Phylogenomic loci define the generic boundaries of Gochnatieae and improve resolution at the species level in Moquiniastrum (Compositae)

Understanding the evolution of the tribe Gochnatieae (Compositae) has been the subject of considerable effort in the past decade. This is due to the key position of this tribe in the phylogeny of the sunflower family and the corresponding implications for biogeographic and morphological evolution of Compositae. Previous studies have confirmed the monophyly of this tribe as well as most of the genera that belong to it. However, phylogenetic resolution of Gochnatieae at both the genus- and species-level has remained poor. A subset of new phylogenomic loci used in this study has proven effective and has improved phylogenetic resolution in this group. The results of this work demonstrate Gochnatieae is a well-supported clade comprised of nine genera (Anastraphia, Cnicothamnus, Cyclolepis, Gochnatia, Moquiniastrum, Nahuatlea,  Pentaphorus, Richterago, Tehuasca). One recently described genus, Vickia, was not included in this study; but its placement in Gochnatieae as a tenth genus in the tribe is well-justified. The monospecific Cyclolepis, which had been circumscribed within the tribe since its inception but was subsequently removed and designated as incertae sedis since 2014, is also shown to belong to Gochnatieae. We confirmed the monophyletic Moquiniastrum with two well-supported subclades. Ancestral area reconstruction analyses show that Gochnatieae originated in Eastern South America about 53 my. Apparently, except for Cyclolepis and Richterago, the ancestors of the other genera of Gochnatieae originated about 44 my from an area that now corresponds to the central Andes. The presence of the genera in the Chaco phytogeographic province, central Chile, and Mexico-United States-Caribbean is a result of dispersal from the central Andes. The ancestral distribution of Moquiniastrum corresponds to a large area comprising Eastern South America and the current central Andes, about 32 my. Ancestral character state reconstruction that included four characters indicates several states associated with complex plant reproductive biology such as gynodioecy, gynomonoecy, and polygamodioecy are derived in Gochnatieae as are heterogamous capitula (in Moquiniastrum and Richterago), dimorphic and subdimorphic corollas (in Cnicothamnus, Moquiniastrum, and Richterago), and the presence of marginal female corollas (in Moquiniastrum and Richterago). Within Moquiniastrum, two subclades (Densicephalum and Polymorphum) exhibit divergent patterns of trait evolution associated with these reproductive characters which suggests this genus can serve as a model to understand the sexual system evolution in plants.

Methods
High-throughput sequencing libraries were generated using microfluidic PCR-based target enrichment and sequenced on an Illumina MiSeq. Sequences were demultiplexed, cleaned, assembled, and then aligned per locus. Geographic areas were selected based on occurrence data gathered from herbarium records for all taxa included in this study. Ancestral character state matrices were constructed from herbarium collections and taxonomic knowledge by the taxonomic specialists who are authors of this manuscript.

近十年来，学界针对帚菊木族（Gochnatieae，菊科Compositae）的演化历程开展了大量研究工作。这是因为该族在菊科系统发育框架中占据关键地位，相关研究成果对菊科的生物地理学与形态演化研究均具有重要参考价值。既往研究已证实该族及其绝大多数归属属类的单系性，但目前该族在属级与物种级的系统发育分辨率仍较为有限。本研究使用的一套全新系统组学位点已被证明可有效提升该类群的系统发育分辨率。

本研究结果显示，帚菊木族（Gochnatieae）为一个得到充分支持的单系支系，包含9个属：Anastraphia、Cnicothamnus、Cyclolepis、Gochnatia、Moquiniastrum、Nahuatlea、Pentaphorus、Richterago、Tehuasca。本次研究未纳入近年新定名的Vickia属，但现有分类学证据已充分支持将其归入该族作为第10个属。此前自该族建立以来便被划入其中、但自2014年起被移出并列为分类位置未定（incertae sedis）的单型属Cyclolepis，本次研究证实其应隶属于帚菊木族。本研究确认了Moquiniastrum的单系性，其下包含两个得到充分支持的亚支系。

祖先区域重建分析显示，帚菊木族起源于南美洲东部，距今约5300万年。除Cyclolepis与Richterago外，该族其余属的祖先类群约于4400万年前起源于现今对应安第斯中部的区域。该族现有类群分布于查科植物地理省、智利中部以及墨西哥-美国-加勒比地区，这一分布格局是从安第斯中部区域扩散而来的结果。Moquiniastrum的祖先分布范围覆盖南美洲东部与现今的安第斯中部区域，距今约3200万年。

针对4个性状的祖先性状状态重建结果显示，与植物复杂生殖生物学相关的多个性状状态——如雌全异株（gynodioecy）、雌全同株（gynomonoecy）、雄全异株（polygamodioecy）——在帚菊木族中均为衍生性状；异花头状花序（仅见于Moquiniastrum与Richterago）、二型与亚二型花冠（见于Cnicothamnus、Moquiniastrum与Richterago）以及边缘雌性花冠（见于Moquiniastrum与Richterago）同样为该族的衍生性状。在Moquiniastrum属下，两个亚支系（Densicephalum与Polymorphum）在上述生殖相关性状上呈现出迥异的演化模式，这表明该属可作为探究植物性系统演化的理想模型类群。

方法
本研究通过基于微流控PCR的靶向富集技术构建高通量测序文库，并在Illumina MiSeq测序平台上完成测序。序列经解复用、质控过滤、拼接及各位点联配处理。研究选取的地理分布区域，基于本研究纳入所有类群的标本馆分布记录数据确定。祖先性状状态矩阵由本研究作者中的分类学专家，通过标本馆馆藏资料与分类学知识构建完成。