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Sprengelmeyer QD, Pool JE. Ethanol resistance in Drosophila melanogaster has increased in parallel cold-adapted populations and shows a variable genetic architecture within and between populations. Ecol Evol 2021; 11:15364-15376. [PMID: 34765183 PMCID: PMC8571616 DOI: 10.1002/ece3.8228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/24/2021] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the genetic properties of adaptive trait evolution is a fundamental crux of biological inquiry that links molecular processes to biological diversity. Important uncertainties persist regarding the genetic predictability of adaptive trait change, the role of standing variation, and whether adaptation tends to result in the fixation of favored variants. Here, we use the recurrent evolution of enhanced ethanol resistance in Drosophila melanogaster during this species' worldwide expansion as a promising system to add to our understanding of the genetics of adaptation. We find that elevated ethanol resistance has evolved at least three times in different cooler regions of the species' modern range-not only at high latitude but also in two African high-altitude regions. Applying a bulk segregant mapping framework, we find that the genetic architecture of ethanol resistance evolution differs substantially not only between our three resistant populations, but also between two crosses involving the same European population. We then apply population genetic scans for local adaptation within our quantitative trait locus regions, and we find potential contributions of genes with annotated roles in spindle localization, membrane composition, sterol and alcohol metabolism, and other processes. We also apply simulation-based analyses that confirm the variable genetic basis of ethanol resistance and hint at a moderately polygenic architecture. However, these simulations indicate that larger-scale studies will be needed to more clearly quantify the genetic architecture of adaptive evolution and to firmly connect trait evolution to specific causative loci.
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Affiliation(s)
| | - John E. Pool
- Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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2
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Leal BSS, Chaves CJN, Graciano VA, Boury C, Huacre LAP, Heuertz M, Palma-Silva C. Evidence of local adaptation despite strong drift in a Neotropical patchily distributed bromeliad. Heredity (Edinb) 2021; 127:203-218. [PMID: 33953353 PMCID: PMC8322333 DOI: 10.1038/s41437-021-00442-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Both genetic drift and divergent selection are predicted to be drivers of population differentiation across patchy habitats, but the extent to which these forces act on natural populations to shape traits is strongly affected by species' ecological features. In this study, we infer the genomic structure of Pitcairnia lanuginosa, a widespread herbaceous perennial plant with a patchy distribution. We sampled populations in the Brazilian Cerrado and the Central Andean Yungas and discovered and genotyped SNP markers using double-digest restriction-site associated DNA sequencing. In addition, we analyzed ecophysiological traits obtained from a common garden experiment and compared patterns of phenotypic and genetic divergence (PST-FST comparisons) in a subset of populations from the Cerrado. Our results from molecular analyses pointed to extremely low genetic diversity and a remarkable population differentiation, supporting a major role of genetic drift. Approximately 0.3% of genotyped SNPs were flagged as differentiation outliers by at least two distinct methods, and Bayesian generalized linear mixed models revealed a signature of isolation by environment in addition to isolation by distance for high-differentiation outlier SNPs among the Cerrado populations. PST-FST comparisons suggested divergent selection on two ecophysiological traits linked to drought tolerance. We showed that these traits vary among populations, although without any particular macro-spatial pattern, suggesting local adaptation to differences in micro-habitats. Our study shows that selection might be a relevant force, particularly for traits involved in drought stress, even for populations experiencing strong drift, which improves our knowledge on eco-evolutionary processes acting on non-continuously distributed species.
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Affiliation(s)
- Bárbara Simões Santos Leal
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Cleber Juliano Neves Chaves
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Vanessa Araujo Graciano
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Christophe Boury
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Luis Alberto Pillaca Huacre
- grid.10800.390000 0001 2107 4576Departamento de Ecología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Myriam Heuertz
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Clarisse Palma-Silva
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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3
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Tarkhnishvili D, Barateli N, Murtskhvaladze M, Iankoshvili G. Estimating phenotypic heritability of sexual and unisexually reproducing rock lizards (genus Darevskia). ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Xia H, Luo Z, Xiong J, Ma X, Lou Q, Wei H, Qiu J, Yang H, Liu G, Fan L, Chen L, Luo L. Bi-directional Selection in Upland Rice Leads to Its Adaptive Differentiation from Lowland Rice in Drought Resistance and Productivity. MOLECULAR PLANT 2019; 12:170-184. [PMID: 30584948 DOI: 10.1016/j.molp.2018.12.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Drought resistance is required in rice breeding to address the challenge of frequent droughts. However, the evolutionary mechanism of rice drought resistance is not fully understood. We investigated the genetic differentiation between upland and lowland rice domesticated in agro-ecosystems with contrasting water-soil conditions using genome-wide SNPs. We estimated morphological differences among upland and lowland rice in drought resistance and productivity through common garden experiments. Upland rice had better drought resistance but poorer productivity. The negative correlations between traits of drought resistance and productivity are attributed to the underlying genetic trade-offs through tight linkages (e.g., DCA1 and OsCesA7) or pleiotropic effects (e.g., LAX1). The genetic trade-offs are common and greatly shape the evolution of drought resistance in upland rice. In genomic regions associated with both productivity and drought resistance, signs of balancing selection were detected in upland rice, while signs of directional selection were detected in lowland rice, potentially contributing to their adaptive differentiation. Signs of balancing selection in upland rice resulted from bi-directional selection during its domestication in drought-prone upland agro-ecosystems. Using genome-wide association analysis, we identified several valuable quantitative trait loci associated with drought resistance, for which highly differentiated genes should be considered candidates. Bi-directional selection breaking tight linkages by accumulating recombination events would be applicable in breeding water-saving and drought-resistance rice.
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Affiliation(s)
- Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Zhi Luo
- Shanghai Agrobiological Gene Center, Shanghai, China; College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Jie Xiong
- Shanghai Agrobiological Gene Center, Shanghai, China; College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Haibin Wei
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jie Qiu
- Institute of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hua Yang
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Guolan Liu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China; College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China.
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5
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Volis S, Ormanbekova D, Shulgina I. Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions. Mol Ecol 2016; 25:1449-64. [PMID: 26841244 DOI: 10.1111/mec.13565] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/17/2016] [Accepted: 01/26/2016] [Indexed: 02/03/2023]
Abstract
Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean. In a multiyear reciprocal transplant experiment, the plants of desert and Mediterranean origin demonstrated home advantage, and population differentiation in several phenotypic traits related to reproduction exceeded neutral predictions, as determined by comparisons of QST values with theoretical FST distributions. Thus, variation in these traits likely resulted from local adaptation to desert and Mediterranean environments. The two separate common garden experiments conducted with different experimental design revealed that two population comparisons, in contrast to multi-population comparisons, are likely to detect population differences in virtually every trait, but many of these differences reflect effects of local rather than regional environment. We detected a general reduction in neutral (SSR) genetic variation but not in adaptive quantitative trait variation in peripheral desert as compared with Mediterranean core populations. On the other hand, the molecular data indicated intensive gene flow from the Mediterranean core towards desert periphery. Although species range position in our study (edge vs. interior) was confounded with climate (desert vs. Mediterranean), the results suggest that the gene flow from the species core does not have negative consequences for either performance of the peripheral plants or their adaptive potential.
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Affiliation(s)
- S Volis
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - D Ormanbekova
- Department of Agricultural Sciences, University of Bologna, Bologna, 40127, Italy
| | - I Shulgina
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
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6
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Decanalization of wing development accompanied the evolution of large wings in high-altitude Drosophila. Proc Natl Acad Sci U S A 2016; 113:1014-9. [PMID: 26755605 DOI: 10.1073/pnas.1515964113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In higher organisms, the phenotypic impacts of potentially harmful or beneficial mutations are often modulated by complex developmental networks. Stabilizing selection may favor the evolution of developmental canalization--that is, robustness despite perturbation--to insulate development against environmental and genetic variability. In contrast, directional selection acts to alter the developmental process, possibly undermining the molecular mechanisms that buffer a trait's development, but this scenario has not been shown in nature. Here, we examined the developmental consequences of size increase in highland Ethiopian Drosophila melanogaster. Ethiopian inbred strains exhibited much higher frequencies of wing abnormalities than lowland populations, consistent with an elevated susceptibility to the genetic perturbation of inbreeding. We then used mutagenesis to test whether Ethiopian wing development is, indeed, decanalized. Ethiopian strains were far more susceptible to this genetic disruption of development, yielding 26 times more novel wing abnormalities than lowland strains in F2 males. Wing size and developmental perturbability cosegregated in the offspring of between-population crosses, suggesting that genes conferring size differences had undermined developmental buffering mechanisms. Our findings represent the first observation, to our knowledge, of morphological evolution associated with decanalization in the same tissue, underscoring the sensitivity of development to adaptive change.
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7
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Ozerov MY, Himberg M, Aykanat T, Sendek DS, Hägerstrand H, Verliin A, Krause T, Olsson J, Primmer CR, Vasemägi A. Generation of a neutral F
ST
baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin. J Evol Biol 2015; 28:1170-83. [DOI: 10.1111/jeb.12645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 01/17/2023]
Affiliation(s)
- M. Y. Ozerov
- Department of Biology; University of Turku; Turku Finland
| | - M. Himberg
- Faculty of Science and Engineering; Åbo Akademi University; Turku Finland
| | - T. Aykanat
- Department of Biology; University of Turku; Turku Finland
| | - D. S. Sendek
- State Research Institute on Lake and River Fisheries (GosNIORKh); St. Petersburg Russia
| | - H. Hägerstrand
- Faculty of Science and Engineering; Åbo Akademi University; Turku Finland
| | - A. Verliin
- Estonian Marine Institute; University of Tartu; Tartu Estonia
| | - T. Krause
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Tartu Estonia
| | - J. Olsson
- Department of Aquatic Resources; Institute for Coastal Research; Swedish University of Agricultural Sciences; Öregrund Sweden
| | - C. R. Primmer
- Department of Biology; University of Turku; Turku Finland
| | - A. Vasemägi
- Department of Biology; University of Turku; Turku Finland
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Tartu Estonia
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8
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Laaksonen T, Sirkiä PM, Calhim S, Brommer JE, Leskinen PK, Primmer CR, Adamík P, Artemyev AV, Belskii E, Both C, Bureš S, Burgess MD, Doligez B, Forsman JT, Grinkov V, Hoffmann U, Ivankina E, Král M, Krams I, Lampe HM, Moreno J, Mägi M, Nord A, Potti J, Ravussin PA, Sokolov L. Sympatric divergence and clinal variation in multiple coloration traits of Ficedula flycatchers. J Evol Biol 2015; 28:779-90. [PMID: 25683091 DOI: 10.1111/jeb.12604] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/23/2015] [Accepted: 02/06/2015] [Indexed: 01/25/2023]
Abstract
Geographic variation in phenotypes plays a key role in fundamental evolutionary processes such as local adaptation, population differentiation and speciation, but the selective forces behind it are rarely known. We found support for the hypothesis that geographic variation in plumage traits of the pied flycatcher Ficedula hypoleuca is explained by character displacement with the collared flycatcher Ficedula albicollis in the contact zone. The plumage traits of the pied flycatcher differed strongly from the more conspicuous collared flycatcher in a sympatric area but increased in conspicuousness with increasing distance to there. Phenotypic differentiation (PST ) was higher than that in neutral genetic markers (FST ), and the effect of geographic distance remained when statistically controlling for neutral genetic differentiation. This suggests that a cline created by character displacement and gene flow explains phenotypic variation across the distribution of this species. The different plumage traits of the pied flycatcher are strongly to moderately correlated, indicating that they evolve non-independently from each other. The flycatchers provide an example of plumage patterns diverging in two species that differ in several aspects of appearance. The divergence in sympatry and convergence in allopatry in these birds provide a possibility to study the evolutionary mechanisms behind the highly divergent avian plumage patterns.
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Affiliation(s)
- T Laaksonen
- Department of Biology, University of Turku, Turku, Finland; Finnish Museum of Natural History, Zoology Unit, University of Helsinki, Helsinki, Finland
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9
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Fabian DK, Lack JB, Mathur V, Schlötterer C, Schmidt PS, Pool JE, Flatt T. Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa. J Evol Biol 2015; 28:826-40. [PMID: 25704153 DOI: 10.1111/jeb.12607] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/12/2015] [Accepted: 02/17/2015] [Indexed: 01/31/2023]
Abstract
Clines in life history traits, presumably driven by spatially varying selection, are widespread. Major latitudinal clines have been observed, for example, in Drosophila melanogaster, an ancestrally tropical insect from Africa that has colonized temperate habitats on multiple continents. Yet, how geographic factors other than latitude, such as altitude or longitude, affect life history in this species remains poorly understood. Moreover, most previous work has been performed on derived European, American and Australian populations, but whether life history also varies predictably with geography in the ancestral Afro-tropical range has not been investigated systematically. Here, we have examined life history variation among populations of D. melanogaster from sub-Saharan Africa. Viability and reproductive diapause did not vary with geography, but body size increased with altitude, latitude and longitude. Early fecundity covaried positively with altitude and latitude, whereas lifespan showed the opposite trend. Examination of genetic variance-covariance matrices revealed geographic differentiation also in trade-off structure, and QST -FST analysis showed that life history differentiation among populations is likely shaped by selection. Together, our results suggest that geographic and/or climatic factors drive adaptive phenotypic differentiation among ancestral African populations and confirm the widely held notion that latitude and altitude represent parallel gradients.
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Affiliation(s)
- D K Fabian
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria; Vienna Graduate School of Population Genetics, Vienna, Austria
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10
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Felappi JF, Vieira RC, Fagundes NJR, Verrastro LV. So far away, yet so close: strong genetic structure in Homonota uruguayensis (Squamata, Phyllodactylidae), a species with restricted geographic distribution in the Brazilian and Uruguayan Pampas. PLoS One 2015; 10:e0118162. [PMID: 25692471 PMCID: PMC4334718 DOI: 10.1371/journal.pone.0118162] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/08/2015] [Indexed: 11/19/2022] Open
Abstract
The Pampas is a biologically rich South American biome, but is poorly represented in phylogeographic studies. While the Pleistocene glacial cycles may have affected the evolutionary history of species distributed in forested biomes, little is known about their effects on the habitats that remained stable through glacial cycles. The South American Pampas have been covered by grasslands during both glacial and interglacial periods and therefore represent an interesting system to test whether the genetic structure in such environments is less pronounced. In this study, we sampled Pampean populations of Homonota uruguayensis from Southern Brazil and Uruguay to assess the tempo and mode of population divergence, using both morphological measurements and molecular markers. Our results indicate that, in spite of its narrow geographic distribution, populations of H. uruguayensis show high levels of genetic structure. We found four major well-supported mtDNA clades with strong geographic associations. Estimates of their divergence times fell between 3.16 and 1.82 million years before the present. Populations from the central portion of the species distribution, on the border between Uruguay and Brazil, have high genetic diversity and may have undergone a population expansion approximately 250,000 years before the present. The high degree of genetic structure is reflected in the analyses of morphological characters, and most individuals could be correctly assigned to their parental population based on morphology alone. Finally, we discuss the biogeographic and conservation implications of these findings.
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Affiliation(s)
- Jéssica F. Felappi
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Renata C. Vieira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Nelson J. R. Fagundes
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Laura V. Verrastro
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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11
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Xia H, Zheng X, Chen L, Gao H, Yang H, Long P, Rong J, Lu B, Li J, Luo L. Genetic differentiation revealed by selective loci of drought-responding EST-SSRs between upland and lowland rice in China. PLoS One 2014; 9:e106352. [PMID: 25286109 PMCID: PMC4186790 DOI: 10.1371/journal.pone.0106352] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 08/05/2014] [Indexed: 12/02/2022] Open
Abstract
Upland and lowland rice (Oryza sativa L.) represent two of the most important rice ecotypes adapted to ago-ecosystems with contrasting soil-water conditions. Upland rice, domesticated in the water-limited environment, contains valuable drought-resistant characters that can be used in water-saving breeding. Knowledge about the divergence between upland and lowland rice will provide valuable cues for the evolution of drought-resistance in rice. Genetic differentiation between upland and lowland rice was explored by 47 Simple Sequence Repeats (SSRs) located in drought responding expressed sequence tags (ESTs) among 377 rice landraces. The morphological traits of drought-resistance were evaluated in the field experiments. Different outlier loci were detected in the japonica and indica subspecies, respectively. Considerable genetic differentiation between upland and lowland rice on these outlier loci was estimated in japonica (Fst = 0.258) and indica (Fst = 0.127). Furthermore, populations of the upland and lowland ecotypes were clustered separately on these outlier loci. A significant correlation between genetic distance matrices and the dissimilarity matrices of drought-resistant traits was determined, indicating a certain relationship between the upland-lowland rice differentiation and the drought-resistance. Divergent selections occur between upland and lowland rice on the drought-resistance as the Qsts of some drought-resistant traits are significantly higher than the neutral Fst. In addition, the upland- and lowland-preferable alleles responded differently among ecotypes or allelic types under osmotic stress. This shows the evolutionary signature of drought resistance at the gene expression level. The findings of this study can strengthen our understanding of the evolution of drought-resistance in rice with significant implications in the improvement of rice drought-resistance.
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Affiliation(s)
- Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Xiaoguo Zheng
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Huan Gao
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hua Yang
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Ping Long
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jun Rong
- Center for Watershed Ecology, Institute of Life Science and Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, China
| | - Baorong Lu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Fudan University, Shanghai, China
| | - Jiajia Li
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China
- * E-mail:
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12
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Variation and signatures of selection on the human face. J Hum Evol 2014; 75:143-52. [PMID: 25186351 DOI: 10.1016/j.jhevol.2014.08.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 08/03/2014] [Accepted: 08/04/2014] [Indexed: 11/22/2022]
Abstract
There has been much debate about why humans throughout the world differ in facial form. Previous studies of human skull morphology found levels of among-population differentiation that were comparable to those of neutral genetic markers, suggesting that genetic drift (neutral processes) played an important role in influencing facial differentiation. However, variation in soft-tissue morphology has not been studied in detail. In this study, we analyzed high-resolution 3D images of soft-tissue facial form in four Eurasian populations: Han Chinese, Tibetans, Uyghur and Europeans. A novel method was used to establish a high-density alignment across all of the faces, allowing facial diversity to be examined at an unprecedented resolution. These data exhibit signatures of population structure and history. However, among-population differentiation was higher for soft-tissue facial form than for genome-wide genetic loci, and high-resolution analyses reveal that the nose, brow area and cheekbones exhibit particularly strong signals of differentiation (Qst estimates: 0.3-0.8) between Europeans and Han Chinese. Our results suggest that local adaptation and/or sexual selection have been important in shaping human soft-tissue facial morphology.
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13
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Gómez GF, Márquez EJ, Gutiérrez LA, Conn JE, Correa MM. Geometric morphometric analysis of Colombian Anopheles albimanus (Diptera: Culicidae) reveals significant effect of environmental factors on wing traits and presence of a metapopulation. Acta Trop 2014; 135:75-85. [PMID: 24704285 DOI: 10.1016/j.actatropica.2014.03.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 01/24/2023]
Abstract
Anopheles albimanus is a major malaria mosquito vector in Colombia. In the present study, wing variability (size and shape) in An. albimanus populations from Colombian Maracaibo and Chocó bio-geographical eco-regions and the relationship of these phenotypic traits with environmental factors were evaluated. Microsatellite and morphometric data facilitated a comparison of the genetic and phenetic structure of this species. Wing size was influenced by elevation and relative humidity, whereas wing shape was affected by these two variables and also by rainfall, latitude, temperature and eco-region. Significant differences in mean shape between populations and eco-regions were detected, but they were smaller than those at the intra-population level. Correct assignment based on wing shape was low at the population level (<58%) and only slightly higher (>70%) at the eco-regional level, supporting the low population structure inferred from microsatellite data. Wing size was similar among populations with no significant differences between eco-regions. Population relationships in the genetic tree did not agree with those from the morphometric data; however, both datasets consistently reinforced a panmictic population of An. albimanus. Overall, site-specific population differentiation is not strongly supported by wing traits or genotypic data. We hypothesize that the metapopulation structure of An. albimanus throughout these Colombian eco-regions is favoring plasticity in wing traits, a relevant characteristic of species living under variable environmental conditions and colonizing new habitats.
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Affiliation(s)
- Giovan F Gómez
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Edna J Márquez
- Facultad de Ciencias, Universidad Nacional de Colombia, Medellín, Colombia.
| | - Lina A Gutiérrez
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Jan E Conn
- Wadsworth Center, New York State Department of Health, Slingerlands, 12159 NY, USA; Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, 12222 NY, USA.
| | - Margarita M Correa
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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Brommer JE, Hanski IK, Kekkonen J, Väisänen RA. Size differentiation in Finnish house sparrows follows Bergmann's rule with evidence of local adaptation. J Evol Biol 2014; 27:737-47. [DOI: 10.1111/jeb.12342] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/09/2014] [Accepted: 01/18/2014] [Indexed: 11/30/2022]
Affiliation(s)
- J. E. Brommer
- Department of Biology; University of Turku; Turku Finland
- Aronia Research and Development Institute; Åbo Akademi and Novia University of Applied Sciences; Ekenäs Finland
| | - I. K. Hanski
- Finnish Museum of Natural History; Helsinki Finland
| | - J. Kekkonen
- Department of Biosciences; University of Helsinki; Helsinki Finland
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15
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Ye Q, Tang F, Wei N, Yao X. Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense. ANNALS OF BOTANY 2014; 113:79-86. [PMID: 24265350 PMCID: PMC3864726 DOI: 10.1093/aob/mct255] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/11/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species. METHODS Population differentiation at five quantitative traits (QST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (FST) in seven populations of P. sinense. QST estimates were derived using a Bayesian hierarchical variance component method. KEY RESULTS Trait-specific QST values were equal to or lower than FST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense. CONCLUSIONS Despite the prevalent empirical evidence for QST > FST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower QST relative to FST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, QST estimates were of the same magnitude as FST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that sophisticated considerations are required for the inference of conservation measures of P. sinense from neutral genetic markers.
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Affiliation(s)
- Qigang Ye
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Feiyan Tang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Na Wei
- Department of Ecology and Evolutional Biology, The University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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16
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DeFaveri J, Merilä J. Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks. J Evol Biol 2013; 26:1700-15. [DOI: 10.1111/jeb.12168] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 12/26/2022]
Affiliation(s)
- J. DeFaveri
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki Finland
| | - J. Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki Finland
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17
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Karhunen M, Merilä J, Leinonen T, Cano JM, Ovaskainen O. driftsel
: an R package for detecting signals of natural selection in quantitative traits. Mol Ecol Resour 2013; 13:746-54. [DOI: 10.1111/1755-0998.12111] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 12/01/2022]
Affiliation(s)
- M. Karhunen
- Department of Biosciences FI‐00014 University of Helsinki PO Box 65 Helsinki Finland
| | - J. Merilä
- Department of Biosciences FI‐00014 University of Helsinki PO Box 65 Helsinki Finland
| | - T. Leinonen
- Department of Biosciences FI‐00014 University of Helsinki PO Box 65 Helsinki Finland
| | - J. M. Cano
- Research Unit of Biodiversity (UO‐CSIC‐PA) Oviedo University Edificio de Investigación C/ Gonzalo Gutiérrez Quirós s/n 33600 Mieres Oviedo Spain
| | - O. Ovaskainen
- Department of Biosciences FI‐00014 University of Helsinki PO Box 65 Helsinki Finland
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18
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Méndez-Vigo B, Gomaa NH, Alonso-Blanco C, Xavier Picó F. Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions. THE NEW PHYTOLOGIST 2013; 197:1332-1343. [PMID: 23252608 DOI: 10.1111/nph.12082] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 11/05/2012] [Indexed: 05/08/2023]
Abstract
The study of the evolutionary and population genetics of quantitative traits requires the assessment of within- and among-population patterns of variation. We carried out experiments including eight Iberian Arabidopsis thaliana populations (10 individuals per population) in glasshouse and field conditions. We quantified among- and within-population variation for flowering time and for several field life-history traits. Individuals were genotyped with microsatellites, single nucleotide polymorphisms and four well-known flowering genes (FRI, FLC, CRY2 and PHYC). Phenotypic and genotypic data were used to conduct Q(ST)-F(ST) comparisons. Life-history traits varied significantly among- and within-populations. Flowering time also showed substantial within- and among-population variation as well as significant genotype × environment interactions among the various conditions. Individuals bearing FRI truncations exhibited reduced recruitment in field conditions and differential flowering time behavior across experimental conditions, suggesting that FRI contributes to the observed significant genotype × environment interactions. Flowering time estimated in field conditions was the only trait showing significantly higher quantitative genetic differentiation than neutral genetic differentiation values. Overall, our results show that these A. thaliana populations are genetically more differentiated for flowering time than for neutral markers, suggesting that flowering time is likely to be under divergent selection.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Nasr H Gomaa
- Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092, Sevilla, Spain
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19
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Gormally CL, Hamrick JL, Donovan LA. Inter-island but not intra-island divergence among populations of sea oats, Uniola paniculata L. (Poaceae). CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0441-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Lamy JB, Plomion C, Kremer A, Delzon S. Q(ST) < F(ST) As a signature of canalization. Mol Ecol 2012; 21:5646-55. [PMID: 23110372 DOI: 10.1111/mec.12017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 02/02/2023]
Abstract
A key aim of evolutionary biology - inferring the action of natural selection on wild species - can be achieved by comparing neutral genetic differentiation between populations (F(ST)) with quantitative genetic variation (Q(ST)). Each of the three possible outcomes of comparisons of Q(ST) and F(ST) (Q(ST) > F(ST), Q(ST) = F(ST), Q(ST) < F(ST)) is associated with an inference (diversifying selection, genetic drift, uniform selection, respectively). However, published empirical and theoretical studies have focused on the Q(ST) > F(ST) outcome. We believe that this reflects the absence of a straightforward biological interpretation of the Q(ST) < F(ST) pattern. We here report recent evidence of this neglected evolutionary pattern, provide guidelines to its interpretation as either a canalization phenomenon or a consequence of uniform selection and discuss the significant importance this issue will have for the area of evolutionary biology.
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21
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Kronholm I, Picó FX, Alonso-Blanco C, Goudet J, de Meaux J. Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1. Evolution 2012; 66:2287-302. [PMID: 22759302 DOI: 10.1111/j.1558-5646.2012.01590.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation.
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Affiliation(s)
- Ilkka Kronholm
- Department Genetics and Plant Breeding, Max Planck Institute for Plant Breeding Research, DE-50829 Cologne, Germany
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22
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Volis S. Adaptive genetic differentiation in a predominantly self-pollinating species analyzed by transplanting into natural environment, crossbreeding and Q(ST)-F(ST) test. THE NEW PHYTOLOGIST 2011; 192:237-248. [PMID: 21729087 DOI: 10.1111/j.1469-8137.2011.03799.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
• Both genetic drift and natural selection result in genetic/phenotypic differentiation over space. I analyzed the role of local adaptation in the genetic differentiation of populations of the annual grass Hordeum spontaneum sampled along an aridity gradient. • The study included the introduction of plants having desert vs nondesert origin into natural (desert) environment, analysis of population differentiation in allozymes and random amplified polymorphic DNA (RAPD) markers vs phenotypic traits (Q(ST) -F(ST) comparison), and planting interpopulation hybrids under simulated desert conditions in a glasshouse. • The results of the home advantage test, Q(ST) -F(ST) comparison and crossbreeding were consistent with local adaptation; that is, that differentiation of the desert plants from plants of nondesert origin in phenotypic traits was adaptive, giving them home advantage. Each method used provided additional, otherwise unavailable, information, meaning that they should be viewed as complementary rather than alternative approaches. • Gene flow from adjacent populations (i.e. populations experiencing the desert environment) via seeds (but not pollen) had a positive effect on fitness by enhancing natural selection and counteracting drift. At the same time, the effect of genes from the species distributional core (nondesert plants) by either seed or pollen had a negative fitness effect despite its enriching effect on neutral diversity. The pattern of outbreeding depression observed in interpopulation hybrids (F(1) ) and their segregating progeny (F(2) ) was inconsistent with underdominance, but indicated the presence of additive, dominance and epistatic effects.
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Affiliation(s)
- S Volis
- The Institutes for Applied Research, Ben-Gurion University of the Negev, POB 653, Beer Sheva 84105, Israel
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23
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Does selection or genetic drift explain geographic differentiation of morphological characters in house sparrows Passer domesticus? Genet Res (Camb) 2011; 93:367-79. [PMID: 21859501 DOI: 10.1017/s0016672311000267] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Understanding the relative influence of genetic drift and selection is fundamental in evolutionary biology. The theory of neutrality predicts that the genetic differentiation of a quantitative trait (QST) equals the genetic differentiation at neutral molecular markers (FST) if the quantitative trait has not been under selection. Thus, the relative magnitude of observed QST and expected QST under neutral expectations suggests the importance of selection and genetic drift for any observed phenotypic divergence. Because QST is based on additive genetic variance, estimating QST based on phenotypic measurements is problematic due to unknown environmental effects. To account for this, we used a model where the environmental component was allowed to vary when estimating QST. The model was used on data from 14 house sparrow (Passer domesticus) populations in Norway. In accordance with the significant phenotypic inter-population differences our analyses suggested that directional selection may have favoured different optimal phenotypes for some morphological traits across populations. In particular, different body mass and male ornamental phenotypes seemed to have been favoured. The conclusions are, however, dependent on assumptions regarding the proportion of the observed inter-population variation that is due to additive genetic differences, showing the importance of collecting such information in natural populations. By estimating QST, allowing the additive genetic proportion of phenotypic inter-population variation to vary, and by making use of recent statistical methods to compare observed QST with neutral expectations, we can use data that are relatively easy to collect to identify adaptive variation in natural populations.
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Brommer JE. Whither Pst? The approximation of Qst by Pst in evolutionary and conservation biology. J Evol Biol 2011; 24:1160-8. [PMID: 21457173 DOI: 10.1111/j.1420-9101.2011.02268.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Local adaptation through natural selection can be inferred in case the additive genetic divergence in a quantitative trait across populations (Q(st)) exceeds the neutral expectation based on differentiation of neutral alleles across these populations (e.g. F(st)). As such, measuring Q(st) in relation to neutral differentiation presents a first-line investigation applicable in evolutionary biology (selection on functional genes) and conservation biology (identification of locally adapted coding genes). However, many species, especially those in need of conservation actions, are not amenable for the kind of breeding design required to estimate either narrow- or broad-sense Q(st). In such cases, Q(st) has been approximated by the phenotypic divergence in a trait across populations (P(st)). I here argue that the critical aspect for how well P(st) approximates Q(st) depends on the extent that additive genetic effects determine variation between populations relative to within populations. I review how the sensitivity of conclusions regarding local adaptation based on P(st) have been evaluated in the literature and find that many studies make a anticonservative null assumption in estimating P(st) and/or use a nonconservative approach to explore sensitivity of their conclusions. Data from two studies that have provided a second, independent assessment of selection in their system suggest that P(st)-F(st) comparisons should be interpreted very conservatively. I conclude with recommendations for improving the robustness of the inferences drawn from comparing P(st) with neutral differentiation.
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Affiliation(s)
- J E Brommer
- Bird Ecology Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland. History
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25
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Edelaar P, Björklund M. If F(ST) does not measure neutral genetic differentiation, then comparing it with Q(ST) is misleading. Or is it? Mol Ecol 2011; 20:1805-12. [PMID: 21410574 DOI: 10.1111/j.1365-294x.2011.05051.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The comparison between neutral genetic differentiation (F(ST) ) and quantitative genetic differentiation (Q(ST) ) is commonly used to test for signatures of selection in population divergence. However, there is an ongoing discussion about what F(ST) actually measures, even resulting in some alternative metrics to express neutral genetic differentiation. If there is a problem with F(ST) , this could have repercussions for its comparison with Q(ST) as well. We show that as the mutation rate of the neutral marker increases, F(ST) decreases: a higher within-population heterozygosity (He) yields a lower F(ST) value. However, the same is true for Q(ST) : a higher mutation rate for the underlying QTL also results in a lower Q(ST) estimate. The effect of mutation rate is equivalent in Q(ST) and F(ST) . Hence, the comparison between Q(ST) and F(ST) remains valid, if one uses neutral markers whose mutation rates are not too high compared to those of quantitative traits. Usage of highly variable neutral markers such as hypervariable microsatellites can lead to serious biases and the incorrect inference that divergent selection has acted on populations. Much of the discussion on F(ST) seems to stem from the misunderstanding that it measures the differentiation of populations, whereas it actually measures the fixation of alleles. In their capacity as measures of population differentiation, Hedrick's G'(ST) and Jost's D reach their maximum value of 1 when populations do not share alleles even when there remains variation within populations, which invalidates them for comparisons with Q(ST) .
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Affiliation(s)
- Pim Edelaar
- Department of Conservation Biology, Estación Biológica de Doñana-CSIC, Av. Americo Vespucio s/n, E-41092 Sevilla, Spain.
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26
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Miner BE, Kerr B. Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations. Proc Biol Sci 2010; 278:1306-13. [PMID: 20943691 DOI: 10.1098/rspb.2010.1663] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system.
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Affiliation(s)
- Brooks E Miner
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195, USA.
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27
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Reduction in the sex ability of worldwide clonal populations of Puccinia striiformis f.sp. tritici. Fungal Genet Biol 2010; 47:828-38. [DOI: 10.1016/j.fgb.2010.07.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Revised: 07/02/2010] [Accepted: 07/04/2010] [Indexed: 01/13/2023]
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Kronholm I, Loudet O, de Meaux J. Influence of mutation rate on estimators of genetic differentiation--lessons from Arabidopsis thaliana. BMC Genet 2010; 11:33. [PMID: 20433762 PMCID: PMC2888750 DOI: 10.1186/1471-2156-11-33] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 05/01/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The analysis of molecular variation within and between populations is crucial to establish strategies for conservation as well as to detect the footprint of spatially heterogeneous selection. The traditional estimator of genetic differentiation (F(ST)) has been shown to be misleading if genetic diversity is high. Alternative estimators of F(ST) have been proposed, but their robustness to variation in mutation rate is not clearly established. We first investigated the effect of mutation and migration rate using computer simulations and examined their joint influence on Q(ST), a measure of genetic differentiation for quantitative traits. We further used experimental data in natural populations of Arabidopsis thaliana to characterize the effect of mutation rate on various estimates of population differentiation. Since natural species exhibit various degrees of self-fertilisation, we also investigated the effect of mating system on the different estimators. RESULTS If mutation rate is high and migration rate low, classical measures of genetic differentiation are misleading. Only Phi(ST), an estimator that takes the mutational distances between alleles into account, is independent of mutation rate, for all migration rates. However, the performance of Phi(ST) depends on the underlying mutation model and departures from this model cause its performance to degrade. We further show that Q(ST) has the same bias. We provide evidence that, in A. thaliana, microsatellite variation correlates with mutation rate. We thereby demonstrate that our results on estimators of genetic differentiation have important implications, even for species that are well established models in population genetics and molecular biology. CONCLUSIONS We find that alternative measures of differentiation like F'(ST) and D are not suitable for estimating effective migration rate and should not be used in studies of local adaptation. Genetic differentiation should instead be measured using an estimator that takes mutation rate into account, such as Phi(ST). Furthermore, in systems where migration between populations is low, such as A. thaliana, Q(ST) < F(ST) cannot be taken as evidence for homogenising selection as has been traditionally thought.
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Affiliation(s)
- Ilkka Kronholm
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78000 Versailles, France
| | - Juliette de Meaux
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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