Resource Article
StAMPP: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations
Abstract
Statistical Analysis of Mixed‐Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed‐ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise FST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed‐ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high‐throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.
Citing Literature
Number of times cited according to CrossRef: 140
- J. W. Ball, T. P. Robinson, G. W. Wardell-Johnson, J. Bovill, M. Byrne, P. G. Nevill, Fine-scale species distribution modelling and genotyping by sequencing to examine hybridisation between two narrow endemic plant species, Scientific Reports, 10.1038/s41598-020-58525-2, 10, 1, (2020).
- Justin C. Bagley, Neander M. Heming, Eliécer E. Gutiérrez, Upendra K. Devisetty, Karen E. Mock, Andrew J. Eckert, Steven H. Strauss, Genotyping‐by‐sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides), Ecology and Evolution, 10.1002/ece3.6214, 10, 11, (4609-4629), (2020).
- Menno J. Jong, Zhipeng Li, Yanli Qin, Erwan Quéméré, Karis Baker, Wen Wang, A. Rus Hoelzel, Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene, Molecular Ecology, 10.1111/mec.15450, 29, 15, (2777-2792), (2020).
- María I. Cádiz, María E. López, Diego Díaz-Domínguez, Giovanna Cáceres, Grazyella M. Yoshida, Daniel Gomez-Uchida, José M. Yáñez, Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus), Scientific Reports, 10.1038/s41598-020-68064-5, 10, 1, (2020).
- Alexis B. Sturm, Ryan J. Eckert, Juliett González Méndez, Patricia González-Díaz, Joshua D. Voss, Population genetic structure of the great star coral, Montastraea cavernosa, across the Cuban archipelago with comparisons between microsatellite and SNP markers, Scientific Reports, 10.1038/s41598-020-72112-5, 10, 1, (2020).
- Nga T. T. Vu, Kyall R. Zenger, Jarrod L. Guppy, Melony J. Sellars, Catarina N. S. Silva, Shannon R. Kjeldsen, Dean R. Jerry, Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis, BMC Genomics, 10.1186/s12864-020-07084-x, 21, 1, (2020).
- EMJ Lee, KG O’Malley, Fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits in the California Current Ecosystem, Marine Ecology Progress Series, 10.3354/meps13453, 649, (67-81), (2020).
- Christer S. Nyinondi, Matern S. P. Mtolera, Aviti J. Mmochi, Fernando A. Lopes Pinto, Ross D. Houston, Dirk J. Koning, Christos Palaiokostas, Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing, Ecology and Evolution, 10.1002/ece3.6664, 10, 18, (10044-10056), (2020).
- Sana Beji, Véronique Fontaine, Rosemonde Devaux, Martine Thomas, Sandra Silvia Negro, Nasser Bahrman, Mathieu Siol, Grégoire Aubert, Judith Burstin, Jean-Louis Hilbert, Bruno Delbreil, Isabelle Lejeune-Hénaut, Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea, BMC Genomics, 10.1186/s12864-020-06928-w, 21, 1, (2020).
- Joseph P Zilko, Dan Harley, Birgita Hansen, Alexandra Pavlova, Paul Sunnucks, Accounting for cryptic population substructure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial, Molecular Ecology, 10.1111/mec.15540, 29, 16, (2978-2993), (2020).
- Jun Inoue, Kanako Hisata, Nina Yasuda, Noriyuki Satoh, An Investigation into the Genetic History of Japanese Populations of Three Starfish, Acanthaster planci , Linckia laevigata , and Asterias amurensis , Based on Complete Mitochondrial DNA Sequences , G3: Genes|Genomes|Genetics, 10.1534/g3.120.401155, 10, 7, (2519-2528), (2020).
- Ángel-David Popa-Báez, Renee Catullo, Siu Fai Lee, Heng Lin Yeap, Roslyn G. Mourant, Marianne Frommer, John A. Sved, Emily C. Cameron, Owain R. Edwards, Phillip W. Taylor, John G. Oakeshott, Genome-wide patterns of differentiation over space and time in the Queensland fruit fly, Scientific Reports, 10.1038/s41598-020-67397-5, 10, 1, (2020).
- Charles Perrier, Quentin Rougemont, Anne Charmantier, Demographic history and genomics of local adaptation in blue tit populations, Evolutionary Applications, 10.1111/eva.13035, 13, 6, (1145-1165), (2020).
- Oliver Berry, Zoe Richards, Glenn Moore, Udhi Hernawan, Mike Travers, Bernd Gruber, Oceanic and coastal populations of a harvested macroinvertebrate Rochia nilotica in north-western Australia are isolated and may be locally adapted, Marine and Freshwater Research, 10.1071/MF19172, 71, 7, (782), (2020).
- Hugo Cayuela, Quentin Rougemont, Martin Laporte, Claire Mérot, Eric Normandeau, Yann Dorant, Ole K. Tørresen, Siv Nam Khang Hoff, Sissel Jentoft, Pascal Sirois, Martin Castonguay, Teunis Jansen, Kim Praebel, Marie Clément, Louis Bernatchez, Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish, Molecular Ecology, 10.1111/mec.15499, 29, 13, (2379-2398), (2020).
- Jennifer Ovenden, Danielle Davenport, Anthony Moore, A perfect storm of genetic drift and divergence may prevent the rebuilding of the gemfish (Rexea solandri) stock on the east Australian coast, Fisheries Research, 10.1016/j.fishres.2020.105645, 230, (105645), (2020).
- Michael T. J. Hague, Amber N. Stokes, Chris R. Feldman, Edmund D. Brodie, Edmund D. Brodie, The geographic mosaic of arms race coevolution is closely matched to prey population structure, Evolution Letters, 10.1002/evl3.184, 4, 4, (317-332), (2020).
- Charlotte Jones, Jose De Vega, David Lloyd, Matthew Hegarty, Sarah Ayling, Wayne Powell, Leif Skøt, Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm, Scientific Reports, 10.1038/s41598-020-64989-z, 10, 1, (2020).
- Megan L. Fritz, Schyler O. Nunziata, Rong Guo, Bruce E. Tabashnik, Yves Carrière, Mutations in a Novel Cadherin Gene Associated with Bt Resistance in Helicoverpa zea , G3: Genes|Genomes|Genetics, 10.1534/g3.120.401053, 10, 5, (1563-1574), (2020).
- Aliki Xanthopoulou, Maria Manioudaki, Christos Bazakos, Christos Kissoudis, Anna-Maria Farsakoglou, Evangelos Karagiannis, Michail Michailidis, Chrysanthi Polychroniadou, Antonios Zambounis, Konstantinos Kazantzis, Athanasios Tsaftaris, Panagiotis Madesis, Filippos Aravanopoulos, Athanassios Molassiotis, Ioannis Ganopoulos, Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species, Horticulture Research, 10.1038/s41438-020-0281-9, 7, 1, (2020).
- Artem V. Nedoluzhko, Natalia V. Slobodova, Fedor Sharko, Gulmira M. Shalgimbayeva, Svetlana V. Tsygankova, Eugenia S. Boulygina, Zsigmond Jeney, Van Q. Nguyen, Thế T. Pham, Đức T. Nguyen, Alexander A. Volkov, Jorge M.O. Fernandes, Sergey M. Rastorguev, A new strain group of common carp: The genetic differences and admixture events between Cyprinus carpio breeds, Ecology and Evolution, 10.1002/ece3.6286, 10, 12, (5431-5439), (2020).
- Selam Meseret, Yonatan A. Mekonnen, Bertram Brenig, Ekkehard Schütz, Olivier Hanotte, Mehmet Gültas, Armin O. Schmitt, Genetic Diversity and Population Structure of Six Ethiopian Cattle Breeds from Different Geographical Regions Using High Density Single Nucleotide Polymorphisms, Livestock Science, 10.1016/j.livsci.2020.103979, (103979), (2020).
- Kara K. S. Layton, Brian Dempson, Paul V. R. Snelgrove, Steven J. Duffy, Amber M. Messmer, Ian G. Paterson, Nicholas W. Jeffery, Tony Kess, John B. Horne, Sarah J. Salisbury, Daniel E. Ruzzante, Paul Bentzen, David Côté, Cameron M. Nugent, Moira M. Ferguson, Jong S. Leong, Ben F. Koop, Ian R. Bradbury, Resolving fine‐scale population structure and fishery exploitation using sequenced microsatellites in a northern fish, Evolutionary Applications, 10.1111/eva.12922, 13, 5, (1055-1068), (2020).
- Takeshi Takeuchi, Tetsuji Masaoka, Hideo Aoki, Ryo Koyanagi, Manabu Fujie, Noriyuki Satoh, Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs, Evolutionary Applications, 10.1111/eva.12905, 13, 4, (837-853), (2020).
- Anne‐Laure Ferchaud, Maeva Leitwein, Martin Laporte, Damien Boivin‐Delisle, Bérénice Bougas, Cécilia Hernandez, Éric Normandeau, Isabel Thibault, Louis Bernatchez, Adaptive and maladaptive genetic diversity in small populations: Insights from the Brook Charr (Salvelinus fontinalis) case study, Molecular Ecology, 10.1111/mec.15566, 29, 18, (3429-3445), (2020).
- Elahe Parvizi, Ceridwen I. Fraser, Ludovic Dutoit, Dave Craw, Jonathan M. Waters, The genomic footprint of coastal earthquake uplift, Proceedings of the Royal Society B: Biological Sciences, 10.1098/rspb.2020.0712, 287, 1930, (20200712), (2020).
- Andrew Ecclestone, Tim J. Haxton, Thomas C. Pratt, Chris C. Wilson, Tom Whillans, Seasonal use of two unregulated Lake Superior tributaries by lake sturgeon, Journal of Great Lakes Research, 10.1016/j.jglr.2020.06.008, (2020).
- John Soghigian, Andrea Gloria‐Soria, Vincent Robert, Gilbert Le Goff, Anna‐Bella Failloux, Jeffrey R. Powell, Genetic evidence for the origin of Aedes aegypti, the yellow fever mosquito, in the southwestern Indian Ocean, Molecular Ecology, 10.1111/mec.15590, 29, 19, (3593-3606), (2020).
- Elizabeth M. J. Lee, Kathleen G. O’Malley, Big Fishery, Big Data, and Little Crabs: Using Genomic Methods to Examine the Seasonal Recruitment Patterns of Early Life Stage Dungeness Crab (Cancer magister) in the California Current Ecosystem, Frontiers in Marine Science, 10.3389/fmars.2019.00836, 6, (2020).
- Seyedeh Narjes Tabatabaei, Asghar Abdoli, Iraj Hashemzadeh Segherloo, Eric Normandeau, Faraham Ahmadzadeh, Farshad Nejat, Louis Bernatchez, Fine-scale population genetic structure of Endangered Caspian Sea trout, Salmo caspius: implications for conservation, Hydrobiologia, 10.1007/s10750-020-04334-7, (2020).
- Stephanie K. Venables, Andrea D. Marshall, Amelia J. Armstrong, Joseph L. Tomkins, W. Jason Kennington, Genome-wide SNPs detect no evidence of genetic population structure for reef manta rays (Mobula alfredi) in southern Mozambique, Heredity, 10.1038/s41437-020-00373-x, (2020).
- Selamawit Ketema, Bizuayehu Tesfaye, Gemechu Keneni, Berhanu Amsalu Fenta, Ermias Assefa, Nicolas Greliche, Eunice Machuka, Nasser Yao, DArTSeq SNP-based markers revealed high genetic diversity and structured population in Ethiopian cowpea [Vigna unguiculata (L.) Walp] germplasms, PLOS ONE, 10.1371/journal.pone.0239122, 15, 10, (e0239122), (2020).
- Carly J. Prior, Nathan C. Layman, Matthew H. Koski, Laura F. Galloway, Jeremiah W. Busch, Westward range expansion from middle latitudes explains the Mississippi River discontinuity in a forest herb of eastern North America, Molecular Ecology, 10.1111/mec.15650, 0, 0, (2020).
- Morgan Gueuning, Juerg E. Frey, Christophe Praz, Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long‐standing systematic enigma in Central European bees, Molecular Ecology, 10.1111/mec.15629, 0, 0, (2020).
- Zhen Fu, Amanda R. Meier, Brendan Epstein, Alan O. Bergland, Carmen I. Castillo Carrillo, William R. Cooper, Regina K. Cruzado, David R. Horton, Andrew S. Jensen, Joanna L. Kelley, Arash Rashed, Stuart R. Reitz, Silvia I. Rondon, Jenita Thinakaran, Erik J. Wenninger, Carrie H. Wohleb, David W. Crowder, William E. Snyder, Host plants and Wolbachia shape the population genetics of sympatric herbivore populations, Evolutionary Applications, 10.1111/eva.13079, 0, 0, (2020).
- Xiaowei Mao, Simona Augyte, Mao Huang, Matthew P. Hare, David Bailey, Schery Umanzor, Michael Marty-Rivera, Kelly R. Robbins, Charles Yarish, Scott Lindell, Jean-Luc Jannink, Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers, Frontiers in Marine Science, 10.3389/fmars.2020.00694, 7, (2020).
- Caitlin E. Morrison, Rebecca N. Johnson, Catherine E. Grueber, Carolyn J. Hogg, Genetic impacts of conservation management actions in a critically endangered parrot species, Conservation Genetics, 10.1007/s10592-020-01292-4, (2020).
- Pierre Feutry, Floriaan Devloo‐Delva, Adrien Tran Lu Y, Stefano Mona, Rasanthi M. Gunasekera, Grant Johnson, Richard D. Pillans, Damian Jaccoud, Andrzej Kilian, David L. Morgan, Thor Saunders, Nicholas J. Bax, Peter M. Kyne, One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark, Molecular Ecology Resources, 10.1111/1755-0998.13204, 0, 0, (2020).
- Ruwani Dissanayake, Shivraj Braich, Noel O. I. Cogan, Kevin Smith, Sukhjiwan Kaur, Characterization of Genetic and Allelic Diversity Amongst Cultivated and Wild Lentil Accessions for Germplasm Enhancement, Frontiers in Genetics, 10.3389/fgene.2020.00546, 11, (2020).
- Morteza Bitaraf Sani, Javad Zare Harofte, Ahmad Bitaraf, Saeid Esmaeilkhanian, Mohammad Hossein Banabazi, Nader Salim, Abbas Teimoori, Ali Shafei Naderi, Mohammad Ali Faghihi, Pamela Anna Burger, Mohammad Silawi, Afsaneh Taghipour Sheshdeh, Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran, Genes, 10.3390/genes11060599, 11, 6, (599), (2020).
- Roberto F. Nespolo, Carlos A. Villarroel, Christian I. Oporto, Sebastián M. Tapia, Franco Vega-Macaya, Kamila Urbina, Matteo De Chiara, Simone Mozzachiodi, Ekaterina Mikhalev, Dawn Thompson, Luis F. Larrondo, Pablo Saenz-Agudelo, Gianni Liti, Francisco A. Cubillos, An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages, PLOS Genetics, 10.1371/journal.pgen.1008777, 16, 5, (e1008777), (2020).
- Soo Hyun Lee, Dong Won Seo, Eun Seok Cho, Bong Hwan Choi, Yong Min Kim, Joon Ki Hong, Hyo Dong Han, Yeon Bok Jung, Dong Jun Kim, Tae Jeong Choi, Seung Hwan Lee, Genetic Diversity and Ancestral Study for Korean Native Pigs Using 60K SNP Chip, Animals, 10.3390/ani10050760, 10, 5, (760), (2020).
- Susanne U Franssen, Caroline Durrant, Olivia Stark, Bettina Moser, Tim Downing, Hideo Imamura, Jean-Claude Dujardin, Mandy J Sanders, Isabel Mauricio, Michael A Miles, Lionel F Schnur, Charles L Jaffe, Abdelmajeed Nasereddin, Henk Schallig, Matthew Yeo, Tapan Bhattacharyya, Mohammad Z Alam, Matthew Berriman, Thierry Wirth, Gabriele Schönian, James A Cotton, Global genome diversity of the Leishmania donovani complex, eLife, 10.7554/eLife.51243, 9, (2020).
- C. Brekke, L. F. Groeneveld, T. H. E. Meuwissen, N. Sæther, S. Weigend, P. Berg, Assessing the genetic diversity conserved in the Norwegian live poultry genebank, Acta Agriculturae Scandinavica, Section A — Animal Science, 10.1080/09064702.2020.1727560, (1-13), (2020).
- Sandra Grünig, Markus Fischer, Christian Parisod, Recent hybrid speciation at the origin of the narrow endemic Pulmonaria helvetica, Annals of Botany, 10.1093/aob/mcaa145, (2020).
- Terry D. Beacham, Colin Wallace, Kim Jonsen, Brenda McIntosh, John R. Candy, Eric B. Rondeau, Jean-Sébastien Moore, Louis Bernatchez, Ruth E. Withler, Accurate estimation of conservation unit contribution to coho salmon mixed-stock fisheries in British Columbia, Canada, using direct DNA sequencing for single nucleotide polymorphisms, Canadian Journal of Fisheries and Aquatic Sciences, 10.1139/cjfas-2019-0339, (1-14), (2020).
- G. Cagnano, I. Lenk, N. Roulund, C. S. Jensen, M. P. Cox, T. Asp, Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue ( Schedonorus pratensis ) , Mycologia, 10.1080/00275514.2020.1746607, (1-17), (2020).
- Gregory Vogel, Michael A. Gore, Christine D. Smart, Genome-wide association study in New York Phytophthora capsici isolates reveals loci involved in mating type and mefenoxam sensitivity , Phytopathology®, 10.1094/PHYTO-04-20-0112-FI, (2020).
- Ingrid Spies, Kristen M. Gruenthal, Daniel P. Drinan, Anne B. Hollowed, Duane E. Stevenson, Carolyn M. Tarpey, Lorenz Hauser, Genetic evidence of a northward range expansion in the eastern Bering Sea stock of Pacific cod, Evolutionary Applications, 10.1111/eva.12874, 13, 2, (362-375), (2019).
- Belén Jiménez‐Mena, Alan Le Moan, Asbjørn Christensen, Mikael Deurs, Henrik Mosegaard, Jakob Hemmer‐Hansen, Dorte Bekkevold, Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea, Evolutionary Applications, 10.1111/eva.12875, 13, 2, (376-387), (2019).
- Christophe Verwimp, Lies Vansteenbrugge, Sofie Derycke, Thomas Kerkhove, Hilde Muylle, Olivier Honnay, Tom Ruttink, Isabel Roldán‐Ruiz, Kris Hostens, Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea, Ecology and Evolution, 10.1002/ece3.5468, 10, 1, (11-25), (2019).
- Ya-Ping Lin, Chu-Yin Liu, Kai-Yi Chen, Assessment of Genetic Differentiation and Linkage Disequilibrium in Solanum pimpinellifolium Using Genome-Wide High-Density SNP Markers , G3: Genes|Genomes|Genetics, 10.1534/g3.118.200862, 9, 5, (1497-1505), (2019).
- Gerard G. Dumancas, Applications of Supercomputers in Population Genetics, Biotechnology, 10.4018/978-1-5225-8903-7, (693-719), (2019).
- Belinda Wright, Katherine A. Farquharson, Elspeth A. McLennan, Katherine Belov, Carolyn J. Hogg, Catherine E. Grueber, From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species, BMC Genomics, 10.1186/s12864-019-5806-y, 20, 1, (2019).
- Tania Chavarria‐Pizarro, Juan Pablo Gomez, Judit Ungvari‐Martin, Rachael Bay, Michael M. Miyamoto, Rebecca Kimball, Strong phenotypic divergence in spite of low genetic structure in the endemic Mangrove Warbler subspecies (Setophaga petechia xanthotera) of Costa Rica, Ecology and Evolution, 10.1002/ece3.5826, 9, 24, (13902-13918), (2019).
- Jarrod Sopniewski, Foyez Shams, Benjamin C. Scheele, Ben J. Kefford, Tariq Ezaz, Identifying sex-linked markers in Litoria aurea: a novel approach to understanding sex chromosome evolution in an amphibian, Scientific Reports, 10.1038/s41598-019-52970-4, 9, 1, (2019).
- Felix Vaux, Leif K. Rasmuson, Lisa A. Kautzi, Polly S. Rankin, Matthew T. O. Blume, Kelly A. Lawrence, Sandra Bohn, Kathleen G. O'Malley, Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus), Ecology and Evolution, 10.1002/ece3.5763, 9, 23, (13153-13173), (2019).
- Marianne Gagnon, Glenn Yannic, Charles Perrier, Steeve D. Côté, No evidence of inbreeding depression in fast declining herds of migratory caribou, Journal of Evolutionary Biology, 10.1111/jeb.13533, 32, 12, (1368-1381), (2019).
- Yi‐Kai Tea, Cara Van Der Wal, William B. Ludt, Anthony C. Gill, Nathan Lo, Simon Y. W. Ho, Boomeranging around Australia: Historical biogeography and population genomics of the anti‐equatorial fish Microcanthus strigatus (Teleostei: Microcanthidae), Molecular Ecology, 10.1111/mec.15172, 28, 16, (3771-3785), (2019).
- Shawn M. Billerman, Carla Cicero, Rauri C. K. Bowie, Matthew D. Carling, Phenotypic and genetic introgression across a moving woodpecker hybrid zone, Molecular Ecology, 10.1111/mec.15043, 28, 7, (1692-1708), (2019).
- Norah P. Saarman, Robert Opiro, Chaz Hyseni, Richard Echodu, Elizabeth A. Opiyo, Kirstin Dion, Thomas Johnson, Serap Aksoy, Adalgisa Caccone, The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda, Molecular Ecology, 10.1111/mec.14957, 28, 1, (66-85), (2019).
- José Luis Blanco‐Pastor, Stéphanie Manel, Philippe Barre, Anna M. Roschanski, Evelin Willner, Klaus J. Dehmer, Mathew Hegarty, Hilde Muylle, Tom Ruttink, Isabel Roldán‐Ruiz, Thomas Ledauphin, Abraham Escobar‐Gutiérrez, Jean‐Paul Sampoux, Pleistocene climate changes, and not agricultural spread, accounts for range expansion and admixture in the dominant grassland species Lolium perenne L., Journal of Biogeography, 10.1111/jbi.13587, 46, 7, (1451-1465), (2019).
- Nobu Sutra, Junko Kusumi, Javier Montenegro, Hirozumi Kobayashi, Shingo Fujimoto, Kawilarang W. A. Masengi, Atsushi J. Nagano, Atsushi Toyoda, Masatoshi Matsunami, Ryosuke Kimura, Kazunori Yamahira, Evidence for sympatric speciation in a Wallacean ancient lake, Evolution, 10.1111/evo.13821, 73, 9, (1898-1915), (2019).
- Xiao Zhang, Hailun Su, Jia Yang, Li Feng, Zhonghu Li, Guifang Zhao, Population genetic structure, migration, and polyploidy origin of a medicinal species Gynostemma pentaphyllum (Cucurbitaceae), Ecology and Evolution, 10.1002/ece3.5618, 9, 19, (11145-11170), (2019).
- Yann Dorant, Laura Benestan, Quentin Rougemont, Eric Normandeau, Brian Boyle, Rémy Rochette, Louis Bernatchez, Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Homarus americanus) as a case study, Ecology and Evolution, 10.1002/ece3.5240, 9, 11, (6606-6623), (2019).
- Ludmila Sromek, Didier Forcioli, Rafal Lasota, Paola Furla, Maciej Wolowicz, Next‐generation phylogeography of the cockle Cerastoderma glaucum: Highly heterogeneous genetic differentiation in a lagoon species, Ecology and Evolution, 10.1002/ece3.5070, 9, 8, (4667-4682), (2019).
- Floriaan Devloo‐Delva, Gregory E. Maes, Sebastián I. Hernández, Jaime D. Mcallister, Rasanthi M. Gunasekera, Peter M. Grewe, Robin B. Thomson, Pierre Feutry, Accounting for kin sampling reveals genetic connectivity in Tasmanian and New Zealand school sharks, Galeorhinus galeus, Ecology and Evolution, 10.1002/ece3.5012, 9, 8, (4465-4472), (2019).
- M. E. Green, S. A. Appleyard, W. White, S. Tracey, F. Devloo-Delva, J. R. Ovenden, Novel multimarker comparisons address the genetic population structure of silvertip sharks (Carcharhinus albimarginatus), Marine and Freshwater Research, 10.1071/MF18296, 70, 7, (1007), (2019).
- Vladimir Salvador De Jesús-Bonilla, Rubi Nelsi Meza-Lázaro, Alejandro Zaldívar-Riverón, 3RAD-based systematics of the transitional Nearctic-Neotropical lubber grasshopper genus Taeniopoda (Orthoptera: Romaleidae), Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2019.04.019, (2019).
- Patrick Monnahan, Filip Kolář, Pierre Baduel, Christian Sailer, Jordan Koch, Robert Horvath, Benjamin Laenen, Roswitha Schmickl, Pirita Paajanen, Gabriela Šrámková, Magdalena Bohutínská, Brian Arnold, Caroline M. Weisman, Karol Marhold, Tanja Slotte, Kirsten Bomblies, Levi Yant, Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa, Nature Ecology & Evolution, 10.1038/s41559-019-0807-4, 3, 3, (457-468), (2019).
- Maulik Upadhyay, Susanne Eriksson, Sofia Mikko, Erling Strandberg, Hans Stålhammar, Martien A. M. Groenen, Richard P. M. A. Crooijmans, Göran Andersson, Anna M. Johansson, Genomic relatedness and diversity of Swedish native cattle breeds, Genetics Selection Evolution, 10.1186/s12711-019-0496-0, 51, 1, (2019).
- Renee A. Catullo, Heng L. Yeap, Siu F. Lee, Jason G. Bragg, Jodie Cheesman, Stefano De Faveri, Owain Edwards, Alvin K. W. Hee, Angel D. Popa, Michele Schiffer, John G. Oakeshott, A genome-wide approach for uncovering evolutionary relationships of Australian Bactrocera species complexes (Diptera: Tephritidae), Invertebrate Systematics, 10.1071/IS18065, (2019).
- Jane Melville, Kirilee Chaplin, Mark Hutchinson, Joanna Sumner, Bernd Gruber, Anna J. MacDonald, Stephen D. Sarre, Taxonomy and conservation of grassland earless dragons: new species and an assessment of the first possible extinction of a reptile on mainland Australia, Royal Society Open Science, 10.1098/rsos.190233, 6, 5, (190233), (2019).
- Simone Andrea Biagini, Neus Solé-Morata, Elizabeth Matisoo-Smith, Pierre Zalloua, David Comas, Francesc Calafell, People from Ibiza: an unexpected isolate in the Western Mediterranean, European Journal of Human Genetics, 10.1038/s41431-019-0361-1, (2019).
- Ross Crates, George Olah, Marcin Adamski, Nicola Aitken, Sam Banks, Dean Ingwersen, Louis Ranjard, Laura Rayner, Dejan Stojanovic, Tomasz Suchan, Brenton von Takach Dukai, Robert Heinsohn, Genomic impact of severe population decline in a nomadic songbird, PLOS ONE, 10.1371/journal.pone.0223953, 14, 10, (e0223953), (2019).
- Andrea Gloria-Soria, John Soghigian, David Kellner, Jeffrey R. Powell, Genetic diversity of laboratory strains and implications for research: The case of Aedes aegypti, PLOS Neglected Tropical Diseases, 10.1371/journal.pntd.0007930, 13, 12, (e0007930), (2019).
- Redempta A. Kajungiro, Christos Palaiokostas, Fernando A. Lopes Pinto, Aviti J. Mmochi, Marten Mtolera, Ross D. Houston, Dirk Jan de Koning, Population Structure and Genetic Diversity of Nile Tilapia (Oreochromis niloticus) Strains Cultured in Tanzania, Frontiers in Genetics, 10.3389/fgene.2019.01269, 10, (2019).
- Anna M. Johansson, Maulik Upadhyay, Erling Strandberg, Susanne Eriksson, Genetic differentiation between subpopulations of Swedish mountain (Fjäll and Fjällnära) cattle, Acta Agriculturae Scandinavica, Section A — Animal Science, 10.1080/09064702.2019.1704857, (1-8), (2019).
- Catharine Prussing, Kevin J. Emerson, Sara A. Bickersmith, Maria Anice Mureb Sallum, Jan E. Conn, Minimal genetic differentiation of the malaria vector Nyssorhynchus darlingi associated with forest cover level in Amazonian Brazil, PLOS ONE, 10.1371/journal.pone.0225005, 14, 11, (e0225005), (2019).
- Mbiru Moses, Matern S. P. Mtolera, Leonard J. Chauka, Fernando A. Lopes, Dirk Jan de Koning, Ross D. Houston, Christos Palaiokostas, Characterizing the genetic structure of introduced Nile tilapia (Oreochromis niloticus) strains in Tanzania using double digest RAD sequencing, Aquaculture International, 10.1007/s10499-019-00472-5, (2019).
- Sara L. Martin, Jean-Sebastien Parent, Martin Laforest, Eric Page, Julia M. Kreiner, Tracey James, Population Genomic Approaches for Weed Science, Plants, 10.3390/plants8090354, 8, 9, (354), (2019).
- Kirilee Chaplin, Joanna Sumner, Christy A Hipsley, Jane Melville, An Integrative Approach Using Phylogenomics and High-Resolution X-Ray Computed Tomography for Species Delimitation in Cryptic Taxa, Systematic Biology, 10.1093/sysbio/syz048, (2019).
- Guillaume Wos, Jana Mořkovská, Magdalena Bohutínská, Gabriela Šrámková, Adam Knotek, Magdalena Lučanová, Stanislav Španiel, Karol Marhold, Filip Kolář, Role of ploidy in colonization of alpine habitats in natural populations of Arabidopsis arenosa, Annals of Botany, 10.1093/aob/mcz070, (2019).
- Mackenzie R. Gavery, Krista M. Nichols, Barry A. Berejikian, Christopher P. Tatara, Giles W. Goetz, Jon T. Dickey, Donald M. Van Doornik, Penny Swanson, Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead (Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment, Genes, 10.3390/genes10050356, 10, 5, (356), (2019).
- Yusuke Fukuda, Grahame Webb, Charlie Manolis, Garry Lindner, Sam Banks, Translocation, genetic structure and homing ability confirm geographic barriers disrupt saltwater crocodile movement and dispersal, PLOS ONE, 10.1371/journal.pone.0205862, 14, 8, (e0205862), (2019).
- B. M. Caruana, L. W. Pembleton, F. Constable, B. Rodoni, A. T. Slater, N. O. I. Cogan, Validation of Genotyping by Sequencing Using Transcriptomics for Diversity and Application of Genomic Selection in Tetraploid Potato, Frontiers in Plant Science, 10.3389/fpls.2019.00670, 10, (2019).
- Shuangshuang Liu, Jared Streich, Justin O. Borevitz, Kevin J. Rice, Tingting Li, Bo Li, Kent J. Bradford, Environmental resource deficit may drive the evolution of intraspecific trait variation in invasive plant populations, Oikos, 10.1111/oik.05548, 128, 2, (171-184), (2018).
- Sarah E. Lower, Kathrin F. Stanger-Hall, David W. Hall, Molecular variation across populations of a widespread North American firefly, Photinus pyralis, reveals that coding changes do not underlie flash color variation or associated visual sensitivity, BMC Evolutionary Biology, 10.1186/s12862-018-1251-9, 18, 1, (2018).
- Luis Inostroza, Mehul Bhakta, Hernán Acuña, Catalina Vásquez, Joel Ibáñez, Gerardo Tapia, Wenbin Mei, Matias Kirst, Marcio Resende, Patricio Munoz, Understanding the Complexity of Cold Tolerance in White Clover using Temperature Gradient Locations and a GWAS Approach, The Plant Genome, 10.3835/plantgenome2017.11.0096, 11, 3, (1-14), (2018).
- Abdulqader Jighly, Zibei Lin, John W. Forster, German C. Spangenberg, Ben J. Hayes, Hans D. Daetwyler, Insights into population genetics and evolution of polyploids and their ancestors, Molecular Ecology Resources, 10.1111/1755-0998.12896, 18, 5, (1157-1172), (2018).
- Arsen V. Dotsev, Tatiana E. Deniskova, Innokentiy M. Okhlopkov, Gabor Mészáros, Johann Sölkner, Henry Reyer, Klaus Wimmers, Gottfried Brem, Natalia A. Zinovieva, Genome‐wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia), Ecology and Evolution, 10.1002/ece3.4350, 8, 16, (8000-8010), (2018).
- Anastasia Klimova, Alfredo Ortega‐Rubio, David L. J. Vendrami, Joseph I. Hoffman, Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence, and long‐distance dispersal in North American palms, Ecology and Evolution, 10.1002/ece3.4125, 8, 11, (5873-5890), (2018).
- Kelly S. Andrews, Krista M. Nichols, Anna Elz, Nick Tolimieri, Chris J. Harvey, Robert Pacunski, Dayv Lowry, K. Lynne Yamanaka, Daniel M. Tonnes, Cooperative research sheds light on population structure and listing status of threatened and endangered rockfish species, Conservation Genetics, 10.1007/s10592-018-1060-0, 19, 4, (865-878), (2018).
- D. P. Karabanov, Yu. V. Kodukhova, Biochemical Polymorphism and Intraspecific Structure in Populations of Kilka Clupeonella cultriventris (Nordmann, 1840) from Natural and Invasive Parts of Its Range, Inland Water Biology, 10.1134/S1995082918040107, 11, 4, (496-500), (2018).
- Bernadette Julier, Philippe Barre, Paola Lambroni, Sabrina Delaunay, Muriel Thomasset, Frédéric Lafaillette, Vincent Gensollen, Use of GBS markers to distinguish among lucerne varieties, with comparison to morphological traits, Molecular Breeding, 10.1007/s11032-018-0891-1, 38, 11, (2018).
- Lubna M. A. Hassan, Danny Arends, Siham A. Rahmatalla, Monika Reissmann, Henry Reyer, Klaus Wimmers, Sumaia M. A. Abukashawa, Gudrun A. Brockmann, Genetic diversity of Nubian ibex in comparison to other ibex and domesticated goat species, European Journal of Wildlife Research, 10.1007/s10344-018-1212-z, 64, 5, (2018).
- Francesca Raffini, Carmelo Fruciano, Axel Meyer, Morphological and genetic correlates in the left–right asymmetric scale-eating cichlid fish of Lake Tanganyika, Biological Journal of the Linnean Society, 10.1093/biolinnean/bly024, 124, 1, (67-84), (2018).
- Jarkko Salojärvi, Computational Tools for Population Genomics, , 10.1007/13836_2018_57, (2018).
- Veronika Ruslanovna Kharzinova, Arsen Vladimirovich Dotsev, Tatiana Evgenievna Deniskova, Anastasiya Dmitrievna Solovieva, Valeriy Ivanovich Fedorov, Kasim Anverovich Layshev, Tatiana Michailovna Romanenko, Innokentiy Michailovich Okhlopkov, Klaus Wimmers, Henry Reyer, Gottfried Brem, Natalia Anatolievna Zinovieva, Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip, PLOS ONE, 10.1371/journal.pone.0207944, 13, 11, (e0207944), (2018).
- Katherine A. Solari, Uma Ramakrishnan, Elizabeth A. Hadly, Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient, PLOS ONE, 10.1371/journal.pone.0207936, 13, 12, (e0207936), (2018).
- See more
