The root of the eukaryote tree of life defines some of the most fundamental relationships among species. It is also critical for defining the last eukaryote common ancestor (LECA), the shared ...heritage of all extant species. The unikont-bikont root has been the reigning paradigm for eukaryotes for more than 10 years 1 but is becoming increasingly controversial 2–4. We developed a carefully vetted data set, consisting of 37 nuclear-encoded proteins of close bacterial ancestry (euBacs) and their closest bacterial relatives, augmented by deep sequencing of the Acrasis kona (Heterolobosea, Discoba) transcriptome. Phylogenetic analysis of these data produces a highly robust, fully resolved global phylogeny of eukaryotes. The tree sorts all examined eukaryotes into three megagroups and identifies the Discoba, and potentially its parent taxon Excavata 5, as the sister group to the bulk of known eukaryote diversity, the proposed Neozoa (Amorphea + Stramenopila+Alveolata+Rhizaria+Plantae SARP 6). All major alternative hypotheses are rejected with as little as ∼50% of the data, and this resolution is unaffected by the presence of fast-evolving alignment positions or distant outgroup sequences. This “neozoan-excavate” root revises hypotheses of early eukaryote evolution and highlights the importance of the poorly studied Discoba for understanding the evolution of eukaryotic diversity and basic cellular processes.
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•A new 37-protein data set produces a robust and rooted eukaryote tree•All examined eukaryotes form three megagroups: Amorphea, SARP, and Excavata•A new neozoan-excavate root is proposed with strong statistical support•Discoba (Excavata) has a long, unique, and largely unknown evolutionary history
He et al. developed a novel data set of 37 eukaryotic proteins of bacterial ancestry (euBacs) to explore the major radiations of eukaryotes. A neozoan-excavate root is found, with the little-known Discoba (and potentially its parent taxon Excavata) identified as sister group to the bulk of known eukaryote diversity.
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•Phylogenomic analyses of 147 proteins identify Rhizaria and Alveolata as sister taxa (R+A).•A relative measure is used to estimate extreme long branch (xLB) content across genes and ...taxa.•Removing xLB-rich genes increases support for R+A, suggesting this grouping is not a long branch attraction artifact.•Some of the highest xLB content in a broad taxonomic sampling of eukaryotes is found in ribosomal proteins.
Rhizaria is a major eukaryotic group of tremendous diversity, including amoebae with spectacular skeletons or tests (Radiolaria and Foraminifera), plasmodial parasites (Plasmodiophorida) and secondary endosymbionts (Chlorarachniophyta). Current phylogeny places Rhizaria in an unresolved trichotomy with Stramenopila and Alveolata (supergroup “SAR”). We assembled a 147-protein data set with extensive rhizarian coverage (M147), including the first transcriptomic data for a euglyphid amoeba. Phylogenetic pre-screening of individual proteins indicated potential problems with radically misplaced sequences due either to contamination of rhizarian sequences amplified from wild collected material and/or extremely long branches (xLBs). Therefore, two data subsets were extracted containing either all proteins consistently recovering rhizarian monophyly (M34) or excluding all proteins with ⩾3 xLBs (defined as ⩾2× the average terminal branch length for the tree). Phylogenetic analyses of M147 give conflicting results depending on the outgroup and method of analysis but strongly support an exclusive Rhizaria+Alveolata (R+A) clade with both data subsets (M34 and M37) regardless of phylogenetic method used. Support for an R+A clade is most consistent when a close outgroup is used and decreases with more distant outgroups, suggesting that support for alternative SAR topologies may reflect a long-branch attraction artifact. A survey of xLB distribution among taxa and protein functional category indicates that small “informational” proteins in particular have highly variable evolutionary rates with no consistent pattern among taxa.
Anthropogenic habitat disturbance is a major threat to tropical forests and understanding the ecological consequences of this disturbance is crucial for the conservation of biodiversity. There have ...been many attempts to determine the ecological traits associated with bird species' vulnerability to disturbance, but no attempt has been made to synthesize these studies to show consensus. We analyzed data from 57 published studies (covering 1214 bird species) that investigated the response of tropical bird assemblages to moderate forest disturbance (e.g., selective logging). Our results show that the mean abundance of species from six commonly reported feeding guilds responded differently to disturbance and that species' ecological traits (body size, local population size, and geographic range size) and evolutionary relationships may influence responses in some guilds. Granivore abundance increased significantly and insectivore and frugivore abundance decreased significantly following disturbance. These general conclusions were robust to the effects of ecological traits and phylogeny. Responses of carnivores, nectarivores, and omnivores were less clear, but analyses that accounted for phylogeny indicated that these guilds declined following disturbance. In contrast to the other guilds, the reported responses of carnivores and nectarivores differed among regions (Asia vs. Neotropics) and were influenced by the sampling protocols used in different studies (e.g., time since disturbance), which may explain the difficulty in detecting general responses to disturbance in these guilds. Overall, general patterns governed the responses of species to habitat disturbance, and the differential responses of guilds suggested that disturbance affects trophic organization and thus ecosystem functioning.
Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein ...trees. However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artifacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, whereas ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi, and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in undersampled lineages, whereas ConWin analyses of Discoba, the most undersampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa. CAT-GTR; Discoba; eukaryote tree of life; HGT; jackknife; mixture models; mosaic genes; phylogenomics; sliding window; supermatrix..
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Current understanding of the higher order systematics of eukaryotes relies largely on analyses of the small ribosomal subunit RNA (SSU rRNA). Independent testing of these results is still limited. We ...have combined the sequences of four of the most broadly taxonomically sampled proteins available to create a roughly parallel data set to that of SSU rRNA. The resulting phylogenetic tree shows a number of striking differences from SSU rRNA phylogeny, including strong support for most major groups and several major supergroups.
Phylogenetic trees seem to be finding ever broader applications, and researchers from very different backgrounds are becoming interested in what they might have to say. This tutorial aims to ...introduce the basics of building and interpreting phylogenetic trees. It is intended for those wanting to understand better what they are looking at when they look at someone else's trees or to begin learning how to build their own. Topics covered include: how to read a tree, assembling a dataset, multiple sequence alignment (how it works and when it does not), phylogenetic methods, bootstrap analysis and long-branch artefacts, and software and resources.
The social amoebas (Dictyostelia) display conditional multicellularity in a wide variety of forms. Despite widespread interest in Dictyostelium discoideum as a model system, almost no molecular data ...exist from the rest of the group. We constructed the first molecular phylogeny of the Dictyostelia with parallel small subunit ribosomal RNA and a-tubulin data sets, and we found that dictyostelid taxonomy requires complete revision. A mapping of characters onto the phylogeny shows that the dominant trend in dictyostelid evolution is increased size and cell type specialization of fruiting structures, with some complex morphologies evolving several times independently. Thus, the latter may be controlled by only a few genes, making their underlying mechanisms relatively easy to unravel.
Social Amoebae or Dictyostelia are eukaryotic microbes with a unique life cycle consisting of both uni- and multicellular stages. They have long fascinated molecular, developmental and evolutionary ...biologists, and Dictyostelium discoideum is now one of the most widely studied eukaryotic microbial models. The first molecular phylogeny of Dictyostelia included most of the species known at the time and suggested an extremely deep taxon with a molecular depth roughly equivalent to Metazoa. The group was also shown to consist of four major clades, none of which correspond to traditional genera. Potential morphological justification was identified for three of the four major groups, on the basis of which tentative names were assigned.
Over the past four years, the Mycetozoan Global Biodiversity Survey has identified many new isolates that appear to be new species of Dictyostelia, along with numerous isolates of previously described species. We have determined 18S ribosomal RNA gene sequences for all of these new isolates. Phylogenetic analyses of these data show at least 50 new species, and these arise from throughout the dictyostelid tree breaking up many previously isolated long branches. The resulting tree now shows eight well-supported major groups instead of the original four. The new species also expand the known morphological diversity of the previously established four major groups, violating nearly all previously suggested deep morphological patterns.
A greatly expanded phylogeny of Dictyostelia now shows even greater morphological plasticity at deep taxonomic levels. In fact, there now seem to be no obvious deep evolutionary trends across the group. However at a finer level, patterns in morphological character evolution are beginning to emerge. These results also suggest that there is a far greater diversity of Dictyostelia yet to be discovered, including novel morphologies.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Members of the eukaryote/archaea specific eRF1 and eRF3 protein families have central roles in translation termination. They are also central to various mRNA surveillance mechanisms, together with ...the eRF1 paralogue Dom34p and the eRF3 paralogues Hbs1p and Ski7p. We have examined the evolution of eRF1 and eRF3 families using sequence similarity searching, multiple sequence alignment and phylogenetic analysis.
Extensive BLAST searches confirm that Hbs1p and eRF3 are limited to eukaryotes, while Dom34p and eRF1 (a/eRF1) are universal in eukaryotes and archaea. Ski7p appears to be restricted to a subset of Saccharomyces species. Alignments show that Dom34p does not possess the characteristic class-1 RF minidomains GGQ, NIKS and YXCXXXF, in line with recent crystallographic analysis of Dom34p. Phylogenetic trees of the protein families allow us to reconstruct the evolution of mRNA surveillance mechanisms mediated by these proteins in eukaryotes and archaea.
We propose that the last common ancestor of eukaryotes and archaea possessed Dom34p-mediated no-go decay (NGD). This ancestral Dom34p may or may not have required a trGTPase, mostly like a/eEF1A, for its delivery to the ribosome. At an early stage in eukaryotic evolution, eEF1A was duplicated, giving rise to eRF3, which was recruited for translation termination, interacting with eRF1. eRF3 evolved nonsense-mediated decay (NMD) activity either before or after it was again duplicated, giving rise to Hbs1p, which we propose was recruited to assist eDom34p in eukaryotic NGD. Finally, a third duplication within ascomycete yeast gave rise to Ski7p, which may have become specialised for a subset of existing Hbs1p functions in non-stop decay (NSD). We suggest Ski7p-mediated NSD may be a specialised mechanism for counteracting the effects of increased stop codon read-through caused by prion-domain PSI+ mediated eRF3 precipitation.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The order Hymenoptera (bees, ants, wasps, sawflies) contains about eight percent of all described species, but no analytical studies have addressed the origins of this richness at family-level or ...above. To investigate which major subtaxa experienced significant shifts in diversification, we assembled a family-level phylogeny of the Hymenoptera using supertree methods. We used sister-group species-richness comparisons to infer the phylogenetic position of shifts in diversification.
The supertrees most supported by the underlying input trees are produced using matrix representation with compatibility (MRC) (from an all-in and a compartmentalised analysis). Whilst relationships at the tips of the tree tend to be well supported, those along the backbone of the tree (e.g. between Parasitica superfamilies) are generally not. Ten significant shifts in diversification (six positive and four negative) are found common to both MRC supertrees. The Apocrita (wasps, ants, bees) experienced a positive shift at their origin accounting for approximately 4,000 species. Within Apocrita other positive shifts include the Vespoidea (vespoid wasps/ants containing 24,000 spp.), Anthophila + Sphecidae (bees/thread-waisted wasps; 22,000 spp.), Bethylidae + Chrysididae (bethylid/cuckoo wasps; 5,200 spp.), Dryinidae (dryinid wasps; 1,100 spp.), and Proctotrupidae (proctotrupid wasps; 310 spp.). Four relatively species-poor families (Stenotritidae, Anaxyelidae, Blasticotomidae, Xyelidae) have undergone negative shifts. There are some two-way shifts in diversification where sister taxa have undergone shifts in opposite directions.
Our results suggest that numerous phylogenetically distinctive radiations contribute to the richness of large clades. They also suggest that evolutionary events restricting the subsequent richness of large clades are common. Problematic phylogenetic issues in the Hymenoptera are identified, relating especially to superfamily validity (e.g. "Proctotrupoidea", "Mymarommatoidea"), and deeper apocritan relationships. Our results should stimulate new functional studies on the causes of the diversification shifts we have identified. Possible drivers highlighted for specific adaptive radiations include key anatomical innovations, the exploitation of rich host groups, and associations with angiosperms. Low richness may have evolved as a result of geographical isolation, specialised ecological niches, and habitat loss or competition.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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