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Luiselli J, Rouzaud-Cornabas J, Lartillot N, Beslon G. Genome Streamlining: Effect of Mutation Rate and Population Size on Genome Size Reduction. Genome Biol Evol 2024; 16:evae250. [PMID: 39566106 DOI: 10.1093/gbe/evae250] [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: 04/08/2024] [Revised: 11/10/2024] [Accepted: 11/14/2024] [Indexed: 11/22/2024] Open
Abstract
Genome streamlining, i.e. genome size reduction, is observed in bacteria with very different life traits, including endosymbiotic bacteria and several marine bacteria, raising the question of its evolutionary origin. None of the hypotheses proposed in the literature is firmly established, mainly due to the many confounding factors related to the diverse habitats of species with streamlined genomes. Computational models may help overcome these difficulties and rigorously test hypotheses. In this work, we used Aevol, a platform designed to study the evolution of genome architecture, to test 2 main hypotheses: that an increase in population size (N) or mutation rate (μ) could cause genome reduction. In our experiments, both conditions lead to streamlining but have very different resulting genome structures. Under increased population sizes, genomes lose a significant fraction of noncoding sequences but maintain their coding size, resulting in densely packed genomes (akin to streamlined marine bacteria genomes). By contrast, under an increased mutation rate, genomes lose both coding and noncoding sequences (akin to endosymbiotic bacteria genomes). Hence, both factors lead to an overall reduction in genome size, but the coding density of the genome appears to be determined by N×μ. Thus, a broad range of genome size and density can be achieved by different combinations of N and μ. Our results suggest that genome size and coding density are determined by the interplay between selection for phenotypic adaptation and selection for robustness.
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Affiliation(s)
- Juliette Luiselli
- INSA-Lyon, CNRS, Université Claude Bernard Lyon 1, ECL, Université Lumière Lyon 2, LIRIS UMR5205, Lyon 69621, France
- Beagle Team, Inria Lyon La Doua, Villeurbanne, France
| | - Jonathan Rouzaud-Cornabas
- INSA-Lyon, CNRS, Université Claude Bernard Lyon 1, ECL, Université Lumière Lyon 2, LIRIS UMR5205, Lyon 69621, France
- Beagle Team, Inria Lyon La Doua, Villeurbanne, France
| | - Nicolas Lartillot
- Laboratoire de Biométrie et de Biologie Évolutive UMR CNRS 5558, Université Claude Bernard Lyon 1, Université Lyon 1, Villeurbanne, France
| | - Guillaume Beslon
- INSA-Lyon, CNRS, Université Claude Bernard Lyon 1, ECL, Université Lumière Lyon 2, LIRIS UMR5205, Lyon 69621, France
- Beagle Team, Inria Lyon La Doua, Villeurbanne, France
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Hull KL, Greenwood MP, Lloyd M, Brink-Hull M, Bester-van der Merwe AE, Rhode C. Drivers of genomic diversity and phenotypic development in early phases of domestication in Hermetia illucens. INSECT MOLECULAR BIOLOGY 2024; 33:756-776. [PMID: 38963286 DOI: 10.1111/imb.12940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
The black soldier fly (BSF), Hermetia illucens, has the ability to efficiently bioremediate organic waste into usable bio-compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its association to phenotypic development across early generations of mass rearing under two selection strategies: selection for greater larval mass (SEL lines) and no direct artificial selection (NS lines). Genome-wide single nucleotide polymorphism (SNP) data were generated using 2bRAD sequencing, while phenotypic traits relating to production and population fitness were measured. Declining patterns of genomic diversity were observed across three generations of captive breeding, with the lowest diversity recorded for the F3 generation of both selection lines, most likely due to founder effects. The SEL cohort displayed statistically significantly greater larval weight com the NS lines with pronounced genetic and phenotypic directional changes across generations. Furthermore, lower genetic and phenotypic diversity, particularly for fitness traits, were evident for SEL lines, illustrating the trade-off between selecting for mass and the resulting decline in population fitness. SNP-based heritability was significant for growth, but was low or non-significant for fitness traits. Genotype-phenotype correlations were observed for traits, but individual locus effect sizes where small and very few of these loci demonstrated a signature for selection. Pronounced genetic drift, due to small effective population sizes, is likely overshadowing the impacts of selection on genomic diversity and consequently phenotypic development. The results hold particular relevance for genetic management and selective breeding for BSF in future.
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Affiliation(s)
- Kelvin L Hull
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Melissa Lloyd
- Research and Development Department, Insect Technology Group Holdings UK Ltd., Guildford, UK
| | - Marissa Brink-Hull
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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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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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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Wakeley J, Fan WT(L, Koch E, Sunyaev S. Recurrent mutation in the ancestry of a rare variant. Genetics 2023; 224:iyad049. [PMID: 36967220 PMCID: PMC10324944 DOI: 10.1093/genetics/iyad049] [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: 01/30/2023] [Revised: 01/30/2023] [Accepted: 03/08/2023] [Indexed: 03/28/2023] Open
Abstract
Recurrent mutation produces multiple copies of the same allele which may be co-segregating in a population. Yet, most analyses of allele-frequency or site-frequency spectra assume that all observed copies of an allele trace back to a single mutation. We develop a sampling theory for the number of latent mutations in the ancestry of a rare variant, specifically a variant observed in relatively small count in a large sample. Our results follow from the statistical independence of low-count mutations, which we show to hold for the standard neutral coalescent or diffusion model of population genetics as well as for more general coalescent trees. For populations of constant size, these counts are distributed like the number of alleles in the Ewens sampling formula. We develop a Poisson sampling model for populations of varying size and illustrate it using new results for site-frequency spectra in an exponentially growing population. We apply our model to a large data set of human SNPs and use it to explain dramatic differences in site-frequency spectra across the range of mutation rates in the human genome.
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Affiliation(s)
- John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Wai-Tong (Louis) Fan
- Department of Mathematics, Indiana University, Bloomington, IN 47405, USA
- Center of Mathematical Sciences and Applications, Harvard University, Cambridge, MA 02138, USA
| | - Evan Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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