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Molecular Ecology Resources

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28029226/meeting-the-challenge-of-dna-barcoding-neotropical-amphibians-polymerase-chain-reaction-optimization-and-new-coi-primers
#12
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
#13
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
#14
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. argue that genome scans using RADseq will miss many loci under selection due to a combination of sparse marker density and low levels of linkage disequilibrium in most species. We agree that marker density and levels of LD are important considerations when designing a RADseq study; however, we dispute that RAD-based genome scans are as prone to failure as Lowry et al...
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
#15
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
#16
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
#17
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
#18
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-expressed-sequence-tag-and-genomic-ssrs
#19
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 SSR 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
#20
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
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