Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tipsthe Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.phylogeny | taxonomy | tree of life | biodiversity | synthesis T he realization that all organisms on Earth are related by common descent (1) was one of the most profound insights in scientific history. The goal of reconstructing the tree of life is one of the most daunting challenges in biology. The scope of the problem is immense: there are ∼1.8 million named species, and most species have yet to be described (2-4). Despite decades of effort and thousands of phylogenetic studies on diverse clades, we lack a comprehensive tree of life, or even a summary of our current knowledge. One reason for this shortcoming is lack of data. GenBank contains DNA sequences for ∼411,000 species, only 22% of estimated named species. Although some gene regions (e.g., rbcL, 16S, COI) have been widely sequenced across some lineages, they are insufficient for resolving relationships across the entire tree (5). Most recognized species have never been included in a phylogenetic analysis because no appropriate molecular or morphological data have been collected.There is extensive publication of new phylogenies, data, and inference methods, but little attention to synthesis. We therefore focus on constructing, to our knowledge, the first comprehensive tree of life through the integration of published phylogenies with taxonomic information. Phylogenies by systematists with expertise in particular taxa likely represent the best estimates of relationships for individual clades. By focusing on trees instead of raw data, we avoid issues of dataset assembly (6). However, most published phylogenies are available only as jour...

Worldwide cooling trends probably played a large role in the diversification and present day distribution of the tribe Mentheae. Additional work is needed to ascertain relationships within some Mentheae genera, especially in the subtribe Menthinae.

Previous molecular phylogenetic research, based on chloroplast and nuclear ribosomal DNA data, has demonstrated that the large genus Salvia (Lamiaceae) is paraphyletic as traditionally circumscribed. However, neither relationships within Salvia s.l. nor within subtribe Salviinae have been evaluated using low‐copy nuclear gene regions. Here, we use two low‐copy nuclear gene regions (PPR‐AT3G09060, GBSSI) to further assess relationships of Salvia and related genera within Salviinae. Our results largely confirm results from previous studies based on chloroplast and nuclear ribosomal DNA. Based upon the phylogenetic results presented here, previous phylogenetic studies, and taxonomic, morphological, and practical considerations, we conclude that the botanical community would be best served by maintaining a broadly defined Salvia, including the five small embedded genera Dorystaechas, Meriandra, Perovskia, Rosmarinus, and Zhumeria as Salvia species. We subsequently present an updated circumscription of Salvia.

Premise of the StudyA key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species‐rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega‐genus Salvia.MethodsA chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared.Key ResultsA well‐resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade.Conclusions Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

Aim Across angiosperm families, the area occupied by a family is strongly correlated with its richness. We explore the causes of this area‐richness correlation using the cosmopolitan family, Cyperaceae Juss., as a model. We test the hypothesis that, despite a proposed tropical origin, temperate lineages in the family diversified at elevated rates. We test the hypothesis that the area‐richness correlation is maintained within intrafamilial clades, and that this relationship could be described as a function of niche space. We also test the hypothesis that the partitioning of geographical and ecological space, not the extent of this space, is the factor most closely associated with clade richness. Location Cosmopolitan. Methods We use molecular data from four genes sequenced in 384 taxa to develop a chronogram of Cyperaceae. We then develop a model of ancestral ranges and measure rates of diversification throughout the history of the family. Integrating data from over 4,800,000 digitized herbarium records, we characterize the range and niche of more than 4500 species and test for correlations of the species richness maintained within clades with range size, range partitioning, range overlap, niche, clade age and rate of diversification. Results Cyperaceae originated in South America in the late Cretaceous and subsequently dispersed throughout the globe. Of three increases in diversification rate, two occurred in the temperate Northern Hemisphere. The variable most closely associated with clade richness is the partitioning of geographical space by species within each clade. Main conclusions We show that species‐rich clades in Cyperaceae are not only more widespread, occupy more niche space, and diversify more quickly, but also exhibit patterns that are consistent with the partitioning of geographical and ecological space as a major correlate to diversification.

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Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: 1) a novel comprehensive global reference taxonomy; and 2) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. While data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. Significance statement Scientists have used gene sequences and morphological data to construct tens of thousands of evolutionary trees that describe the evolutionary history of animals, plants and microbes. This study is the first to apply an efficient and automated process for assembling published trees into a complete tree of life. This tree, and the underlying data, are available to browse and download from the web, facilitating subsequent analyses that require evolutionary trees. The tree can be easily updated with newly-. CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not. http://dx.doi.org/10.1101/012260 doi: bioRxiv preprint first posted online Dec. 5, 2014; published data. Our analysis of coverage not only reveals gaps in sampling and naming biodiversity, but also further demonstrates that most published phylogenies are not available in digital formats that can be summarized into a tree of life.