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Molecular Ecology Resources

Yu-Long Li, Jin-Xian Liu
Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program STUCTURE has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (MedMedK, MedMeaK, MaxMedK, MaxMeaK) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data...
September 16, 2017: Molecular Ecology Resources
Helmut Bayerl, Robert H S Kraus, Carsten Nowak, Daniel W Foerster, Joerns Fickel, Ralph Kuehn
Biodiversity has suffered a dramatic global decline during the past decades and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and a genetic level. However, in wild species the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in non-model species by semi-deep sequencing of random amplicons...
September 15, 2017: Molecular Ecology Resources
Gang Hou, Wei-Tao Chen, Huo-Sheng Lu, Fei Cheng, Song-Guang Xie
DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2-parameter (K2P) distances within species, genera, and families were 0.31%, 8.71%, and 14.52%, respectively. A Neighbor-joining (NJ) tree, Bayesian inference (BI) and maximum-likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single-species-representing clusters, respectively. Barcoding Gap Analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95...
September 15, 2017: Molecular Ecology Resources
Song-Zhi Xu, Zhen-Yu Li, Xiao-Hua Jin
Invasive plants have aroused attention globally for causing ecological damage and having a negative impact on the economy and human health. However, it can be extremely challenging to rapidly and accurately identify invasive plants based on morphology because they are an assemblage of many different families and many plant materials lack sufficient diagnostic characteristics during border inspections. It is therefore urgent to evaluate candidate loci and build a reliable genetic library to prevent invasive plants from entering China...
September 2, 2017: Molecular Ecology Resources
Jesse R Lasky, Brenna R Forester, Matthew Reimherr
Local adaptation is often studied via 1) multiple common garden experiments comparing performance of genotypes in different environments and 2) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome-wide association model of genotype interactions with continuous environmental gradients (G×E), i...
September 1, 2017: Molecular Ecology Resources
Gregory L Owens, Marco Todesco, Emily B M Drummond, Sam Yeaman, Loren H Rieseberg
High throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that 'index switching', where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole genome shotgun dataset sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may...
August 17, 2017: Molecular Ecology Resources
Anna Tigano, Timothy B Sackton, Vicki L Friesen
Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats, and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick-billed murre (Uria lomvia), an arctic colonial seabird...
August 16, 2017: 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 1,084 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
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