Molecular Ecology Resources

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Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data
Molecular Ecology Resources - Tập 20 Số 2 - Trang 481-497 - 2020
Joshua G. Harrison, W. John Calder, Vivaswat Shastry, C. Alex Buerkle
AbstractMolecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modelled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features...... hiện toàn bộ
Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs
Molecular Ecology Resources - Tập 14 Số 5 - Trang 1024-1031 - 2014
Jun‐Bo Yang, Li D, Hongtao Li
AbstractChloroplast genomes supply indispensable information that helps improve the phylogenetic resolution and even as organelle‐scale barcodes. Next‐generation sequencing technologies have helped promote sequencing of complete chloroplast genomes, but compared with the number of angiosperms, relatively few chloroplast genomes have been sequenced. There are two ma...... hiện toàn bộ
DNA barcoding Indian marine fishes
Molecular Ecology Resources - Tập 11 Số 1 - Trang 60-71 - 2011
W. S. Lakra, Mukti Verma, Mukunda Goswami, J. K. Jena, Vindhya Mohindra, Peyush Punia, A. Gopalakrishnan, Karan Veer Singh, Robert Ward, Paul D. N. Hebert
AbstractDNA barcoding has been adopted as a global bio‐identification system for animals in recent years. A major national programme on DNA barcoding of fish and marine life was initiated in India by the authors during 2006 and 115 species of marine fish covering Carangids, Clupeids, Scombrids, Groupers, Sciaenids, Silverbellies, Mullids, Polynemids and Silurids re...... hiện toàn bộ
coancestry: a program for simulating, estimating and analysing relatedness and inbreeding coefficients
Molecular Ecology Resources - Tập 11 Số 1 - Trang 141-145 - 2011
Jinliang Wang
AbstractThe software package coancestry implements seven relatedness estimators and three inbreeding estimators to estimate relatedness and inbreeding coefficients from multilocus genotype data. Two likelihood estimators that allow for inbred individuals and account for genotyping errors are for the first time included in this user‐friendly progr...... hiện toàn bộ
Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files
Molecular Ecology Resources - Tập 21 Số 2 - Trang 584-595 - 2021
Milan Malinsky, Michael Matschiner, Hannes Svardal
AbstractPatterson's D, also known as the ABBA‐BABA statistic, and related statistics such as the f4‐ratio, are commonly used to assess evidence of gene flow between populations or closely related species. Currently available implementations often require custom file formats, implement only s...... hiện toàn bộ
The genome of the marine medaka Oryzias melastigma
Molecular Ecology Resources - Tập 18 Số 3 - Trang 656-665 - 2018
Hui‐Su Kim, Bo‐Young Lee, Jeonghoon Han, Chang‐Bum Jeong, Dae‐Sik Hwang, Min‐Chul Lee, Hye‐Min Kang, Duck‐Hyun Kim, Dong Soo Lee, Jaebum Kim, Ik‐Young Choi, Jae‐Seong Lee
AbstractMarine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field‐based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole‐genome draft of O...... hiện toàn bộ
Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development
Molecular Ecology Resources - Tập 11 Số 6 - Trang 1093-1101 - 2011
M. Gardner, Alison Fitch, Terry Bertozzi, Andrew J. Lowe
AbstractNext generation sequencing is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. Here, we summarize the results of the large‐scale development of microsatellites for 54 nonmodel species using next generation sequencing and show that there are clear differences amongst plants, invertebrat...... hiện toàn bộ
Removing external DNA contamination from arthropod predators destined for molecular gut‐content analysis
Molecular Ecology Resources - Tập 12 Số 3 - Trang 464-469 - 2012
Matthew H. Greenstone, Donald C. Weber, Thomas A. Coudron, Mark E. Payton, Jing Hu
AbstractEcological research requires large samples for statistical validity, typically hundreds or thousands of individuals, which are most efficiently gathered by mass‐collecting techniques. For the study of interspecific interactions, molecular gut‐content analysis enables detection of arthropod predation with minimal disruption of community interactions. Field e...... hiện toàn bộ
genepop’007: a complete re‐implementation of the genepop software for Windows and Linux
Molecular Ecology Resources - Tập 8 Số 1 - Trang 103-106 - 2008
François Rousset
AbstractThis note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previ...... hiện toàn bộ
Next‐generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
Molecular Ecology Resources - Tập 11 Số s1 - Trang 117-122 - 2011
Paul A. Hohenlohe, Stephen J. Amish, Julian Catchen, Fred W. Allendorf, Gordon Luikart
AbstractThe increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction‐site‐associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between intr...... hiện toàn bộ
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