda, Masayuki Sakata, Satoshi Yamamoto, Toshifumi Minamoto
The advent of environmental DNA (eDNA) analysis methods has enabled rapid and wide-range ecological monitoring in aquatic ecosystems, but there is a dearth of information on eDNA degradation. The results of previous studies suggest that the decay rate of eDNA varies depending on the length of DNA fragments. To examine this hypothesis, we compared temporal change in copy number of long eDNA fragments (719 bp) with that of short eDNA fragments (127 bp). First, we isolated rearing water from a target fish species, Japanese Jack Mackerel (Trachurus japonicus), and then quantified the copy number of the long and short eDNA fragments in 1 L water samples after isolating the water from the fish...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28613017/small-and-large-scale-heterogeneity-in-genetic-variation-across-the-collard-flycatcher-genome-implications-for-estimating-genetic-diversity-in-nonmodel-organisms
#19
Pär K Ingvarsson, Jing Wang
Population genetic studies in nonmodel organisms are often hampered by a lack of reference genomes that are essential for whole-genome resequencing. In the light of this, genotyping methods have been developed to effectively eliminate the need for a reference genome, such as genotyping by sequencing or restriction site-associated DNA sequencing (RAD-seq). However, what remains relatively poorly studied is how accurately these methods capture both average and variation in genetic diversity across an organism's genome...
July 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28497651/harnessing-the-power-of-digital-droplet-pcr-to-conduct-real-world-microbial-competitions
#20
Helen A Murphy
The budding yeast, Saccharomyces cerevisiae, has a long and storied history as a model organism for genetic, cellular and molecular biological research. More recently, researchers have sought to understand the ecology and evolution of its sister species, Saccharomyces paradoxus, in part to put our vast knowledge of the model yeast into its natural context (Replansky et al. ). However, the research tools have been limited, and most investigations into natural populations have either been descriptions of patterns of biogeography or taken the organism back into the laboratory for mating, growth and competition assays (Kuehne et al...
May 2017: Molecular Ecology Resources
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