U.S. flag

An official website of the United States government

Dot gov

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Https

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

PubAg

Main content area

You searched for: Journal name Molecular ecology resources Remove constraint Journal name: Molecular ecology resources Publication year rev 7984-2016 Remove constraint Publication year rev: 7984-2016 Source 2016 v.16 no.3 Remove constraint Source: 2016 v.16 no.3
Start Over

Search

20  Search Results

1 - 20 of 20
Number of results to display per page

Search Results

1. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

Author:
Paul D. Blischak; Laura S. Kubatko; Andrea D. Wolfe
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 742-754
ISSN:
1755-098X
Subject:
alleles; autopolyploidy; computer software; data collection; gene frequency; heterozygosity; hexaploidy; high-throughput nucleotide sequencing; restriction endonucleases; single nucleotide polymorphism; statistical models; tetraploidy; uncertainty
Abstract:
... Despite the increasing opportunity to collect large‐scale data sets for population genomic analyses, the use of high‐throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty–ADU), which complicates the calculation of ...
DOI:
10.1111/1755-0998.12493

2. Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont‐rich aphid genus

Author:
E. Jousselin; A.‐L. Clamens; M. Galan; M. Bernard; S. Maman; B. Gschloessl; G. Duport; A. S. Meseguer; F. Calevro; A. Coeur d'acier
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 628-640
ISSN:
1755-098X
Subject:
Buchnera aphidicola; Cinara; DNA; Serratia; arthropods; bacteria; bacterial communities; endosymbionts; hosts; microbiome; nucleotide sequences; polymerase chain reaction; ribosomal RNA; sequence analysis; species diversity
Abstract:
... The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the res ...
DOI:
10.1111/1755-0998.12478

3. Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA‐seq

Author:
R. Pérez‐Portela; X. Turon; A. Riesgo
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 794-808
ISSN:
1755-098X
Subject:
Arbacia; animal ovaries; cDNA libraries; complementary DNA; energy; gene expression; gene expression regulation; genes; genomics; immune response; lipid metabolism; littoral zone; messenger RNA; muscle contraction; proteins; somatic cells; testes; tissues; transcriptome
Abstract:
... The sea urchin Arbacia lixula is a keystone species in Mediterranean ecosystems that drive landscape changes in littoral communities. However, genomic information available for the whole order Arbacioida is very limited. Using RNA‐seq techniques, we have characterized the transcriptome of four different tissue types in A. lixula: the ‘somatic’ tissues (coelomocytes and digestive tissue) and the ‘r ...
DOI:
10.1111/1755-0998.12500

4. Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD‐seq for the small yellow croaker (Larimichthys polyactis)

Author:
Bai‐Dong Zhang; Dong‐Xiu Xue; Juan Wang; Yu‐Long Li; Bing‐Jian Liu; Jin‐Xian Liu
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 755-768
ISSN:
1755-098X
Subject:
DNA; Larimichthys polyactis; actin; adaptive radiation; data collection; genes; genetic variation; genomics; high-throughput nucleotide sequencing; loci; oxidative stress; population size; single nucleotide polymorphism; synapse
Abstract:
... Recent advances in high‐throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27 556 single nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) us ...
DOI:
10.1111/1755-0998.12476

5. Establishing a community‐wide DNA barcode library as a new tool for arctic research

Author:
H. Wirta; G. Várkonyi; C. Rasmussen; R. Kaartinen; N. M. Schmidt; P. D. N. Hebert; M. Barták; G. Blagoev; H. Disney; S. Ertl; P. Gjelstrup; D. J. Gwiazdowicz; L. Huldén; J. Ilmonen; J. Jakovlev; M. Jaschhof; J. Kahanpää; T. Kankaanpää; P. H. Krogh; R. Labbee; C. Lettner; V. Michelsen; S. A. Nielsen; T. R. Nielsen; L. Paasivirta; S. Pedersen; J. Pohjoismäki; J. Salmela; P. Vilkamaa; H. Väre; M. Tschirnhaus; T. Roslin
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 809-822
ISSN:
1755-098X
Subject:
DNA; DNA barcoding; DNA libraries; Malaise traps; arthropods; ecosystems; fauna; insect communities; internal transcribed spacers; monophyly; phenology; space and time; summer; vascular plants; Arctic region; Greenland
Abstract:
... DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to‐date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we ap ...
DOI:
10.1111/1755-0998.12489

6. Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly

Author:
Nobuaki Kono; Hiroyuki Nakamura; Yusuke Ito; Masaru Tomita; Kazuharu Arakawa
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 662-672
ISSN:
1755-098X
Subject:
Araneae; RNA; ambient temperature; cost effectiveness; ethanol; gene expression; genome; guidelines; high-throughput nucleotide sequencing; preservatives; storage conditions; transcriptome; transcriptomics
Abstract:
... With advances in high‐throughput sequencing technologies, de novo transcriptome sequencing and assembly has become a cost‐effective method to obtain comprehensive genetic information of a species of interest, especially in nonmodel species with large genomes such as spiders. However, high‐quality RNA is essential for successful sequencing, and sample preservation conditions require careful conside ...
DOI:
10.1111/1755-0998.12485

7. Genomewide gene‐associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex

Author:
Yaping Lin; Yiyong Chen; Wei Xiong; Aibin Zhan
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 784-793
ISSN:
1755-098X
Subject:
Ciona intestinalis; alleles; bioinformatics; coasts; expressed sequence tags; genetic markers; heterozygosity; loci; microsatellite repeats; models; South Africa; Spain
Abstract:
... The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genomewide genetic markers are still lacking. Here, we characterized a large set of genomewide gene‐associated microsatellite markers for C. intestinalis spA (=C. robusta). Bioinfo ...
DOI:
10.1111/1755-0998.12481

8. How to limit false positives in environmental DNA and metabarcoding?

Author:
Gentile Francesco Ficetola; Pierre Taberlet; Eric Coissac
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 604-607
ISSN:
1755-098X
Subject:
DNA; biogeography; bioinformatics; ecosystems; statistical models
Abstract:
... Environmental DNA (eDNA) and metabarcoding are boosting our ability to acquire data on species distribution in a variety of ecosystems. Nevertheless, as most of sampling approaches, eDNA is not perfect. It can fail to detect species that are actually present, and even false positives are possible: a species may be apparently detected in areas where it is actually absent. Controlling false positive ...
DOI:
10.1111/1755-0998.12508

9. Identifying the number of population clusters with structure: problems and solutions

Author:
Kimberly J. Gilbert
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 601-603
ISSN:
1755-098X
Subject:
algorithms; ancestry; landscapes; population structure
Abstract:
... The program structure has been used extensively to understand and visualize population genetic structure. It is one of the most commonly used clustering algorithms, cited over 11 500 times in Web of Science since its introduction in 2000. The method estimates ancestry proportions to assign individuals to clusters, and post hoc analyses of results may indicate the most likely number of clusters, or ...
DOI:
10.1111/1755-0998.12521

10. Measuring the immune system of the three‐spined stickleback – investigating natural variation by quantifying immune expression in the laboratory and the wild

Author:
Shaun Robertson; Janette E. Bradley; Andrew D. C. MacColl
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 701-713
ISSN:
1755-098X
Subject:
Gasterosteus aculeatus; genes; immune response; immune system; innate immunity; quantitative polymerase chain reaction; wild fish; Scotland
Abstract:
... Current understanding of the immune system comes primarily from laboratory‐based studies. There has been substantial interest in examining how it functions in the wild, but studies have been limited by a lack of appropriate assays and study species. The three‐spined stickleback (Gasterosteus aculeatus L.) provides an ideal system in which to advance the study of wild immunology, but requires the d ...
DOI:
10.1111/1755-0998.12497
PubMed:
26646722
PubMed Central:
PMC4991546

11. Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

Author:
Austen C. Thomas; Bruce E. Deagle; J. Paige Eveson; Corie H. Harsch; Andrew W. Trites
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 714-726
ISSN:
1755-098X
Subject:
DNA; Phoca vitulina; biomass; field experimentation; fish; nucleotide sequences; seals
Abstract:
... DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high‐throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in ...
DOI:
10.1111/1755-0998.12490

12. Whole‐genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations

Author:
Marty Kardos; Arild Husby; S. Eryn McFarlane; Anna Qvarnström; Hans Ellegren
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 727-741
ISSN:
1755-098X
Subject:
genes; genotyping; linkage disequilibrium; loci; males; phenotype; phenotypic variation; population size; quantitative trait loci; quantitative traits; single nucleotide polymorphism
Abstract:
... Dissecting the genetic basis of phenotypic variation in natural populations is a long‐standing goal in evolutionary biology. One open question is whether quantitative traits are determined only by large numbers of genes with small effects, or whether variation also exists in large‐effect loci. We conducted genomewide association analyses of forehead patch size (a sexually selected trait) on 81 who ...
DOI:
10.1111/1755-0998.12498

13. A framework for estimating the sensitivity of eDNA surveys

Author:
Elise M. Furlan; Dianne Gleeson; Christopher M. Hardy; Richard P. Duncan
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 641-654
ISSN:
1755-098X
Subject:
DNA; Misgurnus anguillicaudatus; autumn; models; polymerase chain reaction; probability; spring; surveys
Abstract:
... Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, wi ...
DOI:
10.1111/1755-0998.12483

14. polypatex: an r package for paternity exclusion in autopolyploids

Author:
Alexander B. Zwart; Carole Elliott; Tara Hopley; David Lovell; Andrew Young
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 694-700
ISSN:
1755-098X
Subject:
alleles; animals; autopolyploidy; computer software; data analysis; data collection; diploidy; fathers; genetic markers; genotype; loci; microsatellite repeats; mothers; paternity; phenotype; plants (botany); progeny
Abstract:
... Microsatellite markers have demonstrated their value for performing paternity exclusion and hence exploring mating patterns in plants and animals. Methodology is well established for diploid species, and several software packages exist for elucidating paternity in diploids; however, these issues are not so readily addressed in polyploids due to the increased complexity of the exclusion problem and ...
DOI:
10.1111/1755-0998.12496

15. The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem

Author:
Sebastien J. Puechmaille
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 608-627
ISSN:
1755-098X
Subject:
algorithms; data collection; microsatellite repeats; models; population structure; wildlife management
Abstract:
... Inferences of population structure and more precisely the identification of genetically homogeneous groups of individuals are essential to the fields of ecology, evolutionary biology and conservation biology. Such population structure inferences are routinely investigated via the program structure implementing a Bayesian algorithm to identify groups of individuals at Hardy–Weinberg and linkage equ ...
DOI:
10.1111/1755-0998.12512

16. Extending RAD tag analysis to microbial ecology: a comparison between MultiLocus Sequence Typing and 2b‐RAD to investigate Listeria monocytogenes genetic structure

Author:
Marianna Pauletto; Lisa Carraro; Massimiliano Babbucci; Rosaria Lucchini; Luca Bargelloni; Barbara Cardazzo
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 823-835
ISSN:
1755-098X
Subject:
genome; high-throughput nucleotide sequencing; bioinformatics; phylogeny; biosafety; multilocus sequence typing; food processing; microbial ecology; molecular epidemiology; Listeria monocytogenes; population genetics; population structure
Abstract:
... The advent of next‐generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole‐genome sequencing, which also remains impractical for large population samples due to the cost of ...
DOI:
10.1111/1755-0998.12495

17. Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs

Author:
D. J. Machado; M. L. Lyra; T. Grant
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 686-693
ISSN:
1755-098X
Subject:
Bufonidae; DNA; Dendrobatidae; baiting; biodiversity; bycatch; frogs; genes; genomics; high-throughput nucleotide sequencing; mitochondria; mitochondrial genome; nucleotide sequences; protein subunits; ribosomal proteins; transfer RNA
Abstract:
... Next‐generation sequencing continues to revolutionize biodiversity studies by generating unprecedented amounts of DNA sequence data for comparative genomic analysis. However, these data are produced as millions or billions of short reads of variable quality that cannot be directly applied in comparative analyses, creating a demand for methods to facilitate assembly. We optimized an in silico strat ...
DOI:
10.1111/1755-0998.12492

18. Recombination patterns reveal information about centromere location on linkage maps

Author:
Morten T. Limborg; Garrett J. McKinney; Lisa W. Seeb; James E. Seeb
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 655-661
ISSN:
1755-098X
Subject:
Oncorhynchus mykiss; Oncorhynchus nerka; barley; centromeres; chromosome mapping; crossover interference; eukaryotic cells; genes; linkage groups; males; meiosis
Abstract:
... Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres – an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference, approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming ...
DOI:
10.1111/1755-0998.12484

19. Statistical approaches to account for false‐positive errors in environmental DNA samples

Author:
José J. Lahoz‐Monfort; Gurutzeta Guillera‐Arroita; Reid Tingley
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 673-685
ISSN:
1755-098X
Subject:
DNA; models; polymerase chain reaction; statistical analysis
Abstract:
... Environmental DNA (eDNA) sampling is prone to both false‐positive and false‐negative errors. We review statistical methods to account for such errors in the analysis of eDNA data and use simulations to compare the performance of different modelling approaches. Our simulations illustrate that even low false‐positive rates can produce biased estimates of occupancy and detectability. We further show ...
DOI:
10.1111/1755-0998.12486

20. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

Author:
G. J. McKinney; L. W. Seeb; W. A. Larson; D. Gomez‐Uchida; M. T. Limborg; M. S. O. Brieuc; M. V. Everett; K. A. Naish; R. K. Waples; J. E. Seeb
Source:
Molecular ecology resources 2016 v.16 no.3 pp. 769-783
ISSN:
1755-098X
Subject:
Salmo salar; quantitative trait loci; heat tolerance; loci; stress response; introduced species; expressed sequence tags; Oncorhynchus tshawytscha; chromosome mapping; genotyping; indigenous species; single nucleotide polymorphism
Abstract:
... Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynch ...
DOI:
10.1111/1755-0998.12479