title: Genomic patterns of species diversity and divergence in Eucalyptus.
abstract: We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology.
authors: School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.|Tasmanian Alkaloids, PO Box 130, Westbury, TAS 7303, Australia.
authors: Corey J
authors: CJ
authors: Hudson
authors: School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.|National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.|Faculty of Science, Health, Education and Engineering, and Collaborative Research Network, University of the Sunshine Coast, Locked Bag 4, Maroochydore, QLD, 4558, Australia.
authors: Jules S
authors: JS
authors: Freeman
authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors: Alexander A
authors: AA
authors: Myburg
authors: School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.|National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
authors: Brad M
authors: BM
authors: Potts
authors: School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.|National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia.
authors: René E
authors: RE
authors: Vaillancourt
mesh_terms: D001499:Bayes Theorem; D032461:Chromosomes, Plant / Q000235:genetics; D005052:Eucalyptus / Q000235:genetics*; D020440:Gene Duplication; D017343:Genes, Plant; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D005843:Geography; D025341:Principal Component Analysis; D013045:Species Specificity; D018709:Statistics, Nonparametric
chemical_list: D005819:Genetic Markers
keywords: Eucalyptus; gene density; genome-scan; genomic architecture; outlier; population genomics; speciation; tandem gene duplication