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| 1 | Chloroplast phylogenomics of the New World grape species (Vitis, Vitaceae)显示文摘Vitis L。(葡萄类) 是经济地很重要的水果庄稼,葡萄和酒的来源。在类以内的种系发生的关系是高度争论的。此处,我们从整个 plastomes 采用顺序数据试图提高 Vitis 种系发生的分辨率。结果作为 monophyletic 支持新世界 Vitis 亚属 Vitis。在 clade 以内, V。californica 是到仍然保持新的姐妹世界 Vitis 亚属 Vitis。在亚属 Vitis 以内,而且,欧亚的 clade 要用体力地被支持并且是到新世界 clade 的姐妹。Vitis vinifera ssp 的 clade。vinifera 和 V。vinifera ssp。sylvestris 是到 Vitis 的核心亚洲人 clade 的姐妹。在北美洲的几普遍的种被发现例如,是在 plastome 树上的 nonmonophyletic 广泛地定义的 Vitis cinerea 和 V。aestivalis 各个需要被分成几种。可能也 nonmonophyly 某种类由于在北美的 Vitis 的杂交的普通出现。由进九个系列的 Munson 的北美的 Vitis 的分类基于种系发生的结果被讨论。分叉时间和系多样化的分析在在晚第三纪开始的北美洲支持 Vitis 的快速的放射。 | Jun Went AJ Harris Yash Kalburgi Ning Zhang Yuan Xu Wei Zheng Stefanie M. Ickert-Bondt Gabriel Johnson Elizabeth A. Zimmer | 2018 | Journal of Systematics and Evolution2018，56，4： | 14 |
| 2 | Announcement of the awards of JSE Outstanding Papers显示文摘 | Song Ge Jun Wen | 2015 | Journal of Systematics and Evolution2015，53，4： | 6 |
| 3 | Phylogenomics,biogeography,and evolution of morphology and ecological niche of the eastern Asian-eastern North American Nyssa(Nyssaceae)显示文摘Nyssa(Nyssaceae,Cornales)represents a classical example of the well-known eastern Asian-eastern North American floristic disjunction.The genus consists of three species in eastern Asia,four species in eastern North America,and one species in Central America.Species of the genus are ecologically important trees in eastern North American and eastern Asian forests.The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian-eastern North American floristic disjunction.However,despite the small number of species,relationships within the genus have remained unclear and have not been elucidated using a molecular approach.Here,we integrate data from 48 nuclear genes,fossils,morphology,and ecological niche to resolve species relationships,elucidate its biogeographical history,and investigate the evolution of morphology and ecological niches,aiming at a better understanding of the well-known EA-ENA floristic disjunction.Results showed that the Central American(CAM)Nyssa talamancana was sister to the remaining species,which were divided among three,rapidly diversified subclades.Estimated divergence times and biogeographical history suggested that Nyssa had an ancestral range in Eurasia and western North America in the late Paleocene.The rapid diversification occurred in the early Eocene,followed by multiple dispersals between and within the Erasian and North American continents.The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene,respectively.The Central American N.talamancana represents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America.The results supported the importance of both the North Atlantic land bridge and the Bering land bridge(BLB)for the Paleogene dispersals of Nyssa and the Neogene dispersals,respectively,as well as the role of Central America as refugia of the Paleogene flora.The totalevidence-based dated phylogeny suggested that the pattern of macroevolution of Nyssa coincided with paleoclimatic changes.We found a number of evolutionary changes in morphology(including wood anatomy and leaf traits)and ecological niches(precipitation and temperature)between the EA-ENA disjunct,supporting the ecological selection driving trait evolutions after geographic isolation.We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories.The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree.However,conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case.Furthermore,we demonstrated that rapid diversification events may not be recovered in the divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available.Our study provides an example of complex bidirectional exchanges of plants between Eurasia and North America in the Paleogene,but “out of Asia” migrations in the Neogene,to explain the present disjunct distribution of Nyssa in EA and ENA. | Wenbin Zhou Qiu-Yun(Jenny)Xiang Jun Wen | 2020 | Journal of Systematics and Evolution2020，58，5： | 4 |
| 4 | A molecular phylogeny of Staphyleaceae: Implications for generic delimitation and classical biogeographic disjunctions in the family显示文摘Staphyleaceae 传统地包括适度、热带的树和灌木的三个类:Euscaphis Siebold 与 Zucc, Staphylea L. ,和 Tuprinia 发泄。这些类被形态学,而是一个最近的分类清楚地基于四叶绿体基因支持并且原子它的享受 Staphylea, Euscaphis,和在 Staphylea s.l 的新世界 Turpinia 和在 Dalrympelea Roxb 的旧世界 Turpinia。在这研究,我们的目的到过(1 ) 在使用二的 Staphyleaceae 以内解决种系发生的关系原子并且六个叶绿体标记,(2 ) 探索词法 synapomorphies 支持主要 clades,并且(3 ) 在通用定界线和生物地理学上讨论我们的结果的含意。我们的种系发生的结果在 Staphyleaceae 显示出五主要 clades:(1 ) 旧世界 Turpinia,(2 ) 新世界 Turpinia,(3 ) 只旧的世界 Staphylea 的 clade,(4 ) 包括所有新世界种类和旧世界的其余部分的 Staphylea 的亚洲北方的美国 clade,并且(5 ) Euscaphis。在 Staphylea 和 Turpinia 的二 clades 各个以内,传统地使用限定类的词法特征可以展出集中。在在这研究检验的词法特征之中,我们发现那花粉不是分类地增进知识的,叶牙齿展示, epicuticular 给表演打蜡分别地,为 Staphylea 和 Tuprinia 的传统的类限制了支持并且花瓣长度(即,花尺寸)在与新世界 Turpinia 相比的旧世界 Turpinia 是显著地更小的。关于生物地理学,我们的结果支持在东方北美洲和喜马拉雅山脉之间的稀罕分离。 | AJ Harris Ping-Ting Chen Xin-Wei Xu Jian-Qiang Zhang Xue Yang Jun Wen | 2017 | Journal of Systematics and Evolution2017，55，2： | 4 |
| 5 | Phylogenomics,biogeography,and evolution of the blue-or white-fruited dogwoods(Cornus)-Insights into morphological and ecological niche divergence following intercontinental geographic isolation显示文摘The eastern Asian(EA)-eastem North American(ENA)floristic disjunction represents a major pattern of phytogeography of the Northern Hemisphere.Despite 20 years of studies dedicated to identification of taxa that display this disjunct pattern,its origin and evolution remain an open question,especially regarding postisolation evolution.The blue-or white-fruited dogwoods(BW)are the most species-rich among the four major clades of Cornus L.,consisting of-35 species divided into three subgenera(subg.Yinquania,subg.Mesomora,and subg.Kraniopsis).The BW group provides an excellent example of the EA-ENA floristic disjunction for biogeographic study due to its diversity distribution centered in eastern Asia and eastern North America,yet its species relationships and delineation have remained poorly understood.In this study,we combined genome-wide markers from RAD-seq,morphology,fossils,and climate data to understand species relationships,biogeographic history,and ecological niche and morphological evolution.Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well-resolved phylogeny of the BW group with three intercontinental disjunct clades in EA and ENA or Eurasia and North America,of which two are newly identified within subg.Kraniopsis.These analyses also recovered a potential new species but failed to resolve relationships within the C.hemsleyi-C.schindleri complex.In an effort to develop an approach to reduce computation time,analysis of different nodal age settings in treePL suggests setting a node's minimum age constraint to the lower bound of a fossil's age range to obtain similar ages to that of BEAST.Divergence time analyses with BEAST and treePL dated the BW stem back to the very Late Cretaceous and the divergence of the three subgenera in the Paleogene.By integrating fossil ages and morphology,a total evidence-based dating approach was used in conjunction with time-slice probabilities of dispersal under a DEC model to resolve ancestral ranges of each disjunct in the Miocene:Eurasia and ENA(disjunct 1),EA and western North America(disjunct 2),and EA(disjunct 3).The dated biogeographic history supports dispersal via the North Atlantic Land Bridge in the late Paleogene in disjunct 1 and dispersal via the Bering Land Bridge in the Miocene for disjuncts 2 and 3.Character mapping with a stochastic model in phytools and comparison of ecological niche,morphospace,and rate of evolution indicated differential divergence patterns in morphology,ecological niche,and molecules between disjunct sisters.Although morphological stasis was observed in most of the characters,evolutionary changes in growth habit and some features of leaf,flower,and fruit morphology occurred in one or both sister clades.A significant differentiation of ecological habitats in temperature,precipitation,and elevation between disjunct sisters was observed,suggesting a role of niche divergence in morphological evolution post-isolation.The patterns of evolutionary rate between morphology and molecules varied among disjunct clades and were not always congruent between morphology and molecules,suggesting cases of non-neutral morphological evolution driven by ecological selection.Our phylogenetic evidence and comparisons of evolutionary rate among disjunct lineages lend new insights into the formation of the diversity anomaly between EA and ENA,with particular support of an early diversification in EA.These findings,in conjunction with previous studies,again suggest that the EA-ENA disjunct floras are an assembly of lineages descended from the Mesophytic Forests that evolved from the early Paleogene“boreotropical flora”through varied evolutionary pathways across lineages. | Kira Lindelof Julieta ALindo Wenbin Zhou Xiang Ji Qiu-Yun(Jenny)Xiang | 2020 | Journal of Systematics and Evolution2020，58，5： | 3 |
| 6 | Maple phylogeny and biogeography inferred from phylogenomic data显示文摘Acer(the maple genus)is one of the diverse tree genera in the Northern Hemisphere with about 152 species,most of which are in eastern Asia.There are roughly a dozen species in Europe/western Asia and a dozen in North America.Several phylogenetic studies of Acer have been conducted since 1998,but none have provided a satisfactory resolution for basal relationships among sections of Acer.Here we report the first well-resolved phylogeny of Acer based on DNA sequences of over 500 nuclear loci generated using the anchored hybrid enrichment method and explore the implications of the robust phylogeny for Acer systematics and biogeography.Our phylogenetic results support the most recent taxonomic treatment of Acer by de Jong with some modifications;section Pentaphylla may be expanded to include section Trifoliata,and A.yangbiense may be included in section Lithocarpa.Sections Spicata,Negundo,Arguta,and Palmata form a clade sister to the rest of the genus where sections Glabra and Parviflora comprise the first clade followed by section Macrantha,sections Ginnala,Lithocarpa,Indivisa,sections Platanoidea and Macrophylla,section Rubra,section Acer,and section Pentaphylla.Monotypic sections Glabra and Macrophylla in North America are sister to the Japanese section Parviflora and Eurasian section Platanoidea,respectively.Ancestral area inferences using statistical dispersal and vicariance analysis(S-DIVA)and dispersal and extinction cladogenesis(DEC)methods suggest that Asia might be the most likely ancestral area of Acer as proposed by Wolfe and Tanai and molecular dating using Bayesian evolutionary analysis by sampling trees(BEAST)indicate that section diversifications of Acer might have completed largely in the late Eocene and the intercontinental disjunctions of Acer between eastern Asia and eastern North America formed mostly in the Miocene. | Jianhua Li Mark Stukel Parker Bussies Kaleb Skinner Alan R.Lemmon Emily Moriarty Lemmon Kenneth Brown Airat Bekmetjev Nathan G.Swenson | 2019 | Journal of Systematics and Evolution2019，57，6： | 3 |
| 7 | Phylogenetics and biogeography of Theaceae based on sequences of plastid genes显示文摘尽管有 Theaceae 的几词法、分子的分析,几个突出的问题在部落之中包括争论关系留在家庭的 phylogenetics 和生物地理学 Gordonieae, Stewartieae 和 Stewartieae。在这研究,我们从除了 Laplacea,进行的种系发生的分析使用吝啬,可能性的,和贝叶斯的方法,代表所有类的 Theaceae 的 27 种类收集了多重质体基因的 DNA 序列,并且与石块刻度和分子的数据在一个贝叶斯的框架以内估计了分叉时间。我们的数据在家庭并且为 Theeae 的姐妹组关系为三个部落提供了进一步的支持给 Stewartieae 正 Gordonieae。在 Gordonieae 以内,我们的学习第一次为 Franklinia 和 Schima 的姐妹关系提供了强壮的分子的支持。在 Stewartieae 以内,我们的数据支持了 paraphyly 包括 Hartia 的 Stewartia。在 Stewartia 以内,我们的数据第一次建议北美人(NA ) 种类 Stewartia ovata 比到另外的 NA 种类 Stewartia malacodendron 与东方亚洲人(EA ) 种类有关仔细是更多。Biogeographic 分析显示 Gordonieae 的那分离的地方性的种可能从 EA 从 Stewartieae 的 NA 和那些发源。在这识别的 EA-NA 分离的对的分叉时间学习(在 Gordonieae 和 S 的 Franklinia 和 Schima。ovata (NA ) 和 Stewartia 的亚洲种类) 被估计在中间中新世。在 Gordonieae 和 Stewartieae 的人口交换可能发生在 Bering 陆地桥上在以前中间中新世。 | Mi-Mi LI Jian-Hua LI Peter DEL TREDICI Jeffrey CORAJOD Cheng-Xin FU | 2013 | Journal of Systematics and Evolution2013，51，4： | 2 |
| 8 | Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq显示文摘Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RAD-seq Allele Dropout Remedy in our study of the gymnosperm genus, Torreya, to mitigate ADO in outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR to supplement Rad-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and tested hypotheses on anomalies of biodiversity of the eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized birth–death model and divergence–extinction–cladogenesis method, we resolved a detailed biogeographic history of Torreya that suggested a Jurassic origin spanning Laurasia and differential speciation and extinction among continents accounting for modern diversity, which is biased toward eastern Asia (EA). The biogeographic results also supported a vicariance origin of modern Torreya from a widespread ancestor in EA and North America (NA) in the mid-Eocene, and cross Beringian exchange in the early Paleogene before the vicariant isolation, in contrast to the “out of NA” pattern common to gymnosperms and to the “out of EA” hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies for Torreya jackii, suggesting differential lineage sorting of plastid genomes among species of Torreya or plastid genome capture in T. jackii. | Wenbin Zhou AJ Harris Qiu-Yun(Jenny)Xiang | 2022 | Journal of Systematics and Evolution2022，60，6： | 1 |
| 9 | Molecular phylogenetic analysis suggests paraphyly and early diversification of Philadelphus (Hydrangeaceae) in western North America: New insights into affinity with Carpenteria显示文摘Philadelphus (Hydrangeaceae ) 包括 60 或在东方亚洲和西方的亚洲分离地散布的更少种类。类高度在园艺被珍视,但是糟糕关于分类,种关系,和 biogeographic 历史理解。现在的学习是第一种系发生并且 Philadelphus 用的 biogeographic 分析原子并且评估分类计划并且阐明的叶绿体 DNA 标记 biogeographic 起源。我们的结果建议 Philadelphus 是有类 Carpenteria 在内嵌套的 monotypic 的一个 paraphyletic 组。三个主要的系在 PhiladelphusCarpenteria clade 被识别,强烈各由分子的数据支持了。用 Bayes 歌剧女主角方法的 Biogeographic 分析(在最新发达的粗锉实现了) 并且带着野兽标明日期的分叉时间在西方的北美洲(包括的墨西哥) 解决了起源和 Philadelphus s.l (包括的 Carpenteria ) 的早多样化在始新世。进亚洲和另外的区域在多样化、随后散布的系晚第三级或获得世界范围的分布的晚第三纪。学习增加一个另外的例子一 out of 北半球的 phylogeographic 历史上的西方的北美洲移植。 | Yue-Long GUO Andrew PAIS Alan S. WEAKLEY Qiu-Yun (Jenny) XIANG* | 2013 | Journal of Systematics and Evolution2013，51，5： | 1 |
| 10 | RAD-seq data provide new insights into biogeography,diversity anomaly,and species delimitation in eastern Asian-North American disjunct clade Benthamidia of Cornus(Cornaceae)显示文摘The big-bracted dogwood clade Benthamidia of Cornus is a typical example of the well-known eastern Asia(EA)and North America(NA)floristic disjunction,with greater species diversity in EA than in NA.The lineage provides an opportunity to explore factors contributing to the plant diversity unevenness between EA and NA and test hypotheses on the origin of disjunct distribution from a phylogenetic perspective.We generated RAD-seq data,conducted phylogenomic and biogeographic analyses for the clade with sampling of all species(9)and subspecies(10)currently recognized in floras.We also assessed species delineation and calculated phylogenetic diversity to evaluate the diversity unevenness between EA and NA.Finally,we examined variation of diversification rates and ecological niches on the phylogeny to explore potential causes underlying the observed diversity pattern.Our results revealed phylogenetic relationships congruent with previous studies and suggested a trans-Beringian ancestral distribution of the clade Benthamidia in the mid-Oligocene,dispersal from Mexico to eastern United States in the mid-Miocene,and early diversification of the EA clade in SW China.Our results also confirmed greater phylogenetic diversity and diversification rate of the EA clade.Species delimitation analysis suggested 17 species in the clade Benthamidia,including all recognized subspecies.By integrating the results of molecular data with morphology,we proposed to retain the subspecies without changing their ranks.Our data suggested increased diversification rate in EA as an intrinsic factor explaining the greater species diversity in the region driven mainly by biogeographic isolation and partially by niche divergence. | Zhi-Yuan Du Jin Cheng Qiu-Yun(Jenny)Xiang | 2024 | Journal of Systematics and Evolution2024，62，1： | 0 |
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