Significance: Early branching events in the diversification of land plants and closely related algal lineages remain fundamental and unresolved questions in plant evolutionary biology. Accurate reconstructions of these relationships are critical for testing hypotheses of character evolution: for example, the origins of the embryo, vascular tissue, seeds, and flowers. We investigated relationships among streptophyte algae and land plants using the largest set of nuclear genes that has been applied to this problem to date. Hypothesized relationships were rigorously tested through a series of analyses to assess systematic errors in phylogenetic inference caused by sampling artifacts and model misspecification. Results support some generally accepted phylogenetic hypotheses, while rejecting others. This work provides a new framework for studies of land plant evolution.

• Premise of the study: Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses.• Methods: We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid).• Key results: Many important questions of deep‐level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep‐level relationships are resolved with strong support.• Conclusions: Our analyses confirm that with large amounts of sequence data, most deep‐level relationships within the angiosperms can be resolved. We anticipate that this well‐resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species,

Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data.

Rare species are typically considered to maintain low levels of genetic variation, and this view has been supported by several reviews of large numbers of isozyme studies. Although these reviews have provided valuable data on levels of variability in plant species in general, and rare species in particular, these broad overviews involve comparisons that may confound the effects of rarity with a multitude of other factors that affect genetic variability. Additionally, the statistical analyses employed assume the data to be independent, which is not the case for organisms that share a common phylogenetic history. As the role of evolutionary history and historical constraints has become better understood, more researchers have studied widespread congeners when investigating the genetic diversity of rare species in an effort to control for these effects. We summarize the available data from such studies, comparing for rare and widespread congeners (1) the levels of genetic variability at the population and species levels and (2) measures of population substructuring. At the population level, we summarized data for percentage polymorphic loci (%P_pop), mean number of alleles per locus (A_pop), and observed heterozygosity (H_o). Species‐level measures used were percentage polymorphic loci (%P_spp), mean number of alleles per locus (A_spp), and total genetic diversity (H_T). Indices of population subdivision (either F_ST or G_ST) were also examined. Using Wilcoxon signed rank tests, we found significant, but small, differences between rare and widespread species for all diversity measures except H_T. However, there does not appear to be a difference between rare and widespread congeners in terms of how genetic variation is partitioned within and among populations. Levels of diversity, for all measures examined, between rare and widespread congeners are highly correlated.