1
|
Wei Q, Wang X, Dong Y, Shang Y, Sun G, Wu X, Zhao C, Sha W, Yang G, Zhang H. Analysis of the Complete Mitochondrial Genome of Pteronura brasiliensis and Lontra canadensis. Animals (Basel) 2023; 13:3165. [PMID: 37893890 PMCID: PMC10603698 DOI: 10.3390/ani13203165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/25/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
P. brasiliensis and L. canadensis are two otter species, which successfully occupied semi-aquatic habitats and diverged from other Mustelidae. Herein, the full-length mitochondrial genome sequences were constructed for these two otter species for the first time. Comparative mitochondrial genome, selection pressure, and phylogenetic independent contrasts (PICs) analyses were conducted to determine the structure and evolutionary characteristics of their mitochondrial genomes. Phylogenetic analyses were also conducted to confirm these two otter species' phylogenetic position. The results demonstrated that the mitochondrial genome structure of P. brasiliensis and L. canadensis were consistent across Mustelidae. However, selection pressure analyses demonstrated that the evolutionary rates of mitochondrial genome protein-coding genes (PCGs) ND1, ND4, and ND4L were higher in otters than in terrestrial Mustelidae, whereas the evolutionary rates of ND2, ND6, and COX1 were lower in otters. Additionally, PIC analysis demonstrated that the evolutionary rates of ND2, ND4, and ND4L markedly correlated with a niche type. Phylogenetic analysis showed that P. brasiliensis is situated at the base of the evolutionary tree of otters, and then L. canadensis diverged from it. This study suggests a divergent evolutionary pattern of Mustelidae mitochondrial genome PCGs, prompting the otters' adaptation to semi-aquatic habitats.
Collapse
Affiliation(s)
- Qinguo Wei
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.W.); (G.Y.)
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Guolei Sun
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Chao Zhao
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Weilai Sha
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.W.); (G.Y.)
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China; (X.W.); (Y.D.); (Y.S.); (G.S.); (X.W.); (C.Z.); (W.S.)
| |
Collapse
|
2
|
The selective constraints of ecological specialization in mustelidae on mitochondrial genomes. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00461-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
3
|
Zhou L, Xiao Q, Bi J, Wang Z, Li Y. RabGTD: a comprehensive database of rabbit genome and transcriptome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5053987. [PMID: 30010730 PMCID: PMC6047408 DOI: 10.1093/database/bay075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/22/2018] [Indexed: 12/28/2022]
Abstract
The rabbit is a very important species for both biomedical research and agriculture animal breeding. They are not only the most-used experimental animals for the production of antibodies, but also widely used for studying a variety of human diseases. Here we developed RabGTD, the first comprehensive rabbit database containing both genome and transcriptome data generated by next-generation sequencing. Genomic variations coming from 79 samples were identified and annotated, including 33 samples of wild rabbits and 46 samples of domestic rabbits with diverse populations. Gene expression profiles of 86 tissue samples were complied, including those from the most commonly used models for hyperlipidemia and atherosclerosis. RabGTD is a web-based and open-access resource, which also provides convenient functions and friendly interfaces of searching, browsing and downloading for users to explore the big data. Database URL: http://www.picb.ac.cn/RabGTD/
Collapse
Affiliation(s)
- Lu Zhou
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Qingyu Xiao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Jie Bi
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,University of Chinese Academy of Sciences, 52 Sanlihe Rd., Xicheng District, Beijing 100049, China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Rd., Xuhui District, Shanghai 200031, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, 1278 Keyuan Rd., Pudong District, Shanghai 201203, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Rd., Yangpu District, Shanghai 200433, China
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Chen J, Ni P, Li X, Han J, Jakovlić I, Zhang C, Zhao S. Population size may shape the accumulation of functional mutations following domestication. BMC Evol Biol 2018; 18:4. [PMID: 29351740 PMCID: PMC5775542 DOI: 10.1186/s12862-018-1120-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e . CONCLUSIONS Our results confirm the classical population genetics theory prediction and highlight the important role of species' N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process.
Collapse
Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, 00100 Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Chengjun Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 People’s Republic of China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| |
Collapse
|
6
|
Vasemägi A, Sulku J, Bruneaux M, Thalmann O, Mäkinen H, Ozerov M. Prediction of harmful variants on mitochondrial genes: Test of habitat-dependent and demographic effects in a euryhaline fish. Ecol Evol 2017; 7:3826-3835. [PMID: 28616179 PMCID: PMC5468147 DOI: 10.1002/ece3.2989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 11/27/2022] Open
Abstract
Both effective population size and life history may influence the efficacy of purifying selection, but it remains unclear if the environment affects the accumulation of weakly deleterious nonsynonymous polymorphisms. We hypothesize that the reduced energetic cost of osmoregulation in brackish water habitat may cause relaxation of selective constraints at mitochondrial oxidative phosphorylation (OXPHOS) genes. To test this hypothesis, we analyzed 57 complete mitochondrial genomes of Pungitius pungitius collected from brackish and freshwater habitats. Based on inter‐ and intraspecific comparisons, we estimated that 84% and 68% of the nonsynonymous polymorphisms in the freshwater and brackish water populations, respectively, are weakly or moderately deleterious. Using in silico prediction tools (MutPred, SNAP2), we subsequently identified nonsynonymous polymorphisms with potentially harmful effect. Both prediction methods indicated that the functional effects of the fixed nonsynonymous substitutions between nine‐ and three‐spined stickleback were weaker than for polymorphisms within species, indicating that harmful nonsynonymous polymorphisms within populations rarely become fixed between species. No significant differences in mean estimated functional effects were identified between freshwater and brackish water nine‐spined stickleback to support the hypothesis that reduced osmoregulatory energy demand in the brackish water environment reduces the strength of purifying selection at OXPHOS genes. Instead, elevated frequency of nonsynonymous polymorphisms in the freshwater environment (Pn/Ps = 0.549 vs. 0.283; Fisher's exact test p = .032) suggested that purifying selection is less efficient in small freshwater populations. This study shows the utility of in silico functional prediction tools in population genetic and evolutionary research in a nonmammalian vertebrate and demonstrates that mitochondrial energy production genes represent a promising system to characterize the demographic, life history and potential habitat‐dependent effects of segregating amino acid variants.
Collapse
Affiliation(s)
- Anti Vasemägi
- Department of Biology University of Turku Turku Finland.,Department of Aquaculture Estonian University of Life Sciences Tartu Estonia
| | - Janne Sulku
- Department of Biology University of Turku Turku Finland
| | - Matthieu Bruneaux
- Department of Biology University of Turku Turku Finland.,Department of Biological and Environmental Science Centre of Excellence in Biological Interactions University of Jyväskylä Jyväskylä Finland
| | - Olaf Thalmann
- Department of Biology University of Turku Turku Finland.,Department of Pediatric Gastroenterology and Metabolic Diseases Poznan University of Medical Sciences Poznan Poland
| | - Hannu Mäkinen
- Department of Biology University of Turku Turku Finland
| | | |
Collapse
|
7
|
Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species. Heredity (Edinb) 2016; 116:506-15. [PMID: 26883183 DOI: 10.1038/hdy.2016.8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/02/2015] [Accepted: 12/30/2015] [Indexed: 12/26/2022] Open
Abstract
Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.
Collapse
|
8
|
Doro MG, Piras D, Leoni GG, Casu G, Vaccargiu S, Parracciani D, Naitana S, Pirastu M, Novelletto A. Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes. PLoS One 2014; 9:e95969. [PMID: 24763315 PMCID: PMC3999278 DOI: 10.1371/journal.pone.0095969] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/01/2014] [Indexed: 11/18/2022] Open
Abstract
We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg) A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.
Collapse
Affiliation(s)
- Maria Grazia Doro
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | - Daniela Piras
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
- Experimental Zoo-prophylactic Institute of Sardinia, Sassari, Italy
| | | | - Giuseppina Casu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | - Simona Vaccargiu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
| | | | - Salvatore Naitana
- Faculty of Veterinary Sciences, University of Sassari, Sassari, Italy
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council (CNR), Sassari, Italy
- Genetic Park of Ogliastra, Perdasdefogu, Italy
| | - Andrea Novelletto
- Department of Biology, University “Tor Vergata”, Rome, Italy
- * E-mail:
| |
Collapse
|
9
|
Wang GD, Xie HB, Peng MS, Irwin D, Zhang YP. Domestication Genomics: Evidence from Animals. Annu Rev Anim Biosci 2014; 2:65-84. [DOI: 10.1146/annurev-animal-022513-114129] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - David Irwin
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| |
Collapse
|
10
|
Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA. Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. ISME JOURNAL 2014; 8:1428-39. [PMID: 24451207 DOI: 10.1038/ismej.2013.248] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 12/11/2013] [Accepted: 12/14/2013] [Indexed: 11/09/2022]
Abstract
The vast majority of surface ocean bacteria are uncultivated. Compared with their cultured relatives, they frequently exhibit a streamlined genome, reduced G+C content and distinct gene repertoire. These genomic traits are relevant to environmental adaptation, and have generally been thought to become fixed in marine bacterial populations through selection. Using single-cell genomics, we sequenced four uncultivated cells affiliated with the ecologically relevant Roseobacter clade and used a composition-heterogeneous Bayesian phylogenomic model to resolve these single-cell genomes into a new clade. This lineage has no representatives in culture, yet accounts for ∼35% of Roseobacters in some surface ocean waters. Analyses of multiple genomic traits, including genome size, G+C content and percentage of noncoding DNA, suggest that these single cells are representative of oceanic Roseobacters but divergent from isolates. Population genetic analyses showed that substitution of physicochemically dissimilar amino acids and replacement of G+C-rich to G+C-poor codons are accelerated in the uncultivated clade, processes that are explained equally well by genetic drift as by the more frequently invoked explanation of natural selection. The relative importance of drift vs selection in this clade, and perhaps in other marine bacterial clades with streamlined G+C-poor genomes, remains unresolved until more evidence is accumulated.
Collapse
Affiliation(s)
- Haiwei Luo
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| |
Collapse
|
11
|
Moray C, Lanfear R, Bromham L. Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives. Genome Biol Evol 2014; 6:161-9. [PMID: 24459286 PMCID: PMC3914681 DOI: 10.1093/gbe/evu005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 11/14/2022] Open
Abstract
Studies of domesticated animals have led to the suggestion that domestication could have significant effects on patterns of molecular evolution. In particular, analyses of mitochondrial genome sequences from domestic dogs and yaks have yielded higher ratios of non-synonymous to synonymous substitutions in the domesticated lineages than in their wild relatives. These results are important because they imply that changes to selection or population size operating over a short timescale can cause significant changes to the patterns of mitochondrial molecular evolution. In this study, our aim is to test whether the impact on mitochondrial genome evolution is a general feature of domestication or whether it is specific to particular examples. We test whether domesticated mammals and birds have consistently different patterns of molecular evolution than their wild relatives for 16 phylogenetically independent comparisons of mitochondrial genome sequences. We find no consistent difference in branch lengths or dN/dS between domesticated and wild lineages. We also find no evidence that our failure to detect a consistent pattern is due to the short timescales involved or low genetic distance between domesticated lineages and their wild relatives. However, removing comparisons where the wild relative may also have undergone a bottleneck does reveal a pattern consistent with reduced effective population size in domesticated lineages. Our results suggest that, although some domesticated lineages may have undergone changes to selective regime or effective population size that could have affected mitochondrial evolution, it is not possible to generalize these patterns over all domesticated mammals and birds.
Collapse
Affiliation(s)
- Camile Moray
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Robert Lanfear
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- National Evolutionary Synthesis Center, Durham, NC
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| |
Collapse
|