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Molecular Ecology Resources

Igor J Chybicki
This paper introduces the NMπ computer program designed for estimation of plant mating system and seed and pollen dispersal kernels. NMπ is a re-implementation of the NM+ program and provides new features such as support for multi-core processors, explicit treatment of dioecy, the possibility of incorporating uniparentally cytoplasmic markers, the possibility of assessing assortative mating due to phenotypic similarity and inference about offspring genealogies. The probability model of parentage (the neighborhood model) accounts for missing data and genotyping errors, which can be estimated along with regular parameters of the mating system...
August 14, 2017: Molecular Ecology Resources
Justin R Eastwood, Ellis Mulder, Simon Verhulst, Anne Peters
Since attrition of telomeres, DNA caps that protect chromosome integrity, is accelerated by various forms of stress, telomere length (TL) has been proposed as an indicator of lifetime accumulated stress. In ecological studies it has been used to provide insights into aging, life-history trade-offs, the costs of reproduction and disease. qPCR is a high throughput and cost effective tool to measure relative TL (rTL) that can be applied to newly-collected and archived ecological samples. However, qPCR is susceptible to error both from the method itself and pre-analytical steps...
August 14, 2017: Molecular Ecology Resources
A J Shirk, E L Landguth, S A Cushman
Anthropogenic migration barriers fragment many populations and limit the ability of species to respond to climate-induced biome shifts. Conservation actions designed to conserve habitat connectivity and mitigate barriers are needed to unite fragmented populations into larger, more viable metapopulations, and to allow species to track their climate envelope over time. Landscape genetic analysis provides an empirical means to infer landscape factors influencing gene flow, and thereby inform such conservation actions...
August 10, 2017: Molecular Ecology Resources
Francisco Pina-Martins, Diogo N Silva, Joana Fino, Octávio S Paulo
Structure_threader is a program to parallelize multiple runs of genetic clustering software that does not make use of multi-threading technology (structure, fastStructure and MavericK) on multi-core computers. Our approach was benchmarked across multiple systems and displayed great speed improvements relative to the single threaded implementation, scaling very close to linearly with the number of physical cores used. Structure_threader was compared to previous software written for the same task - ParallelStructure and StrAuto, and was proven to be the faster (up to 25% faster) wrapper under all tested scenarios...
August 4, 2017: Molecular Ecology Resources
Andrew P A Oxley, Sarah R Catalano, Melissa L Wos-Oxley, Emma L Westlake, Gretchen L Grammer, Mike A Steer
The capacity to reliably identify fish eggs is critical in the application of the daily egg production method (DEPM) to estimate biomass of commercially important species. This application has largely been confined to species that have easily identifiable eggs. Various molecular strategies have been used to extend the DEPM to a broader range of species, with recent approaches like in situ hybridisation (ISH) that preserves the integrity of whole eggs, embryos, or larvae recommended as a suitable alternative over destructive procedures like PCR...
August 4, 2017: Molecular Ecology Resources
Jinliang Wang
Many molecular ecology analyses assume the genotyped individuals are sampled at random from a population and thus are representative of the population. Realistically, however, a sample may contain excessive close relatives (ECR) because, for example, localized juveniles are drawn from fecund species. Our knowledge is limited about how ECR affect the routinely conducted elementary genetics analyses, and how ECR are best dealt with to yield unbiased and accurate parameter estimates. This study quantifies the effects of ECR on some popular population genetics analyses of marker data, including the estimation of allele frequencies, F-statistics, expected heterozygosity (He ), effective and observed numbers of alleles, and the tests of Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE)...
August 4, 2017: Molecular Ecology Resources
Bettina Thalinger, Johannes Oehm, Armin Obwexer, Michael Traugott
Molecular methods allow non-invasive assessment of vertebrate predator-prey systems at high taxonomic resolution by examining dietary samples such as faeces and pellets. To facilitate the interpretation of field-derived data, feeding trials, investigating the impacts of biological, methodological, and environmental factors on prey DNA detection have been conducted. The effect of meal size, however, has not yet been explicitly considered for vertebrate consumers. Moreover, different non-invasively obtained sample types remain to be compared in such experiments...
August 4, 2017: Molecular Ecology Resources
Emmanuel Corse, Emese Meglécz, Gaït Archambaud, Morgane Ardisson, Jean-François Martin, Christelle Tougard, Rémi Chappaz, Vincent Dubut
The main objective of this work was to develop and validate a robust and reliable 'from benchtop-to-desktop' metabarcoding workflow to investigate the diet of invertebrate-eaters. We applied our workflow to fecal DNA samples of an invertebrate-eating fish species. A fragment of the COI gene was amplified by combining two minibarcoding primer sets to maximize the taxonomic coverage. Amplicons were sequenced by an Illumina MiSeq platform. We developed a filtering approach based on a series of non-arbitrary thresholds established from control samples and from molecular replicates in order to address the elimination of cross-contamination, PCR/sequencing errors and mistagging artifacts...
August 4, 2017: Molecular Ecology Resources
Kaitlyn M Gaynor, Joseph W Solomon, Stefanie Siller, Linnet Jessell, J Emmett Duffy, Dustin R Rubenstein
Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication...
August 4, 2017: Molecular Ecology Resources
Brendan F Wringe, Ryan R E Stanley, Nicholas W Jeffery, Eric C Anderson, Ian R Bradbury
The ability to detect and characterize hybridization in nature has long been of interest to many fields of biology and often has direct implications for wildlife management and conservation. The capacity to identify the presence of hybridization, and quantify the numbers of individuals belonging to different hybrid classes, permits inference on the magnitude of, and time scale over which, hybridization has been, or is occurring. Here we present an R package and associated workflow developed for the detection, with estimates of efficiency and accuracy, of multi-generational hybrid individuals using genetic or genomic data in conjunction with the program NEWHYBRIDS...
August 4, 2017: Molecular Ecology Resources
Torrey W Rodgers, Charles C Y Xu, Jacalyn Giacalone, Karen M Kapheim, Kristin Saltonstall, Marta Vargas, Douglas W Yu, Panu Somervuo, W Owen McMillan, Patrick A Jansen
Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq...
July 31, 2017: Molecular Ecology Resources
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 data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU 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
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-level 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
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 noninvasively 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 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee...
July 4, 2017: Molecular Ecology Resources
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
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
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
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
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
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
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