Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You and Your Team.

Learn More →

RADseq approaches and applications for forest tree genetics

RADseq approaches and applications for forest tree genetics As tree species vary extensively in genome size, complexity, and resource development, reduced representation methods have been increasingly employed for the generation of population genomic data. By allowing rapid marker discovery and genotyping for thousands of genomic regions in many individuals without requiring genomic resources, restriction site-associated DNA sequencing (RADseq) methods have dramatically improved our ability to bring population genomic perspectives to non-model trees. The rapid recent increase in studies of trees utilizing RADseq suggests that it is likely to become among the most common approaches for generating genome-wide data for a variety of applications. Here we provide a practical review of RADseq and its application to research areas of tree genetics. We briefly review RADseq laboratory methods and consider analytical approaches for assembly, variant calling, and bioinformatic processing. To guide considerations for study design, we use in silico analyses of eight available tree genomes to illustrate how expected marker number and density vary across laboratory approaches and genome sizes, and to consider the ability of RADseq designs to query coding regions. We review the empirical use of RADseq for different research objectives, considering its strengths and limitations. Many studies have used RADseq data to perform genome scans for selection, although limited marker density and linkage disequilibrium will often compromise its utility for such analyses. Regardless of this limitation, RADseq offers a powerful and inexpensive technique for generating genome-wide SNP data that can greatly contribute to research spanning phylogenetic and population genetic inference, linkage mapping, and quantitative genetic parameter estimation for tree genetics. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Tree Genetics & Genomes Springer Journals

RADseq approaches and applications for forest tree genetics

Download PDF
25 pages
Read Article

Loading next page...
 
/lp/springer_journal/radseq-approaches-and-applications-for-forest-tree-genetics-xbnG0BUcop
Publisher
Springer Journals
Copyright
Copyright © 2018 by Springer-Verlag GmbH Germany, part of Springer Nature
Subject
Life Sciences; Forestry; Plant Genetics and Genomics; Plant Breeding/Biotechnology; Tree Biology; Biotechnology
ISSN
1614-2942
eISSN
1614-2950
DOI
10.1007/s11295-018-1251-3
Publisher site
See Article on Publisher Site

Abstract

As tree species vary extensively in genome size, complexity, and resource development, reduced representation methods have been increasingly employed for the generation of population genomic data. By allowing rapid marker discovery and genotyping for thousands of genomic regions in many individuals without requiring genomic resources, restriction site-associated DNA sequencing (RADseq) methods have dramatically improved our ability to bring population genomic perspectives to non-model trees. The rapid recent increase in studies of trees utilizing RADseq suggests that it is likely to become among the most common approaches for generating genome-wide data for a variety of applications. Here we provide a practical review of RADseq and its application to research areas of tree genetics. We briefly review RADseq laboratory methods and consider analytical approaches for assembly, variant calling, and bioinformatic processing. To guide considerations for study design, we use in silico analyses of eight available tree genomes to illustrate how expected marker number and density vary across laboratory approaches and genome sizes, and to consider the ability of RADseq designs to query coding regions. We review the empirical use of RADseq for different research objectives, considering its strengths and limitations. Many studies have used RADseq data to perform genome scans for selection, although limited marker density and linkage disequilibrium will often compromise its utility for such analyses. Regardless of this limitation, RADseq offers a powerful and inexpensive technique for generating genome-wide SNP data that can greatly contribute to research spanning phylogenetic and population genetic inference, linkage mapping, and quantitative genetic parameter estimation for tree genetics.

Journal

Tree Genetics & Genomes – Springer Journals

Published: May 21, 2018

References

  • Assisted gene flow to facilitate local adaptation to climate change
    Aitken, SN; Whitlock, MC
  • Adaptation, migration or extirpation: climate change outcomes for tree populations
    Aitken, SN; Yeaman, S; Holliday, JA; Wang, T; Curtis-McLane, S
  • The Amborella genome and the evolution of flowering plants
    Albert, VA; Barbazuk, WB; Der, JP; Leebens-Mack, J; Ma, H; Palmer, JD; Rounsley, S; Sankoff, D; Schuster, SC; Soltis, DE; Soltis, PS
  • Potential for evolutionary responses to climate change—evidence from tree populations
    Alberto, FJ; Aitken, SN; Alía, R; González-Martínez, SC; Hänninen, H; Kremer, A; Lefèvre, F; Lenormand, T; Yeaman, S; Whetten, R; Savolainen, O
  • Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River
    Alter, SE; Munshi-South, J; Stiassny, ML
  • Marker-based quantitative genetics in the wild? The heritability and genetic correlation of chemical defenses in Eucalyptus
    Andrew, RL; Peakall, R; Wallis, IR; Wood, JT; Knight, EJ; Foley, WJ
  • Harnessing the power of RADseq for ecological and evolutionary genomics
    Andrews, KR; Good, JM; Miller, MR; Luikart, G; Hohenlohe, PA
  • RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
    Arnold, B; Corbett-Detig, RB; Hartl, D; Bomblies, K
  • Rapid SNP discovery and genetic mapping using sequenced RAD markers
    Baird, NA; Etter, PD; Atwood, TS; Currey, MC; Shiver, AL; Lewis, ZA; Selker, EU; Cresko, WA; Johnson, EA
  • High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly
    Bartholomé, J; Mandrou, E; Mabiala, A; Jenkins, J; Nabihoudine, I; Klopp, C; Schmutz, J; Plomion, C; Gion, JM
  • RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)
    Benestan, L; Gosselin, T; Perrier, C; Sainte-Marie, B; Rochette, R; Bernatchez, L
  • Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
    Bérénos, C; Ellis, PA; Pilkington, JG; Pemberton, JM
  • Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus× domestica Borkh)
    Bianco, L; Cestaro, A; Sargent, DJ; Banchi, E; Derdak, S; Guardo, M; Salvi, S; Jansen, J; Viola, R; Gut, I
  • Genotyping by sequencing for SNP-based linkage map construction and QTL analysis of chilling requirement and bloom date in peach [Prunus persica (L.) Batsch]
    Bielenberg, DG; Rauh, B; Fan, S; Gasic, K; Abbott, AG; Reighard, GL; Okie, WR; Wells, CE
  • Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data
    Birol, I; Raymond, A; Jackman, SD; Pleasance, S; Coope, R; Taylor, GA; Yuen, MMS; Keeling, CI; Brand, D; Vandervalk, BP; Kirk, H; Pandoh, P; Moore, RA; Zhao, Y; Mungall, AJ; Jaquish, B; Yanchuk, A; Ritland, C; Boyle, B; Bousquet, J; Ritland, K; MacKay, J; Bohlmann, J; Jones, SJM
  • TASSEL: software for association mapping of complex traits in diverse samples
    Bradbury, PJ; Zhang, Z; Kroon, DE; Casstevens, TM; Ramdoss, Y; Buckler, ES
  • Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration
    Brelsford, A; Toews, DP; Irwin, DE
  • Population genomics based on low coverage sequencing: how low should we go?
    Buerkle, AC; Gompert, Z
  • The cellular and molecular biology of conifer embryogenesis
    Cairney, J; Pullman, GS
  • Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization
    Cariou, M; Duret, L; Charlat, S
  • How and how much does RAD-seq bias genetic diversity estimates?
    Cariou, M; Duret, L; Charlat, S
  • Effects of interspecific recombination on functional traits in trees revealed by metabolomics and genotyping-by-resequencing
    Caseys, C; Glauser, G; Stölting, KN; Christe, C; Albrectsen, BR; Lexer, C
  • Field heritability of a plant adaptation to fire in heterogeneous landscapes
    Castellanos, M; González-Rodríguez, S; Pausas, J
  • Stacks: building and genotyping loci de novo from short-read sequences
    Catchen, JM; Amores, A; Hohenlohe, P; Cresko, W; Postlethwait, JH
  • Stacks: an analysis tool set for population genomics
    Catchen, JM; Hohenlohe, PA; Bassham, S; Amores, A; Cresko, WA
  • Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations
    Catchen, JM; Hohenlohe, PA; Bernatchez, L; Funk, WC; Andrews, KR; Allendorf, FW
  • Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach
    Cavender-Bares, J; González-Rodríguez, A; Eaton, DA; Hipp, AA; Beulke, A; Manos, PS
  • Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform
    Chen, C; Mitchell, SE; Elshire, RJ; Buckler, ES; El-Kassaby, YA
  • Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F1 fertility and recurrent gene flow
    Christe, C; Stölting, KN; Bresadola, L; Fussi, B; Heinze, B; Wegmann, D; Lexer, C
  • Testing marker-based estimates of heritability in the wild
    Coltman, DW
  • Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae
    Comeault, AA; Soria-Carrasco, V; Gompert, Z; Farkas, TE; Buerkle, CA; Parchman, TL; Nosil, P
  • Expression of additive genetic variances and covariances for wild radish floral traits: comparison between field and greenhouse environments
    Conner, JK; Franks, R; Stewart, C
  • GBStools: a statistical method for estimating allelic dropout in reduced representation sequencing data
    Cooke, TF; Yee, M; Muzzio, M; Sockell, A; Bell, R; Cornejo, OE; Kelley, JL; Bailliet, G; Bravi, CM; Bustamante, CD
  • Heritabilities and additive genetic coefficients of variation in forest trees
    Cornelius, J
  • Empirical assessment of RAD sequencing for interspecific phylogeny
    Cruaud, A; Gautier, M; Galan, M; Foucaud, J; Sauné, L; Genson, G; Dubois, E; Nidelet, S; Deuve, T; Rasplus, JY
  • RADIS: analysis of RAD-seq for interspecific phylogeny
    Cruaud, A; Gautier, M; Rossi, JP; Rasplus, J-Y; Gouzy, J
  • Performance of marker-based relatedness estimators in natural populations of outbred vertebrates
    Csilléry, K; Johnson, T; Beraldi, D; Clutton-Brock, T; Coltman, D; Hansson, B; Spong, G; Pemberton, JM
  • Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population
    Daetwyler, HD; Hickey, JM; Henshall, JM; Dominik, S; Gredler, B; Werf, JH; Hayes, BJ
  • Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences—a case study in the tree genus Milicia
    Daïnou, K; Blanc-Jolivet, C; Degen, B; Kimani, P; Ndiade-Bourobou, D; Donkpegan, AS; Tosso, F; Kaymak, E; Bourland, N; Doucet, JL; Hardy, OJ
  • The variant call format and VCFtools
    Danecek, P; Auton, A; Abecasis, G; Albers, CA; Banks, E; DePristo, MA; Handsaker, RE; Lunter, G; Marth, GT; Sherry, ST
  • RAD-seq phylogenomics recovers a well-resolved phylogeny of a rapid radiation of mutualistic and antagonistic yucca moths
    Darwell, CT; Rivers, DM; Althoff, DM
  • Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    Davey, JW; Hohenlohe, PA; Etter, PD; Boone, JQ; Catchen, JM; Blaxter, ML
  • Special features of RAD sequencing data: implications for genotyping
    Davey, JW; Cezard, T; Fuentes-Utrilla, P; Eland, C; Gharbi, K; Blaxter, ML
  • An evaluation of seed zone delineation using phenotypic and population genomic data on black alder Alnus glutinosa
    Kort, H; Mergeay, J; Vander Mijnsbrugge, K; Decocq, G; Maccherini, S; Bruun, HHK; Honnay, O; Vandepitte, K
  • Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa
    Kort, H; Vandepitte, K; Bruun, HH; Closset-Kopp, D; Honnay, O; Mergeay, J
  • Isolation, characterization and genotyping of single nucleotide polymorphisms in the non-model tree species Frangula alnus (Rhamnaceae)
    Kort, H; Vandepitte, K; Mergeay, J; Honnay, O
  • Evolution, plasticity and evolving plasticity of phenology in the tree species Alnus glutinosa
    Kort, H; Vander Mijnsbrugge, K; Vandepitte, K; Mergeay, J; Ovaskainen, O; Honnay, O
  • Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia
    Deng, M; Jiang, XL; Hipp, AL; Manos, PS; Hahn, M
  • Genomic selection: genome-wide prediction in plant improvement
    Desta, ZA; Ortiz, R
  • PyRAD: assembly of de novo RADseq loci for phylogenetic analyses
    Eaton, DA
  • Historical introgression among the American live oaks and the comparative nature of tests for introgression
    Eaton, DA; Hipp, AL; González-Rodríguez, A; Cavender-Bares, J
  • Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants
    Eaton, DA; Spriggs, EL; Park, B; Donoghue, MJ
  • Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies
    Ebel, ER; DaCosta, JM; Sorenson, MD; Hill, RI; Briscoe, AD; Willmott, KR; Mullen, SP
  • Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits
    Eckert, AJ; Bower, AD; Wegrzyn, JL; Pande, B; Jermstad, KD; Krutovsky, KV; Clair, JBS; Neale, DB
  • Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae)
    Eckert, AJ; Heerwaarden, J; Wegrzyn, JL; Nelson, CD; Ross-Ibarra, J; González-Martínez, SC; Neale, DB
  • The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae)
    Eckert, AJ; Wegrzyn, JL; Liechty, JD; Lee, JM; Cumbie, WP; Davis, JM; Goldfarb, B; Loopstra, CA; Palle, SR; Quesada, T; Langley, CH
  • Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing
    El-Dien, OG; Ratcliffe, B; Klápště, J; Chen, C; Porth, I; El-Kassaby, YA
  • Implementation of the realized genomic relationship matrix to open-pollinated white spruce family testing for disentangling additive from nonadditive genetic effects
    El-Dien, OG; Ratcliffe, B; Klápště, J; Porth, I; Chen, C; El-Kassaby, YA
  • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    Elshire, RJ; Glaubitz, JC; Sun, Q; Poland, JA; Kawamoto, K; Buckler, ES; Mitchell, SE
  • Rapid evolutionary response to a transmissible cancer in Tasmanian devils
    Epstein, B; Jones, M; Hamede, R; Hendricks, S; McCallum, H; Murchison, EP; Schönfeld, B; Wiench, C; Hohenlohe, P; Storfer, A
  • Molecular methods for evolutionary genetics
    Etter, PD; Bassham, S; Hohenlohe, PA; Johnson, EA; Cresko, WA
  • Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations
    Evans, LM; Slavov, GT; Rodgers-Melnick, E; Martin, J; Ranjan, P; Muchero, W; Brunner, AM; Schackwitz, W; Gunter, L; Chen, J
  • Robust demographic inference from genomic and SNP data
    Excoffier, L; Dupanloup, I; Huerta-Sánchez, E; Sousa, VC; Foll, M
  • Introduction to quantitative genetics
    Falconer, DS; Mackay, TF
  • Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools
    Fierst, JL
  • Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus subgenus Quercus)
    Fitz-Gibbon, S; Hipp, AL; Pham, KK; Manos, PS; Sork, V
  • Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates
    Fountain, ED; Pauli, JN; Reid, BN; Palsbøll, PJ; Peery, MZ
  • The genetic architecture of local adaptation I: the genomic landscape of foxtail pine (Pinus balfouriana Grev. & Balf.) as revealed from a high-density linkage map
    Friedline, CJ; Lind, BM; Hobson, EM; Harwood, DE; Mix, AD; Maloney, PE; Eckert, AJ
  • QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data
    Fuentes-Utrilla, P; Goswami, C; Cottrell, J; Pong-Wong, R; Law, A; A’Hara, S; Lee, S; Woolliams, J
  • Quantifying population genetic differentiation from next-generation sequencing data
    Fumagalli, M; Vieira, FG; Korneliussen, TS; Linderoth, T; Huerta-Sánchez, E; Albrechtsen, A; Nielsen, R
  • The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing
    Gagnaire, PA; Pavey, SA; Normandeau, E; Bernatchez, L
  • Construction of a framework genetic linkage map in Gleditsia triacanthos L.
    Gailing, O; Staton, ME; Lane, T; Schlarbaum, SE; Nipper, R; Owusu, SA; Carlson, JE
  • Fast and cost-effective genetic mapping in apple using next-generation sequencing
    Gardner, KM; Brown, P; Cooke, TF; Cann, S; Costa, F; Bustamante, C; Velasco, R; Troggio, M; Myles, S
  • The effect of RAD allele dropout on the estimation of genetic variation within and between populations
    Gautier, M; Gharbi, K; Cezard, T; Foucaud, J; Kerdelhué, C; Pudlo, P; Cornuet, JM; Estoup, A
  • Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap
    Gayral, P; Melo-Ferreira, J; Glémin, S; Bierne, N; Carneiro, M; Nabholz, B; Lourenco, JM; Alves, PC; Ballenghien, M; Faivre, N; Belkhir, K; Cahais, V; Loire, E; Bernard, A; Galtier, N
  • A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species
    Geraldes, A; DiFazio, SP; Slavov, GT; Ranjan, P; Muchero, W; Hannemann, J; Gunter, LE; Wymore, AM; Grassa, CJ; Farzaneh, N
  • Genomic quantitative genetics to study evolution in the wild
    Gienapp, P; Fior, S; Guillaume, F; Lasky, JR; Sork, VL; Csilléry, K
  • TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline
    Glaubitz, JC; Casstevens, TM; Lu, F; Harriman, J; Elshire, RJ; Sun, Q; Buckler, ES
  • Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species
    Gompert, Z; Lucas, LK; Nice, CC; Fordyce, JA; Forister, ML; Buerkle, CA
  • Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants
    Gompert, Z; Lucas, LK; Buerkle, CA; Forister, ML; Fordyce, JA; Nice, CC
  • Forest-tree population genomics and adaptive evolution
    González-Martínez, SC; Krutovsky, KV; Neale, DB
  • Plant speciation
    Grant, V
  • Genomics of plant genetic resources
    Grattapaglia, D
  • Genomic selection in forest tree breeding
    Grattapaglia, D; Resende, MD
  • Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS)
    Guajardo, V; Solís, S; Sagredo, B; Gainza, F; Muñoz, C; Gasic, K; Hinrichsen, P
  • Construction of a SNP-based high-density genetic map for pummelo using RAD sequencing
    Guo, F; Yu, H; Tang, Z; Jiang, X; Wang, L; Wang, X; Xu, Q; Deng, X
  • Population genomic evidence for adaptive differentiation in the Baltic Sea herring
    Guo, B; Li, Z; Merilä, J
  • Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
    Gutenkunst, RN; Hernandez, RD; Williamson, SH; Bustamante, CD
  • Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species
    Hamon, P; Grover, CE; Davis, AP; Rakotomalala, JJ; Raharimalala, NE; Albert, VA; Sreenath, HL; Stoffelen, P; Mitchell, SE; Couturon, E; Hamon, S; de Kochko, A; Crouzillat, D; Rigoreau, M; Sumirat, U; Akaffou, S; Guyot, R
  • GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome
    Hapke, A; Thiele, D
  • Genome-wide association and genomic selection in animal breeding
    Hayes, B; Goddard, M
  • Evolutionary potential and adaptation of Banksia attenuata (Proteaceae) to climate and fire regime in southwestern Australia, a global biodiversity hotspot
    He, T; D’Agui, H; Lim, SL; Enright, NJ; Luo, Y
  • Predicting RAD-seq marker numbers across the eukaryotic tree of life
    Herrera, S; Reyes-Herrera, PH; Shank, TM
  • Understanding and using quantitative genetic variation
    Hill, WG
  • Variation in actual relationship as a consequence of Mendelian sampling and linkage
    Hill, WG; Weir, BS
  • Using phylogenomics to infer the evolutionary history of oaks
    Hipp, AL; Manos, PS; Cavender-Bares, J; Eaton, D; Nipper, R
  • A framework phylogeny of the American oak clade based on sequenced RAD data
    Hipp, AL; Eaton, DA; Cavender-Bares, J; Fitzek, E; Nipper, R; Manos, PS
  • Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering
    Hodel, RGJ; Chen, S; Payton, AC; McDaniel, SF; Soltis, P; Soltis, DE
  • Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags
    Hohenlohe, PA; Bassham, S; Etter, PD; Stiffler, N; Johnson, EA; Cresko, WA
  • Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes
    Hohenlohe, PA; Bassham, S; Currey, M; Cresko, WA
  • Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing
    Hohenlohe, PA; Day, MD; Amish, SJ; Miller, MR; Kamps-Hughes, N; Boyer, MC; Muhlfeld, CC; Allendorf, FW; Johnson, EA; Luikart, G
  • Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis)
    Holliday, JA; Ritland, K; Aitken, SN
  • Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients in Populus trichocarpa
    Holliday, JA; Zhou, L; Bawa, R; Zhang, M; Oubida, RW
  • Thousands of RAD-seq loci fully resolve the phylogeny of the highly disjunct arctic-alpine genus Diapensia (Diapensiaceae)
    Hou, Y; Nowak, MD; Mirré, V; Bjorå, CS; Brochmann, C; Popp, M
  • Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan
    Imai, A; Yoshioka, T; Hayashi, T
  • Towards integration of population and comparative genomics in forest trees
    Ingvarsson, PK; Hvidsten, TR; Street, NR
  • The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)
    Izuno, A; Kitayama, K; Onoda, Y; Tsujii, Y; Hatakeyama, M; Nagano, AJ; Honjo, MN; Shimizu-Inatsugi, R; Kudoh, H; Shimizu, KK; Isagi, Y
  • Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L
    Jeffries, DL; Copp, GH; Handley, LL; Olsén, KH; Sayer, CD; Hänfling, B
  • Landscape genomic insights into the historic migration of mountain hemlock in response to Holocene climate change
    Johnson, JS; Gaddis, KD; Cairns, DM; Konganti, K; Krutovsky, KV
  • Seed dispersal at alpine treeline: an assessment of seed movement within the alpine treeline ecotone
    Johnson, JS; Gaddis, KD; Cairns, DM; Krutovsky, KV
  • Targeted capture in evolutionary and ecological genomics
    Jones, MR; Good, JM
  • Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq
    Karam, MJ; Lefévre, F; Dagher-Kharrat, MB; Pinosio, S; Vendramin, G
  • High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra
    Konar, A; Choudhury, O; Bullis, R; Fiedler, L; Kruser, JM; Stephens, MT; Gailing, O; Schlarbaum, S; Coggeshall, MV; Staton, ME; Carlson, JE; Emrich, S; Romero-Severson, J
  • ANGSD: analysis of next generation sequencing data
    Korneliussen, TS; Albrechtsen, A; Nielsen, R
  • Genomic selection for fruit quality traits in apple (Malus x domestica Borkh.)
    Kumar, S; Chagné, D; Bink, MCAM; Volz, RK; Whitworth, C; Carlisle, C
  • RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic eels
    Laporte, M; Pavey, SA; Rougeux, C; Pierron, F; Lauzent, M; Budzinski, H; Labadie, P; Geneste, E; Couture, P; Baudrimont, M; Bernatchez, L
  • Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)
    Larson, WA; Seeb, LW; Everett, MV; Waples, RK; Templin, WD; Seeb, JE
  • The utility of single nucleotide polymorphism (SNP) data in phylogenetics
    Leaché, AD; Oaks, JR
  • SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches
    Lepais, O; Weir, JT
  • Fast and accurate short read alignment with burrows-wheeler transform
    Li, H; Durbin, R
  • The sequence alignment/map format and SAMtools
    Li, H; Handsaker, B; Wysoker, A; Fennell, T; Ruan, J; Homer, N; Marth, G; Abecasis, G; Durbin, R
  • Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA
    Lind, BM; Friedline, CJ; Wegrzyn, JL; Maloney, PE; Vogler, DR; Neale, DB; Eckert, AJ
  • Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species
    Lindtke, D; Gompert, Z; Lexer, C; Buerkle, CA
  • Epigenetic regulation of transposable elements in plants
    Lisch, D
  • How important are transposons for plant evolution?
    Lisch, D
  • Phylogeny of Morella rubra and its relatives (Myricaceae) and genetic resources of Chinese bayberry using RAD sequencing
    Liu, L; Jin, X; Chen, N; Li, X; Li, P; Fu, C
  • Estimating phylogenetic trees from genome-scale data
    Liu, L; Xi, Z; Wu, S; Davis, CC; Edwards, SV
  • Construction of a SNP-based genetic linkage map for kiwifruit using next-generation restriction-site-associated DNA sequencing (RADseq)
    Liu, CY; Li, DW; Zhou, JH; Zhang, Q; Tian, H; Yao, XH
  • Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation
    Lowry, DB; Hoban, S; Kelley, JL; Lotterhos, KE; Reed, LK; Antolin, MF; Storfer, A
  • Responsible RAD: striving for best practices in population genomic studies of adaptation
    Lowry, DB; Hoban, S; Kelley, JL; Lotterhos, KE; Reed, LK; Antolin, MF; Storfer, A
  • Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol
    Lu, F; Lipka, AE; Glaubitz, J; Elshire, R; Cherney, JH; Casler, MD; Buckler, ES; Costich, DE
  • Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.)
    Lu, M; Krutovsky, KV; Nelson, CD; Koralewski, TE; Byram, TD; Loopstra, CA
  • Highly variable reproductive isolation among pairs of Catostomus species
    Mandeville, EG; Parchman, TL; McDonald, DB; Buerkle, CA
  • The first high-density sequence characterized SNP-based linkage map of olive (Olea europaea L. subsp. europaea) developed using genotyping by sequencing
    Marchese, A
  • Next-generation sequencing platforms
    Mardis, ER
  • Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case study in Carex sect. Racemosae
    Massatti, R; Reznicek, AA; Knowles, LL
  • Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
    Mastretta-Yanes, A; Arrigo, N; Alvarez, N; Jorgensen, T; Piñero, D; Emerson, B
  • Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations
    McGee, MD; Neches, RY; Seehausen, O
  • The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    McKenna, A; Hanna, M; Banks, E; Sivachenko, A; Cibulskis, K; Kernytsky, A; Garimella, K; Altshuler, D; Gabriel, S; Daly, M; DePristo, MA
  • RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on breaking RAD by Lowry et al. (2016)
    McKinney, GJ; Larson, WA; Seeb, LW; Seeb, JE
  • Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa
    McKown, AD; Guy, RD; Klápště, J; Geraldes, A; Friedmann, M; Cronk, QC; El-Kassaby, YA; Mansfield, SD; Douglas, CJ
  • A genetic legacy of introgression confounds phylogeny and biogeography in oaks
    McVay, JD; Hipp, AL; Manos, PS
  • Adaptation in plant genomes: bigger is different
    Mei, W; Stetter, MG; Gates, DJ; Stitzer, MC; Ross-Ibarra, J
  • GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data
    Melo, AT; Bartaula, R; Hale, I
  • Genomic selection: a paradigm shift in animal breeding
    Meuwissen, T; Hayes, B; Goddard, M
  • Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
    Miller, MR; Dunham, JP; Amores, A; Cresko, WA; Johnson, EA
  • ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments
    Mora-Márquez, F; García-Olivares, V; Emerson, B; López de Heredia, U
  • Geographic variation in forest trees: genetic basis and application of knowledge in silviculture
    Morgenstern, EK
  • Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)
    Mori, K; Shirasawa, K; Nogata, H; Hirata, C; Tashiro, K; Habu, T; Kim, S; Himeno, S; Kuhara, S; Ikegami, H
  • Multiplexed-shotgun-genotyping data resolve phylogeny within a very recently derived insular lineage
    Mort, ME; Crawford, DJ; Kelly, JK; Santos-Guerra, A; Sequeira, MM; Moura, M; Caujapé-Castells, J
  • De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies
    Mousavi, M; Tong, C; Liu, F; Tao, S; Wu, J; Li, H; Shi, J
  • The genome of Eucalyptus grandis
    Myburg, AA; Grattapaglia, D; Tuskan, GA; Hellsten, U; Hayes, RD; Grimwood, J; Jenkins, J; Lindquist, E; Tice, H; Bauer, D; Goodstein, DM; Dubchak, I; Poliakov, A; Mizrachi, E; Kullan, ARK; Hussey, SG; Pinard, D; van der Merwe, K; Singh, P; van Jaarsveld, I; Silva-Junior, OB; Togawa, RC; Pappas, MR; Faria, DA; Sansaloni, CP; Petroli, CD; Yang, X; Ranjan, P; Tschaplinski, TJ; Ye, CY; Li, T; Sterck, L; Vanneste, K; Murat, F; Soler, M; Clemente, HS; Saidi, N; Cassan-Wang, H; Dunand, C; Hefer, CA; Bornberg-Bauer, E; Kersting, AR; Vining, K; Amarasinghe, V; Ranik, M; Naithani, S; Elser, J; Boyd, AE; Liston, A; Spatafora, JW; Dharmwardhana, P; Raja, R; Sullivan, C; Romanel, E; Alves-Ferreira, M; Külheim, C; Foley, W; Carocha, V; Paiva, J; Kudrna, D; Brommonschenkel, SH; Pasquali, G; Byrne, M; Rigault, P; Tibbits, J; Spokevicius, A; Jones, RC; Steane, DA; Vaillancourt, RE; Potts, BM; Joubert, F; Barry, K; Pappas, GJ; Strauss, SH; Jaiswal, P; Grima-Pettenati, J; Salse, J; van de Peer, Y; Rokhsar, DS; Schmutz, J
  • Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato
    Nadeau, NJ; Ruiz, M; Salazar, P; Counterman, B; Medina, JA; Ortiz-Zuazaga, H; Morrison, A; McMillan, WO; Jiggins, CD; Papa, R
  • Phylogenetic relationships of Aurantioideae (Rutaceae) based on RAD-Seq
    Nagano, Y; Mimura, T; Kotoda, N; Matsumoto, R; Nagano, AJ; Honjo, MN; Kudoh, H; Yamamoto, M
  • Genotyping-by-sequencing in ecological and conservation genomics
    Narum, SR; Buerkle, CA; Davey, JW; Miller, MR; Hohenlohe, PA
  • Population, quantitative and comparative genomics of adaptation in forest trees
    Neale, DB; Ingvarsson, PK
  • Forest tree genomics: growing resources and applications
    Neale, DB; Kremer, A
  • Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
    Neale, DB; Wegrzyn, JL; Stevens, KA; Zimin, AV; Puiu, D; Crepeau, MW; Cardeno, C; Koriabine, M; Holtz-Morris, AE; Liechty, JD; Martínez-García, PJ; Vasquez-Gross, HA; Lin, BY; Zieve, JJ; Dougherty, WM; Fuentes-Soriano, S; Wu, LS; Gilbert, D; Marçais, G; Roberts, M; Holt, C; Yandell, M; Davis, JM; Smith, KE; Dean, JFD; Lorenz, W; Whetten, RW; Sederoff, R; Wheeler, N; McGuire, PE; Main, D; Loopstra, CA; Mockaitis, K; deJong, PJ; Yorke, JA; Salzberg, SL; Langley, CH
  • The Douglas-fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae
    Neale, DB; McGuire, PE; Wheeler, NC; Stevens, KA; Crepeau, MW; Cardeno, C; Zimin, AV; Puiu, D; Pertea, GM; Sezen, UU
  • Hybrid speciation and independent evolution in lineages of alpine butterflies
    Nice, CC; Gompert, Z; Fordyce, JA; Forister, ML; Lucas, LK; Buerkle, CA
  • Genotype and SNP calling from next-generation sequencing data
    Nielsen, R; Paul, JS; Albrechtsen, A; Song, YS
  • SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data
    Nielsen, R; Korneliussen, T; Albrechtsen, A; Li, Y; Wang, J
  • The Norway spruce genome sequence and conifer genome evolution
    Nystedt, B; Street, NR; Wetterbom, A; Zuccolo, A; Lin, Y; Scofield, DG; Vezzi, F; Delhomme, N; Giacomello, S; Alexeyenko, A
  • Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories
    O’Loughlin, SM; Magesa, S; Mbogo, C; Mosha, F; Midega, J; Lomas, S; Burt, A
  • Genotyping by sequencing reveals the interspecific C. maxima/C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits
    Oueslati, A; Slhi-Hannachi, A; Luro, F; Vignes, H; Mournet, P; Ollitrault, P
  • Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing
    Pais, AL; Whetten, RW; Xiang, QYJ
  • Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers
    Pan, J; Wang, B; Pei, ZY; Zhao, W; Gao, J; Mao, JF; Wang, XR
  • Genome-wide association genetics of an adaptive trait in lodgepole pine
    Parchman, TL; Gompert, Z; Mudge, J; Schilkey, FD; Benkman, CW; Buerkle, C
  • Lost in parameter space: a road map for stacks
    Paris, JR; Stevens, JR; Catchen, JM
  • Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot
    Paun, O; Turner, B; Trucchi, E; Munzinger, J; Chase, MW; Samuel, R
  • Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners
    Pavy, N; Gagnon, F; Rigault, P; Blais, S; Deschênes, A; Boyle, B; Pelgas, B; Deslauriers, M; Clément, S; Lavigne, P; Lamothe, M; Cooke, JEK; Jaramillo-Correa, JP; Beaulieu, J; Isabel, N; Mackay, J; Bousquet, J
  • Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species
    Peterson, BK; Weber, JN; Kay, EH; Fisher, HS; Hoekstra, HE
  • Some evolutionary consequences of being a tree
    Petit, RJ; Hampe, A
  • A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny
    Pham, KK; Hipp, AL; Manos, PS; Cronn, RC
  • First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill
    Pinosio, S; González-Martínez, S; Bagnoli, F; Cattonaro, F; Grivet, D; Marroni, F; Lorenzo, Z; Pausas, J; Verdú, M; Vendramin, G
  • High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)
    Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, JM; Grivet, D; de Miguel, M; de María, N; Cervera, MT; Bagnoli, F; Isik, F; Vendramin, GG; González-Martínez, SC
  • Genotyping-by-sequencing for plant breeding and genetics
    Poland, JA; Rife, TW
  • Population genetic inference from genomic sequence variation
    Pool, JE; Hellmann, I; Jensen, JD; Nielsen, R
  • Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)
    Pootakham, W; Jomchai, N; Ruang-areerate, P; Shearman, JR; Sonthirod, C; Sangsrakru, D; Tragoonrung, S; Tangphatsornruang, S
  • Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)
    Pootakham, W; Ruang-Areerate, P; Jomchai, N; Sonthirod, C; Sangsrakru, D; Yoocha, T; Theerawattanasuk, K; Nirapathpongporn, K; Romruensukharom, P; Tragoonrung, S
  • Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms
    Porth, I; Klapšte, J; Skyba, O; Hannemann, J; McKown, AD; Guy, RD; DiFazio, SP; Muchero, W; Ranjan, P; Tuskan, GA
  • The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation
    Pritchard, JK; Pickrell, JK; Coop, G
  • dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
    Puritz, JB; Hollenbeck, CM; Gold, JR
  • Demystifying the RAD fad
    Puritz, JB; Matz, MV; Toonen, RJ; Weber, JN; Bolnick, DI; Bird, CE
  • Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations
    Pyhäjärvi, T; Garcia-Gil, MR; Knürr, T; Mikkonen, M; Wachowiak, W; Savolainen, O
  • Revisiting protein heterozygosity in plants—nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris
    Pyhäjärvi, T; Kujala, ST; Savolainen, O
  • Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.)
    Quesada, T; Gopal, V; Cumbie, WP; Eckert, AJ; Wegrzyn, JL; Neale, DB; Goldfarb, B; Huber, DA; Casella, G; Davis, JM
  • A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods
    Ratcliffe, B; El-Dien, OG; Klápště, J; Porth, I; Chen, C; Jaquish, B; El-Kassaby, Y
  • Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees
    Resende, MDV; Resende, MFR; Sansaloni, CP; Petroli, CD; Missiaggia, AA; Aguiar, AM; Abad, JM; Takahashi, EK; Rosado, AM; Faria, DA
  • Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments
    Resende, MFR; Muñoz, P; Acosta, JJ; Peter, G; Davis, JM; Grattapaglia, D; Resende, MDV; Kirst, M
  • Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.)
    Resende, MFR; Muñoz, P; Resende, MDV; Garrick, DJ; Fernando, RL; Davis, JM; Jokela, EJ; Martin, TA; Peter, GF; Kirst, M
  • A marker-based method for inferences about quantitative inheritance in natural populations
    Ritland, K
  • Marker-inferred relatedness as a tool for detecting heritability in nature
    Ritland, K
  • Partitioning of genetic variation across the genome using multimarker methods in a wild bird population
    Robinson, MR; Santure, AW; DeCauwer, I; Sheldon, BC; Slate, J
  • Sampling strategies for frequency spectrum-based population genomic inference
    Robinson, JD; Coffman, AJ; Hickerson, MJ; Gutenkunst, RN
  • Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection
    Rodríguez-Ezpeleta, N; Bradbury, IR; Mendibil, I; Álvarez, P; Cotano, U; Irigoien, X
  • Genome divergence during evolutionary diversification as revealed in replicate lake–stream stickleback population pairs
    Roesti, M; Hendry, AP; Salzburger, W; Berner, D
  • Inferring phylogenies from RAD sequence data
    Rubin, BE; Ree, RH; Moreau, CS
  • A role for migration-linked genes and genomic islands in divergence of a songbird
    Ruegg, K; Anderson, EC; Boone, J; Pouls, J; Smith, TB
  • High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species
    Sakaguchi, S; Sugino, T; Yoshihiko, T; Ito, M; Crisp, MD; Bowman, DMJS; Nagano, AJ; Honjo, MN; Yasugi, M; Kudoh, H
  • Gene flow and local adaptation in trees
    Savolainen, O; Pyhäjärvi, T; Knürr, T
  • Ecological genomics of local adaptation
    Savolainen, O; Lascoux, M; Merilä, J
  • A RAD-based linkage map of kiwifruit (Actinidia chinensis Pl.) as a tool to improve the genome assembly and to scan the genomic region of the gender determinant for the marker-assisted breeding
    Scaglione, D; Fornasiero, A; Pinto, C; Cattonaro, F; Spadotto, A; Infante, R; Meneses, C; Messina, R; Lain, O; Cipriani, G
  • Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus
    Shafer, ABA; Gattepaille, LM; Stewart, REA; Wolf, JBW
  • Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference
    Shafer, A; Peart, CR; Tusso, S; Maayan, I; Brelsford, A; Wheat, CW; Wolf, JB
  • Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of Eucalyptus grandis
    Silva-Junior, OB; Grattapaglia, D
  • A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species
    Silva-Junior, OB; Faria, DA; Grattapaglia, D
  • Estimating individual admixture proportions from next generation sequencing data
    Skotte, L; Korneliussen, TS; Albrechtsen, A
  • Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa
    Slavov, GT; DiFazio, SP; Martin, J; Schackwitz, W; Muchero, W; Rodgers-Melnick, E; Lipphardt, MF; Pennacchio, CP; Hellsten, U; Pennacchio, LA
  • Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis
    Slavov, GT; Nipper, R; Robson, P; Farrar, K; Allison, GG; Bosch, M; Clifton-Brown, JC; Donnison, IS; Jensen, E
  • Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate
    Sork, V; Aitken, S; Dyer, R; Eckert, A; Legendre, P; Neale, D
  • First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Née (Fagaceae)
    Sork, VL; Fitz-Gibbon, ST; Puiu, D; Crepeau, M; Gugger, PF; Sherman, R; Stevens, K; Langley, CH; Pellegrini, M; Salzberg, SL
  • AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data
    Sovic, MG; Fries, AC; Gibbs, HL
  • RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    Stamatakis, A
  • The loci of evolution: how predictable is genetic evolution?
    Stern, DL; Orgogozo, V
  • Sequence of the sugar pine megagenome
    Stevens, KA; Wegrzyn, JL; Zimin, A; Puiu, D; Crepeau, M; Cardeno, C; Paul, R; Gonzalez-Ibeas, D; Koriabine, M; Holtz-Morris, AE; Martínez-García, PJ; Sezen, UU; Marçais, G; Jermstad, K; McGuire, PE; Loopstra, CA; Davis, JM; Eckert, A; de Jong, P; Yorke, JA; Salzberg, SL; Neale, DB; Langley, CH
  • Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species
    Stölting, KN; Nipper, R; Lindtke, D; Caseys, C; Waeber, S; Castiglione, S; Lexer, C
  • Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae)
    Sun, Y; Surget-Groba, Y; Gao, S
  • The use of marker-based relationship information to estimate the heritability of body weight in a natural population: a cautionary tale
    Thomas, SC; Coltman, DW; Pemberton, JM
  • Advances and limits of using population genetics to understand local adaptation
    Tiffin, P; Ross-Ibarra, J
  • Construction of high-density linkage maps of Populus deltoides × P. simonii using restriction-site associated DNA sequencing
    Tong, C; Li, H; Wang, Y; Li, X; Ou, J; Wang, D; Xu, H; Ma, C; Lang, X; Liu, G
  • Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data
    Torkamaneh, D; Laroche, J; Bastien, M; Abed, A; Belzile, F
  • The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    Tuskan, GA; DiFazio, S; Jansson, S; Bohlmann, J; Grigoriev, I; Hellsten, U; Putnam, N; Ralph, S; Rombauts, S; Salamov, A; Schein, J; Sterck, L; Aerts, A; Bhalerao, RR; Bhalerao, RP; Blaudez, D; Boerjan, W; Brun, A; Brunner, A; Busov, V; Campbell, M; Carlson, J; Chalot, M; Chapman, J; Chen, GL; Cooper, D; Coutinho, PM; Couturier, J; Covert, S; Cronk, Q; Cunningham, R; Davis, J; Degroeve, S; Dejardin, A; dePamphilis, C; Detter, J; Dirks, B; Dubchak, I; Duplessis, S; Ehlting, J; Ellis, B; Gendler, K; Goodstein, D; Gribskov, M; Grimwood, J; Groover, A; Gunter, L; Hamberger, B; Heinze, B; Helariutta, Y; Henrissat, B; Holligan, D; Holt, R; Huang, W; Islam-Faridi, N; Jones, S; Jones-Rhoades, M; Jorgensen, R; Joshi, C; Kangasjarvi, J; Karlsson, J; Kelleher, C; Kirkpatrick, R; Kirst, M; Kohler, A; Kalluri, U; Larimer, F; Leebens-Mack, J; Leple, JC; Locascio, P; Lou, Y; Lucas, S; Martin, F; Montanini, B; Napoli, C; Nelson, DR; Nelson, C; Nieminen, K; Nilsson, O; Pereda, V; Peter, G; Philippe, R; Pilate, G; Poliakov, A; Razumovskaya, J; Richardson, P; Rinaldi, C; Ritland, K; Rouze, P; Ryaboy, D; Schmutz, J; Schrader, J; Segerman, B; Shin, H; Siddiqui, A; Sterky, F; Terry, A; Tsai, CJ; Uberbacher, E; Unneberg, P; Vahala, J; Wall, K; Wessler, S; Yang, G; Yin, T; Douglas, C; Marra, M; Sandberg, G; van de Peer, Y; Rokhsar, D
  • The genome of the domesticated apple (Malus domestica Borkh.)
    Velasco, R; Zharkikh, A; Affourtit, J; Dhingra, A; Cestaro, A; Kalyanaraman, A; Fontana, P; Bhatnagar, SK; Troggio, M; Pruss, D; Salvi, S; Pindo, M; Baldi, P; Castelletti, S; Cavaiuolo, M; Coppola, G; Costa, F; Cova, V; Dal Ri, A; Goremykin, V; Komjanc, M; Longhi, S; Magnago, P; Malacarne, G; Malnoy, M; Micheletti, D; Moretto, M; Perazzolli, M; Si-Ammour, A; Vezzulli, S; Zini, E; Eldredge, G; Fitzgerald, LM; Gutin, N; Lanchbury, J; Macalma, T; Mitchell, JT; Reid, J; Wardell, B; Kodira, C; Chen, Z; Desany, B; Niazi, F; Palmer, M; Koepke, T; Jiwan, D; Schaeffer, S; Krishnan, V; Wu, C; Chu, VT; King, ST; Vick, J; Tao, Q; Mraz, A; Stormo, A; Stormo, K; Bogden, R; Ederle, D; Stella, A; Vecchietti, A; Kater, MM; Masiero, S; Lasserre, P; Lespinasse, Y; Allan, AC; Bus, V; Chagné, D; Crowhurst, RN; Gleave, AP; Lavezzo, E; Fawcett, JA; Proost, S; Rouzé, P; Sterck, L; Toppo, S; Lazzari, B; Hellens, RP; Durel, CE; Gutin, A; Bumgarner, RE; Gardiner, SE; Skolnick, M; Egholm, M; van de Peer, Y; Salamini, F; Viola, R
  • The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
    Verde, I; Abbott, AG; Scalabrin, S; Jung, S; Shu, S; Marroni, F; Zhebentyayeva, T; Dettori, MT; Grimwood, J; Cattonaro, F
  • Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.
    Verdu, CF; Guichoux, E; Quevauvillers, S; Thier, O; Laizet, Y; Delcamp, A; Gévaudant, F; Monty, A; Porté, AJ; Lejeune, P
  • Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation
    Vieira, FG; Fumagalli, M; Albrechtsen, A; Nielsen, R
  • Heritability in the genomics era—concepts and misconceptions
    Visscher, PM; Hill, WG; Wray, NR
  • Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
    Wagner, CE; Keller, I; Wittwer, S; Selz, OM; Mwaiko, S; Greuter, L; Sivasundar, A; Seehausen, O
  • Pedigrees or markers: which are better in estimating relatedness and inbreeding coefficient?
    Wang, J
  • Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers
    Wang, N; Thomson, M; Bodles, WJ; Crawford, RM; Hunt, HV; Featherstone, AW; Pellicer, J; Buggs, RJ
  • Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species
    Wang, J; Street, NR; Scofield, DG; Ingvarsson, PK
  • Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation
    Wegrzyn, JL; Liechty, JD; Stevens, KA; Wu, LS; Loopstra, CA; Vasquez-Gross, HA; Dougherty, WM; Lin, BY; Zieve, JJ; Martínez-García, PJ
  • Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)
    Yeaman, S; Hodgins, KA; Suren, H; Nurkowski, KA; Rieseberg, LH; Holliday, JA; Aitken, SN
  • Convergent local adaptation to climate in distantly related conifers
    Yeaman, S; Hodgins, KA; Lotterhos, KE; Suren, H; Nadeau, S; Degner, JC; Nurkowski, KA; Smets, P; Wang, T; Gray, LK
  • SNP markers trace familial linkages in a cloned population of Pinus taeda—prospects for genomic selection
    Zapata-Valenzuela, J; Isik, F; Maltecca, C; Wegrzyn, J; Neale, D; McKeand, S; Whetten, R
  • Construction of a high-density genetic map of Ziziphus jujuba
    Zhang, Z; Wei, T; Zhong, Y; Li, X; Huang, J
  • Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology
    Zhigunov, AV; Ulianich, PS; Lebedeva, MV; Chang, PL; Nuzhdin, SV; Potokina, EK
  • Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)
    Zhou, L; Bawa, R; Holliday, JA
  • Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers
    Zohren, J; Wang, N; Kardailsky, I; Borrell, JS; Joecker, A; Nichols, RA; Buggs, RJ