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Sympatric Speciation of Wild Emmer Wheat Driven by Ecology and Chromosomal Rearrangements

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Sympatric Speciation of Wild Emmer Wheat Driven by Ecology and Chromosomal Rearrangements Sympatric speciation of wild emmer wheat driven by ecology and chromosomal rearrangements Hongwei Wanga,1,2, Huayan Yinb,1, Chengzhi Jiaoc,1, Xiaojian Fanga,1, Guiping Wanga,1, Guangrong Lid, Fei Nia, Penghuan Lia, Peisen Sua, Wenyang Gea, Zhongfan Lyua, Shoushen Xua, Yanhong Yanga, Yongchao Haoa, Xinxin Chenga, Jinxiao Zhaoa, Cheng Liua,3, Fengfeng Xuc, Xin Maa, Silong Suna, Yan Zhaoa, Yinguang Baoa, Cheng Liue,4, Jingjing Zhangf, Tomas Pavlicekg, Anfei Lia, Zujun Yangd,1,2, Eviatar Nevog,2, and Lingrang Konga,2 aState Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 271018 Tai’an, China; bCollege of Agronomy, Qingdao Agricultural University, 266109 Qingdao, China; cNovogene Bioinformatics Institute, 100083 Beijing, China; dCenter for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054 Chengdu, China; eCrop Research Institute, Shandong Academy of Agricultural Sciences, 250100 Jinan, China; fSchool of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; and gInstitute of Evolution, University of Haifa, Haifa 3498838, Israel Contributed by Eviatar Nevo, December 27, 2019 (sent for review November 26, 2019; reviewed by Eugene V. Koonin, James Shapiro, and Alan Robert Templeton) In plants, the mechanism for ecological sympatric speciation (SS) is nature by the examples in animals (e.g., resource competition, little known. Here, after ruling out the possibility of secondary assortative mating, etc.) (5, 7, 8). In plants, which are stressed contact, we show that wild emmer wheat, at the microclimatically constantly by a diversity of biotic and abiotic stresses, ecological divergent microsite of “Evolution Canyon” (EC), Mt. Carmel, Israel, divergence was presumed essential in driving speciation. How- underwent triple SS. Initially, it split following a bottleneck of an ever, accepted examples of ecological SS are still limited in ancestral population, and further diversified to three isolated pop- plants, and evolutionary mechanisms for such speciation have ulations driven by disruptive ecological selection. Remarkably, two not been well established. One compelling case is that of sister postzygotically isolated populations (SFS1 and SFS2) sympatrically species of palm (Howea) that seem to have split on a tiny iso- branched within an area less than 30 m at the tropical hot and dry lated island in the Tasman Sea, possibly driven by divergent soil savannoid south-facing slope (SFS). A series of homozygous chro- preference, yet any underlying cellular and genetic mechanisms mosomal rearrangements in the SFS1 population caused hybrid associated with this split have not been demonstrated (9). EVOLUTION sterility with the SFS2 population. We demonstrate that these two populations developed divergent adaptive mechanisms against Significance severe abiotic stresses on the tropical SFS. The SFS2 population evolved very early flowering, while the SFS1 population alterna- In plants, which are stressed constantly by diverse abiotic and tively evolved a direct tolerance to irradiance by improved ROS biotic stresses, ecological divergence is substantial in driving scavenging activity that potentially accounts for its evolutionary speciation, yet its demonstration under sympatry is still limited fate with unstable chromosome status. Moreover, a third prezygoti- in plants and needs elaboration. By analyzing wild emmer cally isolated sympatric population adapted on the abutting tem- wheat at the Evolution Canyon microsite, a hot spot of sym- perate, humid, cool, and forested north-facing slope (NFS), patric speciation, we highlighted how disruptive ecological separated by 250 m from the SFS wild emmer wheat populations. selection drives primary sympatric speciation in situ. Natural The NFS population evolved multiple resistant loci to fungal dis- selection, overruling the homogenizing effects of gene flow, eases, including powdery mildew and stripe rust. Our study illus- split the metapopulation of wild emmer wheat into three re- trates how plants sympatrically adapt and speciate under disruptive productively isolated populations. Each population evolved ecological selection of abiotic and biotic stresses. unique evolutionary trajectory with divergent adaptive strat- egies, including fungal disease resistance, irradiance tolerance, sympatric speciation | wild emmer wheat | Robertsonian translocation | and divergent flowering time. Our work provides a model for abiotic stress | biotic stress plant adaptive ecological sympatric speciation under biotic and abiotic stressors. nderstanding the mechanisms underlying speciation, the Usplitting of a group of interbreeding populations into two Author contributions: H.W., E.N., and L.K. designed research; H.Y., G.W., G.L., P.L., P.S., reproductively isolated groups, has been a major focus of evo- W.G., Z.L., S.X., Y.Y., Y.H., X.C., J. Zhao, C.L.3, X.M., Y.B., A.L., and Z.Y. performed research; 4 lutionary biology (1). In the widespread process known as C.L. , J. Zhang, and T.P. contributed new reagents/analytic tools; C.J., X.F., F.N., F.X., S.S., and Y.Z. analyzed data; and H.W. wrote the paper. “allopatric speciation,” populations that become geographically Reviewers: E.V.K., National Institutes of Health; J.S., University of Chicago; and A.R.T., isolated experience selective pressures and/or genetic drift that Washington University in St. Louis. ultimately give rise to two reproductively isolated new species (2). The authors declare no competing interest. In contrast, there are dramatically fewer known instances of spe- ciation occurring without geographical isolation, a concept known Published under the PNAS license. as sympatric speciation (SS) proposed by Darwin (2–4). It is Data deposition: The resequencing and SNP data generated in this work are deposited in the Genome Sequence Archive in the BIG Data Center, Beijing Institute of Genomics, generally agreed that an instance of SS must be substantiated with Chinese Academy of Sciences, under the accession no. CRA001873. evidence showing that the relevant species occur in the same 1H.W., H.Y., C.J., X.F., G.W., and Z.Y. contributed equally to this work. geographic location, are in reproductive isolation, and display a 2To whom correspondence may be addressed. Email: [email protected], sister relationship (3). Claims of SS are bolstered by evidence that [email protected], [email protected], or [email protected]. any earlier periods of allopatric speciation are unlikely (5). Major 3State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Col- questions about SS typically center on how reproductive isolation lege of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong, China. has arisen in sympatry and on the nature of the selection pressures 4Crop Research Institute, Shandong Academy of Agricultural Sciences, 250100 Jinan, and genetic drift that has driven the speciation (6). China. An increasing number of mathematical models have been This article contains supporting information online at https://www.pnas.org/lookup/suppl/ established to sustain the plausibility of SS, often including the doi:10.1073/pnas.1920415117/-/DCSupplemental. influence of disruptive selection that is particularly validated in www.pnas.org/cgi/doi/10.1073/pnas.1920415117 PNAS Latest Articles | 1of9 Downloaded by guest on September 27, 2021 Guided by the widely held speculation that divergent selection incipient SS is under way at EC-I between populations present via microcosmic ecological differences are likely essential in fa- on the SFS or NFS. cilitating SS, a long-term research project since 1990 in Israel has Here, seeking to apply modern genome-scale technologies to enabled tracking of evolutionary histories at a microscale by examine potential speciation events in tetraploid wheat pop- designating four natural laboratories: the so-called “Evolution ulations at EC-I, we collected 47 accessions of wild emmer wheat Canyon” microsites (EC-I to EC-IV). At each of these EC sites, (Triticum dicoccoides Koern), the progenitor of bread wheat, there are sharp ecological contrasts within minuscule interslope from EC-I. Using genomics, cytogenetics, analysis of hybrid distances (6). The EC-I microsite comprises twin slopes with sterility patterns, and both observational and hypothesis-driven extremely sharp ecological contrasts: the south-facing slope confirmatory studies addressing observed divergence for eco- (SFS) and north-facing slope (NFS) are only separated by an logically important traits, we assessed the possibility of SS of wild average of 250 m, but the SFS receives 200 to 800% higher solar emmer wheat at EC-I. radiation than the NFS, resulting in a substantially hotter and Results drier slope (Fig. 1A). In contrast, the higher relative humidity Three Distinct Populations of Wild Emmer Wheat Have Diverged and reduced solar radiation of the NFS results in cooler and within EC-I following a Recent Population Bottleneck. To apply wetter conditions (10). These dramatic differences in microcli- modern high-resolution genetic analysis methods to the excep- mates in extremely close proximity have enabled very high spatial tionally diverse populations of species known to exist at the EC-I resolution studies unfolding the influence of environmental site, we collected 47 accessions from the tropical hot and dry gradients on fitness-related phenotypic traits, and
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