Epistasis between cytoplasmic and nuclear genes is the primary genetic component of complex quantitative traits.Genetic dissection of cytonuclear epistasis is fundamentally important to understand the genetic architec...Epistasis between cytoplasmic and nuclear genes is the primary genetic component of complex quantitative traits.Genetic dissection of cytonuclear epistasis is fundamentally important to understand the genetic architecture of complex traits.In this study,a two-dimensional genome scan strategy was employed to evaluate the contribution of cytoplasm,quantitative trait loci (QTL),QTL×QTL interactions and QTL×QTL×cytoplasm interactions to the phenotypic variation.The p-value and parameter value for each genetic effect were calculated by multiple regression analysis.A stepwise approach was suggested to build confidence in candidate QTL on the basis of q-value estimation,false discovery rate calculation and Bonferroni adjustment.A fine-scale grid scan strategy was proposed for further analysis of peaks of interest.Plant height in maize was used as an example to illustrate the efficiency of the two-dimensional genome scan strategy.展开更多
The angiosperm family Elaeagnaceae comprises three genera and ca.100 species distributed mainly in Eurasia and North America.Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducte...The angiosperm family Elaeagnaceae comprises three genera and ca.100 species distributed mainly in Eurasia and North America.Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted,limiting the application and preservation of natural genetic resources.Here,we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand interand intrageneric relationships,as well as the origin and biogeographical history of the family.For this purpose,we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and,along with current distributional data,infer historical biogeographical processes.Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera.Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia.The intrageneric relationships of Elaeagnus and Hippophae were also well resolved.High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus,and our analyses suggest putative ancient and recent hybridization.We inferred that Elaeagnaceae originated at ca.90.48 Ma(95%CI?89.91e91.05 Ma),and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution.This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date,offers new insights into previously unresolved relationships in Elaeagnus,and provides a foundation for further studies on classification,evolution,biogeography,and conservation of Elaeagnaceae.展开更多
A single small population of chasmophytic plants is described as Mojiangia oreophila,a monotypic genus in the subtribe Crepidinae,characterised by a unique combination of morphological features,in particular densely l...A single small population of chasmophytic plants is described as Mojiangia oreophila,a monotypic genus in the subtribe Crepidinae,characterised by a unique combination of morphological features,in particular densely long-papillose homomorphic achenes with five main ribs each accompanied by two secondary ribs,coarse brownish pappus bristles,moderately many-flowered capitula,a small involucre with numerous outer phyllaries,perennial rosette herb growth and brown-woolly caudex and leaf axils.Molecular phylogenetic analysis detected that in the nrlTS phylogeny M.oreophila forms a clade of its own in the Crepidinae;in the plastid DNA phylogeny it is nested in the clade formed by the hybrid-ogenous genus Faberia,the maternal ancestor of which comes from the Crepidinae and the paternal ancestor from the Lactucinae,where Faberia is placed in nrlTS phylogenies.M.oreophila shares several morphological features with Faberia and also shares the expected chromosome number of 2n=16 with its hitherto unknown maternal ancestor.M.oreophila may therefore be a successor of the maternal ancestor of Faberia.Alternatively,cytonuclear discordance is to be assumed in Mojiangia,caused by chloroplast capture as a result of hybridisation and introgression with Faberia.展开更多
The complex interactions of historical,geological and climatic events on plant evolution have been an important research focus for many years.However,the role of desert formation and expansion in shaping the genetic s...The complex interactions of historical,geological and climatic events on plant evolution have been an important research focus for many years.However,the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored.In the present study,we investigated the phylogeography of Arnebia szechenyi,a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China.We measured genetic diversity of populations using three maternally inherited chloroplast DNA(cpDNA)fragments and seven bi-paternally inherited nuclear DNA(nDNA)loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species.Our data indicated a considerably high level of genetic variation within A.szechenyi and noteworthy asymmetry in historical migration from the east to the west.Moreover,two nuclear genetic groups of populations were revealed,corresponding to the two geographic regions separated by the Tengger Desert.However,analysis of cpDNA data did not show significant geographic structure.The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A.szechenyi populations experienced long periods of geographic isolation followed by range expansion,which would have promoted generalized recombination of the nuclear genome.Our findings further highlight the important role that the Tengger Desert,together with the Helan Mountains,has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.展开更多
Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought,little work has been devoted to uncovering the extent,timeline,and geographic and ecological context of ancien...Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought,little work has been devoted to uncovering the extent,timeline,and geographic and ecological context of ancient hybridization.Using an expansive new dataset of nuclear and chloroplast DNA sequences,we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks(Quercus).We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae.Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting,with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation,dated to the Early-Middle Eocene.Ancestral reconstructions including fossils suggest ancestors of Castanea+Castanopsis,Lithocarpus,and the Old World oak clade probably co-occurred in North America and Eurasia,while the ancestors of Chrysolepis,Notholithocarpus,and the New World oak clade co-occurred in North America,offering ample opportunity for hybridization in each region.Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives.Concomitantly,this study provides a methodological framework for detecting ancient hybridization in other groups.展开更多
基金supported by the National Basic Research Program of China(2011CB100106)the National Natural Science Foundation of China(30971846and31171187)+1 种基金the Vital Project of Natural Science of Universities in Jiangsu Province(09KJA210002) to C.Xufrom the National Natural Science Foundation of China(31100882) to Z.Tang
文摘Epistasis between cytoplasmic and nuclear genes is the primary genetic component of complex quantitative traits.Genetic dissection of cytonuclear epistasis is fundamentally important to understand the genetic architecture of complex traits.In this study,a two-dimensional genome scan strategy was employed to evaluate the contribution of cytoplasm,quantitative trait loci (QTL),QTL×QTL interactions and QTL×QTL×cytoplasm interactions to the phenotypic variation.The p-value and parameter value for each genetic effect were calculated by multiple regression analysis.A stepwise approach was suggested to build confidence in candidate QTL on the basis of q-value estimation,false discovery rate calculation and Bonferroni adjustment.A fine-scale grid scan strategy was proposed for further analysis of peaks of interest.Plant height in maize was used as an example to illustrate the efficiency of the two-dimensional genome scan strategy.
基金supported by the National Natural Science Foundation of China,Key International(regional)Cooperative Research Project(no.31720103903)the Science and Technology Basic Resources Investigation Program of China(no.2019FY100900)+6 种基金the Strategic Priority Research Program of Chinese Academy of Sciences(no.XDB31000000)the National Natural Science Foundation of China(no.31270274)the Yunling International High-end Experts Program of Yunnan Province,China(no.YNQR-GDWG-2017-002 and no.YNQR-GDWG-2018-012)the China Scholarship Council(202004910775)the Chinese Academy of Sciences(CAS)President's International Fellowship Initiative(no.2020PB0009)the China Postdoctoral Science Foundation(CPSF)the United States Department of Energy(grant no.DESC0018247 to PSS,RPG,and DES).
文摘The angiosperm family Elaeagnaceae comprises three genera and ca.100 species distributed mainly in Eurasia and North America.Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted,limiting the application and preservation of natural genetic resources.Here,we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand interand intrageneric relationships,as well as the origin and biogeographical history of the family.For this purpose,we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and,along with current distributional data,infer historical biogeographical processes.Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera.Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia.The intrageneric relationships of Elaeagnus and Hippophae were also well resolved.High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus,and our analyses suggest putative ancient and recent hybridization.We inferred that Elaeagnaceae originated at ca.90.48 Ma(95%CI?89.91e91.05 Ma),and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution.This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date,offers new insights into previously unresolved relationships in Elaeagnus,and provides a foundation for further studies on classification,evolution,biogeography,and conservation of Elaeagnaceae.
文摘A single small population of chasmophytic plants is described as Mojiangia oreophila,a monotypic genus in the subtribe Crepidinae,characterised by a unique combination of morphological features,in particular densely long-papillose homomorphic achenes with five main ribs each accompanied by two secondary ribs,coarse brownish pappus bristles,moderately many-flowered capitula,a small involucre with numerous outer phyllaries,perennial rosette herb growth and brown-woolly caudex and leaf axils.Molecular phylogenetic analysis detected that in the nrlTS phylogeny M.oreophila forms a clade of its own in the Crepidinae;in the plastid DNA phylogeny it is nested in the clade formed by the hybrid-ogenous genus Faberia,the maternal ancestor of which comes from the Crepidinae and the paternal ancestor from the Lactucinae,where Faberia is placed in nrlTS phylogenies.M.oreophila shares several morphological features with Faberia and also shares the expected chromosome number of 2n=16 with its hitherto unknown maternal ancestor.M.oreophila may therefore be a successor of the maternal ancestor of Faberia.Alternatively,cytonuclear discordance is to be assumed in Mojiangia,caused by chloroplast capture as a result of hybridisation and introgression with Faberia.
基金supported by the National Natural Science Foundation of China(41861008)Science Foundation of Yunnan Education Department(2018JS347)the Ten-thousand Talents Program of Yunnan Province(YNWR-QNBJ-2020).
文摘The complex interactions of historical,geological and climatic events on plant evolution have been an important research focus for many years.However,the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored.In the present study,we investigated the phylogeography of Arnebia szechenyi,a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China.We measured genetic diversity of populations using three maternally inherited chloroplast DNA(cpDNA)fragments and seven bi-paternally inherited nuclear DNA(nDNA)loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species.Our data indicated a considerably high level of genetic variation within A.szechenyi and noteworthy asymmetry in historical migration from the east to the west.Moreover,two nuclear genetic groups of populations were revealed,corresponding to the two geographic regions separated by the Tengger Desert.However,analysis of cpDNA data did not show significant geographic structure.The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A.szechenyi populations experienced long periods of geographic isolation followed by range expansion,which would have promoted generalized recombination of the nuclear genome.Our findings further highlight the important role that the Tengger Desert,together with the Helan Mountains,has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.
基金National Natural Science Foundation of China with a key international(regional)cooperative research project(No.31720103903 to T.-S.Y.and D.E.S)the Strategic Priority Research Program of the Chinese Academy of Sciences(CAS)(grant No.XDB31000000 to D.-Z.L.)+6 种基金the Science and Technology Basic Resources Investigation Program of China(2019FY100900 to H.-L.L.)the National Natural Science Foundation of China(No.32270247 to R.Z.)the Yunling International High-end Experts Program of Yunnan Province,China(grant No.YNQR-GDWG-2017-002 to P.S.S.and T.-S.Y.and YNQR-GDWG-2018-012 to D.E.S.and T.-S.Y.)the USA Department of Energy(grant DE-SC0018247 to P.S.S.,D.E.S.,R.P.G.,and R.A.F.)the USA National Science Foundation(grant DEB-1916632 to R.A.F.,R.P.G.,D.E.S.,and P.S.S.)the Natural Environment Research Council of the UK(grant No.NE/X015505/1 to A.F.and P.J.V.)Leverhulme Research Project(grant RPG-2019-365 to A.F.and P.J.V.).
文摘Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought,little work has been devoted to uncovering the extent,timeline,and geographic and ecological context of ancient hybridization.Using an expansive new dataset of nuclear and chloroplast DNA sequences,we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks(Quercus).We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae.Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting,with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation,dated to the Early-Middle Eocene.Ancestral reconstructions including fossils suggest ancestors of Castanea+Castanopsis,Lithocarpus,and the Old World oak clade probably co-occurred in North America and Eurasia,while the ancestors of Chrysolepis,Notholithocarpus,and the New World oak clade co-occurred in North America,offering ample opportunity for hybridization in each region.Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives.Concomitantly,this study provides a methodological framework for detecting ancient hybridization in other groups.
