Circumscription of Primula subgenus Auganthus (Primulaceae) based on chloroplast DNA sequences

Recent molecular phylogenetic analyses of Primula have greatly enhanced our understanding of the infrageneric relationships of the genus,but the subgenera Auganthus and Carolinella remain meagerly sampled and poorly understood.In the present study,nucleotide sequence data of three chloroplast DNA regions (matK,rps16,and trnL-F) were used to infer phylogenetic relationships of the subgenera Auganthus and Carolinella.Sequence data were acquired and analyzed for 70 species of Primula and its close relatives.Th...     

Pollen morphology in Primula sect. Carolinella (Primulaceae) and its taxonomic implications

Pollen morphology in Primula section Carolinella has been investigated for the first time. Seven of the nine species constituting the section were available for study, i. e., P. cardioeides, P. chapaensis, P. intanoensis, P. kwangtungensis, P. kweichouensis, P. partschiana , and P. rugosa, A considerable variation in pollen morphology was found among the investigated species, particularly in number and arrangement of the apertures. Pollen of different species were either tricolpate, tricolporate, trisyncolpate, or polycolpate. Within Primula , the section Carolinella is diagnosed by having calyptrate capsules and leaves with revolute vernation, but the variation in pollen morphology indicates that this group is heterogeneous, and that either polycolpate pollen or a capsular lid has evolved more than once in the genus Primula.     

Robustness of compound Dirichlet priors for Bayesian inference of branch lengths

We modified the phylogenetic program MrBayes 3.1.2 to incorporate the compound Dirichlet priors for branch lengths proposed recently by Rannala, Zhu, and Yang (2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.) as a solution to the problem of branch-length overestimation in Bayesian phylogenetic inference. The compound Dirichlet prior specifies a fairly diffuse prior on the tree length (the sum of branch lengths) and uses a Dirichlet distribution to partition the tree length into branch lengths. Six problematic data sets originally analyzed by Brown, Hedtke, Lemmon, and Lemmon (2010. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Syst. Biol. 59:145-161) are reanalyzed using the modified version of MrBayes to investigate properties of Bayesian branch-length estimation using the new priors. While the default exponential priors for branch lengths produced extremely long trees, the compound Dirichlet priors produced posterior estimates that are much closer to the maximum likelihood estimates. Furthermore, the posterior tree lengths were quite robust to changes in the parameter values in the compound Dirichlet priors, for example, when the prior mean of tree length changed over several orders of magnitude. Our results suggest that the compound Dirichlet priors may be useful for correcting branch-length overestimation in phylogenetic analyses of empirical data sets.     

报春花属藏报春组、毛茛叶报春组的界定和系统发育关系 :核糖体DNAITS序列证据(英文)

报春花属 (PrimulaL .)藏报春组 (sect.AuganthusPaxexBalf.f.)和毛茛叶报春组 (sect.RanunculoidesChenetC .M .Hu)的界定一直是没有解决的问题。应用核糖体DNAITS序列数据探讨其系统发育关系。取样包括藏报春组和毛茛叶报春组的全部 5个种以及其他一些相关组的代表种。ITS系统树表明 ,陕西羽叶报春 (P .filchneraeKnuth)应与藏报春 (P .sinensisSabineexLindl.)和野藏报春 (P .rupestrisBalf.f.etFarrer)一起置于藏报春组 ;毛茛叶报春组只含两种 :毛茛叶报春 (P .cicutariifoliaPax)和安徽羽叶报春 (P .merrillianaSchltr.)。这两组并不具密切亲缘关系 ,它们在报春花属中与其他组的关系还需进一步研究。研究也表明ITS序列可以为报春花属的系统发育重建提供大量可靠资料     

Chromosomal variability in the genus Primula (Primulaceae)

Chromosome numbers and measurements were recorded in 47 individuals of ten taxa of Primula , representing eight species and two subspecies from ten populations. The basic numbers of chromosomes were x  = 8, 9 or 11, and they were mostly metacentric, medium-long to medium-small, ranging in length from c . 3.6 µm to 1.6 µm. Diploid chromosome numbers of 2 n  = 2 x  = 24 and 22 were scored for the first time in P. loeseneri Kitag. and P. prenantha Balf. & Sm., respectively. A new ploidy level of 2 n  = 4 x  = 44 was found in P. burmanica Balf. & King. The recorded diploid numbers of the remaining species confirmed earlier reports. Interspecific variability in chromosome numbers was correlated with heterogeneity in their mean length. Comparison of the data with those in the literature revealed that the observed variability of chromosomal characters was compatible with the other taxonomic criteria and supports the current taxonomic delimitation. Chromosomal variation at the diploid level is the predominant feature in Primula evolution, and allopatric speciation has played a major role in its specific diversity. Subgen. Aleuritia could represent the main clade from which the other subgenera have evolved. The origin of the chromosome numbers, geographical distribution and evolution of the species were assessed, and the parallel polyphyletic mode of evolution in the genus was confirmed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 211–219.     

报春花属藏报春组、毛茛叶报春组的界定和系统发育关系:核糖体DNA ITS序列证据

报春花属(Primula L.)藏报春组(sect. Auganthus Pax ex Balf. f.)和毛茛叶报春组(sect. Ranunculoides Chen et C. M. Hu)的界定一直是没有解决的问题.应用核糖体DNA ITS序列数据探讨其系统发育关系.取样包括藏报春组和毛茛叶报春组的全部5个种以及其他一些相关组的代表种.ITS系统树表明,陕西羽叶报春(P.filchnerae Knuth)应与藏报春(P. sinensis Sabine ex Lindl.)和野藏报春(P. rupestris Balf. f. et Farrer)一起置于藏报春组;毛茛叶报春组只含两种:毛茛叶报春(P. cicutariifolia Pax)和安徽羽叶报春(P. merrilliana Schltr.).这两组并不具密切亲缘关系,它们在报春花属中与其他组的关系还需进一步研究.研究也表明ITS序列可以为报春花属的系统发育重建提供大量可靠资料.     

七种灯台报春组植物的细胞学研究

对报春花科（Primulaceae）报春花属（Primula）灯台报春组植物Section Proliferoe的7种报春进行了细胞学研究,其中腾冲灯台报春和川东灯台报春的核型分析为首次报道,结合已报道的灯台报春组其它植物的细胞学资料进行统计分析,结果表明灯台报春组植物在染色体基数、染色体形态、着丝点位置及染色体对称性上都具有很高的一致性,在灯台报春组有核型记录的种类中,其核型都属于Stebbins的2A型或2B型,核型差异很小,染色体基数均为x=11,推测其可能与报春花属中具有相同染色体基数的组亲缘关系更近。结合已发表的灯台报春组植物的细胞学资料及它们的形态特征,对其系统演化关系进行了比较分析,以期对该组的系统学及演化关系提供一些证据。     

On the occurrence of unilateral incompatibility in Primula section Aleuritia Duby and the origin of Primula scotica Hook

The occurrence of unilateral incompatibility was tested for a distylous heteromorphic system, using crosses between a self-sterile and three self-fertile species in Primula L. section Aleuritia Duby. The crosses showed non-reciprocity but not in the same direction as would be predicted in the case of unilateral incompatibility. Pollen from the self-compatible (s-c) species was not always inhibited on the style of the self-incompatible (s-i) species, and cross-fertility between s-i and s-c crosses more resembled that between different s-c species, which was also non-reciprocal. Cytoplasmic-nuclear DNA interactions and the possibility of embryo-endosperm imbalance could both explain these results. In crosses between Primula farinosa L. (s-i diploid) and P. scotica Hook. (s-c hexaploid), heterostylous pin tetraploid offspring were produced. This result is discussed in relation to the genome of P. scotica and the possibility that pin morph plants may occur in wild P scotica populations.     

Integrating species distribution models (SDMs) and phylogeography for two species of Alpine Primula

The major intention of the present study was to investigate whether an approach combining the use of niche-based palaeodistribution modeling and phylo-geography would support or modify hypotheses about the Quaternary distributional history derived from phylogeographic methods alone. Our study system comprised two closely related species of Alpine Primula. We used species distribution models based on the extant distribution of the species and last glacial maximum (LGM) climate models to predict the distribution of the two species during the LGM. Phylogeographic data were generated using amplified fragment length polymorphisms (AFLPs). In Primula hirsuta, models of past distribution and phylogeographic data are partly congruent and support the hypothesis of widespread nunatak survival in the Central Alps. Species distribution models (SDMs) allowed us to differentiate between alpine regions that harbor potential nunatak areas and regions that have been colonized from other areas. SDMs revealed that diversity is a good indicator for nunataks, while rarity is a good indicator for peripheral relict populations that were not source for the recolonization of the inner Alps. In P. daonensis, palaeo-distribution models and phylogeographic data are incongruent. Besides the uncertainty inherent to this type of modeling approach (e.g., relatively coarse 1-km grain size), disagreement of models and data may partly be caused by shifts of ecological niche in both species. Nevertheless, we demonstrate that the combination of palaeo-distribution modeling with phylogeographical approaches provides a more differentiated picture of the distributional history of species and partly supports (P. hirsuta) and partly modifies (P. daonensis and P. hirsuta) hypotheses of Quaternary distributional history. Some of the refugial area indicated by palaeodistribution models could not have been identified with phylogeographic data.     

Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference

Recent studies have observed that Bayesian analyses of sequence data sets using the program MrBayes sometimes generate extremely large branch lengths, with posterior credibility intervals for the tree length (sum of branch lengths) excluding the maximum likelihood estimates. Suggested explanations for this phenomenon include the existence of multiple local peaks in the posterior, lack of convergence of the chain in the tail of the posterior, mixing problems, and misspecified priors on branch lengths. Here, we analyze the behavior of Bayesian Markov chain Monte Carlo algorithms when the chain is in the tail of the posterior distribution and note that all these phenomena can occur. In Bayesian phylogenetics, the likelihood function approaches a constant instead of zero when the branch lengths increase to infinity. The flat tail of the likelihood can cause poor mixing and undue influence of the prior. We suggest that the main cause of the extreme branch length estimates produced in many Bayesian analyses is the poor choice of a default prior on branch lengths in current Bayesian phylogenetic programs. The default prior in MrBayes assigns independent and identical distributions to branch lengths, imposing strong (and unreasonable) assumptions about the tree length. The problem is exacerbated by the strong correlation between the branch lengths and parameters in models of variable rates among sites or among site partitions. To resolve the problem, we suggest two multivariate priors for the branch lengths (called compound Dirichlet priors) that are fairly diffuse and demonstrate their utility in the special case of branch length estimation on a star phylogeny. Our analysis highlights the need for careful thought in the specification of high-dimensional priors in Bayesian analyses.     

Genetic structure of the forest herb Primula elatior in a changing landscape

To investigate whether changes in land use and associated forest patch turnover affected genetic diversity and structure of the forest herb Primula elatior, historical data on landscape changes were combined with a population genetic analysis using dominant amplified fragment length polymorphism markers. Based on nine topographic maps, landscape history was reconstructed and forest patches were assigned to two age classes: young (less than 35 years) and old (more than 35 years). The level of differentiation among Primula populations in recently established patches was compared with the level of differentiation among populations in older patches. Genetic diversity was independent of population size (P > 0.05). Most genetic variation was present within populations. Within-population diversity levels tended to be higher for populations located in older forests compared with those for populations located in young forests (Hj = 0.297 and 0.285, respectively). Total gene diversity was also higher for old than for young populations (Ht = 0.2987 and 0.2828, respectively). The global fixation index FST averaged over loci was low, but significant. Populations in older patches were significantly more differentiated from each other than were populations in recently established patches and they showed significant isolation by distance. In contrast, no significant correlations between pairwise geographical distance and FST were found for populations in recently established patches. The location of young and old populations in the studied system and altered gene flow because of increased population density and decreased inter-patch distances between extant populations may explain the observed lower genetic differentiation in the younger populations. This study exemplifies the importance of incorporating data on historical landscape changes in population genetic research at the landscape scale.     

Primula jiugongshanensis sp. nov. (Primulaceae) from China,based on morphological and molecular evidence

Primula jiugongshanensis J. W. Shao, a new species from Mt Jiugongshan in Hubei Province, China, is described and illustrated. This species is a biennial glabrous herb with pinnately compound leaves, and affiliated to P. sect. Ranunculoides C. M. Hu. It is distinguished from other species of the section by outer simple leaves ovate, flowers distylous, corolla lobe apex conspicuously emarginate, and lack of bulblets. Molecular phylogenetic analysis of nrDNA internal transcribed spacer sequences (ITS) was conducted and the results also supported the recognition of P. jiugongshanensis as a new species. The species is known from only three separated unprotected populations and is categorized as ‘Endangered’ (EN).     

Reappraisal of Primula ranunculoides (Primulaceae), an endangered species endemic to China,based on morphological,molecular genetic and reproductive characters

The taxonomic status of Primula ranunculoides and other members of section Ranunuculoides is reappraised here based on data from morphological, reproductive and molecular characters. Multivariate analysis of morphological characters indicates that P. ranunculoides is a coherent species that can be distinguished from its sectional congeners P. cicutariifolia and P. merrilliana by the characters of simple kidney‐shaped outer leaves and the unique clonal reproductive ability by which apices of the scape differentiate into bulblets at the late phases of flowering. Recognition of P. ranunculoides at the specific level is also supported by palynological characters, breeding system, cross pollination results and molecular phylogenetic analysis of nrDNA internal transcribed spacer sequences. A taxonomic revision of section Ranunuculoides is presented and a possible mechanism of speciation discussed. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 338–349.     

毛茛叶报春高分化的谱系地理结构

毛茛叶报春（Primula ranunculoides Chen）是我国特有的珍稀濒危花卉,其野生种质资源已十分稀少。为了揭示其谱系地理结构,本文对11个居群114个个体的叶绿体trnL-F和trnS-G基因片段进行了测序分析。结果共检测到10个单倍型,除YJPA和YJPB两居群共享一个单倍型（H9）外,其余各居群均仅有一个特有单倍型,居群内不存在单倍型多样性。毛茛叶报春具高分化的谱系地理结构,居群间的总平均遗传距离达0.015,单倍型间的平均突变次数高达31.2步,两者均显著高于同属的近缘种。其种子散布能力弱、生境片断化和地理隔离明显及两年生的生活史可能是导致其高分化谱系地理结构产生的主要原因。Samova、Structure以及TCS分析均支持将毛茛叶报春11个居群的遗传结构分为6组,它们与地形（山脉）关系密切对应,彼此间分化明显,因此建议不同山体的居群应视为不同的保护单元进行遗传管理。     

Fine-scale genetic structure of the common Primula elatior (Primulaceae) at an early stage of population fragmentation

Many rare species are threatened by habitat fragmentation; however, less is known about effects of fragmentation on common species, despite their potential role in ecosystem productivity and functioning. We identified key factors and processes influencing gene flow in a large population of Primula elatior, a common distylous perennial herb, at an early stage of the fragmentation process, i.e., when fragmentation is taking place. Using 19 allozyme loci, we investigated genetic variation and fine-scale spatial genetic structure (SGS) at seedling and adult life stages in relation to fragmentation history (recent bottlenecks), selection, clonal propagation, sexual reproduction (seed and pollen dispersal, distyly), and patchy structure (patch size, plant density, and morph ratio). The main factors contributing to the strong SGS are seed and (to a lesser extent) pollen dispersal, through a spatial Wahlund effect and biparental inbreeding. Significant differences in allele frequencies between seedlings and adults indicate a temporal Wahlund effect. Patch plant density and biased morph ratio also affect the genetic patterns. Our results show that if P. elatior populations evolve into patchworks of small, isolated remnants, genetic erosion, reduced gene flow, and increased inbreeding can be expected, suggesting that such common plant species might require large population sizes to remain viable.     

Primula tschuktschorum and Primula eximia (Primulaceae: Section Crystallophlomis): A distylous species and its homostylous derivative from the Bering Strait region,Alaska

Primula tschuktschorum Kjellman s. lat., known from Alaska and northeastern Siberia, has been the subject of many nomenclatural combinations. This paper argues the case for treating it as two species on the basis of morphology and reproductive biology.Primula tschuktschorum Kjellman s. str. is a distylous species endemic to the Bering Strait region andP. eximia Greene is a more widely distributed homostylous species. The polymorphism seen inP. eximia is attributed to ecological and phenological factors and a high degree of self-fertilization. In contrast to its distylous relative, the ability of this homostylous species to self-fertilize has enabled it to colonize recently deglaciated areas in Alaska. Because of the intramorph incompatibility system associated with distyly,P. tschuktschorum is an obligate outcrosser. Its apparent rarity may be due to a dependence on inefficient pollinators. The species deserves further study to determine if there is a need for protected status in Alaska.     

Comparative study of pollination biology of two closely related alpine Primula species,namely Primula beesiana and P. bulleyana (Primulaceae)

Abstract The comparative pollination biology of a population of Primula beesiana, a population of P. bulleyana, and an overlapping population of these two species in Yulong Shan, Yunnan Province, China, was studied in 2004 and 2005. The results indicate that both P. beesiana and P. bulleyana are typical heterostylous and obligate outcrossing species; the main pollinators of the two species were bees and butterflies. At the sites of all three populations, the main pollinating visitors of the two species showed preference for one of the two species, resulting in the ethological isolation of the two species by the pollinators. This ethological isolation contributes to the reproductive isolation of the two species, which supports the hypothesis that P. beesiana and P. bulleyana are two distinct species. The reproductive isolation of the two species (ethological isolation) is probably an important mechanism in maintaining species boundaries in the genus and has contributed to the species diversification of Primula in the area. In addition, gene exchanges between P. beesiana and P. bulleyana has occurred to some extent in the overlapping population, but whether natural hybridization has contributed to species diversification in Primula remains to be determined.     

The distyly in Primula elatior (L.) Hill (Primulaceae), with a study of flowering phenology and pollen flow

Flowers of Primula elatior exhibit all the dimorphic traits typical of distyly. The difference in pollen production between pin and thrum flowers is not thought to be caused by the pollen size dimorphism. The percentage of pin pollen which is probably viable exceeds that of thrum pollen. In the population studied the morph ratio is 1:1, and plants are randomly dispersed with regard to morph type. Bumblebees are the main pollinators, and analysis of the stigmatic pollen load in naturally |xjllinated flowers shows that pin stigmas receive many more pollen grains than thrum stigmas. Intramorph pollination is considerable in pins, while thrums are subject to some differential pollination. Emasculation experiments have shown that intraflower pollination in the thrum morph is negligible. Aging of pin flowers has a reducing effect on their total pollen loads, while in thrums there is no change in total pollen load after the first days of anthesis.     

Buzz-pollinated Dodecatheon originated from within the heterostylous Primula subgenus Auriculastrum (Primulaceae): a seven-region cpDNA phylogeny and its implications for floral evolution

We sequenced seven cpDNA regions from 70 spp. in Dodecatheon, Primula subgenus Auriculastrum, and outgroups, reconstructed their cpDNA phylogeny with maximum parsimony, and determined branch support with bootstrap frequencies and Bayesian posterior probabilities. Strongly supported conclusions include the (1) paraphyly of Primula subgenus Auriculastrum with respect to a monophyletic Dodecatheon, (2) sister relationship between the North American Dodecatheon and the Californian P. suffrutescens, (3) novel basal split in Dodecatheon to produce one clade with rugose and one clade with smooth anther connectives, (4) monophyly of all sections of Primula subgenus Auriculastrum, and (5) exclusion of the enigmatic Primula section Amethystina from the similar Primula subgenus Auriculastrum. These results support the origin of the monomorphic, buzz-pollinated flower of Dodecatheon from the heterostylous flower of Primula. We marshal evidence to support the novel hypothesis that the solanoid flower of Dodecatheon represents the fixation of recessive alleles at the heterostyly linkage group (pin phenotype). Of the remaining traits associated with their solanoid flowers, we recognize at least six likely to have arisen with the origin of Dodecatheon, one that preceded it (flower coloration, a transfer exaptation in Dodecatheon), and one that followed it (rugose anther connectives, an adaptation to buzz pollination).     

Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast TRNT-TRNF region and nuclear rDNA

The species of the genus Populus, collectively known as poplars, are widely distributed over the northern hemisphere and well known for their ecological, economical, and evolutionary importance. The extensive interspecific hybridization and high morphological diversity in this group pose difficulties in identifying taxonomic units for comparative evolutionary studies and systematics. To understand the evolutionary relationships among poplars and to provide a framework for biosystematic classification, we reconstructed a phylogeny of the genus Populus based on nucleotide sequences of three noncoding regions of the chloroplast DNA (intron of trnL and intergenic regions of trnT-trnL and trnL-trnF) and ITS1 and ITS2 of the nuclear rDNA. The resulting phylogenetic trees showed polyphyletic relationships among species in the sections Tacamahaca and Aigeiros. Based on chloroplast DNA sequence data, P. nigra had a close affinity to species of section Populus, whereas nuclear DNA sequence data suggested a close relationship between P. nigra and species of the section Aigeiros, suggesting a possible hybrid origin for P. nigra. Similarly, the chloroplast DNA sequences of P. tristis and P. szechuanica were similar to that of the species of section Aigeiros, while the nuclear sequences revealed a close affinity to species of the section Tacamahaca, suggesting a hybrid origin for these two Asiatic balsam poplars. The incongruence between phylogenetic trees based on nuclear- and chloroplast-DNA sequence data suggests a reticulate evolution in the genus Populus.