1
|
Zhang WW, Weng ZY, Wang X, Yang Y, Li D, Wang L, Liu XC, Meng ZN. Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics. Zool Res 2024; 45:314-328. [PMID: 38485502 PMCID: PMC11017090 DOI: 10.24272/j.issn.2095-8137.2023.222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/05/2023] [Indexed: 03/19/2024] Open
Abstract
Animal body size variation is of particular interest in evolutionary biology, but the genetic basis remains largely unknown. Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size, providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates. Herein, we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea. Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size, respectively. A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups. Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups. These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks. Based on our results, we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection, leading to genetic variations in metabolic patterns, organ development, and lifespan, resulting in body size divergence between the two locally adapted populations. These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.
Collapse
Affiliation(s)
- Wei-Wei Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zhuo-Ying Weng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong SAR 999077, China
| | - Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Duo Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Le Wang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, Singapore City 117604, Singapore
| | - Xiao-Chun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, Guangdong 519000, China
| | - Zi-Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, Guangdong 519000, China. E-mail:
| |
Collapse
|
2
|
Silva FA, Picorelli ACR, Veiga GS, Nery MF. Patterns of enrichment and acceleration in evolutionary rates of promoters suggest a role of regulatory regions in cetacean gigantism. BMC Ecol Evol 2023; 23:62. [PMID: 37872505 PMCID: PMC10594719 DOI: 10.1186/s12862-023-02171-5] [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: 02/10/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Cetaceans (whales, porpoises, and dolphins) are a lineage of aquatic mammals from which some species became giants. Only recently, gigantism has been investigated from the molecular point of view. Studies focused mainly on coding regions, and no data on the influence of regulatory regions on gigantism in this group was available. Accordingly, we investigated the molecular evolution of non-coding regulatory regions of genes already described in the literature for association with size in mammals, focusing mainly on the promoter regions. For this, we used Ciiider and phyloP tools. Ciiider identifies significantly enriched transcription factor binding sites, and phyloP estimates the molecular evolution rate of the promoter. RESULTS We found evidence of enrichment of transcription binding factors related to large body size, with distinct patterns between giant and non-giant cetaceans in the IGFBP7 and NCAPG promoters, in which repressive agents are present in small cetaceans and those that stimulate transcription, in giant cetaceans. In addition, we found evidence of acceleration in the IGF2, IGFBP2, IGFBP7, and ZFAT promoters. CONCLUSION Our results indicate that regulatory regions may also influence cetaceans' body size, providing candidate genes for future research to understand the molecular basis of the largest living animals.
Collapse
Affiliation(s)
- Felipe A Silva
- Dept of Genetics, Evolution, Microbiology & Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, 13083-862, SP, Brazil
| | - Agnello C R Picorelli
- Dept of Genetics, Evolution, Microbiology & Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, 13083-862, SP, Brazil
| | - Giovanna S Veiga
- Dept of Genetics, Evolution, Microbiology & Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, 13083-862, SP, Brazil
| | - Mariana F Nery
- Dept of Genetics, Evolution, Microbiology & Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, 13083-862, SP, Brazil.
| |
Collapse
|
3
|
Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis. Animals (Basel) 2023; 13:ani13060992. [PMID: 36978532 PMCID: PMC10044097 DOI: 10.3390/ani13060992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Body size is one of the most economically important traits of dairy cattle, as it is significantly associated with cow longevity, production, health, fertility, and environmental adaptation. The identification and application of genetic variants using a novel genetic approach, such as genome-wide association studies (GWASs), may give more insights into the genetic architecture of complex traits. The identification of genes, single nucleotide polymorphisms (SNPs), and pathways associated with the body size traits may offer a contribution to genomic selection and long-term planning for selection in dairy cows. In this study, we performed GWAS analysis to identify the genetic markers and genes associated with four body size traits (body height, body depth, chest width, and angularity) in 1000 Chinese Holstein cows. We performed SNPs genotyping in 1000 individuals, based on the GeneSeek Genomic Profiler Bovine 100 K. In total, we identified 11 significant SNPs in association with body size traits at the threshold of Bonferroni correction (5.90 × 10−7) using the fixed and random model circulating probability unification (FarmCPU) model. Several genes within 200 kb distances (upstream or downstream) of the significant SNPs were identified as candidate genes, including MYH15, KHDRBS3, AIP, DCC, SQOR, and UBAP1L. Moreover, genes within 200 kb of the identified SNPs were significantly enriched (p ≤ 0.05) in 25 Gene Ontology terms and five Kyoto Encyclopedia of Genes and Genomes pathways. We anticipate that these results provide a foundation for understanding the genetic architecture of body size traits. They will also contribute to breeding programs and genomic selection work on Chinese Holstein cattle.
Collapse
|
4
|
Magpali L, Bielawski JP. Why are whales big? Genes behind ocean giants. Trends Genet 2023; 39:436-438. [PMID: 36997429 DOI: 10.1016/j.tig.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023]
Abstract
Gigantism is prevalent in animals, but it has never reached more extreme levels than in aquatic mammals such as whales, dolphins, and porpoises. A new study by Silva et al. has uncovered five genes underlying this gigantism, a phenotype with important connections to aging and cancer suppression in long-lived animals.
Collapse
|
5
|
Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
Collapse
Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
| |
Collapse
|
6
|
Silva FA, Souza ÉMS, Ramos E, Freitas L, Nery MF. The molecular evolution of genes previously associated with large sizes reveals possible pathways to cetacean gigantism. Sci Rep 2023; 13:67. [PMID: 36658131 PMCID: PMC9852289 DOI: 10.1038/s41598-022-24529-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/16/2022] [Indexed: 01/21/2023] Open
Abstract
Cetaceans are a group of aquatic mammals with the largest body sizes among living animals, including giant representatives such as blue and fin whales. To understand the genetic bases of gigantism in cetaceans, we performed molecular evolutionary analyses on five genes (GHSR, IGF2, IGFBP2, IGFBP7, and EGF) from the growth hormone/insulin-like growth factor axis, and four genes (ZFAT, EGF, LCORL, and PLAG1) previously described as related to the size of species evolutionarily close to cetaceans, such as pigs, cows, and sheep. Our dataset comprised 19 species of cetaceans, seven of which are classified as giants because they exceed 10 m in length. Our results revealed signs of positive selection in genes from the growth hormone/insulin-like growth factor axis and also in those related to body increase in cetacean-related species. In addition, pseudogenization of the EGF gene was detected in the lineage of toothless cetaceans, Mysticeti. Our results suggest the action of positive selection on gigantism in genes that act both in body augmentation and in mitigating its consequences, such as cancer suppression when involved in processes such as division, migration, and cell development control.
Collapse
Affiliation(s)
- Felipe André Silva
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| | - Érica M. S. Souza
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| | - Elisa Ramos
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| | - Lucas Freitas
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| | - Mariana F. Nery
- grid.411087.b0000 0001 0723 2494Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, 255, Monteiro Lobato, Cidade Universitária, IB, Bloco H, Campinas, SP 13083-862 Brazil
| |
Collapse
|
7
|
Oliveira-Rodrigues C, Correia AM, Valente R, Gil Á, Gandra M, Liberal M, Rosso M, Pierce G, Sousa-Pinto I. Assessing data bias in visual surveys from a cetacean monitoring programme. Sci Data 2022; 9:682. [DOI: 10.1038/s41597-022-01803-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
AbstractLong-term monitoring datasets are fundamental to understand physical and ecological responses to environmental changes, supporting management and conservation. The data should be reliable, with the sources of bias identified and quantified. CETUS Project is a cetacean monitoring programme in the Eastern North Atlantic, based on visual methods of data collection. This study aims to assess data quality and bias in the CETUS dataset, by 1) applying validation methods, through photographic confirmation of species identification; 2) creating data quality criteria to evaluate the observer’s experience; and 3) assessing bias to the number of sightings collected and to the success in species identification. Through photographic validation, the species identification of 10 sightings was corrected and a new species was added to the CETUS dataset. The number of sightings collected was biased by external factors, mostly by sampling effort but also by weather conditions. Ultimately, results highlight the importance of identifying and quantifying data bias, while also yielding guidelines for data collection and processing, relevant for species monitoring programmes based on visual methods.
Collapse
|
8
|
Tejada-Martinez D, de Magalhães JP, Opazo JC. Positive selection and gene duplications in tumour suppressor genes reveal clues about how cetaceans resist cancer. Proc Biol Sci 2021; 288:20202592. [PMID: 33622125 DOI: 10.1098/rspb.2020.2592] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cetaceans are the longest-living species of mammals and the largest in the history of the planet. They have developed mechanisms against diseases such cancer, although the underlying molecular bases of these remain unknown. The goal of this study was to investigate the role of natural selection in the evolution of 1077 tumour suppressor genes (TSGs) in cetaceans. We used a comparative genomic approach to analyse two sources of molecular variation in the form of dN/dS rates and gene copy number variation. We found a signal of positive selection in the ancestor of cetaceans within the CXCR2 gene, an important regulator of DNA damage, tumour dissemination and immune system. Further, in the ancestor of baleen whales, we found six genes exhibiting positive selection relating to diseases such as breast carcinoma, lung neoplasm (ADAMTS8) and leukaemia (ANXA1). The TSGs turnover rate (gene gain and loss) was almost 2.4-fold higher in cetaceans when compared with other mammals, and notably even faster in baleen whales. The molecular variants in TSGs found in baleen whales, combined with the faster gene turnover rate, could have favoured the evolution of their particular traits of anti-cancer resistance, gigantism and longevity. Additionally, we report 71 genes with duplications, of which 11 genes are linked to longevity (e.g. NOTCH3 and SIK1) and are important regulators of senescence, cell proliferation and metabolism. Overall, these results provide evolutionary evidence that natural selection in TSGs could act on species with large body sizes and extended lifespan, providing novel insights into the genetic basis of disease resistance.
Collapse
Affiliation(s)
- Daniela Tejada-Martinez
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.,Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Valdivia, Chile.,Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
| |
Collapse
|
9
|
Sendell-Price AT, Ruegg KC, Clegg SM. Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection. Heredity (Edinb) 2020; 124:535-549. [PMID: 32080374 PMCID: PMC7080774 DOI: 10.1038/s41437-020-0298-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/25/2023] Open
Abstract
Theory predicts that when populations are established by few individuals, random founder effects can facilitate rapid phenotypic divergence even in the absence of selective processes. However, empirical evidence from historically documented colonisations suggest that, in most cases, drift alone is not sufficient to explain the rate of morphological divergence. Here, using the human-mediated introduction of the silvereye (Zosterops lateralis) to French Polynesia, which represents a potentially extreme example of population founding, we reassess the potential for morphological shifts to arise via drift alone. Despite only 80 years of separation from their New Zealand ancestors, French Polynesian silvereyes displayed significant changes in body and bill size and shape, most of which could be accounted for by drift, without the need to invoke selection. However, signatures of selection at genes previously identified as candidates for bill size and body shape differences in a range of bird species, also suggests a role for selective processes in driving morphological shifts within this population. Twenty-four SNPs in our RAD-Seq dataset were also found to be strongly associated with phenotypic variation. Hence, even under population founding extremes, when it is difficult to reject drift as the sole mechanism based on rate tests of phenotypic shifts, the additional role of divergent natural selection in novel environments can be revealed at the level of the genome.
Collapse
Affiliation(s)
- Ashley T Sendell-Price
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Kristen C Ruegg
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sonya M Clegg
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK
- Environmental Futures Research Institute, Griffith University, Queensland, 4111, Australia
| |
Collapse
|