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Joo-hwan Kim - One of the best experts on this subject based on the ideXlab platform.
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Historical Biogeography of Melanthiaceae: A Case of Out-of-North America Through the Bering Land Bridge.
Frontiers in plant science, 2019Co-Authors: Changkyun Kim, Sang-chul Kim, Joo-hwan KimAbstract:Intercontinental floristic disjunction between East Asia and North America in the Northern Hemisphere has received much attention during the past decades, but few studies have focused on the family level. Melanthiaceae, containing 196 species and 17 genera circumscribed in five tribes, is disjunctly distributed in Eurasia and North America. It is one of the excellent models for studying the evolution of biogeographic patterns in this region. Here, we present a fossil calibrated, molecular phylogeny of Melanthiaceae based on two chloroplast DNA datasets: one dataset includes extensive sampling (94 species representing all 17 genera of Melanthiaceae) of four chloroplast DNA regions (atpB, rbcL, matK, and ndhF) and the other includes six species representing all tribes of the the family for 78 coding genes of the chloroplast genome. Within these framework, we infer the historical biogeography of Melanthiaceae. Both datasets produce well resolved phylogenies of Melanthiaceae showing the monophyly of the family and the relationships among the five tribes. Melanthieae is found to be sister to the rest of the tribes of the family and the remaining taxa are divided into two major clades consisting of the Chionographideae + Heloniadeae clade and the Parideae + Xerophylleae clade. The molecular dating and the ancestral area analyses suggest that Melanthiaceae most likely originated in North America with its crown group dated at 92.1 mya in late Cretaceous. The favored ancestral areas at the crown lineages of tribes are also North America. In the family, seven independent migrations into East Asia from North America are inferred to have occurred in the Oligocene and the Miocene-Pliocene via historical paleo-land bridge connections. Cooling trends during the Oligocene resulted in the present East Asia-North America disjunct distribution, while the warm period during the middle Miocene and habitat heterogeneity stimulated diversification in East Asia. Our study provides the phylogenetic and biogeographical history of the Melanthiaceae and adds an example of ‘out of North America’ migration in the biogeographic history of the northern Hemisphere.
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Image_1_Historical Biogeography of Melanthiaceae: A Case of Out-of-North America Through the Bering Land Bridge.TIF
2019Co-Authors: Changkyun Kim, Sang-chul Kim, Joo-hwan KimAbstract:Intercontinental floristic disjunction between East Asia and North America in the Northern Hemisphere has received much attention during the past decades, but few studies have focused on the family level. Melanthiaceae, containing 196 species and 17 genera circumscribed in five tribes, is disjunctly distributed in Eurasia and North America. It is one of the foremost models for studying the evolution of biogeographic patterns in this region. Here, we present a fossil-calibrated, molecular phylogeny of Melanthiaceae based on two chloroplast DNA datasets: one dataset includes extensive sampling (94 species representing all 17 genera of Melanthiaceae) of four chloroplast DNA regions (atpB, rbcL, matK, and ndhF) and the other includes six species representing all tribes of the family for 78 coding genes of the chloroplast genome. Within this framework, we infer the historical biogeography of Melanthiaceae. Both datasets produce well-resolved phylogenies of Melanthiaceae showing the monophyly of the family and the relationships among the five tribes. Melanthieae is found to be sister to the rest of the tribes of the family and the remaining taxa are divided into two major clades consisting of the Chionographideae + Heloniadeae clade and the Parideae + Xerophylleae clade. The molecular dating and the ancestral area analyses suggest that Melanthiaceae most likely originated in North America with its crown group dated at 92.1 mya in the late Cretaceous. The favored ancestral areas at the crown lineages of tribes are also in North America. In the family, seven independent migrations into East Asia from North America are inferred to have occurred in the Oligocene and the Miocene-Pliocene via historical paleo-land bridge connections. Cooling trends during the Oligocene resulted in the present East Asia-North America disjunct distribution, while the warm period during the middle Miocene and habitat heterogeneity stimulated diversification in East Asia. Our study provides the phylogenetic and biogeographical history of the Melanthiaceae and adds an example of “out of North America” migration in the biogeographic history of the Northern Hemisphere.
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Historical Biogeography of Melanthiaceae: A Case of Out-of-North America Through the Bering Land Bridge
Frontiers Media S.A., 2019Co-Authors: Changkyun Kim, Sang-chul Kim, Joo-hwan KimAbstract:Intercontinental floristic disjunction between East Asia and North America in the Northern Hemisphere has received much attention during the past decades, but few studies have focused on the family level. Melanthiaceae, containing 196 species and 17 genera circumscribed in five tribes, is disjunctly distributed in Eurasia and North America. It is one of the foremost models for studying the evolution of biogeographic patterns in this region. Here, we present a fossil-calibrated, molecular phylogeny of Melanthiaceae based on two chloroplast DNA datasets: one dataset includes extensive sampling (94 species representing all 17 genera of Melanthiaceae) of four chloroplast DNA regions (atpB, rbcL, matK, and ndhF) and the other includes six species representing all tribes of the family for 78 coding genes of the chloroplast genome. Within this framework, we infer the historical biogeography of Melanthiaceae. Both datasets produce well-resolved phylogenies of Melanthiaceae showing the monophyly of the family and the relationships among the five tribes. Melanthieae is found to be sister to the rest of the tribes of the family and the remaining taxa are divided into two major clades consisting of the Chionographideae + Heloniadeae clade and the Parideae + Xerophylleae clade. The molecular dating and the ancestral area analyses suggest that Melanthiaceae most likely originated in North America with its crown group dated at 92.1 mya in the late Cretaceous. The favored ancestral areas at the crown lineages of tribes are also in North America. In the family, seven independent migrations into East Asia from North America are inferred to have occurred in the Oligocene and the Miocene-Pliocene via historical paleo-land bridge connections. Cooling trends during the Oligocene resulted in the present East Asia-North America disjunct distribution, while the warm period during the middle Miocene and habitat heterogeneity stimulated diversification in East Asia. Our study provides the phylogenetic and biogeographical history of the Melanthiaceae and adds an example of “out of North America” migration in the biogeographic history of the Northern Hemisphere
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Table_1_Historical Biogeography of Melanthiaceae: A Case of Out-of-North America Through the Bering Land Bridge.DOCX
2019Co-Authors: Changkyun Kim, Sang-chul Kim, Joo-hwan KimAbstract:Intercontinental floristic disjunction between East Asia and North America in the Northern Hemisphere has received much attention during the past decades, but few studies have focused on the family level. Melanthiaceae, containing 196 species and 17 genera circumscribed in five tribes, is disjunctly distributed in Eurasia and North America. It is one of the foremost models for studying the evolution of biogeographic patterns in this region. Here, we present a fossil-calibrated, molecular phylogeny of Melanthiaceae based on two chloroplast DNA datasets: one dataset includes extensive sampling (94 species representing all 17 genera of Melanthiaceae) of four chloroplast DNA regions (atpB, rbcL, matK, and ndhF) and the other includes six species representing all tribes of the family for 78 coding genes of the chloroplast genome. Within this framework, we infer the historical biogeography of Melanthiaceae. Both datasets produce well-resolved phylogenies of Melanthiaceae showing the monophyly of the family and the relationships among the five tribes. Melanthieae is found to be sister to the rest of the tribes of the family and the remaining taxa are divided into two major clades consisting of the Chionographideae + Heloniadeae clade and the Parideae + Xerophylleae clade. The molecular dating and the ancestral area analyses suggest that Melanthiaceae most likely originated in North America with its crown group dated at 92.1 mya in the late Cretaceous. The favored ancestral areas at the crown lineages of tribes are also in North America. In the family, seven independent migrations into East Asia from North America are inferred to have occurred in the Oligocene and the Miocene-Pliocene via historical paleo-land bridge connections. Cooling trends during the Oligocene resulted in the present East Asia-North America disjunct distribution, while the warm period during the middle Miocene and habitat heterogeneity stimulated diversification in East Asia. Our study provides the phylogenetic and biogeographical history of the Melanthiaceae and adds an example of “out of North America” migration in the biogeographic history of the Northern Hemisphere.
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A Dynamic Tandem Repeat in Monocotyledons Inferred from a Comparative Analysis of Chloroplast Genomes in Melanthiaceae
Frontiers in plant science, 2017Co-Authors: Hoang Dang Khoa, Joo-hwan KimAbstract:Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore ‘hot spots’ for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the rps16 region across the Melanthiaceae. Based on the partial or complete loss of rps16 gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections (Veratrum and Fuscoveratrum) of Veratrum. Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from trnH_GUG to a part of rps3. Our results show an accumulation of tandem repeats in the rpl23-ycf2 regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during slipped-strand mispairing (SSM) events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.
Spencer C. H. Barrett - One of the best experts on this subject based on the ideXlab platform.
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Post-glacial history of Trillium grandiflorum (Melanthiaceae) in eastern North America: inferences from phylogeography
American journal of botany, 2004Co-Authors: Steven R. Griffin, Spencer C. H. BarrettAbstract:Dispersal and migration are important processes affecting the evolutionary history and genetics of species. Here we investigate post-glacial migration and gene flow in Trillium grandiflorum (Melanthiaceae), a wide-ranging, forest herb from eastern North America. Using phylogeographic approaches, we examined cpDNA and allozyme diversity in 35 populations of T. grandiflorum sampled from throughout the geographic range of the species. Nested clade analysis (NCA) of cpDNA haplotypes indicated that T. grandiflorum likely survived in two refugia in the southeastern US during the last glaciation and that long-distance dispersal characterized the post-glacial recolonization of northern areas. There was no evidence for reduced allozyme diversity in populations from glaciated compared to ice-free regions, probably because of the greater abundance and larger effective size of populations in the north. An analysis of isolation-by-distance based on the allozyme data suggested a pattern of population differentiation consistent with restricted gene flow. Notwithstanding the significance of rare seed dispersal events for migration, a comparison of allozyme and cpDNA genetic structure indicates that pollen flow between populations is more likely than seed dispersal. These results for T. grandiflorum represent the first phylogeographic analysis of a temperate woodland herb in eastern North America and support the importance of occasional long-distance dispersal events in the post-glacial migration of plants.
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Genetic variation in Trillium erectum (Melanthiaceae), a widespread forest herb in eastern North America
Canadian Journal of Botany, 2004Co-Authors: Steven R. Griffin, Spencer C. H. BarrettAbstract:Trillium erectum L. is an insect-pollinated understory herb widespread in forests of eastern North America. Marker gene studies indicate that the species has a mixed mating system, but aspects of population genetic structure have not been investigated. Using 10 allozyme loci, we measured genetic variation within and among 23 populations sampled from throughout the species' range. Overall, T. erectum displayed moderate levels of genetic diversity in comparison with other herbaceous plants. The percentage of loci that were polymorphic was 52%, with average values (±SE) of 1.20 ± 0.02, 0.08 ± 0.01, and 0.13 ± 0.01 for the number of alleles per locus (A), observed heterozygosity (Ho), and expected heterozygosity (He), respectively. There was evidence of inbreeding within populations (Fis = 0.39, 95% CI 0.260.55) and significant population differentiation (Fst = 0.16, 0.050.24). Analysis of genetic data provided no evidence of isolation by distance, and together with the occurrence of population subdivision,...
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Factors Affecting Low Seed:Ovule Ratios in a Spring Woodland Herb, Trillium grandiflorum (Melanthiaceae)
International Journal of Plant Sciences, 2002Co-Authors: Steven R. Griffin, Spencer C. H. BarrettAbstract:Female fertility in flowering plants is commonly observed to be submaximal. The fraction of ovules in a flower that produce seeds is commonly less than 1.00, particularly in outcrossing species. Here we investigate through controlled pollinations factors that may contribute toward low seed:ovule ratios in Trillium grandiflorum, a self‐incompatible woodland herb from eastern North America. Reduced fruit and seed set in open‐pollinated plants in comparison with hand cross‐pollinated plants demonstrated that pollen limitation was a contributing factor to low female fertility. However, seed:ovule ratios of hand cross‐pollinated flowers averaged only 0.66. Experimental pollinations involving the manipulation of pollen age, the number of pollen donors, the timing of pollination, and the application of self‐pollen before cross‐pollen each had no effect on fertility. This indicated that aspects of pollen delivery were not responsible for low seed:ovule ratios and that resources might influence variation in seed:o...
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Stigmatic Self-Incompatibility and Mating Patterns in Trillium grandiflorum and Trillium erectum(Melanthiaceae)
Annals of Botany, 2001Co-Authors: Tammy L. Sage, Steven R. Griffin, Vincenza Pontieri, Peter Drobac, William W. Cole, Spencer C. H. BarrettAbstract:Post-pollination processes governing mating patterns in Trillium, a well-known genus of insect-pollinated woodland herbs, are poorly understood. Mechanisms influencing outcrossing were investigated in T. grandiflorumand T. erectum, two widespread species native to eastern North America. In southern Ontario, Canada, the two species are often sympatric; they flower in early May, and are pollinated by diAerent assemblages of insects. Controlled cross- and selfpollinations and structural observations of pollen germination and pollen tube growth were conducted to determine whether the two species possess a self-incompatibility (SI) system and, if so, the specific site(s) of self-rejection. Controlled pollinations indicated that both species set significantly more seeds from cross-pollination than self-pollination, implicating the action of SI. This was confirmed by structural studies which demonstrated that selfrecognition and rejection reactions occurred on dry-type stigmatic papillae. Observations of pollen hydration revealed that self-rejection was rapid, being initiated within 10 min of pollination and prior to pollen tube emergence. Final selfrejection resulted in failure of pollen tube growth at the base of stigmatic papillae. SI was expressed more weakly in T. erectum and thereby resulted in considerable self-seed set in some individuals. Estimates of outcrossing rates using allozyme markers indicated that T. erectum displayed a mixed-mating system whereas T. grandiflorum was more highly outcrossed. Structural studies of pollen traits indicated that the two species diAered with respect to the size of grains and their aggregation with implications for pollen dispersal and mating. The ecological and evolutionary implications of the variable expression of SI in Trillium are discussed. # 2001 Annals of Botany Company
Steven R. Griffin - One of the best experts on this subject based on the ideXlab platform.
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Post-glacial history of Trillium grandiflorum (Melanthiaceae) in eastern North America: inferences from phylogeography
American journal of botany, 2004Co-Authors: Steven R. Griffin, Spencer C. H. BarrettAbstract:Dispersal and migration are important processes affecting the evolutionary history and genetics of species. Here we investigate post-glacial migration and gene flow in Trillium grandiflorum (Melanthiaceae), a wide-ranging, forest herb from eastern North America. Using phylogeographic approaches, we examined cpDNA and allozyme diversity in 35 populations of T. grandiflorum sampled from throughout the geographic range of the species. Nested clade analysis (NCA) of cpDNA haplotypes indicated that T. grandiflorum likely survived in two refugia in the southeastern US during the last glaciation and that long-distance dispersal characterized the post-glacial recolonization of northern areas. There was no evidence for reduced allozyme diversity in populations from glaciated compared to ice-free regions, probably because of the greater abundance and larger effective size of populations in the north. An analysis of isolation-by-distance based on the allozyme data suggested a pattern of population differentiation consistent with restricted gene flow. Notwithstanding the significance of rare seed dispersal events for migration, a comparison of allozyme and cpDNA genetic structure indicates that pollen flow between populations is more likely than seed dispersal. These results for T. grandiflorum represent the first phylogeographic analysis of a temperate woodland herb in eastern North America and support the importance of occasional long-distance dispersal events in the post-glacial migration of plants.
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Genetic variation in Trillium erectum (Melanthiaceae), a widespread forest herb in eastern North America
Canadian Journal of Botany, 2004Co-Authors: Steven R. Griffin, Spencer C. H. BarrettAbstract:Trillium erectum L. is an insect-pollinated understory herb widespread in forests of eastern North America. Marker gene studies indicate that the species has a mixed mating system, but aspects of population genetic structure have not been investigated. Using 10 allozyme loci, we measured genetic variation within and among 23 populations sampled from throughout the species' range. Overall, T. erectum displayed moderate levels of genetic diversity in comparison with other herbaceous plants. The percentage of loci that were polymorphic was 52%, with average values (±SE) of 1.20 ± 0.02, 0.08 ± 0.01, and 0.13 ± 0.01 for the number of alleles per locus (A), observed heterozygosity (Ho), and expected heterozygosity (He), respectively. There was evidence of inbreeding within populations (Fis = 0.39, 95% CI 0.260.55) and significant population differentiation (Fst = 0.16, 0.050.24). Analysis of genetic data provided no evidence of isolation by distance, and together with the occurrence of population subdivision,...
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Factors Affecting Low Seed:Ovule Ratios in a Spring Woodland Herb, Trillium grandiflorum (Melanthiaceae)
International Journal of Plant Sciences, 2002Co-Authors: Steven R. Griffin, Spencer C. H. BarrettAbstract:Female fertility in flowering plants is commonly observed to be submaximal. The fraction of ovules in a flower that produce seeds is commonly less than 1.00, particularly in outcrossing species. Here we investigate through controlled pollinations factors that may contribute toward low seed:ovule ratios in Trillium grandiflorum, a self‐incompatible woodland herb from eastern North America. Reduced fruit and seed set in open‐pollinated plants in comparison with hand cross‐pollinated plants demonstrated that pollen limitation was a contributing factor to low female fertility. However, seed:ovule ratios of hand cross‐pollinated flowers averaged only 0.66. Experimental pollinations involving the manipulation of pollen age, the number of pollen donors, the timing of pollination, and the application of self‐pollen before cross‐pollen each had no effect on fertility. This indicated that aspects of pollen delivery were not responsible for low seed:ovule ratios and that resources might influence variation in seed:o...
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Stigmatic Self-Incompatibility and Mating Patterns in Trillium grandiflorum and Trillium erectum(Melanthiaceae)
Annals of Botany, 2001Co-Authors: Tammy L. Sage, Steven R. Griffin, Vincenza Pontieri, Peter Drobac, William W. Cole, Spencer C. H. BarrettAbstract:Post-pollination processes governing mating patterns in Trillium, a well-known genus of insect-pollinated woodland herbs, are poorly understood. Mechanisms influencing outcrossing were investigated in T. grandiflorumand T. erectum, two widespread species native to eastern North America. In southern Ontario, Canada, the two species are often sympatric; they flower in early May, and are pollinated by diAerent assemblages of insects. Controlled cross- and selfpollinations and structural observations of pollen germination and pollen tube growth were conducted to determine whether the two species possess a self-incompatibility (SI) system and, if so, the specific site(s) of self-rejection. Controlled pollinations indicated that both species set significantly more seeds from cross-pollination than self-pollination, implicating the action of SI. This was confirmed by structural studies which demonstrated that selfrecognition and rejection reactions occurred on dry-type stigmatic papillae. Observations of pollen hydration revealed that self-rejection was rapid, being initiated within 10 min of pollination and prior to pollen tube emergence. Final selfrejection resulted in failure of pollen tube growth at the base of stigmatic papillae. SI was expressed more weakly in T. erectum and thereby resulted in considerable self-seed set in some individuals. Estimates of outcrossing rates using allozyme markers indicated that T. erectum displayed a mixed-mating system whereas T. grandiflorum was more highly outcrossed. Structural studies of pollen traits indicated that the two species diAered with respect to the size of grains and their aggregation with implications for pollen dispersal and mating. The ecological and evolutionary implications of the variable expression of SI in Trillium are discussed. # 2001 Annals of Botany Company
Jun-bo Yang - One of the best experts on this subject based on the ideXlab platform.
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Ultra-Barcoding Discovers a Cryptic Species in Paris yunnanensis (Melanthiaceae), a Medicinally Important Plant
Frontiers in plant science, 2020Co-Authors: Changkun Liu, Zhenyan Yang, Jin Yang, Lei Jin, Jun-bo YangAbstract:Ultra-barcoding is a technique using whole plastomes and nuclear ribosomal DNA (nrDNA) sequences for plant species identification. Paris yunnanensis is a medicinal plant of great economic importance for the pharmaceutical industry. However, the alpha taxonomy of P. yunnanensis is still uncertain, hindering effective conservation and management of the germplasm. To resolve long-standing taxonomic disputes regarding this species, we newly generated the complete plastomes and nrDNA sequences from 22 P. yunnanensis accessions. Ultra-barcoding analyses suggest that P. yunnanensis as currently circumscribed is made up of two distinct genetic lineages, corresponding to the two phenotypes ("typical" and "high stem" form) identified early in our study. With distinct morphologies and distribution, the "high stem" form should be recognized as a previously unrecognized species; here it is described as a new species, P. liiana sp. nov. Moreover, the ultra-barcoding data do not support treatment of P. yunnanensis as a conspecific variety under Paris polyphylla. Our study represents a guiding practical application of ultra-barcoding for discovery of cryptic species in taxonomically challenging plant taxa. The findings highlight the great potential of ultra-barcoding as an effective tool for resolving perplexing problems in plant taxonomy.
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Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)
BMC plant biology, 2019Co-Authors: Lifang Yang, Mark W. Chase, Zhenyan Yang, Changkun Liu, Jin Yang, Jun-bo YangAbstract:Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.
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Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)
2019Co-Authors: Lifang Yang, Mark W. Chase, Zhenyan Yang, Changkun Liu, Jin Yang, Jun-bo YangAbstract:Abstract Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. Results: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. Conclusions: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris . Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris . Our findings challenge the theoretical prediction that large genome sizes may limit speciation.
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Phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)
2019Co-Authors: Lifang Yang, Mark W. Chase, Zhenyan Yang, Changkun Liu, Jin Yang, Jun-bo YangAbstract:Abstract Background Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. Results All 29 species currently recognized in Paris were sampled. Complete plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the late Miocene. Conclusions Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.
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Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae)
BMC plant biology, 2019Co-Authors: Lifang Yang, Zhenyan Yang, Changkun Liu, Zhi-rong Zhang, Jing Yang, Haiyang Liu, Jun-bo YangAbstract:Robust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms. Paris japonica (Melanthiaceae) has the largest genome that has been confirmed in eukaryotes to date; however, its phylogenetic position remains unresolved. As a result, the evolutionary history of the genomic gigantisms in P. japonica remains poorly understood. We used next-generation sequencing to generate complete plastomes of P. japonica, P. verticillata, Trillium govanianum, Ypsilandra thibetica and Y. yunnanensis. Together with published plastomes, the infra-familial relationships in Melanthiaceae and infra-generic phylogeny in Paris were investigated, and their divergence times were calculated. The results indicated that the expansion of the ancestral genome of extant Paris and Trillium occurred approximately from 59.16 Mya to 38.21 Mya. The sister relationship between P. japonica and the section Euthyra was recovered, and they diverged around the transition of the Oligocene/Miocene (20 Mya), when the Japan Islands were separated from the continent of Asia. The genome size expansion in the most recent common ancestor for Paris and Trillium was most possibly a gradual process that lasted for approximately 20 million years. The divergence of P. japonica (section Kinugasa) and other taxa with thick rhizome may have been triggered by the isolation of the Japan Islands from the continent of Asia. This long-term separation, since the Oligocene/Miocene boundary, would have played an important role in the formation and evolution of the genomic gigantism in P. japonica. Moreover, our results support the taxonomic treatment of Paris as a genus rather than dividing it into three genera, but do not support the recognition of T. govanianum as the separate genus Trillidium.
Masashi Ohara - One of the best experts on this subject based on the ideXlab platform.
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Mechanisms of reproductive isolation of interspecific hybridization between Trillium camschatcense and T. tschonoskii (Melanthiaceae)
Plant Species Biology, 2012Co-Authors: Satomi Ishizaki, Tamayo Abe, Masashi OharaAbstract:Reproductive isolation plays a significant role in the prevention of gene flow between different plant species. Isolation factors can vary, acting either pre- or postzygotically. Trillium camschatcense and T. tschonoskii are herbaceous perennials which frequently grow together in Hokkaido, Japan. Natural hybrid formation, T. × hagae, between these species is common, and occurs asymmetrically with T. camschatcense as the maternal parent and T. tschonoskii as the paternal. Here, we examined the efficiency of each reproductive isolation factor to clarify which factor was responsible for the frequency and asymmetry of the hybridization. We found that prezygotic barriers, self fertilization and conspecific pollen precedence, are major isolation factors in both parental species, and that T. tschonoskii as a maternal parent has more effective prezygotic barriers than T. camschatcense. In addition, hybrids with T. tschonoskii as the maternal parent were not observed to reach the flowering stage. We concluded that prezygotic isolation factors in the both species act as main barriers to prevent natural hybridization, and that asymmetry of the isolating barriers between these species would promote T. camschatcense as the maternal parent of the hybrids.
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Breeding system and floral visitors of Veratrum album subsp. oxysepalum (Melanthiaceae).
Plant Species Biology, 2009Co-Authors: Yuuki Kato, Kiwako S. Araki, Masashi OharaAbstract:Veratrum album subsp. oxysepalum is an andromonoecious perennial woodland herb. In the present study, to clarify the essential life-history characteristics of this species, sexual reproduction was examined and breeding experiments were carried out along with observations of floral visitors in the field. The results of the breeding experiments showed that this species has a high level of self-incompatibility. As various Coleoptera and Diptera visited the flowers, the seed production of V. album subsp. oxysepalum possibly depends on outcrossing pollination by insects.
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Adaptive significance of self-fertilization in a hermaphroditic perennial, Trillium camschatcense (Melanthiaceae).
American journal of botany, 2008Co-Authors: Shosei Kubota, Yoshiaki Kameyama, Akira S. Hirao, Masashi OharaAbstract:The evolution of self-fertilization from primarily outcrossing ancestors is one of the most common evolutionary transitions in plants; however, the ecological mechanisms that maintain self-fertilization have remained controversial. Theoretical studies suggest that selfing is advantageous over outcrossing in terms of genetic transmission and assurance of seed production under pollen-limited circumstances. Trillium camschatcense is a herbaceous perennial distributed in Hokkaido and northern Honshu, Japan. Geographical variation in the breeding system (self-compatible, SC; or self-incompatible, SI) has been reported in populations in Hokkaido. Here, we used several SC and SI populations of T. camschatcense to investigate the adaptive significance and the evolutionary basis of self-fertilization. Pollination experiments and genetic analyses demonstrated that the potential availability of outcross pollen in SC populations was sufficient and that the number of pollen donors was equal to that of SI populations. However, despite the high availability of outcross pollen, the SC populations produced seeds predominantly by selfing and so underwent severe inbreeding depression. Although none of the suggested advantages for self-fertilization were supported by our analyses, we propose two possible scenarios for the evolution of self-fertilization in T. camschatcense.