1). To examine the genetic subdivision of six pairs of populations, we conducted Bayesian clustering analysis using STRUCTURE 2.23 (Pritchard et al. 2013) by randomly drawing the parameter sets from the parameter space. Richards TJ, Walter GM, McGuigan K, Ortiz-Barrientos D. Roda F, Ambrose L, Walter GM, Liu HL, Schaul A, Lowe A, Pelser PB, Prentis P, Rieseberg LH, Ortiz-Barrientos D. Roda F, Walter GM, Nipper R, Ortiz‐Barrientos D. Ru D, Mao K, Zhang L, Wang X, Lu Z, Sun Y. Rundle HD, Nagel L, Boughman JW, Schluter D. Ryan PG, Bloomer P, Moloney CL, Grant TJ, Delport W. Schlötterer C, Tobler R, Kofler R, Nolte V. Servedio MR, Doorn GSV, Kopp M, Frame AM, Nosil P. Soria-Carrasco V, Gompert Z, Comeault AA, Farkas TE, Parchman TL, Johnston JS, Buerkle CA, Feder JL, Bast J, Schwander T, The green star and cross show the locations where the common garden experiment and the artificial crossing study were conducted, respectively. For this subset of SNPs, we compared allele frequency estimates by Pool-Seq with estimates based on genotyping, and found high consistency between the two estimates (Pearson’s correlation coefficient r = 0.90, ranging from 0.86 to 0.91 for individual populations; determination coefficient in linear regression R2 = 0.82, ranging from 0.74 to 0.98), which validated the accuracy of allele frequencies determined by the Pool-Seq approach (Rellstab et al. This difference in flowering time between species was consistent in two consecutive years under standard common garden conditions (supplementary fig. 2008). Stärke: GlasGestaltungselement (GF) Street, Thomas William Walpole, Dave R. Vaughan, Anne Marie Swanton, Thomas A. 1992; Zheng and Ge 2010; Banaticla-Hilario et al. These results remained the same when different genetic distances, different criteria of grouping SNPs, and various missing levels were used (supplementary figs. 2016; Ru et al. GlasGestaltungselement (GF) One particular challenge to demonstrate parallel speciation is to distinguish between the multiple origin and the single origin following gene flow between species (Quesada et al. However, we found that the information on variation from the summary statistics could not be recovered with subset of the PLS components, probably because of the lack of multicollinearity of our statistics. We thank Tao Sang, Bao-Rong Lu, Yong-Qing Zhu, and Disna Ratnasekera for their help in field collections and phenotyping. Together, these results indicated that at least two independent origins of O. nivara occurred, with one in South Asia and the other in Southeast Asia. 2014) on first two PCs and all 18 phenotypic traits, with habitat/species and region (Nepal, Myanmar, Laos, and Cambodia) as fixed factors, and locality (six sites where pairs of species populations were sampled) as a random factor within the interaction between fixed factors. Pattis, 218 Carbon St, Weatherly, PA 18255. This work was supported by the National Natural Science Foundation of China (91731301; 91231201; 31800186), the grants from the Chinese Academy of Sciences (XDB31000000; XDA08020103; CAS/SAFEA International Partnership Program for Creative Research Teams), and China Postdoctoral Science Foundation (2017M620950). As a special form of parallel evolution, parallel speciation involves independent formations of reproductive isolation in separate but closely related lineages/populations as by-products of adaptation to similar divergent environments, providing a convincing case for ecological speciation and for natural selection in generating reproductive isolation (Schluter and Nagel 1995; Johannesson 2001; Nosil 2012). To summarize, this system provides an outstanding scenario for testing the underlying mechanisms of ecological speciation as well as what genes and gene networks and to what extent selection acts repeatedly during speciation. 2014), we also applied different cut-off levels (i.e., 0.03, 0.05, 0.07) to rare alleles of the Pool-Seq data and obtained the same results in terms of the tree topology. In the MO model, outlier sites would group populations either by species or by geography; whereas the neutral and linked sites would produce a phylogenetic pattern in which populations are clustered by geography rather than by species (Roda et al. Further analysis based on a three-way ANOVA revealed significant differences in flowering time for populations between species but not for populations within species whether they were from same or different regions (table 1). Nolte Küchen Eco 2016. Based on the sequences of 16 neutral genes, we obtained an average FST value of 0.300 between species across six paired populations, with individual pair values ranging from 0.195 to 0.393 (supplementary fig. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. Linear mixed-effect models detected that 14 of 19 traits showed significant differences, and only three grain traits (weight, length, and thickness of grains), awn length, and the flag leaf length were not significantly different between species (fig. 2012; Liu et al. Over 30 individuals, each descended from separately collected maternal plants, were used for all populations (supplementary table S1, Supplementary Material online). 2016). 5b and supplementary table S4, Supplementary Material online), suggesting that phenotypic difference between the paired populations is associated with habitat differentiation. A three-way analysis of variance (ANOVA) (Butlin et al. S7, top panel, Supplementary Material online) and in two additional more complex scenarios, the history of population size (i.e., the demography scenario) and gene flow (i.e., the migration scenario) were modeled separately (supplementary fig. In contrast, O. nivara is characterized by its short stature, predominant self-fertilization, and photoperiod insensitivity (early flowering) (Morishima et al. 2013). S10 and table S4, Supplementary Material online). The summary statistics of the raw data were calculated using FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). As a perennial, O. rufipogon is widely distributed throughout southern China, South and Southeast Asia, Papua New Guinea, and northern Australia, and grows in areas with year-round water, such as swamps and lakes; whereas O. nivara is an annual found within a more restricted distribution in South and Southeast Asia and usually inhabits ponds and swamps that dry up completely during the dry season (Sharma and Shastry 1965; Morishima et al. 1992; Kuroda et al. To distinguish between the alternative models, we followed the methods by Roda et al. As such, flowering time is usually investigated as a measure of drought escape because earlier flowering results in greater fitness during the shortened growing season (Kooyers 2015). 2017; Trucchi et al. Fast and accurate short read alignment with Burrows–Wheeler transform, The Sequence Alignment/Map format and SAMtools, DnaSP v5: A software for comprehensive analysis of DNA polymorphism data, Factors affecting phenological patterns of bombacaceous trees in seasonal forests in Costa Rica and Mexico, The strength and genetic basis of reproductive isolating barriers in flowering plants, Population-genetic inference from pooled-sequencing data, Adaptive population divergence: markers, QTL and traits, Demographic modelling with whole-genome data reveals parallel origin of similar, ASTRAL: genome-scale coalescent-based species tree estimation, Evolutionary studies in cultivated rice and its wild relatives, Remarkable life history polymorphism may be evolving under divergent selection in the silverleaf sunflower, Estimation of fixation indices and gene diversities, Mathematical model for studying genetic variation in terms of restriction endonucleases, Host-plant adaptation drives the parallel evolution of reproductive isolation. Achtung! To further validate the reliability of our SNP calling and, hence, our allele frequency estimation, we genotyped 271 individuals sampled from four population pairs (i.e., NEP1, NEP2, KHM, and LAO1) and one Chinese O. rufipogon population (rGX-bh) using Illumina Infinium BeadChip (Illumina Inc.). We calculated average seed set and F1 viability at the population and species levels and performed the t-test for significance by R language v3.1.2 (https://www.R-project.org/). 4a andsupplementary table S4, Supplementary Material online). L.Z., N.-N.R., R.L., Y.-S.D., M.-X.W., C.-B.C., H.-Z.Z., and Y.-T.L. The posterior probabilities among three MO models were further compared with test which MO model was more likely. R package abc (Csilléry et al. 2c) generated a similar phylogeny to that based on neutral SNPs (fig. Separate analyses on individual genes clearly indicated that none of genes supports the reciprocal monophyly of the two species (supplementary fig. To assess the potential mapping bias in our data, we compared the mapping rate, genome coverage (with sites where the mapping depth ≥10), mismatch, and indel rate between mapped reads and the reference (supplementary table S2, Supplementary Material online) and did not find significant differences between species in these features (t-test, P = 0.075 for mapping rate, P = 0.203 for genome coverage, P = 0.317 for mismatch, and P = 0.172 for indels). 2015), we then used the combined sequences of 16 neutral genes to reconstruct the phylogenetic relationship of six population pairs of the two species (see Materials and Methods). Three-Way ANOVA for PC1, PC2, and 18 Phenotypic Traits. Although all these fragments did not show significant derivation from neutrality at the population level, we found significant values for either Tajima’s D or Fu and Li’s D* and F* at one or a few of the specific populations for four loci (GELP80, P14, PK, T4) (supplementary table S10, Supplementary Material online). . First, we conducted phylogenetic analyses based on Pool-Seq data and revealed that the O. nivara populations did not form a monophyletic clade but rather grouped together in accordance to the geographic region where they were collected (fig. 2012). Diesen qualitativ hochwertigen Metall - Griff Nr. Single-headed arrows stand for colonization or migration, and double-headed arrows indicate the gene flow between populations. We used two approaches to distinguish between the SO and MO models. We examined the extent of postmating isolation by determining the seed set of crosses and the viability of F1 hybrids following the methods of Sobel and Streisfeld (2015). 218-637-8683 Buckly Stritzel. Singletons produced by direct sequencing were confirmed through repeated PCR amplification and sequencing (Zheng and Ge 2010; Liu et al. One exception is the population pair in Myanmar (MMR1), where the flowering time of the two species entirely overlapped (fig. 2009; Banaticla-Hilario et al. We produced 268-Gb high-quality data after trimming with an average sequencing depth of 30× per pooled sample and finally retained 6,168,151 polymorphic sites for subsequent analyses (supplementary table S2, Supplementary Material online; see Materials and Methods). Griff Aldrich. The consistency of allele frequencies between Pool-Seq and genotyping data was evaluated by Pearson’s correlation coefficient and linear regression. As shown in figure 3a, under the SO model, an ancestral population diverged into different species before they colonized in multiple regions, with or without an initial period of allopatry; in contrast, under the MO model, an ancestral population colonized multiple regions and then diverged into different species within regions. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments. 2013; Richards et al. S.G. designed the study. 2007; Vaughan et al. 914-218-8254 Candi Frydman. Despite the fact that significant values for the parameters might arise from different factors other than nonneutrality, we conducted our population genetic analyses by excluding these four loci. (2009) found that a total of 30 QTLs, with effect sizes ranging from 2.9% to 36.5%, contributed to the major phenotypic differentiation between O. rufipogon and O. nivara, with >80% QTL alleles of O. nivara acting in the same direction of phenotypic evolution. Genotyping calling was analyzed using software Genome Studio (Illumina Inc.). 2012). This explanation is in agreement with the phylogenetic trees based on the Pool-Seq data (fig. Boxes and horizontal bars represent the central 50% and the median of the data, respectively. 2007; Zheng and Ge 2010); thus their speciation process is incomplete. (a) Species divergence may arise in face of gene flow after secondary contact between two species that were already divergent in allopatry (the SO model) or may occur multiple times in sympatry (the MO model). 2014), we performed approximate Bayesian computation (ABC) that is likelihood-free and widely used in the parameter estimation and model selection of complicated evolutionary scenarios (Beaumont 2010; Csilléry et al. Furthermore, phylogenetic analyses under different distances and various levels of missing data (from 10% to 60% of 276 pairwise comparisons of 24 populations) did not change our conclusion (supplementary figs. The single handle 218 is characterised by its clean edges and brass look. . eBook: The Court of Justice of the Economic Community of West African States as a Constitutional Court (ISBN 978-3-8487-6051-0) von aus dem Jahr 2019 Phylogenetic trees were then constructed using the data sets from different combinations of the SNP grouping criteria. N.-N.R., L.Z., L.H., C.-Y.J., J.G., and F.-M.Z. We found marked between-species differences in first heading and flowering peak for five out of the six population pairs (fig. In all six combinations of population pairs between regions, the posterior probability (PP) was much higher for the MO models than for the SO models (supplementary table S3, Supplementary Material online; see Materials and Methods). 1; supplementary table S1, Supplementary Material online; see Materials and Methods). (2003). Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. These nuclear genes are unlinked loci randomly distributed on all 12 chromosomes of rice, and most of them were demonstrated to evolve neutrally in previous studies (Zhu et al. Given the potential limitation of the Pool-Seq approach in detecting low-frequency alleles (Lynch et al. Search for other works by this author on: Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China, State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China, Blowin’ in the wind – the transition from ecotype to species, Genome size is not correlated with effective population size in the.

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