Molecular Ecology Resources

Cover image for Vol. 16 Issue 5

Early View (Online Version of Record published before inclusion in an issue)

Edited By: Shawn Narum

Impact Factor: 5.298

ISI Journal Citation Reports © Ranking: 2015: 6/45 (Evolutionary Biology); 14/149 (Ecology); 46/289 (Biochemistry & Molecular Biology)

Online ISSN: 1755-0998

Associated Title(s): Molecular Ecology


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  1. Resource Articles

    1. Experimental conditions improving in-solution target enrichment for ancient DNA

      Diana I. Cruz-Dávalos, Bastien Llamas, Charleen Gaunitz, Antoine Fages, Cristina Gamba, Julien Soubrier, Pablo Librado, Andaine Seguin-Orlando, Mélanie Pruvost, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A. S. Al-Rasheid, Amelie Scheu, Norbert Beneke, Arne Ludwig, Alan Cooper, Eske Willerslev and Ludovic Orlando

      Version of Record online: 18 SEP 2016 | DOI: 10.1111/1755-0998.12595

  2. Special Issue: Population Genomics in R

    1. pcadapt: an R package to perform genome scans for selection based on principal component analysis

      Keurcien Luu, Eric Bazin and Michael G. B. Blum

      Version of Record online: 7 SEP 2016 | DOI: 10.1111/1755-0998.12592

  3. Genomic Resources Notes

    1. Whole genome sequence resource of Indian Zaprionus indianus

      Radhika Khanna and Sujata Mohanty

      Version of Record online: 6 SEP 2016 | DOI: 10.1111/1755-0998.12582

  4. Special Issue: Population Genomics in R

    1. minotaur: A platform for the analysis and visualization of multivariate results from genome scans with R Shiny

      Robert Verity, Caitlin Collins, Daren C. Card, Sara M. Schaal, Liuyang Wang and Katie E. Lotterhos

      Version of Record online: 31 AUG 2016 | DOI: 10.1111/1755-0998.12579

  5. Resource Articles

    1. Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio

      Toshifumi Minamoto, Kimiko Uchii, Teruhiko Takahara, Takumi Kitayoshi, Satsuki Tsuji, Hiroki Yamanaka and Hideyuki Doi

      Version of Record online: 31 AUG 2016 | DOI: 10.1111/1755-0998.12586

  6. Genomic Resources Notes

    1. Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)

      V. A. C. Pavinato, G. R. A. Margarido, A. J. Wijeratne, S. Wijeratne, T. Meulia, A. P. Souza, A. P. Michel and M. I. Zucchi

      Version of Record online: 30 AUG 2016 | DOI: 10.1111/1755-0998.12583

  7. News and Views

    1. Opinion

      You have full text access to this OnlineOpen article
      The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes

      Matheus Sanitá Lima, Laura C. Woods, Matthew W. Cartwright and David Roy Smith

      Version of Record online: 30 AUG 2016 | DOI: 10.1111/1755-0998.12585

  8. Resource Articles

    1. angsd-wrapper: utilities for analysing next-generation sequencing data

      Arun Durvasula, Paul J. Hoffman, Tyler V. Kent, Chaochih Liu, Thomas J. Y. Kono, Peter L. Morrell and Jeffrey Ross-Ibarra

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12578

  9. Special Issue: Population Genomics in R

    1. Linking genomics and population genetics with r

      Emmanuel Paradis, Thierry Gosselin, Jérôme Goudet, Thibaut Jombart and Klaus Schliep

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12577

  10. Resource Articles

    1. wisepair: a computer program for individual matching in genetic tracking studies

      Andrew P. Rothstein, Ryan McLaughlin, Alejandro Acevedo-Gutiérrez and Dietmar Schwarz

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12590

    2. High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA

      M. De Barba, C. Miquel, S. Lobréaux, P. Y. Quenette, J. E. Swenson and P. Taberlet

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12594

    3. Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites

      Jean P. Elbers, Rachel W. Clostio and Sabrina S. Taylor

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12591

    4. Arbovirus and insect-specific virus discovery in Kenya by novel six genera multiplex high-resolution melting analysis

      Jandouwe Villinger, Martin K. Mbaya, Daniel Ouso, Purity N. Kipanga, Joel Lutomiah and Daniel K. Masiga

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12584

    5. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

      Gautier Sarah, Felix Homa, Stéphanie Pointet, Sandy Contreras, François Sabot, Benoit Nabholz, Sylvain Santoni, Laure Sauné, Morgane Ardisson, Nathalie Chantret, Christopher Sauvage, James Tregear, Cyril Jourda, David Pot, Yves Vigouroux, Hana Chair, Nora Scarcelli, Claire Billot, Nabila Yahiaoui, Roberto Bacilieri, Bouchaib Khadari, Michel Boccara, Adéline Barnaud, Jean-Pierre Péros, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin and Manuel Ruiz

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12587

    6. A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird

      Sara A. Kaiser, Scott A. Taylor, Nancy Chen, T. Scott Sillett, Eliana R. Bondra and Michael S. Webster

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12589

    7. Draft genome of an iconic Red Sea reef fish, the blacktail butterflyfish (Chaetodon austriacus): current status and its characteristics

      Joseph D. DiBattista, Xin Wang, Pablo Saenz-Agudelo, Marek J. Piatek, Manuel Aranda and Michael L. Berumen

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12588

    8. Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

      E. E. Nielsen, J. A. T. Morgan, S. L. Maher, J. Edson, M. Gauthier, J. Pepperell, B. J. Holmes, M. B. Bennett and J. R. Ovenden

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12580

    9. Real-time PCR detection of Didemnum perlucidum (Monniot, 1983) and Didemnum vexillum (Kott, 2002) in an applied routine marine biosecurity context

      Tiffany J. S. Simpson, P. Joana Dias, Michael Snow, Julieta Muñoz and Tina Berry

      Version of Record online: 29 AUG 2016 | DOI: 10.1111/1755-0998.12581

    10. discomark: Nuclear marker discovery from orthologous sequences using draft genome data

      Sereina Rutschmann, Harald Detering, Sabrina Simon, Jakob Fredslund and Michael T. Monaghan

      Version of Record online: 23 AUG 2016 | DOI: 10.1111/1755-0998.12576

    11. Comparative performance of double-digest RAD sequencing across divergent arachnid lineages

      Mercedes Burns, James Starrett, Shahan Derkarabetian, Casey H. Richart, Allan Cabrero and Marshal Hedin

      Version of Record online: 18 AUG 2016 | DOI: 10.1111/1755-0998.12575

  11. Special Issue: Population Genomics in R

    1. You have full text access to this OnlineOpen article
      apex: phylogenetics with multiple genes

      Thibaut Jombart, Frederick Archer, Klaus Schliep, Zhian Kamvar, Rebecca Harris, Emmanuel Paradis, Jérome Goudet and Hilmar Lapp

      Version of Record online: 12 AUG 2016 | DOI: 10.1111/1755-0998.12567

    2. genepopedit: a simple and flexible tool for manipulating multilocus molecular data in R

      Ryan R. E. Stanley, Nicholas W. Jeffery, Brendan F. Wringe, Claudio DiBacco and Ian R. Bradbury

      Version of Record online: 11 AUG 2016 | DOI: 10.1111/1755-0998.12569

  12. Resource Articles

    1. You have full text access to this OnlineOpen article
      Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel

      Elmira Mohandesan, Camilla F. Speller, Joris Peters, Hans-Peter Uerpmann, Margarethe Uerpmann, Bea De Cupere, Michael Hofreiter and Pamela A. Burger

      Version of Record online: 1 AUG 2016 | DOI: 10.1111/1755-0998.12551

  13. Genomic Resources Notes

    1. Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays

      Vanessa P. Cruz, Manuel Vera, Belén G. Pardo, John Taggart, Paulino Martinez, Claudio Oliveira and Fausto Foresti

      Version of Record online: 28 JUL 2016 | DOI: 10.1111/1755-0998.12564

  14. Resource Articles

    1. Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica

      Zhongying Qiu, Fei Liu, Huimeng Lu and Yuan Huang

      Version of Record online: 20 JUL 2016 | DOI: 10.1111/1755-0998.12553

    2. A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa

      S. Guimaraes, M. Pruvost, J. Daligault, E. Stoetzel, E. A. Bennett, N. M.-L. Côté, V. Nicolas, A. Lalis, C. Denys, E.-M. Geigl and T. Grange

      Version of Record online: 20 JUL 2016 | DOI: 10.1111/1755-0998.12565

  15. Special Issue: Population Genomics in R

    1. stratag: An r package for manipulating, summarizing and analysing population genetic data

      Frederick I. Archer, Paula E. Adams and Brita B. Schneiders

      Version of Record online: 20 JUL 2016 | DOI: 10.1111/1755-0998.12559

  16. Resource Articles

    1. megasat: automated inference of microsatellite genotypes from sequence data

      Luyao Zhan, Ian G. Paterson, Bonnie A. Fraser, Beth Watson, Ian R. Bradbury, Praveen Nadukkalam Ravindran, David Reznick, Robert G. Beiko and Paul Bentzen

      Version of Record online: 19 JUL 2016 | DOI: 10.1111/1755-0998.12561

  17. From the Cover

    1. You have full text access to this OnlineOpen article
      Measuring microbial fitness in a field reciprocal transplant experiment

      Primrose J. Boynton, Rike Stelkens, Vienna Kowallik and Duncan Greig

      Version of Record online: 15 JUL 2016 | DOI: 10.1111/1755-0998.12562

  18. Resource Articles

    1. ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments

      F. Mora-Márquez, V. García-Olivares, B. C. Emerson and U. López de Heredia

      Version of Record online: 12 JUL 2016 | DOI: 10.1111/1755-0998.12550

    2. Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding

      Arthur Kocher, Jean-Charles Gantier, Pascal Gaborit, Lucie Zinger, Helene Holota, Sophie Valiere, Isabelle Dusfour, Romain Girod, Anne-Laure Bañuls and Jerome Murienne

      Version of Record online: 12 JUL 2016 | DOI: 10.1111/1755-0998.12556

    3. De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis

      Rebekah L. Horn, Thiruvarangan Ramaraj, Nicholas P. Devitt, Faye D. Schilkey and David E. Cowley

      Version of Record online: 12 JUL 2016 | DOI: 10.1111/1755-0998.12555

  19. Special Issue: Population Genomics in R

    1. vcfr: a package to manipulate and visualize variant call format data in r

      Brian J. Knaus and Niklaus J. Grünwald

      Version of Record online: 12 JUL 2016 | DOI: 10.1111/1755-0998.12549

    2. Developing educational resources for population genetics in r: an open and collaborative approach

      Zhian N. Kamvar, Margarita M. López-Uribe, Simone Coughlan, Niklaus J. Grünwald, Hilmar Lapp and Stéphanie Manel

      Version of Record online: 12 JUL 2016 | DOI: 10.1111/1755-0998.12558

  20. Resource Articles

    1. Partial genotyping at polymorphic markers can improve heritability estimates in sibling groups

      J. Gauzere, S. Oddou-Muratorio, L. Gay and E. K. Klein

      Version of Record online: 6 JUL 2016 | DOI: 10.1111/1755-0998.12536

    2. A high-throughput detection method for invasive fruit fly (Diptera: Tephritidae) species based on microfluidic dynamic array

      Fan Jiang, Wei Fu, Anthony R. Clarke, Mark Kurt Schutze, Agus Susanto, Shuifang Zhu and Zhihong Li

      Version of Record online: 5 JUL 2016 | DOI: 10.1111/1755-0998.12542

  21. From the Cover

  22. Resource Articles

    1. A universal and reliable assay for molecular sex identification of three-spined sticklebacks (Gasterosteus aculeatus)

      E.-A. Toli, F.C.F. Calboli, T. Shikano and J. Merilä

      Version of Record online: 30 JUN 2016 | DOI: 10.1111/1755-0998.12543

    2. Identification of novel microRNA genes in freshwater and marine ecotypes of the three-spined stickleback (Gasterosteus aculeatus)

      S. M. Rastorguev, A. V. Nedoluzhko, F. S. Sharko, E. S. Boulygina, A. S. Sokolov, N. M. Gruzdeva, K. G. Skryabin and E. B. Prokhortchouk

      Version of Record online: 30 JUN 2016 | DOI: 10.1111/1755-0998.12545

    3. Lessons from genome skimming of arthropod-preserving ethanol

      B. Linard, P. Arribas, C. Andújar, A. Crampton-Platt and A. P. Vogler

      Version of Record online: 23 JUN 2016 | DOI: 10.1111/1755-0998.12539

    4. CoMuS: simulating coalescent histories and polymorphic data from multiple species

      S. Papadantonakis, P. Poirazi and P. Pavlidis

      Version of Record online: 23 JUN 2016 | DOI: 10.1111/1755-0998.12544

    5. metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data

      Guillaume Louvel, Clio Der Sarkissian, Kristian Hanghøj and Ludovic Orlando

      Version of Record online: 22 JUN 2016 | DOI: 10.1111/1755-0998.12546

    6. Family-assisted inference of the genetic architecture of major histocompatibility complex variation

      A. Gaigher, R. Burri, W. H. Gharib, P. Taberlet, A. Roulin and L. Fumagalli

      Version of Record online: 4 JUN 2016 | DOI: 10.1111/1755-0998.12537

    7. A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada

      M. Castelin, N. Van Steenkiste, E. Pante, R. Harbo, G. Lowe, S. R. Gilmore, T. W. Therriault and C. L. Abbott

      Version of Record online: 19 MAY 2016 | DOI: 10.1111/1755-0998.12534

    8. Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa

      M. O. Burford Reiskind, K. Coyle, H. V. Daniels, P. Labadie, M. H. Reiskind, N. B. Roberts, R. B. Roberts, J. Schaff and E. L. Vargo

      Version of Record online: 17 MAY 2016 | DOI: 10.1111/1755-0998.12527

    9. TEMPLE: analysing population genetic variation at transcription factor binding sites

      Maria Litovchenko and Stefan Laurent

      Version of Record online: 9 MAY 2016 | DOI: 10.1111/1755-0998.12535

    10. A genes eye view of ontogeny: de novo assembly and profiling of the Gryllus rubens transcriptome

      Emma L. Berdan, Thomas Blankers, Isabelle Waurick, Camila J. Mazzoni and Frieder Mayer

      Version of Record online: 24 APR 2016 | DOI: 10.1111/1755-0998.12530

    11. Evaluation of TagSeq, a reliable low-cost alternative for RNAseq

      Brian K. Lohman, Jesse N. Weber and Daniel I. Bolnick

      Version of Record online: 22 APR 2016 | DOI: 10.1111/1755-0998.12529

    12. Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species

      Hadi Dahruddin, Aditya Hutama, Frédéric Busson, Sopian Sauri, Robert Hanner, Philippe Keith, Renny Hadiaty and Nicolas Hubert

      Version of Record online: 19 APR 2016 | DOI: 10.1111/1755-0998.12528

    13. Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication

      Jun Huang, Youjun Gao, Haitao Jia and Zuxin Zhang

      Version of Record online: 31 MAR 2016 | DOI: 10.1111/1755-0998.12526

    14. Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika

      Floris C. Breman, Sara Loix, Kurt Jordaens, Jos Snoeks and Maarten Van Steenberge

      Version of Record online: 29 MAR 2016 | DOI: 10.1111/1755-0998.12523

    15. Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions

      Anaïs Lacoursière-Roussel, Maikel Rosabal and Louis Bernatchez

      Version of Record online: 28 MAR 2016 | DOI: 10.1111/1755-0998.12522

  23. Special Issue: Population Genomics in R


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