ALBERT

Description: The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: approximately 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, approximately 3.5 x 10(9) yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Povolotskaya, Inna S -- Kondrashov, Fyodor A -- England -- Nature. 2010 Jun 17;465(7300):922-6. doi: 10.1038/nature09105. Epub 2010 May 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Calle Dr Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20485343" target="_blank"〉PubMed〈/a〉

Description: The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337882/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337882/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moroz, Leonid L -- Kocot, Kevin M -- Citarella, Mathew R -- Dosung, Sohn -- Norekian, Tigran P -- Povolotskaya, Inna S -- Grigorenko, Anastasia P -- Dailey, Christopher -- Berezikov, Eugene -- Buckley, Katherine M -- Ptitsyn, Andrey -- Reshetov, Denis -- Mukherjee, Krishanu -- Moroz, Tatiana P -- Bobkova, Yelena -- Yu, Fahong -- Kapitonov, Vladimir V -- Jurka, Jerzy -- Bobkov, Yuri V -- Swore, Joshua J -- Girardo, David O -- Fodor, Alexander -- Gusev, Fedor -- Sanford, Rachel -- Bruders, Rebecca -- Kittler, Ellen -- Mills, Claudia E -- Rast, Jonathan P -- Derelle, Romain -- Solovyev, Victor V -- Kondrashov, Fyodor A -- Swalla, Billie J -- Sweedler, Jonathan V -- Rogaev, Evgeny I -- Halanych, Kenneth M -- Kohn, Andrea B -- 1R01GM097502/GM/NIGMS NIH HHS/ -- 1S10RR027052/RR/NCRR NIH HHS/ -- 55007424/Howard Hughes Medical Institute/ -- 5R21DA030118/DA/NIDA NIH HHS/ -- P30 DA018310/DA/NIDA NIH HHS/ -- R01 AG029360/AG/NIA NIH HHS/ -- R01 GM097502/GM/NIGMS NIH HHS/ -- R01 MH097062/MH/NIMH NIH HHS/ -- R01MH097062/MH/NIMH NIH HHS/ -- R21 DA030118/DA/NIDA NIH HHS/ -- R21 RR025699/RR/NCRR NIH HHS/ -- R21RR025699/RR/NCRR NIH HHS/ -- S10 RR027052/RR/NCRR NIH HHS/ -- England -- Nature. 2014 Jun 5;510(7503):109-14. doi: 10.1038/nature13400. Epub 2014 May 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, Florida 32080, USA [2] Department of Neuroscience & McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, USA [3] Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington 98250, USA. ; Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences, Auburn, Alabama 36849, USA. ; The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, Florida 32080, USA. ; 1] The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, Florida 32080, USA [2] Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington 98250, USA. ; 1] Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain. ; 1] Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, 303 Belmont Street, Worcester, Massachusetts 01604, USA [2] Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Gubkina 3, Moscow 119991, Russia. ; Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA. ; European Research Institute for the Biology of Ageing, University of Groningen Medical Center, Antonius Deusinglaan 1, Building 3226, Room 03.34, 9713 AV Groningen, The Netherlands. ; Department of Medical Biophysics and Department of Immunology, University of Toronto, Sunnybrook Research Institute 2075 Bayview Avenue, Toronto, Ontario M4N 3M5, Canada. ; Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Gubkina 3, Moscow 119991, Russia. ; Department of Neuroscience & McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, USA. ; Genetic Information Research Institute, 1925 Landings Dr., Mountain View, California 94043, USA. ; Program in Molecular Medicine, University of Massachusetts Medical School, 222 Maple Avenue, Shrewsbury, Massachusetts 01545, USA. ; Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington 98250, USA. ; Department of Computer Science, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK. ; 1] Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain [3] Institucio Catalana de Recerca i Estudis Avancats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain. ; 1] Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, 303 Belmont Street, Worcester, Massachusetts 01604, USA [2] Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Gubkina 3, Moscow 119991, Russia [3] Center for Brain Neurobiology and Neurogenetics and Institute of Cytology and Genetics, RAS, Lavrentyev Avenue, 10, Novosibirsk 630090, Russia [4] Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, 119991 Moscow, Russia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24847885" target="_blank"〉PubMed〈/a〉

Description: The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.

Description: The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.