Table_1_Eriobotrya Belongs to Rhaphiolepis (Maleae, Rosaceae): Evidence From Chloroplast Genome and Nuclear Ribosomal DNA Data.docx

The Eriobotrya-Rhaphiolepis (ER) clade consists of about 46 species distributed in East and Southeast Asia. Although Eriobotrya and Rhaphiolepis have been supported to form a clade, the monophyly of Eriobotrya and Rhaphiolepis at the genus level has never been well tested and their phylogenetic positions in Maleae still remain uncertain. This study aims to reconstruct a robust phylogeny of the ER clade in the framework of Maleae with a broad taxon sampling and clarify the phylogenetic relationship between Eriobotrya and Rhaphiolepis. This study employed sequences of the whole plastome (WP) and entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach and included 83 samples representing 76 species in 32 genera of Rosaceae, especially Maleae. The Maximum Likelihood (ML) and Bayesian Analysis (BI) based on three datasets, i.e., WP, coding sequences of plastome (CDS), and nrDNA, strongly supported the paraphyly of Eriobotrya, within which Rhaphiolepis was nested. Our plastid tree supported the sister relationship between the ER clade and Heteromeles, and the nrDNA tree, however, did not resolve the phylogenetic placement of the ER clade in Maleae. Strong incongruence between the plastid and the nuclear trees is most likely explained by hybridization events, which may have played an important role in the evolutionary history of the ER clade. Molecular, morphological, and geographic evidence all supports the merge of Eriobotrya with Rhaphiolepis, which has the nomenclatural priority. We herein transferred 36 taxa of Eriobotrya to Rhaphiolepis. We also proposed a new name, Rhaphiolepis loquata B.B.Liu & J.Wen, for the economically important loquat, as the specific epithet “japonica” was pre-occupied in Rhaphiolepis.

枇杷属-石斑木属（Eriobotrya-Rhaphiolepis, ER）进化支包含约46个物种，分布于东亚及东南亚地区。尽管枇杷属（Eriobotrya）与石斑木属（Rhaphiolepis）被证实可构成一个进化支，但二者的属级单系性尚未得到充分检验，且它们在苹果族（Maleae）中的系统发育位置仍不明确。本研究旨在以苹果族为研究框架，通过广泛的类群取样构建ER进化支的高支持度系统发育树，并阐明枇杷属与石斑木属之间的系统发育关系。本研究采用了从基因组浅层测序（genome skimming）技术组装得到的全质体基因组（whole plastome, WP）序列以及完整核核糖体DNA（nuclear ribosomal DNA, nrDNA）重复序列，共纳入蔷薇科（Rosaceae）32属76种的83份样本，其中重点涵盖苹果族类群。基于全质体基因组、质体编码序列（coding sequences of plastome, CDS）以及核核糖体DNA三套数据集的最大似然法（Maximum Likelihood, ML）分析与贝叶斯推断（Bayesian Inference, BI）均强烈支持枇杷属为并系群，石斑木属嵌套于枇杷属内。本研究的质体系统发育树支持ER进化支与红果树属（Heteromeles）互为姊妹群，但核核糖体DNA系统发育树未能明确ER进化支在苹果族中的系统发育位置。质体与核基因系统发育树之间的显著冲突，最可能由杂交事件所致，这类事件可能在ER进化支的演化历史中发挥了关键作用。分子、形态及地理证据均支持将枇杷属并入具有命名优先权的石斑木属。本研究将36个枇杷属类群转移至石斑木属。鉴于“japonica”这一种加词在石斑木属中已被占用，本研究还为具有重要经济价值的枇杷发表了新名称：Rhaphiolepis loquata B.B.Liu & J.Wen。