被子植物系统发育深层关系研究: 进展与挑战

被子植物系统发育学是研究被子植物及其各类群间亲缘关系与进化历史的学科。从20世纪90年代起, 核苷酸和氨基酸序列等分子数据开始被广泛运用于被子植物系统发育研究, 经过20多年的发展, 从使用单个或联合少数几个细胞器基因, 到近期应用整个叶绿体基因组来重建被子植物的系统发育关系, 目、科水平上的被子植物系统发育框架已被广泛接受。在这个框架中, 基部类群、主要的5个分支(即真双子叶植物、单子叶植物、木兰类、金粟兰目和金鱼藻目)、每个分支所包含的目以及几个大分支包括的核心类群等都具有高度支持。与此同时, 细胞器基因还存在一些固有的问题, 例如单亲遗传、系统发育信息量有限等, 因此近年来双亲遗传的核基因在被子植物系统发育研究中的重要性逐渐得到关注, 并在不同分类阶元的研究中都取得了一定进展。但是, 被子植物系统发育中仍然存在一些难以确定的关系, 例如被子植物5个分支之间的关系、真双子叶植物内部某些类群的位置等。本文简述了20多年来被子植物系统发育深层关系的主要研究进展, 讨论了被子植物系统发育学常用的细胞器基因和核基因的选用, 已经确定和尚未确定系统发育位置的主要类群, 以及研究中尚存在的问题和可能的解决方法。     

花同源异型MADS-box 基因在被子植物中的功能保守性和多样性

MADS-box基因家族成员作为转录调控因子在被子植物花发育调控中发挥关键作用。本文以模式植物拟南芥(Arabidopsis thaliana) 和水稻 (Oryza sativa)为例, 综述了近10年来对被子植物(又称有花植物)两大主要类群——核心真 双子叶植物和单子叶植物花同源异型MADS-box基因的研究成果, 分析MADS-box基因在被子植物中的功能保守性和多样性,同时探讨双子叶植物花发育的ABCDE模型在多大程度上适用于单子叶植物。     

植物LEAFY 同源基因的研究进展

本文就近10年来LEAFY(简写为LFY)同源基因的研究进展做了综合分析。通过对19种植物中已分离到的LFY同源基因的序列比较分析发现: LFY同源基因编码区核苷酸和氨基酸序列同源性都较高;在双子叶植物基因组中, 拷贝数却有所不同。该基因的表达特性显示其在不同植物中表达的时间和空间有所差异。根据已知序列推导的氨基酸序列构建的系统进化树表明, 单子叶植物与裸子植物的亲缘关系近于双子叶与裸子植物的亲缘关系。上述研究资料为植物成花机理研究提供了重要参考, 且在研究植物系统进化方面也具有重要的意义。     

植物LEAFY同源基因的研究进展

本文就近10年来LEAFY(简写为LFY)同源基因的研究进展做了综合分析.通过对19种植物中已分离到的LFY同源基因的序列比较分析发现:LFY同源基因编码区核苷酸和氨基酸序列同源性都较高;在双子叶植物基因组中,拷贝数却有所不同.该基因的表达特性显示其在不同植物中表达的时间和空间有所差异.根据已知序列推导的氨基酸序列构建的系统进化树表明,单子叶植物与裸子植物的亲缘关系近于双子叶与裸子植物的亲缘关系.上述研究资料为植物成花机理研究提供了重要参考,且在研究植物系统进化方面也具有重要的意义.     

花同源异型MADS-box基因在被子植物中的功能保守性和多样性

MADS-box基因家族成员作为转录调控因子在被子植物花发育调控中发挥关键作用。本文以模式植物拟南芥（Arabidopsis thaliana）和水稻（Oryza sativa）为例,综述了近10年来对被子植物（又称有花植物）两大主要类群——核心真双子叶植物和单子叶植物花同源异型MADS-box基因的研究成果,分析MADS-box基因在被子植物中的功能保守性和多样性,同时探讨双子叶植物花发育的ABCDE模型在多大程度上适用于单子叶植物。     

利用全测序基因组数据对被子植物纤维素合成酶基因的进化分析

利用已经分离的植物纤维素合成酶基因的Cellulose_synt结构域为检索序列,从NCBI和其他数据库中调取已完成测序的物种的纤维素合成酶的氨基酸序列,共涉及10个物种的171个基因,基于以上氨基酸序列,应用MEGA4.0生成系统进化树。结果表明:CesA基因和Csl基因直向的相似度远大于平行的相似度,且它们的分化可能在单子叶和真双子叶植物分化之前,单子叶和真双子叶植物的最近共同祖先中至少存在7个CesA基因,综合已知的模式植物CesA基因的功能(初生壁或次生壁形成特异性),可为推测其他物种中该基因的功能提供帮助。     

猴欢喜叶绿体全基因组及杜英科系统地位分析

最新的分子系统发育(APG IV)研究中以猴欢喜属(Sloanea L.)为代表的杜英科(Elaeocarpaceae)所在的酢浆草目(Oxalidales)被置于豆类分支(Fabids),且与卫矛目(Celastrales)、金虎尾目(Malpighiales)组成一支(COM分支),但支持率较低.为提高COM分支支...     

利用植物DNA条形码构建亚热带森林群落系统发育关系——以鼎湖山样地为例

在群落水平上重建植物系统发育关系是当前植物系统学研究的一项重要内容;DNA条形码技术的出现为这一工作的开展提供了便利。本文选取国际通用的植物DNA条形码（rbcL,matK和psbA trnH）,对鼎湖山大样地的183个物种（隶属于24目51科110属）进行测序;分别利用两位点和三位点DNA条形码组合构建该样地植物群落的系统发育关系,并比较不同位点组合构建出的群落系统发育关系的拓扑结构和节点支持率;最后选出一个具有最好拓扑结构和最高节点支持率的鼎湖山大样地群落系统发育关系。在目、科和属这三个水平上,三位点条形码片段组合构建的群落系统发育关系与APG系统获得较好匹配;有些进化分支在相应的APG系统位置解决得不好,却在条形码序列构建的系统发育关系中得到了较好解决。表明综合使用不同进化速率的DNA条形码片段并采取三位点超级矩阵的组合策略,在未采用APG系统大框架的情况下,也能快速而又相对准确地构建出鼎湖山南亚热带森林植物群落的系统发育关系。     

利用植物DNA条形码构建亚热带森林群落系统发育关系——以鼎湖山样地为例

在群落水平上重建植物系统发育关系是当前植物系统学研究的一项重要内容;DNA条形码技术的出现为这一工作的开展提供了便利。本文选取国际通用的植物DNA条形码（rbcL,matK和psbA trnH）,对鼎湖山大样地的183个物种（隶属于24目51科110属）进行测序;分别利用两位点和三位点DNA条形码组合构建该样地植物群落的系统发育关系,并比较不同位点组合构建出的群落系统发育关系的拓扑结构和节点支持率;最后选出一个具有最好拓扑结构和最高节点支持率的鼎湖山大样地群落系统发育关系。在目、科和属这三个水平上,三位点条形码片段组合构建的群落系统发育关系与APG系统获得较好匹配;有些进化分支在相应的APG系统位置解决得不好,却在条形码序列构建的系统发育关系中得到了较好解决。表明综合使用不同进化速率的DNA条形码片段并采取三位点超级矩阵的组合策略,在未采用APG系统大框架的情况下,也能快速而又相对准确地构建出鼎湖山南亚热带森林植物群落的系统发育关系。     

拟南芥耐盐基因ENH1在陆生植物中的进化

[目的]ENH1是最近鉴定的拟南芥耐盐基因,编码一个叶绿体定位的蛋白,N末端具有一个PZD结构域,C末端具有一个RUBR结构域;功能上与活性氧自由基的脱毒有关,本文研究ENH1基因的进化历史和功能分化。[方法]从陆地植物基因组中获得同源蛋白,重建这个基因家族的系统发生,通过生物信息学手段研究其蛋白质结构域组织,蛋白质相互作用和表达谱。[结果]总共获得35个ENH1同源蛋白序列,大多数物种保持一个基因拷贝,系统发育上单子叶与双子叶被明确划分,并获得高度的支持,在进化过程EHN1蛋白获得了PDZ结构域。[结论]功能上,这个基因家族通过获得PZD结构域适应被子植物细胞的复杂功能要求,ENH1样基因可能涉及叶绿体的多种功能,此外,ENH1基因家族适合作为系统发育重建的分子标记。     

Bees diversified in the age of eudicots

Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113–132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.     

Using nuclear genes to reconstruct angiosperm phylogeny at the species level: A casestudy with Brassicaceae species

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.     

A multilocus phylogeny of the Sulidae (Aves: Pelecaniformes)

Gene trees will often differ from the true species history, the species tree, as a result of processes such as incomplete lineage sorting. New methods such as Bayesian Estimation of the Species Tree (BEST) use the multispecies coalescent to model lineage sorting, and directly infer the species tree from multilocus DNA sequence data. The Sulidae (Aves: Pelecaniformes) is a family of ten booby and gannet species with a global distribution. We sequenced five nuclear intron loci and one mitochondrial locus to estimate a species tree for the Sulidae using both BEST and by concatenating nuclear loci. We also used fossil calibrated strict and relaxed molecular clocks in BEAST to estimate divergence times for major nodes in the sulid phylogeny. Individual gene trees showed little phylogenetic conflict but varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. On the other hand, both the BEST and concatenated species trees were highly resolved, strongly supported, and topologically consistent with each other. The three sulid genera (Morus, Sula, Papasula) were monophyletic and the relationships within genera were mostly consistent with both a previously estimated mtDNA gene tree and the mtDNA gene tree estimated here. However, our species trees conflicted with the mtDNA gene trees in the relationships among the three genera. Most notably, we find that the endemic and endangered Abbott's booby (Papasula abbotti) is likely basal to all other members of the Sulidae and diverged from them approximately 22 million years ago.     

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.     

Phylogeny and biogeography of the freshwater crab genus Johora (Crustacea: Brachyura: Potamidae) from the Malay Peninsula, and the origins of its insular fauna

The phylogeny and biogeography of the Malayan freshwater crab genus Johora was studied using two mitochondrial genes, 16S rRNA (560 bp) and cytochrome oxidase subunit I (COI) (616 bp), and one nuclear gene, histone 3 (H3) (328 bp). Johora is shown to be monophyletic and composed of three clades that correspond with the topography of the Malay Peninsula. The three clades were estimated to be of similar age ( c . 11 million years ago (mya)). The Malayan island of Pulau Tioman (with five species) was determined to have been colonised independently by two separate clades (at c . 11 and 5 mya, respectively), one of which evolved semiterrestrial habits, possibly in response to competition by the second. A partitioned Bremer support (PBS) analysis reveals that most of the support for the phylogenetic tree comes from the COI gene fragment and that the nuclear protein-encoding genes H3 is useful for reconstructing the relationships of Johora .     

Viburnum phylogeny based on combined molecular data: implications for taxonomy and biogeography

We investigated Viburnum phylogeny using separate and combined analyses of DNA sequence data from two chloroplast and three nuclear loci. Separate analyses of nuclear and chloroplast data sets resulted in gene trees that were generally congruent with one another and with trees from two previous analyses. Our gene trees do differ in the position of section Pseudotinus, as well as in species relationships within sections Pseudotinus and Lentago. However, tests for incongruence indicate that differences between the nuclear and chloroplast data are not significant. Furthermore, gene trees from combined analyses were highly similar to those found in separate analyses, suggesting that these localized differences do not affect other parts of the tree. Our analyses provide convincing support for numerous relationships, although there is still uncertainty at the base of the tree. To facilitate future study, we propose informal names for 12 well-supported species groups, as well as for several higher-level clades. We also discuss the biogeographic implications of our phylogeny, focusing on repeated, although apparently temporally incongruent, patterns of disjunction between the Old and New Worlds.     

Phylogeographical and speciation patterns in subterranean worm lizards of the genus Blanus (Amphisbaenia: Blanidae)

The peculiar lifestyle of subterranean reptiles must determine their modes of speciation and diversification. To further understand the evolutionary biology of subterranean reptiles, we studied the phylogeny of worm lizards of the genus Blanus and the phylogeography of its Iberian representatives. We used mitochondrial (ND4 and 16S rRNA) and nuclear (anonymous) partial gene sequences to resolve phylogenetic relationships within Blanus. The Eastern Mediterranean Blanus strauchi was recovered as sister group of Western Mediterranean species. Iberian and North African Blanus were recovered as reciprocally monophyletic groups. The same genes were used to determine phylogeography of 47 populations of Blanus cinereus. Mitochondrial and nuclear sequence data recovered two highly supported Iberian clades. Parapatry and high sequence divergences between them suggest that these clades may represent independent taxonomic units. A molecular clock was calibrated considering that the split between Iberian and North African Blanus was due to the re-opening of the Betic Strait in the Upper Tortonian (8-9 million years ago). Differentiation between the two Iberian clades was estimated to date back to 5.2 million years ago. The Central Iberian clade included five mitochondrial haplotype lineages (A-E). Geographical ranges of two of them broadly overlap in the central Iberian plateau. After testing alternative hypotheses, the most likely explanation for this striking phylogeographical pattern involves recent dispersal of one of the lineages (C) over the geographical range of the other (B). The inferred recent dispersal of this fossorial reptile is explained in terms of demographic advantages associated to underground lifestyle.     

Assessing phylogenetic resolution among mitochondrial, nuclear, and morphological datasets in Nothonotus darters (Teleostei: Percidae)

External morphological characters are the basis of our understanding of diversity and species relationships in many darter clades. The past decade has seen the publication of many studies utilizing mtDNA sequence data to investigate darter phylogenetics, but only recently have nuclear genes been used to investigate darter relationships. Despite a long tradition of use in darter systematics few studies have examined the phylogenetic utility of external morphological characters in estimating relationships among species in darter clades. We present DNA sequence data from the mitochondrial cytochrome b (cytb) gene, the nuclear encoded S7 intron 1, and discretely coded external morphological characters for all 20 species in the darter clade Nothonotus. Bayesian phylogenetic analyses result in phylogenies that are in broad agreement with previous studies. The cytb gene tree is well resolved, while the nuclear S7 gene tree lacks phylogenetic resolution, node support, and is characterized by a lack of reciprocal monophyly for many of the Nothonotus species. The phylogenies resulting from analysis of the morphological dataset lack resolution, but nodes present are found in the cytb and S7 gene trees. The highest resolution and node support is found in the Bayesian combined data phylogeny. Based on our results we propose continued exploration of the phylogenetic utility of external morphological characters in other darter clades. Given the extensive lack of reciprocal monophyly of species observed in the S7 gene tree we predict that nuclear gene sequences may have limited utility in intraspecific phylogeographic studies of Nothonotus darters.