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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/29352511/draft-genome-and-reference-transcriptomic-resources-for-the-urticating-pine-defoliator-thaumetopoea-pityocampa-lepidoptera-notodontidae
#1
B Gschloessl, F Dorkeld, H Berges, G Beydon, O Bouchez, M Branco, A Bretaudeau, C Burban, E Dubois, P Gauthier, E Lhuillier, J Nichols, S Nidelet, S Rocha, L Sauné, R Streiff, M Gautier, C Kerdelhué
The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity, and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture...
January 20, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29330936/give-me-a-sample-of-air-and-i-will-tell-which-species-are-found-from-your-region-molecular-identification-of-fungi-from-airborne-spore-samples
#2
Nerea Abrego, Veera Norros, Panu Halme, Panu Somervuo, Heini Ali-Kovero, Otso Ovaskainen
Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning, and are important for human health, food production, and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise...
January 13, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29328547/blow-flies-as-urban-wildlife-sensors
#3
Constanze Hoffmann, Kevin Merkel, Andreas Sachse, Pablo Rodríguez, Fabian H Leendertz, Sébastien Calvignac-Spencer
Wildlife detection in urban areas is very challenging. Conventional monitoring techniques such as direct observation are faced with the limitation that urban wildlife is extremely elusive. It was recently shown that invertebrate-derived DNA (iDNA) can be used to assess wildlife diversity in tropical rainforests. Flies, which are ubiquitous and very abundant in most cities, may also be used to detect wildlife in urban areas. In urban ecosystems, however, overwhelming quantities of domestic mammal DNA could completely mask the presence of wild mammal DNA...
January 12, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29314756/sorting-specimen-rich-invertebrate-samples-with-cost-effective-ngs-barcodes-validating-a-reverse-workflow-for-specimen-processing
#4
Wendy Y Wang, Amrita Srivathsan, Maosheng Foo, Seiki Yamane, Rudolf Meier
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0...
January 5, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29314766/gpsit-an-automated-method-for-evolutionary-analysis-of-nonculturable-ciliated-microeukaryotes
#5
Xiao Chen, Yurui Wang, Yalan Sheng, Alan Warren, Shan Gao
Microeukaryotes are among the most important components of the microbial food web in almost all aquatic and terrestrial ecosystems worldwide. In order to gain a better understanding their roles and functions in ecosystems, sequencing coupled with phylogenomic analyses of entire genomes or transcriptomes are increasingly used to reconstruct the evolutionary history and classification of these microeukaryotes and thus provide a more robust framework for determining their systematics and diversity. More importantly, phylogenomic research usually requires high levels of hands-on bioinformatics experience...
January 4, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29288544/metabarcoding-for-the-parallel-identification-of-several-hundred-predators-and-their-preys-application-to-bat-species-diet-analysis
#6
Maxime Galan, Jean-Baptiste Pons, Orianne Tournayre, Éric Pierre, Maxime Leuchtmann, Dominique Pontier, Nathalie Charbonnel
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the 'all at once' taxonomic identification of bats and their arthropod preys for several hundreds of samples...
December 30, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29288525/multi-allelic-exact-tests-for-hardy-weinberg-equilibrium-that-account-for-gender
#7
Jan Graffelman, Bruce S Weir
Statistical tests for Hardy-Weinberg equilibrium are important elementary tools in genetic data analysis. X-chromosomal variants have long been tested by applying autosomal test procedures to females only, and gender is usually not considered when testing autosomal variants for equilibrium. Recently, we proposed specific X-chromosomal exact test procedures for bi-allelic variants that include the hemizygous males, as well as autosomal tests that consider gender. In this paper we present the extension of the previous work for variants with multiple alleles...
December 30, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29282875/evaluating-methods-to-visualize-patterns-of-genetic-differentiation-on-a-landscape
#8
Geoffrey L House, Matthew W Hahn
With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model-based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long-distance migration, EEMS' model is more sensitive to short-distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations...
December 28, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29271609/reducing-cryptic-relatedness-in-genomic-datasets-via-a-central-node-exclusion-algorithm
#9
Pablo A S Fonseca, Thiago P Leal, Fernanda C Santos, Mateus H Gouveia, Samir Id-Lahoucine, Izinara C Rosse, Ricardo V Ventura, Frank A T Bruneli, Marco A Machado, Maria Gabriela C D Peixoto, Eduardo Tarazona-Santos, Maria Raquel S Carvalho
Cryptic relatedness is a confounding factor in genetic diversity and genetic association studies. Development of strategies to reduce cryptic relatedness in a sample is a crucial step for downstream genetic analyzes. The present study uses a node selection algorithm, based on network degrees of centrality, to evaluate its applicability and impact on evaluation of genetic diversity and population stratification. 1,036 Guzerá (Bos indicus) females were genotyped using Illumina Bovine SNP50 v2 BeadChip. Four strategies were compared...
December 22, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29266847/dartr-an-r-package-to-facilitate-analysis-of-snp-data-generated-from-reduced-representation-genome-sequencing
#10
B Gruber, P J Unmack, O Berry, A Georges
Though vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new R package, dartR, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. DartR provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy-Weinberg equilibrium, gametic-phase disequilibrium, and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis, and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e...
December 20, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29205893/measuring-the-gut-microbiome-in-birds-comparison-of-faecal-and-cloacal-sampling
#11
Elin Videvall, Maria Strandh, Anel Engelbrecht, Schalk Cloete, Charlie K Cornwallis
The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing...
December 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29194981/ddrage-a-dataset-generator-to-evaluate-ddradseq-analysis-software
#12
Henning Timm, Hannah Weigand, Martina Weiss, Florian Leese, Sven Rahmann
High throughput sequencing makes it possible to evaluate thousands of genetic markers across genomes and populations. Reduced-representation sequencing approaches, like ddRADseq (double digest restriction site associated DNA sequencing), are frequently applied to screen for genetic variation. In particular in non-model organisms where whole-genome sequencing is not yet feasible, ddRADseq has become popular as it allows genome-wide assessment of variation patterns even in the absence of other genomic resources...
December 1, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29172252/prospects-on-the-evolutionary-mitogenomics-of-plants-a-case-study-on-the-olive-family-oleaceae
#13
Céline Van de Paer, Olivier Bouchez, Guillaume Besnard
The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high-throughput techniques, we reconstructed complete mitogenomes (ca...
November 24, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29171165/readtools-a-universal-toolkit-for-handling-sequence-data-from-different-sequencing-platforms
#14
D Gómez-Sánchez, C Schlötterer
Sequencing whole genomes has become a standard research tool in many disciplines including Molecular Ecology, but the rapid technological advances in combination with several competing platforms has resulted in a confusing diversity of formats. This lack of standard formats causes several problems, such as undocumented pre-processing steps or the loss of information in downstream software tools, which do not account for the specifics of the different available formats. ReadTools is an open source Java toolkit designed to standardize and pre-process read data from different platforms...
November 24, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29171158/genetic-monitoring-of-open-ocean-biodiversity-an-evaluation-of-dna-metabarcoding-for-processing-continuous-plankton-recorder-samples
#15
Bruce E Deagle, Laurence J Clarke, John A Kitchener, Andrea M Polanowski, Andrew T Davidson
DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programs, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterised biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n= 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker...
November 23, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29160928/genotyping-by-sequencing-for-estimating-relatedness-in-non-model-organisms-avoiding-the-trap-of-precise-bias
#16
Catherine R M Attard, Luciano B Beheregaray, Luciana M Möller
There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e. RADseq and similar methods) datasets for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of dataset that could lead to downward-biased, yet precise, estimates of relatedness. Here we assess the applicability of genotyping-by-sequencing datasets for relatedness inferences given their relatively high genotyping error rates...
November 21, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29154499/fuzzyid2-a-software-package-for-large-dataset-species-identification-via-barcoding-and-metabarcoding-using-hidden-markov-models-and-fuzzy-set-methods
#17
Z Y Shi, C Q Yang, M D Hao, X Y Wang, R D Ward, A B Zhang
Species identification through DNA barcoding or metabarcoding has become a key approach for biodiversity evaluation and ecological studies. However, the rapid accumulation of barcoding data has created some difficulties: for instance, global enquiries to a large reference library can take a very long time. We here devise a two-step searching strategy to speed identification procedures of such queries. This firstly uses a Hidden Markov Model (HMM) algorithm to narrow the searching scope to genus level, and then determines the corresponding species using minimum genetic distance...
November 20, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29143457/microhaplotypes-provide-increased-power-from-short-read-dna-sequences-for-relationship-inference
#18
Diana S Baetscher, Anthony J Clemento, Thomas C Ng, Eric C Anderson, John Carlos Garza
The accelerating rate at which DNA sequence data is now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by these sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine "microhaplotypes" and then call these microhaplotypes as alleles at each locus...
November 16, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29131534/universal-target-enrichment-baits-for-anthozoan-cnidaria-phylogenomics-new-approaches-to-long-standing-problems
#19
A M Quattrini, B C Faircloth, L F Dueñas, T C L Bridge, M R Brugler, I F Calixto-Botía, D M DeLeo, S Forêt, S Herrera, S Lee, D J Miller, C Prada, G Rádis-Baptista, C Ramírez-Portilla, J A Sánchez, E Rodríguez, C S McFadden
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,306 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was performed on 33 taxa from all orders within the class Anthozoa...
November 13, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29120090/ednaoccupancy-an-r-package-for-multi-scale-occupancy-modeling-of-environmental-dna-data
#20
Robert M Dorazio, Richard A Erickson
In this article we describe eDNAoccupancy, an R package for fitting Bayesian, multi-scale occupancy models. These models are appropriate for occupancy surveys that include three, nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit, and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). eDNAoccupancy allows users to specify and fit multi-scale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria...
November 9, 2017: Molecular Ecology Resources
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