Data from: Phylogenomics in Cactaceae: a case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan/Sonoran Deserts

PREMISE OF THE STUDY: Although numerous phylogenetic studies have been conducted in Cactaceae, whole plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age and morphological evolution. METHODS: We developed a plastome dataset for most known diploid members of the chollas, 42 taxa, as well as for other members of Cylindropuntieae. Paired-end, raw reads from genome skimming were referenced-mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, which were used to build our plastome dataset that was analyzed using various methods. KEY RESULTS: Our plastome dataset resolved the phylogeny of the chollas, including most inter- and intraspecific relationships. Tribe Cylindropuntieae arose during the early Miocene in southern South America, ca. 18 mya, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya, and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series (e.g., spiny fruit) in Cylindropuntia are mostly homoplasious. CONCLUSIONS: This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although widespread throughout western North American deserts, the most recent common ancestor of the chollas s.l. likely arose in the Chihuahuan Desert region during the mid-Miocene, with much of their species diversity arising in the early to mid-Pliocene, showing a strikingly similar pattern to other western North American Desert groups.

研究背景：尽管针对仙人掌科（Cactaceae）已开展大量系统发育研究，但尚未有研究采用完整质体基因组（plastome）数据集。本研究以团扇仙人掌类（chollas）为研究对象，构建质体基因组数据集用于系统发育重建，以解析类群亲缘关系、生物地理格局、支系起源时间及形态演化规律。
研究方法：我们针对绝大多数已知二倍体团扇仙人掌类类群（共计42个分类单元）以及圆柱仙人掌族（Cylindropuntieae）的其他类群，构建了质体基因组数据集。本研究通过基因组浅层测序（genome skimming）获取双端原始读段，将其参考映射至一种团扇仙人掌——比格罗夫圆柱掌（Cylindropuntia bigelovii）的从头组装（de novo assembly）质体基因组，以此完成本研究质体基因组数据集的构建，并采用多种分析方法开展数据解析。
主要结果：本研究的质体基因组数据集成功解析了团扇仙人掌类的系统发育关系，涵盖绝大多数种间及种内亲缘关系。圆柱仙人掌族起源于南美洲南部的中新世早期，距今约18百万年，且被支持为南美支系特弗罗仙人掌族（Tephrocacteae）的姊妹群。（小团扇属（Micropuntia）+（圆柱掌属（Cylindropuntia）+克鲁松掌属（Grusonia）））支系最有可能起源于奇瓦瓦沙漠区域，距今约16百万年，随后扩散至北美其他沙漠区域。传统上用于识别圆柱掌属（Cylindropuntia）类群的关键形态性状（如具刺果实）大多为同塑性状。
结论：本研究首次为仙人掌科内的任意类群提供了全面的质体基因组系统发育框架。尽管团扇仙人掌类广泛分布于北美西部沙漠区域，其广义类群（sensu lato，s.l.）的最近共同祖先很可能起源于中新世中期的奇瓦瓦沙漠区域，绝大多数物种多样性形成于上新世早中期，这一演化模式与北美西部沙漠其他类群的演化规律极为相似。