Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization

PeerJ

article

Aaron Liston¹  Kevin A. Weitemier¹  Lucas Letelier¹  János Podani³  Yu Zong¹  Lang Liu⁵  Timothy A. Dickinson⁶ 

[1] Department of Botany and Plant Pathology, Oregon State University;Department of Fisheries and Wildlife, Oregon State University;Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Lorand University;College of Chemistry & Life Sciences, Zhejiang Normal University;Department of Cell and Systems Biology, University of Toronto;Department of Natural History, Royal Ontario Museum;Department of Ecology and Evolutionary Biology, University of Toronto

关键词: Crataegus;    Rosaceae;    Phylogeny;    Hyb-Seq;    Target capture phylogenetics;    Plastomes;    Nuclear loci;    Hybridization;    Tree-tree comparisons;   

DOI  :  10.7717/peerj.12418

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundHawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups.MethodsWe used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies.ResultsWe obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.

【 授权许可】

CC BY