Qiuyue Zhang, M. Deng, Y. Bouchenak‐Khelladi, Zhekun Zhou, G. Hu, Yaowu Xing
Ulmaceae is a woody family widespread in northern temperate forests. Despite the ecological importance of this family, its phylogeny and biogeographic history are poorly understood. In this study, we reconstruct phylogenetic relationships within the family and infer spatio‐temporal diversification patterns based on chloroplast genome (complete cpDNA) and nuclear ribosomal DNA sequences (nrDNA). The seven Ulmaceae genera are resolved in two main clades (temperate vs. tropical) by both cpDNA and nrDNA sequences. The temperate clade includes four genera, Hemiptelea, Zelkova, Planera, and Ulmus. The relationships among Planera and other genera are controversial because of inconsistent topologies between plastid and nuclear data. The tropical clade includes three genera ((Ampelocera, Phyllostylon), Holoptelea). Molecular dating and diversification analyses show that Ulmaceae originated in the Early Cretaceous (ca. 110–125 Ma) with the main lineages establishing from the Late Cretaceous to the early Eocene. The diversification rate slowed during the middle to the late Paleogene (ca. 23–45 Ma), followed by a rapid diversification of the East Asian temperate group in the Neogene, congruent with a global cooling event. The ancestral state optimization analysis suggests an East Asian origin of the temperate Ulmaceae clade during the Paleocene, which is consistent with the fossil record. Both phylogenomic and fossil evidence support East Asia as a center of origin and diversification for the temperate woody lineages.
{"title":"The diversification of the northern temperate woody flora – A case study of the Elm family (Ulmaceae) based on phylogenomic and paleobotanical evidence","authors":"Qiuyue Zhang, M. Deng, Y. Bouchenak‐Khelladi, Zhekun Zhou, G. Hu, Yaowu Xing","doi":"10.1111/jse.12720","DOIUrl":"https://doi.org/10.1111/jse.12720","url":null,"abstract":"Ulmaceae is a woody family widespread in northern temperate forests. Despite the ecological importance of this family, its phylogeny and biogeographic history are poorly understood. In this study, we reconstruct phylogenetic relationships within the family and infer spatio‐temporal diversification patterns based on chloroplast genome (complete cpDNA) and nuclear ribosomal DNA sequences (nrDNA). The seven Ulmaceae genera are resolved in two main clades (temperate vs. tropical) by both cpDNA and nrDNA sequences. The temperate clade includes four genera, Hemiptelea, Zelkova, Planera, and Ulmus. The relationships among Planera and other genera are controversial because of inconsistent topologies between plastid and nuclear data. The tropical clade includes three genera ((Ampelocera, Phyllostylon), Holoptelea). Molecular dating and diversification analyses show that Ulmaceae originated in the Early Cretaceous (ca. 110–125 Ma) with the main lineages establishing from the Late Cretaceous to the early Eocene. The diversification rate slowed during the middle to the late Paleogene (ca. 23–45 Ma), followed by a rapid diversification of the East Asian temperate group in the Neogene, congruent with a global cooling event. The ancestral state optimization analysis suggests an East Asian origin of the temperate Ulmaceae clade during the Paleocene, which is consistent with the fossil record. Both phylogenomic and fossil evidence support East Asia as a center of origin and diversification for the temperate woody lineages.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"4 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2021-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84260824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. He, Mengge Wang, Yingxiang Li, Xing Zou, Hui-Yuan Yeh, Renkuan Tang, Xiao-min Yang, Z. Wang, Jianxin Guo, Ting Luo, J. Zhao, Jin Sun, Rong Hu, Lan-Hai Wei, Gang Chen, Yingrui Hou, Chuan‐Chao Wang
The Han Chinese are the world's largest ethnic group residing across China. Shaanxi province in northern China was a pastoral–agricultural interlacing region sensitive to climate change since Neolithic times, which makes it a vital place for studying population dynamics. However, genetic studies of Shaanxi Han are underrepresented due to the lack of high‐density sampling and genome‐wide data. Here, we genotyped 700 000 single nucleotide polymorphisms (SNPs) in 200 Han individuals from nine populations in Shaanxi and compared with available modern and ancient Eurasian individuals. We revealed a north–south genetic cline in Han Chinese with Shaanxi Han locating at the northern side of the cline. We detected the western Eurasian‐related admixture in Shaanxi populations, especially in Guanzhong and Shanbei Han Chinese in proportions of 2%–4.6%. Shaanxi Han were suggested to derive a large part of ancestry (39%–69%) from a lineage that also contributed largely to ancient and present‐day Tibetans (85%) as well as southern Han, supporting the common northern China origin of modern Sino‐Tibetan‐speaking populations and southwestward expansion of millet farmers from the middle‐upper Yellow River Basin to the Tibetan Plateau and to southern China. The rest of the ancestry of Shaanxi Han was from a lineage closely related to ancient and present‐day Austronesian and Tai‐Kadai speaking populations in southern China and Southeast Asia. We also observed a genetic substructure in Shaanxi Han in terms of north–south‐related ancestry corresponding well to the latitudes. Maternal mitochondrial DNA and paternal Y‐chromosome lineages further demonstrated the aforementioned admixture pattern of Han Chinese in Shaanxi province.
{"title":"Fine‐scale north‐to‐south genetic admixture profile in Shaanxi Han Chinese revealed by genome‐wide demographic history reconstruction","authors":"G. He, Mengge Wang, Yingxiang Li, Xing Zou, Hui-Yuan Yeh, Renkuan Tang, Xiao-min Yang, Z. Wang, Jianxin Guo, Ting Luo, J. Zhao, Jin Sun, Rong Hu, Lan-Hai Wei, Gang Chen, Yingrui Hou, Chuan‐Chao Wang","doi":"10.1111/jse.12715","DOIUrl":"https://doi.org/10.1111/jse.12715","url":null,"abstract":"The Han Chinese are the world's largest ethnic group residing across China. Shaanxi province in northern China was a pastoral–agricultural interlacing region sensitive to climate change since Neolithic times, which makes it a vital place for studying population dynamics. However, genetic studies of Shaanxi Han are underrepresented due to the lack of high‐density sampling and genome‐wide data. Here, we genotyped 700 000 single nucleotide polymorphisms (SNPs) in 200 Han individuals from nine populations in Shaanxi and compared with available modern and ancient Eurasian individuals. We revealed a north–south genetic cline in Han Chinese with Shaanxi Han locating at the northern side of the cline. We detected the western Eurasian‐related admixture in Shaanxi populations, especially in Guanzhong and Shanbei Han Chinese in proportions of 2%–4.6%. Shaanxi Han were suggested to derive a large part of ancestry (39%–69%) from a lineage that also contributed largely to ancient and present‐day Tibetans (85%) as well as southern Han, supporting the common northern China origin of modern Sino‐Tibetan‐speaking populations and southwestward expansion of millet farmers from the middle‐upper Yellow River Basin to the Tibetan Plateau and to southern China. The rest of the ancestry of Shaanxi Han was from a lineage closely related to ancient and present‐day Austronesian and Tai‐Kadai speaking populations in southern China and Southeast Asia. We also observed a genetic substructure in Shaanxi Han in terms of north–south‐related ancestry corresponding well to the latitudes. Maternal mitochondrial DNA and paternal Y‐chromosome lineages further demonstrated the aforementioned admixture pattern of Han Chinese in Shaanxi province.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"424 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84939298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene duplication provides raw material for functional innovation, but gene duplicability varies considerably. Previous studies have found widespread asymmetrical sequence evolution between paralogs. However, it remains unknown whether the rate of evolution among paralogs affects their propensity of being retained after another round of whole‐genome duplication (WGD). In this study, we investigated gene groups that have experienced two successive WGDs to determine which of two older duplicates with different evolutionary rates was more likely to retain both younger duplicates. To uncouple the measurement of evolutionary rates from any assignment of duplicate or singleton status, we measured the evolutionary rates of singleton genes in out‐lineages but classified these singleton genes according to whether they are retained or not in a crown group of species. We found that genes that retained younger duplicates in the crown group of genomes were more constrained prior to the younger duplication event than those that failed to leave duplicates. In addition, we also found that the retained clades have more genes in out‐lineages. Subsequent analyses showed that genes in the retained clades were expressed more broadly and highly than genes in the singleton clades. We concluded that the set of repeatedly retained genes after two WGDs is biased toward slowly evolving genes in angiosperms, suggesting that the potential of genes for both functional conservation and divergence likely affects their propensity of being retained after WGD in angiosperms.
{"title":"Preferential retention of the slowly evolving gene in pairs of duplicates in angiosperm genomes","authors":"Linbo Wang, Hong Ma, Juan Lin","doi":"10.1111/jse.12712","DOIUrl":"https://doi.org/10.1111/jse.12712","url":null,"abstract":"Gene duplication provides raw material for functional innovation, but gene duplicability varies considerably. Previous studies have found widespread asymmetrical sequence evolution between paralogs. However, it remains unknown whether the rate of evolution among paralogs affects their propensity of being retained after another round of whole‐genome duplication (WGD). In this study, we investigated gene groups that have experienced two successive WGDs to determine which of two older duplicates with different evolutionary rates was more likely to retain both younger duplicates. To uncouple the measurement of evolutionary rates from any assignment of duplicate or singleton status, we measured the evolutionary rates of singleton genes in out‐lineages but classified these singleton genes according to whether they are retained or not in a crown group of species. We found that genes that retained younger duplicates in the crown group of genomes were more constrained prior to the younger duplication event than those that failed to leave duplicates. In addition, we also found that the retained clades have more genes in out‐lineages. Subsequent analyses showed that genes in the retained clades were expressed more broadly and highly than genes in the singleton clades. We concluded that the set of repeatedly retained genes after two WGDs is biased toward slowly evolving genes in angiosperms, suggesting that the potential of genes for both functional conservation and divergence likely affects their propensity of being retained after WGD in angiosperms.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"49 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75346005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qing‐Hua Wang, S. Dong, Jin-Long Zhang, Yang Liu, Yu Jia
Orthotrichum Hedw. s.l. and Ulota Mohr s.l. are two of the most speciose genera of the xerophytic moss family Orthotrichaceae. We reconstructed the phylogeny of these two genera using three data matrices: (i) organellar genomes and 33 taxa; (ii) six loci from three genomes and 144 taxa; and (iii) two plastid loci and 163 taxa. The present phylogeny, based on the maximum sampling of genes or taxa to date, generally confirms the new classification of Orthotrichum and Ulota, and indicated that all Ulota species, except Ulota phyllantha Brid., form a clade and three lineages comprise the cryptoporous Orthotrichum clade. We provided new morphological characters that support the present division of the two genera. Ancestral state reconstruction of stoma indicates that superficial stomata in Orthotrichum represent a plesiomorphic character and semi‐immersed stomata were derived from immersed stomata. The results also suggest that immersed stomata independently arose once in Orthotrichum, whereas semi‐immersed stomata probably arose more than once. Molecular dating analysis reveals that the occurrence of immersed stomata is probably related to arid environments during the early Oligocene to late Miocene, whereas the appearance of semi‐immersed stomata might be associated with the mesic–xeric or semiarid environments during the middle Miocene to Pliocene. Ancestral state reconstruction of habitat indicates that the saxicolous habitat is apomorphic and independently evolved multiple times in Orthotrichum and Ulota, which supports the former hypothesis. Considering morphological statistics, the development of the cryptopore in Orthotrichum could provide increased resilience to dry habitats, and might promote their habitat shift during evolution.
{"title":"Phylogeny of Orthotrichum s.l. and Ulota s.l. (Orthotrichaceae, Bryophyta): Insights into stomatal evolution","authors":"Qing‐Hua Wang, S. Dong, Jin-Long Zhang, Yang Liu, Yu Jia","doi":"10.1111/jse.12713","DOIUrl":"https://doi.org/10.1111/jse.12713","url":null,"abstract":"Orthotrichum Hedw. s.l. and Ulota Mohr s.l. are two of the most speciose genera of the xerophytic moss family Orthotrichaceae. We reconstructed the phylogeny of these two genera using three data matrices: (i) organellar genomes and 33 taxa; (ii) six loci from three genomes and 144 taxa; and (iii) two plastid loci and 163 taxa. The present phylogeny, based on the maximum sampling of genes or taxa to date, generally confirms the new classification of Orthotrichum and Ulota, and indicated that all Ulota species, except Ulota phyllantha Brid., form a clade and three lineages comprise the cryptoporous Orthotrichum clade. We provided new morphological characters that support the present division of the two genera. Ancestral state reconstruction of stoma indicates that superficial stomata in Orthotrichum represent a plesiomorphic character and semi‐immersed stomata were derived from immersed stomata. The results also suggest that immersed stomata independently arose once in Orthotrichum, whereas semi‐immersed stomata probably arose more than once. Molecular dating analysis reveals that the occurrence of immersed stomata is probably related to arid environments during the early Oligocene to late Miocene, whereas the appearance of semi‐immersed stomata might be associated with the mesic–xeric or semiarid environments during the middle Miocene to Pliocene. Ancestral state reconstruction of habitat indicates that the saxicolous habitat is apomorphic and independently evolved multiple times in Orthotrichum and Ulota, which supports the former hypothesis. Considering morphological statistics, the development of the cryptopore in Orthotrichum could provide increased resilience to dry habitats, and might promote their habitat shift during evolution.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"37 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89561764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zheng‐Zhen Wang, Zixiao Guo, C. Zhong, Haomin Lyu, Xinnian Li, N. Duke, S. Shi
Subspecies is used to designate taxa below species but above geographical populations. What patterns of genomic variation are expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina (Forssk.) Vierh. of the Indo‐West Pacific coasts. This species has three subspecies, distinguished by morphological traits and geographical distribution. We collected samples from 16 populations (577 individuals) covering all three subspecies and sequenced 94 nuclear genes. We reveal comprehensive genetic divergence among subspecies, generally higher than among geographical populations within subspecies. The level of genetic diversity differs among the three subspecies, possibly hinting at a degree of separation among their gene pools. We observed that divergence varies from locus to locus across the genome. A small portion of the genome is most informative about subspecies delineation, whereas the rest is undifferentiated or slightly differentiated, hinting at uneven gene flow and incomplete isolation. The three subspecies likely split simultaneously with gene flow among lineages. This reticulate evolution results in some discordance between morphology and genetics in areas of population contact. In short, A. marina subspecies show species‐like patterns in some respects and population‐like patterns in others. We propose that the subspecies designated in A. marina are informative in predicting genetic divergences and useful in making conservation decisions.
{"title":"Genomic variation patterns of subspecies defined by phenotypic criteria: Analyses of the mangrove species complex, Avicennia marina","authors":"Zheng‐Zhen Wang, Zixiao Guo, C. Zhong, Haomin Lyu, Xinnian Li, N. Duke, S. Shi","doi":"10.1111/jse.12709","DOIUrl":"https://doi.org/10.1111/jse.12709","url":null,"abstract":"Subspecies is used to designate taxa below species but above geographical populations. What patterns of genomic variation are expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina (Forssk.) Vierh. of the Indo‐West Pacific coasts. This species has three subspecies, distinguished by morphological traits and geographical distribution. We collected samples from 16 populations (577 individuals) covering all three subspecies and sequenced 94 nuclear genes. We reveal comprehensive genetic divergence among subspecies, generally higher than among geographical populations within subspecies. The level of genetic diversity differs among the three subspecies, possibly hinting at a degree of separation among their gene pools. We observed that divergence varies from locus to locus across the genome. A small portion of the genome is most informative about subspecies delineation, whereas the rest is undifferentiated or slightly differentiated, hinting at uneven gene flow and incomplete isolation. The three subspecies likely split simultaneously with gene flow among lineages. This reticulate evolution results in some discordance between morphology and genetics in areas of population contact. In short, A. marina subspecies show species‐like patterns in some respects and population‐like patterns in others. We propose that the subspecies designated in A. marina are informative in predicting genetic divergences and useful in making conservation decisions.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"112 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80812368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Xue, S. Dong, Ming‐Qiang Wang, Tianqiang Song, G. Zhou, Zhen Li, Y. Van de Peer, Zhu-Qing Shao, Wen Wang, Min Chen, Yan-mei Zhang, Xiaoqin Sun, Hongfeng Chen, Yongxia Zhang, Shouzhou Zhang, Fei Chen, Liangsheng Zhang, C. Cox, Yang Liu, Qiang Wang, Y. Hang
The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon‐sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon‐usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony‐informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.
{"title":"Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants","authors":"J. Xue, S. Dong, Ming‐Qiang Wang, Tianqiang Song, G. Zhou, Zhen Li, Y. Van de Peer, Zhu-Qing Shao, Wen Wang, Min Chen, Yan-mei Zhang, Xiaoqin Sun, Hongfeng Chen, Yongxia Zhang, Shouzhou Zhang, Fei Chen, Liangsheng Zhang, C. Cox, Yang Liu, Qiang Wang, Y. Hang","doi":"10.1111/jse.12708","DOIUrl":"https://doi.org/10.1111/jse.12708","url":null,"abstract":"The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon‐sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon‐usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony‐informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"202 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83555436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chenyang Liao, Qing Gao, D. S. Katz‐Downie, S. R. Downie
Angelica is a taxonomically complex genus widespread throughout the North Temperate Zone. Previous phylogenetic studies of the genus have focused primarily on its East Asian species. The relationships among its North American members, the monophyly of these species, and the value of fruit morphology in circumscribing its taxa have yet to be examined. This study represents the most comprehensive sampling of Angelica to date (100 species) and includes all 26 species in North America. Relationships are inferred using Bayesian inference, maximum likelihood, and maximum parsimony analyses of ITS sequences and, for multiple accessions of each North American species, cpDNA ndhF‐rpl32, rpl32‐trnL, and psbM‐psbD sequences. The fruit morphological characters examined were those considered phylogenetically important in East Asian Angelica. The results revealed that the North American species fell into three major clades: North American Angelica clade, Archangelica clade, and the Eurasian Angelica clade. Angelica dawsonii has affinities with Lomatium brandegeei. Fourteen species within the North American Angelica clade were strongly supported as monophyletic. Two paraphyletic species resulted in new combinations in A. lineariloba and A. venenosa. Conflict between the ITS‐derived and cpDNA‐derived phylogenies and the lack of resolution in portions of the trees may be due to chloroplast capture and rapid species radiation. Fruit morphology supported some interspecific relationships based on molecular data, and relationships revealed by ITS and cpDNA data were roughly in accordance with fruit classification type and geographic distribution region, respectively. A diagnostic key based on fruit morphology is provided for the identification of the North American Angelica taxa.
{"title":"A systematic study of North American Angelica species (Apiaceae) based on nrDNA ITS and cpDNA sequences and fruit morphology","authors":"Chenyang Liao, Qing Gao, D. S. Katz‐Downie, S. R. Downie","doi":"10.1111/jse.12702","DOIUrl":"https://doi.org/10.1111/jse.12702","url":null,"abstract":"Angelica is a taxonomically complex genus widespread throughout the North Temperate Zone. Previous phylogenetic studies of the genus have focused primarily on its East Asian species. The relationships among its North American members, the monophyly of these species, and the value of fruit morphology in circumscribing its taxa have yet to be examined. This study represents the most comprehensive sampling of Angelica to date (100 species) and includes all 26 species in North America. Relationships are inferred using Bayesian inference, maximum likelihood, and maximum parsimony analyses of ITS sequences and, for multiple accessions of each North American species, cpDNA ndhF‐rpl32, rpl32‐trnL, and psbM‐psbD sequences. The fruit morphological characters examined were those considered phylogenetically important in East Asian Angelica. The results revealed that the North American species fell into three major clades: North American Angelica clade, Archangelica clade, and the Eurasian Angelica clade. Angelica dawsonii has affinities with Lomatium brandegeei. Fourteen species within the North American Angelica clade were strongly supported as monophyletic. Two paraphyletic species resulted in new combinations in A. lineariloba and A. venenosa. Conflict between the ITS‐derived and cpDNA‐derived phylogenies and the lack of resolution in portions of the trees may be due to chloroplast capture and rapid species radiation. Fruit morphology supported some interspecific relationships based on molecular data, and relationships revealed by ITS and cpDNA data were roughly in accordance with fruit classification type and geographic distribution region, respectively. A diagnostic key based on fruit morphology is provided for the identification of the North American Angelica taxa.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"23 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90864547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study attempts to understand the biogeographic history of the Western Ghats forests by investigating decoupling between phylogenetic and taxonomic diversity. We specifically test whether the deciduous forests have been recently established, whether the southern region was a refuge, and whether the deciduous and evergreen forest species have disparate evolutionary histories. We used species composition data from 23 forest types along the Western Ghats for all woody angiosperms above 10‐cm diameter at breast height. Forests were broadly grouped as either evergreen or deciduous. Mean phylogenetic distances corrected for species richness and mean phylogenetic beta diversity corrected for shared species were assessed using z‐scores from null distributions. Null distributions were generated by randomizing the species relationships on the phylogeny. We found that all evergreen forests showed a greater phylogenetic diversity as compared with null expectations. Deciduous forests showed the inverse pattern. Within the evergreen belt, there was a decreasing phylogenetic diversity from south to north, as predicted by the southern refuge hypothesis. The phylogenetic beta diversity across evergreen–deciduous forests was lesser than the null expectation, whereas it was much higher across forests within the evergreen belt. This study provides the first phylogenetic evidence for the antiquity of evergreen forests as well as the southern refuge hypothesis in the Western Ghats. The deciduous forests species have shared evolutionary histories with the evergreen forest species, suggesting multiple shifts between evergreen and deciduous states through the lineages. Conversely, the evergreen species exhibited a disparate evolutionary history across these forests, possibly owing to sharper ecological or climatic gradients.
{"title":"Contrasting patterns of phylogenetic diversity across climatic zones of Western Ghats: A biodiversity hotspot in peninsular India","authors":"D. B., R. B.R, K. Karanth","doi":"10.1111/jse.12663","DOIUrl":"https://doi.org/10.1111/jse.12663","url":null,"abstract":"This study attempts to understand the biogeographic history of the Western Ghats forests by investigating decoupling between phylogenetic and taxonomic diversity. We specifically test whether the deciduous forests have been recently established, whether the southern region was a refuge, and whether the deciduous and evergreen forest species have disparate evolutionary histories. We used species composition data from 23 forest types along the Western Ghats for all woody angiosperms above 10‐cm diameter at breast height. Forests were broadly grouped as either evergreen or deciduous. Mean phylogenetic distances corrected for species richness and mean phylogenetic beta diversity corrected for shared species were assessed using z‐scores from null distributions. Null distributions were generated by randomizing the species relationships on the phylogeny. We found that all evergreen forests showed a greater phylogenetic diversity as compared with null expectations. Deciduous forests showed the inverse pattern. Within the evergreen belt, there was a decreasing phylogenetic diversity from south to north, as predicted by the southern refuge hypothesis. The phylogenetic beta diversity across evergreen–deciduous forests was lesser than the null expectation, whereas it was much higher across forests within the evergreen belt. This study provides the first phylogenetic evidence for the antiquity of evergreen forests as well as the southern refuge hypothesis in the Western Ghats. The deciduous forests species have shared evolutionary histories with the evergreen forest species, suggesting multiple shifts between evergreen and deciduous states through the lineages. Conversely, the evergreen species exhibited a disparate evolutionary history across these forests, possibly owing to sharper ecological or climatic gradients.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"5 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74894839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meifang Wang, Chun-Yan Jing, Xiu-Hua Wang, Zhe Cai, Lian Zhou, Mu-Fan Geng, Jing-Dan Han, Jie Guo, Fu-min Zhang, S. Ge
Parallel domestication has been widely acknowledged but its genetic basis remains largely unclear. As an important rice ecotype, upland rice was assumedly domesticated multiple times in two rice subspecies (Indica and Japonica) and provides a feasible system to explore the genetic basis of parallel domestication. To uncover the genome‐wide pattern of genetic differentiation between upland and lowland rice and explore the parallelism of genetic changes during upland rice domestication, we obtained whole‐genome sequences of 95 rice landraces and yielded genome‐wide expression data for five tissues of representative accessions of upland and lowland rice. Our phylogenetic analyses confirmed multiple domestications of the upland ecotype in two rice subspecies. Genomic scans based on resequencing data identified substantial differentiation between the upland and lowland ecotypes with 11.4% and 14.8% of the genome diverged between the two ecotypes in Indica and Japonica, respectively. Further genome‐wide gene expression analyses found that 30% of effectively expressed genes were significantly differentiated between two ecotypes, indicating the importance of regulation changes in the domestication of upland rice. Importantly, we found that only 1.8% of differentiated genomes and 1.6% of differentially expressed genes were shared by upland Indica and upland Japonica, suggestive of largely unparallel genetic alterations during upland rice domestication. These findings not only provide new insights into the genetic basis of parallel domestication at the genome scale but could also facilitate genetic improvement and breeding of rice and crops in general.
{"title":"Genomic landscape of parallel domestication of upland rice and its implications","authors":"Meifang Wang, Chun-Yan Jing, Xiu-Hua Wang, Zhe Cai, Lian Zhou, Mu-Fan Geng, Jing-Dan Han, Jie Guo, Fu-min Zhang, S. Ge","doi":"10.1111/jse.12636","DOIUrl":"https://doi.org/10.1111/jse.12636","url":null,"abstract":"Parallel domestication has been widely acknowledged but its genetic basis remains largely unclear. As an important rice ecotype, upland rice was assumedly domesticated multiple times in two rice subspecies (Indica and Japonica) and provides a feasible system to explore the genetic basis of parallel domestication. To uncover the genome‐wide pattern of genetic differentiation between upland and lowland rice and explore the parallelism of genetic changes during upland rice domestication, we obtained whole‐genome sequences of 95 rice landraces and yielded genome‐wide expression data for five tissues of representative accessions of upland and lowland rice. Our phylogenetic analyses confirmed multiple domestications of the upland ecotype in two rice subspecies. Genomic scans based on resequencing data identified substantial differentiation between the upland and lowland ecotypes with 11.4% and 14.8% of the genome diverged between the two ecotypes in Indica and Japonica, respectively. Further genome‐wide gene expression analyses found that 30% of effectively expressed genes were significantly differentiated between two ecotypes, indicating the importance of regulation changes in the domestication of upland rice. Importantly, we found that only 1.8% of differentiated genomes and 1.6% of differentially expressed genes were shared by upland Indica and upland Japonica, suggestive of largely unparallel genetic alterations during upland rice domestication. These findings not only provide new insights into the genetic basis of parallel domestication at the genome scale but could also facilitate genetic improvement and breeding of rice and crops in general.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"77 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81398053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-04-28DOI: 10.1080/13651501.2020.1757277
Lilia Coronato
Abend, M. Adhikary, Amitava Aerts, An Ainsbury, Elizabeth Akar, Ayşeg€ ul Al-Bachir, M. Alexander, Andrew Aliru, Maureen Aly, A. Anastasov, Natasa Anderson, Rhona Ando, K. Antovic, N. M. Antunes Soares, Felix Aravindan, Natarajan Aronov, Stella Arora, Rajesh Ayinoglu, Fatima Ayrapetyan, Sinerik Azimzadeh, Omid Azizova, Tamara Azizullah, Azizullah Azzam, Edouard Balajee, Adayabalam Ballarini, Francesca Ballhausen, Hendrik Bao, J. Baranova, Ancha Barquinero, Joan Francesc Baulch, Janet E. Baumann, Michael Bazak, Remon Beaugelin-Seiller, Karine Bebas, Piotr Behari, J. Bekeschus, S. Belyaev, Igor Benderitter, M. Blakely, William Boege, Fritz Boehm, D. Boga, Ayper Bond, Andrew Boreham, D. R. Bouffler, Simon Bouville, A. Braby, Leslie Broadhurst, J. H. Brooks, Antone Brown, Stephen Cadet, Jean Cammaerts, Marie-Claire Candas, Demet Cand eias, Serge Carty, Michael P. Castresana, Javier Celli, Janathan Chandna, Sudhir Chaudhury, Nabo Chodick, G. Chung, Byung Yeoup Coelho, L. A. Coleman, William B. Collins, Andrew Cooke, Marcus Cosic, Irena Coulter, Jonathan Courrol, Lilia Coronato Cucinotta, Francis Dadachova, E. Dale, Roger Dasdag, Suleyman Datta, K. Dauer, L. T. Deckbar, Dorothee Depauw, Nicolas DiGiorgio, Marina Dingfelder, M. Down, J. D. Drouet, M. Durante, Marco Dynlacht, J R Eberhardt, J. Ebert, Steven N. Edeline, Julien Efstathopoulos, E. P. ElAchy, Samar Erfani, Mostafa Eriksson, D. Esnault, Marie-Andree Feinendegen, Ludwig Fernandez-Palomo, Cristian Fischer, Manfred Flegal, Farrah N. Fokas, Emmanouil Franken, Nicolaas Fukumoto, Manabu Furtado Filho, Orlando Gaipl, Udo Galisteo J unior, Andr es Garcia, O. Garty, G. Georgakilas, A. G. George, K. A. Geras’kin, Stanislav Geso, M. Gewirtz, D. A. Giorgi, G. Gomolka, Maria Goodhead, Dudley Gorbunov, Nikolai Grdina, David Greenberger, Joel Gudkov, D.I. Guha, Chandan Gupta, Manju Hallahan, D. E. Harms-Ringdahl, Mats Hashem, H. A. Haston, Christina Held, Kathryn Hendry, Jolyon Henshaw, Denis Herskind, Carsten Herv e du Penhoat, Marie-Anne Hideghety, Katalin Higashitani, Atsushi Hill, Colin Hill, Richard Hinrikus, Hiie Hoeye, Ellen Marie Hofer, Michal Ita, K. Jacob, Naduparambil Jang, Cheol Seong Jenrow, Kenneth Jensen, Mark Jeon, You-Jin
{"title":"List of Reviewers","authors":"Lilia Coronato","doi":"10.1080/13651501.2020.1757277","DOIUrl":"https://doi.org/10.1080/13651501.2020.1757277","url":null,"abstract":"Abend, M. Adhikary, Amitava Aerts, An Ainsbury, Elizabeth Akar, Ayşeg€ ul Al-Bachir, M. Alexander, Andrew Aliru, Maureen Aly, A. Anastasov, Natasa Anderson, Rhona Ando, K. Antovic, N. M. Antunes Soares, Felix Aravindan, Natarajan Aronov, Stella Arora, Rajesh Ayinoglu, Fatima Ayrapetyan, Sinerik Azimzadeh, Omid Azizova, Tamara Azizullah, Azizullah Azzam, Edouard Balajee, Adayabalam Ballarini, Francesca Ballhausen, Hendrik Bao, J. Baranova, Ancha Barquinero, Joan Francesc Baulch, Janet E. Baumann, Michael Bazak, Remon Beaugelin-Seiller, Karine Bebas, Piotr Behari, J. Bekeschus, S. Belyaev, Igor Benderitter, M. Blakely, William Boege, Fritz Boehm, D. Boga, Ayper Bond, Andrew Boreham, D. R. Bouffler, Simon Bouville, A. Braby, Leslie Broadhurst, J. H. Brooks, Antone Brown, Stephen Cadet, Jean Cammaerts, Marie-Claire Candas, Demet Cand eias, Serge Carty, Michael P. Castresana, Javier Celli, Janathan Chandna, Sudhir Chaudhury, Nabo Chodick, G. Chung, Byung Yeoup Coelho, L. A. Coleman, William B. Collins, Andrew Cooke, Marcus Cosic, Irena Coulter, Jonathan Courrol, Lilia Coronato Cucinotta, Francis Dadachova, E. Dale, Roger Dasdag, Suleyman Datta, K. Dauer, L. T. Deckbar, Dorothee Depauw, Nicolas DiGiorgio, Marina Dingfelder, M. Down, J. D. Drouet, M. Durante, Marco Dynlacht, J R Eberhardt, J. Ebert, Steven N. Edeline, Julien Efstathopoulos, E. P. ElAchy, Samar Erfani, Mostafa Eriksson, D. Esnault, Marie-Andree Feinendegen, Ludwig Fernandez-Palomo, Cristian Fischer, Manfred Flegal, Farrah N. Fokas, Emmanouil Franken, Nicolaas Fukumoto, Manabu Furtado Filho, Orlando Gaipl, Udo Galisteo J unior, Andr es Garcia, O. Garty, G. Georgakilas, A. G. George, K. A. Geras’kin, Stanislav Geso, M. Gewirtz, D. A. Giorgi, G. Gomolka, Maria Goodhead, Dudley Gorbunov, Nikolai Grdina, David Greenberger, Joel Gudkov, D.I. Guha, Chandan Gupta, Manju Hallahan, D. E. Harms-Ringdahl, Mats Hashem, H. A. Haston, Christina Held, Kathryn Hendry, Jolyon Henshaw, Denis Herskind, Carsten Herv e du Penhoat, Marie-Anne Hideghety, Katalin Higashitani, Atsushi Hill, Colin Hill, Richard Hinrikus, Hiie Hoeye, Ellen Marie Hofer, Michal Ita, K. Jacob, Naduparambil Jang, Cheol Seong Jenrow, Kenneth Jensen, Mark Jeon, You-Jin","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"1990 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2020-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82333635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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