Target Capture Sequencing UnravelsRubusEvolution

Abstract

6Background: Rubus (Rosaceae) comprises more than 500 species with additional commercially 7 cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic 8 treatment of the genus defined 12 subgenera; two subgenera were subsequently described and 9 some species were rearranged. Intra-and interspecific ploidy levels and hybridization make 10 phylogenetic estimation of Rubus challenging. Our objectives were to: estimate the phylogeny 11 of 94 geographically diverse species and 3 cultivars using chloroplast DNA sequences and target 12 capture of approximately 1,000 low copy nuclear genes; estimate divergence times between 13 major Rubus clades; and examine the historical biogeography of species diversification. 14 15 Results: Target capture sequencing identified eight major groups within Rubus. Subgenus 16 Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were 17 para-or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at 18 subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. 19 Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known 20 cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus 21 Rubus species were examined using limited nuclear and chloroplast loci by Wang et al. (18). 63 Species from Dalibardastrum and Idaeobatus were nested within the paraphyletic 64 Malachobatus. These authors hypothesized that the allopolyploid species in Malachobatus may 65 be derived from crosses between Idaeobatus and Cylactis species (8, 18). Similarly, 66 Dalibardastrum species may be derived from Malachobatus ancestors. Idaeobatus was 67 polyphyletic with members in four clades. Current phylogenies consistently indicate that 68subgeneric labels rarely represent monophyletic groups (17, 18). 69 Hybridization and polyploidization are major evolutionary forces in Rubus. Intraspecific 70 morphological and ploidial variability and the capability of many species to hybridize widely 71 across the genus complicate traditional taxonomic classification (8,(19)(20)(21). Past phylogenetic 72 analyses of the genus were based on nuclear ribosomal DNA internal transcribed spacer (ITS) 73 sequence data and a few other nuclear and chloroplast loci, including GBSSI-2, PEPC, trnL/F, 74 rbcL, rpl20-rps12, and trnG-trnS (17, 18, 22). Relying on a limited number of loci to determine 75 relationships in this genus with prevalent hybridization and polyploidy has resulted in low 76 phylogenetic resolution. Additionally, single gene trees may not represent species trees due to 77 hybridization, incomplete lineage sorting (ILS), and gene duplication (23). 79Two contrasting views of Rubus evolution exist. One view uses a nuclear ribosomal ITS-based 80 genus-wide phylogeny (17) to suggest that the ancestral area for the genus was North America, 81 Eastern Europe (possibly Russia) or Asia (possibly Korea or Japan). In contrast, the treatme...

Museomics Unveil the Phylogeny and Biogeography of the Neglected Juan Fernandez Archipelago Megalachne and Podophorus Endemic Grasses and Their Connection With Relict Pampean-Ventanian Fescues

“…Genomic data are increasingly called upon to elucidate evolutionary and taxonomic challenges posed by several cryptic or ambiguously related organisms, which could not be resolved using traditional approaches, such as morphometrics or standard molecular methods ( Harrison and Kidner, 2011 ; Straub et al, 2012 ; Carter et al, 2020 ; Larridon et al, 2020 ). The advent of the high-throughput sequencing (HTS) methods have outpaced classical molecular barcoding and phylogenetic procedures based on few molecular markers that have served to build phylogenies with constrained resolution limits ( Diaz-Perez et al, 2018 ; Sancho et al, 2018 ).…”

Target Capture Sequencing Unravels Rubus Evolution

“…Finn for technical assistance and meaningful discussion on this manuscript. This manuscript has been released as a pre-print at biorXiv (Carter et al, 2019).…”

Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental Geodynamics

“…Despite this progress, several relationships within the Andean tetraploid clade were unresolved or weakly supported in these previous studies. Sequence capture using anchored hybrid enrichment, also known as Hyb-Seq ( Cronn et al, 2012 ; Lemmon et al, 2012 ; Lemmon and Lemmon, 2013 ; Weitemier et al, 2014 ) has been informative at various taxonomic levels in plants ( Fragoso-Martínez et al, 2017 ; Wanke et al, 2017 ; Carter et al, 2019 ; Granados Mendoza et al, 2020 ; Larridon et al, 2020 ; Murphy et al, 2020 ). The methodology yields sequences of hundreds of single or low copy nuclear loci.…”