Stacks: an analysis tool set for population genomics (scientific article published on 24 May 2013)

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Q64114717	GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity
Q92658081	Gene Flow in the Müllerian Mimicry Ring of a Poisonous Papuan Songbird Clade (Pitohui; Aves)
Q34472524	Gene duplication, population genomics, and species-level differentiation within a tropical mountain shrub
Q104073650	Genes, pathways and networks responding to drought stress in oil palm roots
Q49227454	Genetic Architecture of Capitate Glandular Trichome Density in Florets of Domesticated Sunflower (Helianthus annuus L.).
Q50421287	Genetic Basis of Body Color and Spotting Pattern in Redheaded Pine Sawfly Larvae (Neodiprion lecontei).
Q35952069	Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing
Q46242535	Genetic Diversity and Connectivity in Maurolicus muelleri in the Bay of Biscay Inferred from Thousands of SNP Markers.
Q55689638	Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus.
Q26314615	Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes
Q91724735	Genetic analysis of Taishu horses on and off Tsushima Island: Implications for conservation
Q49417345	Genetic and morphological support for possible sympatric origin of fish from subterranean habitats
Q37692331	Genetic architecture of threshold reaction norms for male alternative reproductive tactics in Atlantic salmon (Salmo salar L.).
Q53098435	Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing.
Q36151657	Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing
Q36367738	Genetic diversity and gene flow decline with elevation in montane mayflies
Q90123793	Genetic diversity and population structure of four Chinese rabbit breeds
Q61443169	Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins
Q110951134	Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations
Q47107651	Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq
Q58775902	Genetic diversity maintained among fragmented populations of a tree undergoing range contraction
Q64052811	Genetic diversity of Nyssorhynchus (Anopheles) darlingi related to biting behavior in western Amazon
Q90003058	Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark
Q35541527	Genetic evidence for ecological divergence in kokanee salmon
Q93014387	Genetic evidence of a northward range expansion in the eastern Bering Sea stock of Pacific cod
Q47558657	Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach
Q34450552	Genetic mapping and QTL analysis of growth-related traits in Pinctada fucata using restriction-site associated DNA sequencing
Q47111111	Genetic mapping of the qSBN7 locus, a QTL controlling secondary branch number per panicle in rice
Q56669711	Genetic parameters and quantitative trait loci analysis associated with body size and timing at metamorphosis into glass eels in captive-bred Japanese eels (Anguilla japonica)
Q90834598	Genetic patterns in peripheral marine populations of the fusilier fish Caesio cuning within the Kuroshio Current
Q35565054	Genetic reconstructions of invasion history
Q92670213	Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude
Q36037448	Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes.
Q92235075	Genetic variation and admixture of red-eared sliders (Trachemys scripta elegans) in the USA
Q94461695	Genome Wide Analysis for Growth at Two Growth Stages in A New Fast-Growing Common Carp Strain (Cyprinus carpio L.).
Q38686190	Genome-Wide Association Study Identifies Loci Associated with Resistance to Viral Nervous Necrosis Disease in Asian Seabass
Q92712580	Genome-Wide Association Study Reveals Candidate Genes for Flowering Time Variation in Common Bean (Phaseolus vulgaris L.).
Q31122855	Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies
Q38650694	Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon) in Northeast China Using Double-Digest Restriction-Site Associated DNA Sequencing
Q36060049	Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus).
Q91638750	Genome-Wide Signatures of Selection in Colletotrichum kahawae Reveal Candidate Genes Potentially Involved in Pathogenicity and Aggressiveness
Q90043924	Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae)
Q41049895	Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae).
Q64282591	Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus
Q28468305	Genome-wide SNP analysis using 2b-RAD sequencing identifies the candidate genes putatively associated with resistance to ivermectin in Haemonchus contortus
Q30388402	Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.
Q89455101	Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function
Q46243724	Genome-wide SNPs identify limits to connectivity in the extreme freshwater disperser, spangled perch Leiopotherapon unicolor (Terapontidae).
Q33622312	Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti
Q31169878	Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis).
Q38846375	Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex.
Q43047339	Genome-wide SNPs reveal the drivers of gene flow in an urban population of the Asian Tiger Mosquito, Aedes albopictus.
Q47549314	Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories.
Q93043890	Genome-wide association study of an unusual dolphin mortality event reveals candidate genes for susceptibility and resistance to cetacean morbillivirus
Q36324539	Genome-wide data delimits multiple climate-determined species ranges in a widespread Australian fish, the golden perch (Macquaria ambigua).
Q31103108	Genome-wide data help identify an avian species-level lineage that is morphologically and vocally cryptic
Q116202034	Genome-wide data implicate terminal fusion automixis in king cobra facultative parthenogenesis
Q31047720	Genome-wide data reveal cryptic diversity and genetic introgression in an Oriental cynopterine fruit bat radiation
Q97549721	Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes
Q92205851	Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats
Q91397452	Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq
Q58748607	Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group
Q88571571	Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus)
Q39032250	Genome-wide selection components analysis in a fish with male pregnancy
Q61443862	Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan
Q52880916	Genome-wide single nucleotide polymorphism scan suggests adaptation to urbanization in an important pollinator, the red-tailed bumblebee (Bombus lapidarius L.).
Q43764049	Genome-wide single-generation signatures of local selection in the panmictic European eel.
Q47698727	Genome-wide single-nucleotide polymorphism data reveal cryptic species within cryptic freshwater snail species-The case of the Ancylus fluviatilis species complex.
Q46253095	Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata
Q31151679	Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River
Q55210189	Genomewide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies.
Q41468649	Genomewide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus).
Q47837310	Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka).
Q92795600	Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes
Q62753278	Genomic Evidence for Cryptic Speciation in Tree Frogs From the Apennine Peninsula, With Description of Hyla perrini sp. nov
Q36100788	Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals.
Q50027502	Genomic Predictions and Genome-Wide Association Study of Resistance Against Piscirickettsia salmonis in Coho Salmon (Oncorhynchus kisutch) Using ddRAD Sequencing.
Q61811047	Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters
Q47094512	Genomic Signature of Adaptive Divergence despite Strong Nonadaptive Forces on Edaphic Islands: A Case Study of Primulina juliae.
Q94453200	Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Scophthalmus maximus)
Q40447709	Genomic Signatures of Historical Allopatry and Ecological Divergence in an Island Lizard
Q92535289	Genomic analyses reveal three independent introductions of the invasive brown rat (Rattus norvegicus) to the Faroe Islands
Q38637391	Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae).
Q47830427	Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands.
Q88525065	Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.).
Q46440259	Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus).
Q41546749	Genomic and phenotypic signatures of climate adaptation in an Anolis lizard
Q57152977	Genomic approaches for studying crop evolution
Q92358502	Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow
Q39370557	Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp., Serranidae).
Q46588570	Genomic characterization of sex-identification markers in Sebastes carnatus and Sebastes chrysomelas rockfishes
Q31151567	Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species.
Q47177870	Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus).
Q94554218	Genomic differentiation and intercontinental population structure of mosquito vectors Culex pipiens pipiens and Culex pipiens molestus
Q39629179	Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens).
Q110697371	Genomic diversity and demographic history of the Dromiciops genus (Marsupialia: Microbiotheriidae)
Q55412812	Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw.
Q46214368	Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis
Q51151596	Genomic evidence for the population genetic differentiation of Misgurnus anguillicaudatus in the Yangtze River basin of China.
Q46380972	Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic.
Q38473522	Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata).
Q44170049	Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group.
Q33897920	Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta
Q57136008	Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes
Q39172678	Genomic islands of divergence linked to ecotypic variation in sockeye salmon
Q42372647	Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America
Q91155442	Genomic pedigree reconstruction identifies predictors of mating and reproductive success in an invasive vertebrate
Q118110161	Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes)
Q100635453	Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants
Q64951914	Genomic reconstruction of 100 000-year grassland history in a forested country: population dynamics of specialist forbs.
Q38629735	Genomic regions and genes related to inter-population differences in body size in the ground beetle Carabus japonicus
Q38631839	Genomic resources and their influence on the detection of the signal of positive selection in genome scans
Q111629796	Genomic signals reveal past evolutionary dynamics of Quercus schottkyana and its response to future climate change
Q37412270	Genomic signatures among Oncorhynchus nerka ecotypes to inform conservation and management of endangered Sockeye Salmon
Q57823840	Genomic signatures of environmental selection despite near-panmixia in summer flounder
Q46312114	Genomic signatures of evolution in Nautilus-An endangered living fossil
Q64285223	Genomic signatures of introgression between commercial and native bumblebees, , in western Iberian Peninsula-Implications for conservation and trade regulation
Q46327292	Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties
Q64889666	Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds.
Q36012909	Genomic signatures of rapid adaptive evolution in the bluespotted cornetfish, a Mediterranean Lessepsian invader.
Q35994521	Genomic signatures of the plateless phenotype in the threespine stickleback
Q35908706	Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki).
Q35611931	Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands
Q90561560	Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon
Q98224922	Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners
Q47684970	Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char
Q44876597	Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agroecosystem.
Q46276723	Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies
Q92796701	Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation
Q31155680	Genotype Calling from Population-Genomic Sequencing Data
Q97067711	Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)
Q37004886	Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy
Q38768198	Genotyping-by-Sequencing and Its Exploitation for Forage and Cool-Season Grain Legume Breeding
Q41978818	Genotyping-by-sequencing in ecological and conservation genomics.
Q36177377	Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae).
Q58618245	Genotyping-by-sequencing supports a genetic basis for wing reduction in an alpine New Zealand stonefly
Q35492595	Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing
Q27316146	Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past
Q44096718	Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower.
Q46368395	Geographically structured genetic variation in the Medicago lupulina-Ensifer mutualism.
Q118110159	Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia
Q54984754	Great tits and the city: Distribution of genomic diversity and gene-environment associations along an urbanization gradient.
Q90352488	Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation
Q26771227	Harnessing the power of RADseq for ecological and evolutionary genomics
Q36370317	Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data.
Q88815217	Hierarchical biogeographical processes largely explain the genomic divergence pattern in a species complex of sea anemones (Metridioidea: Sagartiidae: Anthothoe)
Q101166118	High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)
Q60918673	High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations
Q64105038	High-Density Linkage Map and QTLs for Growth in Snapper ()
Q60935922	High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing
Q34370890	High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers
Q37678615	High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus.
Q50979717	High-density linkage maps fail to detect any genetic component to sex determination in a Rana temporaria family.
Q36726469	High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex.
Q90322442	High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.).
Q46712146	High-throughput SNPs for all: genotyping-in-thousands
Q60296477	Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly
Q41085609	Historical demography and genetic differentiation of the giant freshwater prawn Macrobrachium rosenbergii in Bangladesh based on mitochondrial and ddRAD sequence variation.
Q98159237	Historical human activities reshape evolutionary trajectories across both native and introduced ranges
Q46439491	History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei).
Q64241965	Hitchhiking the high seas: Global genomics of rafting crabs
Q41971204	Homogeneous nuclear background for mitochondrial cline in northern range of Notochthamalus scabrosus
Q110697261	Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex
Q38733016	Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut.
Q93174827	Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi
Q89524246	How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish
Q36320229	How Do Cold-Adapted Plants Respond to Climatic Cycles? Interglacial Expansion Explains Current Distribution and Genomic Diversity in Primula farinosa L.
Q110697283	How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)
Q104736881	How rapidly do self-compatible populations evolve selfing? Mating system estimation within recently evolved self-compatible populations of Azorean Tolpis succulenta (Asteraceae)
Q57824790	Human activities and landscape features interact to closely define the distribution and dispersal of an urban commensal
Q39641210	Hybrid dynamics in a species group of swallowtail butterflies
Q98177762	Hybridization Between Yuccas From Baja California: Genomic and Environmental Patterns
Q35964819	Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens
Q100437375	Hybridization and introgression between toads with different sex chromosome systems
Q58129575	Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles
Q40306834	Hybridization promotes speciation in Coenonympha butterflies.
Q30372766	Hyperdiverse gene cluster in snail host conveys resistance to human schistosome parasites
Q46516175	Identification and Characterization of Sex-Associated Loci in Sockeye Salmon Using Genotyping-by-Sequencing and Comparison with a Sex-Determining Assay Based on the sdY Gene
Q93154042	Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo
Q38927074	Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map.
Q37194944	Identification of Quantitative Trait Loci Controlling Root and Shoot Traits Associated with Drought Tolerance in a Lentil (Lens culinaris Medik.) Recombinant Inbred Line Population.
Q98946191	Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads
Q46261655	Identification of genomic regions associated with sex in Pacific halibut
Q92898954	Identification of sex-linked markers in the sexually cryptic coco de mer: are males and females produced in equal proportions?
Q36176883	Identifying homomorphic sex chromosomes from wild-caught adults with limited genomic resources
Q35911845	Identifying signatures of sexual selection using genomewide selection components analysis
Q35963644	Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions
Q90352498	Impact of supplementation on deleterious mutation distribution in an exploited salmonid
Q35579962	Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq).
Q58670490	Improved reference genome of Aedes aegypti informs arbovirus vector control
Q47192676	Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies
Q36263529	Incipient speciation driven by hypertrophied lips in Midas cichlid fishes?
Q35532749	Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox).
Q28830326	Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats?
Q92072973	Increased Adaptive Variation Despite Reduced Overall Genetic Diversity in a Rapidly Adapting Invader
Q98164355	Individual-based population genomics reveal different drivers of adaptation in sympatric fish
Q47316436	Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes
Q38674952	Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches.
Q111630374	Inflorescence characteristics as function-valued traits: Analysis of heritability and selection on architectural effects
Q57471095	Inheritance, distribution and genetic differentiation of a color polymorphism in Panamanian populations of the tortoise beetle, Chelymorpha alternans (Coleoptera: Chrysomelidae)
Q33789176	Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes
Q103826076	Insights into genomic structure and evolutionary processes of coastal Suaeda species in East Asia using cpDNA, nDNA, and genome-wide SNPs
Q96136411	Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust (Dociostaurus maroccanus)
Q34402716	Integrating evolutionary and functional tests of adaptive hypotheses: a case study of altitudinal differentiation in hemoglobin function in an Andean Sparrow, Zonotrichia capensis
Q92784646	Integrating hybrid zone analyses in species delimitation: lessons from two anuran radiations of the Western Mediterranean
Q58585817	Integrating phylogenomics, phylogenetics, morphometrics, relative genome size and ecological niche modelling disentangles the diversification of Eurasian Euphorbia seguieriana s. l. (Euphorbiaceae)
Q47720655	Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids.
Q101440812	Integrative taxonomy at the nexus of population divergence and speciation in insular speckled rattlesnakes
Q103805634	Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations
Q35232364	Intraspecific polymorphism, interspecific divergence, and the origins of function-altering mutations in deer mouse hemoglobin.
Q35729535	Introgression between invasive and native blue mussels (genus Mytilus) in the central California hybrid zone
Q64101043	Isolation by Distance, Source-Sink Population Dynamics and Dispersal Facilitation by Trade Routes: Impact on Population Genetic Structure of a Stored Grain Pest
Q90249880	Land bridges in the Pleistocene contributed to flora assembly on the continental islands of South China: Insights from the evolutionary history of Quercus championii
Q46267203	Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss).
Q93254970	Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa
Q90475013	Landscape limits gene flow and drives population structure in Agassiz's desert tortoise (Gopherus agassizii)
Q28822567	Large-Scale Genotyping-by-Sequencing Indicates High Levels of Gene Flow in the Deep-Sea Octocoral Swiftia simplex (Nutting 1909) on the West Coast of the United States
Q97545696	Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea
Q90170459	Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin
Q57143276	Lessons from a natural experiment: Allopatric morphological divergence and sympatric diversification in the Midas cichlid species complex are largely influenced by ecology in a deterministic way
Q30000065	Limitations of climatic data for inferring species boundaries: insights from speckled rattlesnakes
Q30994494	Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data
Q46273521	Linking micro- and macroevolutionary perspectives to evaluate the role of Quaternary sea-level oscillations in island diversification
Q89818407	Local adaptation fuels cryptic speciation in terrestrial annelids
Q55000091	Loci under selection and markers associated with host plant and host-related strains shape the genetic structure of Brazilian populations of Spodoptera frugiperda (Lepidoptera, Noctuidae).
Q36015906	Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?
Q98159224	Long-lived marine species may be resilient to environmental variability through a temporal portfolio effect
Q59795961	Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish
Q46244099	Long-term in situ persistence of biodiversity in tropical sky-islands revealed by landscape genomics.
Q93195725	Long-term isolation of European steppe outposts boosts the biome's conservation value
Q30564568	Long-term sperm storage in the brownbanded bamboo shark Chiloscyllium punctatum
Q102152317	Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance
Q46261889	Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems.
Q46325908	Male and female contributions to behavioral isolation in darters as a function of genetic distance and color distance.
Q90608358	Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp
Q89702746	Mapping of Quantitative Trait Loci for Growth and Carcass-Related Traits in Chickens Using a Restriction-Site Associated DNA Sequencing Method
Q63976746	Mapping of multiple complementary sex determination loci in a parasitoid wasp
Q61450434	Matching the genetics of released and local Aedes aegypti populations is critical to assure Wolbachia invasion
Q60935140	Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing
Q91791675	Metapopulation dynamics and foraging plasticity in a highly vagile seabird, the southern rockhopper penguin
Q90754394	Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/adenine methylation changes
Q47665611	MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation
Q37640637	Microgeographical structure in the major Neotropical malaria vector Anopheles darlingi using microsatellites and SNP markers.
Q46864358	Microhabitat differences impact phylogeographic concordance of codistributed species: genomic evidence in montane sedges (Carex L.) from the Rocky Mountains
Q46260554	Microhaplotypes provide increased power from short-read DNA sequences for relationship inference
Q46433692	Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species.
Q41336934	Mining sequence variations in representative polyploid sugarcane germplasm accessions
Q91791997	Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea)
Q100727563	Miocene diversification of a golden-thread nanmu tree species (Phoebe zhennan, Lauraceae) around the Sichuan Basin shaped by the East Asian monsoon
Q35831299	Mitochondrial DNA variants help monitor the dynamics of Wolbachia invasion into host populations.
Q90081425	Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development
Q41081052	Mixed population genomics support for the central marginal hypothesis across the invasive range of the cane toad (Rhinella marina) in Australia.
Q46307561	Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis).
Q48106847	Molecular Ecology continues to perform well according to the major publication metrics. Introduction
Q35610003	Molecular Mapping of Restriction-Site Associated DNA Markers In Allotetraploid Upland Cotton
Q46402131	Molecular ecology studies of species radiations: current research gaps, opportunities and challenges
Q52668061	Molecular evidence for the first records of facultative parthenogenesis in elapid snakes.
Q116672870	Molecular phylogeny and systematics of bald uakaris, genus Cacajao (Primates: Pitheciidae), with the description of a new species
Q58782127	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
Q92023523	More than the eye can see: Genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean
Q35736891	Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation
Q111629854	Morphological distinctiveness of Ligularia tongolensis and L. cymbulifera is maintained between habitats despite bidirectional and asymmetrical introgression in multiple hybrid zones
Q57179152	Morphometric and genetic differentiation among populations of flat-headed cusimanse () in Nigeria
Q89531563	Multiple Loci Control Eyespot Number Variation on the Hindwings of Bicyclus anynana Butterflies
Q92219926	Multiple auto- and allopolyploidisations marked the Pleistocene history of the widespread Eurasian steppe plant Astragalus onobrychis (Fabaceae)
Q31103371	Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae).
Q92406848	Multiple introductions and population structure during the rapid expansion of the invasive Sahara mustard (Brassica tournefortii)
Q90620490	Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype
Q28597003	Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids
Q51278699	Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers.
Q58612158	Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains
Q52624453	Navigating the Interface Between Landscape Genetics and Landscape Genomics.
Q97094132	New genomic resources for three exploited Mediterranean fishes
Q91061003	New insights from RADseq data on differentiation in the Hottentot golden mole species complex from South Africa
Q46598811	New view of population genetics of zooplankton: RAD-seq analysis reveals population structure of the North Atlantic planktonic copepod Centropages typicus.
Q46867729	Next generation phylogeography of cave and surface Astyanax mexicanus
Q41085653	No evidence for adaptation to local rhizobial mutualists in the legume Medicago lupulina.
Q57153210	No evidence for maintenance of a sympatric species barrier by chromosomal inversions
Q57139481	Nonclonal coloniality: Genetically chimeric colonies through fusion of sexually produced polyps in the hydrozoan
Q37549988	Normal chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora crassa
Q58707921	Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis
Q56654710	Novel insights on colonization routes and evolutionary potential of Colletotrichum kahawae, a severe pathogen of Coffea arabica
Q44751831	Novel trophic niches drive variable progress towards ecological speciation within an adaptive radiation of pupfishes
Q96641130	On the causes of geographically heterogeneous parallel evolution in sticklebacks
Q35558575	Optimization of multiplexed RADseq libraries using low-cost adaptors
Q92358458	Optimizing genomic selection for blight resistance in American chestnut backcross populations: A trade-off with American chestnut ancestry implies resistance is polygenic
Q36345463	Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird.
Q90726566	PMERGE: Computational filtering of paralogous sequences from RAD-seq data
Q31135647	PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data
Q60296522	Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot ()
Q96578702	Parallel flowering time clines in native and introduced ragweed populations are likely due to adaptation
Q39878246	Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact.
Q90171616	Parallel selection on thermal physiology facilitates repeated adaptation of city lizards to urban heat islands
Q31137982	Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations
Q89983911	Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing
Q39225188	Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback
Q90617643	Patterns of Genome-Wide Variation, Population Differentiation and SNP Discovery of the Red Banded Stink Bug (Piezodorus guildinii)
Q47118351	Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia River.
Q33877314	Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize
Q57187478	Phenotypic and life-history diversification in Amazonian frogs despite past introgressions
Q56894031	Phenotypic plasticity and local adaptation favor range expansion of a Neotropical palm
Q92287023	Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)
Q90138971	Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae)
Q55689727	Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation.
Q36327058	Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus).
Q98216464	Phylogenomic test of mitochondrial clues to archaic ancestors in a group of hybridizing swallowtail butterflies
Q60912389	Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries
Q35558051	Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing
Q40923249	Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture.
Q51151184	Phylogeographic analysis suggests two origins for the riparian azalea Rhododendron indicum (L.) Sweet.
Q36034291	Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.
Q41140865	Phylogeography and larval spine length of the dragonfly Leucorhinia dubia in Europe.
Q92220679	Phylogeography and population genetics of pine butterflies: Sky islands increase genetic divergence
Q94600793	Phylogeography of the iconic Australian red-tailed black-cockatoo (Calyptorhynchus banksii) and implications for its conservation
Q57824793	Physiological and genomic signatures of evolutionary thermal adaptation in redband trout from extreme climates
Q58705527	Pleistocene climate cycling and host plant association shaped the demographic history of the bark beetle Pityogenes chalcographus
Q52690794	Pleistocene land bridges act as semipermeable agents of avian gene flow in Wallacea.
Q33590815	Pollutants and Insecticides Drive Local Adaptation in African Malaria Mosquitoes
Q49725092	Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant-plant, Acacia (Vachellia) drepanolobium.
Q93081188	Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback
Q97883617	Population Genetic Structure and Demographic History of Primula fasciculata in Southwest China
Q59487549	Population Genomic Analysis of North American Eastern Wolves (Canis lycaon) Supports Their Conservation Priority Status
Q90192580	Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature
Q90226616	Population Genomic Approaches for Weed Science
Q89616427	Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop
Q92811816	Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region
Q64934524	Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus).
Q64892984	Population divergence and gene flow in two East Asian shorebirds on the verge of speciation.
Q44039088	Population genetic structure is shaped by historical, geographic, and environmental factors in the leguminous shrub Caragana microphylla on the Inner Mongolia Plateau of China
Q59128402	Population genetic structure of the deep-sea mussel s (Bivalvia: Mytilidae) in the Northwest Pacific
Q99608431	Population genetic structure of the great star coral, Montastraea cavernosa, across the Cuban archipelago with comparisons between microsatellite and SNP markers
Q43713275	Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis).
Q38917340	Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits
Q50067243	Population genomic footprints of host adaptation, introgression and recombination in Coffee Leaf Rust
Q33575087	Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas
Q58768359	Population genomics of Culiseta melanura, the principal vector of Eastern equine encephalitis virus in the United States
Q92424276	Population genomics of an exceptional hybridogenetic system of Pelophylax water frogs
Q92402654	Population genomics of an outbreak of the potato late blight pathogen, Phytophthora infestans, reveals both clonality and high genotypic diversity
Q36490100	Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect
Q28834686	Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae)
Q36797657	Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations
Q57825256	Population genomics of the introduced and cultivated Pacific kelp : Marinas-not farms-drive regional connectivity and establishment in natural rocky reefs
Q91657042	Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitats types
Q51275635	Population genomics reveals multiple drivers of population differentiation in a sex-role-reversed pipefish.
Q37271776	Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis.
Q64924725	Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise.
Q58862787	Population history provides foundational knowledge for utilizing and developing native plant restoration materials
Q38804860	Population structure and gene flow in the global pest, Helicoverpa armigera.
Q42671322	Population structure and genetic diversity of Bromus tectorum within the small grain production region of the Pacific Northwest.
Q39952715	Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection
Q111629665	Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L.—Insights from GWAS and GBS data
Q35666752	Possible Human Papillomavirus 38 Contamination of Endometrial Cancer RNA Sequencing Samples in The Cancer Genome Atlas Database
Q60487960	Potential limits to the benefits of admixture during biological invasion
Q99579761	Power of a dual-use SNP panel for pedigree reconstruction and population assignment
Q54986973	Practical considerations for plant phylogenomics.
Q91511120	Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region
Q28603248	Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life
Q54973409	Predicting the genetic impact of stocking in Brook Charr (Salvelinus fontinalis) by combining RAD sequencing and modeling of explanatory variables.
Q91585667	Predicting the success of an invader: Niche shift versus niche conservatism
Q57814566	Pushing the limits of whole genome amplification: successful sequencing of RADseq library from a single microhymenopteran (Chalcidoidea, )
Q35113428	PyRAD: assembly of de novo RADseq loci for phylogenetic analyses
Q92022772	QTL Mapping of Intestinal Neutrophil Variation in Threespine Stickleback Reveals Possible Gene Targets Connecting Intestinal Inflammation and Systemic Health
Q48316705	QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods
Q59339916	Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions
Q28603162	R-gene variation across Arabidopsis lyrata subspecies: effects of population structure, selection and mating system
Q57173967	RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding
Q46728354	RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus).
Q91909292	RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean
Q34518965	RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa.
Q33575137	RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic
Q35839806	RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels
Q64055139	RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories
Q46261663	RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata).
Q42042959	RAD-Seq analysis of typical and minor Citrus accessions, including Bhutanese varieties
Q39693112	RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas.
Q59795240	RAD-seq reveals genetic structure of the F-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression
Q31108650	RADIS: analysis of RAD-seq data for interspecific phylogeny
Q31114729	RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data
Q50104536	RADpainter and fineRADstructure: population inference from RADseq data
Q92888358	RADseq analyses reveal concordant Indian Ocean biogeographic and phylogeographic boundaries in the reef fish Dascyllus trimaculatus
Q42372765	RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia
Q38674762	RADseq provides evidence for parallel ecotypic divergence in the autotetraploid Cochlearia officinalis in Northern Norway
Q89793423	RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics
Q45786943	Radiation of the polymorphic Little Devil poison frog (Oophaga sylvatica) in Ecuador
Q99581564	Range reduction of Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns
Q92967071	Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools
Q34323524	Rapid SNP discovery and a RAD-based high-density linkage map in jujube (Ziziphus Mill.).
Q35364084	Rapid evolution of a native species following invasion by a congener
Q33784954	Rapid evolution of phenotypic plasticity and shifting thresholds of genetic assimilation in the nematode Caenorhabditis remanei
Q34538897	Rapid evolutionary response to a transmissible cancer in Tasmanian devils
Q98225865	Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids
Q30274894	Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish, Cyprinodon bovinus.
Q89811423	Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection
Q46259266	Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest
Q58765793	Recent advances in conservation and population genomics data analysis
Q30748146	Recent novel approaches for population genomics data analysis
Q38159797	Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools.
Q59666645	Rediscovery of Red Wolf Ghost Alleles in a Canid Population Along the American Gulf Coast
Q46732748	Reed frog diversification in the Gulf of Guinea: overseas dispersal, the progression rule, and in situ speciation
Q57093794	Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback
Q100569639	Repeated hybridisation increased diversity in the door snail complex Charpentieria itala in the Southern Alps
Q91912433	Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)
Q52327961	Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling.
Q46257729	Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling
Q55442805	Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection.
Q36116109	Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae).
Q55259779	Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish (Silurus meridionalis).
Q45779590	Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.
Q92606325	Restriction-site associated DNA markers provide new insights into the evolutionary history of the bark beetle genus Dendroctonus
Q92634945	Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae)
Q55278956	Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes.
Q53637417	SNP discovery and genotyping using restriction-site-associated DNA sequencing in chickens.
Q38369087	SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus).
Q104704961	Safeguarding the genetic integrity of native pollinators requires stronger regulations on commercial lines
Q36273104	Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps
Q92857959	Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing
Q38732742	Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome
Q90027364	Sea Turtle Population Genomic Discovery: Global and Locus-Specific Signatures of Polymorphism, Selection, and Adaptive Potential
Q58404713	Seascape genetics of saithe (Pollachius virens) across the North Atlantic using single nucleotide polymorphisms
Q92088539	Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada
Q31122640	Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus).
Q92700706	Selecting RAD-Seq Data Analysis Parameters for Population Genetics: The More the Better?
Q36049287	Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics
Q46748059	Sequence-tagged high-density genetic maps of Zoysia japonica provide insights into genome evolution in Chloridoideae
Q22121997	Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
Q36154852	Serial sequencing of isolength RAD tags for cost-efficient genome-wide profiling of genetic and epigenetic variations
Q94460489	Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23
Q38704386	Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems.
Q92220538	Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)
Q90194588	Sex-specific impact of inbreeding on pathogen load in the striped dolphin
Q47556300	Sex-specific markers developed by next-generation sequencing confirmed an XX/XY sex determination system in bighead carp (Hypophthalmichehys nobilis) and silver carp (Hypophthalmichthys molitrix).
Q35723011	Shared and nonshared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale
Q101632240	Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles
Q91868278	Shedding Light on Specificity: Population Genomic Structure of a Symbiosis Between a Coral Reef Fish and Luminous Bacterium
Q35744553	Signatures of natural selection between life cycle stages separated by metamorphosis in European eel.
Q46294943	Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity.
Q46896670	SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches
Q35543826	Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species
Q50333883	Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant
Q60043885	Small and genetically highly structured populations in a long-legged bee, Rediviva longimanus, as inferred by pooled RAD-seq
Q99595113	Small-scale population divergence is driven by local larval environment in a temperate amphibian
Q46256093	Spatial population genomics of the brown rat (Rattus norvegicus) in New York City
Q46260546	Spatial variation in the parasite communities and genomic structure of urban rats in New York City.
Q28596878	Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise
Q64994562	Speciation and hybridization in invasive fire ants.
Q46262184	Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier
Q93003073	Speciation with gene flow: Evidence from a complex of alpine butterflies (Coenonympha, Satyridae)
Q46321965	Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs
Q110697273	Species limits and phylogeographic structure in two genera of solitary African mole-rats Georychus and Heliophobius
Q31095987	Species limits, interspecific hybridization and phylogeny in the cryptic land snail complex Pyramidula: The power of RADseq data
Q90045164	Species-Specific Marker Discovery in Tilapia
Q90068757	Spontaneous whole-genome duplication restores fertility in interspecific hybrids
Q90438287	Stable species boundaries despite ten million years of hybridization in tropical eels
Q96303655	Strong Selection Against Early Generation Hybrids in Joshua Tree Hybrid Zone Not Explained by Pollinators Alone
Q92646908	Strong phenotypic divergence in spite of low genetic structure in the endemic Mangrove Warbler subspecies (Setophaga petechia xanthotera) of Costa Rica
Q35535064	Strong premating reproductive isolation drives incipient speciation in Mimulus aurantiacus
Q47614411	Substantial differences in bias between single-digest and double-digest RAD-seq libraries: A case study
Q89998847	Supplementation stocking of Lake Trout (Salvelinus namaycush) in small boreal lakes: Ecotypes influence on growth and condition
Q58695562	Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach)
Q52370373	Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java.
Q91776459	Taming the Red Bastards: Hybridisation and species delimitation in the Rhodanthemum arundanum-group (Compositae, Anthemideae)
Q38792657	Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences
Q39511840	Tempo and mode of speciation in Holacanthus angelfishes based on RADseq markers
Q90731468	Testing morphological trait evolution and assessing species delimitations in the grape genus using a phylogenomic framework
Q92668343	The Apennines as a cryptic Pleistocene refugium of the bark beetle Pityogenes chalcographus (Coleoptera: Curculionidae)
Q58744003	The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Q41383276	The Integrated Genomic Architecture and Evolution of Dental Divergence in East African Cichlid Fishes (Haplochromis chilotes x H. nyererei).
Q91529511	The Interplay between Incipient Species and Social Polymorphism in the Desert Ant Cataglyphis
Q57922403	The State of "" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization
Q28602365	The aggregate site frequency spectrum for comparative population genomic inference
Q36367589	The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins.
Q91656413	The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes
Q99616759	The conservation value of admixed phenotypes in a critically endangered species complex
Q61814089	The cryptic origins of evolutionary novelty: 1,000-fold-faster trophic diversification rates without increased ecological opportunity or hybrid swarm
Q46468051	The cryptic origins of evolutionary novelty: 1000-fold faster trophic diversification rates without increased ecological opportunity or hybrid swarm
Q37272530	The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland
Q88137080	The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis)
Q36371156	The effects of Pleistocene climate change on biotic differentiation in a montane songbird clade from Wallacea
Q64900108	The effects of agent hybridization on the efficacy of biological control of tansy ragwort at high elevations.
Q91236067	The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus
Q30928623	The evolutionary history of the embiotocid surfperch radiation based on genome-wide RAD sequence data
Q91168851	The genetic architecture of adaptation: convergence and pleiotropy in Heliconius wing pattern evolution
Q30275367	The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation
Q47848466	The genetic architecture of tristyly and its breakdown to self-fertilization
Q30396631	The genome of the Gulf pipefish enables understanding of evolutionary innovations
Q64109196	The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system
Q57152521	The genomic basis of cichlid fish adaptation within the deepwater "twilight zone" of Lake Malawi
Q55425765	The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.
Q40378176	The geography of divergence with gene flow facilitates multitrait adaptation and the evolution of pollinator isolation in Mimulus aurantiacus.
Q53089587	The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments.
Q47223083	The phylogeography of the cycad genus Dioon (Zamiaceae) clarifies its Cenozoic expansion and diversification in the Mexican transition zone.
Q58734505	The population genomics of yellowfin tuna (Thunnus albacares) at global geographic scale challenges current stock delineation
Q42117347	The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing.
Q27927983	The queenslandensis and the type Form of the Dengue Fever Mosquito (Aedes aegypti L.) Are Genomically Indistinguishable
Q91216167	The role of ecotype-environment interactions in intraspecific trophic niche partitioning subsequent to stocking
Q90776971	The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization
Q34714372	The transgenerational effects of heat stress in the nematode Caenorhabditis remanei are negative and rapidly eliminated under direct selection for increased stress resistance in larvae
Q39767166	Towards understanding the genetic basis of mouth asymmetry in the scale-eating cichlid Perissodus microlepis
Q66680669	Tracking genetic invasions: Genome-wide single nucleotide polymorphisms reveal the source of pyrethroid-resistant (yellow fever mosquito) incursions at international ports
Q38951281	Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals.
Q46310690	Trans-species variation in Dmrt1 is associated with sex determination in four European tree-frog species
Q28601592	Transition in sexual system and sex chromosome evolution in the tadpole shrimp Triops cancriformis
Q41091752	Tumor diversity and evolution revealed through RADseq.
Q57493037	Two's company, three's a crowd: new insights on spruce budworm species boundaries using genotyping-by-sequencing in an integrative species assessment (Lepidoptera: Tortricidae)
Q58601401	Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata
Q61796124	Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrel
Q64230589	Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited
Q90697498	Urban hubs of connectivity: contrasting patterns of gene flow within and among cities in the western black widow spider
Q46244310	Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive
Q28601584	Use of RAD sequencing for delimiting species
Q38942611	Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish
Q57159850	Using high-throughput sequencing to investigate the factors structuring genomic variation of a Mediterranean grasshopper of great conservation concern
Q64285371	Using host-associated differentiation to track source population and dispersal distance among insect vectors of plant pathogens
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P356	DOI	10.1111/MEC.12354
P932	PMC publication ID	3936987
P698	PubMed publication ID	23701397

P50	author	William A Cresko	Q51549606
		Julian Catchen	Q61163717
		Susan Bassham	Q88793512
P2093	author name string	Angel Amores
		Paul A Hohenlohe
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P433	issue	11
P921	main subject	genomics	Q222046
P304	page(s)	3124-3140
P577	publication date	2013-05-24
P1433	published in	Molecular Ecology	Q6895946
P1476	title	Stacks: an analysis tool set for population genomics
P478	volume	22

Stacks: an analysis tool set for population genomics

scientific article published on 24 May 2013

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