Origins of major archaeal clades correspond to gene acquisitions from bacteria
Shijulal Nelson-Sathi,Filipa L. Sousa,Mayo Roettger,Nabor Lozada-Chávez,Thorsten Thiergart,Arnold Janssen,David Bryant,Giddy Landan,Peter Schönheit,Bettina Siebers,James O. McInerney,William Martin +11 more
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TLDR
To investigate the origin of higher taxa in archaea, gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes are determined in the context of their homologues from 1,847 reference bacterial genomes.Abstract:
The mechanisms that underlie the origin of major prokaryotic groups are poorly understood In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxaread more
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Complex archaea that bridge the gap between prokaryotes and eukaryotes
Anja Spang,Jimmy H. Saw,Steffen Leth Jørgensen,Katarzyna Zaremba-Niedzwiedzka,Joran Martijn,Anders E. Lind,Roel van Eijk,Christa Schleper,Christa Schleper,Lionel Guy,Lionel Guy,Thijs J. G. Ettema +11 more
TL;DR: The discovery of ‘Lokiarchaeota’ is described, a novel candidate archaeal phylum which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eUKaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities.
Journal ArticleDOI
Horizontal gene transfer: building the web of life.
TL;DR: How HGT has shaped the web of life is described using examples of HGT among prokaryotes, between proKaryotes and eukaryote, and even between multicellular eukaries, to discuss replacement and additive HGT.
Journal ArticleDOI
The physiology and habitat of the last universal common ancestor
Madeline C. Weiss,Filipa L. Sousa,Natalia Mrnjavac,Sinje Neukirchen,Mayo Roettger,Shijulal Nelson-Sathi,William Martin +6 more
TL;DR: The data support the theory of an autotrophic origin of life involving the Wood–Ljungdahl pathway in a hydrothermal setting and identify clostridia and methanogens, whose modern lifestyles resemble that of LUCA, as basal among their respective domains.
Journal ArticleDOI
Synthesis of phylogeny and taxonomy into a comprehensive tree of life
Cody E. Hinchliff,Stephen A. Smith,James F. Allman,J. Gordon Burleigh,Ruchi Chaudhary,Lyndon M. Coghill,Keith A. Crandall,Jiabin Deng,Bryan T. Drew,Romina Gazis,Karl Gude,David S. Hibbett,Laura A. Katz,H. Dail Laughinghouse,Emily Jane McTavish,Peter E. Midford,Christopher L. Owen,Richard H. Ree,Jonathan Rees,Douglas E. Soltis,Tiffani L. Williams,Karen Cranston +21 more
TL;DR: This study is the first, to the knowledge, to apply an efficient and automated process for assembling published trees into a complete tree of life, and presents a draft tree containing 2.3 million tips—the Open Tree of Life.
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Evolution by gene loss
Ricard Albalat,Cristian Cañestro +1 more
TL;DR: These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
References
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