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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/28603873/environmental-dna-enables-detection-of-terrestrial-mammals-from-forest-pond-water
#1
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
https://www.readbyqxmd.com/read/28544559/pipecraft-flexible-open-source-toolkit-for-bioinformatics-analysis-of-custom-high-throughput-amplicon-sequencing-data
#2
Sten Anslan, Mohammad Bahram, Indrek Hiiesalu, Leho Tedersoo
High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analyzed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user friendly graphical interface that links several public tools for analyzing amplicon sequencing data...
May 25, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28503747/friends-and-family-a-software-program-for-identification-of-unrelated-individuals-from-molecular-marker-data
#3
Deon de Jager, Petrus Swarts, Cindy Harper, Paulette Bloomer
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations...
May 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28488798/a-comparison-of-sedimentary-dna-and-pollen-from-lake-sediments-in-recording-vegetation-composition-at-the-siberian-treeline
#4
Bastian Niemeyer, Laura S Epp, Kathleen R Stoof-Leichsenring, Luidmila A Pestryakova, Ulrike Herzschuh
Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes...
May 10, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28477337/comparative-analysis-of-dna-extraction-methods-to-study-the-body-surface-microbiota-of-insects-a-case-study-with%C3%A2-ant-cuticular-bacteria
#5
Caroline Birer, Niklas Tysklind, Lucie Zinger, Christophe Duplais
High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behavior of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties to working with low bacterial DNA quantities as in individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm)...
May 6, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449359/transcriptomic-responses-of-solanum-dulcamara-to-natural-and-simulated-herbivory
#6
Tobias Lortzing, Vivien Firtzlaff, Duy Nguyen, Ivo Rieu, Sandra Stelzer, Martina Schad, Jim Kallarackal, Anke Steppuhn
Plants are attacked by diverse herbivores and respond with manifold defense responses. To study transcriptional and other early regulation events of these plant responses, herbivory is often simulated to standardize the temporal and spatial dynamics that vary tremendously for natural herbivory. Yet to what extent such simulations of herbivory are able to elicit the same plant response as real herbivory remains largely undetermined. We examined the transcriptional response of a wild model plant to herbivory by lepidopteran larvae and to a commonly used herbivory simulation by applying the larvae's oral secretions to standardized wounds...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449317/a-comparison-of-individual-based-genetic-distance-metrics-for-landscape-genetics
#7
A J Shirk, E L Landguth, S A Cushman
A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between pairwise genetic distances and landscape distances among sampled individuals in a population...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449274/a-dna-barcode-library-for-germany-s-mayflies-stoneflies-and-caddisflies-ephemeroptera-plecoptera-trichoptera
#8
Jérôme Morinière, Lars Hendrich, Michael Balke, Arne J Beermann, Tobias König, Monika Hess, Stefan Koch, Reinhard Müller, Florian Leese, Paul D N Hebert, Axel Hausmann, Christoph F Schubart, Gerhard Haszprunar
Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. However, a comprehensive DNA barcode library based upon taxonomically well-curated specimens can overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient, and reliable DNA-based identifications and assessments of ecological status...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449263/multi-dice-r-package-for-comparative-population-genomic-inference-under-hierarchical-co-demographic-models-of-independent-single-population-size-changes
#9
Alexander T Xue, Michael J Hickerson
Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis while benefiting in statistical power from aggregating datasets. This approach has been applied to classical phylogeographic datasets such as mitochondrial barcodes as well as reduced-genome polymorphism datasets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449215/rapid-degradation-of-longer-dna-fragments-enables-the-improved-estimation-of-distribution-and-biomass-using-environmental-dna
#10
Toshiaki Jo, Hiroaki Murakami, Reiji Masuda, Masayuki Sakata, Satoshi Yamamoto, Toshifumi Minamoto
The advent of environmental DNA (eDNA) analysis methods has enabled rapid and wide-range ecological monitoring in aquatic ecosystems, but there is a dearth of information on eDNA degradation. The results of previous studies suggest that the decay rate of eDNA varies depending on the length of DNA fragments. To examine this hypothesis, we compared temporal change in copy number of long eDNA fragments (719 bp) with that of short eDNA fragments (127 bp). First, we isolated rearing water from a target fish species, Japanese Jack Mackerel (Trachurus japonicus), and then quantified the copy number of the long and short eDNA fragments in 1 L water samples after isolating the water from the fish...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28417603/squamate-conserved-loci-sqcl-a-unified-set-of-conserved-loci-for-phylogenomics-and-population-genetics-of-squamate-reptiles
#11
Sonal Singhal, Maggie Grundler, Guarino Colli, Daniel L Rabosky
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches - anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) - and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics...
April 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28417591/effective-mosquito-and-arbovirus-surveillance-using-metabarcoding
#12
J Batovska, S E Lynch, N O I Cogan, K Brown, J M Darbro, E A Kho, M J Blacket
Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernise vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding'. The aim of our study was to establish a metabarcoding protocol to characterise pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%...
April 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28407448/draft-genomes-of-the-corallimorpharians-amplexidiscus-fenestrafer-and-discosoma-sp
#13
Xin Wang, Yi Jin Liew, Yong Li, Didier Zoccola, Sylvie Tambutte, Manuel Aranda
Corallimorpharia are the closest non-calcifying relatives of reef-building corals. Aside from their popularity among aquarium hobbyists, their evolutionary position between the Actiniaria (sea anemones) and the Scleractinia (hard corals) makes them ideal candidates for comparative studies aiming at understanding the evolution of hexacorallian orders in general and reef-building corals in particular. Here we have sequenced and assembled two draft genomes for the Corallimorpharia species Amplexidiscus fenestrafer and Discosoma sp...
April 13, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28394451/ancient-dna-analysis-identifies-marine-mollusc-shells-as-new-metagenomic-archives-of-the-past
#14
Clio Der Sarkissian, Vianney Pichereau, Catherine Dupont, Peter C Ilsøe, Mickael Perrigault, Paul Butler, Laurent Chauvaud, Jón Eiríksson, James Scourse, Christine Paillard, Ludovic Orlando
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity, and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories...
April 10, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28382730/responsible-rad-striving-for-best-practices-in-population-genomic-studies-of-adaptation
#15
LETTER
David B Lowry, Sean Hoban, Joanna L Kelley, Katie E Lotterhos, Laura K Reed, Michael F Antolin, Andrew Storfer
We thank McKinney et al. (2017) and Catchen et al. (2017) for their recent commentaries on Lowry et al (2017), "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." Both articles argued that we overstated the limitations of RADseq for studies of local adaptation and McKinney et al. (2017) argued that "RADseq provides unprecedented insights" into mechanisms of evolutionary adaptations. While we agree with some of the comments made by the authors of the two papers, we still believe caution should be employed in RADseq studies that aim to detect loci that contribute to adaptation...
April 6, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28382652/a-new-promising-phylogenetic-marker-to-study-the-diversity-of-fungal-communities-the-glycoside-hydrolase-63-gene
#16
L Pérez-Izquierdo, E Morin, J P Maurice, F Martin, A Rincón, M Buée
In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for Fungi, but this marker was criticized for idel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in Basidiomycetes...
April 6, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28374552/treespace-statistical-exploration-of-landscapes-of-phylogenetic-trees
#17
Thibaut Jombart, Michelle Kendall, Jacob Almagro-Garcia, Caroline Colijn
The increasing availability of large genomic datasets as well as the advent of Bayesian phylogenetics facilitate the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes...
April 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28374569/graphics-for-relatedness-research
#18
Iván Galván-Femenía, Jan Graffelman, Carles Barceló-I-Vidal
Studies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article is to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS and IBD based allele sharing studies are considered. Furthermore, we propose two additional graphical methods from the field of compositional data analysis: the ternary diagram and scatterplots of isometric log-ratios of IBS and IBD probabilities...
April 3, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28371384/unlocking-the-story-in-the-swab-a-new-genotyping-assay-for-the-amphibian-chytrid-fungus-batrachochytrium-dendrobatidis
#19
Allison Q Byrne, Andrew P Rothstein, Thomas J Poorten, Jesse Erens, Matthew L Settles, Erica Bree Rosenblum
One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity of Bd in natural systems...
April 2, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28613017/small-and-large-scale-heterogeneity-in-genetic-variation-across-the-collard-flycatcher-genome-implications-for-estimating-genetic-diversity-in-nonmodel-organisms
#20
Pär K Ingvarsson, Jing Wang
Population genetic studies in nonmodel organisms are often hampered by a lack of reference genomes that are essential for whole-genome resequencing. In the light of this, genotyping methods have been developed to effectively eliminate the need for a reference genome, such as genotyping by sequencing or restriction site-associated DNA sequencing (RAD-seq). However, what remains relatively poorly studied is how accurately these methods capture both average and variation in genetic diversity across an organism's genome...
July 2017: Molecular Ecology Resources
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