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Evolutionary Biology

Section edited by Fyodor Kondrashov and Puri Lopez-Garcia

This section aims to yield an integrative and interdisciplinary view of evolution. Suitable research directions include molecular and mechanistic aspects of evolution as well as studies focusing on the evolutionary process, such as phylogenetic patterns and relationships. Conceptual, experimental and theoretical studies are equally appreciated as long as the central research direction is any aspect of evolution. Evolutionary hypotheses are welcome as long as they are based on the most rigorous scientific standards.

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  1. Content type: Research

    Determining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic...

    Authors: Begoña Dobon, Ludovica Montanucci, Juli Peretó, Jaume Bertranpetit and Hafid Laayouni

    Citation: Biology Direct 2019 14:17

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  2. Content type: Commentary

    A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mit...

    Authors: Michael Lynch and Georgi K. Marinov

    Citation: Biology Direct 2018 13:26

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    The Comment to this article has been published in Biology Direct 2018 13:21

  3. Content type: Research

    The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteri...

    Authors: Dino Osmanovic, David A. Kessler, Yitzhak Rabin and Yoav Soen

    Citation: Biology Direct 2018 13:24

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  4. Content type: Comment

    The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondr...

    Authors: Marie Gerlitz, Michael Knopp, Nils Kapust, Joana C. Xavier and William F. Martin

    Citation: Biology Direct 2018 13:21

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    The Commentary to this article has been published in Biology Direct 2018 13:26

  5. Content type: Opinion

    Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic ...

    Authors: Eugene V. Koonin, Yuri I. Wolf and Mikhail I. Katsnelson

    Citation: Biology Direct 2017 12:31

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  6. Content type: Research

    During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present...

    Authors: Güleycan Lutfullahoğlu-Bal, Abdurrahman Keskin, Ayşe Bengisu Seferoğlu and Cory D. Dunn

    Citation: Biology Direct 2017 12:16

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  7. Content type: Research

    Acanthamoebidae is a “family” level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the ...

    Authors: Alexander K. Tice, Lora L. Shadwick, Anna Maria Fiore-Donno, Stefan Geisen, Seungho Kang, Gabriel A. Schuler, Frederick W. Spiegel, Katherine A. Wilkinson, Michael Bonkowski, Kenneth Dumack, Daniel J. G. Lahr, Eckhard Voelcker, Steffen Clauß, Junling Zhang and Matthew W. Brown

    Citation: Biology Direct 2016 11:69

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  8. Content type: Research

    The Tim17 family of proteins plays a fundamental role in the biogenesis of mitochondria. Three Tim17 family proteins, Tim17, Tim22, and Tim23, are the central components of the widely conserved multi-subunit p...

    Authors: Vojtěch Žárský and Pavel Doležal

    Citation: Biology Direct 2016 11:54

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  9. Content type: Research

    Evolutionary game theory (EGT) has been widely used to simulate tumour processes. In almost all studies on EGT models analysis is limited to two or three phenotypes. Our model contains four main phenotypes. Mo...

    Authors: Andrzej Świerniak and Michał Krześlak

    Citation: Biology Direct 2016 11:53

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  10. Content type: Comment

    Although biology has achieved great successes in recent years, we have not got a clear idea on “what is life?” Actually, as explained here, the main reason for this situation is that there are two completely d...

    Authors: Wentao Ma

    Citation: Biology Direct 2016 11:49

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  11. Content type: Hypothesis

    Species-rich adaptive radiations arising from rare plant and animal colonizers are common on remote volcanic archipelagoes. However, they present a paradox. The severe genetic bottleneck of founder events and ...

    Authors: Elysse M. Craddock

    Citation: Biology Direct 2016 11:44

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  12. Content type: Review

    For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have per...

    Authors: Johann-Mattis List, Jananan Sylvestre Pathmanathan, Philippe Lopez and Eric Bapteste

    Citation: Biology Direct 2016 11:39

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  13. Content type: Research

    The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomy...

    Authors: Sandrine Pinos, Pierre Pontarotti, Didier Raoult, Jean Pierre Baudoin and Isabelle Pagnier

    Citation: Biology Direct 2016 11:38

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  14. Content type: Discovery notes

    Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α p...

    Authors: Mauro Degli Esposti, Diego Cortez, Luis Lozano, Simon Rasmussen, Henrik Bjørn Nielsen and Esperanza Martinez Romero

    Citation: Biology Direct 2016 11:34

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  15. Content type: Research

    While commonly assumed in the biochemistry community that the control of metabolic pathways is thought to be critical to cellular function, it is unclear if metabolic pathways generally have evolutionarily sta...

    Authors: Alena Orlenko, Ashley I. Teufel, Peter B. Chi and David A. Liberles

    Citation: Biology Direct 2016 11:31

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  16. Content type: Hypothesis

    The discovery of the viroid in 1971, which initiated the third major expansion of the biosphere towards smaller living entities—after discovery of the “subvisual” microorganisms in 1675 and that of the “submic...

    Authors: Theodor O. Diener

    Citation: Biology Direct 2016 11:15

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  17. Content type: Research

    The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have sh...

    Authors: Daniel A. Power, Richard A. Watson, Eörs Szathmáry, Rob Mills, Simon T. Powers, C. Patrick Doncaster and BłaŻej Czapp

    Citation: Biology Direct 2015 10:69

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    The Erratum to this article has been published in Biology Direct 2016 11:29

  18. Content type: Discovery notes

    Many proteins of viruses infecting hyperthermophilic Crenarchaeota have no detectable homologs in current databases, hampering our understanding of viral evolution. We used sensitive database search methods an...

    Authors: Mart Krupovic, Virginija Cvirkaite-Krupovic, David Prangishvili and Eugene V. Koonin

    Citation: Biology Direct 2015 10:65

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  19. Content type: Research

    The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalow...

    Authors: Avigdor Beiles, Shmuel Raz, Yuval Ben-Abu and Eviatar Nevo

    Citation: Biology Direct 2015 10:58

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  20. Content type: Research

    Transposable elements (TEs) play an important role in genome function and evolution. It has been shown that TEs are a considerable source of adaptive changes in the genome of Drosophila melanogaster. Specifically...

    Authors: Josefa González, Jose Martínez and Wojciech Makalowski

    Citation: Biology Direct 2015 10:50

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  21. Content type: Discovery notes

    The interaction between the ribosome and the endoplasmic reticulum-located Sec61 protein translocon is mediated through an arginine residue of Sec61α, which is conserved in all prokaryotic and eukaryotic ortho...

    Authors: Abhishek Sinha, Atrayee Ray, Sandipan Ganguly, Shubhra Ghosh Dastidar and Srimonti Sarkar

    Citation: Biology Direct 2015 10:56

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  22. Content type: Research

    Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the...

    Authors: Alexander V. Badyaev, Erin S. Morrison, Virginia Belloni and Michael J. Sanderson

    Citation: Biology Direct 2015 10:45

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  23. Content type: Comment

    “Which came first, the Chicken or the Egg?” We suggest this question is not a paradox. The Modern Synthesis envisions speciation through genetic changes in germ cells via random mutations, an “Egg first” scena...

    Authors: Yitzhak Pilpel and Oded Rechavi

    Citation: Biology Direct 2015 10:34

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  24. Content type: Hypothesis

    Fundamental problems faced by the protocells and their modern descendants include how to go from one phenotypic state to another; escape from a basin of attraction in the space of phenotypes; reconcile conflic...

    Authors: Vic Norris, Rosetta N Reusch, Kazuei Igarashi and Robert Root-Bernstein

    Citation: Biology Direct 2014 10:28

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  25. Content type: Research

    Internalization-based hypotheses of eukaryotic origin require close physical association of host and symbiont. Prior hypotheses of how these associations arose include chance, specific metabolic couplings betw...

    Authors: Scott L Hooper and Helaine J Burstein

    Citation: Biology Direct 2014 9:24

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    The Erratum to this article has been published in Biology Direct 2015 10:11

  26. Content type: Discovery notes

    Through the course of their evolution, viruses with large genomes have acquired numerous host genes, most of which perform function in virus reproduction in a manner that is related to their original activitie...

    Authors: Natalya Yutin, Guilhem Faure, Eugene V Koonin and Arcady R Mushegian

    Citation: Biology Direct 2014 9:22

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