Wei Wang, D. Dilcher, G. Sun, Hongshan Wang, Zhiduan Chen
The new discovery of angiosperm remains in the Jehol Biota of northeastern China contributes to our understanding of the origin and early evolution of flowering plants. The earliest eudicot genus with reproductive organs, Leefructus, was recently documented from the Lower Cretaceous Yixian Formation at 125.8–123.0 Ma, and was reconsidered to be close to the extant family Ranunculaceae based on gross morphology. However, this hypothesis has not been tested using a cladistic approach. To determine the possible allies of Leefructus within extant eudicots, we constructed a 66 morphological data matrix. Molecular and morphological analyses of extant Ranunculales combined with the fossil suggest that it has an affinity with the Ranunculaceae. The earliest fossil record of the eudicots is 127–125 Ma based on tricolpate pollen grains. Thus, we suggest a hypothesis that the basal eudicots might have experienced an accelerated evolution and diversification during the latest Barremian and earliest Aptian, leading to the stem groups of at least six extant families or lineages, 10–15 Myr earlier than currently documented. Angiosperms have undergone multiple uneven pulses of radiation since their origin. Many key character innovations occurred in different stages that could have triggered those radiations in concert with various biotic and abiotic factors.
{"title":"Accelerated evolution of early angiosperms: Evidence from ranunculalean phylogeny by integrating living and fossil data","authors":"Wei Wang, D. Dilcher, G. Sun, Hongshan Wang, Zhiduan Chen","doi":"10.1111/jse.12090","DOIUrl":"https://doi.org/10.1111/jse.12090","url":null,"abstract":"The new discovery of angiosperm remains in the Jehol Biota of northeastern China contributes to our understanding of the origin and early evolution of flowering plants. The earliest eudicot genus with reproductive organs, Leefructus, was recently documented from the Lower Cretaceous Yixian Formation at 125.8–123.0 Ma, and was reconsidered to be close to the extant family Ranunculaceae based on gross morphology. However, this hypothesis has not been tested using a cladistic approach. To determine the possible allies of Leefructus within extant eudicots, we constructed a 66 morphological data matrix. Molecular and morphological analyses of extant Ranunculales combined with the fossil suggest that it has an affinity with the Ranunculaceae. The earliest fossil record of the eudicots is 127–125 Ma based on tricolpate pollen grains. Thus, we suggest a hypothesis that the basal eudicots might have experienced an accelerated evolution and diversification during the latest Barremian and earliest Aptian, leading to the stem groups of at least six extant families or lineages, 10–15 Myr earlier than currently documented. Angiosperms have undergone multiple uneven pulses of radiation since their origin. Many key character innovations occurred in different stages that could have triggered those radiations in concert with various biotic and abiotic factors.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":" 10","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91412619","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}
Hong‐Lei Li, Wei Wang, Rui‐Qi Li, Jing-Bo Zhang, Miao-miao Sun, R. Naeem, Junyan Su, X. Xiang, P. Mortimer, De-Zhu Li, K. Hyde, Jian-chu Xu, D. Soltis, P. Soltis, Jianhua Li, Shouzhou Zhang, Hong Wu, Zhiduan Chen, An‐ming Lu
There has been increasing interest in integrating a regional tree of life with community assembly rules in the ecological research. This raises questions regarding the impacts of taxon sampling strategies at the regional versus global scales on the topology. To address this concern, we constructed two trees for the nitrogen‐fixing clade: (i) a genus‐level global tree including 1023 genera; and (ii) a regional tree comprising 303 genera, with taxon sampling limited to China. We used the supermatrix approach and performed maximum likelihood analyses on combined matK, rbcL, and trnL‐F plastid sequences. We found that the topology of the global and the regional tree of the N‐fixing clade were generally congruent. However, whereas relationships among the four orders obtained with the global tree agreed with the accepted topology obtained in focused analyses with more genes, the regional topology obtained different relationships, albeit weakly supported. At a finer scale, the phylogenetic position of the family Myricaceae was found to be sensitive to sampling density. We expect that internal support throughout the phylogeny could be improved with denser taxon sampling. The taxon sampling approach (global vs. regional) did not have a major impact on fine‐level branching patterns of the N‐fixing clade. Thus, a well‐resolved phylogeny with relatively dense taxon sampling strategy at the regional scale appears, in this case, to be a good representation of the overall phylogenetic pattern and could be used in ecological research. Otherwise, the regional tree should be adjusted according to the correspondingly reliable global tree.
{"title":"Global versus Chinese perspectives on the phylogeny of the N‐fixing clade","authors":"Hong‐Lei Li, Wei Wang, Rui‐Qi Li, Jing-Bo Zhang, Miao-miao Sun, R. Naeem, Junyan Su, X. Xiang, P. Mortimer, De-Zhu Li, K. Hyde, Jian-chu Xu, D. Soltis, P. Soltis, Jianhua Li, Shouzhou Zhang, Hong Wu, Zhiduan Chen, An‐ming Lu","doi":"10.1111/jse.12201","DOIUrl":"https://doi.org/10.1111/jse.12201","url":null,"abstract":"There has been increasing interest in integrating a regional tree of life with community assembly rules in the ecological research. This raises questions regarding the impacts of taxon sampling strategies at the regional versus global scales on the topology. To address this concern, we constructed two trees for the nitrogen‐fixing clade: (i) a genus‐level global tree including 1023 genera; and (ii) a regional tree comprising 303 genera, with taxon sampling limited to China. We used the supermatrix approach and performed maximum likelihood analyses on combined matK, rbcL, and trnL‐F plastid sequences. We found that the topology of the global and the regional tree of the N‐fixing clade were generally congruent. However, whereas relationships among the four orders obtained with the global tree agreed with the accepted topology obtained in focused analyses with more genes, the regional topology obtained different relationships, albeit weakly supported. At a finer scale, the phylogenetic position of the family Myricaceae was found to be sensitive to sampling density. We expect that internal support throughout the phylogeny could be improved with denser taxon sampling. The taxon sampling approach (global vs. regional) did not have a major impact on fine‐level branching patterns of the N‐fixing clade. Thus, a well‐resolved phylogeny with relatively dense taxon sampling strategy at the regional scale appears, in this case, to be a good representation of the overall phylogenetic pattern and could be used in ecological research. Otherwise, the regional tree should be adjusted according to the correspondingly reliable global tree.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"32 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74994734","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}
The phylogenetic relationships of pteridophytes occurring in China were reconstructed using DNA sequences of the three plastid genes, atpA, atpB, and rbcL. The sampling comprised all genera of Chinese pteridophytes—including ferns and lycophytes—with the exception of four small genera. The effort to sample all recorded families and genera in a phylogenetic framework enabled the phylogenetic relationships of all Chinese pteridophytes to be addressed for the first time in a single phylogenetic hypothesis. The results provided strong evidence to support the continuing impact of Ren‐Chang Ching's integrative classification of pteridophytes. Ten out of 11 orders accepted by Ching were consistent with the phylogeny, whereas four new orders were introduced to avoid paraphyletic taxa in the leptosporangiate ferns. Of the 63 families considered by Ching, 36 families were supported by molecular data, 22 of those had the same or nearly the same circumscription, and the remaining 14 families were supported but substantially revised. Twenty‐eight small families were now accepted as synonyms. A consistent pattern was observed at the generic level. Among the 223 genera considered by Ching, 133 genera were recognized by the phylogeny, although some of them were substantially changed in the context of circumscription, and 90 were now accepted as synonyms. Three endemic genera were incorporated here for the first time in DNA‐based phylogenetic analyses, namely Blechnidium, Saxiglossum, and Sinephropteris, which were shown to be nested in Blechnum, Pyrrosia, and Asplenium respectively. This paper tentatively accepts 40 families and 151 genera of ferns and lycophytes occurring in China; the importance of phylodiversity of Chinese pteridophytes is also briefly discussed.
{"title":"Embracing the pteridophyte classification of Ren‐Chang Ching using a generic phylogeny of Chinese ferns and lycophytes","authors":"Hong‐Mei Liu","doi":"10.1111/jse.12184","DOIUrl":"https://doi.org/10.1111/jse.12184","url":null,"abstract":"The phylogenetic relationships of pteridophytes occurring in China were reconstructed using DNA sequences of the three plastid genes, atpA, atpB, and rbcL. The sampling comprised all genera of Chinese pteridophytes—including ferns and lycophytes—with the exception of four small genera. The effort to sample all recorded families and genera in a phylogenetic framework enabled the phylogenetic relationships of all Chinese pteridophytes to be addressed for the first time in a single phylogenetic hypothesis. The results provided strong evidence to support the continuing impact of Ren‐Chang Ching's integrative classification of pteridophytes. Ten out of 11 orders accepted by Ching were consistent with the phylogeny, whereas four new orders were introduced to avoid paraphyletic taxa in the leptosporangiate ferns. Of the 63 families considered by Ching, 36 families were supported by molecular data, 22 of those had the same or nearly the same circumscription, and the remaining 14 families were supported but substantially revised. Twenty‐eight small families were now accepted as synonyms. A consistent pattern was observed at the generic level. Among the 223 genera considered by Ching, 133 genera were recognized by the phylogeny, although some of them were substantially changed in the context of circumscription, and 90 were now accepted as synonyms. Three endemic genera were incorporated here for the first time in DNA‐based phylogenetic analyses, namely Blechnidium, Saxiglossum, and Sinephropteris, which were shown to be nested in Blechnum, Pyrrosia, and Asplenium respectively. This paper tentatively accepts 40 families and 151 genera of ferns and lycophytes occurring in China; the importance of phylodiversity of Chinese pteridophytes is also briefly discussed.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"07 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86012950","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}
Angiosperm phylogeny has been investigated extensively using organellar sequences; recent efforts using nuclear genes have also been successful in reconstructing angiosperm phylogenies at family or deeper levels. However, it is not clear whether nuclear genes are also effective in understanding relationships between species in a genus. Here we present a case study of phylogeny at generic and specific levels with nuclear genes, using Brassicaceae taxa as examples. Brassicaceae includes various crops and the model plant Arabidopsis thaliana. A recent study showed that nuclear genes can provide well‐resolved relationships between tribes and larger lineages in Brassicaceae, but few species were included in any given genus. We present a phylogeny with multiple species in each of five genera within Brassicaceae for a total of 65 taxa, using three protein‐coding nuclear genes, MLH1, SMC2, and MCM5, with up to approximately 10 200 base pairs (in both exons and introns). Maximum likelihood and Bayesian analyses of the separate gene regions and combined data reveal high resolution at various phylogenetic depths. The relationships between genera here were largely congruent with previous results, with further resolution at the species level. Also, we report for the first time the affinity of Cardamine rockii with tribe Camelineae instead of other Cardamine members. In addition, we report sequence divergence at three levels: across angiosperms, among Brassicaceae species, and between Arabidopsis ecotypes. Our results provide a robust species‐level phylogeny for a number of Brassicaceae members and support an optimistic perspective on the phylogenetic utility of conserved nuclear data for relatively recent clades.
{"title":"Using nuclear genes to reconstruct angiosperm phylogeny at the species level: A case study with Brassicaceae species","authors":"L. Cai, Hong Ma","doi":"10.1111/jse.12204","DOIUrl":"https://doi.org/10.1111/jse.12204","url":null,"abstract":"Angiosperm phylogeny has been investigated extensively using organellar sequences; recent efforts using nuclear genes have also been successful in reconstructing angiosperm phylogenies at family or deeper levels. However, it is not clear whether nuclear genes are also effective in understanding relationships between species in a genus. Here we present a case study of phylogeny at generic and specific levels with nuclear genes, using Brassicaceae taxa as examples. Brassicaceae includes various crops and the model plant Arabidopsis thaliana. A recent study showed that nuclear genes can provide well‐resolved relationships between tribes and larger lineages in Brassicaceae, but few species were included in any given genus. We present a phylogeny with multiple species in each of five genera within Brassicaceae for a total of 65 taxa, using three protein‐coding nuclear genes, MLH1, SMC2, and MCM5, with up to approximately 10 200 base pairs (in both exons and introns). Maximum likelihood and Bayesian analyses of the separate gene regions and combined data reveal high resolution at various phylogenetic depths. The relationships between genera here were largely congruent with previous results, with further resolution at the species level. Also, we report for the first time the affinity of Cardamine rockii with tribe Camelineae instead of other Cardamine members. In addition, we report sequence divergence at three levels: across angiosperms, among Brassicaceae species, and between Arabidopsis ecotypes. Our results provide a robust species‐level phylogeny for a number of Brassicaceae members and support an optimistic perspective on the phylogenetic utility of conserved nuclear data for relatively recent clades.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"62 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84057921","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}
Zhixi Fu, BO-HAN Jiao, Bao Nie, Guojin Zhang, TIAN-GANG Gao
The sunflower family (Asteraceae) is the largest and the most diverse flowering plant family, comprising 24 000–30 000 species and 1600–1700 genera. In China, Asteraceae are also the largest family, with approximately 2336 indigenous species in 248 genera. In the past two decades, molecular phylogenetic analyses has contributed greatly to our understanding of the systematics of Asteraceae. Nevertheless, the large‐scale analyses and knowledge about the relationships of Chinese Asteraceae at the generic level as a whole are far from complete due to difficulties in sampling. In this study, we presented a three‐marker (rbcL, ndhF, and matK) phylogeny of Asteraceae, including 506 genera (i.e., approximately one‐third of Asteraceae genera). The study sampled 200 Chinese genera (i.e., approximately 80% of Chinese Asteraceae genera). The backbones of the new phylogeny were largely congruent with earlier studies, with 13 subfamilies and 45 tribes recognized. Chinese Asteraceae were distributed in 7 subfamilies (Mutisioideae, Wunderlichioideae, Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, and Asteroideae) and 22 tribes (Mutiseae, Hyalideae, Cardueae, Pertyeae, Gymnarrheneae, Vernonieae, Cichorieae, Doroniceae, Senecioneae, Astereae, Anthemideae, Gnaphalieae, Calenduleae, Inuleae, Athroismeae, Helenieae, Coreopsideae, Neurolaeneae, Tageteae, Millieae, Eupatorieae, and Heliantheae). Chinese Asteraceae lacked 6 basal subfamilies and 23 tribes. Several previously ambiguous relationships were clarified. Our analyses also resolved some unplaced genera within Chinese Asteraceae. Finally, our phylogenetic tree was used to revise the classification for all genera of Chinese Asteraceae. In total, 255 genera, 22 tribes, and 7 subfamilies in China are recognized.
{"title":"A comprehensive generic‐level phylogeny of the sunflower family: Implications for the systematics of Chinese Asteraceae","authors":"Zhixi Fu, BO-HAN Jiao, Bao Nie, Guojin Zhang, TIAN-GANG Gao","doi":"10.1111/jse.12216","DOIUrl":"https://doi.org/10.1111/jse.12216","url":null,"abstract":"The sunflower family (Asteraceae) is the largest and the most diverse flowering plant family, comprising 24 000–30 000 species and 1600–1700 genera. In China, Asteraceae are also the largest family, with approximately 2336 indigenous species in 248 genera. In the past two decades, molecular phylogenetic analyses has contributed greatly to our understanding of the systematics of Asteraceae. Nevertheless, the large‐scale analyses and knowledge about the relationships of Chinese Asteraceae at the generic level as a whole are far from complete due to difficulties in sampling. In this study, we presented a three‐marker (rbcL, ndhF, and matK) phylogeny of Asteraceae, including 506 genera (i.e., approximately one‐third of Asteraceae genera). The study sampled 200 Chinese genera (i.e., approximately 80% of Chinese Asteraceae genera). The backbones of the new phylogeny were largely congruent with earlier studies, with 13 subfamilies and 45 tribes recognized. Chinese Asteraceae were distributed in 7 subfamilies (Mutisioideae, Wunderlichioideae, Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, and Asteroideae) and 22 tribes (Mutiseae, Hyalideae, Cardueae, Pertyeae, Gymnarrheneae, Vernonieae, Cichorieae, Doroniceae, Senecioneae, Astereae, Anthemideae, Gnaphalieae, Calenduleae, Inuleae, Athroismeae, Helenieae, Coreopsideae, Neurolaeneae, Tageteae, Millieae, Eupatorieae, and Heliantheae). Chinese Asteraceae lacked 6 basal subfamilies and 23 tribes. Several previously ambiguous relationships were clarified. Our analyses also resolved some unplaced genera within Chinese Asteraceae. Finally, our phylogenetic tree was used to revise the classification for all genera of Chinese Asteraceae. In total, 255 genera, 22 tribes, and 7 subfamilies in China are recognized.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"104 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76048827","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}
Zhiduan Chen, An‐ming Lu, Shouzhou Zhang, Qing‐Feng Wang, Zhongjian Liu, De-Zhu Li, Hong Ma, Jianhua Li, D. Soltis, P. Soltis, J. Wen
The knowledge of evolutionary relationships is fundamental to all disciplines of biology, yielding novel and profound insights across plant sciences, from comparative genomics, molecular evolution, and plant development, to the study of adaptation, speciation, community assembly, and ecosystem functioning (Forest et al., 2007; Donoghue, 2008; Gehrke & Linder, 2011). Phylogeny (the Tree of Life, TOL) has become the foundation of evolutionary biology. It is accurate to say “Evolutionary biology makes much more sense in the light of phylogeny”, as a corollary to Dobzhansky’s (1973) famous statement “Nothing in biologymakes sense except in the light of evolution.” China harbors 31 362 species, 3328 genera, and 312 families of vascular plants (Wu et al., 1994–2013) and has the richest flora of the Northern Hemisphere (Wu et al., 2003). A well-resolved phylogeny of vascular plants of China has many potential uses in various areas of biology—ecology, conservation genetics, and agriculture—as well as stimulates new research at the interface of evolutionary ecology, phylogenetics, and biogeography, thus clarifying processes that shaped patterns of distribution and diversity of such a rich flora of the Northern Hemisphere (Qian & Ricklefs, 2000; Wang et al., 2009; L opezPujol et al., 2011). Understanding the phylogeny of vascular plants andphylogenetic diversity at this scalewill help elucidate fundamental processes underlying plant/animal associations and the assembly of entire ecosystems, and help manage the impact of global challenges to biodiversity and the maintenance of natural resources to humankind. In June 2007, an international symposium on the TOL was held in Beijing, China. Journal of Systematics and Evolution (JSE) organized and published the symposium special issue: Patterns of Evolution and the Tree of Life (JSE vol. 46, no. 3, 2008). Since then, the Chinese botanical community has continued to make contributions to TOL studies. The present special issue aims to present recent progress in reconstructing TOL of the vascular plant genera in China, including the assembly of DNA materials, establishment of co-operation, data generation, tree reconstruction, on how to use the China TOL as a framework to further examine the origin and evolution of major clades in vascular plants, and the floristic relationship between China and other regions of the world as all vascular plants share a common ancestor (Wen et al., 2010; Xiang et al., 2015). This special issue consists of 11 papers all related to the “giant” phylogeny of the Chinese vascular plants. Chen et al. (2016) sampled 6098 species representing 3114 genera of vascular plants and five genera of bryophytes as out-groups to reconstruct the TOL of the Chinese vascular plants at the generic level. To facilitate further application of such a largescale phylogeny to other biology fields, the SoTree software was introduced to enable the efficient generation of the phylogenetic trees by providing sub-
进化关系的知识是生物学所有学科的基础，从比较基因组学、分子进化和植物发育到适应、物种形成、群落组装和生态系统功能的研究，在植物科学领域产生了新颖而深刻的见解(Forest等人，2007;多诺霍,2008;Gehrke & Linder, 2011)。系统发育(生命之树，TOL)已经成为进化生物学的基础。“进化生物学在系统发育方面更有意义”是准确的，这是Dobzhansky(1973)著名论断的必然结果，“生物学中没有任何东西在进化的角度下是有意义的”。中国有维管植物312科3328属3362种(Wu et al.， 1994-2013)，是北半球植物区系最丰富的国家(Wu et al.， 2003)。对中国维管植物系统发育的完整研究在生物学生态学、保护遗传学和农业等各个领域都有许多潜在的用途，同时也刺激了进化生态学、系统发育学和生物地理学领域的新研究，从而阐明了形成北半球如此丰富的植物群分布模式和多样性的过程(Qian & Ricklefs, 2000;Wang et al.， 2009;L opezPujol et al.， 2011)。在这个尺度上理解维管植物的系统发育和系统发育多样性将有助于阐明植物/动物关联和整个生态系统组装的基本过程，并有助于管理全球挑战对生物多样性和自然资源维护对人类的影响。2007年6月，TOL国际研讨会在中国北京举行。《系统学与进化》(JSE)组织出版了专题讨论会特刊《进化模式与生命之树》(JSE第46卷第6期)。3, 2008)。从那时起，中国植物学界继续为TOL研究做出贡献。目前特刊旨在重建托尔目前的最新进展的维管植物属在中国,包括DNA的组装材料,建立合作,数据生成,树重建,中国如何使用托尔作为一个框架,进一步检查主要演化支在维管植物的起源和演化,以及中国和世界其他地区植物区系之间的关系,因为所有维管植物共享一个共同的祖先(温家宝et al ., 2010;Xiang等人，2015)。本期特刊收录了11篇有关中国维管植物“巨型”系统发育的论文。Chen et al.(2016)以维管植物3114属6098种和苔藓植物5属为外类群，在属水平上重建了中国维管植物的TOL。为了将这种大规模的系统发育进一步应用于其他生物学领域，我们引入了SoTree软件，通过提供包含感兴趣物种列表的子数据集来高效地生成系统发育树，用于研究中国当地植物群的起源、生态学和生物地理学。Liu(2016)利用3个质体基因的DNA序列，对259属蕨类植物进行了系统发育分析，为庆仁昌蕨类植物综合分类的影响提供了证据。在Ching的系统中，11个目中有10个与现代基于dna的系统发育一致，而在细孢蕨类植物中引入了4个新目以避免副葡萄目。Wang等人(2016)将Leefructus -一种最早的大戟属化石-整合到现存毛茛属的详尽形态学数据集中，以提高我们对该谱系在戟属中的多样性的理解。由于这一化石的整合，作者们发现，在早白垩纪被子植物辐射开始的时候，基底长尾科植物经历了加速的多样化。Du等人(2016)取样了139个属(43科)，代表了全世界大多数水生植物科。结果表明，在被子植物的早期辐射中，水生栖息地至少被三次殖民，即Nymphaeales, Ceratophyllales和mono子科。其中三篇论文论述了被子植物在序位或序位以上的系统发育。本文特别关注蔷薇科，因为蔷薇科不仅贡献了四分之一现存被子植物的多样性，包括相当重要的经济作物和大多数优势的森林树木，而且被认为是中国被子植物多样性的主要贡献者。Sun et al.(2016)采用超矩阵方法，采用密集采样方案(4个基因，共9300个分类群，代表2775个属，138个科，17目)，解决了全球Rosidae的系统发育问题。他们发现了一些新的关系，并确认了两个家族和467个属是非单系的。 固氮支系是被子植物中最大的支系之一，包含1300余属，约3万种，是现存温带和热带森林的重要组成部分。Li等人(2016a)利用超矩阵构建了迄今为止最全面、最稳健的固氮进化枝全局树，并与中国维管植物TOL的局部树进行了比较。通过密集采样，全局树和局部树的拓扑结构基本一致，并且大多数内部支持都得到了极大的改善。Yang et al.(2016)利用8个叶绿体标记和1个线粒体基因，组装了649个属的11,951个性状的矩阵，覆盖了龙胆属的约54%，重建了龙胆属的系统发育。全球龙胆树和中国龙胆树的拓扑结构主要是JSE系统与进化杂志
{"title":"The Tree of Life: China project","authors":"Zhiduan Chen, An‐ming Lu, Shouzhou Zhang, Qing‐Feng Wang, Zhongjian Liu, De-Zhu Li, Hong Ma, Jianhua Li, D. Soltis, P. Soltis, J. Wen","doi":"10.1111/jse.12215","DOIUrl":"https://doi.org/10.1111/jse.12215","url":null,"abstract":"The knowledge of evolutionary relationships is fundamental to all disciplines of biology, yielding novel and profound insights across plant sciences, from comparative genomics, molecular evolution, and plant development, to the study of adaptation, speciation, community assembly, and ecosystem functioning (Forest et al., 2007; Donoghue, 2008; Gehrke & Linder, 2011). Phylogeny (the Tree of Life, TOL) has become the foundation of evolutionary biology. It is accurate to say “Evolutionary biology makes much more sense in the light of phylogeny”, as a corollary to Dobzhansky’s (1973) famous statement “Nothing in biologymakes sense except in the light of evolution.” China harbors 31 362 species, 3328 genera, and 312 families of vascular plants (Wu et al., 1994–2013) and has the richest flora of the Northern Hemisphere (Wu et al., 2003). A well-resolved phylogeny of vascular plants of China has many potential uses in various areas of biology—ecology, conservation genetics, and agriculture—as well as stimulates new research at the interface of evolutionary ecology, phylogenetics, and biogeography, thus clarifying processes that shaped patterns of distribution and diversity of such a rich flora of the Northern Hemisphere (Qian & Ricklefs, 2000; Wang et al., 2009; L opezPujol et al., 2011). Understanding the phylogeny of vascular plants andphylogenetic diversity at this scalewill help elucidate fundamental processes underlying plant/animal associations and the assembly of entire ecosystems, and help manage the impact of global challenges to biodiversity and the maintenance of natural resources to humankind. In June 2007, an international symposium on the TOL was held in Beijing, China. Journal of Systematics and Evolution (JSE) organized and published the symposium special issue: Patterns of Evolution and the Tree of Life (JSE vol. 46, no. 3, 2008). Since then, the Chinese botanical community has continued to make contributions to TOL studies. The present special issue aims to present recent progress in reconstructing TOL of the vascular plant genera in China, including the assembly of DNA materials, establishment of co-operation, data generation, tree reconstruction, on how to use the China TOL as a framework to further examine the origin and evolution of major clades in vascular plants, and the floristic relationship between China and other regions of the world as all vascular plants share a common ancestor (Wen et al., 2010; Xiang et al., 2015). This special issue consists of 11 papers all related to the “giant” phylogeny of the Chinese vascular plants. Chen et al. (2016) sampled 6098 species representing 3114 genera of vascular plants and five genera of bryophytes as out-groups to reconstruct the TOL of the Chinese vascular plants at the generic level. To facilitate further application of such a largescale phylogeny to other biology fields, the SoTree software was introduced to enable the efficient generation of the phylogenetic trees by providing sub-","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"26 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78773183","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}
Although aquatic plants are discussed as a unified biological group, they are phylogenetically well dispersed across the angiosperms. In this study, we annotated the aquatic taxa on the tree of vascular plants, and extracted the topology of these aquatic lineages to construct the tree of aquatic angiosperms. We also reconstructed the ancestral areas of aquatic families. We found that aquatic angiosperms could be divided into two different categories: the four aquatic orders and the aquatic taxa in terrestrial orders. Aquatic lineages evolved early in the radiation of angiosperms, both in the orders Nymphaeales and Ceratophyllales and among basal monocots (Acorales and Alismatales). These aquatic orders do not have any extant terrestrial relatives. They originated from aquatic habitats during the Early Cretaceous. Asia would have been one of the centers for early diversification of aquatic angiosperms. The aquatic families within terrestrial orders may originate from other areas besides Asia, such as America or Australia. The lineages leading to extant angiosperms diversified early in underexploited freshwater habitats. The four extant aquatic orders were relicts of an early radiation of angiosperm in aquatic environments. Their extinct ancestors might be aquatic early angiosperms.
{"title":"Phylogenetic tree of vascular plants reveals the origins of aquatic angiosperms","authors":"Zhi‐Yuan Du, Qing‐Feng Wang","doi":"10.1111/jse.12182","DOIUrl":"https://doi.org/10.1111/jse.12182","url":null,"abstract":"Although aquatic plants are discussed as a unified biological group, they are phylogenetically well dispersed across the angiosperms. In this study, we annotated the aquatic taxa on the tree of vascular plants, and extracted the topology of these aquatic lineages to construct the tree of aquatic angiosperms. We also reconstructed the ancestral areas of aquatic families. We found that aquatic angiosperms could be divided into two different categories: the four aquatic orders and the aquatic taxa in terrestrial orders. Aquatic lineages evolved early in the radiation of angiosperms, both in the orders Nymphaeales and Ceratophyllales and among basal monocots (Acorales and Alismatales). These aquatic orders do not have any extant terrestrial relatives. They originated from aquatic habitats during the Early Cretaceous. Asia would have been one of the centers for early diversification of aquatic angiosperms. The aquatic families within terrestrial orders may originate from other areas besides Asia, such as America or Australia. The lineages leading to extant angiosperms diversified early in underexploited freshwater habitats. The four extant aquatic orders were relicts of an early radiation of angiosperm in aquatic environments. Their extinct ancestors might be aquatic early angiosperms.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"13 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87680089","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}
Miao-miao Sun, R. Naeem, Junyan Su, Zhisheng Cao, J. G. Burleigh, P. Soltis, D. Soltis, Zhiduan Chen
Rosidae, a clade of approximately 90 000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas of poor resolution and/or support, and there have been few attempts to synthesize the available data into a comprehensive view of Rosidae phylogeny. We aim to improve understanding of the phylogeny of Rosidae with a dense sampling scheme using both newly generated sequences and data from GenBank of the chloroplast rbcL, atpB, and matK genes and the mitochondrial matR gene. We combined sequences from 9300 species, representing 2775 genera, 138 families, and 17 orders into a supermatrix. Although 59.26% of the cells in the supermatrix have no data, our results generally agree with previous estimates of Rosidae phylogeny and provide greater resolution and support in several areas of the topology. Several noteworthy phylogenetic relationships are recovered, including some novel relationships. Two families (Euphorbiaceae and Salvadoraceae) and 467 genera are recovered as non‐monophyletic in our sampling, suggesting the need for future systematic studies of these groups. Our study shows the value of a botanically informed bioinformatics approach and dense taxonomic sampling for resolving rosid relationships. The resulting tree provides a starting point for large‐scale analyses of the evolutionary patterns within Rosidae.
{"title":"Phylogeny of the Rosidae: A dense taxon sampling analysis","authors":"Miao-miao Sun, R. Naeem, Junyan Su, Zhisheng Cao, J. G. Burleigh, P. Soltis, D. Soltis, Zhiduan Chen","doi":"10.1111/jse.12211","DOIUrl":"https://doi.org/10.1111/jse.12211","url":null,"abstract":"Rosidae, a clade of approximately 90 000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas of poor resolution and/or support, and there have been few attempts to synthesize the available data into a comprehensive view of Rosidae phylogeny. We aim to improve understanding of the phylogeny of Rosidae with a dense sampling scheme using both newly generated sequences and data from GenBank of the chloroplast rbcL, atpB, and matK genes and the mitochondrial matR gene. We combined sequences from 9300 species, representing 2775 genera, 138 families, and 17 orders into a supermatrix. Although 59.26% of the cells in the supermatrix have no data, our results generally agree with previous estimates of Rosidae phylogeny and provide greater resolution and support in several areas of the topology. Several noteworthy phylogenetic relationships are recovered, including some novel relationships. Two families (Euphorbiaceae and Salvadoraceae) and 467 genera are recovered as non‐monophyletic in our sampling, suggesting the need for future systematic studies of these groups. Our study shows the value of a botanically informed bioinformatics approach and dense taxonomic sampling for resolving rosid relationships. The resulting tree provides a starting point for large‐scale analyses of the evolutionary patterns within Rosidae.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"58 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76140458","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}
Utilization of ferns by phytophagous insects is widely considered to be less common and less specialized compared to the phytophagous insect community feeding on angiosperms. In this study, this assumption is challenged by exploring the evolution of pteridophagy (fern‐feeding) in the larval stages of sawflies (Symphyta). To achieve this, phylogenetic frameworks were assembled based on published phylogenetic studies and newly reconstructed phylogenies based on cytochrome oxidase subunit I (COI) barcoding data that allowed the reconstruction of the ancestral feeding preferences by plotting reported host plants of sawflies. Evidence was found for two exclusively pteridophagous lineages of sawflies that probably originated before the Cretaceous Terrestrial Revolution, whereas the third lineage comprising several exclusively pteridophagous sawfly genera is nested in the derived sawfly clade feeding predominantly on eudicots. Thus, the evolution of pteridophagy in the clade was probably connected with the transformation of terrestrial habitats associated with the rise of angiosperms during the Cretaceous. The observed phylogenetic patterns are consistent with the hypothesis of “larval diet conservatism” resulting in the establishment of genera and lineages that feed exclusively, or at least predominantly, on conifers, eudicots, ferns, and monocots. Only a small percentage of sawfly genera were found to be polyphylophagous. The results suggest a low frequency of switches between host plants belonging to different major plant lineages such as angiosperms, conifers, and ferns. Successful switches between hosts belonging to different major lineages of land plants coincide with the reorganization of the phylogenetic composition of terrestrial vegetation in the late Mesozoic.
{"title":"The ghost of the Cretaceous terrestrial revolution in the evolution of fern–sawfly associations","authors":"Harald Schneider","doi":"10.1111/jse.12194","DOIUrl":"https://doi.org/10.1111/jse.12194","url":null,"abstract":"Utilization of ferns by phytophagous insects is widely considered to be less common and less specialized compared to the phytophagous insect community feeding on angiosperms. In this study, this assumption is challenged by exploring the evolution of pteridophagy (fern‐feeding) in the larval stages of sawflies (Symphyta). To achieve this, phylogenetic frameworks were assembled based on published phylogenetic studies and newly reconstructed phylogenies based on cytochrome oxidase subunit I (COI) barcoding data that allowed the reconstruction of the ancestral feeding preferences by plotting reported host plants of sawflies. Evidence was found for two exclusively pteridophagous lineages of sawflies that probably originated before the Cretaceous Terrestrial Revolution, whereas the third lineage comprising several exclusively pteridophagous sawfly genera is nested in the derived sawfly clade feeding predominantly on eudicots. Thus, the evolution of pteridophagy in the clade was probably connected with the transformation of terrestrial habitats associated with the rise of angiosperms during the Cretaceous. The observed phylogenetic patterns are consistent with the hypothesis of “larval diet conservatism” resulting in the establishment of genera and lineages that feed exclusively, or at least predominantly, on conifers, eudicots, ferns, and monocots. Only a small percentage of sawfly genera were found to be polyphylophagous. The results suggest a low frequency of switches between host plants belonging to different major plant lineages such as angiosperms, conifers, and ferns. Successful switches between hosts belonging to different major lineages of land plants coincide with the reorganization of the phylogenetic composition of terrestrial vegetation in the late Mesozoic.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"279 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76997816","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}
Utricularia sect. Foliosa Kamiénski comprises three recognized species, U. amethystina Salzm. ex A.St.‐Hil. & Girard, U. tricolor A.St.‐Hil., and U. tridentata Sylvén, delimited based mainly on shape and structure of the corolla. In comparison with the two latter members of the section, U. amethystina forms a complex of morphological variants, reflected taxonomically by the previous recognition of 31 synonyms. In his monograph of the genus, Taylor synonymized these taxa based primarily on his observation of continuous morphological variation of the flowers. In the same treatment he also suggested a future taxonomic re‐evaluation could re‐establish two, three or more taxa. Here we examine this question utilizing morphometric analyses of floral variation across most of the synonyms mentioned above, within populations from across their Neotropical distribution. Based on both morphological and geographic characters we identify strongly differentiated morphotypes. Our data provide support for both the maintenance of taxa previously recognised as synonyms under U. amethystina, and the resurrection of taxa to species status, namely U. bicolor, U. damazioi, U. lindmanii and U. hirtella, and four other putative new taxa.
{"title":"Morphometric approach to address taxonomic problems: The case of Utricularia sect. Foliosa (Lentibulariaceae)","authors":"Paulo Baleeiro, R. W. Jobson, P. Sano","doi":"10.1111/jse.12186","DOIUrl":"https://doi.org/10.1111/jse.12186","url":null,"abstract":"Utricularia sect. Foliosa Kamiénski comprises three recognized species, U. amethystina Salzm. ex A.St.‐Hil. & Girard, U. tricolor A.St.‐Hil., and U. tridentata Sylvén, delimited based mainly on shape and structure of the corolla. In comparison with the two latter members of the section, U. amethystina forms a complex of morphological variants, reflected taxonomically by the previous recognition of 31 synonyms. In his monograph of the genus, Taylor synonymized these taxa based primarily on his observation of continuous morphological variation of the flowers. In the same treatment he also suggested a future taxonomic re‐evaluation could re‐establish two, three or more taxa. Here we examine this question utilizing morphometric analyses of floral variation across most of the synonyms mentioned above, within populations from across their Neotropical distribution. Based on both morphological and geographic characters we identify strongly differentiated morphotypes. Our data provide support for both the maintenance of taxa previously recognised as synonyms under U. amethystina, and the resurrection of taxa to species status, namely U. bicolor, U. damazioi, U. lindmanii and U. hirtella, and four other putative new taxa.","PeriodicalId":101317,"journal":{"name":"JOURNAL OF SYSTEMATICS AND EVOLUTION","volume":"110 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75331697","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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