Molecular Ecology Resources

Cover image for Vol. 17 Issue 1

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: 6/46 (Evolutionary Biology); 14/150 (Ecology); 46/289 (Biochemistry & Molecular Biology)

Online ISSN: 1755-0998

Associated Title(s): Molecular Ecology


  1. 1 - 69
  1. Resource Articles

    1. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

      Roberto Arrigoni, Benoît Vacherie, Francesca Benzoni, Fabrizio Stefani, Eric Karsenti, Olivier Jaillon, Fabrice Not, Flavia Nunes, Claude Payri, Patrick Wincker and Valérie Barbe

      Version of Record online: 23 JAN 2017 | DOI: 10.1111/1755-0998.12640

    2. A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy

      Manuela Winkler, Pedro Escobar García, Andreas Gattringer, Michaela Sonnleitner, Karl Hülber, Peter Schönswetter and Gerald M. Schneeweiss

      Version of Record online: 5 JAN 2017 | DOI: 10.1111/1755-0998.12641

    3. eDNA metabarcoding: a promising method for anuran surveys in highly diverse tropical forests

      Carla M. Lopes, Thais Sasso, Alice Valentini, Tony Dejean, Marcio Martins, Kelly R. Zamudio and Célio F. B. Haddad

      Version of Record online: 5 JAN 2017 | DOI: 10.1111/1755-0998.12643

    4. SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)

      Irene Muñoz, Dora Henriques, Laura Jara, J. Spencer Johnston, Julio Chávez-Galarza, Pilar De La Rúa and M. Alice Pinto

      Version of Record online: 26 DEC 2016 | DOI: 10.1111/1755-0998.12637

  2. News and Views

    1. Opinion

      You have free access to this content
      Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

      David B. Lowry, Sean Hoban, Joanna L. Kelley, Katie E. Lotterhos, Laura K. Reed, Michael F. Antolin and Andrew Storfer

      Version of Record online: 16 DEC 2016 | DOI: 10.1111/1755-0998.12635

  3. Resource Articles

    1. Combining bleach and mild predigestion improves ancient DNA recovery from bones

      Sanne Boessenkool, Kristian Hanghøj, Heidi M. Nistelberger, Clio Der Sarkissian, Agata T. Gondek, Ludovic Orlando, James H. Barrett and Bastiaan Star

      Version of Record online: 15 DEC 2016 | DOI: 10.1111/1755-0998.12623

    2. DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland

      O. Hawlitschek, J. Morinière, G. U. C. Lehmann, A. W. Lehmann, M. Kropf, A. Dunz, F. Glaw, M. Detcharoen, S. Schmidt, A. Hausmann, N. U. Szucsich, S. A. Caetano-Wyler and G. Haszprunar

      Version of Record online: 5 DEC 2016 | DOI: 10.1111/1755-0998.12638

    3. You have full text access to this OnlineOpen article
      Strategies for complete plastid genome sequencing

      Alex D. Twyford and Rob W. Ness

      Version of Record online: 28 NOV 2016 | DOI: 10.1111/1755-0998.12626

    4. You have full text access to this OnlineOpen article
      High performance computation of landscape genomic models including local indicators of spatial association

      S. Stucki, P. Orozco-terWengel, B. R. Forester, S. Duruz, L. Colli, C. Masembe, R. Negrini, E. Landguth, M. R. Jones, The NEXTGEN Consortium, M. W. Bruford, P. Taberlet and S. Joost

      Version of Record online: 28 NOV 2016 | DOI: 10.1111/1755-0998.12629

    5. DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep

      Abdolbaset Ghorbani, Barbara Gravendeel, Sugirthini Selliah, Shahin Zarré and Hugo de Boer

      Version of Record online: 28 NOV 2016 | DOI: 10.1111/1755-0998.12615

    6. Controlling for P-value inflation in allele frequency change in experimental evolution and artificial selection experiments

      Petri Kemppainen, Bernt Rønning, Thomas Kvalnes, Ingerid J. Hagen, Thor Harald Ringsby, Anna M. Billing, Henrik Pärn, Sigbjørn Lien, Arild Husby, Bernt-Erik Sæther and Henrik Jensen

      Version of Record online: 25 NOV 2016 | DOI: 10.1111/1755-0998.12631

    7. Resources for phylogenomic analyses of Australian terrestrial vertebrates

      Jason G. Bragg, Sally Potter, Ke Bi, Renee Catullo, Stephen C. Donnellan, Mark D. B. Eldridge, Leo Joseph, J. Scott Keogh, Paul Oliver, Kevin C. Rowe and Craig Moritz

      Version of Record online: 25 NOV 2016 | DOI: 10.1111/1755-0998.12633

    8. varver: a database of microsatellite variation in vertebrates

      Akiko Sato Yashima and Hideki Innan

      Version of Record online: 21 NOV 2016 | DOI: 10.1111/1755-0998.12625

    9. A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales

      Brent C. Emerson, Juliane Casquet, Heriberto López, Pedro Cardoso, Paulo A. V. Borges, Noémy Mollaret, Pedro Oromí, Dominique Strasberg and Christophe Thébaud

      Version of Record online: 20 NOV 2016 | DOI: 10.1111/1755-0998.12617

    10. Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations

      Garrett J. McKinney, Ryan K. Waples, Lisa W. Seeb and James E. Seeb

      Version of Record online: 20 NOV 2016 | DOI: 10.1111/1755-0998.12613

    11. Detection limits of quantitative and digital PCR assays and their influence in presence–absence surveys of environmental DNA

      Margaret E. Hunter, Robert M. Dorazio, John S. S. Butterfield, Gaia Meigs-Friend, Leo G. Nico and Jason A. Ferrante

      Version of Record online: 20 NOV 2016 | DOI: 10.1111/1755-0998.12619

    12. High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

      James Starrett, Shahan Derkarabetian, Marshal Hedin, Robert W. Bryson Jr., John E. McCormack and Brant C. Faircloth

      Version of Record online: 19 NOV 2016 | DOI: 10.1111/1755-0998.12621

    13. You have full text access to this OnlineOpen article
      Identification of sawflies and horntails (Hymenoptera, ‘Symphyta’) through DNA barcodes: successes and caveats

      Stefan Schmidt, Andreas Taeger, Jérôme Morinière, Andrew Liston, Stephan M. Blank, Katja Kramp, Manfred Kraus, Olga Schmidt, Erik Heibo, Marko Prous, Tommi Nyman, Tobias Malm and Julie Stahlhut

      Version of Record online: 19 NOV 2016 | DOI: 10.1111/1755-0998.12614

    14. Identifying homomorphic sex chromosomes from wild-caught adults with limited genomic resources

      Alan Brelsford, Guillaume Lavanchy, Roberto Sermier, Anna Rausch and Nicolas Perrin

      Version of Record online: 18 NOV 2016 | DOI: 10.1111/1755-0998.12624

    15. Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird

      Aleksandra Biedrzycka, Alvaro Sebastian, Magdalena Migalska, Helena Westerdahl and Jacek Radwan

      Version of Record online: 18 NOV 2016 | DOI: 10.1111/1755-0998.12612

    16. Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues

      Jean-René Arseneau, Royce Steeves and Mark Laflamme

      Version of Record online: 18 NOV 2016 | DOI: 10.1111/1755-0998.12616

    17. A comparison of DNA extraction methods for high-throughput DNA analyses

      Lauren M. Schiebelhut, Sarah S. Abboud, Liza E. Gómez Daglio, Holly F. Swift and Michael N Dawson

      Version of Record online: 16 NOV 2016 | DOI: 10.1111/1755-0998.12620

    18. Draft genome of the American Eel (Anguilla rostrata)

      Scott A. Pavey, Martin Laporte, Eric Normandeau, Jérémy Gaudin, Louis Letourneau, Sébastien Boisvert, Jacques Corbeil, Céline Audet and Louis Bernatchez

      Version of Record online: 14 NOV 2016 | DOI: 10.1111/1755-0998.12608

  4. From the Cover

    1. You have full text access to this OnlineOpen article
      Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome

      Ludovic Dutoit, Reto Burri, Alexander Nater, Carina F. Mugal and Hans Ellegren

      Version of Record online: 14 NOV 2016 | DOI: 10.1111/1755-0998.12602

  5. Resource Articles

    1. swinger: a user-friendly computer program to establish captive breeding groups that minimize relatedness without pedigree information

      Jonathan Sandoval-Castillo, Catherine R. M. Attard, Shashikanth Marri, Chris J. Brauer, Luciana M. Möller and Luciano B. Beheregaray

      Version of Record online: 14 NOV 2016 | DOI: 10.1111/1755-0998.12609

    2. Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes

      Fátima Sánchez Barreiro, Filipe G. Vieira, Michael D. Martin, James Haile, M. Thomas P. Gilbert and Nathan Wales

      Version of Record online: 7 NOV 2016 | DOI: 10.1111/1755-0998.12610

    3. DNA barcodes of the native ray-finned fishes in Taiwan

      Chia-Hao Chang, Kwang-Tsao Shao, Han-Yang Lin, Yung-Chieh Chiu, Mao-Ying Lee, Shih-Hui Liu and Pai-Lei Lin

      Version of Record online: 2 NOV 2016 | DOI: 10.1111/1755-0998.12601

    4. Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers

      Sanna Olsson, Pedro Seoane-Zonjic, Rocío Bautista, M. Gonzalo Claros, Santiago C. González-Martínez, Ivan Scotti, Caroline Scotti-Saintagne, Olivier J. Hardy and Myriam Heuertz

      Version of Record online: 27 OCT 2016 | DOI: 10.1111/1755-0998.12605

    5. You have full text access to this OnlineOpen article
      Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology

      Roman V. Briskine, Timothy Paape, Rie Shimizu-Inatsugi, Tomoaki Nishiyama, Satoru Akama, Jun Sese and Kentaro K. Shimizu

      Version of Record online: 26 OCT 2016 | DOI: 10.1111/1755-0998.12604

    6. Residual eDNA detection sensitivity assessed by quantitative real-time PCR in a river ecosystem

      Katherine D. Balasingham, Ryan P. Walter and Daniel D. Heath

      Version of Record online: 12 OCT 2016 | DOI: 10.1111/1755-0998.12598

    7. Complete mitochondrial genomes of eleven extinct or possibly extinct bird species

      Jarl A. Anmarkrud and Jan T. Lifjeld

      Version of Record online: 11 OCT 2016 | DOI: 10.1111/1755-0998.12600

    8. 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

  6. 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

  7. 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

  8. 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

  9. 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

    12. 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

  10. 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

  11. 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

    3. 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

  12. 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

  13. 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

  14. From the Cover

  15. Resource Articles

    1. 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


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