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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/29131534/universal-target-enrichment-baits-for-anthozoan-cnidaria-phylogenomics-new-approaches-to-long-standing-problems
#1
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
#2
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
https://www.readbyqxmd.com/read/29120082/substantial-differences-in-bias-between-single-digest-and-double-digest-rad-seq-libraries-a-case-study
#3
Sarah P Flanagan, Adam G Jones
The tradeoffs of using single-digest versus double-digest restriction site associated DNA sequencing (RAD-seq) protocols have been widely discussed. However, no direct empirical comparisons of the two methods have been conducted. Here, we sampled a single population of Gulf pipefish (Syngnathus scovelli) and genotyped 444 individuals using RAD-seq. Sixty individuals were subjected to single-digest RAD-seq (sdRAD-seq), and the remaining 384 individuals were genotyped using a double-digest RAD-seq (ddRAD-seq) protocol...
November 9, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29098789/gene-expression-differs-in-co-dominant-prairie-grasses-under-drought
#4
Ava M Hoffman, Melinda D Smith
Grasslands of the Central US are expected to experience severe droughts and other climate extremes in the future, yet we know little about how these grasses will respond in terms of gene expression. We compared gene expression in Andropogon gerardii and Sorghastrum nutans, two closely related co-dominant C4 grasses responsible for the majority of ecosystem function, using RNA-seq. We compared Trinity assemblies within each species to determine annotated functions of transcripts responding to drought. Subsequently, we compared homologous annotated gene-groups across the two species using cross-species meta-level analysis and functional clustering based on key terms...
November 3, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29091348/validation-of-loop-mediated-isothermal-amplification-lamp-for-fast-and-portable-sex-determination-across-the-phylogeny-of-birds
#5
A Centeno-Cuadros, J L Tella, M Delibes, P Edelaar, M Carrete
PCR is a universal tool for the multiplication of specific DNA sequences. For example, PCR-based sex determination is widely used, and a diversity of primer sets is available. However, this protocol requires thermal cycling and electrophoresis so results are typically obtained in laboratories and several days after sampling. Loop-mediated isothermal amplification (LAMP) is an alternative to PCR that can take molecular ecology outside the laboratory. Although its application has been successfully probed for sex determination in three species of a single avian Family (Raptors, Accipitridae), its generality remains untested and suitable primers across taxa are lacking...
November 1, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29091345/a-method-for-the-direct-detection-of-airborne-dispersal-in-lichens
#6
S Eaton, C Zuniga, J Czyzewski, C J Ellis, D Genney, D Haydon, N Mirzai, R Yahr
This paper sets out a novel method to determine dispersal distances in lichens. Direct measurement of dispersal often remains difficult for lichens and other small inconspicuous species because of the need to track microscopic reproductive propagules, which even if they can be captured, cannot be identified using traditional morphological approaches. A low-cost device (<£200) was developed in order to trap the reproductive propagules of lichens, capable of sampling around 0.1m(3) of air per minute. In parallel, molecular techniques were developed to enable species specific detection of propagules caught by the devices, with identification using novel species-specific primers and optimization of a standard DNA extraction and nested PCR protocol...
November 1, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29058814/new-barcoded-primers-for-efficient-retrieval-of-cercozoan-sequences-in-high-throughput-environmental-diversity-surveys-with-emphasis-on-worldwide-biological-soil-crusts
#7
Anna Maria Fiore-Donno, Christian Rixen, Martin Rippin, Karin Glaser, Elena Samolov, Ulf Karsten, Burkhard Becker, Michael Bonkowski
We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hyper-variable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (ca...
October 23, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29058809/combining-noninvasive-genetics-and-a-new-mammalian-sex-linked-marker-provides-new-tools-to-investigate-population-size-structure-and-individual-behaviour-an-application-to-bats
#8
D Zarzoso-Lacoste, P-L Jan, L Lehnen, T Girard, A-L Besnard, S J Puechmaille, E J Petit
Monitoring wild populations is crucial for their effective management. Noninvasive genetic methods provide robust data from individual free-ranging animals, which can be used in capture-mark-recapture (CMR) models to estimate demographic parameters without capturing or disturbing them. However, sex- and status-specific behaviour, which may lead to differences in detection probabilities, is rarely considered in monitoring. Here, we investigated population size, sex ratio, sex- and status-related behaviour in 19 Rhinolophus hipposideros maternity colonies (Northern France) with a noninvasive genetic CMR approach (using faeces) combined with parentage assignments...
October 23, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29058768/the-impact-of-endogenous-content-replicates-and-pooling-on-genome-capture-from-fecal-samples
#9
J Hernandez-Rodriguez, M Arandjelovic, J Lester, C de Filippo, A Weihmann, M Meyer, S Angedakin, F Casals, A Navarro, L Vigilant, H S Kühl, K Langergraber, C Boesch, D Hughes, T Marques-Bonet
Target capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of non-invasive samples such as feces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution, and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries...
October 23, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29024430/impact-of-sequence-processing-and-taxonomic-classification-approaches-on-eukaryotic-community-structure-from-environmental-samples-with-emphasis-on-diatoms
#10
K Hardge, S Neuhaus, E S Kilias, C Wolf, K Metfies, S Frickenhaus
Next-generation sequencing is a common method for analyzing microbial community diversity and composition. Configuring an appropriate sequence processing strategy within the variety of tools and methods is a non-trivial task and can considerably influence the resulting community characteristics. We analyzed the V4 region of 18S rRNA gene sequences of marine samples by 454-pyrosequencing. Along this process, we generated several data sets with QIIME, mothur and a custom-made pipeline based on DNAStar and the phylogenetic-tree based PhyloAssigner...
October 12, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29024429/genetic-barcoding-of-dark-spored-myxomycetes-amoebozoa-identification-evaluation-and-application-of-a-sequence-similarity-threshold-for-species-differentiation-in-ngs-studies
#11
Mathilde Borg Dahl, Asker Daniel Brejnrod, Martin Unterseher, Thomas Hoppe, Yun Feng, Yuri Novozhilov, Søren Johannes Sørensen, Martin Schnittler
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime molds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation...
October 12, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28987008/mvmapper-interactive-spatial-mapping-of-genetic-structures
#12
Julian R Dupuis, Forest T Bremer, Thibaut Jombart, Sheina B Sim, Scott M Geib
Characterizing genetic structure across geographic space is a fundamental challenge in population genetics. Multivariate statistical analyses are powerful tools for summarizing genetic variability, but geographic information and accompanying metadata are not always easily integrated into these methods in a user-friendly fashion. Here, we present a deployable Python-based web-tool, mvmapper, for visualizing and exploring results of multivariate analyses in geographic space. This tool can be used to map results of virtually any multivariate analysis of georeferenced data, and routines for exporting results from a number of standard methods have been integrated in the R package adegenet, including principal components analysis (PCA), spatial PCA, discriminant analysis of principal components, principal coordinates analysis, nonmetric dimensional scaling and correspondence analysis...
October 7, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28977733/how-to-optimize-the-precision-of-allele-and-haplotype-frequency-estimates-using-pooled-sequencing-data
#13
Nicolas O Rode, Yan Holtz, Karine Loridon, Sylvain Santoni, Joëlle Ronfort, Laurène Gay
Sequencing pools of individuals rather than individuals separately reduces the costs of estimating allele frequencies at many loci in many populations. Theoretical and empirical studies show that pool-sequencing a limited number of individuals (typically fewer than 50) provides reliable allele frequency estimates, provided that the DNA pooling and DNA sequencing steps are carefully controlled. Unequal contributions of different individuals to the DNA pool and the mean and variance in sequencing depth both can affect the standard error of allele frequency estimates...
October 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28960889/esnail-a-transcriptome-based-molecular-resource-of-the-central-nervous-system-for-terrestrial-gastropods
#14
Min Zhao, Tianfang Wang, Michael J Stewart, Utpal Bose, Saowaros Suwansa-Ard, Kenneth B Storey, Scott F Cummins
To expand on emerging terrestrial gastropod molecular resources, we have undertaken transcriptome-based sequencing of the central nervous system (CNS) from six ecologically invasive terrestrial gastropods. Focusing on snail species Cochlicella acuta and Helix aspersa, and reticulated slugs Deroceras invadens, Deroceras reticulatum, Lehmannia nyctelia, and Milax gagates, we obtained a total of 367,869,636 high quality reads and compared them with existing CNS transcript resources for the invasive Mediterranean snail, Theba pisana...
September 28, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28941033/baitstools-software-for-hybridization-capture-bait-design
#15
Michael G Campana
Nucleic acid hybridization capture is a principal technology in molecular ecology and genomics. Bait design, however, is a non-trivial task and few resources currently exist to automate the process. Here, I present BaitsTools, an open-source, user-friendly software package to facilitate the design of nucleic acid baits for hybridization capture. This article is protected by copyright. All rights reserved.
September 20, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28926213/whole-genome-amplification-and-sequencing-of-a-daphnia-resting-egg
#16
Justin B Lack, Lawrence J Weider, Punidan D Jeyasingh
Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Though a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well-known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA...
September 19, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28921901/structureselector-a-web-based-software-to-select-and-visualize-the-optimal-number-of-clusters-using-multiple-methods
#17
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 structure 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 and 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
https://www.readbyqxmd.com/read/28921927/fast-and-cost-effective-single-nucleotide-polymorphism-snp-detection-in-the-absence-of-a-reference-genome-using-semi-deep-next-generation-random-amplicon-sequencing-ramseq
#18
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
https://www.readbyqxmd.com/read/28921904/developing-a-dna-barcode-library-for-perciform-fishes-in-the-south-china-sea-species-identification-accuracy-and-cryptic-diversity
#19
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
https://www.readbyqxmd.com/read/28865184/dna-barcoding-of-invasive-plants-in-china-a-resource-for-identifying-invasive-plants
#20
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
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