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Premise: The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed., Methods: We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses., Results: Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes., Conclusions: Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution., (© 2021 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Premise of the Study: Cruciferous vegetables, many of which are in the genus Brassica (Brassicaceae), are prized for their nutritive value and have been cultivated for thousands of years. There are numerous wild northwestern Mediterranean species in the tribe Brassiceae, and it is therefore assumed this center of diversity is also the region of origin. Within the tribe, the Nigra and Oleracea clades contain the three diploid Brassica crops, B. oleracea, B. rapa, and B. nigra. These three species hybridized in the past to form the tetraploid crop species B. juncea, B. carinata, and B. napus. Collectively, these crop Brassicas have been thought to be closely related because they can still hybridize., Methods: Using a combination of molecular phylogenetics, diversification analysis, and historical biogeography, we evaluated the relationships and origins of four nested clades: the tribe Brassiceae, the Nigra-Oleracea clade, the core Oleracea (includes B. oleracea + B. rapa and their respective wild relatives), and Brassica oleracea and relatives., Key Results: We found evidence that the tribe originated around the intersection forming between the Arabian Peninsula and Saharan Africa approximately 24 million years ago (Mya). Our data also suggest that the maternal genomes of the three diploid crop Brassicas are not closely related and that the Nigra-Oleracea clade diverged 20 Mya. Finally, our analyses indicate that the core Oleracea lineage giving rise to B. oleracea + B. rapa originated ≈3 Mya in the northeastern Mediterranean, from where ancestors of B. oleracea spread through Europe and B. rapa to Asia., Conclusions: These results challenge previous hypotheses about the biogeographic origins of the tribe Brassiceae and the crop Brassica species and appear to be correlated with major geological and climatic events in the Mediterranean basin.

The vast majority of flowering plant seeds contain a triploid endosperm formed by fertilization of a monosporic, Polygonum-type female gametophyte. However, evolutionary transitions to six other genetic constructs of endosperm are widespread, and six of seven known patterns are found in the order Piperales. Within Piperaceae, Manekia has not been described, and we report its female gametophyte to be tetrasporic and 16-nucleate at maturity. Manekia ontogeny is generally characterized by early establishment of a bipolar or weakly bipolar body plan and a binucleate central cell at maturity (Drusa-type pattern); however, ca. 16% of early stages had distinctly tetrapolar organization, and ca. 21% of mature specimens had a tetranucleate central cell (Penaea-type pattern, not previously reported in Piperaceae). An evolutionary developmental analysis indicates heterochrony, heterotopy, novelties, and sequence deletions have each played roles in modulating variation within Piperales. Our data suggest the common ancestor of Piperaceae was tetrasporic and retained a plesiomorphic bipolar body plan, producing a "functionally bisporic" form of triploid endosperm derived from the lineal descendants of two megaspores and a sperm. Developmental modifications of this tetrasporic, bipolar ontogeny can account for the origin of all three other known "true" tetrasporic endosperm genetic constructs, formed from derivatives of all four megaspores and a sperm. These derived endosperms in turn have higher ploidy, higher potential heterozygosity, and reduced genetic conflicts.