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Escorcia-Rodríguez JM, Esposito M, Freyre-González JA, Moreno-Hagelsieb G. Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty. PeerJ 2022; 10:e13843. [PMID: 36065404 PMCID: PMC9440661 DOI: 10.7717/peerj.13843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 07/14/2022] [Indexed: 01/18/2023] Open
Abstract
Orthologs separate after lineages split from each other and paralogs after gene duplications. Thus, orthologs are expected to remain more functionally coherent across lineages, while paralogs have been proposed as a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synonymous to synonymous substitutions (dN/dS), as proxy for functional divergence. We used five working definitions of orthology, including reciprocal best hits (RBH), among other definitions based on network analyses and clustering. The results showed that orthologs, by all definitions tested, had values of dN/dS noticeably lower than those of paralogs, suggesting that orthologs generally tend to be more functionally stable than paralogs. The differences in dN/dS ratios remained suggesting the functional stability of orthologs after eliminating gene comparisons with potential problems, such as genes with high codon usage biases, low coverage of either of the aligned sequences, or sequences with very high similarities. Separation by percent identity of the encoded proteins showed that the differences between the dN/dS ratios of orthologs and paralogs were more evident at high sequence identity, less so as identity dropped. The last results suggest that the differences between dN/dS ratios were partially related to differences in protein identity. However, they also suggested that paralogs undergo functional divergence relatively early after duplication. Our analyses indicate that choosing orthologs as probably functionally coherent remains the right approach in comparative genomics.
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Affiliation(s)
- Juan M. Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autonóma de México, Cuernavaca, Morelos, México
| | - Mario Esposito
- Department of Biology, Wilfrid Laurier University, Waterloo, Canada
| | - Julio A. Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autonóma de México, Cuernavaca, Morelos, México
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Zheng J, Wang J, Gong Z, Han GZ. Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water. PLoS Pathog 2021; 17:e1009730. [PMID: 34252162 PMCID: PMC8297934 DOI: 10.1371/journal.ppat.1009730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/22/2021] [Accepted: 06/18/2021] [Indexed: 11/18/2022] Open
Abstract
The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history.
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Affiliation(s)
- Jialu Zheng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jianhua Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhen Gong
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
- * E-mail:
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3
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Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda. Sci Rep 2018; 8:17964. [PMID: 30568252 PMCID: PMC6299273 DOI: 10.1038/s41598-018-36428-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/19/2018] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial DNA hyperdiversity is primarily caused by high mutation rates (µ) and has potential implications for mitogenome architecture and evolution. In the hyperdiverse mtDNA of Melarhaphe neritoides (Gastropoda: Littorinidae), high mutational pressure generates unusually large amounts of synonymous variation, which is expected to (1) promote changes in synonymous codon usage, (2) reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. The mitogenome of M. neritoides was sequenced, compared to closely related littorinids and put in the phylogenetic context of Caenogastropoda, to assess the influence of mtDNA hyperdiversity and high µ on gene content and gene order. Most mitogenome features are in line with the trend in Mollusca, except for the atypical secondary structure of the methionine transfer RNA lacking the TΨC-loop. Therefore, mtDNA hyperdiversity and high µ in M. neritoides do not seem to affect its mitogenome architecture. Synonymous sites are under positive selection, which adds to the growing evidence of non-neutral evolution at synonymous sites. Under such non-neutrality, substitution rate involves neutral and non-neutral substitutions, and high µ is not necessarily associated with high substitution rate, thus explaining that, unlike high µ, a high substitution rate is associated with gene order rearrangement.
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Chen J, Ni P, Tran Thi TN, Kamaldinov EV, Petukhov VL, Han J, Liu X, Šprem N, Zhao S. Selective constraints in cold-region wild boars may defuse the effects of small effective population size on molecular evolution of mitogenomes. Ecol Evol 2018; 8:8102-8114. [PMID: 30250687 PMCID: PMC6144961 DOI: 10.1002/ece3.4221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/25/2018] [Accepted: 05/11/2018] [Indexed: 12/15/2022] Open
Abstract
Spatial range expansion during population colonization is characterized by demographic events that may have significant effects on the efficiency of natural selection. Population genetics suggests that genetic drift brought by small effective population size (Ne) may undermine the efficiency of selection, leading to a faster accumulation of nonsynonymous mutations. However, it is still unknown whether this effect might be balanced or even reversed by strong selective constraints. Here, we used wild boars and local domestic pigs from tropical (Vietnam) and subarctic region (Siberia) as animal model to evaluate the effects of functional constraints and genetic drift on shaping molecular evolution. The likelihood-ratio test revealed that Siberian clade evolved significantly different from Vietnamese clades. Different datasets consistently showed that Siberian wild boars had lower Ka/Ks ratios than Vietnamese samples. The potential role of positive selection for branches with higher Ka/Ks was evaluated using branch-site model comparison. No signal of positive selection was found for the higher Ka/Ks in Vietnamese clades, suggesting the interclade difference was mainly due to the reduction in Ka/Ks for Siberian samples. This conclusion was further confirmed by the result from a larger sample size, among which wild boars from northern Asia (subarctic and nearby region) had lower Ka/Ks than those from southern Asia (temperate and tropical region). The lower Ka/Ks might be due to either stronger functional constraints, which prevent nonsynonymous mutations from accumulating in subarctic wild boars, or larger Ne in Siberian wild boars, which can boost the efficacy of purifying selection to remove functional mutations. The latter possibility was further ruled out by the Bayesian skyline plot analysis, which revealed that historical Ne of Siberian wild boars was smaller than that of Vietnamese wild boars. Altogether, these results suggest stronger functional constraints acting on mitogenomes of subarctic wild boars, which may provide new insights into their local adaptation of cold resistance.
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Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinois
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
| | - Thuy Nhien Tran Thi
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
- National Institute of Animal SciencesHanoiVietnam
| | - Evgeniy Varisovich Kamaldinov
- Federal State Budgetary Educational Institution of Higher EducationNovosibirsk State Agrarian UniversityNovosibirskRussia
| | - Valeriy Lavrentyevich Petukhov
- Federal State Budgetary Educational Institution of Higher EducationNovosibirsk State Agrarian UniversityNovosibirskRussia
| | - Jianlin Han
- International Livestock Research Institute (ILRI)NairobiKenya
- CAAS‐ILRI Joint Laboratory on Livestock and Forage Genetic ResourcesInstitute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiangdong Liu
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
| | - Nikica Šprem
- Department of Fisheries, Beekeeping, Game Management and Special ZoologyFaculty of AgricultureUniversity of ZagrebZagrebCroatia
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
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Parker DJ, Wiberg RAW, Trivedi U, Tyukmaeva VI, Gharbi K, Butlin RK, Hoikkala A, Kankare M, Ritchie MG. Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation. Genome Biol Evol 2018; 10:2086-2101. [PMID: 30010752 PMCID: PMC6107330 DOI: 10.1093/gbe/evy147] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 12/25/2022] Open
Abstract
The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here, we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species known. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm-adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We also look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, but do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. Finally, we also resequenced three populations of D. montana from across its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.
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Affiliation(s)
- Darren J Parker
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
- Department of Ecology and Evolution, University of Lausanne, Biophore, Switzerland
| | - R Axel W Wiberg
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Venera I Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Karim Gharbi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences, The University of Sheffield, UK
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Michael G Ritchie
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
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6
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Gayk ZG, Le Duc D, Horn J, Lindsay AR. Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation. BMC Evol Biol 2018; 18:64. [PMID: 29703132 PMCID: PMC5921391 DOI: 10.1186/s12862-018-1181-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/16/2018] [Indexed: 11/12/2022] Open
Abstract
Background The common loon (Gavia immer) is one of five species that comprise the avian order Gaviiformes. Loons are specialized divers, reaching depths up to 60 m while staying submerged for intervals up to three minutes. In this study we used comparative genomics to investigate the genetic basis of the common loon adaptations to its ecological niche. We used Illumina short read DNA sequence data from a female bird to produce a draft assembly of the common loon (Gavia immer) genome. Results We identified 14,169 common loon genes, which based on well-resolved avian genomes, represent approximately 80.7% of common loon genes. Evolutionary analyses between common loon and Adelie penguin (Pygoscelis adeliae), red-throated loon (Gavia stellata), chicken (Gallus gallus), northern fulmar (Fulmarus glacialis), and rock pigeon (Columba livia) show 164 positively selected genes in common and red-throated loons. These genes were enriched for a number of protein classes, including those involved in muscle tissue development, immunoglobulin function, hemoglobin iron binding, G-protein coupled receptors, and ATP metabolism. Conclusions Signatures of positive selection in these areas suggest the genus Gavia may have adapted for underwater diving by modulating their oxidative and metabolic pathways. While more research is required, these adaptations likely result in (1) compensations in oxygen respiration and energetic metabolism, (2) low-light visual acuity, and (3) elevated solute exchange. This work represents the first effort to understand the genomic adaptations of the common loon as well as other Gavia and may have implications for subsequent studies that target particular genes for loon population genetic, ecological or conservation studies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1181-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zach G Gayk
- Biology Department, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, 49950, Michigan, USA. .,Biology Department, University of Windsor, 401 Sunset Avenue, Windsor, N9B 3P4, Ontario, Canada.
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jeffrey Horn
- Department of Mathematics and Computer Science, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, 49950, Michigan, USA
| | - Alec R Lindsay
- Biology Department, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, 49950, Michigan, USA
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Oda H, Ota M, Toh H. Profile comparison revealed deviation from structural constraint at the positively selected sites. Biosystems 2016; 147:67-77. [PMID: 27443483 DOI: 10.1016/j.biosystems.2016.07.007] [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: 01/11/2015] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 11/18/2022]
Abstract
The amino acid substitutions at a site are affected by mixture of various constraints. It is also known that the amino acid substitutions are accelerated at sites under positive selection. However, the relationship between the substitutions at positively selected sites and the constraints has not been thoroughly examined. The advances in computational biology have enabled us to divide the mixture of the constraints into the structural constraint and the remainings by using the amino acid sequences and the tertiary structures, which is expressed as the deviation of the mixture of constraints from the structural constraint. Here, two types of profiles, or matrices with the size of 20 x (site length), are compared. One of the profiles represents the mixture of constraints, and is generated from a multiple amino acid sequence alignment, whereas the other is designed to represent the structural constraints. We applied the profile comparison method to proteins under positive selection to examine the relationship between the positive selection and constraints. The results suggested that the constraint at a site under positive selection tends to be deviated from the structural constraint at the site.
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Affiliation(s)
- Hiroyuki Oda
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan.
| | - Motonori Ota
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya City, Aichi 464-8601, Japan
| | - Hiroyuki Toh
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
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Echave J, Spielman SJ, Wilke CO. Causes of evolutionary rate variation among protein sites. Nat Rev Genet 2016; 17:109-21. [PMID: 26781812 DOI: 10.1038/nrg.2015.18] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It has long been recognized that certain sites within a protein, such as sites in the protein core or catalytic residues in enzymes, are evolutionarily more conserved than other sites. However, our understanding of rate variation among sites remains surprisingly limited. Recent progress to address this includes the development of a wide array of reliable methods to estimate site-specific substitution rates from sequence alignments. In addition, several molecular traits have been identified that correlate with site-specific mutation rates, and novel mechanistic biophysical models have been proposed to explain the observed correlations. Nonetheless, current models explain, at best, approximately 60% of the observed variance, highlighting the limitations of current methods and models and the need for new research directions.
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Affiliation(s)
- Julian Echave
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires, Argentina
| | - Stephanie J Spielman
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Claus O Wilke
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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