Incongruence among mitochondrial,chloroplast and nuclear gene trees in <Emphasis Type="Italic">Pinus</Emphasis> subgenus <Emphasis Type="Italic">Strobus</Emphasis> (Pinaceae)

Introgression has been considered to be one of main factors leading to phylogenetic incongruence among different datasets at lower taxonomic levels. In the plants of Pinaceae, the mtDNA, cpDNA, and nuclear DNA (nrDNA) may have different evolutionary histories through introgression because they are inherited maternally, paternally and biparentally, respectively. We compared mtDNA, cpDNA, and two low-copy nrDNA phylogenetic trees in the genus Pinus subgenus Strobus, in order to detect unknown past introgression events in this group. nrDNA trees were mostly congruent with the cpDNA tree, and supported the recent sectional and subsectional classification system. In contrast, mtDNA trees split the members of sect. Quinquefoliae into two groups that were not observed in the other gene trees. The factors constituting incongruence may be divided into the following two categories: the different splits within subsect. Strobus, and the non-monophyly of subsect. Gerardianae. The former was hypothesized to have been caused by the past introgression of cpDNA, mtDNA or both between Eurasian and North American species through Beringia. The latter was likely caused by the chimeric structure of the mtDNA sequence of P. bungeana, which might have originated through past hybridization, or through a horizontal transfer event and subsequent recombination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A taxonomic reassessment of the Vittiaceae (Hypnales, Bryopsida): evidence from phylogenetic analyses of combined chloroplast and nuclear sequence data

The Vittiaceae are a small family of aquatic mosses that are defined based on gametophytic traits whose interpretation has led to conflicting taxonomic arrangements. Phylogenetic analyses of two cpDNA regions, trnL-trnF and atpB-rbcL, indicate that Vittia is nested within the Amblystegiaceae s. str., suggesting that the family Vittiaceae should not be recognized. Platylomella lescurii appears nested within the Thuidiaceae/Leskeaceae. This suggests that the series of character states shared by Vittia and Platylomella, including a differentiated leaf border, short laminal cells, stiff stems, and a thick costa, are convergent features that arose independently in unrelated lineages of aquatic Hypnales. Within the Amblystegiaceae, phylogenetic analyses of the two cpDNA regions combined with ITS sequence data show that Hypnobartlettia, Vittia elimbata spec. nov., V. pachyloma, and V. salina, despite their strong morphological similarity to aquatic Amblystegium species, form a clade that is sister to the Drepanocladus/Pseudo-calliergon complex. This combined clade is unresolved at a polytomy that includes Amblystegium serpens and a clade including all the other Amblystegium species. The occurrence of A. serpens outside the strongly supported clade including other Amblystegium species suggests that A. serpens may be better accommodated in a distinct genus. Amblystegium serpens is the type species of Amblystegium and thus retains the name. The other species are accommodated in their own genus, Hygroamblystegium, including H. fluviatile, H. humile comb. nov., H. noterophyllum, H. tenax, and H. varium.     

Biosystematic studies inTulipa sect.Eriostemones (Liliaceae)

Evolutionary relationships and infra- and interspecific variability within the species ofTulipa sect.Eriostemones Boissier were studied. Measurements of 35 morphological characters were used for principal component and canonical variate analyses. Crossing experiments and chromosome counts were carried out. Two axes of morphological variation were encountered within the principal component plot. Variation of subsect.Biflores was traced along one axis, the species of subsect.Australes as well asSaxatiles were found along the other axis. The nomenclature of names of subsect.Biflores was considered on the basis of their geography, specific morphological characteristics and polyploidy. Conspecificity of names of all species was tested based on both morphology and crossability.     

Karyotypic and chloroplast genomic diversity inMedicago sect.Lupularia (Leguminosae)

Studies were made on the chromosome complements and chloroplast genomes ofMedicago lupulina andM. secundiflora, which comprise sectionLupularia ofMedicago. Both types of analyses indicated more substantial differences between these species than suggested by external morphology.Medicago lupulina has a relatively asymmetrical karyotype in terms of centromeric position and relative length. The karyotype ofM. secundiflora is comparatively more asymmetrical in centromeric position and reduced in absolute size but exhibits greater symmetry in relative length. The restriction endonuclease fragmentation patterns of the chloropiast DNA of these two species (with Bam HI, Eco RI, Bgl II, and Xho I) show little similarity, with only 17% of the fragments matching in size. The lack of interspecific congruence among data of morphology, karyology and cpDNA inLupularia is contrary to consistency exhibited among these data inMedicago subsect.Intertextae.     

基于3种基因序列对百合属Leucolirion组的系统发育与种间关系研究

中国拥有丰富的野生百合种质资源,但有关百合属的系统发育与进化关系研究相对较少。该研究基于ITS、cpDNA(trnV-ndhC、petL-psbE)及单拷贝核基因AKT等3个基因片段,选取特有分布于西南地区的百合属6个近缘类群共48份样本及GenBank获得的数据,对百合属Leucolirion组进行了系统发育与种间关系研究。结果表明:(1)ITS结果支持前人的处理,即将Leucolirion组细分为2个亚组,subsect.Leucolirion6a和subsect.Leucolirion6b。建议将湖北百合(L.henryi)和南川百合(L.rosthornii)归入到subsect.Leucolirion 6a,与泸定百合(L.sargentiae)、淡黄花百合(L.sulphureum)、宜昌百合(L.leucanthum)和岷江百合(L.regale)等4个种一起组成Leucolirion组;原本属于Archelirion组的野百合(L.brownii)与subsect.Leucolirion6b聚为一支,故将它与台湾百合(L.longiflorm)、麝香百合(L.formosanum)等组成一个新组,命名为百合组(sect.Lilium)。(2)组间关系上,Leucolirion组与百合组的系统发育关系较远,前者与分布于日本的Archelirion组形成姐妹类群,而后者与Sinomartagon组的亲缘关系更近。(3)基于叶绿体联合基因和单拷贝核基因AKT的6个近缘种的遗传距离显示,湖北百合与南川百合明显区别于Leucolirion组内拥有白色管状花的4个类群。叶绿体联合基因树和单拷贝核基因树结果表明,泸定百合、淡黄花百合、岷江百合和宜昌百合在遗传水平上表现出了极高的相似性,遗传关系十分相近,这可能与百合属植物特殊的繁育系统有关,影响了物种间遗传变异与分化。     

Protecting evolutionary significant units for the remnant populations of <Emphasis Type="Italic">Berchemiella wilsonii</Emphasis> var. <Emphasis Type="Italic">pubipetiolata</Emphasis> (Rhamnaceae)

Berchemiella wilsonii var. pubipetiolata (Rhamnaceae) is an endangered tree in eastern China. Habitat destruction has resulted in fragmentation of remnant populations and extinction of local populations. AFLP and cpDNA markers were used to determine the population structure of remnant populations of B. wilsonii var. pubipetiolata. Moderate nuclear genomic diversity was found within each of the four remnant populations (H _S = 0.141–0.172), while the cpDNA haplotype diversity in each population ranged from 0.356 to 0.681. Six haplotypes were identified by a combined cpRFLP and cpSSR analysis in a total of 89 individuals. AMOVA revealed significantly AFLP genetic differentiation within and between regions (Φ_SC = 0.196, Φ_CT = 0.396, respectively), and a high cpDNA haplotype differentiation between regions (Φ_CT = 0.849). The results suggest low gene flow between populations of B. wilsonii var. pubipetiolata. Strong genetic divergence between two regional populations as revealed by both AFLP and cpDNA markers provided convincing evidence that two distinct evolutionary lineages existed, and should be recognized as ‘evolutionary significant units’ (ESUs) for conservation concerns.     

Molecular phylogeny ofIva (Asteraceae,Heliantheae) based on chloroplast DNA restriction site variation

Iva s.str. (comprising ten species) was examined by cpDNA restriction site variation to determine phyletic relationships within the group. The results were compared with relationships proposed from other data. A total of 86 restriction site mutations was detected, 47 of which proved phylogenetically informative. A single most parsimonious tree was obtained using both Wagner and Dollo parsimony. The tree revealed three main lineages that are congruent with the three chromosome lineages (base numbers of x = 16, 17, 18). The monophyly of the x = 16 and 18 groups was supported strongly by molecular data, while the monophyly of x = 17 lineage was only supported moderately. Relationships among the three lineages indicate that the sect.Iva is paraphyletic because sect.Linearbractea is nested within it. Both morphological data and the secondary chemical data are in agreement with the proposed cpDNA phylogeny. Because of this agreement, sect.Iva is revised such that,I. axillaris was excluded and positioned within the newly proposed sect.Rhizoma. Patterns and rates of cpDNA evolution were also examined. The results indicated an uneven evolution in the chloroplast genome with different rates of cpDNA evolution in at least a few species ofIva. However, the evolutionary clock hypothesis can not be rejected within most of the lineages inIva.     

Phylogenetic analysis of Fosterella L.B. Sm. (Pitcairnioideae, Bromeliaceae) based on four chloroplast DNA regions

The about 31 species of Fosterella L.B. Sm. (Bromeliaceae) are terrestrial herbs with a centre of diversity in the central South American Andes. To resolve infra- and intergeneric relationships among Fosterella and their putative allies, we conducted a phylogenetic analysis based on sequence data from four chloroplast DNA regions (matK gene, rps16 intron, atpB-rbcL and psbB-psbH intergenic spacers). Sequences were generated for 96 accessions corresponding to 60 species from 18 genera. Among these, 57 accessions represented 22 of the 31 recognized Fosterella species and one undescribed morphospecies. Maximum parsimony and Bayesian inference methods yielded well-resolved phylogenies. The monophyly of Fosterella was strongly supported, as was its sister relationship with a clade comprising Deuterocohnia, Dyckia and Encholirium. Six distinct evolutionary lineages were distinguished within Fosterella. Character mapping indicated that parallel evolution of identical character states is common in the genus. Relationships between species and lineages are discussed in the context of morphological, ecological and biogeographical data as well as the results of a previous amplified fragment length polymorphism (AFLP) study.     

Geographic structuring of chloroplast DNA genotypes inTiarella trifoliata (Saxifragaceae)

Tiarella trifoliata comprises varietieslaciniata, trifoliata, andunifoliata, and is distributed from southeastern Alaska to northern California. We analyzed restriction site variation of chloroplast DNA (cpDNA) using 23 endonucleases in 76 populations representing the entire geographic range of the species and the three recognized varieties. We also employed comparative restriction site mapping of PCR-amplified chloroplast DNA fragments using 16 restriction endonucleases. This species exhibits low cpDNA restriction site variation. No differentiation is evident among varieties of this species based on cpDNA data; some plants of each variety were characterized by each of the two major cpDNA types detected. The two major cpDNA clades, which differ by only a single restriction site mutation, are geographically structured. A northern clade comprises populations from Alaska to central Oregon; most populations analyzed from southern Oregon and California form a southern clade. Populations that possess the typical northern cpDNA type also occur disjunctly to the south at high elevations in the Siskiyou—Klamath Mountain area of southern Oregon and northern California. Conversely, the southern cpDNA type is found disjunctly to the north in the Olympic Peninsula of Washington. Both geographic areas characterized by disjunct cytoplasms are considered glacial refugia.Tiarella trifoliata joins two other species,Tolmiea menziesii andTellima grandiflora, in having well-demarcated northern and southern cpDNA lineages. All three species have similar life-history traits and geographic distributions. We suggest that glaciation may have played a major role in the formation of the cpDNA discontinuities present in these three taxa. The pronounced relationship between cpDNA variation and geographic distribution suggests the potential applicability of intraspecific phylogeography to plants via the analysis of intraspecific cpDNA variation. These three examples also join a rapidly growing data base which indicates that cytoplasms are often geographically structured within species and species complexes.     

Phylogenetic relationships of the monotypic Peruvian genus Laccopetalum (Ranunculaceae)

Laccopetalum giganteum (Ranunculaceae) is a rare endemic buttercup from the montane regions of the Peruvian Andes. The systematic position of this monotypic genus within Ranunculaceae was investigated using cpDNA matK sequence data. Our findings indicate that L. giganteum forms a highly supported clade together with Krapfia. Several morphological characters are shared by these genera; large subglobose and fleshy flowers, presence of androgynophore with a separated staminal and carpellate region and many tiny achenes. The Laccopetalum-Krapfia clade is sister to the core Ranunculus group with a high bootstrap support. The number of sepals and similar characteristics of achene morphology support an affinity of Laccopetalum with Ranunculus s.s tr.     

Chloroplast DNA variation inCoreopsis nuecensoides andC. nuecensis (Asteraceae), a presumed progenitor-derivative species pair

Coreopsis nuecensoides andC. nuecensis are narrowly distributed endemics of southeastern Texas. While they overlap in range, they differ in chromosome number, and F₁ hybrids exhibit strong sterility barriers. Previous morphological, cytogenetic, and allozyme studies suggested thatC. nuecensoides andC. nuecensis are very closely related members of a progenitor-derivative species pair. The two species differ substantially in terms of their leaf flavonoid chemistry, but the flavonoid data do not address the exact nature of the relationship between them. We have further examined the relationship between the species by analyzing genetic diversity within both species using chloroplast DNA (cpDNA) restriction site data. Sixteen restriction site changes were used to define thirteen distinct cpDNA haplotypes. The pattern of relationships among haplotypes provides some support for the presumed ancestor-descendent relationship, but other interpretations are possible. Only one cpDNA haplotype was shared by the two species; of the remaining twelve, seven were unique to one species and five to the other. This result is consistent with results of flavonoid studies, in which each species exhibited flavonoid compounds not seen in the other, but differs from the allozyme results, in which the vast majority of alleles were shared by both species and only the presumed progenitor exhibited unique alleles. Taken together, the data support a very close relationship between the species, but are equivocal with regard to a progenitor-derivative relationship.     

Analysis of the fruit surfaces in Bupleurum L. (Umbelliferae) with SEM

20 Bupleurum L. taxa were investigated for micromorphological typology of the fruit surfaces with SEM. Considerably different types of sculpturing at species and subspecies level and similarities between related taxa were observed. A dichotomic key was prepared using the diagnostic surface patterns. Reticulate (sect. Bupleurum), rugose (sect. Aristata Godron subsect. Aristata) and rugulose-colliculate-verrucate (subsect. Juncea Briq.) types of surface structures were distinguished. Micromorphological characteristics may be valuable additional taxonomical criteria for the delimitation of infrageneric groups of species.     

Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences

Dunnia sinensis, a monotypic genus of theRubiaceae endemic to the southeast mainlandChina, is an endangered species due to habitatdestruction over the past decades. Informationon levels and apportionment of geneticvariation across populations and geographicalregions is fundamental to conservation. In thepresent study, we used organelle DNA variationand nested phylogeographic analyses to test theisolation-by-distance model in this specieswith wind-mediated seed-dispersal and todistinguish ongoing gene flow from historicalprocesses. As expected, low levels of geneticvariation were detected at the ribosomal ITSregion of mtDNA ( = 0.0019± 0.0002) and the atpB-rbcLintergenic spacer of cpDNA ( =0.0022 ± 0.0009) in the rare species. Sixand seven haplotypes of mt- and cpDNA wereidentified from 125 individuals, respectively,according to the reconstructed neighbor-joiningtrees. Both data sets suggested consistentphylogenies that recovered two differentiatedlineages corresponding to western (Yangchun)and eastern (four others populations) portionsof the range. Hierarchical analyses of themolecular variance (AMOVA) of mt- and cpDNAindicated that molecular variance wasattributable to the difference between regions(ct = 0.911 and 0.771 for mt- and cpDNA,respectively) in D. sinensis. Based ongeographic distributions of haplotypes in thehaplotype networks, significant geneticdifferentiation between the two geographicregions, which can be seen as evolutionarilyconservation units, was associated withhistorical fragmentation. In contrast, limitedgene flow with occasional long-range dispersalshaped the apportionment of organelle DNAalleles among populations of the easternregion, within which two incompletely isolatedphylogeographic groups can be recognized asconservation units for management.     

Classifying seedlots of Picea sitchensis and P. glauca in zones of introgression using restriction analysis of chloroplast DNA

Summary Chloroplast DNA (cpDNA) restriction analysis was used to classify five reforestation seedlots as to species. The material included two Sitka spruce (Picea sitchensis (Bong.) Carr.), one white spruce (P. glauca (Moench) Voss) from interior British Columbia, and two putative hybrid seedlots from the coast-interior introgression zone in British Columbia. The cpDNA patterns generated by Bam-HI and Bc1-I from individual trees of Sitka spruce, white spruce, western white spruce (P. glauca var. albertiana (S. Brown)), and Engelmann spruce (P. engelmanni (Parry)) were species-specific. They were used as reference patterns for comparisons. In addition, two controlled crosses between white and Sitka spruce were analyzed to demonstrate the paternal inheritance of cpDNA in spruces. The cpDNA restriction patterns for the five seedlots were obtained from composite samples of seedlings from each lot and compared to the typical cpDNA patterns of each species. Restriction patterns for the two Sitka spruce seedlots agreed with those from the Sitka spruce tree, while patterns for the white spruce seedlots from British Columbia agreed with those from the white spruce tree, lacking evidence of any Engelmann spruce component in the sample. On the other hand, one putative hybrid seedlot showed cpDNA patterns similar to white spruce while the other showed fragments unique to both Sitka and white spruce, indicating that this was a hybrid seedlot. The analysis of cpDNA restriction polymorphism has proven to be an effective tool for classifying seedlots in regions of introgression. To our knowledge, these results provide the first demonstration of the use of cpDNA analysis for solving practical forestry problems.     

RAPD characterisation of two neotropical hybrid legumes

An investigation of randomly amplified polymorphic DNA (RAPD) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) marker distribution was made for two well-characterised hybrids and their parents,Leucaena leucocephala andL. esculenta andParkinsonia aculeata andCercidium praecox. Three chloroplast DNA (cpDNA) markers identified the maternal parent of eachL. leucocephala ×L. esculenta hybrid. Fifteen species-diagnostic RAPD markers (invariant in one taxon and absent from the other) were always present in theLeucaena hybrid and assumed to be of nuclear origin, whilst three RAPD markers showed expression patterns identical to the cpDNA markers and were assumed to be of organellar origin. No RAPD or PCR-RFLP taxon-diagnostic markers were discovered for eitherP. aculeata orC. praecox. However, 21 RAPD markers were species-specific (polymorphic within one taxon but absent from the other) and Southern analysis indicated that none of the markers were of organellar origin. Only 67% additivity of markers specific toP. aculeata andC. praecox was demonstrated in the hybrids between these two species, whilst inLeucaena 97% additivity was demonstrated. Differences between the two hybridising situations were related to the behaviour of the molecular markers and the biology of the species.     

Paternal plastid DNA can be inherited in lentil

Restriction fragment analysis was used to study the inheritance of chloroplast DNA (cpDNA) in F₁ progeny from crosses between Lens culinaris ssp. orientalis and L. culinaris ssp. culinaris. Twenty-five combinations of 11 restriction enzymes and three heterologous probes from Petunia hybrida cpDNA were used to screen six accessions of L.c. culinaris and one accession of L. c. orientalis for restriction fragment length polymorphisms (RFLPs). No variation in cpDNA was observed within the subspecies L. c. culinaris, but the L. c. orientalis accession was unambiguously distinguished from all six L. c. culinaris accessions by two RFLPs. Of ten F₁ progeny from L. c. orientalis x L. c. culinaris crosses, nine had only maternal cpDNA restriction fragments but one F₁ plant inherited cpDNA fragments from both parents. Nuclear DNA inheritance was biparental in all ten F₁ progeny.     

10种杜鹃亚属植物种间杂交的可育性研究

为探索杜鹃花亚属内异种杂交的可育性及其规律,对杜鹃亚属有鳞大花亚组(subsect. Maddenia)、三花杜鹃亚组(subsect. Triflora)、亮鳞杜鹃亚组(subsect. Heliolepida)及腋花杜鹃亚组(subsect. Scabrifolia)等4亚组10个杜鹃花种类的22个杂交组合(其中18个数据完整组合)的可育性进行了研究。结果表明:(1)所涉及的杜鹃亚属不同亚组间及三花杜鹃亚组内杂交均较困难,在18个数据完整组合中高可育与可育组合比率明显偏低,不育比率高(55.6%)。(2)在10个不可育或败育组合中,不能坐果(Cab型)、不能结实(Sab型)和可结实而种子不能发芽(Sng型)的数量分布为6∶1∶3,其不亲和或败育发生的阶段可能涵盖了从前合子期到后合子期的整个阶段。(3)亲本一方为多倍体组合的可育率(41.6%),尤其是母本为多倍体时,比二倍体组合的可育率(50.0%)低且无高可育组合出现,部分印证了倍性是导致该亚属植物不同种类杂交不亲和、不育与育性下降的重要原因,但不是唯一原因,亚组间杂交的可育率(16.7%)明显低于亚组内(三花杜鹃亚组内,58.3%)。(4)与相应的母本自然授粉结果相比,杂交明显导致多数可育组合绿苗率比率和单位可育种子数量比率的大幅度下降,这是双亲遗传差异及多倍体亲本介入后所导致的杂交衰退hybrid weakness现象。(5)在多倍体作母本的情况下,杂交单向不育或非对称遗传渗透现象明显。     

The chloroplast genome arrangement ofLobelia thuliniana (Lobeliaceae): Expansion of the inverted repeat in an ancestor of theCampanulales

A clone-bank ofSac I restriction fragments was constructed from the chloroplast DNA (cpDNA) ofLobelia thuliniana E. B. Knox (Lobeliaceae). These cloned fragments and a set of 106 clones spanning the tobacco chloroplast genome were used as probes to determine the cpDNA restriction fragment arrangement forSac I and six other restriction enzymes (BamH I,EcoR V,Hind III,Nci I,Pst I, andXho I) and the chloroplast genome arrangement ofL. thuliniana relative to tobacco, which has been fully sequenced and is collinear with the hypothesized ancestral genome arrangement of angiosperms. The results confirm and refine our previous understanding of the chloroplast genome arrangement in the large single-copy region (LSC) and reveal (1) a roughly 11 kilobase (kb) expansion of the inverted repeat (IR) into the small single-copy region (SSC) and (2) apparent sequence divergence of the DNA segment inL. thuliniana that corresponds to ORF1901 in tobacco. The expansion of the IR into the SSC is present in all other examined members ofLobeliaceae, Cyphiaceae, andCampanulaceae, which indicates that the IR expansion was an early event in the cpDNA evolution of theCampanulales. The IR expansion into the SSC was not present inSphenoclea, which additionally supports exclusion of this genus from theCampanulaceae.     

Molecular phylogeny and biogeography of the bipolar Euphrasia (Orobanchaceae): recent radiations in an old genus

Euphrasia includes perennial or annual green parasitic plants, and has a disjunct bipolar distribution except for one transtropical connection across the high mountains of Oceania. The disjunction is coupled with strikingly contrasting patterns of morphological diversity between the southern and northern hemispheres, making it an exciting model to study processes of evolutionary diversification which shaped present floras. We inferred the relationships among 51 species representing 14 of the 15 sections of the genus based on nrDNA ITS and cpDNA trnL intron, trnL-trnF and atpB-rbcL intergenic spacers. Maximum parsimony and Bayesian inference support monophyly of the genus and of several intrageneric groups characterized by morphology, ploidy level, and geographic range. Molecular phylogenetic dating using Bayesian “relaxed” clock methods suggests that the earliest Euphrasia radiations occurred minimum 11–8 Mya with bipolarity being achieved 7–5 Mya. Biogeographic analyses using explicit model-based approach inferred Eurasia as an ancestral area for the genus. The most parsimonious reconstruction found by a dispersal-vicariance analysis requires 17 dispersals to account for the current biogeographic pattern and supports Eurasian origin for Euphrasia. Both long-distance dispersal and across land vicariance can be invoked to explain the diversification in the genus, which experienced rapid radiations driven by new ecological opportunities of the late Pliocene and Pleistocene but also retained a set of local endemic or relict species of an earlier origin.