title: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae).
abstract: As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar.
authors: Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.|Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada.
authors: Daisie I
authors: DI
authors: Huang
authors: Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.|Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada.
authors: Charles A
authors: CA
authors: Hefer
authors: Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
authors: Natalia
authors: N
authors: Kolosova
authors: Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
authors: Carl J
authors: CJ
authors: Douglas
authors: Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.|Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada.
authors: Quentin C B
authors: QCB
authors: Cronk
mesh_terms: D001483:Base Sequence; D002170:Canada; D003710:Demography; D018506:Gene Expression Regulation, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D032107:Populus / Q000235:genetics*; D016415:Sequence Alignment; D013045:Species Specificity; D014481:United States
keywords: Populus; Salix; cytonuclear discordance; phylogenomics; plastome