Archaea: The First Domain of Diversified Life

The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston’s generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.

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A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

BMC Ecology and Evolution ◽

10.1186/s12862-021-01952-0 ◽

2022 ◽

Vol 22 (1) ◽

Author(s):

Monique Aouad ◽

Jean-Pierre Flandrois ◽

Frédéric Jauffrit ◽

Manolo Gouy ◽

Simonetta Gribaldo ◽

...

Keyword(s):

Phylogenetic Signal ◽

Single Gene ◽

Tree Of Life ◽

Divide And Conquer ◽

Data Sets ◽

Gene Trees ◽

Tree Reconstruction ◽

Taxonomic Rank ◽

Domains Of Life ◽

Origin Of Eukaryotes

Abstract Background The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal. Results We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study. Conclusions We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.

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The role of public goods in planetary evolution

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2016.0359 ◽

2017 ◽

Vol 375 (2109) ◽

pp. 20160359 ◽

Cited By ~ 4

Author(s):

James O. McInerney ◽

Douglas H. Erwin

Keyword(s):

Public Goods ◽

Phylogenetic Signal ◽

Eukaryotic Cell ◽

Early History ◽

Evolutionary Transition ◽

Direct Graph ◽

Planetary Evolution ◽

History Of ◽

Life On Earth

Biological public goods are broadly shared within an ecosystem and readily available. They appear to be widespread and may have played important roles in the history of life on Earth. Of particular importance to events in the early history of life are the roles of public goods in the merging of genomes, protein domains and even cells. We suggest that public goods facilitated the origin of the eukaryotic cell, a classic major evolutionary transition. The recognition of genomic public goods challenges advocates of a direct graph view of phylogeny, and those who deny that any useful phylogenetic signal persists in modern genomes. Ecological spillovers generate public goods that provide new ecological opportunities. This article is part of the themed issue ‘Reconceptualizing the origins of life’.

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Indagando aspectos evolutivos con filogenias: reloj molecular y otras técnicas útiles en biología comparada

Tequio ◽

10.53331/teq.v4i11.3158 ◽

2021 ◽

Vol 4 (11) ◽

pp. 53-68

Author(s):

Carlos Luis Leopardi-Verde ◽

Guadalupe Jeanett Escobedo-Sarti

Keyword(s):

Principal Component Analysis ◽

Molecular Clock ◽

Phylogenetic Signal ◽

Principal Component ◽

Study Group ◽

Signal Estimation ◽

Independent Contrasts ◽

Wide Range ◽

Evolutionary Studies ◽

Phylogenetic Framework

The first step for evolutionary studies is usually to establish a hypothesis of relationships between members of the study group. After this, there is a wide range of possibilities depending on the researcher's interest. This contribution presents the generalities of some of the methodologies most commonly used in macroevolutionary studies: the molecular clock and the reconstruction of ancestral characters. Information on other useful techniques for comparative studies that use a phylogenetic framework is also presented, such as phylogenetic signal estimation, independent contrasts, orthonormal decomposition, and phylogenetic principal component analysis.

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Linking Leaf Spectra to the Plant Tree of Life

Remote Sensing of Plant Biodiversity ◽

10.1007/978-3-030-33157-3_7 ◽

2020 ◽

pp. 155-172 ◽

Cited By ~ 1

Author(s):

José Eduardo Meireles ◽

Brian O’Meara ◽

Jeannine Cavender-Bares

Keyword(s):

Spectral Reflectance ◽

Biological Diversity ◽

Phylogenetic Signal ◽

Tree Of Life ◽

Evolutionary Trees ◽

Form And Function ◽

History Of ◽

Leaf Evolution ◽

Plant Form ◽

And Function

AbstractEvolutionary trees recount the history of how biological diversity came to be and how evolution gave rise to the incredible variation in plant form and function that can be captured by spectral reflectance. Understanding plant spectra in light of evolution is thus important for assessing biodiversity and critical for explaining how spectral diversity is generated. Here, we focus on leaf spectra and how they are linked to the plant tree of life. We review what evolutionary trees (phylogenies) are and how to interpret them. We then describe how to model the evolution of quantitative traits, discuss which evolutionary processes are involved, and explain specific concepts and metrics, such as phylogenetic signal and evolutionary rates, and how they can be applied to reflectance spectra. Next, we describe a framework that links phylogenies and leaf spectra by coupling models of evolution and radiative transfer models. In doing so, we review some of the challenges of subjecting spectra to evolutionary analyses. We then discuss how spectra can help us to understand leaf evolution and to differentiate plant taxa at different phylogenetic scales from populations to lineages, advancing our potential to remotely detect biodiversity.

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Some early history of replica techniques for electron microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100130018 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1076-1077

Author(s):

Robert M. Fisher

Keyword(s):

Thin Film ◽

Electron Microscopy ◽

Optical Microscope ◽

Early History ◽

Bulk Materials ◽

Thin Sections ◽

Transmission Electron ◽

Reflected Light ◽

History Of ◽

Electron Microscopes

By 1940, a half dozen or so commercial or home-built transmission electron microscopes were in use for studies of the ultrastructure of matter. These operated at 30-60 kV and most pioneering microscopists were preoccupied with their search for electron transparent substrates to support dispersions of particulates or bacteria for TEM examination and did not contemplate studies of bulk materials. Metallurgist H. Mahl and other physical scientists, accustomed to examining etched, deformed or machined specimens by reflected light in the optical microscope, were also highly motivated to capitalize on the superior resolution of the electron microscope. Mahl originated several methods of preparing thin oxide or lacquer impressions of surfaces that were transparent in his 50 kV TEM. The utility of replication was recognized immediately and many variations on the theme, including two-step negative-positive replicas, soon appeared. Intense development of replica techniques slowed after 1955 but important advances still occur. The availability of 100 kV instruments, advent of thin film methods for metals and ceramics and microtoming of thin sections for biological specimens largely eliminated any need to resort to replicas.

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