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 in an underlying Dirichlet distr... 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 major reasons for the paucity of co... 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 representing 79 Genera and 37 Famil... hiện toàn bộ
Microsatellite markers for the diploid basidiomycete fungus Armillaria mellea
Molecular Ecology Resources - Tập 9 Số 3 - Trang 943-946 - 2009
Kendra Baumgartner, Lisa C. Grubisha, Phillip Fujiyoshi, Matteo Garbelotto, Sarah E. Bergemann
AbstractWe isolated and characterized 12 microsatellite markers for two North American populations (California, Pennsylvania) of Armillaria mellea, a fungal pathogen responsible for Armillaria root disease of numerous woody plants. Allele frequency ranged from two to nine alleles per locus, and gene diversity ranged from 0.05 to 0.86. Of the 12 loci, eight loci were polymorphic in the California a... hiện toàn bộ
Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009–31 July 2009
Molecular Ecology Resources - Tập 9 Số 6 - Trang 1460-1466 - 2009
Glenn R. Almany, Maurício P. Arruda, Wolfgang Arthofer, Zahi K. Atallah, Steven R. Beissinger, Michael L. Berumen, Steven M. Bogdanowicz, Stacy D. Brown, Michael W. Bruford, Charles Burdine, Jeremiah W. Busch, Nathan R. Campbell, David W. Carey, Bryan C. Carstens, Ka Hou Chu, Marc A. Cubeta, J. P. CUDA, Zhaoxia Cui, L. E. Datnoff, José A. Dávila, EMILY S. DAVIS, R. M. Davis, Onno E. Diekmann, Eduardo Eizirik, Juan A. Fargallo, F.A. Fernandes, Hideo Fukuda, Liane Rosewich Gale, Elizabeth Gallagher, Y. R. Gao, Philippe Girard, Anna Godhe, Evonnildo Costa Gonçalves, Licínia Gouveia, AMBER M. GRAJCZYK, Michael J. Grose, Zhifeng Gu, Andreas Hillarp, Karolina Härnström, Amanda Heather Hemmingsen, Gerald J. Holmes, Cheng‐Hua Huang, CHUAN‐CHIN HUANG, Stephen P. Hudman, Geoffrey P. Jones, Loukas Kanetis, Iddya Karunasagar, Indrani Karunasagar, Nusha Keyghobadi, Steve J. Klosterman, Page E. Klug, Jennifer Koch, Margaret M. Koopman, Kirsten Köppler, Eriko Koshimizu, Susanne Krumböck, Thomas L. Kubisiak, Jacob B. Landis, Mario Lasta, Chow‐Yang Lee, Qianqian Li, Shou‐Hsien Li, Rong‐Chien Lin, Mandi Liu, NA LIU, Wenliang Liu, Yuan Liu, Anne Loiseau, Weisha Luan, K. K. MARUTHACHALAM, Helen McCormick, Rohan Mellick, Patrick J. Monnahan, Eliana Morielle‐Versute, Tomás E. Murray, Shawn R. Narum, K. N. Neufeld, P. Nová, P. S. Ojiambo, Nobuaki Okamoto, Ahmad Sofiman Othman, William A. Overholt, Renata Pardini, Ian G. Paterson, OLIVIA A. PATTY, Robert J. Paxton, Serge Planes, Carolyn Porter, Morgan S. Pratchett, Thomas Püttker, Gordana Rašić, Bilal Rasool, Olivier Rey, Markus Riegler, Christina Riehl, John M. K. Roberts, Pamela D. Roberts, Elisabeth Rochel, Kevin J. Roe, Maurizio Rossetto, Daniel E. Ruzzante, Takashi Sakamoto, V. Saravanan, Cladinara Roberts Sarturi, Anke Schmidt, Maria Paula Cruz Schneider, Hannes Schuler, Jeanne M. Serb, Ester Á. Serrão, Yao Shi, Artur Silva, Simon Yung Wa Sin, Simone Sommer, Christian Stauffer, Carlos Augusto Strüssmann, Krishna V. Subbarao, Craig Syms, Feng Tan, Eugenio Daniel Tejedor, Simon R. Thorrold, Robert N. Trigiano, María Inés Trucco, Mirian T. N. Tsuchiya, Pablo M. Vergara, Mirjam S. van de Vliet, Phillip A. Wadl, Aimin Wang, Hongxia Wang, R. X. WANG, Xinwang Wang, Yan Wang, Andrew R. Weeks, Fuwen Wei, W.J. Werner, E. O. Wiley, Dean A. Williams, R.J. Wilkins, Samantha M. Wisely, Kimberly A. With, Dengsheng Wu, Cheng‐Te Yao, Cynthia Yau, Beng-Keok Yeap, Baoping Zhai, Xiangjiang Zhan, Guoyan Zhang, S. Y. ZHANG, Ru Zhao, Lifeng Zhu
AbstractThis article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes ... hiện toàn bộ
A comparative assessment ofSNPand microsatellite markers for assigning parentage in a socially monogamous bird
Molecular Ecology Resources - Tập 17 Số 2 - Trang 183-193 - 2017
Sara A. Kaiser, Scott A. Taylor, Nancy Chen, T. Scott Sillett, Eliana R. Bondra, Michael S. Webster
AbstractSingle‐nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations ofSNPs and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex ... hiện toàn bộ
related: an R package for analysing pairwise relatedness from codominant molecular markers
Molecular Ecology Resources - Tập 15 Số 3 - Trang 557-561 - 2015
Jack Pew, P. H. Muir, Jinliang Wang, Timothy R. Frasier
AbstractAnalyses of pairwise relatedness represent a key component to addressing many topics in biology. However, such analyses have been limited because most available programs provide a means to estimate relatedness based on only a single estimator, making comparison across estimators difficult. Second, all programs to date have been platform specific, working only on a specific operating system... 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 program for PCs running Windows operating system. A simul... hiện toàn bộ
Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy
Molecular Ecology Resources - Tập 13 Số 6 - Trang 1058-1068 - 2013
Raquel Pino‐Bodas, María P. Martín, Ana Rosa Burgaz, H. Thorsten Lumbsch
AbstractThe lichen‐forming fungal genus Cladonia is species‐rich with approximately 500 described species. The accepted barcode for fungi (ITS rDNA) often fails in identifying Cladonia spp. In order to find other markers that, in combination with the ITS rDNA region can be used for species identification in Cladonia, we studied the loci IGS rDNA, ef1α, rpb2 and cox1. A total of 782 sequences from ... 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 small subsets of the available statistics, and are impractical to evaluate all gene flow hypotheses across da... hiện toàn bộ
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