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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/29791787/dna-barcoding-of-microgastrine-parasitoid-wasps-hymenoptera-braconidae-using-high-throughput-methods-more-than-doubles-the-number-of-species-known-for-australia
#1
Erinn P Fagan-Jeffries, Steven J B Cooper, Terry Bertozzi, Tessa M Bradford, Andrew D Austin
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents, and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 100 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29791785/expressed-exome-capture-sequencing-eecseq-a-method-for-cost-effective-exome-sequencing-for-all-organisms
#2
Jonathan B Puritz, Katie E Lotterhos
Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called "EecSeq", eliminates the need for costly probe design and synthesis. We tested EecSeq in the eastern oyster, Crassostrea virginica, using a controlled exposure experiment. Four adult oysters were heat shocked at 36° C for 1 hour along with four control oysters kept at 14° C...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29786943/integrating-a-comprehensive-dna-barcode-reference-library-with-a-global-map-of-yews-taxus-l-for-forensic-identification
#3
Jie Liu, Richard I Milne, Michael Möller, Guang-Fu Zhu, Lin-Jiang Ye, Ya-Huang Luo, Jun-Bo Yang, Moses Cheloti Wambulwa, Chun-Neng Wang, De-Zhu Li, Lian-Ming Gao
Rapid and accurate identification of endangered species is a critical component of bio-surveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or pre-processed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa...
May 22, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29782705/wild-gwas-association-mapping-in-natural-populations
#4
Anna W Santure, Dany Garant
The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such 'gene mapping' studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment...
May 21, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29768738/unlocking-biodiversity-and-conservation-studies-in-high-diversity-environments-using-environmental-dna-edna-a-test-with-guianese-freshwater-fishes
#5
Kévin Cilleros, Alice Valentini, Luc Allard, Tony Dejean, Roselyne Etienne, Gaël Grenouillet, Amaia Iribar, Pierre Taberlet, Régis Vigouroux, Sébastien Brosse
Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and non-destructive method to assess biodiversity in tropical freshwaters is highly important...
May 16, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29766663/the-effect-of-filtration-method-on-the-efficiency-of-environmental-dna-capture-and-quantification-via-metabarcoding
#6
Jianlong Li, Lori-Jayne Lawson Handley, Daniel S Read, Bernd Hänfling
Environmental DNA (eDNA) is a promising tool for rapid and non-invasive biodiversity monitoring. eDNA density is low in environmental samples, and a capture method, such as filtration, is often required to concentrate eDNA for downstream analyses. In this study, six treatments, with differing filter types and pore sizes for eDNA capture, were compared for their efficiency and accuracy to assess fish community structure with known fish abundance and biomass via eDNA metabarcoding. Our results showed that different filters (with the exception of 20 μm large-pore filters) were broadly consistent in their DNA capture ability...
May 16, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29697894/a-geography-aware-reconciliation-method-to-investigate-diversification-patterns-in-host-parasite-interactions
#7
V Berry, F Chevenet, J-P Doyon, E Jousselin
Cospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and are not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data...
April 26, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29697892/insights-into-population-genetics-and-evolution-of-polyploids-and-their-ancestors
#8
Abdulqader Jighly, Zibei Lin, John W Forster, German C Spangenberg, Ben J Hayes, Hans D Daetwyler
We have developed the first comprehensive simulator for polyploid genomes (PolySim), and demonstrated its value by performing large-scale simulations to examine the effect of different population parameters on the evolution of polyploids. PolySim is unlimited in terms of ploidy, population size, or number of simulated loci. Our process considered the evolution of polyploids from diploid ancestors, polysomic inheritance, inbreeding, recombination rate change in polyploids and gene flow from lower to higher ploidies...
April 26, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29673105/linkage-disequilibrium-clustering-based-approach-for-association-mapping-with-tightly-linked-genome-wide-data
#9
Zitong Li, Petri Kemppainen, Pasi Rastas, Juha Merilä
Genome-wide association studies (GWAS) aim to identify genetic markers strongly associated with quantitative traits by utilizing linkage disequilibrium (LD) between candidate genes and markers. However, because of LD between nearby genetic markers, the standard GWAS approaches typically detect a number of correlated SNPs covering long genomic regions, making corrections for multiple testing overly conservative. Additionally, the high dimensionality of modern GWAS data poses considerable challenges for GWAS procedures such as permutation tests, which are computationally intensive...
April 19, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29673092/using-dna-metabarcoding-for-simultaneous-inference-of-common-vampire-bat-diet-and-population-structure
#10
Kristine Bohmann, Shyam Gopalakrishnan, Martin Nielsen, Luisa Dos Santos Bay Nielsen, Gareth Jones, Daniel G Streicker, M Thomas P Gilbert
Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses. Techniques to determine large scale variation in vampire bat diet and bat population structure would empower locality- and species-specific projections of disease transmission risks...
April 19, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29673087/naturalgwas-an-r-package-for-evaluating-genome-hyphen-wide-association-methods-with-empirical-data
#11
Olivier François, Kevin Caye
Association studies of polygenic traits are notoriously difficult when those studies are conducted at large geographic scales. The difficulty arises as genotype frequencies often vary in geographic space and across distinct environments. Those large{\hyphen}scale variations are known to yield false positives in standard association testing approaches. Although several methods alleviate this problem, no tools have been proposed to evaluate the power that association tests could achieve for a specific study design and set of genotypes...
April 19, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29673082/a-minion-based-pipeline-for-fast-and-cost-effective-dna-barcoding
#12
Amrita Srivathsan, Bilgenur Baloğlu, Wendy Wang, Wei Xin Tan, Denis Bertrand, Amanda Hui Qi Ng, Esther Jia Hui Boey, Jayce Jia Yu Koh, Niranjan Nagarajan, Rudolf Meier
DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory, is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and demonstrate that one flowcell can generate barcodes for ~500 specimens despite the high base-call error rates of MinION™ reads. The pipeline overcomes these errors by first summarizing all reads for the same tagged amplicon as a consensus barcode...
April 19, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29673081/sequence-clustering-threshold-has-little-effect-on-the-recovery-of-microbial-community-structure
#13
Synnøve Smebye Botnen, Marie Louise Davey, Rune Halvorsen, Håvard Kauserud
Analysis of microbial community structure by multivariate ordination methods, using data obtained by high throughput sequencing of amplified markers (i.e., DNA metabarcoding), often requires clustering of DNA sequences into operational taxonomic units (OTUs). Parameters for the clustering procedure tend not to be justified but are set by tradition rather than being based on explicit knowledge. In this study, we explore the extent to which ordination results are affected by variation in parameter settings for the clustering procedure...
April 19, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667364/heritability-of-body-size-in-the-polar-bears-of-western-hudson-bay
#14
René M Malenfant, Corey S Davis, Evan S Richardson, Nicholas J Lunn, David W Coltman
Among polar bears (Ursus maritimus), fitness is dependent on body size through males' abilities to win mates, females' abilities to provide for their young, and all bears' abilities to survive increasingly longer fasting periods caused by climate change. In the Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar bears have declined in body size and condition, but nothing is known about the genetic underpinnings of body size variation, which may be subject to natural selection. Here, we combine a 4449-individual pedigree and an array of 5433 single-nucleotide polymorphisms (SNPs) to provide the first quantitative genetics study of polar bears...
April 18, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667329/performance-of-amplicon-and-shotgun-sequencing-for-accurate-biomass-estimation-in-invertebrate-community-samples
#15
Iliana Bista, Gary R Carvalho, Min Tang, Kerry Walsh, Xin Zhou, Mehrdad Hajibabaei, Shadi Shokralla, Mathew Seymour, David Bradley, Shanlin Liu, Martin Christmas, Simon Creer
New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here we used a set of documented mock communities comprising 13 species of freshwater macroinvertebrates of estimated individual biomass, to compare the detection efficiency of COI metabarcoding (3 different amplicons) and shotgun mitogenome sequencing...
April 18, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667323/clades-a-classification-based-machine-learning-method-for-species-delimitation-from-population-genetic-data
#16
Jingwen Pei, Chong Chu, Xin Li, Bin Lu, Yufeng Wu
Species are considered to be the basic unit of ecological and evolutionary studies. Since multi-locus genomic data are increasingly available there has been considerable interests in the use of DNA sequence data to delimit species. In this paper, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes...
April 18, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29667373/heritability-estimates-from-genome-wide-relatedness-matrices-in-wild-populations-application-to-a-passerine-using-a-small-sample-size
#17
C Perrier, B Delahaie, A Charmantier
Genomic developments have empowered the investigation of heritability in wild populations directly from genome wide relatedness matrices (GRM). Such GRM based approaches can in particular be used to improve or substitute approaches based on social pedigree (PED-social). However, measuring heritability from GRM in the wild has not been widely applied yet, especially using small samples and in non-model species. Here, we estimated heritability for four quantitative traits (tarsus length, wing length, bill length and body mass), using PED-social, a pedigree corrected by genetic data (PED-corrected) and a GRM from a small sample (n = 494) of blue tits from natural populations in Corsica genotyped at nearly 50,000 filtered SNPs derived from RAD-seq...
April 17, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29658173/contrasting-results-from-gwas-and-qtl-mapping-on-wing-length-in-great-reed-warblers
#18
Bengt Hansson, Hanna Sigeman, Martin Stervander, Maja Tarka, Suvi Ponnikas, Maria Strandh, Helena Westerdahl, Dennis Hasselquist
A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re-evaluate the genetic basis of wing length in great reed warblers using a genome-wide association study (GWAS) approach based on restriction site-associated DNA sequencing (RADseq) data...
April 15, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29633537/himap-robust-phylogenomics-from-highly-multiplexed-amplicon-sequencing
#19
Julian R Dupuis, Forest T Bremer, Angela Kauwe, Michael San Jose, Luc Leblanc, Daniel Rubinoff, Scott M Geib
High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment...
April 6, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29633534/utility-of-pooled-sequencing-for-association-mapping-in-non-model-organisms
#20
Steven J Micheletti, Shawn R Narum
High density genome-wide sequencing increases the likelihood of discovering genes of major effect and genomic structural variation in organisms. While there is an increasing availability of reference genomes across broad taxa, the greatest limitation to whole-genome sequencing of multiple individuals continues to be the costs associated with sequencing. To alleviate excessive costs, pooling multiple individuals with similar phenotypes and sequencing the homogenized DNA (Pool-Seq) can achieve high genome coverage, but at the loss of individual genotypes...
April 6, 2018: Molecular Ecology Resources
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