Phycella (Amaryllidaceae) is a clade of lilies endemic to the Mediterranean-type ecosystem of Chile. To approach the evolutionary history of Phycella, we sampled a total of 137 individuals from 47 populations, including all described taxa throughout the geographic range of the group, and sampled 893 nuclear genes (1135 exons) through hybrid capture. These data largely resolved the phylogeny of Phycella with high support and demonstrated substantial phylogenetic resolution at the population level. Near-complete plastomes were extracted from raw reads and assembled for all samples to compare with the nuclear framework and examine complex evolutionary processes. Using phylogenetic network and modeling approaches, we identified major cytonuclear discord, attributable to proximity-based gene flow among recently diverged species through the speciation process, largely involving cytoplasmic DNA. Analyses of niche overlap among species and nuclear clades suggest that the diversification of Phycella was associated with niche divergence, supporting a predominantly geographic mode of speciation in the group, likely driven by the mountainous landscape characteristic of diversity and endemism center of this clade in central Chile. The combination of high-resolution molecular data Finally, we present a major integrative taxonomic proposal that divides Phycella into 18 species on the basis of molecular, morphological, and ecological data. Overall, our findings highlight the value of strong sampling of both populations/individuals and genetic loci for speciation studies, which in combination with morphological and ecological data was key to identifying both evolutionary processes and a confident taxonomic framework for contextualizing these processes.

Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an “expanded” malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.

Aim: Higher elevation habitats contribute substantially to global biodiversity. Nevertheless, we know comparatively little about how diversity patterns differ among alpine and montane communities across different mountain ranges. Here, we characterized the realized niche space of American seed plants to ask whether or not montane or alpine community compositions define climatically distinct species pools at this regional scale. Location: Americas. Time Period: Contemporary. Major taxa studied: Seed plants. Methods: We assembled a niche model dataset of 72,372 American seed plants based on digitized and georeferenced specimen records. We used this dataset to quantify occupied abiotic niche space with regards to temperature, precipitation, and elevation. This approach further permitted differentiation of higher-elevation specialists (i.e., ranges centered at high elevations) from generalists (i.e., ranges centered at lower elevations but extending into mountain areas). Results: Montane communities did not differ from the regional species pool in terms of richness patterns, occupied climatic niche space, or niche breadth. In contrast, alpine communities were characterized by a bimodal latitudinal diversity gradient, drastically reduced climatic niche space, and broader temperature but narrower precipitation niche breadth. Alpine generalists further showed statistically significant differences in temperature, but not precipitation, niche breadth from both alpine specialists and lowland taxa. We also highlight non-alpine species whose climatic niche space otherwise overlapped with that of alpine plants. These species were geographically concentrated in the southern US and Mexico, tended to have a greater fraction of their ranges in frost-exposed mountain foothills, and less of their range in lowland, frost-free, areas, compared to other non-alpine species. Main conclusions: These results suggest that ecological and physiological barriers, rather than dispersal limitation might better explain alpine community assembly and that alpine, but not montane, communities form a climatically distinct species pool in the Americas.