Molecular Phylogeny of Asian Meconopsis Based on Nuclear Ribosomal and Chloroplast DNA Sequence Data

The taxonomy and phylogeny of Asian Meconopsis (Himalayan blue poppy) remain largely unresolved. We used the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and the chloroplast DNA (cpDNA) trnL-F region for phylogenetic reconstruction of Meconopsis and its close relatives Papaver, Roemeria, and Stylomecon. We identified five main clades, which were well-supported in the gene trees reconstructed with the nrDNA ITS and cpDNA trnL-F sequences. We found that 41 species of Asian Meconopsis did not constitute a monophyletic clade, but formed two solid clades (I and V) separated in the phylogenetic tree by three clades (II, III and IV) of Papaver and its allies. Clade V includes only four Asian Meconopsis species, with the remaining 90 percent of Asian species included in clade I. In this core Asian Meconopsis clade, five subclades (Ia–Ie) were recognized in the nrDNA ITS tree. Three species (Meconopsis discigera, M. pinnatifolia, and M. torquata) of subgenus Discogyne were imbedded in subclade Ia, indicating that the present definition of subgenera in Meconopsis should be rejected. These subclades are inconsistent with any series or sections of the present classifications, suggesting that classifications of the genus should be completely revised. Finally, proposals for further revision of the genus Meconopsis were put forward based on molecular, morphological, and biogeographical evidences.     

Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae)

The genus Lespedeza (Fabaceae) consists of 40 species disjunctively distributed in East Asia and eastern North America. Phylogenetic relationships of all Lespedeza species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses of sequence data from five chloroplast (rpl16, rpl32-trnL, rps16-trnQ, trnL-F, and trnK/matK) and one nuclear (ITS) DNA regions. All analyses yielded consistent relationships among major lineages. Our results suggested that Campylotropis, Kummerowia, and Lespedeza are monophyletic, respectively. Lespedeza is resolved as sister to Kummerowia and these two together are further sister to Campylotropis. Neither of the two subgenera, subgen. Lespedeza and subgen. Macrolespedeza, in Lespedeza based on morphological characters, is recovered as monophyletic. Within Lespedeza, the North American clade is retrieved as sister to the Asian clade. The nuclear and chloroplast markers showed incongruent phylogenetic signals at shallow-level phylogeny, which may point to either introgression or incomplete lineage sorting in Lespedeza. The divergence times within Lespedeza and among related genera were estimated using Bayesian approach with BEAST. It is assumed that following the divergence between Kummerowia and Lespedeza in Asia in the late Miocene, the ancestor of Lespedeza diverged into the North American and the Asian lineages. The North American ancestor quickly migrated to North America through the Bering land bridge in the late Miocene. The North American and Asian lineages started to diversify almost simultaneously in the late Miocene but resulted in biased numbers of species in two continents.     

Phylogenetic split of Larix: evidence from paternally inherited cpDNA trnT-trnF region

A molecular phylogeny of Larix comprising 12 species was constructed from the sequence analysis of the paternally inherited cpDNA trnT-trnF region of 46 individuals. The most parsimonious tree split Larix into three sister clades: one clade was composed of two North American species, the other two were short-bracted and long-bracted species of Eurasia respectively except that L. sibirica was clustered in the long-bracted clade. The difference between the present cpDNA phylogeny and previous nrDNA ITS phylogeny in the position of L. sibirica seems to suggest that ancient cytoplasmic gene flow might exist between sections Larix and Multiserialis. The short-bracted L. laricina and long-bracted L. occidentalis have an identical sequence of the trnT-trnF region, which implies that the bract length divergence among North American larches might have occurred recently or chloroplast capture happened during the early differentiation of the two species. The cpDNA results also shed some light on the biogeography of Larix.     

THE PHYLOGENY OF CAULERPA BASED ON RDNA INTERNAL TRANSCRIBED SPACER SEQUENCES

Phylogenetic hypotheses for the pantropical marine green algal genus, Caulerpa , were inferred based on analyses of nuclear-encoded rDNA internal transcribed spacer (ITS) sequences. Results of these analyses were used to assess the correspondence between rDNA phylogeny and traditional sectional taxonomy, to identify synapomorphic morphological characters (including assimilator morphology and chloroplast ultrastructure), and to examine marine biogeographic hypotheses for the genus. Ribosomal DNA ITS sequences were aligned for thirty-three species and intraspecific taxa of Caulerpa. Results indicate limited correspondence between phylogeny and sectional taxonomy for the genus, (e.g., the sections Filicoideae and Sedoideae were not monophyletic). In contrast, chloroplast morphology could be mapped to the tree topology with limited homoplasy. Pantropical isolates of the filicoidean species, Caulerpa sertularioides and Caulerpa mexicana each formed monophyletic groups. Caulerpa reyesii was included as a derived taxon within the Caulerpa taxifolia clade, suggesting that these species were conspecific and affirmed the lack of correspondence between phylogeny and assimilator morphology. Isolates and various intraspecific taxa of Caulerpa racemosa did not form a monophyletic group. Instead, these taxa formed a heterogeneous assemblage with other sedoidean and filicoidean taxa. Within the C. sertularioides clade, Caribbean and Atlantic isolates formed a basal paraphyletic group, whereas eastern and western Pacific isolates formed a more derived monophyletic group. Therefore, these results are not consistent with an Indo-West Pacific origin of this species.     

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.     

鳇亚科似鳇属鱼类的物种界定和系统发育关系

逗亚科似逗属鱼类的物种界定保持争议, 系统发育关系尚待解决。研究取样似逗属鱼类所有种, 使用核基因多位点序列重建似逗属鱼类的系统发育关系, 运用分子的物种界定方法并结合形态特征分析厘定我国似逗属鱼类的分类。贝叶斯系统发育树结果表明: 桂林似逗与平江似逗是单系种; 似逗与扁嘴似逗是多系种, 前者包括五个谱系A至E, 后者包括两个谱系A与B。POFAD距离分析和Structurama分析的结果表明似逗和扁嘴似逗的每个谱系是独立遗传种群, BP & P分析结果强烈支持它们是不同种。*Beast物种树结果揭示: 扁嘴似逗谱系B位于似逗属鱼类的基部位置; 似逗谱系A与B是姊妹群关系, 似逗谱系C是扁嘴似逗谱系A的姊妹群, 它们一起与桂林似逗形成姊妹群关系; 似逗谱系D与E是姊妹群关系, 它们一起是平江似逗的姊妹群。结合形态证据, 对我国似逗属鱼类分类厘定如下: 限定严格意义似逗包括似逗谱系A+B; 恢复长吻似逗(Pseudogobio longirostris Mori, 1934)给予似逗谱系C分类名; 似逗谱系D与E是隐存种, 桂林似逗与平江似逗是有效种。     

Phylogeny of Carpinus and subfamily Coryloideae (Betulaceae) based on chloroplast and nuclear ribosomal sequence data

Phylogenetic studies were conducted for Carpinus and the subfamily Coryloideae (Betulaceae) using sequences of the chloroplast matK gene, the trnL-trnF region (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer) and the psbA-trnH intergenic spacer, and the nuclear ribosomal ITS regions. The combined analyses of the three chloroplast regions suggest that Coryloideae is monophyletic; Ostryopsis is sister to the Carpinus - Ostrya clade; Corylus is monophyletic and sister to the Ostrya - Carpinus - Ostryopsis clade; Ostrya is paraphyletic; and within Carpinus, species of sect. Carpinus from eastern Asia form a monophyletic group, whereas the positions of C. betulus from Europe and C. caroliniana from eastern North America are unresolved within the Carpinus clade. The cpDNA tree generated in this study is largely congruent with the previously published ITS results, but the ITS tree places Carpinus sect. Distegocarpus as sister to the Ostrya - Carpinus sect. Carpinus clade. Future work is needed to examine the relationships within the Ostrya - Carpinus clade, evaluate the generic status of Ostrya, and test the phylogenetic position of Ostryopsis.     

Phylogenetic reticulation in subtribe Helianthinae

Incongruence between phylogenetic estimates based on nuclear and chloroplast DNA (cpDNA) markers was used to infer that there have been at least two instances of chloroplast transfer, presumably through wide hybridization, in subtribe Helianthinae. One instance involved Simsia dombeyana, which exhibited a cpDNA restriction site phenotype that was markedly divergent from all of the other species of the genus that were surveyed but that matched the restriction site pattern previously reported for South American species of Viguiera. In contrast, analysis of sequence data from the nuclear ribosomal DNA internal transcribed spacer (ITS) region showed Simsia to be entirely monophyletic and placed samples of S. dombeyana as the sister group to the relatively derived S. foetida, a result concordant with morphological information. A sample of a South American species of Viguiera was placed by ITS sequence data as the sister group to a member of V. subg. Amphilepis, which was consistent with cpDNA restriction site data. Samples of Tithonia formed a single monophyletic clade based on ITS sequence data, whereas they were split between two divergent clades based on cpDNA restriction site analysis. The results suggested that cpDNA transfer has occurred between taxa diverged to the level of morphologically distinct genera, and highlight the need for careful and complete assessment of molecular data as a source of phylogenetic information.     

Phylogeny and infrageneric classification of Symplocos (Symplocaceae) inferred from DNA sequence data

Symplocos comprises ～300 species of woody flowering plants with a disjunct distribution between the warm-temperate to tropical regions of eastern Asia and the Americas. Phylogenetic analyses of 111 species of Symplocos based on the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast genes rpl16, matK, and trnL-trnF yielded topologies in which only one of the four traditionally recognized subgenera (Epigenia; Neotropics) is monophyletic. Section Cordyloblaste (subgenus Symplocos; eastern Asia) is monophyletic and sister to a group comprising all other samples of Symplocos. Section Palura (subgenus Hopea; eastern Asia) is sister to a group comprising all other samples of Symplocos except those of section Cordyloblaste. Symplocos wikstroemiifolia (eastern Asia) and S. tinctoria (southeastern United States), both of subgenus Hopea, form a clade that groups with S. longipes (tropical North America) and the species of subgenus Epigenia. The remaining samples of subgenus Hopea (eastern Asia) form a clade. Section Neosymplocos (subgenus Microsymplocos; Neotropics) is well nested within a clade otherwise comprising the samples of section Symplocastrum (subgenus Symplocos; Neotropics). Section Urbaniocharis (subgenus Microsymplocos; Antilles) groups as sister to the clade comprising Symplocastrum and Neosymplocos. The data support the independent evolution of deciduousness among section Palura and S. tinctoria. The early initial divergence of sections Cordyloblaste and Palura from the main group warrants their recognition at taxonomic levels higher than those at which they are currently placed. An inferred eastern Asian origin for Symplocos with subsequent dispersal to the Americas is consistent with patterns from other phylogenetic studies of eastern Asian-American disjunct plant groups but contrary to a North American origin inferred from the earliest fossil occurrences of the genus.     

Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America

The genus Castanea (Fagaceae) is widely distributed in the deciduous forests of the Northern Hemisphere. The striking similarity between the floras of eastern Asia and those of eastern North America and the difference in chestnut blight resistance among species has been of interest to botanists for a century. To infer the biogeographical history of the genus, the phylogeny of Castanea was estimated using DNA sequence data from different regions of the chloroplast genome. Sequencing results support the genus Castanea as a monophyletic group with Castanea crenata as basal. The three Chinese species form a strongly supported sister clade to the North American and European clade. A unique westward expansion of extant Castanea species is hypothesized with Castanea originating in eastern Asia, an initial diversification within Asia during the Eocene followed by intercontinental dispersion and divergence between the Chinese and the European/North American species during the middle Eocene and a split between the European and the North American species in the late Eocene. The differentiation within North America and China might have occurred in early or late Miocene. The North America species are supported as a clade with C. pumila var. ozarkensis, the Ozark chinkapin, as the basal lineage, sister to the group comprising C. pumila var. pumila, the Allegheny chinkapin, and Castanea dentata, the American chestnut. Morphological evolution of one nut per bur in the genus may have occurred independently on two continents.     

Phylogenetic analysis of the grape family (Vitaceae) based on three chloroplast markers

Seventy-nine species representing 12 genera of Vitaceae were sequenced for the trnL-F spacer, 37 of which were subsequently sequenced for the atpB-rbcL spacer and the rps16 intron. Phylogenetic analysis of the combined data provided a fairly robust phylogeny for Vitaceae. Cayratia, Tetrastigma, and Cyphostemma form a clade. Cyphostemma and Tetrastigma are each monophyletic, and Cayratia may be paraphyletic. Ampelopsis is paraphyletic with the African Rhoicissus and the South American Cissus striata nested within it. The pinnately leaved Ampelopsis form a subclade, and the simple and palmately leaved Ameplopsis constitutes another with both subclades containing Asian and American species. Species of Cissus from Asia and Central America are monophyletic, but the South American C. striata does not group with other Cissus species. The Asian endemic Nothocissus and Pterisanthes form a clade with Asian Ampelocissus, and A. javalensis from Central America is sister to this clade. Vitis is monophyletic and forms a larger clade with Ampelocissus, Pterisanthes, and Nothocissus. The eastern Asian and North American disjunct Parthenocissus forms a clade with Yua austro-orientalis, a species of a small newly recognized genus from China to eastern Himalaya. Vitaceae show complex multiple intercontinental relationships within the northern hemisphere and between northern and southern hemispheres.     

Phylogenetic relationships of the Rhizophoraceae in China based on sequences of the chloroplast gene matK and the internal transcribed spacer regions of nuclear ribosomal DNA and combined data set

The chloroplast gene matK and the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced from 17 samples of 13 species representing 6 genera of the angiosperm family Rhizophoraceae from China. Phylogenetic analyses were initially conducted based on sequences of the matK gene and the ITS regions, respectively, using Byrsonima crassifolia and Bunchosia armeniaca (Malpighiaceae) as outgroups. The partition–homogeneity test indicated that the two data sets are homogeneous. A combined analysis of the matK and ITS data generated a well supported phylogeny, which is topologically congruent with the two gene trees based on the Templeton test. The combined phylogeny shows that each genus formed a monophyletic group and the monophyletic relationships of the mangrove genera and of the inland genera were strongly supported.     

Die Cypriniden (Teleostei: Cypriniformes) des oberoligozänen Maares von Enspel nebst Bemerkungen zur Phylogenie und Biogeographie der Phoxininae

Palaeorutilus enspelensis (Böhme 1996), the only fish species from the Upper Oligocene maar lake Enspel (Westerwald), is described and its phylogenetical position within the subfamily Phoxininae is discussed. The cladistic analysis of osteological and lepidological features indicates that the genusPalaeorutilus Gaudant 1988 is a member of the Chub Clade. Furthermore, including of the recent Eurasian taxaLagowskiella andEupallasella in the analysis, the Chub Clade can be divided into two monophyletic Clades: the EurasianPhoxinus Clade (including the holarcticPhoxinus) and the eastern North American Creek Chub Clade which includes the fossil genusPalaeorutilus as its basal sister taxon. These phylogenetical investigation as well as the recent and fossil distribution pattern of the Phoxininae support the following biogeographical hypothesis: The settlement of cyprinids in North America took place in several waves and different directions. The separation of Western Clade and Chub Clade did not occur in North America but in Eocene times in Asia. Members of the Creek Chub Clade migrated from Europe to eastern North America via a transatlantic route prior to the Middle Miocene.     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了15种杜鹃属(Rhododendron)植物、1种杜香属(Ledum)植物和Cassiope fastigiata的内转录间隔区(ITS) (包括5.8S)序列.加上从GenBank下载的13种杜鹃属植物和Bajiaria racemosa的ITS序列,以C. fastigiata和B. racemosa为外类群,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析.结果表明: 1)杜鹃属是一个单系类群,叶状苞亚属为杜鹃属的基部类群; 2)杜香属确应归并到杜鹃属中,且与有鳞杜鹃亚属有较近的亲缘关系; 3)有鳞杜鹃亚属和杜香构成一个单系分支,该分支是其余无鳞杜鹃花的姐妹群; 4)由无鳞杜鹃花组成的一个分支的内部支持率较低,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群,而羊踯躅亚属和马银花亚属均为多系类群; 5)在马银花亚属中,长蕊杜鹃组和马银花组均分别得到强烈支持,马银花组与异蕊杜鹃亚属可能构成姐妹群关系,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系.     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了 15种杜鹃属 (Rhododendron)植物、1种杜香属 (Ledum)植物和Cassiopefastigiata的内转录间隔区(ITS) (包括 5 .8S)序列。加上从GenBank下载的 13种杜鹃属植物和Bajiariaracemosa的ITS序列 ,以C .fastigiata和B .racemosa为外类群 ,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析。结果表明 :1)杜鹃属是一个单系类群 ,叶状苞亚属为杜鹃属的基部类群 ;2 )杜香属确应归并到杜鹃属中 ,且与有鳞杜鹃亚属有较近的亲缘关系 ;3)有鳞杜鹃亚属和杜香构成一个单系分支 ,该分支是其余无鳞杜鹃花的姐妹群 ;4 )由无鳞杜鹃花组成的一个分支的内部支持率较低 ,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群 ,而羊踯躅亚属和马银花亚属均为多系类群 ;5 )在马银花亚属中 ,长蕊杜鹃组和马银花组均分别得到强烈支持 ,马银花组与异蕊杜鹃亚属可能构成姐妹群关系 ,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系。     

A phylogeny of Lophocoleaceae-Plagiochilaceae-Brevianthaceae and a revised classification of Plagiochilaceae

The Lophocoleaceae-Plagiochilaceae-Brevianthaceae clade is a largely terrestrial, subcosmopolitan lineage of jungermannialean leafy liverworts that may include significantly more than 1000 species. Here we present the most comprehensively sampled phylogeny available to date based on the nuclear ribosomal internal transcribed spacer region and the chloroplast markers rbcL and rps4 of 372 accessions. Brevianthaceae (consisting of Brevianthus and Tetracymbaliella) form a sister relationship with Lophocoleaceae; this lineage is in turn sister to Plagiochilaceae. Plagiochila is resolved monophyletic subsequent to exclusion of Plagiochila radiculosa; this species is placed in a new genus Cryptoplagiochila. Chiastocaulon and a polyphyletic Acrochila nest in Plagiochilion; these three genera are united under Chiastocaulon to include the Plagiochilaceae species with dominating or exclusively ventral branching. The generic classification of the Lophocoleaceae is still unresolved. We discuss alternative approaches to obtain strictly monophyletic genera by visualizing their consistence with the obtained consensus topology. The presented phylogeny will serve as a basis for follow-up studies including several thousand accessions. These studies will enable revision of current hypotheses on species diversity and distribution of Lophocoleaceae-Plagiochilaceae-Brevianthaceae and allow for a reconstruction of their evolution in time and space.     

Exploring generic delimitation within the fern family Thelypteridaceae

Thelypteridaceae is one of the largest families of polypodioid ferns. The generic classification of the family is still controversial because of high levels of convergent or parallel evolution of morphological characters and a lack of molecular phylogenetic studies. In the present study, phylogenetic analyses of three chloroplast regions (rbcL, rps4 and trnL-trnF intergenic spacer region) for 115 taxa, representing 27 recognized segregates in the family, were conducted to explore infrafamilial relationships and gain further understanding of generic boundaries. The phylogenetic reconstructions resolved six distinct clades (Clade I-VI) with strong support. Seven genera: Cyclogramma, Macrothelypteris, Oreopteris, Phegopteris, Pseudophegopteris, Stegnogramma, and Thelypteris are recognized from Clades I, II, IV, and V. In Clade III, Metathelypteris was supported as monophyletic, but the other segregates Amauropelta, Coryphopteris, and Parathelypteris were polyphyletic or paraphyletic, preventing clear recognition of generic boundaries within this clade without additional sampling. Considering great morphological homoplasy within Clade VI, a large genus Cyclosorus is recognized to comprise several small recognized segregates. Within this clade, Pronephrium, and Christella were revealed to be polyphyletic, but several Asian-endemic segregates, such as Glaphyropteridopsis, Mesopteris, and Pseudocyclosorus were strongly supported as monophyletic. Analyses of the evolution of morphological character states on the molecular phylogeny showed extremely high levels of homoplastic evolution for many diagnostic characters.     

Phylogenetic relationships and evolution in Chrysosplenium (Saxifragaceae) based on matK sequence data

Chrysosplenium (Saxifragaceae) consists of 57 species widely distributed in temperate and arctic regions of the Northern Hemisphere, with two species restricted to the southern part of South America. Species relationships within the genus are highly problematic. The genus has traditionally been divided into two groups, sometimes recognized as sections (Oppositifolia and Alternifolia), based on leaf arrangement, or, alternatively, into 17 series. Based on morphological features, Hara suggested that the genus originated in South America and then subsequently migrated to the Northern Hemisphere. We conducted phylogenetic analyses of DNA sequences of the chloroplast gene matK for species of Chrysosplenium to elucidate relationships, test Hara's biogeographic hypothesis for the genus, and examine chromosomal and gynoecial diversification. These analyses revealed that both sections Oppositifolia and Alternifolia are monophyletic and form two large sister clades. Hence, leaf arrangement is a good indicator of relationships within this genus. Hara's series Pilosa and Macrostemon are each also monophyletic; however, series Oppositifolia, Alternifolia, and Nepalensia are clearly not monophyletic. MacClade reconstructions suggest that the genus arose in Eastern Asia, rather than in South America, with several independent migration events from Asia to the New World. In one well-defined subclade, species from eastern and western North America form a discrete clade, with Old World species as their sister group, suggesting that the eastern and western North American taxa diverged following migration to that continent. The South American species forms a clade with species from eastern Asia; this disjunction may be the result of ancient long-distance dispersal. Character mapping demonstrated that gynoecial diversification is dynamic, with reversals from inferior to half-inferior ovaries, as well as to ovaries that appear superior. Chromosomal evolution also appears to be labile with several independent origins of n = 12 (from an original number of n = 11) and multiple episodes of aneuploidy.     

Phylogeny of firs (genus <Emphasis Type="Italic">Abies</Emphasis>, Pinaceae) based on multilocus nuclear markers (AFLP)

To study the phylogenetic relationships, evolutionary history, and molecular systematics of firs (genus Abies), the phylogenetic reconstruction, based on nuclear multilocus markers—amplified fragment length polymorphism (AFLP)—was conducted. Using seven combinations of selective primers, 84 samples of 39 taxa were genotyped for 553 polymorphic AFLP loci. A comparison with our earlier chloroplast and mitochondrial phylogenies of the genus (in 2014) shows that the nuclear phylogeny generally is more congruent to the chloroplast tree. Most of the clades resolved by the chloroplast phylogeny were supported also in the AFLP tree. Employing the nuclear DNA-based tree, we revealed the presence of new groups and the differences in the topology of several clades. AFLP confirmed the monophyly of Asian species of section Balsamea and their sister position in relation to the American group of species of this section. As shown by the tree of chloroplast DNA, Asian species of section Balsamea do not form a monophyletic group, but belong to the clade comprising the majority of Asian species. Phylogenetically mitochondrial DNA data to a large extent are not congruent to the nuclear and chloroplast DNA trees, and are more in line with geographical distribution of species. Conflicts between nuclear and cytoplasmic phylogeny were analyzed. Taking them into account, we consider the hypothesis of a hybrid origin of particular groups of firs, including ancient hybridization in section Balsamea. A comparison of molecular data with traditional taxonomy of the genus is discussed.