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...

In ciliates, chromosomal rearrangements occur during the development of the somatic macronuclear genome from the germline micronuclear genome. These rearrangements are extensive in three ciliate classes -Armophorea, Spirotrichea and Phyllopharyngea -generating a macronucleus with up to 20,000,000 gene-sized chromosomes. Previously, we have shown that these three classes also share elevated rates of protein evolution relative to other ciliates. To assess the evolution of germline-limited sequences in the class Phyllopharyngea, we used a combination of traditional and walking PCR to analyze micronuclear copies of multiple genes from two lines of the morphospecies Chilodonella uncinata for which we had previously characterized macronuclear sequences. Analyses of the resulting data yield three main results: 1) conserved macronuclear (somatic) regions are found within rapidly evolving micronuclear (germline) regions; 2) gene scrambling exists within this ciliate lineage; and 3) alternative processing of micronuclear regions yields diverse macronuclear β-tubulin paralogs. To our knowledge, this is the first study to demonstrate gene scrambling outside of the non-sister class Spirotrichea, and to show that alternative processing of scrambled genes generates diversity in gene families. Intriguingly, the Spirotrichea and Phyllopharyngea are also united in having transient 'giant' polytene chromosomes, gene-sized somatic chromosomes, and elevated rates of protein evolution. We hypothesize that this suite of characters enables these ciliates to enjoy the benefits of asexuality while still maintaining the ability to go through sexual cycles. The data presented here add to the growing evidence of the dynamic nature of eukaryotic genomes within diverse lineages across the tree of life.

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Most eukaryotic lineages are microbial, and many have only recently been sampled for phylogenetic studies or remain in the "dark area" of the tree of life where there are no molecular data. To assess relationships among eukaryotic lineages, we perform a taxon-rich phylogenomic analysis including 232 eukaryotes selected to maximize taxonomic diversity and up to 1554 genes chosen as vertically inherited based on their broad distribution among eukaryotes. We also include sequences from 486 bacteria and 84 archaea to assess the impact of endosymbiotic gene transfer (EGT) from plastids and to detect contamination. Overall, our analyses are consistent with other less taxon-rich estimates of the eukaryotic tree of life, and we recover strong support for five major clades: Amoebozoa, Excavata (without the genus Malawimonas), Opisthokonta, Archaeplastida, and SAR (Stramenopila, Alveolata, and Rhizaria). Our analyses also highlight the existence of "orphan" lineages, lineages that lack robust placement in the eukaryotic tree of life, and indicate the possibility of as yet undiscovered diversity. In analyses including bacteria and archaea, we find that approximately 10% of the 1554 genes, which we choose because they are found in four or five of the five major eukaryotic clades and hence may be more likely to be inherited vertically, appear to have been acquired from cyanobacteria through EGT in photosynthetic lineages. Removing these EGT genes places the green algae as sister to the glaucophytes instead of the red algae, suggesting that unknowingly including genes of plastid origin, and combining them with genes of nuclear origin, may mislead phylogenetic estimates. Finally, the large size of our data set allows comparative analyses of subsets of data; alignments built from randomly sampled sites provide greater support, particularly for deep relationships, than do equivalent-sized data sets built from randomly sampled genes.