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Molecular Ecology Resources

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https://www.readbyqxmd.com/read/28319339/unbroken-radseq-remains-a-powerful-tool-for-understanding-the-genetics-of-adaptation-in-natural-populations
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28236665/using-a-butterflyfish-genome-as-a-general-tool-for-rad-seq-studies-in-specialized-reef-fish
#9
Joseph D DiBattista, Pablo Saenz-Agudelo, Marek J Piatek, Xin Wang, Manuel Aranda, Michael L Berumen
Data from a large-scale restriction site associated DNA (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction-site (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see if it improves the quality of RAD-Seq markers...
February 25, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28213940/estimating-mating-rates-in-wild-drosophila-melanogaster-females-by-decay-rates-of-male-reproductive-proteins-in-their-reproductive-tracts
#10
Thomas J Giardina, Andrew G Clark, Anthony C Fiumera
Female Drosophila melanogaster frequently mate with multiple males in nature as shown through parentage analysis. Although polyandry is well documented, we know little about the timing between mating events in wild Drosophila populations due to the challenge of following behaviors of individual females. In this study we used the presence of a male reproductive protein that is transferred to the female during mating (Sex Peptide, SP) to determine whether she had recently mated. We sampled females throughout the day, conducted control matings to determine the decay rate of SP within the female reproductive tract and performed computer simulations to fit the observed proportion of mated females to a non-homogenous Poisson process that defined the expected time between successive matings for a given female...
February 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28199781/sequencing-historical-specimens-successful-preparation-of-small-specimens-with-low-amounts-of-degraded-dna
#11
John S Sproul, David R Maddison
Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3-6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58-159 years, and for which few or no suitable replacement specimens exist...
February 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28181736/high-throughput-mining-of-e-genome-specific-snps-for-characterizing-thinopyrum-elongatum-introgressions-in-common-wheat
#12
Haijuan Lou, Lingli Dong, Kunpu Zhang, Da-Wei Wang, Maolin Zhao, Yiwen Li, Chaowu Rong, Huanju Qin, Aimin Zhang, Zhenying Dong, Daowen Wang
Diploid Thinopyrum elongatum (EE, 2n = 2x = 14) and related polyploid species constitute an important gene pool for improving Triticeae grain and forage crops. However, the genomic and molecular marker resources are generally poor for these species. To aid the genetic, molecular, breeding and ecological studies involving Thinopyrum species, we developed a strategy for mining and validating E-genome specific SNPs using Th. elongatum and common wheat (Triticum aestivum, AABBDD, 2n = 6x = 42) as experimental materials...
February 9, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28161911/cryptic-diversity-and-discordance-in-single-locus-species-delimitation-methods-within-horned-lizards-phrynosomatidae-phrynosoma
#13
Christopher Blair, Robert W Bryson
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data...
February 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28150424/detection-of-individual-ploidy-levels-with-genotyping-by-sequencing-gbs-analysis
#14
Zachariah Gompert, Karen E Mock
Ploidy levels sometimes vary among individuals or populations, particularly in plants. When such variation exists, accurate determination of cytotype can inform studies of ecology or trait variation and is required for population genetic analyses. Here we propose and evaluate a statistical approach for distinguishing low-level ploidy variants (e.g., diploids, triploids and tetraploids) based on genotyping-by-sequencing data. The method infers cytotypes based on observed heterozygosity and the ratio of DNA sequences containing different alleles at thousands of heterozygous SNPs (i...
February 1, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28130873/polymorphism-aware-protein-databases-a-pre-requisite-for-an-unbiased-proteomic-analysis-of-natural-populations
#15
Kathrin A Otte, Christian Schlötterer
Recent technological advances have increased the throughput of proteomics, facilitating the characterization of molecular phenotypes on the population level, thus bearing the potential to complement transcriptomic analyses. Reference protein databases are crucial for the analysis and quantification, since only peptides in the protein database can be identified. Any peptide carrying an amino acid variant cannot be identified. Because most proteomic studies, even of natural populations, do not account for polymorphisms, we analyzed the influence of variant peptides on quantitative proteomic analyses...
January 28, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28118515/phylogenomics-using-formalin-fixed-and-100-year-old-intractable-natural-history-specimens
#16
Sara Ruane, Christopher C Austin
Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin-fixed and fluid-preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time-consuming and produce low data quality and quantity. Here we use a modified DNA extraction protocol combined with high-throughput sequencing to recover DNA from formalin-fixed and fluid-preserved snakes that were collected over a century ago and for which little or no modern genetic materials exist in public collections...
January 24, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28078808/minimum-sample-sizes-for-population-genomics-an-empirical-study-from-an-amazonian-plant-species
#17
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
#18
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
#19
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
#20
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 nonmodel species. Utilizing genotype data in the absence of a reference genome, however, presents a number of challenges. One major challenge is the trade-off between splitting alleles at a single locus into separate clusters (loci), creating inflated homozygosity, and lumping multiple loci into a single contig (locus), creating artefacts and inflated heterozygosity...
January 2, 2017: Molecular Ecology Resources
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