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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/28417603/squamate-conserved-loci-sqcl-a-unified-set-of-conserved-loci-for-phylogenomics-and-population-genetics-of-squamate-reptiles
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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/28339169/gesp-a-computer-program-for-modeling-genetic-effective-population-size-inbreeding-and-divergence-in-substructured-populations
#10
Fredrik Olsson, Linda Laikre, Ola Hössjer, Nils Ryman
The genetically effective population size (Ne) is of key importance for quantifying rates of inbreeding and genetic drift, and is often used in conservation management to set targets for genetic viability. The concept was developed for single, isolated populations and the mathematical means for analyzing the expected Ne in complex, subdivided populations have previously not been available. We recently developed such analytical theory and central parts of that work have now been incorporated into a freely available software tool presented here...
March 24, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28332322/design-of-character-based-dna-barcode-motif-for-species-identification-a-computational-approach-and-its-validation-in-fishes
#11
Mohua Chakraborty, Bishal Dhar, Sankar Kumar Ghosh
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa since the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters...
March 23, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28323394/feeding-preference-as-a-main-determinant-of-microscale-patchiness-among-terrestrial-nematodes
#12
Casper W Quist, Gerrit Gort, Christian Mulder, Ruud H P Wilbers, Aad J Termorshuizen, Jaap Bakker, Johannes Helder
Soil biota are responsible for essential ecosystem services such as carbon storage, nutrient cycling and water retention. However, assessment of the condition of soil biota is hampered by an overwhelming level of diversity. With representatives in all trophic levels of the food web, nematode communities can be used as bio-indicators. Accurate assessment of nematode assemblages requires insight in the distribution of specimens with distinct food preferences. With the availability of taxon-specific quantitative-PCR assays, distribution patterns of multiple nematode groups can be investigated simultaneously...
March 21, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28319339/unbroken-radseq-remains-a-powerful-tool-for-understanding-the-genetics-of-adaptation-in-natural-populations
#13
LETTER
Julian M Catchen, Paul A Hohenlohe, Louis Bernatchez, W Chris Funk, Kimberly R Andrews, Fred W Allendorf
Recently, Lowry et al. (2016) addressed the ability of RADseq approaches to detect loci under selection in genome scans. While the authors raise an important consideration for designing studies and interpreting RADseq data, we strongly disagree with their overall view of the ability of RADseq to inform our understanding of the genetic basis of adaptation. RADseq is one of several techniques for population genomic studies, and all of them come with important trade-offs and limitations. This article is protected by copyright...
March 20, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28316149/detecting-alternatively-spliced-transcript-isoforms-from-single-molecule-long-read-sequences-without-a-reference-genome
#14
Xiaoxian Liu, Wenbin Mei, Pamela S Soltis, Douglas E Soltis, W Brad Barbazuk
Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq(™) data for isoform-level transcriptome analysis, including the study of AS and gene fusion. We applied Iso-Seq(™) to investigate AS in Amborella trichopoda, a phylogenetically pivotal species that is sister to all other living angiosperms. Our data show that, compared with RNA-Seq data, the Iso-Seq(™) platform provides better recovery on large transcripts, new gene locus identification, and gene model correction...
March 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28296353/methodological-considerations-for-detection-of-terrestrial-small-body-salamander-edna-and-implications-for-biodiversity-conservation
#15
Donald M Walker, Jacob E Leys, Kelly E Dunham, Joshua C Oliver, Emily E Schiller, Kelsey S Stephenson, John T Kimrey, Jessica Wooten, Mark W Rogers
Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: 1) detect spiked salamander DNA in soil, 2) quantify eDNA degradation over time, 3) determine detectability of salamander eDNA in a terrestrial environment using soil, feces, and skin swabs, 4) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of fecal samples and concentrations did not differ between the two sources...
March 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28296259/taxonomy-free-molecular-diatom-index-for-high-throughput-edna-biomonitoring
#16
Laure Apothéloz-Perret-Gentil, Arielle Cordonier, François Straub, Jennifer Iseli, Philippe Esling, Jan Pawlowski
Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution...
March 14, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28281323/demerelate-calculating-inter-individual-relatedness-for-kinship-analysis-based-on-co-dominant-diploid-genetic-markers-using-r
#17
Philipp Kraemer, Gabriele Gerlach
The Demerelate package offers algorithms to calculate different inter-individual relatedness measurements. Three different allele sharing indices, five pairwise weighted estimates of relatedness and four pairwise weighted estimates with sample size correction are implemented to analyze kinship structures within populations. Statistics are based on randomization tests; modeling relatedness coefficients by logistic regression, modeling relatedness with geographic distance by mantel correlation and comparing mean relatedness between populations using pairwise t-tests...
March 9, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28271620/pedigree-reconstruction-from-snp-data-parentage-assignment-sibship-clustering-and-beyond
#18
Jisca Huisman
Data on hundreds or thousands of Single Nucleotide Polymorphisms (SNPs) provides detailed information about the relationships between individuals, but currently few tools can turn this information into a multi-generational pedigree. I present the R package sequoia, which assigns parents, clusters half-siblings sharing an unsampled parent, and assigns grandparents to half-sibships. Assignments are made after consideration of the likelihoods of all possible first, second and third degree relationships between the focal individuals, as well as the traditional alter native of being unrelated...
March 7, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28258659/genome-wide-survey-of-nuclear-protein-coding-markers-for-beetle-phylogenetics-and-their-application-in-resolving-both-deep-and-shallow-level-divergences
#19
Li-Heng Che, Shao-Qian Zhang, Yun Li, Dan Liang, Hong Pang, Adam Ślipiński, Peng Zhang
Beetles (Coleoptera) are the most diverse and species-rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of "traditional markers" (e.g., mitochondrial genes and nuclear rDNAs) for beetle phylogenetics is small and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome-wide survey to search nuclear protein-coding (NPC) genes suitable for research on beetle phylogenetics...
March 3, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28241394/the-empirical-bayes-estimators-of-fine-scale-population-structure-in-high-gene-flow-species
#20
Shuichi Kitada, Reiichiro Nakamichi, Hirohisa Kishino
An empirical Bayes (EB) pairwise FST estimator was previously introduced and evaluated for its performance by numerical simulation. In this study, we conducted coalescent simulations and generated genetic population structure mechanistically, and compared the performance of the EBFST with Nei's GST , Nei & Chesser's bias-corrected GST (GST _NC ), Weir & Cockerham's ϴ (ϴWC ),( and ϴ with finite sample correction (ϴWC _F ). We also introduced EB estimators for Hedrick' G'ST and Jost' D. We applied these estimators to publicly available SNP genotypes of Atlantic herring...
February 27, 2017: Molecular Ecology Resources
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