A new analysis aims to uncover the root of the bacterial tree of life
The ability to sequence genes and, more recently, whole genomes has transformed our understanding of the tree of life by ...elucidating the tremendous diversity of microorganisms and by placing plants, animals, and fungi as branches nested among microbial lineages (
1
–
3
). The resulting evolutionary tree divides life into three domains: the exclusively microbial Bacteria and Archaea, and Eukarya, organisms whose cells contain nuclei (including ciliates, amoebae, and animals). Yet, the ordering of the earliest branching events on the tree and the nature of now-extinct ancestors remains unclear. On page 588 of this issue, Coleman
et al.
(
4
) provide a new estimate of the root of the bacterial tree of life, that is, the ancestor from which all bacterial species are derived. Knowledge of the root of the bacterial tree is important because it defines the evolutionary starting point for the tremendous diversity of Bacteria and offers glimpses into the nature of the first bacterial cells.
Many species of plants have evolved structures called phytotelmata that store water and trap detritus and prey. These structures house diverse communities of organisms, the inquiline microbiome, that ...aids breakdown of litter and prey. The invertebrate and bacterial food webs in these systems are well characterized, but less is known about microbial eukaryotic community dynamics. In this study we focus on microbes in the SAR clade (Stramenopila, Alveolata, Rhizaria) inhabiting phytotelmata. Using small subunit rDNA amplicon sequencing from repeated temporal and geographic samples of wild and cultivated plants across the Northeast U.S.A., we demonstrate that communities are variable within and between host plant type. Across habitats, communities from tropical bromeliads grown in a single room of a greenhouse were nearly as heterogeneous as wild pitcher plants spread across hundreds of kilometers. At the scale of pitcher plants in a single bog, analyses of samples from three time points suggest that seasonality is a major driver of protist community structure, with variable spring communities transitioning to more homogeneous communities that resemble the surrounding habitat. Our results indicate that protist communities in phytotelmata are variable, likely due to stochastic founder events and colonization/competition dynamics, leading to tremendous heterogeneity in inquiline microeukaryotic communities.
Although macroscopic plants, animals, and fungi are the most familiar eukaryotes, the bulk of eukaryotic diversity is microbial. Elucidating the timing of diversification among the more than 70 ...lineages is key to understanding the evolution of eukaryotes. Here, we use taxon-rich multigene data combined with diverse fossils and a relaxed molecular clock framework to estimate the timing of the last common ancestor of extant eukaryotes and the divergence of major clades. Overall, these analyses suggest that the last common ancestor lived between 1866 and 1679 Ma, consistent with the earliest microfossils interpreted with confidence as eukaryotic. During this interval, the Earth's surface differed markedly from today; for example, the oceans were incompletely ventilated, with ferruginous and, after about 1800 Ma, sulfidic water masses commonly lying beneath moderately oxygenated surface waters. Our time estimates also indicate that the major clades of eukaryotes diverged before 1000 Ma, with most or all probably diverging before 1200 Ma. Fossils, however, suggest that diversity within major extant clades expanded later, beginning about 800 Ma, when the oceans began their transition to a more modern chemical state. In combination, paleontological and molecular approaches indicate that long stems preceded diversification in the major eukaryotic lineages.
The first book to comprehensively address private equity and health care, Ethically Challenged raises the curtain on an industry notorious for its secrecy, exposing the nefarious side of its ...maneuvers.
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•A taxon-rich phylogenomic strategy was used to assess the evolutionary relationships within ciliates.•537 taxa combined with a moderate number of proteins were accessed from GenBank ...and recently released transcriptome data.•Full data matrix as well as six submatrices were analyzed to assess the impact of taxon sampling and missing data.•The multigene phylogenies support the bifurcation of ciliates into two major clades as suggested by SSU-rDNA.
Ciliates are a diverse assemblage of eukaryotes that have been the source of many discoveries including self-splicing RNAs, telomeres and trans-splicing. While analyses of ciliate morphology have given rise to robust hypotheses on relatively shallow level relationships, the deeper evolutionary history of ciliates is largely unknown. This is in part because studies to date have focused on only a single locus, small subunit ribosomal DNA (SSU-rDNA). In the present study, we use a taxon-rich strategy based on multiple loci from GenBank and recently completed transcriptomes to assess deep phylogenetic relationships among ciliates. Our phylogenomic data set includes up to 537 taxa, all of which have been sampled for SSU-rDNA and a subset of which have LSU-rDNA and up to 7 protein-coding sequences. Analyses of these data support the bifurcation of ciliates as suggested by SSU-rDNA, with one major clade defined by having somatic macronuclei that divide with intranuclear microtubules (Intramacronucleata) and the other clade containing lineages that either divide their macronuclei with microtubules external to the macronucleus or are unable to divide their macronuclei (Postciliodesmatophora). These multigene phylogenies provide a robust framework for interpreting the evolution of innovations across the ciliate tree of life.
The bulk of the diversity of eukaryotic life is microbial. Although the larger eukaryotes-namely plants, animals, and fungi-dominate our visual landscapes, microbial lineages compose the greater part ...of both genetic diversity and biomass, and contain many evolutionary innovations. Our understanding of the origin and diversification of eukaryotes has improved substantially with analyses of molecular data from diverse lineages. These data have provided insight into the nature of the genome of the last eukaryotic common ancestor (LECA). Yet, the origin of key eukaryotic features, namely the nucleus and cytoskeleton, remains poorly understood. In contrast, the past decades have seen considerable refinement in hypotheses on the major branching events in the evolution of eukaryotic diversity. New insights have also emerged, including evidence for the acquisition of mitochondria at the time of the origin of eukaryotes and data supporting the dynamic nature of genomes in LECA.
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: (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.
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•Thirty seven sequences for three genes are characterized from 21 taxa of Pleuronematida and Loxocephalida.•BI and ML trees are constructed to assess the relationships of ...Pleuronematida and Loxocephalida.•AU tests are performed to test the hypothesis of morphology-based classifications.•Secondary structures of ITS2 and V4 region of the SSU-rDNA are predicted.•Some conclusions are drawn by comparison among gene trees and morphological systems.
Relationships among members of the ciliate subclass Scuticociliatia (Ciliophora, Oligohymenophorea) are largely unresolved. Phylogenetic studies of its orders Pleuronematida and Loxocephalida were initially based on small subunit ribosomal RNA gene (SSU-rDNA) analyses of a limited number of taxa. Here we characterized 37 sequences (SSU-rDNA, ITS-5.8S and LSU-rDNA) from 21 taxonomically controversial members of these orders. Phylogenetic trees constructed to assess the inter- and intra-generic relationships of pleuronematids and loxocephalids reveal the following: (1) the order Loxocephalida and its two families Loxocephalidae and Cinetochilidae are not monophyletic when more taxa are added; (2) the core pleuronematids are divided into two fully supported clades, however, the order Pleuronematida is not monophyletic because Cyclidium glaucoma is closer to Thigmotrichida; (3) the family Pleuronematidae and the genus Schizocalyptra are monophyletic, though rDNA sequences of Pleuronema species are highly variable; (4) Pseudoplatynematum and Sathrophilus are closely related to the subclass Astomatia, while Cinetochilum forms a monophyletic group with the subclass Apostomatia; and (5) Hippocomos falls in the order Pleuronematida and is closely related to Eurystomatellidae and Cyclidium plouneouri. Further, in an effort to provide a better resolution of evolutionary relationships, the secondary structures of ITS2 transcripts and the variable region 4 (V4) of the small subunit ribosomal RNA (SSU-rRNA) are predicted, revealing that ITS2 structures are conserved at the order level while V4 region structures are more variable than ITS2 structures.
While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of ...interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.
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