Quercus species divergence is driven by natural selection on evolutionarily less integrated traits
Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
33110229
PubMed Central
PMC8027598
DOI
10.1038/s41437-020-00378-6
PII: 10.1038/s41437-020-00378-6
Knihovny.cz E-zdroje
- MeSH
- biologická evoluce MeSH
- dub (rod) * genetika MeSH
- fyziologická adaptace MeSH
- lidé MeSH
- listy rostlin genetika MeSH
- selekce (genetika) MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Functional traits are organismal attributes that can respond to environmental cues, thereby providing important ecological functions. In addition, an organism's potential for adaptation is defined by the patterns of covariation among groups of functionally related traits. Whether an organism is evolutionarily constrained or has the potential for adaptation is based on the phenotypic integration or modularity of these traits. Here, we revisited leaf morphology in two European sympatric white oaks (Quercus petraea (Matt.) Liebl. and Quercus robur L.), sampling 2098 individuals, across much of their geographical distribution ranges. At the phenotypic level, leaf morphology traditionally encompasses discriminant attributes among different oak species. Here, we estimated in situ heritability, genetic correlation, and integration across such attributes. Also, we performed Selection Response Decomposition to test these traits for potential differences in oak species' evolutionary responses. Based on the uncovered functional units of traits (modules) in our study, the morphological module "leaf size gradient" was highlighted among functionally integrated traits. Equally, this module was defined in both oaks as being under "global regulation" in vegetative bud establishment and development. Lamina basal shape and intercalary veins' number were not, or, less integrated within the initially defined leaf functional unit, suggesting more than one module within the leaf traits' ensemble. Since these traits generally show the greatest species discriminatory power, they potentially underwent effective differential response to selection among oaks. Indeed, the selection of these traits could have driven the ecological preferences between the two sympatric oaks growing under different microclimates.
INRA UMR Biodiversité Gènes et Communautés 69 route d'Arcachon 33612 Cestas Cedex France
Pharmacognosy Department Faculty of Pharmacy Alexandria University Alexandria Egypt
Scion 49 Sala Street Whakarewarewa Rotorua 3010 New Zealand
University of Bordeaux UMR 1202 Biodiversité Gènes et Communautés F 33400 Talence France
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Abadie P, Roussel G, Dencausse B, Bonnet C, Bertocchi E, Louvet JM, et al. Strength, diversity and plasticity of postmating reproductive barriers between two hybridizing oak species (Quercus robur L. and Quercus petraea (Matt) Liebl.) J Evol Biol. 2012;25(1):157–173. PubMed
Alberch P (1982) Developmental constraints in evolutionary processes. In: Bonner JT (eds) Evolution and development. Dahlem workshop reports (Life science research report), vol 22. Springer, Berlin, Heidelberg.
Armbruster WS, Pélabon C, Bolstad GH, Hansen TF. Integrated phenotypes: understanding trait covariation in plants and animals. Philos Trans R Soc B. 2014;369(1649):20130245. PubMed PMC
Arnold SJ. Constraints on phenotypic evolution. Am Nat. 1992;140:S85–S107. PubMed
Arnold SJ. The ultimate causes of phenotypic integration: lost in translation. Evolution. 2005;59(9):2059–2061.
Arnold SJ, Pfender ME, Jones AG. The adaptive landscape as a conceptual bridge between micro- and macroevolution. Genetica. 2001;112–113:9–32. PubMed
Barnola P, Alatou D, Lacointe A, Lavarenne S. Etude biologique et biochimique du determinisme de la croissance rythmique du chene pedoncule (Quercus robur L.). Effets de l’ablation des feuilles. Ann For Sci. 1990;47(6):619–631.
Berg R. The ecological significance of correlation pleiades. Evolution. 1960;14(2):171–180.
Bijarpasi MM, Shahraji TR, Lahiji HS. Genetic variability and heritability of some morphological and physiological traits in Fagus orientalis Lipsky along an elevation gradient in Hyrcanian forests. Folia Oecol. 2019;46(1):45–53.
Bijma P, Bastiaansen JW. Standard error of the genetic correlation: how much data do we need to estimate purebred-crossbred genetic correlations? Genet Sel Evol. 2014;46:1–6. PubMed PMC
Bissell E, Diggle P. Modular genetic architecture of floral morphology in Nicotiana: quantitative genetic and comparative phenotypic approaches to floral integration. J Evol Biol. 2010;23(8):1744–1758. PubMed
Bodénés C, Chancerel E, Ehremann F, Kremer A, Plomion C. High-density linkage mapping and distribution of segregation distortion regions in the oak genomes. DNA Res. 2016;23:115–124. PubMed PMC
Brock MT, Weinig C. Plasticity and environment-specific covariances: an investigation of floral – vegetative and within flower correlations. Evolution. 2007;61(12):2913–2924. PubMed
Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2009) ASReml-R reference manual. The State of Queensland, Department of Primary Industries and Fisheries, Brisbane.
Cheverud JM. Phenotypic, genetic, and environmental morphological integration in the cranium. Evolution. 1982;36(3):499–516. PubMed
Cheverud JM. Quantitative fanatic analysis of cranial morphology in the cotton-top (Saguinus oedipus) and saddle-back (S. fuscicollis) tamaris. J Evol Biol. 1996;9:5–42.
Conner JK, Via S. Patterns of phenotypic and genetic correlation among morphological and life-history traits in wild radish, Raphanus raphanastrum. Evolution. 1993;47:704–711. PubMed
Couturier E, Du Pont SC, Douady S. A global regulation inducing the shape of growing folded leaves. PLoS ONE. 2009;4(11):e7968. PubMed PMC
de los Campos G, Pérez-Rodríguez P (2013) BGLR: Bayesian generalized linear regression. R package version 1(3). Accessed 24 Apr 2016
de los Campos G, Sorensen D, Gianola D. Genomic heritability: what it is? PLoS Genet. 2015;11:e1005048. PubMed PMC
de los Campos G, Grüneberg A (2016) MTM (multiple-trait model) package. http://quantgen.github.io/MTM/vignette.html. Accessed 10 May 2018
De Micco V, Aronne G. Morpho-anatomical traits for plant adaptation to drought. In: Aroca R, editor. Plant responses to drought stress. Berlin, Heidelberg: Springer; 2012.
Dow DB, Ashley MV, Howe HF. Characterization of highly variable (GA/CT)n microsatellites in the bur oak, Quercus macrocarpa. Theor Appl Genet. 1995;91:137–141. PubMed
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE. 2011;6:e19379. PubMed PMC
Esteve-Altava B. In search of morphological modules: a systematic review. Biol Rev. 2017;92:1332–1347. PubMed
Feng C, Feng C, Yang L, Kang M, Rausher MD. Genetic architecture of quantitative flower and leaf traits in a pair of sympatric sister species of Primulina. Heredity. 2019;122(6):864–876. PubMed PMC
Fu G, Dai X, Symanzik J, Bushman S. Quantitative gene-gene and gene-environment mapping for leaf shape variation using tree-based models. N Phytol. 2017;213:455–469. PubMed
Gailing O. QTL analysis of leaf morphological characters in Quercus robur full-sib family (Q. robur x Q. robur ssp. slavonica) Plant Biol. 2008;10(5):624–634. PubMed
Gianola D, Norton H. Scaling threshold characters. Genetics. 1981;99(2):357–364. PubMed PMC
Hadfield JD. MCMC methods for multi-response generalized linear models: the MCMCglmm R package. J Stat Softw. 2010;33(2):1–22. PubMed
Hammond D. The expression of genes for leaf shape in Gossypium hirsutum L. Am J Bot. 1941;28(2):124–138.
Hansen TF. Stabilizing selection and the comparative analysis of adaptation. Evolution. 1997;51:1341–1351. PubMed
Hansen TF. The evolution of genetic architecture. Annu Rev Ecol Evol Syst. 2006;37:123–157.
Hansen TF, Houle D. Measuring and comparing evolvability and constraint in multivariate characters. J Evol Biol. 2008;21(5):1201–1219. PubMed
Healy TM, Brennan RS, Whitehead A, Schulte PM. Tolerance traits related to climate change resilience are independent and polygenic. Glob Change Biol. 2018;24:5348–5360. PubMed
Hermant M, Prinzing A, Vernon P, Convey P, Hennion F. Endemic species have highly integrated phenotypes, environmental distributions and phenotype-environment relationship. J Biogeogr. 2013;40(8):1583–1594.
Hill WG, Zhang J. On the pleiotropic structure of the genotype-phenotype map and the evolvability of complex organisms. Genetics. 2012;190(3):1131–1137. PubMed PMC
Hodel RG, Segovia-Salcedo MC, Landis JB, Crowl AA, Sun M, Liu X, et al. The report of my death was an exaggeration: a review for researchers using microsatellites in 21st century. Appl Plant Sci. 2016;4(6):1600025. PubMed PMC
Hubert F, Grimm GW, Jousselin E, Berry V, Franc A, Kremer A. Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus. Syst Biodivers. 2014;12:405–423.
Hunt J, Blows MW, Zajitschek F, Jennions MD, Brooks R. Reconciling strong stabilizing selection with the maintenance of genetic variation in a natural population of black field crickets (Teleogryllus commodus) Genetics. 2007;177(2):875–880. PubMed PMC
Johnson T, Barton N. Theoretical models of selection and mutation on quantitative traits. Philos Transl R Soc B. 2005;360(1459):1411–1425. PubMed PMC
Jombart T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2008;24(11):1403–1405. PubMed
Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010;11(1):1. PubMed PMC
Jones AG, Arnold SJ, Bürger R. Stability of the G-matrix in a population experiencing stabilizing selection, pleiotropic mutation, and genetic drift. Evolution. 2003;57:1747–1760. PubMed
Jones AG, Arnold SJ, Bürger R. Evolution and stability of the G-matrix on a landscape with a moving optimum. Evolution. 2004;58:1639–1654. PubMed
Kanage MK, Ryel RJ, Mock KE, Pfrender ME. Quantitative-genetic variation in morphological and physiological traits within a quaking aspen (Populus tremuloides) population. Can J For Res. 2008;38:1690–1694.
Karaman E, Lund MS, Anche MT, Janss L, Su G. Genomic predictions using multitrait weighted GBLUP accounting for heterogeneous variances and covariances across genome. Genes Genomes Genet. 2018;8:3549–3558. PubMed PMC
Kashtan N, Alon U. Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci USA. 2005;102(39):13773–13778. PubMed PMC
Klápště J, Lstibůrek M, El-Kassaby YA. Estimates of genetic parameters and breeding values from western larch open-pollinated families using marker-based relationship. Tree Genet Genomes. 2014;10(2):241–249.
Klingenberg CP. Morphological integration and developmental modularity. Annu Rev Ecol Evol Syst. 2008;39:115–132.
Kremer A, Dupouey JL, Deans JD, Cottrell J, Csaikl U, Finkeldey R, et al. Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across Western European mixed oak stands. Ann For Sci. 2002;59(7):777–787.
Kremer A, Hipp AL. Oak: an evolutionary success story. N Phytol. 2019;226:987–1011. PubMed PMC
Kremer A, Lowe AJ, Munro RC, Dick J, Cavers S et al. (2008) Intra and interspecific gene flows in oaks as mechanisms promoting genetic diversity and adaptive potential. OAKFLOW. Final report (2001–2005). European Commission, 73 pp (Quality of life and management of living resources (1.1.1.), CEH Project Number:C01615)
Lande R. The genetic covariances between characters maintained by pleiotropic mutation. Genetics. 1980;94:203–215. PubMed PMC
Lang T, Abadie P, Leger V, Decourcelle T, Frigerio J-M, Burban C et al. (2018) High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur). bioRxiv 10.1101/388447
Laughlin DC, Messier J. Fitness of multidimensional phenotypes in dynamic adaptive landscape. Trends Ecol Evol. 2015;30(8):487–496. PubMed
Lepoittevin C, Bodénés E, Chancerel E, Villate L, Lang T, Lesur I, et al. Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks. Mol Ecol Resour. 2015;15(6):1446–1459. PubMed
Leroy T, Louvet J-M, Lalanne C, Le Provost G, Labadie K, Aury J-M et al. (2020) Adaptive introgression as a driver of local adaptation to climate in European white oaks. N Phytol 226:943–946 PubMed PMC
Lesur I, Alexandre H, Boury C, Chancerel E, Plomion C, Kremer A. Development of target sequence capture and estimation of genomic relatedness in a mixed oak stands. Front Plant Sci. 2018;9:996. PubMed PMC
Lesur I, Le Provost G, Bento P, Da Silva C, Leplé J-C, Murat F, et al. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics. 2015;16:112. PubMed PMC
Lévy G, Becker M, Duhamel D. A comparison of the ecology of pedunculate and sessile oaks: radial growth in the Centre and NW of France. For Ecol Manag. 1992;55:51–63.
Lewis MC. The physiological significance of variation in leaf structure. Sci Prog. 1972;60(237):25–51.
Lewontin RC. Adaptation. Sci Am. 1978;239:212–231.. PubMed
Lickliter R. Developmental evolution and the origins of phenotypic variation. Biomol Concepts. 2014;5(4):343–352. PubMed
Lippert C, Quon G, Kang EY, Kadie CM, Listgarten J, Heckerman D. The benefits of selecting phenotype-specific variants for applications of mixed models in genomics. Sci Rep. 2013;3:1815. PubMed PMC
Lipson H, Pollack JB, Suh NP. On the origin of modular variation. Evolution. 2002;56(8):1549–1556. PubMed
Lo Gullo MA, Salleo S. Different strategies of drought resistance in three Mediterranean sclerophyllous trees growing in the same environmental conditions. N Phytol. 1988;108:267–276. PubMed
Lucas LK, Nice CC, Gompert Z. Genetic constraints on wing pattern variation in Lycaeides butterflies: a case study on mapping complex, multifaceted traits in structured populations. Mol Ecol Resour. 2018;18:892–907. PubMed
Lynch M, Ritland K. Estimation of pairwise relatedness with molecular markers. Genetics. 1999;152(4):1753–1766. PubMed PMC
Mariette S, Cottrell J, Csaikl UM, Goikoechea P, Konig A, Lowe AJ, et al. Comparison of levels of genetic diversity detected with AFLP and microsatellite markers within and among mixed Q. petraea (Matt.) Liebl. and Q. robur L. stands. Silvae Genet. 2002;51:72–79.
Marroig G, Melo D, Porto A, Sebastiao H, Garcia G. Selection Response Decomposition (SRD): a new tool for dissecting differences and similarities between matrices. Evol Biol. 2011;38(2):225–241.
McKown AD, Cochard H, Sack L. Decoding leaf hydraulics with a spatially explicit model: principles of venation architecture and implications for its evolution. Am Nat. 2010;175:447–460. PubMed
Melo D, Garcia G, Hubbe A, Assis AP, Marroig G. EvolQG—an R package for evolutionary quantitative genetics. F1000Research. 2015;4:925. PubMed PMC
Muñoz F, Sanchez L (2017) breedR: statistical methods for forest genetic resources analysis. R package version 0.12-2. Accessed 12 Feb 2018
Murren CJ. Penotypic integration in plants. Plant Species Biol. 2002;17(2-3):89–99.
Murren CJ. The integrated phenotype. Integr Comp Biol. 2012;52(1):64–76. PubMed
Olson EC, Miller RL. Morphological integration. Chicago: University of Chicago Press; 1958.
Ordano M, Fornoni J, Boege K, Domínguez CA. The adaptive value of phenotypic floral integration. N Phytol. 2008;179(4):1183–1192. PubMed
Pepper JW. The evolution of evolvability in genetic linkage patterns. Biosystems. 2003;69(2-3):115–126. PubMed
Pew J, Muir PH, Wang J, Frasier TR. Related: an R package for analysing pairwise relatedness from codominant molecular markers. Mol Ecol Resour. 2015;15(3):557–561. PubMed
Phillips PC, Arnold SJ. Visualizing multivariate selection. Evolution. 1989;43(6):1209–1222. PubMed
Pigliucci M. Phenotypic integration: studying the ecology and evolution of complex phenotypes. Ecol Lett. 2003;6(3):265–272.
Pires ND, Dolan L. Morphological evolution in land plants: new designs with old genes. Philos Trans R Soc B. 2012;367(1588):508–518. PubMed PMC
Plomion C, Aury J-M, Amselem J, Leroy T, Murat F, Duplessis S, et al. Oak genome reveals facets of long lifespan. Nat Plants. 2018;4:440–452. PubMed PMC
Ponton S, Dupouey J-L, Bréda N, Dreyer E. Comparison of water-use efficiency of seedlings from two sympatric oak species: genotype x environment interactions. Tree Physiol. 2002;22:413–422. PubMed
Ponton S, Dupouey J-L, Dreyer E. Leaf morphology as species indicator in seedling of Quercus robur L. and Q. petraea (Matt.) Liebl.: modulation by irradiance and growth flush. Ann For Sci. 2004;61(1):73–80.
Porth I, Koch M, Berenyi M, Burg A, Burg K. Identification of adaptation-specific differences in mRNA expression of sessile and pedunculate oak based on osmotic stress-induced genes. Tree Physiol. 2005;25(10):1317–1329. PubMed
Porth I, Klápště J, McKown AD, La Mantia J, Hamelin R, Skyba O, et al. Extensive functional pleiotropy of REVOLUTA substantiated through forward genetics. Plant Physiol. 2014;164(2):548–554. PubMed PMC
Porth I, Garnier-Géré P, Klápště J, Scotti-Saintagne C, El-Kassaby YA, Burg K, et al. Species-specific alleles at a β-tubulin gene show significant associations with leaf morphological variation within Quercus petraea and Q. robur populations. Tree Genet Genomes. 2016;12(4):81.
Porth I, Scotti-Saintagne C, Barreneche T, Kremer A, Burg K. Linkage mapping of osmotic stress induced genes of oak. Tree Genet Genomes. 2005;1(1):31–40.
Press MC. The functional significance of leaf structure: a search for generalizations. N Phytol. 1999;143(1):213–219.
Queller DC, Goodnight KF. Estimating relatedness using genetic markers. Evolution. 1989;43(2):258–275. PubMed
Ramírez-Valiente JA, Lorenzo Z, Soto A, Valladares F, Gil L, Aranda I. Elucidating the role of genetic drift and natural selection in cork oak differentiation regarding drought tolerance. Mol Ecol. 2009;18(18):3803–3815. PubMed
Roff DA (2012) Evolutionary quantitative genetics. Springer Science & Business Media, Dordrecht
Royer DL, Wilf P, Janesko DA, Kowalski EA, Dilcher DL. Correlations of climate and plant ecology to leaf size and shape: potential proxies for the fossil record. Am J Bot. 2005;92:1141–1151. PubMed
Rupp AIKS, Gruber P. Biomimetic groundwork for thermal exchange structures inspired by plant leaf design. Biomimetics. 2019;4:75. PubMed PMC
Sack L, Scoffoni C. Leaf venation: structure, function, development, evolution, ecology and adaptation in the past, present and future. N Phytol. 2013;198:983–1000. PubMed
Saintagne C, Bodenes C, Barreneche T, Pot D, Plomion C, Kremer A. Distribution of genomic regions differentiating oak species assessed by QTL detection. Heredity. 2004;92(1):20–30. PubMed
Savell KR, Auerbach BM, Roseman CC. Constraint, natural selection, and the evolution of human body form. Proc Natl Acad Sci USA. 2016;113(34):9492–9497. PubMed PMC
Schluter D. Adaptive radiation along genetic lines of least resistance. Evolution. 1996;50:1766–1774. PubMed
Scotti-Saintagne C, Mariette S, Porth I, Goicoechea PG, Barreneche T, Bodénès C, et al. Genome scanning for interspecific differentiation between two closely related oak species (Quercus robur L. and Q. petraea (Matt.) Liebl.) Genetics. 2004;168:1615–1626. PubMed PMC
Sinervo B, Svensson E. Correlational selection and the evolution of genomic architecture. Heredity. 2002;89:329–338. PubMed
Smith SD. Pleiotropy and the evolution of floral integration. N Phytol. 2016;209:80–85. PubMed
Steinkellner H, Fluch S, Turetschek E, Lexer C, Streiff R, Kremer A, et al. Identification and characterization of (GA/CT)n microsatellite loci from Quercus petraea. Plant Mol Biol. 1997;33:1093–1096. PubMed
Streiff R, Labbe T, Bacilieri R, Steinkellner H, Glossl J, Kremer A. Within-population genetic structure in Quercus robur L. and Quercus petraea (Matt.) Liebl. assessed with isozymes and microsatellites. Mol Ecol. 1998;7(3):317–328.
Thomas SC. The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations. Philos Trans R Soc B. 2005;360:1457–1467. PubMed PMC
Ueno S, Le Provost G, Leger V, Klopp C, Noirot C, Frigerio J-M, et al. Bioinformatics analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics. 2010;11:650. PubMed PMC
Van de Casteele T, Galbusera P, Matthysen E. A comparison of microsatellite-based pairwise relatedness estimators. Mol Ecol. 2001;10(6):1539–1549. PubMed
VanRaden PM. Efficient methods to compute genomic prediction. J Dairy Sci. 2008;91:4414–4423. PubMed
Viscosi V, Lepais O, Gerber S, Fortini P. Leaf morphological analyses in four European oak species (Quercus) and their hybrids: a comparison of traditional and geometric morphometric methods. Plant Biosyst. 2009;143(3):564–574.
Wagner GP, Pavlicev M, Cheverud JM. The road to modularity. Nat Rev Genet. 2007;8(12):921–931. PubMed
Wagner GP, Zhang J. The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms. Nat Rev Genet. 2011;12(3):204–213. PubMed
Wang Z, Liao B-Y, Zhang J. Genomic patterns of pleiotropy and the evolution of complexity. Proc Natl Acad Sci USA. 2010;107:18034–18039. PubMed PMC
Weissing FJ, Edelaar P, Sander van Doorn G. Adaptive speciation theory: a conceptual review. Behav Ecol Sociobiol. 2011;65(3):461–480. PubMed PMC
Young RL, Badyaev AV. Evolutionary persistence of phenotypic integration: influence of developmental and functional relationships on complex trait evolution. Evolution. 2006;60:1291–1299. PubMed
Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, et al. A unified mixed-model method for association mapping that accounts formultiple levels of relatedness. Nature Genetics. 2006;38:203–208. PubMed