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.

Climate change has led to major changes in the phenology (the timing of seasonal activities, such as flowering) of some species but not others. The extent to which flowering-time response to temperature is shared among closely related species might have important consequences for community-wide patterns of species loss under rapid climate change. Henry David Thoreau initiated a dataset of the Concord, Massachusetts, flora that spans Ϸ150 years and provides information on changes in species abundance and flowering time. When these data are analyzed in a phylogenetic context, they indicate that change in abundance is strongly correlated with flowering-time response. Species that do not respond to temperature have decreased greatly in abundance, and include among others anemones and buttercups [Ranunculaceae pro parte (p.p.)], asters and campanulas (Asterales), bluets (Rubiaceae p.p.), bladderworts (Lentibulariaceae), dogwoods (Cornaceae), lilies (Liliales), mints (Lamiaceae p.p.), orchids (Orchidaceae), roses (Rosaceae p.p.), saxifrages (Saxifragales), and violets (Malpighiales). Because flowering-time response traits are shared among closely related species, our findings suggest that climate change has affected and will likely continue to shape the phylogenetically biased pattern of species loss in Thoreau's woods.conservation ͉ extinction ͉ phenology ͉ phylogenetic conservatism ͉ phylogeny T he impact of climate change on species and communities has been well documented. Arctic forests are shifting poleward and alpine tree lines are shifting upward (1-3); spring flowering time is advancing rapidly (4-7); pest outbreaks are spreading (8); and numerous species are declining in abundance and risk extinction (9). However, despite these generalized trends, species vary dramatically in their responses to climate change. For example, although the spring flowering times of many temperate plants are advancing, some are not changing and others are flowering later in the season (5, 10, 11). Understanding the evolutionary (i.e., phylogenetic) history of traits that are influenced by climate (e.g., flowering phenology) has been an underexplored area of climate change biology, despite the fact that it could prove especially useful in predicting how species and communities will respond to future climate change. Closely related species often share similar traits, a pattern known as phylogenetic conservatism (12)(13)(14)(15)(16)17). If closely related species share similar traits that make them more susceptible to climate change (14, 17), species loss may not be random or uniform, but rather biased against certain lineages in the Tree of Life (i.e., phylogenetic selectivity; see ref. 18). However, a deeper inquiry into these patterns has been hampered largely because adequate datasets documenting community-wide responses to climate change are exceedingly rare.During the mid-19th century, the naturalist and conservationist Henry David Thoreau spent decades exploring the temperate fields, wetlands, and deciduous forests of Concord...

In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent (MSC) model in phylogenomics, popularly known as "species tree" methods. After pointing out errors in alignments and gene tree rooting in recent phylogenomic data sets, particularly in Song et al. (2012) on mammals and Xi et al. (2014) on plants, they suggest that these errors seriously compromise the conclusions of these studies. Additionally, S&G enumerate numerous perceived violated assumptions and deficiencies in the application of the MSC model in phylogenomics, such as its assumption of neutrality and in particular the use of transcriptomes, which are deemed inappropriate for the MSC because the constituent exons often subtend large regions of chromosomes within which recombination is substantial. We acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of S&G's excessively combative and taunting tone. We show that these errors, as well as two nucleotide sorting methods used in the analysis of Amborella, have little impact on the conclusions of those papers. Moreover, several concepts introduced by S&G and an appeal to "first principles" of phylogenetics in an attempt to discredit MSC models are invalid and reveal numerous misunderstandings of the MSC. Contrary to the claims of S&G we show that recent computer simulations used to test the robustness of MSC models are not circular and do not unfairly favor MSC models over concatenation. In fact, although both concatenation and MSC models clearly perform well in regions of tree space with long branches and little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when subjected to data subsampling and its tendency to produce spuriously confident yet conflicting results in regions of parameter space where MSC models still perform well. S&G's claims that MSC models explain little or none (0-15%) of the observed gene tree heterogeneity observed in a mammal data set and that MSC models assume ILS as the only source of gene tree variation are flawed. Overall many of their criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is a special case of emerging network models in phylogenomics. We reiterate that there is enormous promise and value in recent implementations and tests of the MSC and look forward to its increased use and refinement in phylogenomics.

The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; >25,000 bp) datasets for >100 rosid species, we provide a greatly improved understanding of rosid phylogeny. Vitaceae are sister to all other rosids, which in turn form 2 large clades, each with a ML bootstrap value of 100%: (i) eurosids I (Fabidae) include the nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighiales, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosomatales, and Picramniaceae. The rosid clade diversified rapidly into these major lineages, possibly over a period of <15 million years, and perhaps in as little as 4 to 5 million years. The timing of the inferred rapid radiation of rosids [108 to 91 million years ago (Mya) and 107-83 Mya for Fabidae and Malvidae, respectively] corresponds with the rapid rise of angiosperm-dominated forests and the concomitant diversification of other clades that inhabit these forests, including amphibians, ants, placental mammals, and ferns. community assembly ͉ divergence time estimates ͉ phylogeny ͉ rapid radiation G reat progress has been made in elucidating deep-level angiosperm relationships during the past decade. The eudicot clade, with Ϸ75% of all angiosperm species, comprises several major subclades: rosids, asterids, Saxifragales, Santalales, and Caryophyllales (1-3). Investigations have converged on the branching pattern of the basalmost angiosperms, revealing that Amborellaceae, Nymphaeales [in the sense of APG II (3) and including Hydatellaceae (4)], and Austrobaileyales are successive sisters to all other extant angiosperms (reviewed in ref.2). Analyses of complete plastid genome sequences have resolved other problematic deep-level relationships, suggesting that Chloranthaceae and magnoliids are sister to a clade of monocots and eudicots plus Ceratophyllaceae (5, 6). Likewise, progress has been made in clarifying relationships within the large monocot (7) and asterid (8) clades.Despite these successes, the rosids stand out as the largest and least-resolved major clade of angiosperms; basal nodes within the clade have consistently received low internal support (1, 2, 9, 10). The rosid clade comprises Ϸ70,000 species and 140 families (2, 11). Containing more than a quarter of total angiosperm and Ϸ39% of eudicot species diversity, the rosid clade is broader in circumscription than the traditional Rosidae or Rosanae (e.g., 12; reviewed in ref.2). The oldest fossil flowers conforming to the rosids are from the late S...

The angiosperm order Malpighiales includes ∼16,000 species and constitutes up to 40% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics during the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 additional clades in Malpighiales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas (Erythroxylaceae), and passion flowers (Passifloraceae). We found that commonly used a priori approaches for partitioning concatenated data in maximum likelihood analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a posteriori using a Bayesian mixture model. We also found better branch support in trees inferred from a taxon-rich, data-sparse matrix, which deeply sampled only the phylogenetically critical placeholders, than in trees inferred from a taxon-sparse matrix with little missing data. Although this matrix has more missing data, our a posteriori partitioning strategy reduced the possibility of producing multiple distinct but equally optimal topologies and increased phylogenetic decisiveness, compared with the strategy of partitioning by gene. These approaches are likely to help improve phylogenetic resolution in other poorly resolved major clades of angiosperms and to be more broadly useful in studies across the Tree of Life. M alpighiales are one of the most surprising clades discovered in broad molecular phylogenetic studies of the flowering plants (1-3). The order contains ∼16,000 species and 42 families (2, 3) that exhibit remarkable morphological and ecological diversity. A few examples include cactus-like succulents (Euphorbiaceae), epiphytes (Clusiaceae), holoparasites (Rafflesiaceae), submerged aquatics (Podostemaceae), and windpollinated trees (temperate Salicaceae). The order is ecologically important: species in Malpighiales constitute up to 40% of the understory tree diversity in tropical rain forests worldwide (4). They also include many economically important species, such as Barbados nut (Jatropha curcas L., Euphorbiaceae), cassava (Manihot esculenta Crantz, Euphorbiaceae), castor bean (Ricinus communis L., Euphorbiaceae), coca (Erythroxylum coca Lam., Erythroxylaceae), flax (Linum usitatissimum L., Linaceae), the poplars (Populus spp., Salicaceae), and the rubber tree (Hevea brasiliensis Müll. Arg., Euphorbiaceae). Partially for this reason, genomic resources for Malpighiales are growing at a rapid pace and include whole-genome sequencing projects completed or near completion for Barbados nut (5), cassava, castor bean (6), flax, and poplar (7). Thus, a resolved phylogeny of Malpighiales is critical not only for evol...