菝葜属和肖菝葜属的核型变异和系统演化研究

基于体细胞染色体核型及花序特征对菝葜科Smilacaceae菝葜属Smilax和肖菝葜属Heterosmilax进行了系统演化研究,报道了国产菝葜科17个分类群的核型。根据已研究的部分形态学特征和已有的核型和分子序列资料,对它们的系统进化进行了分析。结果显示：（1）整个类群的核型变异表现在二型化、多倍化、染色体的微变异以及染色体基数递减（从16-15-13）,16为菝葜类群的基本染色体基数。（2）草本菝葜的核型对称性在东亚到北美种类中,表现出从对称到不对称的变化,而木本菝葜的各组间并未表现出这种趋势。（3）先出叶（prophy11）是宿存的芽鳞,因此在菝葜组sect．China和土茯苓组sect．Coilanthus中具花序的分枝（该分枝基部具先出叶）与圆锥菝葜组sect．Macranthae和穗菝葜组sect．Smilax中着生叶腋的花序分枝或者具关节的单伞形花序是同源的;结合ITS资料,推测花序原始类型是具伞形花序无总花梗呈穗状排列的种类。从祖先类型,花序的分化朝两个方向：一为菝葜属的菝葜组和土茯苓组以及肖菝葜属的全部种类为代表的生于叶腋的单伞形花序,另一为菝葜属的圆锥菝葜组sect．Macranthae的全部种类构成的圆锥．伞形花序。（4）肖菝葜属的核型和ITS数据都表明其为非单系类群,与草本菝葜和土茯苓组成员为姐妹群,首次发现花被2／3联合的过渡类型——筐条菝葜S.corbularia,建议将肖菝葜属降为亚属,置于菝葜属。（5）核型特点支持草本菝葜是东亚起源,扩展到北美,与土茯苓组种类有共同祖先．来自于x=16的木本菝葜,赞同恢复草本组sect．Nemexia。（6）在广布种菝葜S.china中首次发现二倍体居群,已知其存在3种倍性（2x、4x和6x）,发现不同倍性居群的分布规律,推测在第三纪至更新世中期日本、台湾岛与大陆分离之前,菝葜的叙居群已广泛分布,而目前广泛分布的缸居群是岛屿与大陆分离后形靠的。（7）我国西南是菝葜科现代分布和分化中心。     

菝葜科基于形态学证据的系统发育分析

对全世界范围分布的菝葜科Smilacaceae的79个代表种(包括了全部的属和组), 以分布于南美洲的Philesia Comm. ex Juss.和Lapageria Ruiz &; Pav.属为外类群, 选取包括花粉和染色体性状在内的47个广义的形态学性状进行了分支分类系统发育分析, 同时以表征分类的方法构建了距离树(NJ)辅助分析, 首次对世界分布的菝葜科各属间及属内的系统发育关系作了探讨。(1)Ripogonum与菝葜属Smilax +肖菝葜属Heterosmilax互为姐妹群, 但是距离较远, 支持将类菝葜属(新拟中文名)Ripogonum独立为科的观点; (2)肖菝葜属在菝葜科内处于较为进化的分支上, 并与菝葜属土茯苓组sect. Coilanthus的部分种组成一个具较高支持率(88%)的单系分支, 分析表明肖菝葜属并非是一个好属, 应归入菝葜属; (3)菝葜属6个组的划分大都没有得到支持, 只有东亚北美间断分布的草本菝葜组sect. Nemexia的单系得到很好的支持(93%); (4)分布于南美洲巴西的种类聚为一个单系类群, 表明它们可能有共同的起源, 但由于取样局限, 南美洲种类的系统地位有待进一步研究。     

Climatic niche evolution in Smilacaceae (Liliales) drives patterns of species diversification and richness between the Old and New World

Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time-calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.     

Phylogenetics and morphological evolution of coral‐dwelling barnacles (Balanomorpha: Pyrgomatidae)

Pyrgomatid barnacles are a family of balanomorphs uniquely adapted to symbiosis on corals. The evolution of the coral‐dwelling barnacles is explored using a multi‐gene phylogeny (COI, 16S, 12S, 18S, and H3) and phenotypic trait‐mapping. We found that the hydrocoral associate Wanella should be excluded, while some archaeobalanids in the genus Armatobalanus should be included in the Pyrgomatidae. Three well supported clades were recovered: clade I is the largest group and is exclusively Indo‐West Pacific, clade II contains two plesiomorphic Indo‐West Pacific genera, while clade III is comprised of East and West Atlantic taxa. Some genera did not form reciprocally monophyletic groups, while the genus Trevathana was found to be paraphyletic and to include members of three other apomorphic genera/tribes. The highly unusual coral‐parasitic hoekiines appear to be of recent origin and rapidly evolving from Trevathana sensu lato. Pyrgomatids include six‐, four‐, and one‐plated forms, and exhibit convergent evolutionary tendencies towards skeletal reduction and fusion, loss of cirral armature, and increased host specificity. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 162–179.     

Born migrators: Historical biogeography of the cosmopolitan family Cannabaceae

Dispersal scenarios have been favored over tectonic vicariance as an explanation for disjunct distributions in many plant taxa during the last two decades. However, this argument has been insufficiently addressed in cosmopolitan groups showing disjunct patterns in both the temperate and tropical regions. In this study, we used the Cannabaceae, an angiosperm family distributed in tropical and temperate regions of both the New World and the Old World, to explore the role of dispersal in shaping disjunct patterns and species diversification of cosmopolitan plants. We reconstructed the phylogenetic relationships of all 10 genera and 75 species of Cannabaceae (ca. 64.1% of recognized species) based on eight DNA regions. Based on fossil calibrations, we estimated the divergence times and net diversification rates. We further inferred the ancestral geographical ranges with several models and compared the fitness of different models. The Cannabaceae and most genera were strongly supported as monophyletic except for the Parasponia being embedded within the Trema. The Celtis were resolved into two strongly supported clades primarily corresponding to temperate and tropical regions. We inferred that the Cannabaceae originated at ca. 93 Ma, and that subsequent rampant and widespread dispersals shaped the intercontinentally disjunct distribution of the Cannabaceae. Dispersal coincides with adaptation to drier and colder climate in the Northern Hemisphere, or humid and warm climate in the tropical regions, followed by rapid species diversification. This study advances our understanding as to the formation of distribution patterns and species diversification of a plant family with tropical to temperate disjunct distributions.     

Multigene‐based phylogeny of Urostylida (Ciliophora,Hypotrichia), with establishment of a novel family

The Urostylida is a major taxon of hypotrichs with many unresolved evolutionary relationships. Due to incomplete or inaccurate character states and a paucity of morphogenetic data, the phylogeny of several taxa within urostylids is unresolved. Molecular phylogeny studies based on single gene (SSU rDNA) data may lead to conflict between morphological classification and SSU rDNA tree. In this work, 20 new sequences (SSU rDNA, ITS1‐5.8S‐ITS2 and LSU rDNA) of five genera of urostylids are provided to further investigate the phylogenetic relationships of this group. The main findings are as follows: (i) the establishment of Hemicycliostylidae, a novel family presently including Hemicycliostyla and Australothrix, is supported by both single gene and concatenated phylogenies; (ii) all molecular data support the exclusion of Eschaneustyla from the family Epiclintidae; (iii) Australothrix, Bergeriella and Thigmokeronopsis are distinctly separated in all gene trees although they share the character that each posterior streak generates the ventral row together with the midventral pair; (iv) compared with closely related genera in all trees, that is Metaurostylopsis and Apourostylopsis, Neourostylopsis is characterized by having more than three frontal cirri arranged in distinct or indistinct corona rather than the length of the midventral complex; (v) Hemicycliostyla and Pseudourostyla, two morphologically similar genera, do not form a monophyletic group in all molecular trees, suggesting that the bicorona, multiple marginal cirral rows and high numbers of dorsal kineties may result from convergent evolution; (vi) species of Bakuella fall into three separate clades in all trees suggesting that this genus needs to be split.     

Plastomic data shed new light on the phylogeny,biogeography, and character evolution of the family Crassulaceae

Crassulaceae is a mid-sized family of angiosperms, most species of which are herbaceous succulents, usually with 5-merous flowers and one or two whorls of stamens. Although previous phylogenetic studies revealed seven major “clades” in Crassulaceae and greatly improved our understanding of the evolutionary history of the family, relationships among major clades are still contentious. In addition, the biogeographic origin and evolution of important morphological characters delimiting infrafamilial taxa have not been subject to formal biogeographic and character evolution analyses based on a well-supported phylogeny backbone. In this study, we used plastomic data of 52 species, representing all major clades revealed in previous studies to reconstruct a robust phylogeny of Crassulaceae, based on which we unraveled the spatiotemporal framework of diversification of the family. We found that the family may originate in southern Africa and then dispersed to the Mediterranean, from there to eastern Asia, Macaronesia, and North America. The crown age of Crassulaceae was dated at ca. 63.93 million years ago, shortly after the Cretaceous–Paleogene (K-Pg) boundary. We also traced the evolution of six important morphological characters previously used to delimit infrafamilial taxa and demonstrated widespread parallel and convergent evolution of both vegetative (life form and phyllotaxis) and floral characters (number of stamen whorls, petals free or fused, and flower merism). Our results provide a robust backbone phylogeny as a foundation for further investigations, and also some important new insights into biogeography and evolution of the family Crassulaceae.     

Phylogenetics and character evolution in the grass family (Poaceae): Simultaneous analysis of morphological and Chloroplast DNA restriction site character sets

A phylogenetic analysis of the grass family (Poaceae) was conducted using two character sets, one representing variation in 364 mapped and cladistically informative restriction sites from all regions of the chloroplast genome, the other representing variation in 42 informative “structural characters.” The structural character set includes morphological, anatomical, chromosomal, and biochemical features, plus structural features of the chloroplast genome. The taxon sample comprises 75 exemplar taxa, including 72 representatives of Poaceae and one representative of each of three related families (Flagellariaceae, Restionaceae, and Join-villeaceae);Flagellaria served as the outgroup for the purpose of cladogram rooting. Among the grasses, 24 tribes and all 16 subfamilies of grasses recognized by various modern authors were sampled. Transformations of structural characters are mapped onto the phylogenetic hypotheses generated by the analysis, and interpreted with respect to biogeography and the evolution of wind pollination in the grass family. A major goal of the study was to test the monophyly of several putatively natural groups, including Bambusoideae, Pooideae, Arundinoideae, and the “PACC clade” (the latter comprising subfamilies Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae), as well as to analyze the phylogenetic structure within these groups and others. Several genera of controversial placement (Amphipogon, Anisopogon, Anomochloa, Brachyelytrum, Diarrhena, Eremitis, Ehrharta, Lithachne, Lygeum, Nardus, Olyra, Pharus, andStreptochaeta) also were included, with the goal of determining their phylogenetic affinities. The two character sets were analyzed separately, and a simultaneous analysis of the combined matrices also was conducted. The combined data set also was analyzed using homoplasy-implied weights. Among major results of the combined unweighted analysis were resolution of a sister-group relationship betweenJoinvillea and Poaceae; resolution of a clade comprisingAnomochloa andStreptochaeta as the sister of all other grasses, withPharus the next group to diverge from the lineage that includes all remaining grasses; and resolution of other taxa often assigned to Bambusoideae s.l. (includingEhrharta and Oryzeae, and excluding a few other taxa as noted) as a paraphyletic assemblage, within which is nested a clade that consists ofBrachyelytrum, the PACC clade (includingAmphipogon), and Pooideae (including Brachypodieae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). Within the PACC clade,Aristida is identified as the sister of all other elements of the group; Chloridoideae, Centothecoideae, and Panicoideae are each resolved as monophyletic, the latter two being sister-groups; and the remaining Arundinoid elements constitute a paraphyletic group within which are nested these three subfamilies. Within the Pooideae, four “core tribes” (Bromeae, Hordeeae [i.e., Triticeae], Agrostideae [i.e., Aveneae], andPoeae, the latter includingSesleria) are resolved as a monophyletic group that is nested among the remaining elements of the subfamily (Brachypodieae, Meliceae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). A second principal goal of the analysis was to identify structural synapomorphies of clades. Among the synapomorphies identified for some of the major clades are the following: gain of a 6.4 kb inversion in the chloroplast genome inJoinvillea and the grasses; reduction to 1 ovule per pistil, gain of a lateral “grass-type” embryo, and gain of an inversion around the gene trnT in the chloroplast genome in the grasses; loss of arm cells in the clade that consists ofBrachyelytrum, Pooideae, and the PACC clade; loss of the epiblast and gain of an elongate mesocotyl internode in the PACC clade; gain of proximal female-sterile florets in female-fertile spikelets, gain of overlapping embryonic leaf margins, and gain ofPanicum- type endosperm starch grains in the clade that comprises Centothecoideae and Panicoideae; and loss of the scutellar tail of the embryo in Pooideae (in one of two alternative placements of Pooideae among other groups). These findings are consistent with an origin and early diversification of grasses as forest understory herbs, followed by one or more radiations into open habitats, concomitant with multiple origins of C₄ photosynthesis and specialization for wind pollination.     

Higher‐level phylogenetic affinities of the Neotropical genus Mastigodryas Amaral, 1934 (Serpentes: Colubridae), species‐group definition and description of a new genus for Mastigodryas bifossatus

Most Neotropical colubrid snakes belong to a single, well‐supported lineage. Relationships between the major constituents of this clade remain. Here, we explore the phylogenetic relationships of Mastigodryas and its affinities to other Neotropical colubrid genera by combining DNA and morphological data. Analyses demonstrate that the concatenation of multiple individuals into a single terminal can mask the detection of new taxa. Further, non‐random missing data and/or taxa in some empirical datasets can bias species tree analyses more than concatenation approaches. Our results place Mastigodryas in a strongly supported clade that includes Drymarchon, Rhinobothryum, Drymoluber, Simophis and Leptodrymus. Mastigodryas bifossatus is more closely related to species of Drymoluber and Simophis than to its congeners. Thus, we erect a new genus to accommodate it and recover a monophyletic Mastigodryas. We highlight the importance of the use of morphological characters to diagnose suprageneric clades by showing that some key external and hemipenial characteristics are phylogenetically informative.     

Evolutionary timescale of monocots determined by the fossilized birth‐death model using a large number of fossil records

Although the phylogenetic relationships between monocot orders are sufficiently understood, a timescale of their evolution is needed. Several studies on molecular clock dating are available, but their results have been biased by their calibration schemes. Recently, the fossilized birth‐death model, a type of Bayesian dating method, was proposed, and it does not require prior calibration and allows the use all available fossils. Using this model, we conducted divergence‐time estimations of monocots to explore their evolutionary timeline without calibration bias. This is the first application of this model to seed plants. The dataset contained the matK and rbcL chloroplast genes of 118 monocot genera covering all extant orders. We employed information from 247 monocot fossils, which exceeded previous dating analyses that used a maximum of 12 monocot fossils. The crown group of monocots was dated to approximately the Late Jurassic–Early Cretaceous periods, and most extant monocot orders were estimated to diverge throughout the Early Cretaceous. Our results overlapped with the divergence time of insect lineages, such as beetles and flies, suggesting an association with pollinators in early monocot evolution. In addition, we proposed three new orders based on divergence time: Orchidales separated from Asparagales and Tofieldiales and Arales separated from Aslimatales.     

Phylogenetics and evolution of phyllotaxy in the Solomon's seal genus Polygonatum (Asparagaceae: Polygonateae)

Polygonatum is the largest and most complex genus in tribe Polygonateae, comprising approximately 57 species widely distributed in the warm temperate, subtropical and boreal zones of the Northern Hemisphere. However, phylogenetic relationships in the genus remain poorly understood. The objectives of this study were to reconstruct the phylogenetic relationships of the genus using four plastid markers, and to examine the evolution of leaf arrangement in Polygonatum in the phylogenetic context of its closely related taxa. Thirty Polygonatum species were sampled to infer phylogenetic relationships using maximum‐likelihood and Bayesian analyses. The evolution of leaf arrangements was reconstructed using Bayesian, parsimony and likelihood methods. The phylogenetic analyses supported the current generic delimitation of Polygonatum, with Heteropolygonatum recognized as a distinct genus. Three major lineages in Polygonatum were well supported, largely correlated with geographical distribution and the most recent classification at the sectional level. However, our results did not support the currently recognized series, especially the two large series Verticillata and Alternifolia. Bayesian analyses support the alternate‐leaf arrangement as the ancestral state for Polygonatum, but parsimony and maximum‐likelihood analyses suggest an equivocal state for crown Polygonatum. Leaf arrangement was found to be evolutionarily labile. A new nomenclatural combination was made: P olygonatum section S ibirica (L.I.Abramova) Y.Meng, comb. nov. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 435–451.     

Exon-intron structure and evolution of the Lipocalin gene family

The Lipocalins are an ancient protein family whose expression is currently confirmed in bacteria, protoctists, plants, arthropods, and chordates. The evolution of this protein family has been assessed previously using amino acid sequence phylogenies. In this report we use an independent set of characters derived from the gene structure (exon-intron arrangement) to infer a new lipocalin phylogeny. We also present the novel gene structure of three insect lipocalins. The position and phase of introns are well preserved among lipocalin clades when mapped onto a protein sequence alignment, suggesting the homologous nature of these introns. Because of this homology, we use the intron position and phase of 23 lipocalin genes to reconstruct a phylogeny by maximum parsimony and distance methods. These phylogenies are very similar to the phylogenies derived from protein sequence. This result is confirmed by congruence analysis, and a consensus tree shows the commonalities between the two source trees. Interestingly, the intron arrangement phylogeny shows that metazoan lipocalins have more introns than other eukaryotic lipocalins, and that intron gains have occurred in the C-termini of chordate lipocalins. We also analyze the relationship of intron arrangement and protein tertiary structure, as well as the relationship of lipocalins with members of the proposed structural superfamily of calycins. Our congruence analysis validates the gene structure data as a source of phylogenetic information and helps to further refine our hypothesis on the evolutionary history of lipocalins.     

A family of short retroposons (Squam1) from squamate reptiles (Reptilia: Squamata): Structure,evolution, and correlation with phylogeny

Sequences of the SINE family specific to squamate reptiles have been isolated from the genomes of lacertid lizards and sequenced. These retroposons, which we called Squam1, are 360–390 bp long and contain a region similar to the tRNA gene sequence at the 5’ end. This family has also been detected in representatives of other reptile families (varanids, iguanids (Anolis), gekkonids, and snakes), being absent from the genomes of crocodiles as well as amphibians, birds, and mammals. The primary structures of Squam1 copies have been comprehensively analyzed and compared with GenBank sequences. The genomes of most taxa contain two to three SINE subfamilies with specific diagnostic features in their primary structures. Individual similarity between the copies within each taxon is about 85%, with intrageneric similarity being only slightly higher. A comparison of consensus sequences between different lizard families has shown that Squam1 may be a convenient phylogenetic marker for this group of reptiles, having a number of both apomorphic and more or less pronounced synapomorphic features. By this criterion, snakes slightly differ from lizards but obviously belong to the same clade. However, they show no special affinity to varanids as the putative closest relatives of snakes, compared to other lizards.     

Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Approximately 1.7 kbp of mitochondrial DNA were sequenced from 29 individuals assignable to 11 Uromastyx species or subspecies and two other agamids. U. ocellata and U. ornata had an insertion between the glutamine and isoleucine tRNA genes, which could be folded into a stable stem-and-loop structure, and the insertion for U. ornata additionally retained a sequence similar to the glutamine tRNA gene. This corroborates the role of tandem duplication in reshaping mitochondrial gene arrangements, and supports the idea that the origin of light-strand replication could be relocated within mitochondrial genomes. Molecular phylogeny from different tree-building methods consistently placed African and Arabian taxa in mutually monophyletic groups, excluding U. hardwickii inhabiting India and Pakistan. Unlike previous studies based on morphology , U. macfadyeni did not cluster with morphologically similar Arabian taxa, suggesting convergent evolution to be responsible for the morphological similarities. Divergence times estimated among the Uromastyx taxa, together with geological and palaeontological evidence, suggest that the Uromastyx agamids originated from Central Asia during the Eocene and colonized Africa after its connection with Eurasia in the early Miocene. Their radiation may have been facilitated by repeated aridification of North Africa since the middle Miocene, and geological events such as the expansion of the Red Sea and the East African Rift Valley.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 247–260.     

Mechanisms of light organ occlusion in flashlight fishes, family Anomalopidae (Teleostei:Beryciformes), and the evolution of the group

The circumtropical, nocturnal, shore-fish family Anomalopidae is characterized by a subocular luminous organ containing symbiotic luminous bacteria. The five known species are placed in four genera, one of which is new. Phthanophaneron is restricted to the eastern Pacific, Kryptophanaron to the western Atlantic, Photoblepharon is Indo-West Pacific in distribution and Anomalops is west Pacific. The symbiotic bacteria emit light continuously, and two superficially different mechanisms of occluding the glowing face of the organ are found. In Photoblepharon a black shutter of elastic skin is drawn up over the face of the organ, whereas in Anomalops the organ is rotated downward, so that only the heavily pigmented back of the organ is exposed. In Phthanophaneron and Kryptophanaron, both rotational and shutter mechanisms are present. Elucidation of the structures and linkages involved in light-organ occlusion reveals that the superficially different mechanisms are based on a common functional complex. In all four genera, the light organ is supported by a cartilaginous cup that articulates anteriorly with a cartilaginous stalk. Motive power for both the shutter and rotational mechanisms is supplied by the adductor mandibulae through a complex biomechanical linkage involving the ethmomaxillary ligament and a ligament unique to anomalopids, the Ligament of Diogenes. The structures involved in shutter erection and organ rotation are illustrated and described in detail for Photoblepharon and Anomalops and are compared with those in the other two forms; a functional hypothesis is advanced. Extrafamilial relationships of the Anomalopidae are discussed, and a hypothesis of the phylogenetic relationships of the four genera is derived from a cladistic analysis involving 19 non-light-organ characters and corroborated by some light-organ characters. Most characters associated with the light-organ complex cannot be polarized by conventional outgroup comparison, and the evolution of the light organ occlusion mechanisms is interpreted in light of the hypothesized phylogeny and a hypothesized ancestral mechanism. We propose that the common ancestor of anomalopids possessed a forced rotational mechanism like that of Phthanophaneron and Kryptophanaron. This was refined to a more efficient flipping rotational mechanism in Anomalops, the sister group of the lineage comprising the other three genera, within which the shutter mechanism was progressively refined. The ostensibly unnecessary complexity of the shutter mechanism is apparently a result of functional-morphological constraints imposed on the system by the pre-existence of a rotational mechanism. A brief zoogeographic scenario is proposed.     

Molecular phylogenetics,character evolution and systematics of the genus Micranthes (Saxifragaceae)

With c. 85 species, the genus Micranthes is among the larger genera of the Saxifragaceae. It is only distantly related to the morphologically similar genus Saxifraga, in which it has frequently been included as Saxifraga section Micranthes. To study the molecular evolution of Micranthes, we analysed nuclear ribosomal (internal transcribed spacer, ITS) and plastid (trnL–trnF) DNA sequences in a comprehensive set of taxa comprising c. 75% of the species. The molecular phylogenetic tree from the combined dataset revealed eight well‐supported clades of Micranthes. These clades agree in part with previously acknowledged subsections or series of Saxifraga section Micranthes. As these eight groups can also be delineated morphologically, we suggest that they should be recognized as sections of Micranthes. New relationships were also detected for some species and species groups, e.g. section Davuricae sister to sections Intermediae and Merkianae, and M. micranthidifolia as a member of section Micranthes. Species proposed to be excluded from the genus Micranthes for morphological reasons were resolved in the molecular tree in Saxifraga. Many morphological characters surveyed were homoplasious to varying extents. Micromorphological characters support comparatively well the clades in the phylogenetic tree. An updated nomenclature and a taxonomic conspectus of sections and species of Micranthes are provided. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 47–66.