Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: ipyrad
https://packages.ecosyste.ms/registries/pypi.org/packages/ipyrad
Interactive assembly and analysis of RADseq data sets
5 versions
Latest release: almost 9 years ago
0 downloads
Papers Mentioning ipyrad 48
10.1093/molbev/msaa266
Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian WatersnakesCited by: 10
Author(s): Rhett M. Rautsaw, Tristan D. Schramer, Rachel Acuña, Lindsay N Arick, Mark DiMeo, Kathryn P. Mercier, Michael Schrum, Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Christopher L. Parkinson
Software Mentions: 9
Published: about 4 years ago
10.1111/1755-0998.13280
The genome of <i>Draba nivalis</i> shows signatures of adaptation to the extreme environmental stresses of the ArcticCited by: 13
Author(s): Michael Nowak, Siri Birkeland, Terezie Mandáková, Rimjhim Roy Choudhury, Xi Guo, Lovisa Gustafsson, Abel Gizaw, Audun Schrøder-Nielsen, Marco Fracassetti, Anne K. Brysting, Loren H. Rieseberg, Tanja Slotte, Christian Parisod, Martin A. Lysak, Christian Brochmann
Software Mentions: 8
Published: about 4 years ago
10.1038/s41598-019-41886-8
Geographic separation and genetic differentiation of populations are not coupled with niche differentiation in threatened Kaiser’s spotted newt (Neurergus kaiseri)Cited by: 24
Author(s): Forough Goudarzi, Mahmoud‐Reza Hemami, Loïs Rancilhac, Mansoureh Malekian, Sima Fakheran, Kathryn R. Elmer, Sebastian Steinfartz
Software Mentions: 7
Published: over 5 years ago
10.1038/s42003-020-01482-3
Evaluating insect-host interactions as a driver of species divergence in palm flower weevilsCited by: 11
Author(s): Bruno A. S. de Medeiros, Brian D. Farrell
Software Mentions: 7
Published: almost 4 years ago
10.1002/ece3.4994
Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibianCited by: 23
Author(s): Kyle A. O’Connell, Kevin P. Mulder, Jose A. Maldonado, Kathleen L. Currie, Dennis M. Ferraro
Software Mentions: 7
Published: over 5 years ago
10.1111/evo.13754
The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate‐driven vicariant diversification across an island archipelagoCited by: 20
Author(s): Jamie R. Oaks, Cameron D. Siler, Rafe M. Brown
Software Mentions: 5
Published: over 5 years ago
10.1111/eva.12766
Population structure, genetic connectivity, and adaptation in the Olympia oyster ( <i>Ostrea lurida</i> ) along the west coast of North AmericaCited by: 35
Author(s): Katherine Silliman
Software Mentions: 5
Published: over 5 years ago
10.1111/eva.12960
Genomic insights into historical population dynamics, local adaptation, and climate change vulnerability of the East Asian Tertiary relict <i>Euptelea</i> (Eupteleaceae)Cited by: 12
Author(s): Yanan Cao, Shanshan Zhu, Jun Chen, Hans Peter Comes, Ian Wang, Luyao Chen, Shota Sakaguchi, Ying‐Xiong Qiu
Software Mentions: 5
Published: over 4 years ago
10.7717/peerj.7484
Phylogenomic analyses confirm a novel invasive North American<i>Corbicula</i>(Bivalvia: Cyrenidae) lineageCited by: 20
Author(s): Amanda E. Haponski, Diarmaid Ó Foighil
Software Mentions: 5
Published: over 5 years ago
10.1002/ece3.7099
Divergent lineages in a semi‐arid mallee species, <i>Eucalyptus behriana</i>, correspond to a major geographic break in southeastern AustraliaCited by: 7
Author(s): Patrick S. Fahey, Rachael M. Fowler, Todd G. B. McLay, Frank Udovicic, David J. Cantrill, Michael J. Bayly
Software Mentions: 5
Published: almost 4 years ago
10.3390/ani11092702
Trait Plasticity among Invasive Populations of the Ant Technomyrmex brunneus in JapanCited by: 3
Author(s): Diyona Putri, Masanori Yokozawa, Toshiro Yamanaka, Adam L. Cronin
Software Mentions: 4
Published: about 3 years ago
10.1093/molbev/msy023
RADpainter and fineRADstructure: Population Inference from RADseq DataCited by: 234
Author(s): Milan Malinsky, Emiliano Trucchi, Daniel J. Lawson, Daniel Falush
Software Mentions: 4
Published: almost 7 years ago
10.7717/peerj.5089
Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced lociCited by: 31
Author(s): Bruno A. S. de Medeiros, Brian D. Farrell
Software Mentions: 4
Published: over 6 years ago
10.1002/ece3.4360
RAD sequencing resolved phylogenetic relationships in European shrub willows (<i>Salix</i>L. subg.<i>Chamaetia</i>and subg.<i>Vetrix</i>) and revealed multiple evolution of dwarf shrubsCited by: 31
Author(s): Natascha D. Wagner, S.M. Gramlich, Elvira Hörandl
Software Mentions: 4
Published: over 6 years ago
10.1002/ece3.6185
Panmixia across elevation in thermally sensitive Andean dung beetlesCited by: 3
Author(s): Ethan Linck Linck, Jorge Celi, Kimberly S. Sheldon
Software Mentions: 4
Published: over 4 years ago
10.1002/ece3.6093
Using genomic information for management planning of an endangered perennial,<i>Viola uliginosa</i>Cited by: 9
Author(s): Kyung Min Lee, Pertti Ranta, Jarmo Saarikivi, Lado Kutnar, Branko Vreš, М. А. Джус, Marko Mutanen, Laura Kvist
Software Mentions: 4
Published: almost 5 years ago
10.1002/ece3.4457
Habitat or temporal isolation: Unraveling herbivore-parasitoid speciation patterns using double digest RADseqCited by: 9
Author(s): Y. Miles Zhang, Amber Bass, Diana Catalina Fernández, Barbara J. Sharanowski
Software Mentions: 4
Published: about 6 years ago
10.1111/eva.12893
Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrateCited by: 20
Author(s): Jamie Hudson, Kerstin Johannesson, Christopher D. McQuaid, Marc Rius
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pgen.1009370
Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endospermCited by: 13
Author(s): Katarzyna Dziasek, Lauriane Simon, Clément Lafon‐Placette, Benjamin Laenen, Cecilia Wärdig, Juan Santos‐González, Tanja Slotte, Claudia Köhler
Software Mentions: 3
Published: almost 4 years ago
10.1002/ece3.8015
Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus <i>Capsella</i> (Brassicaceae)Cited by: 7
Author(s): Anže Žerdoner Čalasan, Herbert Hurka, Dmitry A. German, Simon Pfanzelt, Frank R. Blattner, Anna Seidl, Barbara Neuffer
Software Mentions: 3
Published: over 3 years ago
10.1186/s12859-020-03701-4
AdmixPipe: population analyses in Admixture for non-model organismsCited by: 17
Author(s): Steven M. Mussmann, Marlis R. Douglas, Tyler K. Chafin
Software Mentions: 3
Published: over 4 years ago
10.3390/genes10090693
Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum)Cited by: 10
Author(s): Fernando Henrique Santos de Souza, Manolo F. Perez, Luiz Antônio Carlos Bertollo, Ezequiel Aguiar de Oliveira, Sébastien Lavoué, Carla C. Gestich, Petr Ráb, Tariq Ezaz, Thomas Liehr, Patrik Ferreira Viana, Eliana Feldberg, Marcelo de Bello Cioffi
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pntd.0007554
Complex interplay of evolutionary forces shaping population genomic structure of invasive Aedes albopictus in southern EuropeCited by: 22
Author(s): Verena Pichler, Panayiota Kotsakiozi, Beniamino Caputo, Paola Serini, Adalgisa Caccone, Alessandra della Torre
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0216992
Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges BankCited by: 12
Author(s): Gemma V. Clucas, Lisa A. Kerr, Steven X. Cadrin, Douglas R. Zemeckis, Graham D. Sherwood, David Goethel, Zachary T. Whitener, Adrienne I. Kovach
Software Mentions: 3
Published: over 5 years ago
10.1093/gbe/evz113
Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of HawkmothsCited by: 35
Author(s): Anna K. Hundsdoerfer, Kyung Min Lee, Ian J. Kitching, Marko Mutanen
Software Mentions: 3
Published: over 5 years ago
10.3389/fgene.2019.00719
Extensive Cryptic Diversity Within the Physalaemus cuvieri–Physalaemus ephippifer Species Complex (Amphibia, Anura) Revealed by Cytogenetic, Mitochondrial, and Genomic MarkersCited by: 7
Author(s): Juliana Damieli Nascimento, Jucivaldo Dias Lima, Pablo Suárez, Diego Baldo, Gilda Vasconcellos de Andrade, Todd W. Pierson, Benjamin M. Fitzpatrick, Célio F. B. Haddad, Shirlei Maria Recco‐Pimentel, Luciana Bolsoni Lourenço
Software Mentions: 2
Published: over 5 years ago
10.3389/fpls.2019.01074
Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient IntrogressionCited by: 33
Author(s): Claudia Paetzold, Kenneth R. Wood, Deren A. R. Eaton, Warren L. Wagner, Marc S. Appelhans
Software Mentions: 2
Published: about 5 years ago
10.1111/eva.12778
Deconstructing an infamous extinction crisis: Survival of <i>Partula</i> species on Moorea and TahitiCited by: 9
Author(s): Amanda E. Haponski, Taehwan Lee, Diarmaid Ó Foighil
Software Mentions: 2
Published: over 5 years ago
10.3389/fpls.2021.662715
Highly Diverse Shrub Willows (Salix L.) Share Highly Similar PlastomesCited by: 11
Author(s): Natascha Wagner, Martin Volf, Elvira Hörandl
Software Mentions: 2
Published: about 3 years ago
10.3389/fpls.2020.01077
Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing DataCited by: 53
Author(s): Natascha Wagner, Li He, Elvira Hörandl
Software Mentions: 2
Published: over 4 years ago
10.3390/genes12020252
High Genetic Diversity despite Conserved Karyotype Organization in the Giant Trahiras from Genus Hoplias (Characiformes, Erythrinidae)Cited by: 4
Author(s): Francisco de Menezes Cavalcante Sassi, Manolo F. Perez, Vanessa Cristina Sales Oliveira, Geize Aparecida Deon, Fernando Henrique Santos de Souza, Pedro H. N. Ferreira, Ezequiel Aguiar de Oliveira, Terumi Hatanaka, Thomas Liehr, Luiz Antônio Carlos Bertollo, Marcelo de Bello Cioffi
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-017-09906-7
Reference-based RADseq resolves robust relationships among closely related species of lichen-forming fungi using metagenomic DNACited by: 29
Author(s): Felix Grewe, Jen-Pen Huang, Steven D. Leavitt, H. Thorsten Lumbsch
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pone.0198882
Reconciling species diversity in a tropical plant clade (Canarium, Burseraceae)Cited by: 12
Author(s): Sarah Federman, Michael J. Donoghue, Douglas C. Daly, Deren A. R. Eaton
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0216903
Genetic and morphological identification of a recurrent Dicksonia tree fern hybrid in New ZealandCited by: 15
Author(s): Lara D. Shepherd, Patrick J. Brownsey, Chris Stowe, Claire L. Newell, Leon R. Perrie
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-021-87244-5
An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropodsCited by: 7
Author(s): Juan Moles, Shahan Derkarabetian, Stefano Schiaparelli, Michael Schrödl, Jesús Souza Troncoso, Nerida G. Wilson, Gonzalo Giribet
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-021-88417-y
Revisiting the hyperdominance of Neotropical tree species under a taxonomic, functional and evolutionary perspectiveCited by: 11
Author(s): Gabriel Damasco, Christopher Baraloto, Alberto Vicentini, Douglas C. Daly, Bruce G. Baldwin, Paul V. A. Fine
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0190440
Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP dataCited by: 18
Author(s): Jacobo Reyes-Velasco, Joseph D. Manthey, Yann Bourgeois, Xenia Freilich, Stéphane Boissinot
Software Mentions: 1
Published: almost 7 years ago
10.1038/s41598-021-90612-w
Discovery of cryptic plant diversity on the rooftops of the AlpsCited by: 11
Author(s): Florian C. Boucher, Cédric Dentant, Sébastien Ibanez, Thibaut Capblancq, Martí Boleda, Louise Boulangeat, Jan Smyčka, Cristina Roquet, Sébastien Lavergne
Software Mentions: 1
Published: over 3 years ago
10.3897/zookeys.927.51142
Revision of the genus Hoplodrina Boursin, 1937 (Lepidoptera, Noctuidae, Xyleninae). I. Hoplodrina octogenaria (Goeze, 1781) and its sister species H. alsinides (Costantini, 1922) sp. rev. in EuropeCited by: 5
Author(s): Peter Huemer, J. Haxaire, Kyung Min Lee, Marko Mutanen, Oleg Pekarsky, Stefano Scalercio, László Ronkay
Software Mentions: 1
Published: over 4 years ago
10.1186/s12864-021-07465-w
Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic speciesCited by: 6
Author(s): Adrián González Casanova, Francesco Maroso, Andrés Blanco, Miguel Hermida, Néstor Ríos, Graciela García, Alice Manuzzi, Lorenzo Zane, Ana Veríssimo, José‐Luis García‐Marín, Carmen Bouza, Manuel Vera, Paulino Martı́nez
Software Mentions: 1
Published: over 3 years ago
10.1111/eva.13275
Testing for evolutionary change in restoration: A genomic comparison between <i>ex situ</i> , native, and commercial seed sources of <i>Helianthus maximiliani</i>Cited by: 3
Author(s): Joseph Braasch, Lionel N Di Santo, Zachary J. Tarble, Jarrad R. Prasifka, John Hamilton
Software Mentions: 1
Published: over 3 years ago
10.1002/evl3.136
Selfing ability and drift load evolve with range expansionCited by: 27
Author(s): Matthew H. Koski, Nathan C. Layman, Carly J. Prior, Jeremiah W. Busch, Laura F. Galloway
Software Mentions: 1
Published: about 5 years ago
10.1186/s12862-020-01605-8
Nuclear phylogeography of the temperate tree species Chiranthodendron pentadactylon (Malvaceae): Quaternary relicts in Mesoamerican cloud forestsCited by: 5
Author(s): Diana Gabriela Hernández-Langford, María Elena Siqueiros-Delgado, Eduardo Ruiz‐Sánchez
Software Mentions: 1
Published: over 4 years ago
10.3389/fpls.2021.631178
Evolution in the Model Genus Antirrhinum Based on Phylogenomics of Topotypic MaterialCited by: 9
Author(s): Ana Otero, Mario Fernández‐Mazuecos, Pablo Vargas
Software Mentions: 1
Published: almost 4 years ago
10.3389/fpls.2020.00750
How Many Tree Species of Birch Are in Alaska? Implications for Wetland DesignationsCited by: 0
Author(s): Carol A. Rowe, Robert W. Lichvar, Paul G. Wolf
Software Mentions: 1
Published: over 4 years ago
10.3390/genes11030265
Geographic Life History Differences Predict Genomic Divergence Better than Mitochondrial Barcodes or PhenotypeCited by: 14
Author(s): Daniel P. Duran, Robert Laroche, Harlan M. Gough, Rodger A. Gwiazdowski, C. Barry Knisley, David P. Herrmann, Stephen J. Roman, Scott P. Egan
Software Mentions: 1
Published: over 4 years ago
10.1098/rspb.2019.1311
The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterflyCited by: 32
Author(s): Vlad Dincă, Kyung Min Lee, Roger Vila, Marko Mutanen
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pone.0232936
Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across WallaceaCited by: 10
Author(s): Joeri S. Strijk, Hoàng Thị Bình, Nguyễn Văn Ngọc, Joan T. Pereira, J. W. Ferry Slik, Rahayu Sukmaria Sukri, Yoshihisa Suyama, Shuichiro Tagane, Jan J. Wieringa, Tetsukazu Yahara, Damien Daniel Hinsinger
Software Mentions: 1
Published: over 4 years ago