Phylogenetic Insights into Chinese Rubus (Rosaceae) from Multiple Chloroplast and Nuclear DNAs

Abstract

Rubus L. is a large and taxonomically complex genus, species of which exhibit apomixis, polyploidy, and frequent hybridization. Most of Chinese Rubus are assigned in two major sections, Idaeobatus and Malachobatus. To explore the phylogenetic relationships within Chinese Rubus, inferences upon three chloroplast DNA (rbcL, rpl20-rps12, and trnG-trnS), nuclear ribosomal ITS, and two low-copy nuclear markers (GBSSI-2 and PEPC) were deduced in 142 Rubus taxa from 17 subsections in 6 sections. nrITS and GBSSI-2 were the most informative among the six DNA regions assessed. Phylogenetic relationships within Rubus were well-resolved by combined nuclear datasets rather than chloroplast markers. The phylogenetic inferences strongly supported that section Idaeobatus was a polyphyletic group with four distant clades. All samples of sect. Malachobatus formed a monophyletic clade, in which R. tsangorum and R. amphidasys of sect. Dalibardastrum, and R. peltatus from subsection Peltati of sect. Idaeobatus were always nested. Rubus pentagonus (2n = 2x = 14) from subsect. Alpestres of sect. Idaeobatus was a sister group to the polyploid sect. Malachobatus, as well as the polytomy of three sect. Cyalctis members. This suggests that some polyploids of Malachobatus might originate from common ancestors, via polyploidization of hybrids between R. pentagonus and sect. Cylactis species. They had experienced species explosion in a short time. Section Dalibardastrum species have potential parental lineages from subsects. Moluccani and Stipulosi of sect. Malachobatus. Based on molecular phylogenies, we also provided recommendations for the taxonomic treatments of four taxa. In addition, our results showed certain incongruence between chloroplast and nuclear markers, which might be due to hybridization and introgression.

Target Capture Sequencing Unravels Rubus Evolution

“…Our target capture sequencing approach enabled resolution of relationships between major groups, confirming or extending previous studies (Alice and Campbell, 1999;Morden et al, 2003;Yang and Pak, 2006;Wang et al, 2016). Subg.…”

“…Idaeobatus was polyphyletic with members in four clades. Current phylogenies consistently indicate that subgeneric labels rarely represent monophyletic groups (Alice and Campbell, 1999;Wang et al, 2016).…”

“…That study underscored the need for additional molecular data to better resolve species level relationships, particularly for polyploids. Asian Rubus species were examined using limited nuclear and chloroplast loci by Wang et al (2016). Species from Dalibardastrum and Idaeobatus were nested within the paraphyletic Malachobatus.…”

“…Species from Dalibardastrum and Idaeobatus were nested within the paraphyletic Malachobatus. These authors hypothesized that the allopolyploid species in Malachobatus may be derived from crosses between Idaeobatus and Cylactis species (Wang et al, 2015;Wang et al, 2016). Idaeobatus was polyphyletic with members in four clades.…”

“…Intraspecific morphological and ploidal variability and the capability of many species to hybridize widely across the genus complicate traditional taxonomic classification (Bammi and Olmo, 1966;Alice et al, 2001;Mimura et al, 2014;Wang et al, 2015). Past phylogenetic analyses of the genus were based on nuclear ribosomal DNA internal transcribed spacer (ITS) sequence data and a few other nuclear and chloroplast loci, including GBSSI-2, PEPC, trnL/F, rbcL, rpl20-rps12, and trnG-trnS (Alice and Campbell, 1999;Yang and Pak, 2006;Wang et al, 2016). Relying on a limited number of loci to determine relationships in this genus with prevalent hybridization and polyploidy has resulted in low phylogenetic resolution.…”