Phylogeny and classification of Rosaceae

Phylogenetic relationships among 88 genera of Rosaceae were investigated using nucleotide sequence data from six nuclear (18S, gbssi1, gbssi2, ITS, pgip, and ppo) and four chloroplast (matK, ndhF, rbcL, and trnL-trnF) regions, separately and in various combinations, with parsimony and likelihood-based Bayesian approaches. The results were used to examine evolution of non-molecular characters and to develop a new phylogenetically based infrafamilial classification. As in previous molecular phylogenetic analyses of the family, we found strong support for monophyly of groups corresponding closely to many previously recognized tribes and subfamilies, but no previous classification was entirely supported, and relationships among the strongly supported clades were weakly resolved and/or conflicted between some data sets. We recognize three subfamilies in Rosaceae: Rosoideae, including Filipendula, Rubus, Rosa, and three tribes; Dryadoideae, comprising the four actinorhizal genera; and Spiraeoideae, comprising Lyonothamnus and seven tribes. All genera previously assigned to Amygdaloideae and Maloideae are included in Spiraeoideae. Three supertribes, one in Rosoideae and two in Spiraeoideae, are recognized.     

NUCLEAR DNA CONTENT VARIATION WITHIN THE ROSACEAE

Nuclear DNA content has been estimated using flow cytometry for 17 species and eight cultivars of Malus and for 44 species of 29 other genera within the Rosaceae. Compared to other angiosperms, diploid genome sizes vary little within the family Rosaceae and within the genus Malus. C-values of genera within the subfamilies Spiraeoideae and Rosoideae are among the smallest of flowering plants thus far reported. In general, the Maloideae have the largest diploid genomes of the family, consistent with their higher chromosome numbers and presumed polyploid origin.     

matK and rbcL gene sequence data indicate that Saxifraga (Saxifragaceae) is polyphyletic

The large genus Saxifraga, which consists of ≈400 morphologically and cytologically diverse species, has long been considered taxonomically complex. Phylogenetic analysis of over 2500 bp of chloroplast sequence data derived from matK and rbcL was employed to examine relationships among sections of Saxifraga, the segregate genera Zahlbrucknera, Saxifragopsis, and Cascadia, and the relationships of these taxa to other Saxifragaceae sensu stricto. Phylogenetic trees resulting from separate analyses of the matK and rbcL sequences were highly congruent; phylogenetic analysis of a combined matK–rbcL data matrix was therefore also conducted. Our analyses indicate that Saxifraga is polyphyletic, comprising two well-differentiated clades. One clade, Saxifraga sensu stricto, is the sister to the remainder of the family and consists of Saxifraga sections Irregulares, Heterisia, Trachyphyllum, Cymbalaria, Mesogyne, Xanthizoon, Porphyrion, Ciliatae, Cotylea, Ligulatae, Saxifraga, and Gymnopera. With the exception of Gymnopera, the species-rich sections of this clade are monophyletic. Also part of this clade is the problematic Zahlbrucknera paradoxa, which is allied with members of section Saxifraga. A second major clade of Saxifraga species, Micranthes sensu lato, comprises the large section Micranthes, as well as the segregate genus Cascadia, and S. tolmiei of section Merkianae. This clade is allied with the Heuchera, Darmera, and Chrysosplenium-Peltoboykinia groups of genera. The segregate genus Saxifragopsis is only distantly related to species of Saxifraga, and is instead the sister to Astilbe. The monotypic Oresitrophe is confirmed as a member of the Darmera group of genera. These results suggest that the floral features used to define Saxifraga may simply be symplesiomorphic in these well-separated Saxifraga lineages. Furthermore, the enormous cytological diversity encompassed by Saxifraga likely represents two independent instances of extensive aneuploidy and polyploidy in Saxifragaceae.     

利用DNA片段测序方法探究枳属和富民枳的分类地位

富民枳(Poncirus polyandra)属于芸香科(Rutaceae)枳属(Poncirus Raf.)。自发表以来,分类地位一直备受争议,其中在Flora of China中认为富民枳为柑橘杂交种(Poncirus polyandra),把枳属归并于柑橘属(Citrus)。该研究选取枳属的富民枳、枳(Poncirus trifoliata)及柑橘属下8个种共10个种47个个体作为研究材料,以九里香(Murraya exotica)为外类群,利用3个叶绿体片段(trn L-trn F、trn S-trn G、rbc L)、ITS片段和1个单拷贝核基因(Chr 5)数据构建系统发育树,探究枳属和富民枳的分类地位。结果表明:基于3个叶绿体片段数据构建的最大似然树(ML)和贝叶斯树(BI)的拓扑结构基本一致,10个物种聚为两大分支,即柑橘属的8个物种聚为一大分支,富民枳和枳聚为另一大分支。其中,富民枳所有个体聚为一小单系分支,枳的所有个体聚为一小单系分支,支持枳属和富民枳独立存在。2个核DNA片段数据结果显示,枳属的两个种与柑橘属的8个物种聚在一个大分支里,无法确立枳属的单系地位,但富民枳的9个个体聚在一起,暗示富民枳在遗传上是一个独立的类群。综上研究认为,无论是叶绿体DNA数据还是核DNA数据均支持富民枳是一个独立的物种,但核DNA数据不支持枳属成立。     

The complex history of the genus Ilex L. (Aquifoliaceae): evidence from the comparison of plastid and nuclear DNA sequences and from fossil data

 A plastid phylogeny of the genus Ilex based on three different loci (the atpB-rbcL spacer, trnL-trnF and rbcL) is compared with its nuclear phylogeny based on two different loci (the ribosomal ITS and the 5S RNA spacer). These two sets of molecular data are then compared to geographical and temporal data from the fossil record. The plastid phylogeny is strongly correlated with the geographic distribution of extant species. However, the nuclear phylogeny is strongly incongruent with the plastid phylogeny, suggesting frequent interlineage hybridizations. Moreover, the comparison of the ribosomal ITS tree and the 5S RNA spacer tree indicates also possible lineage sorting. Particularly interesting is the finding of two different Ilex lineages in the plastid American clade showing different biogeographic patterns in South America. One of them has a simple North American/South American biogeographical relationship. The other has complex biogeographical relationships, some species showing direct Asian/South American biogeographical relationships. During its history, the genus Ilex probably experienced frequent lineage sorting and interlineage hybridization with subsequent nuclear or cytoplasmic introgression, making the study of its history very complex. Received September 24, 2001; accepted August 19, 2002 Published online: November 28, 2002 Addresses of the authors: Jean-Fran?ois Manen (e-mail: manen@cjb.ville-ge.ch), Yamama Naciri-Graven, Conservatoire et Jardin Botaniques, Impératrice 1, CH-1292 Chambésy/Genève, Switzerland. Michael C. Boulter, Palaeobiology Research Unit, University of East London, Romford Road, London E15 4LZ, UK.     

Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

An effective DNA marker for authenticating the genus Salvia was screened using seven DNA regions (rbcL, matK, trnL–F, and psbA–trnH from the chloroplast genome, and ITS, ITS1, and ITS2 from the nuclear genome) and three combinations (rbcL + matK, psbA–trnH + ITS1, and trnL–F + ITS1). The present study collected 232 sequences from 27 Salvia species through DNA sequencing and 77 sequences within the same taxa from the GenBank. The discriminatory capabilities of these regions were evaluated in terms of PCR amplification success, intraspecific and interspecific divergence, DNA barcoding gaps, and identification efficiency via a tree-based method. ITS1 was superior to the other marker for discriminating between species, with an accuracy of 81.48%. The three combinations did not increase species discrimination. Finally, we found that ITS1 is a powerful barcode for identifying Salvia species, especially Salvia miltiorrhiza.     

Molecular phylogenetic and molecular dating of the New Zealand Gleicheniaceae

The Gleicheniaceae are an ancient family of ferns, with three of the six extant genera occurring in New Zealand:Dicranopteris, Gleichenia, andSticherus. The biogeographic origins of this family in New Zeland are unknown, and the taxonomy ofGleichenia in particular is still unclear. To address aspects of these two issues, DNA sequences from thetrnL-trnF locus and therbcL gene were produced for all of the common Gleicheniaceae species in New Zealand, as well as forGleichenia alpina from Tasmania andSticherus cryptocarpus from Chile. SeveraltrnL-trnF haplotypes were found amongst New ZealandG. dicarpa. One of these haplotypes was also observed in TasmanianG. alpina, while the other New ZealandG. dicarpa trnL-trnF haplotypes were more similar to those ofG. microphylla. These results suggest the taxonomy of New ZealandGleichenia may be more complex than presently recognized. Molecular dating of therbcL sequences with the program r8s rejected vicariant explanations for the disjunct distributions between New Zealand and elsewhere for each ofDicranopteris, Gleichenia, andSticherus. However, the direction of the inferred long-distance dispersal was not resolved.     

Distribution of sorbitol in rosaceae

77 leaf samples representing 68 taxa of Rosaceae were investigated for the presence of sorbitol. A procedure for the quantitative estimation of sorbitol in dry plant tissues was elaborated; it made use of extraction by percolation and capillary GLC analysis of the silylated extracts. All Maloideae and Prunoideae and most Spiraeoideae were found to accumulate sorbitol. The subfamily Rosoideae was found to be heterogeneous in this respect; in most tribes sorbitol is totally lacking, but in Kerrieae, Adenostomeae and part of Dryadeae sorbitol is present in variable amounts. A clear-cut correlation between sorbitol accumulation and basic chromosome number seems to exist in Rosaceae.     

Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective

The eastern Asian and eastern North American disjunction in Juglans offers an opportunity to estimate the time since divergence of the Eurasian and American lineages and to compare it with paleobotanical evidence. Five chloroplast DNA noncoding spacer (NCS) sequences: trnT−trnF, psbA−trnH, atpB−rbcL, trnV-16S rRNA, and trnS-trnfM and data from earlier studies (matK, ITS, and nuclear RFLP) were used to reconstruct phylogeny and to estimate the divergence time of major lineages. Seventeen taxa from four sections of Juglans and two outgroup taxa, Pterocarya stenoptera and Carya illinoiensis were included. NCS data was congruent only with matK data. Both maximum parsimony (MP) and maximum likelihood (ML) cladograms were concordant at the sectional level and revealed three well-supported monophyletic clades corresponding to sections Juglans, Cardiocaryon, and Rhysocaryon in both NCS and combined analyses. The single extant American butternut, Juglans cinerea was placed within the poorly resolved, but well-supported Rhysocaryon. Placement of taxa within Rhysocaryon and Cardiocaryon were inconsistent between NCS and combined analyses. Overall, the results suggest that: (1) the NCS sequence divergence observed within and between sections of Juglans is low and the addition of matK data only marginally improved resolution within Rhysocaryon; (2) the early divergence of section Juglans in both MP and ML analyses of NCS and combined data implies its ancient origin in contrast to fossil evidence, which suggests the earliest divergence of sections Rhysocaryon and Cardiocaryon; and (3) the extant taxa may not hold the footprints to unravel the evolutionary history of the genus.     

Relationships and evolution of Hydrangeaceae based on RBCl sequence data

Phylogenetic analyses of rbcL sequences were used to address both systematic and evolutionary questions posed by the angiosperm family Hydrangeaceae. Our analyses suggest the presence of a monophyletic Hydrangeaceae most closely allied with Loasaceae, a finding in agreement with other molecular as well as morphological analyses. Molecular data indicate that Hydrangeaceae comprise Decumaria, Pileostegia, Schizophragma, Hydrangea, Dichroa, Broussaisia, Platycrater, Cardiandra, Deinanthe, Carpenteria, Philadelphus, Deutzia, Fendlerella, Whipplea, Fendlera, Jamesia, and the enigmatic Kirengeshoma. A particularly close relationship of Kirengeshoma and Deutzia is indicated. Analysis of rbcL sequences suggests that Fendlera and Jamesia are sister to the remainder of the family, lending support to the hypothesis that at least some Carpenterieae are basal in the family and that Hydrangeaceae may have originated in xeric habitats. If this phylogenetic placement of Jamesia and Fendlera is correct, the rbcL trees also suggest that the level of epigyny has decreased in these genera, as well as in the Fendlerella- Whipplea clade and Carpenteria when compared to the outgroup taxa, which are wholly epigynous. Furthermore, the rbcL trees support proposed evolutionary trends in wood anatomy, suggesting, for example, that upland tropical taxa have evolved longer vessel elements with more numerous bars on scalariform perforation plates. The xerophytic basal members of Hydrangeaceae, like the closely related Loasaceae, have short, narrow vessel elements with scalariform perforation plates bearing few bars. Following Jamesia and Fendlera, the remaining hydrangeoids are divided into two large subclades that closely parallel the traditional division of the family into Philadelpheae and Hydrangeae. Both rbcL sequences and morphological data suggest close relationships between: 1) Fendlerella and Whipplea; 2) Decumaria, Pileostegia, and Schizophragma; 3) Carpenteria and Philadelphus; 4) Deinanthe and Cardiandra; 5) Dichroa, Broussaisia, and Hydrangea macrophylla. Molecular and morphological data also concur in demonstrating that the large genus Hydrangea is not a monophyletic assemblage.     

Simaroubaceae,an artificial construct: evidence from rbcL sequence variation

Phylogenetic analyses of rbcL sequence data of representatives of all subfamilies indicate that Simaroubaceae sensu lato is polyphyletic. It represents at least five separate lineages, only three of which (Simarouboideae, Harrisonia, and Kirkioideae) cluster within a robust sapindalean clade. The family is monophyletic only when comprised of members of the subfamily Simarouboideae plus Leitneriaceae, but excluding Harrisonia. Harrisonia is most closely related to Cneorum and Rutaceae. Kirkioideae is distant from Simaroubaceae sensu stricto, although its affinities remain within Sapindales. The other two lineages show an affinity to taxa at some distance from Sapindales: lrvingia with a group of poorly sampled rosid I taxa comprising in part members of Linales and Malphigiales; Picramnia and Alvaradoa cluster together in an isolated position between the broadly comprised groups of rosid I and rosid II. Support for the affinities suggested here is also evident in nonmolecular data sources: wood anatomy, pericarp structure, pollen, and phytochemistry. The elevation of the picramnioid clade, comprising Picramnia and Alvaradoa, to family rank is signaled, and the recognition of Kirkiaceae and Irvingiaceae is substantiated.     

New insights into DNA barcoding of seagrasses

Taxonomists find some plant genera challenging because of the few morphological differences or unclear characters among closely related species, which leads to the misidentification of taxa. DNA barcoding is an approach to identify species by using short orthologous DNA sequences, known as ‘DNA barcodes’. Concatenated rbcL and matK sequences are considered DNA barcodes for seagrasses. However, these markers are not applicable to all members of seagrasses at the species level, especially within the genus Halophila. Our previous studies indicated that the internal transcribed spacer (ITS) showed higher species resolution than the concatenated rbcL and matK sequences in the case of Halophila ovalis and closely related species. In this study, 26 ITS, two rbcL and two matK consensus sequences from 18 seagrass taxa belonging to four families collected in India, Vietnam, Germany, Croatia and Egypt were processed. Molecular ITS analysis resolved five clades. The results also indicate that the Cymodoceaceae family might be a non-monophyletic group. In conclusion, ITS could be applied as a DNA barcode for seagrasses instead of the rbcL/matK system previously proposed.     

Molecular identification of species in Prunus sect. Persica (Rosaceae), with emphasis on evaluation of candidate barcodes for plants

Abstract Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no reliable morphological characters are available. Nowadays, the technique of DNA barcoding has the potential to meet such requirements. In this study, we evaluated the suitability of 11 DNA loci (atpB‐rbcL, trnH‐psbA, trnL‐F, trnS‐G, atpF‐H, rbcL, matK, rpoB, rpoC1, nad1, and internal transcribed spacer [ITS]) as candidate DNA barcodes for peaches, using samples from 38 populations, covering all the species in sect. Persica. On the whole, the primers worked well in this group and sequencing difficulties were met only in the case of ITS locus. Five loci (rbcL, matK, rpoB, rpoC, and nad1) have very low variation rates, whereas atpB‐rbcL, atpF‐H, trnH‐psbA, trnL‐F and trnS‐G show more variability. The most variable loci, atpB‐rbcL and trnH‐psbA, can distinguish three of the five species. Two two‐locus combinations, atpB‐rbcL+trnL‐F and atpB‐rbcL+atpF‐H, can resolve all five species. We also find that identification powers of the loci are method‐dependent. The NeighborNet method shows higher species identification power than maximum parsimony, neighbor joining, and unweighted pair group method with arithmetic mean methods.     

Phylogenetic relationships between disjunctly occurring groups of Tristicha trifaria (Podostemaceae)

Aim To reveal the phylogeographic relationship of disjunct specimens of Tristicha trifaria (Bory ex Willd.) Spreng., a member of the Podostemaceae river‐weed family, which is distributed exceptionally widely, but disjunctly, in Africa and the Americas. Location Brazil, Mexico, Ghana, Tanzania and Madagascar. Methods The chloroplast matK and rbcL genes, a trnK intron, the trnS‐trnG intergenic spacer (IGS), the two IGSs of trnT‐trnL‐trnF, a trnL intron, and nuclear ribosomal ITS regions were sequenced and analysed. Phylogenetic analyses were conducted using maximum likelihood and maximum parsimony methods. Results The T. trifaria samples analysed were separated into two groups in a rooted tree based on a combined matK/rbcL/ITS dataset; one contained the West African and all of the American samples, and the other contained the East African and Madagascan samples. An unrooted tree obtained from a combined analysis of all the chloroplast DNA and nuclear ITS data showed that a sample from West Africa was sister to an American T. trifaria group. Main conclusions The American and West African T. trifaria are closely related, despite the great distance between their locations. This observation, along with a tree of the whole Tristichoideae subfamily and estimated divergence times, suggests that an ancestor of T. trifaria migrated from Asia to Africa during the early Tertiary, and that this was followed by further westward migration to the Americas at the end of the Miocene or in the early Pliocene.     

The systematic identity of Chiloscyphus trichocoleoides,a new liverwort species from New Zealand,uncovered by morphological and molecular evidence

Abstract

A new liverwort species from Western Nelson Ecological Province of New Zealand known from a single sterile specimen is described. It is unusual in having well-developed stem paraphyllia, and the leaves and underleaves are divided with three levels of ciliate division in a pinnate manner. This morphology suggested membership of Trichocoleaceae or Trichotemnomaceae, but other features of the plant made placement in either family seem unnatural. We determined its position by conducting phylogenetic analyses of rbcL, rps4 and trnL–F sequence datasets from 35 exemplars, and further confirmation of the position was carried out by an extended analysis using rbcL sequence dataset of 59 exemplars. The surprising result is that it belongs within the genus Chiloscyphus, where it is unique in these features. We describe this new species as Chiloscyphus trichocoleoides. Placing the new species in Chiloscyphus has broadened the generic concept of Chiloscyphus, and its phylogenetic relationship within and to other genera such as Clasmatocolea and Heteroscyphus needs further investigation. The results also show that the same morphological features seen in Chiloscyphus and in Trichocoleaceae and Trichotemnomaceae have developed independently.