Molecular Ecology Resources Journal Impact Factor & Information

Publisher: Wiley

Journal description

Current impact factor: 3.71

Impact Factor Rankings

2015 Impact Factor Available summer 2016
2014 Impact Factor 3.712
2013 Impact Factor 5.626
2012 Impact Factor 7.432
2011 Impact Factor 3.062
2010 Impact Factor 1.631
2009 Impact Factor 1.251
2008 Impact Factor 0

Impact factor over time

Impact factor

Additional details

5-year impact 4.99
Cited half-life 4.50
Immediacy index 1.63
Eigenfactor 0.03
Article influence 1.65
Other titles Molecular ecology resources (Online)
ISSN 1755-0998
OCLC 190864867
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details


  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author cannot archive a post-print version
  • Restrictions
    • 12 months embargo
  • Conditions
    • Some journals have separate policies, please check with each journal directly
    • On author's personal website, institutional repositories, arXiv, AgEcon, PhilPapers, PubMed Central, RePEc or Social Science Research Network
    • Author's pre-print may not be updated with Publisher's Version/PDF
    • Author's pre-print must acknowledge acceptance for publication
    • Non-Commercial
    • Publisher's version/PDF cannot be used
    • Publisher source must be acknowledged with citation
    • Must link to publisher version with set statement (see policy)
    • If OnlineOpen is available, BBSRC, EPSRC, MRC, NERC and STFC authors, may self-archive after 12 months
    • If OnlineOpen is available, AHRC and ESRC authors, may self-archive after 24 months
    • Publisher last contacted on 07/08/2014
    • This policy is an exception to the default policies of 'Wiley'
  • Classification
    ​ yellow

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Recent developments in genotyping technologies coupled with the growing desire to characterise genome variation in Anopheles populations opens the opportunity to develop more effective genotyping strategies for high-throughput screening. A major bottleneck of this goal is nucleic acid extraction. Here, we examined the feasibility of using intact portions of a mosquito's leg as sources of template DNA for whole genome amplification (WGA) by Primer-Extension Pre-amplification. We used the Agena Biosciences MassARRAY platform (formerly Sequenom) to genotype 78 SNPs for 265 WGA leg samples. We performed nucleic acid extraction on 36 mosquito carcasses and compared the genotype call concordance with their corresponding legs, and observed full concordance. Using three legs instead of one improved genotyping success rates (96% versus 89%, respectively), although this difference was not significant. We provide a proof of concept that WGA reactions can be performed directly on mosquito legs, thereby eliminating the need to extract nucleic acid. This approach is straightforward, sensitive and allows both species determination and genotyping of Anopheles mosquitoes to be performed in a high-throughput manner. Our protocol also leaves the mosquito body intact facilitating other experimental analysis to be undertaken on the same sample. Based on our findings, this method would also be suitable for use with other insect species. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 10/2015; DOI:10.1111/1755-0998.12473
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    ABSTRACT: HybridCheck is a software package to visualise the recombination signal in large DNA sequence dataset, and it can be used to analyse recombination, genetic introgression, hybridisation and horizontal gene transfer. It can scan large (multiple kb) contigs and whole genome sequences of three or more individuals. HybridCheck is written in the R software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface (GUI). In addition, the R code can be readily incorporated in scripts and analysis pipelines. HybridCheck implements several ABBA-BABA tests and visualises the effects of hybridisation and the resulting mosaic-like genome structure in high-density graphics. The package also reports: (1) the breakpoint positions, (2) the number of mutations in each introgressed block, (3) the probability that the identified region is not caused by recombination, and (4) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY, or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridisation and incomplete lineage sorting. HybridCheck is libré software and it and its manual are free to download from This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 09/2015; DOI:10.1111/1755-0998.12469
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    ABSTRACT: New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5,060 UCE loci in 27 Western Scrub-Jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3,749 UCE loci containing 4,460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures we used for SNP calling. This study and other recent studies on the genomics of museums specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 09/2015; DOI:10.1111/1755-0998.12466
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    ABSTRACT: Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly-multiplexed single-nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from i) a three-generation inbred (F2) pedigree, ii) the French breeding population, and iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2,052 / 8,410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5,016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3,981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 09/2015; DOI:10.1111/1755-0998.12464
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    ABSTRACT: Geography and landscape are important determinants of genetic variation in natural populations, and several ancestry estimation methods have been proposed to investigate population structure using genetic and geographic data simultaneously. Those approaches are often based on computer-intensive stochastic simulations, and do not scale with the dimensions of the data sets generated by high-throughput sequencing technologies. There is a growing demand for faster algorithms able to analyze genome-wide patterns of population genetic variation in their geographic context.In this study, we present TESS3, a major update of the spatial ancestry estimation program TESS. By combining matrix factorization and spatial statistical methods, TESS3 provides estimates of ancestry coefficients with accuracy comparable to TESS and with run-times much faster than the Bayesian version. In addition, the TESS3 program can be used to perform genome scans for selection, and separate adaptive from non-adaptive genetic variation using ancestral allele frequency differentiation tests. The main features of TESS3 are illustrated using simulated data and analyzing genomic data from European lines of the plant species Arabidopsis thaliana.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 09/2015; DOI:10.1111/1755-0998.12471
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    ABSTRACT: Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is done by hand. With the rise of Next Generation Sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruitflies (a model species) and red deers (a non-model species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 09/2015; DOI:10.1111/1755-0998.12467
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    ABSTRACT: Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programs for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97 075 highly reliable in silico SNPs. These SNPs were distributed across 14 909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2%, for in silico SNPs compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 09/2015; DOI:10.1111/1755-0998.12468
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    ABSTRACT: The invasion of non-native species that are closely related to native species can lead to competitive elimination of the native species and/or genomic extinction through hybridization. Such invasions often become serious before they are detected, posing unprecedented threats to biodiversity. A Japanese native strain of common carp (Cyprinus carpio) has become endangered owing to the invasion of non-native strains introduced from the Eurasian continent. Here, we propose a rapid environmental DNA-based approach to quantitatively monitor the invasion of non-native genotypes. Using this system, we developed a method to quantify the relative proportion of native and non-native DNA based on a single nucleotide polymorphism by using cycling probe technology in real-time PCR. The efficiency of this method was confirmed in aquarium experiments, where the quantified proportion of native and non-native DNA in the water was well correlated to the biomass ratio of native and non-native genotypes. This method provided quantitative estimates for the proportion of native and non-native DNA in natural rivers and reservoirs, which allowed us to estimate the degree of invasion of non-native genotypes without catching and analysing individual fish. Our approach would dramatically facilitate the process of quantitatively monitoring the invasion of non-native conspecifics in aquatic ecosystems, thus revealing a promising method for risk assessment and management in biodiversity conservation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 08/2015; DOI:10.1111/1755-0998.12460