Volume 5, Issue 1

hierfstat, a package for r to compute and test hierarchical F‐statistics

JÉRÔME GOUDET

Corresponding Author

Department of Ecology and Evolution, BB, UNIL, CH‐1015 Lausanne, Switzerland

Jérôme Goudet, E‐mail: jerome.goudet@unil.chSearch for more papers by this author
First published: 13 December 2004
Citations: 808

Abstract

The package hierfstat for the statistical software r, created by the R Development Core Team, allows the estimate of hierarchical F‐statistics from a hierarchy with any numbers of levels. In addition, it allows testing the statistical significance of population differentiation for these different levels, using a generalized likelihood‐ratio test. The package hierfstat is available at http://www.unil.ch/popgen/softwares/hierfstat.htm.

Number of times cited according to CrossRef: 808

  • Sea ice loss increases genetic isolation in a high Arctic ungulate metapopulation, Global Change Biology, 10.1111/gcb.14965, 26, 4, (2028-2041), (2020).
  • Genetic, morphological and ecological variation across a sharp hybrid zone between two alpine butterfly species, Evolutionary Applications, 10.1111/eva.12925, 13, 6, (1435-1450), (2020).
  • Phylogeographic and population genetic analyses of Cucurbita moschata reveal divergence of two mitochondrial lineages linked to an elevational gradient, American Journal of Botany, 10.1002/ajb2.1424, 107, 3, (510-525), (2020).
  • Cryptic and extensive hybridization between ancient lineages of American crows, Molecular Ecology, 10.1111/mec.15377, 29, 5, (956-969), (2020).
  • Effects of habitat loss on the genetic diversity of Embiratermes neotenicus (Isoptera) in a fragmented landscape of the Atlantic Forest, Brazil, Insect Conservation and Diversity, 10.1111/icad.12414, 13, 4, (351-359), (2020).
  • Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk production traits in Chinese buffalo breeds, Journal of Dairy Science, 10.3168/jds.2019-17364, (2020).
  • The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs, Scientific Reports, 10.1038/s41598-020-62382-4, 10, 1, (2020).
  • Intercontinental long‐distance seed dispersal across the Mediterranean Basin explains population genetic structure of a bird‐dispersed shrub, Molecular Ecology, 10.1111/mec.15413, 29, 8, (1408-1420), (2020).
  • 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).
  • Natural tags identify nursery origin of a coastal elasmobranch Carcharhinus leucas, Journal of Applied Ecology, 10.1111/1365-2664.13627, 57, 7, (1222-1232), (2020).
  • Genetic population structure of anchovy (Engraulis encrasicolus) in North-western Europe and variability in the seasonal distribution of the stocks, Fisheries Research, 10.1016/j.fishres.2020.105619, 229, (105619), (2020).
  • Cryptic speciation in gentoo penguins is driven by geographic isolation and regional marine conditions: Unforeseen vulnerabilities to global change, Diversity and Distributions, 10.1111/ddi.13072, 26, 8, (958-975), (2020).
  • Population genetic diversity and historical dynamics of Fraser’s dolphins Lagenodelphis hosei, Marine Ecology Progress Series, 10.3354/meps13268, 643, (183-195), (2020).
  • Ecological, genetic and evolutionary drivers of regional genetic differentiation in Arabidopsis thaliana, BMC Evolutionary Biology, 10.1186/s12862-020-01635-2, 20, 1, (2020).
  • Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species, Molecular Ecology, 10.1111/mec.15537, 29, 16, (3022-3037), (2020).
  • Hybridization and introgression between toads with different sex chromosome systems, Evolution Letters, 10.1002/evl3.191, 4, 5, (444-456), (2020).
  • Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History, G3: Genes|Genomes|Genetics, 10.1534/g3.120.400886, 10, 9, (3061), (2020).
  • Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation, Journal of Evolutionary Biology, 10.1111/jeb.13581, 33, 4, (468-494), (2020).
  • Demographic, Taxonomic, and Genetic Characterization of the Snook Species Complex (Centropomus spp.) along the Leading Edge of Its Range in the Northwestern Gulf of Mexico, North American Journal of Fisheries Management, 10.1002/nafm.10394, 40, 1, (190-208), (2020).
  • Genetic diversity and domestication of hazelnut (Corylus avellana L.) in Turkey, PLANTS, PEOPLE, PLANET, 10.1002/ppp3.10078, 2, 4, (326-339), (2020).
  • Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection, BMC Genomics, 10.1186/s12864-020-6489-0, 21, 1, (2020).
  • 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).
  • Ocean currents and the population genetic signature of fish migrations, Ecology, 10.1002/ecy.2967, 101, 3, (2020).
  • Contrast‐enhanced sonographic appearances of two primary hepatic epithelioid angiomyolipomas, Journal of Clinical Ultrasound, 10.1002/jcu.22819, 48, 5, (283-286), (2020).
  • Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding, BMC Genomics, 10.1186/s12864-020-6536-x, 21, 1, (2020).
  • Rapid climate-driven evolution of the invasive species Mytilus galloprovincialis over the past century , Anthropocene Coasts, 10.1139/anc-2019-0012, 3, 1, (14-29), (2020).
  • Subtle precipitation differences yield adaptive adjustments in the mesic Nothofagus dombeyi, Forest Ecology and Management, 10.1016/j.foreco.2020.117931, 461, (117931), (2020).
  • Fine‐scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multimodelling approach, Evolutionary Applications, 10.1111/eva.12932, 13, 8, (1854-1867), (2020).
  • Local adaptation across a complex bioclimatic landscape in two montane bumble bee species, Molecular Ecology, 10.1111/mec.15376, 29, 5, (920-939), (2020).
  • The evolution of metabolism: how to test evolutionary hypotheses at the genomic level, Computational and Structural Biotechnology Journal, 10.1016/j.csbj.2020.02.009, (2020).
  • Seascape genomics as a new tool to empower coral reef conservation strategies: An example on north‐western Pacific Acropora digitifera, Evolutionary Applications, 10.1111/eva.12944, 13, 8, (1923-1938), (2020).
  • The genetic legacy of extreme exploitation in a polar vertebrate, Scientific Reports, 10.1038/s41598-020-61560-8, 10, 1, (2020).
  • A small NGS–SNP panel of ancestry inference designed to distinguish African, European, East, and South Asian populations, ELECTROPHORESIS, 10.1002/elps.201900231, 41, 9, (649-656), (2020).
  • Canadian polar bear population structure using genome‐wide markers, Ecology and Evolution, 10.1002/ece3.6159, 10, 8, (3706-3714), (2020).
  • Biome stability predicts population structure of a southern African aridland bird species, Ecology and Evolution, 10.1002/ece3.6175, 10, 9, (4066-4081), (2020).
  • Linking local movement and molecular analysis to explore philopatry and population connectivity of the southern stingray Hypanus americanus, Journal of Fish Biology, 10.1111/jfb.14325, 96, 6, (1475-1488), (2020).
  • Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high‐throughput genotyping approaches, Molecular Ecology, 10.1111/mec.15405, 29, 12, (2189-2203), (2020).
  • Relative importance of isolation‐by‐environment and other determinants of gene flow in an alpine amphibian, Evolution, 10.1111/evo.13955, 74, 5, (962-978), (2020).
  • Using multiple natural tags provides evidence for extensive larval dispersal across space and through time in summer flounder, Molecular Ecology, 10.1111/mec.15414, 29, 8, (1421-1435), (2020).
  • A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice, Molecular Plant, 10.1016/j.molp.2020.03.009, (2020).
  • “A cleaner break”: Genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse (Labrus bergylta), Ecology and Evolution, 10.1002/ece3.6404, 10, 12, (6120-6135), (2020).
  • Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales), New Phytologist, 10.1111/nph.16669, 228, 1, (285-301), (2020).
  • Breaking ecological barriers: Anthropogenic disturbance leads to habitat transitions, hybridization, and high genetic diversity, Science of The Total Environment, 10.1016/j.scitotenv.2020.140046, 740, (140046), (2020).
  • 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).
  • Stepping into the past to conserve the future: Archived skin swabs from extant and extirpated populations inform genetic management of an endangered amphibian, Molecular Ecology, 10.1111/mec.15515, 29, 14, (2598-2611), (2020).
  • Migration dynamics of an important rice pest: The brown planthopper (Nilaparvata lugens) across Asia—Insights from population genomics, Evolutionary Applications, 10.1111/eva.13047, 13, 9, (2449-2459), (2020).
  • Species diversity and phylogeography of Cornus kousa (Asian dogwood) captured by genomic and genic microsatellites, Ecology and Evolution, 10.1002/ece3.6537, 10, 15, (8299-8312), (2020).
  • Using genomics to design and evaluate the performance of underwater forest restoration, Journal of Applied Ecology, 10.1111/1365-2664.13707, 57, 10, (1988-1998), (2020).
  • Environmental pressure rather than ongoing hybridization is responsible for an altitudinal cline in the morphologies of two oaks, Journal of Plant Ecology, 10.1093/jpe/rtaa028, 13, 4, (413-422), (2020).
  • Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes, Communications Biology, 10.1038/s42003-020-1098-7, 3, 1, (2020).
  • School systems as breeding grounds for shadow education: Factors contributing to private supplementary tutoring in West Bengal, India, European Journal of Education, 10.1111/ejed.12412, 55, 3, (342-360), (2020).
  • Landscape does matter: Disentangling founder effects from natural and human‐aided post‐introduction dispersal during an ongoing biological invasion, Journal of Animal Ecology, 10.1111/1365-2656.13284, 89, 9, (2027-2042), (2020).
  • The genetic variation of different developmental stages of Schistosoma japonicum: do the distribution in snails and pairing preference benefit the transmission?, Parasites & Vectors, 10.1186/s13071-020-04240-w, 13, 1, (2020).
  • Genetic diversity and structure of circumtropical almaco jack, : tool for conservation and management, Journal of Fish Biology, 10.1111/jfb.14450, 97, 3, (882-894), (2020).
  • Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France, Annals of Forest Science, 10.1007/s13595-020-00982-w, 77, 3, (2020).
  • Power of a dual‐use SNP panel for pedigree reconstruction and population assignment, Ecology and Evolution, 10.1002/ece3.6645, 10, 17, (9522-9531), (2020).
  • Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple, Horticulture Research, 10.1038/s41438-020-00370-5, 7, 1, (2020).
  • Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm, Theoretical and Applied Genetics, 10.1007/s00122-020-03674-1, (2020).
  • Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta) in relation to taxonomy and geography, American Journal of Botany, 10.1002/ajb2.1525, 107, 9, (1283-1295), (2020).
  • 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).
  • Genotypic similarities among the parthenogenetic Darevskia rock lizards with different hybrid origins, BMC Evolutionary Biology, 10.1186/s12862-020-01690-9, 20, 1, (2020).
  • Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster Crassostrea gigas throughout the Northern Hemisphere, Evolutionary Applications, 10.1111/eva.12965, 13, 6, (1380-1399), (2020).
  • Sexual selection and population divergence III: Interspecific and intraspecific variation in mating signals, Journal of Evolutionary Biology, 10.1111/jeb.13631, 33, 7, (990-1005), (2020).
  • Population genomic SNPs from epigenetic RADs: Gaining genetic and epigenetic data from a single established next‐generation sequencing approach, Methods in Ecology and Evolution, 10.1111/2041-210X.13395, 11, 7, (839-849), (2020).
  • Natural selection drives population divergence for local adaptation in a wheat pathogen, Fungal Genetics and Biology, 10.1016/j.fgb.2020.103398, (103398), (2020).
  • 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).
  • Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland, Molecular Ecology Resources, 10.1111/1755-0998.13167, 20, 5, (1191-1205), (2020).
  • Identification of clonemates and genetic lineages using next-generation sequencing (ddRADseq) guides conservation of a rare species, Bossiaea vombata (Fabaceae), Perspectives in Plant Ecology, Evolution and Systematics, 10.1016/j.ppees.2020.125544, (125544), (2020).
  • Long‐lived marine species may be resilient to environmental variability through a temporal portfolio effect, Ecology and Evolution, 10.1002/ece3.6378, 10, 13, (6435-6448), (2020).
  • Microsatellite marker development in the crop wild relative Linum bienne using genome skimming, Applications in Plant Sciences, 10.1002/aps3.11349, 8, 5, (2020).
  • Bighorn Sheep Genetic Structure in Wyoming Reflects Geography and Management, The Journal of Wildlife Management, 10.1002/jwmg.21882, 84, 6, (1072-1090), (2020).
  • Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L.—Insights from GWAS and GBS data, Journal of Systematics and Evolution, 10.1111/jse.12592, 58, 5, (546-570), (2020).
  • Combining herbarium databases and genetic methods to evaluate the invasion of a popular horticultural species, baby’s breath (Gypsophila paniculata), in the United States, Biological Invasions, 10.1007/s10530-020-02354-x, (2020).
  • Analyzing population structure for forensic STR markers in next generations sequencing data, Forensic Science International: Genetics, 10.1016/j.fsigen.2020.102364, (102364), (2020).
  • Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene), Molecular Ecology, 10.1111/mec.15571, 29, 18, (3511-3525), (2020).
  • Adaptive genetic variation to drought in a widely distributed conifer suggests a potential for increasing forest resilience in a drying climate, New Phytologist, 10.1111/nph.16551, 227, 2, (427-439), (2020).
  • Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae), Scientific Reports, 10.1038/s41598-020-73748-z, 10, 1, (2020).
  • High conservation combined with high plasticity: genomics and evolution of Borrelia bavariensis, BMC Genomics, 10.1186/s12864-020-07054-3, 21, 1, (2020).
  • Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations, BMC Genetics, 10.1186/s12863-020-00921-8, 21, 1, (2020).
  • The role of agro‐ecological factors and transboundary transhumance in shaping the genetic diversity in four indigenous cattle populations of Benin, Journal of Animal Breeding and Genetics, 10.1111/jbg.12495, 137, 6, (622-640), (2020).
  • Species complex diversification by host plant use in an herbivorous insect: The source of Puerto Rican cactus mealybug pest and implications for biological control, Ecology and Evolution, 10.1002/ece3.6702, 10, 19, (10463-10480), (2020).
  • Seasonal use of two unregulated Lake Superior tributaries by lake sturgeon, Journal of Great Lakes Research, 10.1016/j.jglr.2020.06.008, (2020).
  • Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra, Molecular Ecology, 10.1111/mec.15614, 29, 20, (3872-3888), (2020).
  • Spatial gradients of introgressed ancestry reveal cryptic connectivity patterns in a high gene flow marine fish, Molecular Ecology, 10.1111/mec.15611, 29, 20, (3857-3871), (2020).
  • Instability of natural selection at candidate barrier loci underlying speciation in wood ants, Molecular Ecology, 10.1111/mec.15606, 29, 20, (3988-3999), (2020).
  • Genetic and demographic vulnerability of adder populations: Results of a genetic study in mainland Britain, PLOS ONE, 10.1371/journal.pone.0231809, 15, 4, (e0231809), (2020).
  • Breeding systems and genetic diversity in tropical carpenter ant colonies: different strategies for similar outcomes in Brazilian Cerrado savanna, Zoological Journal of the Linnean Society, 10.1093/zoolinnean/zlaa035, (2020).
  • Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils, PeerJ, 10.7717/peerj.9220, 8, (e9220), (2020).
  • Genetic structure of the long-snouted seahorse, Hippocampus guttulatus, in the Central–Western Mediterranean Sea, Biological Journal of the Linnean Society, 10.1093/biolinnean/blaa074, (2020).
  • Impact of biased sex ratio on genetic diversity, structure and differentiation of Populus nigra populations, Botany, 10.1139/cjb-2020-0046, (2020).
  • Outcrossing Mating System of the Early-Divergent Moonwort Fern ( Botrychium lunaria , Ophioglossaceae) Revealed in the European Alps , International Journal of Plant Sciences, 10.1086/710491, (000-000), (2020).
  • Cropland connectivity affects genetic divergence of Colorado potato beetle along an invasion front, Evolutionary Applications, 10.1111/eva.13140, 0, 0, (2020).
  • Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance, Genes, 10.3390/genes11010057, 11, 1, (57), (2020).
  • 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).
  • Origin of planted Eucalyptus benthamii trees in Camden NSW: checking the effectiveness of circa situm conservation measures using molecular markers, Biodiversity and Conservation, 10.1007/s10531-020-01936-4, (2020).
  • A species-discriminatory single-nucleotide polymorphism set reveals maintenance of species integrity in hybridizing European white oaks (Quercus spp.) despite high levels of admixture, Annals of Botany, 10.1093/aob/mcaa001, (2020).
  • Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed, PLOS Genetics, 10.1371/journal.pgen.1008593, 16, 2, (e1008593), (2020).
  • Natural Selection Towards Wild-Type in Composite Cross Populations of Winter Wheat, Frontiers in Plant Science, 10.3389/fpls.2019.01757, 10, (2020).
  • Human Plasmodium vivax diversity, population structure and evolutionary origin, PLOS Neglected Tropical Diseases, 10.1371/journal.pntd.0008072, 14, 3, (e0008072), (2020).
  • Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication, Genes, 10.3390/genes11030266, 11, 3, (266), (2020).
  • See more

The full text of this article hosted at iucr.org is unavailable due to technical difficulties.