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"Tree of life"

Zackary J Jay, Jacob P Beam, Mensur Dlakić, Douglas B Rusch, Mark A Kozubal, William P Inskeep
The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and characterization of a phylum-level archaeal lineage proposed and herein referred to as the 'Marsarchaeota', after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50-80 °C...
May 14, 2018: Nature Microbiology
Alexandre Antonelli, Alexander Zizka, Fernanda Antunes Carvalho, Ruud Scharn, Christine D Bacon, Daniele Silvestro, Fabien L Condamine
The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
(no author information available yet)
No abstract text is available yet for this article.
2018: PloS One
Stephen A Smith, Joseph W Brown
PREMISE OF THE STUDY: Large phylogenies can help shed light on macroevolutionary patterns that inform our understanding of fundamental processes that shape the tree of life. These phylogenies also serve as tools that facilitate other systematic, evolutionary, and ecological analyses. Here we combine genetic data from public repositories (GenBank) with phylogenetic data (Open Tree of Life project) to construct a dated phylogeny for seed plants. METHODS: We conducted a hierarchical clustering analysis of publicly available molecular data for major clades within the Spermatophyta...
March 2018: American Journal of Botany
James B Pease, Joseph W Brown, Joseph F Walker, Cody E Hinchliff, Stephen A Smith
PREMISE OF THE STUDY: Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative. METHODS: We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches...
March 2018: American Journal of Botany
Jeremy M Beaulieu, Brian C O'Meara
PREMISE OF THE STUDY: The study of very large and very old clades holds the promise of greater insights into evolution across the tree of life. However, there has been a fair amount of criticism regarding the interpretations and quality of studies to date, with some suggesting that detailed studies carried out on smaller, tractable scales should be preferred over the increasingly grand syntheses of these data. METHODS: We provided in detail our trials and tribulations of compiling a large, sparsely sampled matrix from GenBank data and inferring a well-supported, time-calibrated phylogeny of Campanulidae...
March 2018: American Journal of Botany
Rosana Zenil-Ferguson, J Gordon Burleigh, José Miguel Ponciano
Premise of the Study: Polyploidy has profound evolutionary consequences for land plants. Despite the availability of large phylogenetic and chromosomal data sets, estimating the rates of polyploidy and chromosomal evolution across the tree of life remains a challenging, computationally complex problem. We introduce the R package chromploid, which allows scientists to perform inference of chromosomal evolution rates across large phylogenetic trees. Methods and Results: chromploid is an open-source package in the R environment that calculates the likelihood function of models of chromosome evolution...
March 2018: Applications in Plant Sciences
Mohammad Vatanparast, Adrian Powell, Jeff J Doyle, Ashley N Egan
Premise of the Study: The development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts. Methods: Using 30 transcriptomes, we compared Hyb-Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation- and coalescent-based methods...
March 2018: Applications in Plant Sciences
Lorena Endara, Hong Cui, J Gordon Burleigh
Premise of the Study: Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms...
March 2018: Applications in Plant Sciences
Hilary A McManus, Karolina Fučíková, Paul O Lewis, Louise A Lewis, Kenneth G Karol
PREMISE OF THE STUDY: Phylogenomic analyses across the green algae are resolving relationships at the class, order, and family levels and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. METHODS: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using next-generation sequencing methods...
May 3, 2018: American Journal of Botany
Tim Janicke, Michael G Ritchie, Edward H Morrow, Lucas Marie-Orleach
Our improving knowledge of the animal tree of life consistently demonstrates that some taxa diversify more rapidly than others, but what contributes to this variation remains poorly understood. An influential hypothesis proposes that selection arising from competition for mating partners plays a key role in promoting speciation. However, empirical evidence showing a link between proxies of this sexual selection and species richness is equivocal. Here, we collected standardized metrics of sexual selection for a broad range of animal taxa, and found that taxonomic families characterized by stronger sexual selection on males show relatively higher species richness...
May 16, 2018: Proceedings. Biological Sciences
Makio Yokono, Soichirou Satoh, Ayumi Tanaka
Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are different than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method...
May 1, 2018: Scientific Reports
Fernando Rodriguez, Irina R Arkhipova
Polyploidy in animals is much less common than in plants, where it is thought to be pervasive in all higher plant lineages. Recent studies have highlighted the impact of polyploidization and the associated process of diploidy restoration on the evolution and speciation of selected taxonomic groups in the animal kingdom: from vertebrates represented by salmonid fishes and African clawed frogs to invertebrates represented by parasitic root-knot nematodes and bdelloid rotifers. In this review, we focus on the unique and diverse roles that transposable elements may play in these processes, from marking and diversifying subgenome-specific chromosome sets before hybridization, to influencing genome restructuring during rediploidization, to affecting subgenome-specific regulatory evolution, and occasionally providing opportunities for domestication and gene amplification to restore and improve functionality...
April 28, 2018: Current Opinion in Genetics & Development
L Lacey Knowles, Huateng Huang, Jeet Sukumaran, Stephen A Smith
PREMISE OF THE STUDY: Discordant gene trees are commonly encountered when sequences from thousands of loci are applied to estimate phylogenetic relationships. Several processes contribute to this discord. Yet, we have no methods that jointly model different sources of conflict when estimating phylogenies. An alternative to analyzing entire genomes or all the sequenced loci is to identify a subset of loci for phylogenetic analysis. If we can identify data partitions that are most likely to reflect descent from a common ancestor (i...
April 30, 2018: American Journal of Botany
Rosa Fernández, Robert J Kallal, Dimitar Dimitrov, Jesús A Ballesteros, Miquel A Arnedo, Gonzalo Giribet, Gustavo Hormiga
Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic...
April 21, 2018: Current Biology: CB
Douglas E Soltis, Michael J Moore, Emily B Sessa, Stephen A Smith, Pamela S Soltis
No abstract text is available yet for this article.
April 27, 2018: American Journal of Botany
Wenpan Dong, Chao Xu, Ping Wu, Tao Cheng, Jing Yu, Shiliang Zhou, De-Yuan Hong
Accurately resolving the phylogeny of enigmatic taxa is always a challenge in phylogenetic inference. Such uncertainties could be due to systematic errors or model violations. Here, we provide an example demonstrating how these factors affect the positioning of Paeoniaceae within Saxifragales based on chloroplast genome data. We newly assembled 14 chloroplast genomes from Saxifragales, and by combining these genomes with those of 63 other angiosperms, three datasets were assembled to test different hypotheses proposed by recent studies...
April 24, 2018: Molecular Phylogenetics and Evolution
Alex Dornburg, Dan L Warren, Katerina L Zapfe, Richard Morris, Teresa L Iglesias, April Lamb, Gabriela Hogue, Laura Lukas, Richard Wong
Trade-offs associated with sexual size dimorphism (SSD) are well documented across the Tree of Life. However, studies of SSD often do not consider potential investment trade-offs between metabolically expensive structures under sexual selection and other morphological modules. Based on the expectations of the expensive tissue hypothesis, investment in one metabolically expensive structure should come at the direct cost of investment in another. Here, we examine allometric trends in the ontogeny of oyster toadfish ( Opsanus tau ) to test whether investment in structures known to have been influenced by strong sexual selection conform to these expectations...
April 2018: Ecology and Evolution
Catarina Nabais, Sónia Gomes Pereira, Mónica Bettencourt-Dias
Centrioles and basal bodies (CBBs) organize centrosomes and cilia within eukaryotic cells. These organelles are composed of microtubules and hundreds of proteins performing multiple functions such as signaling, cytoskeleton remodeling, and cell motility. The CBB is present in all branches of the eukaryotic tree of life and, despite its ultrastructural and protein conservation, there is diversity in its function, occurrence (i.e., presence/absence), and modes of biogenesis across species. In this review, we provide an overview of the multiple pathways through which CBBs are formed in nature, with a special focus on the less studied, noncanonical ways...
April 23, 2018: Cold Spring Harbor Symposia on Quantitative Biology
Ryan A Folk, Pamela S Soltis, Douglas E Soltis, Robert Guralnick
Assessing the relative importance of the various pathways to diversification is a central goal of biodiversity researchers. For plant biologists, and increasingly across the spectrum of biological sciences, among these pathways of interest is hybridization. New methodological developments are moving the field away from questions of whether natural hybridization occurs or hybrids can persist and toward more direct assessments of the long-term impact of hybridization on diversification and genome organization...
February 14, 2018: American Journal of Botany
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