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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/28078808/minimum-sample-sizes-for-population-genomics-an-empirical-study-from-an-amazonian-plant-species
#1
Alison G Nazareno, Jordan B Bemmels, Christopher W Dick, Lúcia G Lohmann
High throughput DNA sequencing facilitates the analysis of large portions of the genome in non-model organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double digest restriction associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a non-model plant species for which no reference genome is available...
January 12, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28067020/spatial-detection-of-outlier-loci-with-moran-eigenvector-maps-mem
#2
Helene H Wagner, Mariana Chávez-Pesqueira, Brenna R Forester
The spatial signature of micro-evolutionary processes structuring genetic variation may play an important role in the detection of loci under selection. However, the spatial location of samples hasn't yet been used to quantify this. Here, we present a new two-step method of spatial outlier detection at the individual and deme levels using the power spectrum of Moran eigenvector maps (MEM). The MEM power spectrum quantifies how the variation in a variable, such as the frequency of an allele at a SNP locus, is distributed across a range of spatial scales defined by MEM spatial eigenvectors...
January 9, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28063202/dna-metabarcoding-reveals-that-200-%C3%AE-m-size-fractionated-filtering-is-unable-to-discriminate-between-planktonic-microbial-and-large-eukaryotes
#3
Lemian Liu, Min Liu, David M Wilkinson, Huihuang Chen, Xiaoqing Yu, Yang Jun
Microeukaryotic plankton (0.2-200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear if we can accurately, effectively, and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analyzed the eukaryotic plankton communities both with, and without, pre-filtering with a 200 μm pore-size sieve - by using SSU rDNA-based high-throughput sequencing on 16 samples with 3 replicates in each sample from two subtropical reservoirs sampled from January to October in 2013...
January 7, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28042915/haplotyping-rad-loci-an-efficient-method-to-filter-paralogs-and-account-for-physical-linkage
#4
Stuart C Willis, Christopher M Hollenbeck, Jonathan B Puritz, John R Gold, David S Portnoy
Next-generation sequencing of reduced-representation genomic libraries provides a powerful methodology for genotyping thousands of single nucleotide polymorphisms (SNPs) among individuals of non-model species. Utilizing genotype data in the absence of a reference genome, however, presents a number of challenges. One major challenge is the tradeoff between splitting alleles at a single locus into separate clusters (loci), creating inflated homozygosity, and lumping multiple loci into a single contig (locus), creating artifacts and inflated heterozygosity...
January 2, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28029226/meeting-the-challenge-of-dna-barcoding-neotropical-amphibians-polymerase-chain-reaction-optimization-and-new-coi-primers
#5
Mariana L Lyra, Célio F B Haddad, Ana Maria L de Azeredo-Espin
Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species...
December 28, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28028941/the-computer-program-structure-for-assigning-individuals-to-populations-easy-to-use-but-easier-to-misuse
#6
Jinliang Wang
The computer program Structure implements a Bayesian method, based on a population genetics model, to assign individuals to their source populations using genetic marker data. It is widely applied in the fields of ecology, evolutionary biology, human genetics and conservation biology for detecting hidden genetic structures, inferring the most likely number of populations (K), assigning individuals to source populations, and estimating admixture and migration rates. Recently, several simulation studies repeatedly concluded that the program yields erroneous inferences when samples from different populations are highly unbalanced in size...
December 27, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28028934/radseq-provides-unprecedented-insights-into-molecular-ecology-and-evolutionary-genetics-comment-on-breaking-rad-by-lowry-et%C3%A2-al-2016
#7
LETTER
Garrett J McKinney, Wesley A Larson, Lisa W Seeb, James E Seeb
In their recently corrected manuscript, "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation", Lowry et al. (2016) detail several concerns with the use of RADseq data for genome scans. Lowry et al. (2016) argue that informative RAD tags are usually distant from each other (100Kbs to MBs), and linkage disequilibrium (LD) in populations can be restricted to small enough haplotype blocks that informative loci may not be in strong enough LD with causal SNPs to be useful in genome scans...
December 27, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27997751/identifying-the-plant-associated-microbiome-across-aquatic-and-terrestrial-environments-the-effects-of-amplification-method-on-taxa-discovery
#8
Sara L Jackrel, Sarah M Owens, Jack A Gilbert, Catherine A Pfister
Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater, and marine environments...
December 20, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27997742/reconstructing-the-plant-mitochondrial-genome-for-marker-discovery-a-case-study-using-pinus
#9
Kevin Donnelly, Joan Cottrell, Richard A Ennos, Giovanni Guiseppe Vendramin, Stuart A'Hara, Sarah King, Annika Perry, Witold Wachowiak, Stephen Cavers
Whole-genome-shotgun (WGS) sequencing of total genomic DNA was used to recover ~1 Mbp of novel mitochondrial (mtDNA) sequence from Pinus sylvestris (L.) and three members of the closely-related Pinus mugo species complex. DNA was extracted from megagametophyte tissue from six mother trees from locations across Europe and 100 bp paired-end sequencing was performed on the Illumina HiSeq platform. Candidate mtDNA sequences were identified by their size and coverage characteristics, and by comparison with published plant mitochondrial genomes...
December 20, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27987268/detecting-invertebrate-species-in-archived-collections-using-next-generation-sequencing
#10
Melissa E Carew, Leon Metzeling, Rosalind StClair, Ary A Hoffmann
Invertebrate biodiversity measured at mostly family level is widely used in biological monitoring programs to assess anthropogenic impacts on ecosystems. However, next generation sequencing (NGS) could allow development of new more sensitive biomonitoring tools by allowing rapid species identification. This could be accelerated if archived invertebrate collections and environmental information from past programs are used to understand species distributions and their environmental responses. In this study, we take archived macroinvertebrate samples from two sites collected on multiple occasions and test if NGS can successfully detect species...
December 17, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27987263/edna-metabarcoding-a-promising-method-for-anuran-surveys-in-highly-diverse-tropical-forests
#11
Carla M Lopes, Thais Sasso, Alice Valentini, Tony Dejean, Marcio Martins, Kelly R Zamudio, Célio F B Haddad
Understanding the geographic distribution and community composition of species is crucial to monitor species persistence and define effective conservation strategies. Environmental DNA (eDNA) has emerged as a powerful noninvasive tool for species detection. However, most eDNA survey methods have been developed and applied in temperate zones. We tested the feasibility of using eDNA to survey anurans in tropical streams in the Brazilian Atlantic forest and compared the results with short-term visual and audio surveys...
December 16, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27978606/level-of-genetic-differentiation-affects-relative-performances-of-est-and-genomic-ssrs
#12
Aurélie Khimoun, Anthony Ollivier, Bruno Faivre, Stéphane Garnier
Microsatellites, also called simple sequence repeats (SSRs) are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers and highly conserved SSRs have recently been developed from Expressed Sequence Tags (EST) to improve SRR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification...
December 15, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27978605/a-novel-method-to-infer-the-origin-of-polyploids-from-aflp-data-reveals-that-the-alpine-polyploid-complex-of-senecio-carniolicus-asteraceae-evolved-mainly-via-autopolyploidy
#13
Manuela Winkler, Pedro Escobar García, Andreas Gattringer, Michaela Sonnleitner, Karl Hülber, Peter Schönswetter, Gerald M Schneeweiss
Despite its evolutionary and ecological relevance the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- versus allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a priori delimited putative parental entities (e...
December 15, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27889948/a-new-sequence-dataset-of-ssu-rrna-gene-for-scleractinia-and-its-phylogenetic-and-ecological-applications
#14
Roberto Arrigoni, Benoît Vacherie, Francesca Benzoni, Fabrizio Stefani, Eric Karsenti, Olivier Jaillon, Fabrice Not, Flavia Nunes, Claude Payri, Patrick Wincker, Valérie Barbe
Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly-used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are largely adopted as barcode marker to investigate marine plankton community structure worldwide...
November 27, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27868358/resolving-microsatellite-genotype-ambiguity-in-populations-of-allopolyploid-and-diploidized-autopolyploid-organisms-using-negative-correlations-between-allelic-variables
#15
Lindsay V Clark, Andrea Drauch Schreier
A major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci...
November 21, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27863055/snps-selected-by-information-content-outperform-randomly-selected-microsatellite-loci-for-delineating-genetic-identification-and-introgression-in-the-endangered-dark-european-honeybee-apis-mellifera-mellifera
#16
Irene Muñoz, Dora Henriques, Laura Jara, J Spencer Johnston, Julio Chávez-Galarza, Pilar De La Rúa, M Alice Pinto
The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies...
November 14, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27863033/dna-barcoding-of-crickets-katydids-and-grasshoppers-orthoptera-from-central-europe-with-focus-on-austria-germany-and-switzerland
#17
O Hawlitschek, J Morinière, G U C Lehmann, A W Lehmann, M Kropf, A Dunz, F Glaw, M Detcharoen, S Schmidt, A Hausmann, N U Szucsich, S A Caetano-Wyler, G Haszprunar
We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes...
November 14, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27860289/breaking-rad-an-evaluation-of-the-utility-of-restriction-site-associated-dna-sequencing-for-genome-scans-of-adaptation
#18
David B Lowry, Sean Hoban, Joanna L Kelley, Katie E Lotterhos, Laura K Reed, Michael F Antolin, Andrew Storfer
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation...
November 12, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27863094/resources-for-phylogenomic-analyses-of-australian-terrestrial-vertebrates
#19
Jason G Bragg, Sally Potter, Ke Bi, Renee Catullo, Stephen C Donnellan, Mark D B Eldridge, Leo Joseph, J Scott Keogh, Paul Oliver, Kevin C Rowe, Craig Moritz
High throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci and we now know that many lineages also exhibit substantial cryptic diversity. Here, we present a set of phylogenetically diverse transcriptome resources to enable exon-based sequence capture studies of Australian vertebrates, including transcriptome sequences for 4 species of birds, 4 frogs, 7 lizards and 7 mammals...
November 8, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27813315/controlling-for-p-value-inflation-in-allele-frequency-change-in-experimental-evolution-and-artificial-selection-experiments
#20
Petri Kemppainen, Bernt Rønning, Thomas Kvalnes, Ingerid J Hagen, Thor-Harald Ringsby, Anna M Billing, Henrik Pärn, Sigbjørn Lien, Arild Husby, Bernt-Erik Saether, Henrik Jensen
Experimental evolution studies can be used to explore genomic response to artificial and natural selection. In such studies, loci that display larger allele frequency change than expected by genetic drift alone are assumed to be directly or indirectly associated with traits under selection. However, such studies report surprisingly many loci under selection, suggesting that current tests for allele frequency change may be subject to p-value inflation and hence be anti-conservative. One factor known from genome wide association (GWA) studies to cause p-value inflation is population stratification, such as relatedness among individuals...
November 4, 2016: Molecular Ecology Resources
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