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Li Y, Wang D, Wang W, Yang W, Gao J, Zhang W, Shan L, Kang M, Chen Y, Ma T. A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination. Mol Ecol 2023; 32:1366-1380. [PMID: 35712997 DOI: 10.1111/mec.16566] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/24/2022] [Accepted: 06/10/2022] [Indexed: 01/17/2023]
Abstract
Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.
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Affiliation(s)
- Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Weiwei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jinwen Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenyan Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lanxing Shan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
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2
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Zhao Q, Zhang R, Xiao Y, Niu Y, Shao F, Li Y, Peng Z. Comparative Transcriptome Profiling of the Loaches Triplophysa bleekeri and Triplophysa rosa Reveals Potential Mechanisms of Eye Degeneration. Front Genet 2020; 10:1334. [PMID: 32010191 PMCID: PMC6977438 DOI: 10.3389/fgene.2019.01334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Eye degeneration is one of the most obvious characteristics of organisms restricted to subterranean habitats. In cavefish, eye degeneration has evolved independently numerous times and each process is associated with different genetic mechanisms. To gain a better understanding of these mechanisms, we compared the eyes of adult individuals of the cave loach Triplophysa rosa and surface loach Triplophysa bleekeri. Compared with the normal eyes of the surface loach, those of the cave loach were found to possess a small abnormal lens and a defective retina containing photoreceptor cells that lack outer segments. Sequencing of the transcriptomes of both species to identify differentially expressed genes (DEGs) and genes under positive selection revealed 4,802 DEGs and 50 genes under positive selection (dN/dS > 1, FDR < 0.1). For cave loaches, we identified one Gene Ontology category related to vision that was significantly enriched in downregulated genes. Specifically, we found that many of the downregulated genes, including pitx3, lim2, crx, gnat2, rx1, rho, prph2, and β|γ-crystallin are associated with lens/retinal development and maintenance. However, compared with those in the surface loach, the lower dS rates but higher dN rates of the protein-coding sequences in T. rosa indicate that changes in amino acid sequences might be involved in the adaptation and visual degeneration of cave loaches. We also found that genes associated with light perception and light-stimulated vision have evolved at higher rates (some genes dN/dS > 1 but FDR > 0.1). Collectively, the findings of this study indicate that the degradation of cavefish vision is probably associated with both gene expression and amino acid changes and provide new insights into the mechanisms underlying the degeneration of cavefish eyes.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yingqi Xiao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yabing Niu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
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3
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Hamabata T, Kinoshita G, Kurita K, Cao PL, Ito M, Murata J, Komaki Y, Isagi Y, Makino T. Endangered island endemic plants have vulnerable genomes. Commun Biol 2019; 2:244. [PMID: 31263788 PMCID: PMC6597543 DOI: 10.1038/s42003-019-0490-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/03/2019] [Indexed: 11/29/2022] Open
Abstract
Loss of genetic diversity is known to decrease the fitness of species and is a critical factor that increases extinction risk. However, there is little evidence for higher vulnerability and extinction risk in endangered species based on genomic differences between endangered and non-endangered species. This is true even in the case of functional loci, which are more likely to relate to the fitness of species than neutral loci. Here, we compared the genome-wide genetic diversity, proportion of duplicated genes (PD), and accumulation of deleterious variations of endangered island endemic (EIE) plants from four genera with those of their non-endangered (NE) widespread congeners. We focused on exhaustive sequences of expressed genes obtained by RNA sequencing. Most EIE species exhibited significantly lower genetic diversity and PD than NE species. Additionally, all endangered species accumulated deleterious variations. Our findings provide new insights into the genomic traits of EIE species.
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Affiliation(s)
- Tomoko Hamabata
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578 Japan
| | - Gohta Kinoshita
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502 Japan
| | - Kazuki Kurita
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502 Japan
| | - Ping-Lin Cao
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578 Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902 Japan
| | - Jin Murata
- Koishikawa Botanical Garden, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 112-0001 Japan
| | - Yoshiteru Komaki
- Koishikawa Botanical Garden, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 112-0001 Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502 Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578 Japan
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4
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Wang K, Shen Y, Yang Y, Gan X, Liu G, Hu K, Li Y, Gao Z, Zhu L, Yan G, He L, Shan X, Yang L, Lu S, Zeng H, Pan X, Liu C, Yuan Y, Feng C, Xu W, Zhu C, Xiao W, Dong Y, Wang W, Qiu Q, He S. Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nat Ecol Evol 2019; 3:823-833. [PMID: 30988486 DOI: 10.1038/s41559-019-0864-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 03/06/2019] [Indexed: 12/30/2022]
Abstract
It is largely unknown how living organisms-especially vertebrates-survive and thrive in the coldness, darkness and high pressures of the hadal zone. Here, we describe the unique morphology and genome of Pseudoliparis swirei-a recently described snailfish species living below a depth of 6,000 m in the Mariana Trench. Unlike closely related shallow sea species, P. swirei has transparent, unpigmented skin and scales, thin and incompletely ossified bones, an inflated stomach and a non-closed skull. Phylogenetic analyses show that P. swirei diverged from a close relative living near the sea surface about 20 million years ago and has abundant genetic diversity. Genomic analyses reveal that: (1) the bone Gla protein (bglap) gene has a frameshift mutation that may cause early termination of cartilage calcification; (2) cell membrane fluidity and transport protein activity in P. swirei may have been enhanced by changes in protein sequences and gene expansion; and (3) the stability of its proteins may have been increased by critical mutations in the trimethylamine N-oxide-synthesizing enzyme and hsp90 chaperone protein. Our results provide insights into the morphological, physiological and molecular evolution of hadal vertebrates.
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Affiliation(s)
- Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yanjun Shen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaoni Gan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guichun Liu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Kuang Hu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yongxin Li
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Zhaoming Gao
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Li Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guoyong Yan
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lisheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xiujuan Shan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao, China
| | - Liandong Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Suxiang Lu
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Honghui Zeng
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiangyu Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chang Liu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yuan Yuan
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Chenguang Feng
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Wenjie Xu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Chenglong Zhu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Wuhan Xiao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yang Dong
- Biological Big Data College, Yunnan Agricultural University, Kunming, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China. .,Qingdao Research Institute, Northwestern Polytechnical University, Qingdao, China. .,Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - Qiang Qiu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China. .,State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China. .,Qingdao Research Institute, Northwestern Polytechnical University, Qingdao, China.
| | - Shunping He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China. .,Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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5
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Subramanian S. Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure. Genome Biol Evol 2018; 10:756-762. [PMID: 29608718 PMCID: PMC5841380 DOI: 10.1093/gbe/evy047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2018] [Indexed: 11/14/2022] Open
Abstract
The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = πN/πS) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (Ne) and selection coefficient (s). Here, we examined the effects of effective population size on ω by comparing protein-coding genes from Mus musculus castaneus and Mus musculus musculus-two mouse subspecies with different Ne. Our results revealed a positive relationship between the magnitude of selection intensity and the ω estimated for genes. For genes under high selective constraints, the ω estimated for the subspecies with small Ne (M. m. musculus) was three times higher than that observed for that with large Ne (M. m. castaneus). However, this difference was only 18% for genes under relaxed selective constraints. We showed that the observed relationship is qualitatively similar to the theoretical predictions. We also showed that, for highly expressed genes, the ω of M. m. musculus was 2.1 times higher than that of M.m. castaneus and this difference was only 27% for genes with low expression levels. These results suggest that the effect of effective population size is more pronounced in genes under high purifying selection. Hence the choice of genes is important when ω is used to infer the effective size of a population.
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Affiliation(s)
- Sankar Subramanian
- GeneCology Research Centre, The University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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6
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Botero-Castro F, Tilak MK, Justy F, Catzeflis F, Delsuc F, Douzery EJP. In Cold Blood: Compositional Bias and Positive Selection Drive the High Evolutionary Rate of Vampire Bats Mitochondrial Genomes. Genome Biol Evol 2018; 10:2218-2239. [PMID: 29931241 PMCID: PMC6127110 DOI: 10.1093/gbe/evy120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial genomes of animals have long been considered to evolve under the action of purifying selection. Nevertheless, there is increasing evidence that they can also undergo episodes of positive selection in response to shifts in physiological or environmental demands. Vampire bats experienced such a shift, as they are the only mammals feeding exclusively on blood and possessing anatomical adaptations to deal with the associated physiological requirements (e.g., ingestion of high amounts of liquid water and iron). We sequenced eight new chiropteran mitogenomes including two species of vampire bats, five representatives of other lineages of phyllostomids and one close outgroup. Conducting detailed comparative mitogenomic analyses, we found evidence for accelerated evolutionary rates at the nucleotide and amino acid levels in vampires. Moreover, the mitogenomes of vampire bats are characterized by an increased cytosine (C) content mirrored by a decrease in thymine (T) compared with other chiropterans. Proteins encoded by the vampire bat mitogenomes also exhibit a significant increase in threonine (Thr) and slight reductions in frequency of the hydrophobic residues isoleucine (Ile), valine (Val), methionine (Met), and phenylalanine (Phe). We show that these peculiar substitution patterns can be explained by the co-occurrence of both neutral (mutational bias) and adaptive (positive selection) processes. We propose that vampire bat mitogenomes may have been impacted by selection on mitochondrial proteins to accommodate the metabolism and nutritional qualities of blood meals.
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Affiliation(s)
- Fidel Botero-Castro
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Marie-Ka Tilak
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Fabienne Justy
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - François Catzeflis
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Emmanuel J P Douzery
- Institut des Sciences de l'Evolution (ISEM), Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
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7
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Abstract
The prevalence of purifying selection in the nature suggests that larger organisms bear a higher number of slightly deleterious mutations because of smaller populations and therefore weaker selection. In this work redistribution of purifying selection in favor of information genes, pathways and processes was found in primates compared with treeshrew and rodents on the ground of genome-wide analysis. The genes which are more favored in primates belong mainly to regulation of gene expression and development, in treeshrew and rodents, to metabolism, transport, energetics, reproduction and olfaction. The former occur predominantly in the nucleus, the latter, in the cytoplasm and membranes. Thus, although purifying selection is on average weaker in the primates, it is stronger concentrated on the "information technology" of life (regulation of gene expression and development). Increased accuracy of information processes probably allows escaping "error catastrophes" in spite of more complex organization, larger body size and higher longevity.
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8
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Fujisawa T, Vogler AP, Barraclough TG. Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles. Proc Biol Sci 2015; 282:20142476. [PMID: 25621335 DOI: 10.1098/rspb.2014.2476] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.
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9
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Zhan J, Thrall PH, Papaïx J, Xie L, Burdon JJ. Playing on a pathogen's weakness: using evolution to guide sustainable plant disease control strategies. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:19-43. [PMID: 25938275 DOI: 10.1146/annurev-phyto-080614-120040] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Wild plants and their associated pathogens are involved in ongoing interactions over millennia that have been modified by coevolutionary processes to limit the spatial extent and temporal duration of disease epidemics. These interactions are disrupted by modern agricultural practices and social activities, such as intensified monoculture using superior varieties and international trading of agricultural commodities. These activities, when supplemented with high resource inputs and the broad application of agrochemicals, create conditions uniquely conducive to widespread plant disease epidemics and rapid pathogen evolution. To be effective and durable, sustainable disease management requires a significant shift in emphasis to overtly include ecoevolutionary principles in the design of adaptive management programs aimed at minimizing the evolutionary potential of plant pathogens by reducing their genetic variation, stabilizing their evolutionary dynamics, and preventing dissemination of pathogen variants carrying new infectivity or resistance to agrochemicals.
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Affiliation(s)
- Jiasui Zhan
- Key Laboratory for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China;
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10
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Deng F, Xia C, Jia X, Song T, Liu J, Lai SJ, Chen SY. Comparative Study on the Genetic Diversity ofGHRGene in Tibetan Cattle and Holstein Cows. Anim Biotechnol 2015; 26:217-21. [DOI: 10.1080/10495398.2014.993082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Luisi P, Alvarez-Ponce D, Pybus M, Fares MA, Bertranpetit J, Laayouni H. Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. Genome Biol Evol 2015; 7:1141-54. [PMID: 25840415 PMCID: PMC4419801 DOI: 10.1093/gbe/evv055] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genes vary in their likelihood to undergo adaptive evolution. The genomic factors that determine adaptability, however, remain poorly understood. Genes function in the context of molecular networks, with some occupying more important positions than others and thus being likely to be under stronger selective pressures. However, how positive selection distributes across the different parts of molecular networks is still not fully understood. Here, we inferred positive selection using comparative genomics and population genetics approaches through the comparison of 10 mammalian and 270 human genomes, respectively. In agreement with previous results, we found that genes with lower network centralities are more likely to evolve under positive selection (as inferred from divergence data). Surprisingly, polymorphism data yield results in the opposite direction than divergence data: Genes with higher centralities are more likely to have been targeted by recent positive selection during recent human evolution. Our results indicate that the relationship between centrality and the impact of adaptive evolution highly depends on the mode of positive selection and/or the evolutionary time-scale.
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Affiliation(s)
- Pierre Luisi
- Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - David Alvarez-Ponce
- Integrative Systems Biology Group, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Spain Biology Department, University of Nevada, Reno Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Marc Pybus
- Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Mario A Fares
- Integrative Systems Biology Group, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Spain Smurfit Institute of Genetics, University of Dublin, Trinity College, Ireland
| | - Jaume Bertranpetit
- Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain Departament de Genètica i de Microbiologia, Grup de Biologia Evolutiva (GBE), Universitat Autonòma de Barcelona, Bellaterra, Spain
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12
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McCandlish DM, Stoltzfus A. Modeling evolution using the probability of fixation: history and implications. QUARTERLY REVIEW OF BIOLOGY 2014; 89:225-52. [PMID: 25195318 DOI: 10.1086/677571] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Many models of evolution calculate the rate of evolution by multiplying the rate at which new mutations originate within a population by a probability of fixation. Here we review the historical origins, contemporary applications, and evolutionary implications of these "origin-fixation" models, which are widely used in evolutionary genetics, molecular evolution, and phylogenetics. Origin-fixation models were first introduced in 1969, in association with an emerging view of "molecular" evolution. Early origin-fixation models were used to calculate an instantaneous rate of evolution across a large number of independently evolving loci; in the 1980s and 1990s, a second wave of origin-fixation models emerged to address a sequence of fixation events at a single locus. Although origin fixation models have been applied to a broad array of problems in contemporary evolutionary research, their rise in popularity has not been accompanied by an increased appreciation of their restrictive assumptions or their distinctive implications. We argue that origin-fixation models constitute a coherent theory of mutation-limited evolution that contrasts sharply with theories of evolution that rely on the presence of standing genetic variation. A major unsolved question in evolutionary biology is the degree to which these models provide an accurate approximation of evolution in natural populations.
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13
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Zhang J, Lou X, Zellmer L, Liu S, Xu N, Liao DJ. Just like the rest of evolution in Mother Nature, the evolution of cancers may be driven by natural selection, and not by haphazard mutations. Oncoscience 2014; 1:580-90. [PMID: 25594068 PMCID: PMC4278337 DOI: 10.18632/oncoscience.83] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022] Open
Abstract
Sporadic carcinogenesis starts from immortalization of a differentiated somatic cell or an organ-specific stem cell. The immortalized cell incepts a new or quasinew organism that lives like a parasite in the patient and usually proceeds to progressive simplification, constantly engendering intermediate organisms that are simpler than normal cells. Like organismal evolution in Mother Nature, this cellular simplification is a process of Darwinian selection of those mutations with growth- or survival-advantages, from numerous ones that occur randomly and stochastically. Therefore, functional gain of growth- or survival-sustaining oncogenes and functional loss of differentiation-sustaining tumor suppressor genes, which are hallmarks of cancer cells and contribute to phenotypes of greater malignancy, are not drivers of carcinogenesis but are results from natural selection of advantageous mutations. Besides this mutation-load dependent survival mechanism that is evolutionarily low and of an asexual nature, cancer cells may also use cell fusion for survival, which is an evolutionarily-higher mechanism and is of a sexual nature. Assigning oncogenes or tumor suppressor genes or their mutants as drivers to induce cancer in animals may somewhat coerce them to create man-made oncogenic pathways that may not really be a course of sporadic cancer formations in the human.
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Affiliation(s)
- Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Lucas Zellmer
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology, Cancer Institute, Chinese Academy of Medical Science, Beijing 100021, P.R. China
| | - D Joshua Liao
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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14
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Szövényi P, Devos N, Weston DJ, Yang X, Hock Z, Shaw JA, Shimizu KK, McDaniel SF, Wagner A. Efficient purging of deleterious mutations in plants with haploid selfing. Genome Biol Evol 2014; 6:1238-52. [PMID: 24879432 PMCID: PMC4041004 DOI: 10.1093/gbe/evu099] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In diploid organisms, selfing reduces the efficiency of selection in removing deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme form of selfing known as intragametophytic selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Here, we ask how effectively deleterious mutations are removed from such plants. Specifically, we study the extent to which deleterious mutations accumulate in a predominantly selfing and a predominantly outcrossing pair of moss species, using genome-wide transcriptome data. We find that the selfing species purge significantly more nonsynonymous mutations, as well as a greater proportion of radical amino acid changes which alter physicochemical properties of amino acids. Moreover, their purging of deleterious mutation is especially strong in conserved regions of protein-coding genes. Our observations show that selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale.
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Affiliation(s)
- Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandInstitute of Systematic Botany, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandMTA-ELTE-MTM Ecology Research Group, ELTE, Biological Institute, Hungary
| | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Zsófia Hock
- Institute of Systematic Botany, University of Zurich, Switzerland
| | | | - Kentaro K Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | | | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandBioinformatics Institute, Agency for Science, Technology and Research (A*STAR), SingaporeThe Santa Fe Institute, Santa Fe NM
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15
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Lou X, Zhang J, Liu S, Xu N, Liao DJ. The other side of the coin: the tumor-suppressive aspect of oncogenes and the oncogenic aspect of tumor-suppressive genes, such as those along the CCND-CDK4/6-RB axis. Cell Cycle 2014; 13:1677-93. [PMID: 24799665 DOI: 10.4161/cc.29082] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although cancer-regulatory genes are dichotomized to oncogenes and tumor-suppressor gene s, in reality they can be oncogenic in one situation but tumor-suppressive in another. This dual-function nature, which sometimes hampers our understanding of tumor biology, has several manifestations: (1) Most canonically defined genes have multiple mRNAs, regulatory RNAs, protein isoforms, and posttranslational modifications; (2) Genes may interact at different levels, such as by forming chimeric RNAs or by forming different protein complexes; (3) Increased levels of tumor-suppressive genes in normal cells drive proliferation of cancer progenitor cells in the same organ or tissue by imposing compensatory proliferation pressure, which presents the dual-function nature as a cell-cell interaction. All these manifestations of dual functions can find examples in the genes along the CCND-CDK4/6-RB axis. The dual-function nature also underlies the heterogeneity of cancer cells. Gene-targeting chemotherapies, including that targets CDK4, are effective to some cancer cells but in the meantime may promote growth or progression of some others in the same patient. Redefining "gene" by considering each mRNA, regulatory RNA, protein isoform, and posttranslational modification from the same genomic locus as a "gene" may help in better understanding tumor biology and better selecting targets for different sub-populations of cancer cells in individual patients for personalized therapy.
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Affiliation(s)
- Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology; Cancer Institute; Chinese Academy of Medical Science; Beijing, PR China
| | - D Joshua Liao
- Hormel Institute; University of Minnesota; Austin, MN USA
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