Parallel Speciation of Wild Rice Associated with Habitat Shifts

Cai, Zhe; Zhou, Lian; Ren, Nanjie; Xu, Xun; Liu, Rong; Huang, Lei; Zheng, Xiaoming; Meng, Qinglin; Du, Yu-Su; Wang, Meixia; Geng, Mu-Fan; Chen, Wenli; Jing, Chun-Yan; Zou, Xinhui; Guo, Jie; Chen, Chengbin; Zeng, Hua-Zhong; Liang, Yuntao; Wei, Xinghua; Guo, Ya‐Long; Zhou, Hang; Zhang, Fu‐Min; Ge, Song

doi:10.1093/molbev/msz029

Cited by 35 publications

(100 citation statements)

References 87 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1a). The exception to clear separation was O. nivara, which nested within rufipogon clades, but this result is consistent with previous analyses based on wide sampling of O. nivara and rufipogon (48). In the phylogeny, rufipogon was represented by two major clades: one that branched next to the outgroups (O. meridionalis and O. longistaminata) and a second that rooted between indica and japonica.…”

Section: Results: the Population Datasetsupporting

confidence: 89%

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

Kou

Liao

Toivainen

et al. 2019

Preprint

View full text Add to dashboard Cite

Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered structural variants (SVs) across a population sample of 358 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read dataset, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among datasets revealed different features of genome variability. For example, genome alignment identified a large (~4.3 Mb) inversion in indica rice varieties relative to an outgroup, and longread analyses suggest that ~9% of genes from this outgroup are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs.However, the site-frequency spectrum of each SV type --which included inversions, duplications, deletions, translocations and mobile element insertions --was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs are predominantly deleterious. The strength of these deleterious effects varied among SV types, with inversions especially deleterious, and across transposable element (TE) families. Among TEs SINE and mariner insertions were especially deleterious, due to stronger selection against their insertions. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ~25% more derived SVs than O. rufipogon, suggesting these deleterious SVs contribute to the cost of domestication. We also used SVs to study the effects of positive selection on the rice genome. Generally, the search for domestication genes were enriched for known candidates, suggesting some utility for SVs towards this purpose. More importantly, we detected hundreds to thousands of genes gained and lost during domestication, many of which are predicted to contribute to traits of agronomic interest.

show abstract

Section: Results: the Population Datasetsupporting

confidence: 89%

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

Kou

Liao

Toivainen

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…When populations independently and repeatedly adapt to similar environments, they often evolve similar phenotypes (Schluter, 2000). This has been observed in a wide variety of animal taxa (e.g., Johannesson et al, 1993;Nosil et al, 2002;Elmer et al, 2010;Ravinet et al, 2013;Soria-Carrasco et al, 2014;Perreault-Payette et al, 2017) and in some plants (e.g., Foster et al, 2007;Trucchi et al, 2017;Cai et al, 2019;Konečná et al, 2019). When independent populations evolve from similar initial conditions, this phenomenon is referred to as 'parallel evolution' (Schluter & Nagel, 1995;Bolnick et al, 2018).…”

Section: Introductionmentioning

confidence: 94%

“…To characterize the extent of phenotypic and genotypic parallelism within a system, it is necessary to rigorously demonstrate that populations adapting to similar environments (collectively referred to as an ecotype) have arisen multiple times independently. We refer the reader to our previous analyses of parallel evolution in Senecio lautus (Roda et al, 2013b;James et al, 2020) and to systems such as the marine snail, Littorina saxatilis (Quesada et al, 2007;Johannesson et al, 2010;Bierne et al, 2013;Butlin et al, 2014;Pérez-Pereira et al, 2017), and the threespine stickleback, Gasterosteus aculeatus (Colosimo et al, 2005;Chan et al, 2010;Dean et al, 2019;Marques et al, 2019) where one can find some of the strongest evidence for the independent origin of populations, and to the increasing number of potential cases of parallel evolution in plants (Foster et al, 2007;Ostevik et al, 2012;Trucchi et al, 2017;Cai et al, 2019;Konečná et al, 2019;Knotek et al, 2020).…”

Section: A Framework To Measure Parallel Evolutionmentioning

confidence: 99%

Phenotypic and genotypic parallel evolution in parapatric ecotypes ofSenecio

James

Wilkinson

Bernal

et al. 2020

Preprint

View full text Add to dashboard Cite

7The independent and repeated adaptation of populations to similar environments often results 8 in the evolution of similar forms. This phenomenon creates a strong correlation between 9 phenotype and environment and is referred to as 'parallel evolution.' However, there is 10 ongoing debate as to when we should call a system either phenotypically or genotypically 11 'parallel.' Here, we suggest a novel and simple framework to quantify parallel evolution at 12 the genotypic and phenotypic levels. We apply this framework to coastal ecotypes of an 13 Australian wildflower, Senecio lautus. Our findings show that S. lautus populations 14 inhabiting similar environments have evolved strikingly similar phenotypes. These 15 phenotypes have arisen via mutational changes affecting common biological functions but 16 occurring in different genes. Our work not only provides a common framework to study the 17

show abstract

“…The RI between Japonica and Indica has been widely reported (Morishima et al, 1992; Ouyang and Zhang, 2013), but the ancestors, O. nivara and O. rufipogon were proved compatible (Cai et al, 2019). Here comes the question that whether the RI appeared during the process of domestication, or the potential RI already existed in the ancestors.…”

Section: Discussionmentioning

confidence: 99%

“…Sa and DPLs both lead to hybrid pollen sterility. On the contrary, the two wild ancestors of rice, O. nivara and O. rufipogon , are compatible (Cai et al, 2019). Rice and the two wild ancestors constitute a excellent system for studying the evolution history of RI genes.…”

Section: Introductionmentioning

confidence: 99%

Independent domestications shape the genetic pattern of a reproductive isolation system in rice

Zhang

2020

Preprint

Self Cite

View full text Add to dashboard Cite

14Severe reproductive isolation (RI) exists between the two subspecies of rice, 15 Indica and Japonica, but in the wild ancestors no post-zygotic RI was found. The 16 studies about the establishment of the interspecies RI of rice are still rear. A pair of 17 rice hybrid sterility genes, DOPPELGANGER 1 (DPL1) and DOPPELGANGER 2 18 (DPL2), offers a convenient example to study the evolutionary history of RI genes. 19 Either of the two loci has one non-functional allele . The hybrid 20 pollen carrying both DPL1-and DPL2-will be sterility. 21 We collected 811 individuals: Oryza sativa (132), the two wild ancestors O. 22 nivara (296) and O. rufipogon (383) as well as 20 DPL1 and 34 DPL2 sequences of O. 23 sativa from on-line databases. We analysed the genetic and geographic pattern of 24DPLs in all three species to determine the origination regions of DPL1-and DPL2-. 25 The neutral test as well as the diversities of nucleotide and haplotype were used to 26 detect if selection shaped the pattern of DPLs. 27 We found that DPL1-and DPL2-of rice emerged from wild ancestor populations 28 in South Asia and South China through two respective domestications. Comparing 29 with the ancestral populations, DPL1-and DPL2-both showed reduce of diversities, 30 however their frequencies increased in rice. We assume that the reduce of diversities 31 due to the bottleneck effect of domestication while the loss of one copy was preferred 32 by artificial selection for cost savings. 33Reproductive isolation (RI) is considered a failure to transmit genetic materials 36 (Futuyma, 2013). Barriers that lead to RI are classified as pre-or postzygotic for 37 practical (Baack et al, 2015; Futuyma, 2013; Lafon-Placette et al, 2016; Rieseberg 38 and Willis, 2007; Widmer et al, 2009). Many genes related to RI have been identified 39 in various species (Fishman and Sweigart, 2018; Masly et al, 2006; Nadir et al, 2018; 40 Ouyang and Zhang, 2018; Zuellig and Sweigart, 2018), yet studies that aim to 41 elucidate the evolutionary histories of RI genes are still rare. 42 Rice (Oryza sativa) is an important crop as well as a model species. Strong 43 postzygotic RI was found between two subspecies of rice, Japonica and Indica. Many 44 loci answering for the hybrid incompatibility have been found (Ouyang et al, 2010; 45 Wang et al, 2014). Hundreds of loci were found related to hybrid incompatibility, 46 indicating that the incompatibility between Japonica and Indica has a complex 47 48 detected: S5 (Chen et al, 2008; Yang et al, 2012b), Sa (Long et al, 2008) and DPLs 49 (Mizuta et al, 2010). S5 leads to endoplasmic reticulum stress. Sa and DPLs both lead 50 to hybrid pollen sterility. On the contrary, the two wild ancestors of rice, O. nivara 51 and O. rufipogon, are compatible (Cai et al, 2019). Rice and the two wild ancestors 52 constitute a excellent system for studying the evolution history of RI genes. 53The DPL system offers a suitable example for exploring this phenomenon. The 54 DPL system contains only two genes, DOPPELGANGER 1 (DPL1)...

show abstract

Parallel Speciation of Wild Rice Associated with Habitat Shifts

Cited by 35 publications

References 87 publications

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

Phenotypic and genotypic parallel evolution in parapatric ecotypes ofSenecio

Independent domestications shape the genetic pattern of a reproductive isolation system in rice

Contact Info

Product

Resources

About