Nevertheless, demonstrating parallel speciation has been a challenging task because it requires in-depth analyses involving phylogenetics, phenotypes, ecology, and particularly the repeated formation of reproductive isolation between species (Schluter and Nagel 1995; Johannesson 2001; Rieseberg and Willis 2007; Nosil 2012). 2013) as the reference and retained reads that were uniquely mapped to this reference with a mapping quality score >30. Blue dots and red triangles represent Oryza rufipogon and O. nivara populations, respectively. 2016). 914-218-9368 Gretchan Cali. Under the SO hypothesis, populations of the two species should indicate reciprocal monophyly; in contrast, for the MO hypothesis, populations from the same region should form a distinct clade. 2013). 2011) and VarScan 2 (Koboldt et al. Because two major models of O. nivara origin (fig. joined the field survey, sample collections, and lab assistances. These natural populations were sampled across four localities (Nepal, Myanmar, Laos, and Cambodia) by the authors, with the distance between two populations of each pair ranging from 1.3 to 44.9 km (supplementary table S1, Supplementary Material online). Specifically, we followed the method proposed by Spitze (1993) to calculate QST according to QST=VB/(VB+2VW) for each trait, where VB and VWare the components of variance between and within species, respectively. To further verify that the nonmonophyly of the O. nivara populations represents multiple origins rather than local gene flow due to secondary contact, we used the sequence data of 16 neutral genes to perform approximate Bayesian computation (ABC) for distinguishing the alternative models of origin for two groups of populations: one group consists of two population pairs in Nepal (NEP1 and NEP2) (hereafter, South Asia) and the other group consists of three population pairs in Cambodia and Laos (KHM, LAO1, and LAO2) (hereafter, Southeast Asia). 2015); thus, they were suitable for a population genetics study. et al. 2015). Sampling locations of Oryza rufipogon (blue) and O. nivara (red) populations used in this study. The mapping and variant calling processes were conducted following the protocol proposed by Schlötterer (Schlötterer et al. Parallel speciation has been reported in animals (Johannesson 2001; Nosil 2012) and strongly suggests the action of natural selection in the process of speciation. In addition, neither premating nor postmating reproductive barriers were observed between populations within both O. rufipogon and O. nivara (figs. Somit können Sie sich sicher sein, dass auch bei einer Erweiterung Ihrer Küche immer ein Ersatzteil vorrätig ist. As the posterior probability was an approximation in ABC method, we performed additional analysis to test the goodness of fit between our models and the data. An in-depth study of the hypothesis on the origin of the Myanmar O. nivara is currently underway and should provide further insights into the origin of this species. We used two approaches to distinguish between the SO and MO models. 1992; Zheng and Ge 2010; Liu et al. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. 218-637-2633 Susy Umbarger. 2017; Trucchi et al. For the linked SNPs, we empirically defined them as the SNPs that were <100/300/500 bp away from the nearest outlier SNPs. 2014), which was overlooked in many previous studies. (2016) to investigate the phylogenetic patterns at neutral, outlier, and linked loci which were assumed to reflect different origin models (fig. 2a), that is, populations from the same region clustered together, which is a pattern consistent with the MO model (fig. Significance after correction for multiple testing is in the parentheses. 2013) and exhibit little interspecific genetic differentiation (Barbier 1989; Zhu et al. 218 Edelstahlfarbig Chrom Glanz OVP 15x. Lots of cost for very little benefit. When the criterion was set to one pair, more SNPs would be defined as outlier even they were neutral in most other pairs; however, when five pairs used as the criterion, more real outliers will be omitted. 2d and supplementary fig. S9 and table S5, Supplementary Material online). 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 div… The outlier SNPs were defined as the sites where allele frequency was significantly different between species for one/three/five pairs of O. rufipogon/O. As a result, a total of 268-Gb high-quality data with a depth of 1.35× for each individual was generated (supplementary table S2, Supplementary Material online); this amount of data ensures the accurate estimation of allele frequencies according to empirical and theoretical studies (Futschik and Schlötterer 2010; Kofler, Orozco-terWengel, et al. Number of individuals (O. nivara/O. Street, Thomas William Walpole, Dave R. Vaughan, Anne Marie Swanton, Thomas A. We used the linear mixed-effects models (nlme package in R) to analyze divergence of morphological traits at the species level. 218-637-7898 Carilyn Bushee. 2015) using Picard (http://broadinstitute.github.io/picard/) and indels together with ten flanking nucleotides to further reduce false positives in variant calling. Zhe Cai, Lian Zhou, Ning-Ning Ren, Xun Xu, Rong Liu, Lei Huang, Xiao-Ming Zheng, Qing-Lin Meng, Yu-Su Du, Mei-Xia Wang, Mu-Fan Geng, Wen-Li Chen, Chun-Yan Jing, Xin-Hui Zou, Jie Guo, Cheng-Bin Chen, Hua-Zhong Zeng, Yun-Tao Liang, Xing-Hua Wei, Ya-Long Guo, Hai-Fei Zhou, Fu-Min Zhang, Song Ge, Parallel Speciation of Wild Rice Associated with Habitat Shifts, Molecular Biology and Evolution, Volume 36, Issue 5, May 2019, Pages 875–889, https://doi.org/10.1093/molbev/msz029. Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C, Schlötterer C. Kuroda Y, Rao SA, Bounphanousay C, Kanyavong K, Iwata A, Tanaka K, Sata Y. Kuroda Y, Sato Y-I, Bounphanousay C, Kono Y, Tanaka K. Leinonen T, McCairns RJS, O’Hara RB, Merila J. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP. 2016) revealed that of the 21,415 expressed genes across three tissues, ∼8% (1,717 genes) differed significantly in expression levels between species and that 62% of the differentially expressed genes exhibited a signature of directional selection. . 2b); whereas the tree that was constructed based on linked SNPs (fig. 1992; Kuroda et al. We further chose three population pairs to conduct a crossing experiment to detect potential postmating isolation (see Materials and Methods). S10, Supplementary Material online). If the QST value significantly exceeded FST, the hypothesis of natural selection driving species divergence was supported; in contrast, the neutral genetic differentiation between species was assumed if the QST values did not differ significantly from FST (McKay and Latta 2002; Whitlock and Guillaume 2009; Leinonen et al. 2012). The nearly complete isolation in flowering time together with a difference in mating system (Sang and Ge 2007; Vaughan et al. Biologically, O. rufipogon is characterized by its tall stature, a mixed mating system, photoperiod sensitivity (late flowering), and profligate vegetative reproduction. Flowering time changes can have widespread ecological consequences and adaptive responses to drought through flowering time shifts have been well-characterized in plant species (Hall and Willis 2006; Franks 2015; Kooyers 2015; Moyers and Rieseberg 2016; Ferris et al. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. Specifically, we divided the genome-wide SNPs into three categories: outlier SNPs (candidates of selection), linked SNPs (tightly linked to outlier SNPs), and neutral SNPs. 218-637-2541 Jeta Kotrba. 2008). Based on a quantitative trait locus (QTL) analysis of eight traits involving life history, mating system, and flowering time, Grillo et al. 0000000 bunyi 10 0000000 bloon 10 0000000 kaca 10 0000000 thii 10 0000000 cabelo 10 0000000 gawa 10 0000000 mintak 10 0000000 tangan 10 0000000 cantora 10 0000000 gmbr 10 0000000 hooy 10 0000000 provas 10 0000000 tirar 10 0000000 kamana 10 0000000 karna 10 0000000 panggil 10 0000000 cuek 10 0000000 heen 10 0000000 sakiit 10 0000000 avanya 10 0000000 bandas 10 … (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. Similarly, PCA showed that the combined samples are organized into two distinct groups (or species), with PC1 and PC2 accounting for 46.1% and 16.9% of the variance, respectively (fig. The green star and cross show the locations where the common garden experiment and the artificial crossing study were conducted, respectively. We removed duplicates showing identical 5′ coordinate (Fracassetti et al. 3b). “N × N” and “R × R” represent crosses between individuals from different populations within the same species. 1; supplementary table S1, Supplementary Material online; see Materials and Methods). Schematic diagram and test for single origin (SO) and multiple origin (MO) models. X.X., Q.-L.M., and M.-F.G. conducted the artificial crossing in Hainan. The QST–FST comparison therefore indicated that the parallel phenotypic divergence between species was an adaptive response to divergent habitats and driven by natural selection. The survival of all organisms depends critically upon interactions with the environment, mediated largely through the action of small molecules. All combined samples (a) and separate analyses on each of six paired populations (b) show the clear parallel phenotypic differentiation between species. The sequenced fragments were assembled by ContigExpress (Informax Inc., North Bethesda, MD) and edited manually. STRUCTURE analysis showed that the best supported clustering (K = 2) suggested the deepest divergence between two regions (South Asia vs. Southeast Asia) rather than between the two species (fig. Die Nobilia Ersatzteile erhalten Sie von uns versandkostenfrei zugesendet. For either MO or SO model, we considered different scenarios involving population split events only (Standard scenarios), fluctuating population sizes through time (Demography scenarios), and gene flow between paired populations (Migration scenarios) (supplementary fig. 218-637-8683 Buckly Stritzel. 2016; Comes et al. Obwohl die Einbauküchen von Nolte mit größter Sorgfalt und aus hochwertigen Materialien hergestellt werden, kann es vorkommen, dass Sie ein Zubehör oder ein Ersatzteil für ihre Nolte Einbauküche benötigen. First, we test for the alternative models by generating phylogenies using different types of SNPs across the genome (Roda et al. To further evaluate which MO model was more likely, we compared the PP values among three MO models and found that the Standard scenario (mean PP of 0.47, ranging from 0.31 to 0.64) and Demography scenario (mean PP of 0.51, ranging from 0.33 to 0.67) were equally supported with much greater possibility than that of the Migration scenario (mean PP was only 0.02), suggesting a negligible level of gene flow between the paired populations. Selfing of the panicles with (28 crosses) and without (40) castration were also conducted (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). 5c), suggesting potential gene flow between populations/localities within species. These observations indicated that mapping bias did not influence SNP calling. Andreas Fritz Hillgruber (18 January 1925 – 8 May 1989) was a conservative German historian who was influential as a military and diplomatic historian who played a leading role in the Historikerstreit of the 1980s.. 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). The summary statistics of the raw data were calculated using FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). 2015) suggested that O. nivara might have originated multiple times, implicative of parallel speciation. S10 and table S4, Supplementary Material online). Rice in Laos, Los Baños, Philippines, IRRI. Selection between the MO and SO models was performed under each scenario by comparing their posterior probabilities (Wegmann et al. The consistency of allele frequencies between Pool-Seq and genotyping data was evaluated by Pearson’s correlation coefficient and linear regression.
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