1
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Timasheva Y, Lepik K, Liska O, Papp B, Kutalik Z. Widespread natural selection on metabolite levels in humans. Genome Res 2024; 34:1121-1129. [PMID: 39152035 PMCID: PMC11444169 DOI: 10.1101/gr.278756.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 08/08/2024] [Indexed: 08/19/2024]
Abstract
Natural selection acts ubiquitously on complex human traits, predominantly constraining the occurrence of extreme phenotypes (stabilizing selection). These constraints propagate to DNA sequence variants associated with traits under selection. The genetic signatures of such evolutionary events can thus be detected via combining effect size estimates from genetic association studies and the corresponding allele frequencies. Although this approach has been successfully applied to high-level traits, the prevalence and mode of selection acting on molecular traits remain poorly understood. Here, we estimate the action of natural selection on genetic variants associated with metabolite levels, an important layer of molecular traits. By leveraging summary statistics of published genome-wide association studies with large sample sizes, we find strong evidence of stabilizing selection for 15 out of 97 plasma metabolites, with nonessential amino acids displaying especially strong selection signatures. Mendelian randomization analysis reveals that metabolites under stronger stabilizing selection display larger effects on a range of clinically relevant complex traits, suggesting that maintaining a disease-free profile may be an important source of selective constraints on the metabolome. Metabolites under strong stabilizing selection in humans are also more conserved in their concentrations among diverse mammalian species, suggesting shared selective forces across micro- and macroevolutionary timescales. Overall, this study demonstrates that variation in metabolite levels among humans is frequently shaped by natural selection and this may act through their causal impact on disease susceptibility.
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Affiliation(s)
- Yanina Timasheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Department of Medical Genetics, Bashkir State Medical University, 450008 Ufa, Russia
- Department of Computational Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Kaido Lepik
- Department of Computational Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
- Center for Primary Care and Public Health, University of Lausanne, CH-1010 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Orsolya Liska
- HCEMM-BRC Metabolic Systems Biology Lab, H-6726 Szeged, Hungary
- Synthetic and Systems Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, HUN-REN, H-6726 Szeged, Hungary
- Doctoral School of Biology, University of Szeged, H-6726 Szeged, Hungary
| | - Balázs Papp
- HCEMM-BRC Metabolic Systems Biology Lab, H-6726 Szeged, Hungary
- Synthetic and Systems Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, HUN-REN, H-6726 Szeged, Hungary
- National Laboratory for Health Security, Institute of Biochemistry, Biological Research Centre, HUN-REN, H-6726 Szeged, Hungary
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, CH-1015 Lausanne, Switzerland;
- Center for Primary Care and Public Health, University of Lausanne, CH-1010 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
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2
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Seitz H. A new perspective on microRNA-guided gene regulation specificity, and its potential generalization to transcription factors and RNA-binding proteins. Nucleic Acids Res 2024; 52:9360-9368. [PMID: 39149906 PMCID: PMC11381331 DOI: 10.1093/nar/gkae694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024] Open
Abstract
Our conception of gene regulation specificity has undergone profound changes over the last 20 years. Previously, regulators were considered to control few genes, recognized with exquisite specificity by a 'lock and key' mechanism. However, recently genome-wide exploration of regulator binding site occupancy (whether on DNA or RNA targets) revealed extensive lists of molecular targets for every studied regulator. Such poor biochemical specificity suggested that each regulator controls many genes, collectively contributing to biological phenotypes. Here, I propose a third model, whereby regulators' biological specificity is only partially due to 'lock and key' biochemistry. Rather, regulators affect many genes at the microscopic scale, but biological consequences for most interactions are attenuated at the mesoscopic scale: only a few regulatory events propagate from microscopic to macroscopic scale; others are made inconsequential by homeostatic mechanisms. This model is well supported by the microRNA literature, and data suggest that it extends to other regulators. It reconciles contradicting observations from biochemistry and comparative genomics on one hand and in vivo genetics on the other hand, but this conceptual unification is obscured by common misconceptions and counter-intuitive modes of graphical display. Profound understanding of gene regulation requires conceptual clarification, and better suited statistical analyses and graphical representation.
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Affiliation(s)
- Hervé Seitz
- Institut de Génétique Humaine (UMR 9002), CNRS, 141, rue de la Cardonille, 34396 Montpellier, France
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3
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Hirst SR, Rautsaw RM, VanHorn CM, Beer MA, McDonald PJ, Rosales García RA, Rodriguez Lopez B, Rubio Rincón A, Franz Chávez H, Vásquez-Cruz V, Kelly Hernández A, Storfer A, Borja M, Castañeda-Gaytán G, Frandsen PB, Parkinson CL, Strickland JL, Margres MJ. Where the "ruber" Meets the Road: Using the Genome of the Red Diamond Rattlesnake to Unravel the Evolutionary Processes Driving Venom Evolution. Genome Biol Evol 2024; 16:evae198. [PMID: 39255072 PMCID: PMC11440179 DOI: 10.1093/gbe/evae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/15/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
Understanding the proximate and ultimate causes of phenotypic variation is fundamental in evolutionary research, as such variation provides the substrate for selection to act upon. Although trait variation can arise due to selection, the importance of neutral processes is sometimes understudied. We presented the first reference-quality genome of the Red Diamond Rattlesnake (Crotalus ruber) and used range-wide 'omic data to estimate the degree to which neutral and adaptive evolutionary processes shaped venom evolution. We characterized population structure and found substantial genetic differentiation across two populations, each with distinct demographic histories. We identified significant differentiation in venom expression across age classes with substantially reduced but discernible differentiation across populations. We then used conditional redundancy analysis to test whether venom expression variation was best predicted by neutral divergence patterns or geographically variable (a)biotic factors. Snake size was the most significant predictor of venom variation, with environment, prey availability, and neutral sequence variation also identified as significant factors, though to a lesser degree. By directly including neutrality in the model, our results confidently highlight the predominant, yet not singular, role of life history in shaping venom evolution.
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Affiliation(s)
- Samuel R Hirst
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rhett M Rautsaw
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Cameron M VanHorn
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Preston J McDonald
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | | | - Bruno Rodriguez Lopez
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Alexandra Rubio Rincón
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | | | - Víctor Vásquez-Cruz
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad Veracruzana, Veracruz, Mexico
- PIMVS Herpetario Palancoatl, Veracruz, Mexico
| | | | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | | | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
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4
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Judson BJ, Kristjánsson BK, Leblanc CA, Ferguson MM. The role of neutral and adaptive evolutionary processes on patterns of genetic diversity across small cave-dwelling populations of Icelandic Arctic charr ( Salvelinus alpinus). Ecol Evol 2024; 14:e11363. [PMID: 38770124 PMCID: PMC11103641 DOI: 10.1002/ece3.11363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/22/2024] Open
Abstract
Understanding the adaptability of small populations in the face of environmental change is a central problem in evolutionary biology. Solving this problem is challenging because neutral evolutionary processes that operate on historical and contemporary timescales can override the effects of selection in small populations. We assessed the effects of isolation by colonization (IBC), isolation by dispersal limitation (IBDL) as reflected by a pattern of isolation by distance (IBD), and isolation by adaptation (IBA) and the roles of genetic drift and gene flow on patterns of genetic differentiation among 19 cave-dwelling populations of Icelandic Arctic charr (Salvelinus alpinus). We detected evidence of IBC based on the genetic affinity of nearby cave populations and the genetic relationships between the cave populations and the presumed ancestral population in the lake. A pattern of IBD was evident regardless of whether high-level genetic structuring (IBC) was taken into account. Genetic signatures of bottlenecks and lower genetic diversity in smaller populations indicate the effect of drift. Estimates of gene flow and fish movement suggest that gene flow is limited to nearby populations. In contrast, we found little evidence of IBA as patterns of local ecological and phenotypic variation showed little association with genetic differentiation among populations. Thus, patterns of genetic variation in these small populations likely reflect localized gene flow and genetic drift superimposed onto a larger-scale structure that is largely a result of colonization history. Our simultaneous assessment of the effects of neutral and adaptive processes in a tractable and replicated system has yielded novel insights into the evolution of small populations on both historical and contemporary timescales and over a smaller spatial scale than is typically studied.
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Affiliation(s)
- Braden J. Judson
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Moira M. Ferguson
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
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5
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Tengölics R, Szappanos B, Mülleder M, Kalapis D, Grézal G, Sajben C, Agostini F, Mokochinski JB, Bálint B, Nagy LG, Ralser M, Papp B. The metabolic domestication syndrome of budding yeast. Proc Natl Acad Sci U S A 2024; 121:e2313354121. [PMID: 38457520 PMCID: PMC10945815 DOI: 10.1073/pnas.2313354121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/11/2023] [Indexed: 03/10/2024] Open
Abstract
Cellular metabolism evolves through changes in the structure and quantitative states of metabolic networks. Here, we explore the evolutionary dynamics of metabolic states by focusing on the collection of metabolite levels, the metabolome, which captures key aspects of cellular physiology. Using a phylogenetic framework, we profiled metabolites in 27 populations of nine budding yeast species, providing a graduated view of metabolic variation across multiple evolutionary time scales. Metabolite levels evolve more rapidly and independently of changes in the metabolic network's structure, providing complementary information to enzyme repertoire. Although metabolome variation accumulates mainly gradually over time, it is profoundly affected by domestication. We found pervasive signatures of convergent evolution in the metabolomes of independently domesticated clades of Saccharomyces cerevisiae. Such recurring metabolite differences between wild and domesticated populations affect a substantial part of the metabolome, including rewiring of the TCA cycle and several amino acids that influence aroma production, likely reflecting adaptation to human niches. Overall, our work reveals previously unrecognized diversity in central metabolism and the pervasive influence of human-driven selection on metabolite levels in yeasts.
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Affiliation(s)
- Roland Tengölics
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Szappanos
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Department of Biotechnology, University of Szeged, Szeged6726, Hungary
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility High-Throughput Mass Spectrometry, Berlin10117, Germany
| | - Dorottya Kalapis
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Gábor Grézal
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Csilla Sajben
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
| | - João Benhur Mokochinski
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Bálint
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - László G. Nagy
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, LondonNW11AT, United Kingdom
| | - Balázs Papp
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- National Laboratory for Health Security, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
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6
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de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
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Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
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7
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Liska O, Boross G, Rocabert C, Szappanos B, Tengölics R, Papp B. Principles of metabolome conservation in animals. Proc Natl Acad Sci U S A 2023; 120:e2302147120. [PMID: 37603743 PMCID: PMC10468614 DOI: 10.1073/pnas.2302147120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/16/2023] [Indexed: 08/23/2023] Open
Abstract
Metabolite levels shape cellular physiology and disease susceptibility, yet the general principles governing metabolome evolution are largely unknown. Here, we introduce a measure of conservation of individual metabolite levels among related species. By analyzing multispecies tissue metabolome datasets in phylogenetically diverse mammals and fruit flies, we show that conservation varies extensively across metabolites. Three major functional properties, metabolite abundance, essentiality, and association with human diseases predict conservation, highlighting a striking parallel between the evolutionary forces driving metabolome and protein sequence conservation. Metabolic network simulations recapitulated these general patterns and revealed that abundant metabolites are highly conserved due to their strong coupling to key metabolic fluxes in the network. Finally, we show that biomarkers of metabolic diseases can be distinguished from other metabolites simply based on evolutionary conservation, without requiring any prior clinical knowledge. Overall, this study uncovers simple rules that govern metabolic evolution in animals and implies that most tissue metabolome differences between species are permitted, rather than favored by natural selection. More broadly, our work paves the way toward using evolutionary information to identify biomarkers, as well as to detect pathogenic metabolome alterations in individual patients.
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Affiliation(s)
- Orsolya Liska
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, 6728Szeged, Hungary
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Doctoral School of Biology, University of Szeged, 6726Szeged, Hungary
| | - Gábor Boross
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Department of Biology, Stanford University, Stanford, City of Palo Alto, CA94305-5020
| | - Charles Rocabert
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Inria, 78150Rocquencourt, 69100Villeurbanne, France
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014Helsinki, Finland
- Institute for Computational Cell Biology, Heinrich-Heine Universität, 40225Düsseldorf, Germany
| | - Balázs Szappanos
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, 6728Szeged, Hungary
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Department of Biotechnology, University of Szeged, 6726Szeged, Hungary
| | - Roland Tengölics
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, 6728Szeged, Hungary
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- Metabolomics Lab, Core facilities, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
| | - Balázs Papp
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, 6728Szeged, Hungary
- National Laboratory of Biotechnology, Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
- National Laboratory for Health Security, Biological Research Centre, Eötvös Loránd Research Network, 6726Szeged, Hungary
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8
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Gates K, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Laporte M, Bernatchez L, Beheregaray LB. Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish. Heredity (Edinb) 2023:10.1038/s41437-023-00612-x. [PMID: 36997655 DOI: 10.1038/s41437-023-00612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractTo conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowfish, Melanotaenia splendida splendida. We used an integrative riverscape genomics and morphometrics framework to assess the influence of these factors on both putative adaptive and non-adaptive spatial divergence. We found that neutral genetic population structure was largely explainable by restricted gene flow among drainages. However, environmental associations revealed that ecological variables had a similar power to explain overall genetic variation, and greater power to explain body shape variation, than the included neutral covariables. Hydrological and thermal variables were the strongest environmental predictors and were correlated with traits previously linked to heritable habitat-associated dimorphism in rainbowfishes. In addition, climate-associated genetic variation was significantly associated with morphology, supporting heritability of shape variation. These results support the inference of evolved functional differences among localities, and the importance of hydroclimate in early stages of diversification. We expect that substantial evolutionary responses will be required in tropical rainforest endemics to mitigate local fitness losses due to changing climates.
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9
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Roberts RJV, Pop S, Prieto-Godino LL. Evolution of central neural circuits: state of the art and perspectives. Nat Rev Neurosci 2022; 23:725-743. [DOI: 10.1038/s41583-022-00644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/09/2022]
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10
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Vasseur F, Westgeest AJ, Vile D, Violle C. Solving the grand challenge of phenotypic integration: allometry across scales. Genetica 2022; 150:161-169. [PMID: 35857239 PMCID: PMC9355930 DOI: 10.1007/s10709-022-00158-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/13/2022] [Indexed: 11/26/2022]
Abstract
Phenotypic integration is a concept related to the cascade of trait relationships from the lowest organizational levels, i.e. genes, to the highest, i.e. whole-organism traits. However, the cause-and-effect linkages between traits are notoriously difficult to determine. In particular, we still lack a mathematical framework to model the relationships involved in the integration of phenotypic traits. Here, we argue that allometric models developed in ecology offer testable mathematical equations of trait relationships across scales. We first show that allometric relationships are pervasive in biology at different organizational scales and in different taxa. We then present mechanistic models that explain the origin of allometric relationships. In addition, we emphasized that recent studies showed that natural variation does exist for allometric parameters, suggesting a role for genetic variability, selection and evolution. Consequently, we advocate that it is time to examine the genetic determinism of allometries, as well as to question in more detail the role of genome size in subsequent scaling relationships. More broadly, a possible-but so far neglected-solution to understand phenotypic integration is to examine allometric relationships at different organizational levels (cell, tissue, organ, organism) and in contrasted species.
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Affiliation(s)
- François Vasseur
- CEFE, University Montpellier, CNRS, EPHE, IRD, Montpellier, France.
| | | | - Denis Vile
- LEPSE, University Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Cyrille Violle
- CEFE, University Montpellier, CNRS, EPHE, IRD, Montpellier, France
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11
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Schroeder L, Elton S, Ackermann RR. Skull variation in Afro-Eurasian monkeys results from both adaptive and non-adaptive evolutionary processes. Sci Rep 2022; 12:12516. [PMID: 35869137 PMCID: PMC9307787 DOI: 10.1038/s41598-022-16734-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
Afro-Eurasian monkeys originated in the Miocene and are the most species-rich modern primate family. Molecular and fossil data have provided considerable insight into their evolutionary divergence, but we know considerably less about the evolutionary processes that underlie these differences. Here, we apply tests developed from quantitative genetics theory to a large (n > 3000) cranio-mandibular morphometric dataset, investigating the relative importance of adaptation (natural selection) and neutral processes (genetic drift) in shaping diversity at different taxonomic levels, an approach applied previously to monkeys of the Americas, apes, hominins, and other vertebrate taxa. Results indicate that natural selection, particularly for differences in size, plays a significant role in diversifying Afro-Eurasian monkeys as a whole. However, drift appears to better explain skull divergence within the subfamily Colobinae, and in particular the African colobine clade, likely due to habitat fragmentation. Small and declining population sizes make it likely that drift will continue in this taxon, with potentially dire implications for genetic diversity and future resilience in the face of environmental change. For the other taxa, many of whom also have decreasing populations and are threatened, understanding adaptive pressures similarly helps identify relative vulnerability and may assist with prioritising scarce conservation resources.
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Affiliation(s)
- Lauren Schroeder
- Department of Anthropology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.
- Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa.
| | - Sarah Elton
- Department of Anthropology, Durham University, Dawson Building, South Road, Durham, DH1 3LE, UK
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, Rondebosch, 7701, South Africa
- Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa
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12
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Langille BL, Tierney SM, Bertozzi T, Beasley-Hall PG, Bradford TM, Fagan-Jeffries EP, Hyde J, Leijs R, Richardson M, Saint KM, Stringer DN, Villastrigo A, Humphreys WF, Austin AD, Cooper SJB. Parallel decay of vision genes in subterranean water beetles. Mol Phylogenet Evol 2022; 173:107522. [PMID: 35595008 DOI: 10.1016/j.ympev.2022.107522] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022]
Abstract
In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.
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Affiliation(s)
- Barbara L Langille
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia.
| | - Simon M Tierney
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Terry Bertozzi
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Perry G Beasley-Hall
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Tessa M Bradford
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Erinn P Fagan-Jeffries
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Josephine Hyde
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Western Australia Department of Biodiversity Conservation and Attractions, Kensington, WA 6151, Australia
| | - Remko Leijs
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Matthew Richardson
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Kathleen M Saint
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Danielle N Stringer
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Adrián Villastrigo
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia; Institute of Evolutionary Biology, Passeig Marítim de la Barceloneta, 37-49, 08003, Spain
| | - William F Humphreys
- Western Australian Museum, Locked Bag 40, Welshpool DC, WA 6986, Australia; School of Animal Biology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
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13
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Wang Y, Jiang B, Wu Y, He X, Liu L. Rapid intraspecies evolution of fitness effects of yeast genes. Genome Biol Evol 2022; 14:6575331. [PMID: 35482054 PMCID: PMC9113246 DOI: 10.1093/gbe/evac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/14/2022] Open
Abstract
Organisms within species have numerous genetic and phenotypic variations. Growing evidences show intraspecies variation of mutant phenotypes may be more complicated than expected. Current studies on intraspecies variations of mutant phenotypes are limited to just a few strains. This study investigated the intraspecies variation of fitness effects of 5,630 gene mutants in ten Saccharomyces cerevisiae strains using CRISPR–Cas9 screening. We found that the variability of fitness effects induced by gene disruptions is very large across different strains. Over 75% of genes affected cell fitness in a strain-specific manner to varying degrees. The strain specificity of the fitness effect of a gene is related to its evolutionary and functional properties. Subsequent analysis revealed that younger genes, especially those newly acquired in S. cerevisiae species, are more likely to be strongly strain-specific. Intriguingly, there seems to exist a ceiling of fitness effect size for strong strain-specific genes, and among them, the newly acquired genes are still evolving and have yet to reach this ceiling. Additionally, for a large proportion of protein complexes, the strain specificity profile is inconsistent among genes encoding the same complex. Taken together, these results offer a genome-wide map of intraspecies variation for fitness effect as a mutant phenotype and provide an updated insight on intraspecies phenotypic evolution.
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Affiliation(s)
- Yayu Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Bei Jiang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xionglei He
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Li Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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14
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Palazzo AF, Kejiou NS. Non-Darwinian Molecular Biology. Front Genet 2022; 13:831068. [PMID: 35251134 PMCID: PMC8888898 DOI: 10.3389/fgene.2022.831068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.
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15
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Zou X, Schaefke B, Li Y, Jia F, Sun W, Li G, Liang W, Reif T, Heyd F, Gao Q, Tian S, Li Y, Tang Y, Fang L, Hu Y, Chen W. Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law. Life Sci Alliance 2022; 5:5/4/e202101333. [PMID: 34969779 PMCID: PMC8739531 DOI: 10.26508/lsa.202101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
This study globally investigates the allelic splicing pattern in multiple tissues of an F1 hybrid mouse and reveals the underlying driving forces shaping such tissue-dependent splicing divergence. Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.
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Affiliation(s)
- Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Bernhard Schaefke
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yisheng Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fujian Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Sun
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Weizheng Liang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Tristan Reif
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Florian Heyd
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Qingsong Gao
- Laboratory for Systems Biology and Functional Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Shuye Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yanping Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yisen Tang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China .,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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16
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Liang W, Zou X, Li G, Zhou S, Tian C, Schaefke B. Systematic Analysis of Monoallelic Gene Expression and Chromatin Accessibility Across Multiple Tissues in Hybrid Mice. Front Cell Dev Biol 2021; 9:717555. [PMID: 34631706 PMCID: PMC8495204 DOI: 10.3389/fcell.2021.717555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
In diploid eukaryotic organisms, both alleles of each autosomal gene are usually assumed to be simultaneously expressed at similar levels. However, some genes can be expressed preferentially or strictly from a single allele, a process known as monoallelic expression. Classic monoallelic expression of X-chromosome-linked genes, olfactory receptor genes and developmentally imprinted genes is the result of epigenetic modifications. Genetic-origin-dependent monoallelic expression, however, is caused by cis-regulatory differences between the alleles. There is a paucity of systematic study to investigate these phenomena across multiple tissues, and the mechanisms underlying such monoallelic expression are not yet fully understood. Here we provide a detailed portrait of monoallelic gene expression across multiple tissues/cell lines in a hybrid mouse cross between the Mus musculus strain C57BL/6J and the Mus spretus strain SPRET/EiJ. We observed pervasive tissue-dependent allele-specific gene expression: in total, 1,839 genes exhibited monoallelic expression in at least one tissue, and 410 genes in at least two tissues. Among these 88 are monoallelic genes with different active alleles between tissues, probably representing genetic-origin-dependent monoallelic expression. We also identified six autosomal monoallelic genes with the active allele being identical in all eight tissues, which are likely novel candidates of imprinted genes. To depict the underlying regulatory mechanisms at the chromatin layer, we performed ATAC-seq in two different cell lines derived from the F1 mouse. Consistent with the global expression pattern, cell-type dependent monoallelic peaks were found, and a higher proportion of C57BL/6J-active peaks were observed in both cell types, implying possible species-specific regulation. Finally, only a small part of monoallelic gene expression could be explained by allelic differences in chromatin organization in promoter regions, suggesting that other distal elements may play important roles in shaping the patterns of allelic gene expression across tissues.
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Affiliation(s)
- Weizheng Liang
- Harbin Institute of Technology, Harbin, China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Shaojie Zhou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Chi Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Bernhard Schaefke
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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17
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Wood ZT, Wiegardt AK, Barton KL, Clark JD, Homola JJ, Olsen BJ, King BL, Kovach AI, Kinnison MT. Meta-analysis: Congruence of genomic and phenotypic differentiation across diverse natural study systems. Evol Appl 2021; 14:2189-2205. [PMID: 34603492 PMCID: PMC8477602 DOI: 10.1111/eva.13264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 01/17/2023] Open
Abstract
Linking genotype to phenotype is a primary goal for understanding the genomic underpinnings of evolution. However, little work has explored whether patterns of linked genomic and phenotypic differentiation are congruent across natural study systems and traits. Here, we investigate such patterns with a meta-analysis of studies examining population-level differentiation at subsets of loci and traits putatively responding to divergent selection. We show that across the 31 studies (88 natural population-level comparisons) we examined, there was a moderate (R 2 = 0.39) relationship between genomic differentiation (F ST ) and phenotypic differentiation (P ST ) for loci and traits putatively under selection. This quantitative relationship between P ST and F ST for loci under selection in diverse taxa provides broad context and cross-system predictions for genomic and phenotypic adaptation by natural selection in natural populations. This context may eventually allow for more precise ideas of what constitutes "strong" differentiation, predictions about the effect size of loci, comparisons of taxa evolving in nonparallel ways, and more. On the other hand, links between P ST and F ST within studies were very weak, suggesting that much work remains in linking genomic differentiation to phenotypic differentiation at specific phenotypes. We suggest that linking genotypes to specific phenotypes can be improved by correlating genomic and phenotypic differentiation across a spectrum of diverging populations within a taxon and including wide coverage of both genomes and phenomes.
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Affiliation(s)
- Zachary T. Wood
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
| | - Andrew K. Wiegardt
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Kayla L. Barton
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Jonathan D. Clark
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
| | - Brian J. Olsen
- Maine Center for Genetics in the EnvironmentOronoMEUSA
- Department of Wildlife, Fisheries, and Conservation BiologyUniversity of MaineOronoMEUSA
| | - Benjamin L. King
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Michael T. Kinnison
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
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18
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Kishi Y, Parker J. Cell type innovation at the tips of the animal tree. Curr Opin Genet Dev 2021; 69:112-121. [PMID: 33784538 DOI: 10.1016/j.gde.2021.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/16/2022]
Abstract
Understanding how organs originate is challenging due to the twin problems of explaining how new cell types evolve and how collective interactions between cell types arise and become selectively advantageous. Animals are assemblages of organs and cell types of different antiquities, and among the most rapidly and convergently evolving are exocrine glands and their constituent secretory cell types. Such structures have arisen independently thousands of times across the Metazoa, impacting how animals chemically interact with their environments. The recurrent evolution of exocrine systems provides a paradigm for examining how qualitative phenotypic novelties arise from variation at the cellular level. Here, we take a hierarchical perspective, focusing on the evolutionary assembly of novel biosynthetic pathways and secretory cell types, and how both selection and non-adaptive molecular processes may combine to build the complex, modular architectures of many animal glands.
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Affiliation(s)
- Yuriko Kishi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Joseph Parker
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125, United States.
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19
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Muñoz-Gómez SA, Bilolikar G, Wideman JG, Geiler-Samerotte K. Constructive Neutral Evolution 20 Years Later. J Mol Evol 2021; 89:172-182. [PMID: 33604782 PMCID: PMC7982386 DOI: 10.1007/s00239-021-09996-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 01/13/2021] [Indexed: 12/29/2022]
Abstract
Evolution has led to a great diversity that ranges from elegant simplicity to ornate complexity. Many complex features are often assumed to be more functional or adaptive than their simpler alternatives. However, in 1999, Arlin Stolzfus published a paper in the Journal of Molecular Evolution that outlined a framework in which complexity can arise through a series of non-adaptive steps. He called this framework Constructive Neutral Evolution (CNE). Despite its two-decade-old roots, many evolutionary biologists still appear to be unaware of this explanatory framework for the origins of complexity. In this perspective piece, we explain the theory of CNE and how it changes the order of events in narratives that describe the evolution of complexity. We also provide an extensive list of cellular features that may have become more complex through CNE. We end by discussing strategies to determine whether complexity arose through neutral or adaptive processes.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA.
| | - Gaurav Bilolikar
- School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
| | - Jeremy G Wideman
- School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
| | - Kerry Geiler-Samerotte
- School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA.
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20
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Manceau M, Marin J, Morlon H, Lambert A. Model-Based Inference of Punctuated Molecular Evolution. Mol Biol Evol 2020; 37:3308-3323. [PMID: 32521005 DOI: 10.1093/molbev/msaa144] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.
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Affiliation(s)
- Marc Manceau
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France.,IBENS, Ecole Normale Supérieure, UMR 8197 CNRS, Paris, France.,DBSSE, ETH Zürich, Basel, Switzerland
| | - Julie Marin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France
| | - Hélène Morlon
- IBENS, Ecole Normale Supérieure, UMR 8197 CNRS, Paris, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France.,Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS UMR 8001, Paris, France
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21
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Muñoz-Gómez SA, Snyder SN, Montoya SJ, Wideman JG. Independent accretion of TIM22 complex subunits in the animal and fungal lineages. F1000Res 2020; 9:1060. [PMID: 33014348 PMCID: PMC7523481 DOI: 10.12688/f1000research.25904.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/21/2020] [Indexed: 12/25/2022] Open
Abstract
Background: The mitochondrial protein import complexes arose early in eukaryogenesis. Most of the components of the protein import pathways predate the last eukaryotic common ancestor. For example, the carrier-insertase TIM22 complex comprises the widely conserved Tim22 channel core. However, the auxiliary components of fungal and animal TIM22 complexes are exceptions to this ancient conservation. Methods: Using comparative genomics and phylogenetic approaches, we identified precisely when each TIM22 accretion occurred. Results: In animals, we demonstrate that Tim29 and Tim10b arose early in the holozoan lineage. Tim29 predates the metazoan lineage being present in the animal sister lineages, choanoflagellate and filastereans, whereas the erroneously named Tim10b arose from a duplication of Tim9 at the base of metazoans. In fungi, we show that Tim54 has representatives present in every holomycotan lineage including microsporidians and fonticulids, whereas Tim18 and Tim12 appeared much later in fungal evolution. Specifically, Tim18 and Tim12 arose from duplications of Sdh3 and Tim10, respectively, early in the Saccharomycotina. Surprisingly, we show that Tim54 is distantly related to AGK suggesting that AGK and Tim54 are extremely divergent orthologues and the origin of AGK/Tim54 interaction with Tim22 predates the divergence of animals and fungi. Conclusions: We argue that the evolutionary history of the TIM22 complex is best understood as the neutral structural divergence of an otherwise strongly functionally conserved protein complex. This view suggests that many of the differences in structure/subunit composition of multi-protein complexes are non-adaptive. Instead, most of the phylogenetic variation of functionally conserved molecular machines, which have been under stable selective pressures for vast phylogenetic spans, such as the TIM22 complex, is most likely the outcome of the interplay of random genetic drift and mutation pressure.
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Affiliation(s)
- Sergio A. Muñoz-Gómez
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Shannon N. Snyder
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Samantha J. Montoya
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Jeremy G. Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
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22
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On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution? Curr Top Dev Biol 2020; 139:375-405. [PMID: 32450967 DOI: 10.1016/bs.ctdb.2020.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The process of multicellular organismal development hinges upon the specificity of developmental programs: for different parts of the organism to form unique features, processes must exist to specify each part. This specificity is thought to be hardwired into gene regulatory networks, which activate cohorts of genes in particular tissues at particular times during development. However, the evolution of gene regulatory networks sometimes occurs by mechanisms that sacrifice specificity. One such mechanism is network co-option, in which existing gene networks are redeployed in new developmental contexts. While network co-option may offer an efficient mechanism for generating novel phenotypes, losses of tissue specificity at redeployed network genes could restrict the ability of the affected traits to evolve independently. At present, there has not been a detailed discussion regarding how tissue specificity of network genes might be altered due to gene network co-option at its initiation, as well as how trait independence can be retained or restored after network co-option. A lack of clarity about network co-option makes it more difficult to speculate on the long-term evolutionary implications of this mechanism. In this review, we will discuss the possible initial outcomes of network co-option, outline the mechanisms by which networks may retain or subsequently regain specificity after network co-option, and comment on some of the possible evolutionary consequences of network co-option. We place special emphasis on the need to consider selectively-neutral outcomes of network co-option to improve our understanding of the role of this mechanism in trait evolution.
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Li Y, Schaefke B, Zou X, Zhang M, Heyd F, Sun W, Zhang B, Li G, Liang W, He Y, Zhou J, Li Y, Fang L, Hu Y, Chen W. Pan-tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation. Mol Syst Biol 2020; 16:e9367. [PMID: 32311237 PMCID: PMC7170663 DOI: 10.15252/msb.20199367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/29/2020] [Accepted: 03/11/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative polyadenylation (APA) is a major layer of gene regulation. However, it has recently been argued that most APA represents molecular noise. To clarify their functional relevance and evolution, we quantified allele-specific APA patterns in multiple tissues from an F1 hybrid mouse. We found a clearly negative correlation between gene expression and APA diversity for the 2,866 genes (24.9%) with a dominant polyadenylation site (PAS) usage above or equal to 90%, suggesting that their other PASs represent molecular errors. Among the remaining genes with multiple PASs, 3,971 genes (34.5%) express two or more isoforms with potentially functional importance. Interestingly, the genes with potentially functional minor PASs specific to neuronal tissues often express two APA isoforms with distinct subcellular localizations. Furthermore, our analysis of cis-APA divergence shows its pattern across tissues is distinct from that of gene expression. Finally, we demonstrate that the relative usage of alternative PASs is not only affected by their cis-regulatory elements, but also by potential coupling between transcriptional and APA regulation as well as competition kinetics between alternative sites.
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Affiliation(s)
- Yisheng Li
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
- Laboratory of RNA BiochemistryInstitute of Chemistry and BiochemistryFreie Universität BerlinBerlinGermany
| | - Bernhard Schaefke
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
- Academy for Advanced Interdisciplinary StudiesSouthern University of Science and TechnologyShenzhenChina
| | - Xudong Zou
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Min Zhang
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Florian Heyd
- Laboratory of RNA BiochemistryInstitute of Chemistry and BiochemistryFreie Universität BerlinBerlinGermany
| | - Wei Sun
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
- Present address:
Department of Pharmaceutical Chemistry and the Cardiovascular Research InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Bin Zhang
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
- Present address:
Cancer Science Institute of SingaporeNational University of SingaporeSingapore CitySingapore
| | - Guipeng Li
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
- Academy for Advanced Interdisciplinary StudiesSouthern University of Science and TechnologyShenzhenChina
| | - Weizheng Liang
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Yuhao He
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Juexiao Zhou
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Yunfei Li
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Liang Fang
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
- Academy for Advanced Interdisciplinary StudiesSouthern University of Science and TechnologyShenzhenChina
| | - Yuhui Hu
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
| | - Wei Chen
- Department of BiologySouthern University of Science and TechnologyShenzhenChina
- Academy for Advanced Interdisciplinary StudiesSouthern University of Science and TechnologyShenzhenChina
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Jiang D, Zhang J. The preponderance of nonsynonymous A-to-I RNA editing in coleoids is nonadaptive. Nat Commun 2019; 10:5411. [PMID: 31776345 PMCID: PMC6881472 DOI: 10.1038/s41467-019-13275-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/31/2019] [Indexed: 01/24/2023] Open
Abstract
A-to-I editing enzymatically converts the base adenosine (A) in RNA molecules to inosine (I), which is recognized as guanine (G) in translation. Exceptionally abundant A-to-I editing was recently discovered in the neural tissues of coleoids (octopuses, squids, and cuttlefishes), with a greater fraction of nonsynonymous sites than synonymous sites subject to high levels of editing. Although this phenomenon is thought to indicate widespread adaptive editing, its potential advantage is unknown. Here we propose an alternative, nonadaptive explanation. Specifically, increasing the cellular editing activity permits some otherwise harmful G-to-A nonsynonymous substitutions, because the As are edited to Is at sufficiently high levels. These high editing levels are constrained upon substitutions, resulting in the predominance of nonsynonymous editing at highly edited sites. Our evidence for this explanation suggests that the prevalent nonsynonymous editing in coleoids is generally nonadaptive, as in species with much lower editing activities. The neural tissues of coleoids have a greater fraction of nonsynonymous sites than synonymous sites subject to high levels of A-to-I RNA editing, a pattern thought to indicate widespread adaptive editing. Here the authors propose and provide evidence for an alternative, nonadaptive explanation.
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Affiliation(s)
- Daohan Jiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA.
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25
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Wideman JG, Novick A, Muñoz-Gómez SA, Doolittle WF. Neutral evolution of cellular phenotypes. Curr Opin Genet Dev 2019; 58-59:87-94. [PMID: 31574422 DOI: 10.1016/j.gde.2019.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/29/2022]
Abstract
Eukaryotes exhibit a great diversity of cellular and subcellular morphologies, but their basic underlying architecture is fairly constant. All have a nucleus, Golgi, cytoskeleton, plasma membrane, vesicles, ribosomes, and all known lineages but one have mitochondrion-related organelles. Moreover, most eukaryotes undergo processes such as mitosis, meiosis, DNA recombination, and often perform feats such as phagocytosis, and amoeboid and flagellar movement. With all of these commonalities, it is obvious that eukaryotes evolved from a common ancestor, but it is not obvious how eukaryotes came to have their diverse structural phenotypes. Are these phenotypes adaptations to particular niches, their evolution dominated by positive natural selection? Or is eukaryotic cellular diversity substantially the product of neutral evolutionary processes, with adaptation either illusory or a secondary consequence? In this paper, we outline how a hierarchical view of phenotype can be used to articulate a neutral theory of phenotypic evolution, involving processes such as gene loss, gene replacement by homologues or analogues, gene duplication followed by subfunctionalization, and constructive neutral evolution. We suggest that neutral iterations of these processes followed by entrenchment of their products can explain much of the diversity of cellular, developmental, and biochemical phenotypes of unicellular eukaryotes and should be explored in addition to adaptive explanations.
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Affiliation(s)
- Jeremy G Wideman
- Centre for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85287, USA; Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Aaron Novick
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Philosophy, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Philosophy, Purdue University, West Lafayette, IN, 47907, USA
| | - Sergio A Muñoz-Gómez
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - W Ford Doolittle
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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Ho WC, Zhang J. Genetic Gene Expression Changes during Environmental Adaptations Tend to Reverse Plastic Changes Even after the Correction for Statistical Nonindependence. Mol Biol Evol 2019; 36:604-612. [PMID: 30649427 DOI: 10.1093/molbev/msz002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Organismal adaptations to new environments often begin with plastic phenotypic changes followed by genetic phenotypic changes, but the relationship between the two types of changes is controversial. Contrary to the view that plastic changes serve as steppingstones to genetic adaptations, recent transcriptome studies reported that genetic gene expression changes more often reverse than reinforce plastic expression changes in experimental evolution. However, it was pointed out that this trend could be an artifact of the statistical nonindependence between the estimates of plastic and genetic phenotypic changes, because both estimates rely on the phenotypic measure at the plastic stage. Using computer simulation, we show that indeed the nonindependence can cause an apparent excess of expression reversion relative to reinforcement. We propose a parametric bootstrap method and show by simulation that it removes the bias almost entirely. Analyzing transcriptome data from a total of 34 parallel lines in 5 experimental evolution studies of Escherichia coli, yeast, and guppies that are amenable to our method confirms that genetic expression changes tend to reverse plastic changes. Thus, at least for gene expression traits, phenotypic plasticity does not generally facilitate genetic adaptation. Several other comparisons of statistically nonindependent estimates are commonly performed in evolutionary genomics such as that between cis- and trans-effects of mutations on gene expression and that between transcriptional and translational effects on gene expression. It is important to validate previous results from such comparisons, and our proposed statistical analyses can be useful for this purpose.
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Affiliation(s)
- Wei-Chin Ho
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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Goloboff PA, Pittman M, Pol D, Xu X. Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model. Syst Biol 2019; 68:494-504. [PMID: 30445627 DOI: 10.1093/sysbio/syy077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/11/2018] [Accepted: 11/13/2018] [Indexed: 01/30/2023] Open
Abstract
The Mkv evolutionary model, based on minor modifications to models of molecular evolution, is being increasingly used to infer phylogenies from discrete morphological data, often producing different results from parsimony. The critical difference between Mkv and parsimony is the assumption of a "common mechanism" in the Mkv model, with branch lengths determining that probability of change for all characters increases or decreases at the same tree branches by the same exponential factor. We evaluate whether the assumption of a common mechanism applies to morphology, by testing the implicit prediction that branch lengths calculated from different subsets of characters will be significantly correlated. Our analysis shows that DNA (38 data sets tested) is often compatible with a common mechanism, but morphology (86 data sets tested) generally is not, showing very disparate branch lengths for different character partitions. The low levels of branch length correlation demonstrated for morphology (fitting models without a common mechanism) suggest that the Mkv model is too unrealistic and inadequate for the analysis of most morphological data sets. [Bayesian analysis; Mkv model; morphological data; phylogenetics.].
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Affiliation(s)
- Pablo A Goloboff
- Unidad Ejecutora Lillo (UEL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), S.M. Tucumán, Argentina
| | - Michael Pittman
- Vertebrate Palaeontology Laboratory, Department of Earth Sciences, University of Hong Kong, Pokfulam, Hong Kong
| | - Diego Pol
- Museo Egidio Feruglio, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Trelew, Argentina
| | - Xing Xu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
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28
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Kiskowski M, Glimm T, Moreno N, Gamble T, Chiari Y. Isolating and quantifying the role of developmental noise in generating phenotypic variation. PLoS Comput Biol 2019; 15:e1006943. [PMID: 31009449 PMCID: PMC6497311 DOI: 10.1371/journal.pcbi.1006943] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 05/02/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Genotypic variation, environmental variation, and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals. Developmental noise, which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fixed, also contributes to phenotypic variation. While evolutionary biology has long focused on teasing apart the relative contribution of genes and environment to phenotypic variation, our understanding of the role of developmental noise has lagged due to technical difficulties in directly measuring the contribution of developmental noise. The influence of developmental noise is likely underestimated in studies of phenotypic variation due to intrinsic mechanisms within organisms that stabilize phenotypes and decrease variation. Since we are just beginning to appreciate the extent to which phenotypic variation due to stochasticity is potentially adaptive, the contribution of developmental noise to phenotypic variation must be separated and measured to fully understand its role in evolution. Here, we show that variation in the component of the developmental process corresponding to environmental and genetic factors (here treated together as a unit called the LALI-type) versus the contribution of developmental noise, can be distinguished for leopard gecko (Eublepharis macularius) head color patterns using mathematical simulations that model the role of random variation (corresponding to developmental noise) in patterning. Specifically, we modified the parameters of simulations corresponding to variation in the LALI-type to generate the full range of phenotypic variation in color pattern seen on the heads of eight leopard geckos. We observed that over the range of these parameters, variation in color pattern due to LALI-type variation exceeds that due to developmental noise in the studied gecko cohort. However, the effect of developmental noise on patterning is also substantial. Our approach addresses one of the major goals of evolutionary biology: to quantify the role of stochasticity in shaping phenotypic variation.
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Affiliation(s)
- Maria Kiskowski
- University of South Alabama, Department of Mathematics and Statistics, Mobile, AL, United States of America
- * E-mail:
| | - Tilmann Glimm
- Western Washington University, Department of Mathematics, Bellingham, WA, United States of America
| | - Nickolas Moreno
- University of South Alabama, Department of Biology, Mobile, AL, United States of America
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States of America
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN, United States of America
- Milwaukee Public Museum, Milwaukee, WI, United States of America
| | - Ylenia Chiari
- University of South Alabama, Department of Biology, Mobile, AL, United States of America
- George Mason University, Department of Biology, Science & Technology Campus, Manassas, VA, United States of America
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29
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Upadhyay A. Structure of proteins: Evolution with unsolved mysteries. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:160-172. [PMID: 31014967 DOI: 10.1016/j.pbiomolbio.2019.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
Abstract
Evolution of macromolecules could be considered as a milestone in the history of life. Nucleic acids are the long stretches of nucleotides that contain all the possible codes and information of life. On the other hand, proteins are their actual translated outcomes, or reflections of modifications in their structure that have occurred at a slow, but steady rate over a very long period of evolution. Over the years of research, biophysicists, biochemists, molecular and structural biologists have unfurled several layers of the structural convolutions in these chemical molecules; however evolutionists look over their structures through a different prism, which may or may not coincide with others. There remains a need to outline several well-known, but less discussed features of protein structures, like intrinsically disordered states, degron signals and different types of ubiquitin chains providing degradation signals, which help the cellular proteolytic machinery to identify and target the proteins towards degradation pathways. There are several important factors, which are critical for folding of proteins into their native three-dimensional conformations by the cytoplasmic chaperones; but in real time how the chaperones fold the newly synthesized polypeptide sequences into a particular three-dimensional shape within a fraction of second is still a mystery for biologists as well as mathematicians. Multiple similar unsolved or unaddressed questions need to be addressed in detail so that future line of research can dig deeper into the finer details of these structures of the proteins.
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Affiliation(s)
- Arun Upadhyay
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India.
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30
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Filippi-Codaccioni O, Beugin MP, de Vienne DM, Portanier E, Fouchet D, Kaerle C, Muselet L, Queney G, Petit EJ, Regis C, Pons JB, Pontier D. Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data. BMC Evol Biol 2018; 18:175. [PMID: 30458712 PMCID: PMC6247516 DOI: 10.1186/s12862-018-1289-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/02/2018] [Indexed: 01/29/2023] Open
Abstract
Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. Results A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1–4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). Conclusions The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1289-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ondine Filippi-Codaccioni
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France.,SEISE 26 bis Barrouil, 33720, Illats, France
| | - Marie-Pauline Beugin
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France.,ANTAGENE, Animal Genomics Laboratory, 6 allée du Levant, 69890, La Tour de Salvagny (Lyon), France
| | - Damien M de Vienne
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France
| | - Elodie Portanier
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, VetAgro Sup - Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, F-69280, Marcy l'Etoile, France.,Office National de la Chasse et de la Faune Sauvage - Unité Faune de Montagne, 147 Route de Lodève, Les Portes du Soleil, F-34990, Juvignac, France
| | - David Fouchet
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France
| | - Cecile Kaerle
- ANTAGENE, Animal Genomics Laboratory, 6 allée du Levant, 69890, La Tour de Salvagny (Lyon), France
| | - Lina Muselet
- ANTAGENE, Animal Genomics Laboratory, 6 allée du Levant, 69890, La Tour de Salvagny (Lyon), France
| | - Guillaume Queney
- ANTAGENE, Animal Genomics Laboratory, 6 allée du Levant, 69890, La Tour de Salvagny (Lyon), France
| | - Eric J Petit
- UMR ESE, Ecology and Ecosystem Health, INRA, Agrocampus Ouest, 65 rue de Saint-Brieuc, 35042, Rennes Cedex, France
| | - Corinne Regis
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France
| | - Jean-Baptiste Pons
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France.,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France
| | - Dominique Pontier
- University Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622, Villeurbanne, France. .,Université de Lyon, LabEx Ecofect, Nadine Cizaire, 92 rue Pasteur, CS 30122 69361, Lyon Cedex 07, France.
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Marsh J, Kollipara A, Timms P, Polkinghorne A. Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus). BMC Microbiol 2011; 11:77. [PMID: 21496349 PMCID: PMC3101125 DOI: 10.1186/1471-2180-11-77] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 04/18/2011] [Indexed: 01/16/2023] Open
Abstract
Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species.
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Affiliation(s)
- James Marsh
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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