High-throughput targeted genotyping using next-generation sequencing applied in Coffea canephora breeding. Euphytica 214:50.
Alkimim ER, Caixeta ET, Sousa TV, et al (2018) – View Publication

Selective efficiency of genome-wide selection in Coffea canephora breeding. Tree Genetics & Genomes 16:41.
Alkimim ER, Caixeta ET, Sousa TV, et al (2020) – View Publication

Impact of dominance effects on autotetraploid genomic prediction. Crop Science 60:656–665.
Amadeu RR, Ferrão LFV, Oliveira I de B, et al (2020) – View Publication

Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula ). G3 10:299–309.
Apuli R-P, Bernhardsson C, Schiffthaler B, et al (2020) – View Publication

Disease Resistance Genetics and Genomics in Octoploid Strawberry. G3 9:3315–3332.
Barbey CR, Lee S, Verma S, et al (2019) – View Publication

How can a high-quality genome assembly help plant breeders? Gigascience 8:.
Benevenuto J, Ferrão LFV, Amadeu RR, Munoz P (2019) – View Publication

QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population. PLOS ONE 11:e0152569.
Carletti G, Carra A, Allegro G, et al (2016) – View Publication

Genomic selection prediction models comparing sequence capture and SNP array genotyping methods. Molecular Breeding 38:115.
de Moraes BFX, dos Santos RF, de Lima BM, et al (2018) – View Publication

Genome‐wide association of volatiles reveals candidate loci for blueberry flavor. New Phytologist 226:1725–1737.
Ferrão LFV, Johnson TS, Benevenuto J, et al (2020) – View Publication

Identifying markers for resistance to sugarcane orange rust (Puccinia kuehnii) via selective genotyping and capture sequencing. Euphytica 215:150.
McCord P, Glynn N, Comstock J (2019) – View Publication

Genome-Wide Exon-Capture Approach Identifies Genetic Variants of Norway Spruce Genes Associated With Susceptibility to Heterobasidion parviporum Infection. Front Plant Sci 9:.
Mukrimin M, Kovalchuk A, Neves LG, et al (2018) – View Publication

Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction. G3: Genes, Genomes, Genetics 9:1189–1198.
Oliveira I de B, Resende MFR, Ferrão LFV, et al (2019) – View Publication

Natural Allelic Variations in Highly Polyploidy Saccharum Complex. Frontiers in Plant Science 7:804.
Song J, Yang X, Resende MFR, et al (2016) – View Publication

Population structure and genetic diversity of coffee progenies derived from Catuaí and Híbrido de Timor revealed by genome-wide SNP marker. Tree Genetics & Genomes 13:124.
Sousa TV, Caixeta ET, Alkimim ER, et al (2017) – View Publication

A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata. PLOS ONE 14:e0222640.
Telfer E, Graham N, Macdonald L, et al (2019) – View Publication

Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species. PLOS ONE 15:e0232201.
Thistlethwaite FR, El-Dien OG, Ratcliffe B, et al (2020) – View Publication

Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform. BMC Genomics 18:930.
Thistlethwaite FR, Ratcliffe B, Klápště J, et al (2017) – View Publication

A chemical genetic roadmap to improved tomato flavor. Science (New York, NY) 355:391–394.
Tieman D, Zhu G, Resende MFR, et al (2017) – View Publication

Design and evaluation of a large sequence-capture probe set and associated SNPs for diploid and haploid samples of Norway spruce ( Picea abies ). Genomics
Vidalis A, Scofield DG, Neves LG, et al (2018a)

Design and evaluation of a large sequence-capture probe set and associated SNPs for diploid and haploid samples of Norway spruce (Picea abies). bioRxiv 291716.
Vidalis A, Scofield DG, Neves LG, et al (2018b) – View Publication

Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of Norway spruce. BMC Genomics 21:323.
Zhou L, Chen Z, Olsson L, et al (2020) – View Publication

Evolutionary Biology

Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study. Molecular Phylogenetics and Evolution 106769.
Bagley JC, Uribe-Convers S, Carlsen MM, Muchhala N (2020) – View Publication

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*. Evolution 73:329–345.
Betancur‐R R, Arcila D, Vari RP, et al (2019) – View Publication

A target enrichment probe set for resolving the flagellate plant tree of life. bioRxiv 2020.05.29.124081.
Breinholt JW, Carey SB, Tiley GP, et al (2020) – View Publication

A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements. Journal of Biogeography 44:2033–2044.
Bryson RW, Linkem CW, Pavón‐Vázquez CJ, et al (2017) – View Publication

Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics. Applications in Plant Sciences 6:e1032.
Chau JH, Rahfeldt WA, Olmstead RG (2018) – View Publication

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade. Evolution 71:913–922.
Crowl AA, Myers C, Cellinese N (2017) – View Publication

Phylogenetic relationships and systematics of the Amazonian poison frog genus Ameerega using ultraconserved genomic elements. Molecular Phylogenetics and Evolution 142:106638.
Guillory WX, French CM, Twomey EM, et al (2020) – View Publication

Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance. Systematic Entomology 45:552–570.
Gustafson GT, Baca SM, Alexander AM, Short AEZ (2020) – View Publication

Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences. Molecular Phylogenetics and Evolution 102:320–330.
Hosner PA, Braun EL, Kimball RT (2016) – View Publication

A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae. Applications in Plant Sciences 8:e11345.
Jantzen JR, Amarasinghe P, Folk RA, et al (2020) – View Publication

Origin and macroevolution of micro-moths on sunken Hawaiian Islands. Proc R Soc B 285:20181047.
Johns CA, Toussaint EFA, Breinholt JW, Kawahara AY (2018) – View Publication

A new target capture phylogeny elucidates the systematics and evolution of wing coupling in sack-bearer moths. Systematic Entomology 45:653–669.
Laurent RAS, Mielke CGC, Herbin D, et al (2020) – View Publication

Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex. Syst Biol 68:956–966.
Linck E, Epperly K, Van Els P, et al (2019) – View Publication

Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White-collared Seedeater complex (Thraupidae: Sporophila torqueola). Ecology and Evolution 8:1867–1881.
Mason NA, Olvera‐Vital A, Lovette IJ, Navarro‐Sigüenza AG (2018) – View Publication

Anchored phylogenomics of burrowing mayflies (Ephemeroptera) and the evolution of tusks. Systematic Entomology 43:692–701.
Miller DB, Bartlett S, Sartori M, et al (2018) – View Publication

Exploring Chihuahuan Desert diversification in the gray-banded kingsnake, Lampropeltis alterna (Serpentes: Colubridae). Molecular Phylogenetics and Evolution 131:211–218.
Myers EA, Bryson RW, Hansen RW, et al (2019) – View Publication

Sequence capture and next-generation sequencing of ultraconserved elements in a large-genome salamander. Molecular Ecology 25:6162–6174.
Newman CE, Austin CC (2016) – View Publication

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes. PloS one 10:e0138446.
Raposo do Amaral F, Neves LG, Resende MFR, et al (2015) – View Publication

Dynamic changes in gene expression and alternative splicing mediate the response to acute alcohol exposure in Drosophila melanogaster. Heredity 121:342–360.
Signor S, Nuzhdin S (2018) – View Publication

et al Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective. Syst Biol.
Singhal S, Colston TJ, Grundler MR, – View Publication

Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae). Cladistics n/a:
Smith CH, Pfeiffer JM, Johnson NA – View Publication

A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae). Front Plant Sci 10:.
Stubbs RL, Folk RA, Xiang C-L, et al (2020) – View Publication

Lost in translation: Population genomics and long-read sequencing reveals relaxation of concerted evolution of the ribosomal DNA cistron. Molecular Phylogenetics and Evolution 148:106804.
Tremble K, Suz LM, Dentinger BTM (2020) – View Publication

Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae). PeerJ 8:e8392.
Valencia-D J, Murillo-A J, Orozco CI, et al (2020) – View Publication

The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck. Molecular Phylogenetics and Evolution 101:294–302.
Zucker MR, Harvey MG, Oswald JA, et al (2016) – View Publication

Characterization and development of microsatellite markers for Echinomastus johnsonii and congeneric taxa. Applications in Plant Sciences 7:e11302.
Zumwalde BA, Dahir JK, Shaw AB, et al (2019) – View Publication