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.     

Molecular phylogeny and biogeography of Malagasy frogs of the genus Gephyromantis

The genus Gephyromantis is a clade within the Malagasy-Comoroan family Mantellidae composed of rainforest frogs that live and breed to varying degrees independently from water. Based on DNA sequences of five mitochondrial and five nuclear genes we inferred the phylogeny of these frogs with full taxon coverage at the species level. Our preferred consensus tree from a partitioned Bayesian analysis of 5843 base pairs of 51 nominal and candidate species supports various major clades within the genus although the basal relationships among these remain unresolved. The data provide strong evidence for the monophyly of the subgenera Gephyromantis (after exclusion of Gephyromantis klemmeri), Laurentomantis, Vatomantis, and Phylacomantis. Species assigned to the subgenus Duboimantis belong to two strongly supported clades of uncertain relationships. G. klemmeri, previously in the subgenus Gephyromantis, was placed with high support sister to the Laurentomantis clade, and the Laurentomantis + G. klemmeri clade was sister to Vatomantis. A reconstruction of ancestral distribution areas indicates a diversification of several subgenera in the northern biogeographic regions of Madagascar and the dispersal out of northern Madagascar for several clades.     

Hidden diversity of Euscorpius (Scorpiones: Euscorpiidae) in Greece revealed by multilocus species‐delimitation approaches

Phylogenetic analysis of the genus Euscorpius (Scorpiones: Euscorpiidae) across the Mediterranean region (86 specimens, 77 localities, four DNA markers: 16S rDNA, COI, COII, and ITS1), focusing on Greek fauna, revealed high variation, deep clade divergences, many cryptic lineages, paraphyly at subgenus level, and sympatry of several new and formerly known lineages. Numerous specimens from mainland and insular Greece, undoubtedly the least studied region of the genus' distribution, have been included. The reconstructed phylogeny covers representative taxa and populations across the entire genus of Euscorpius. The deepest clades detected within Euscorpius correspond (partially) to its current subgeneric division, outlining subgenera Tetratrichobothrius and Alpiscorpius. The rest of the genus falls into several clades, including subgenus Polytrichobothrius and a paraphyletic subgenus Euscorpius s.s. Several cryptic lineages are recovered, especially on the islands. The inadequacy of the morphological characters used in the taxonomy of the genus to delineate species is discussed. Finally, the time frame of differentiation of Euscorpius in the study region is estimated and the distributional patterns of the lineages are contrasted with those of other highly diversified invertebrate genera occurring in the study region. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 728–748.     

Phylogenetic Relationships of American Willows (Salix L., Salicaceae)

Salix L. is the largest genus in the family Salicaceae (450 species). Several classifications have been published, but taxonomic subdivision has been under continuous revision. Our goal is to establish the phylogenetic structure of the genus using molecular data on all American willows, using three DNA markers. This complete phylogeny of American willows allows us to propose a biogeographic framework for the evolution of the genus. Material was obtained for the 122 native and introduced willow species of America. Sequences were obtained from the ITS (ribosomal nuclear DNA) and two plastid regions, matK and rbcL. Phylogenetic analyses (parsimony, maximum likelihood, Bayesian inference) were performed on the data. Geographic distribution was mapped onto the tree. The species tree provides strong support for a division of the genus into two subgenera, Salix and Vetrix. Subgenus Salix comprises temperate species from the Americas and Asia, and their disjunction may result from Tertiary events. Subgenus Vetrix is composed of boreo-arctic species of the Northern Hemisphere and their radiation may coincide with the Quaternary glaciations. Sixteen species have ambiguous positions; genetic diversity is lower in subg. Vetrix. A molecular phylogeny of all species of American willows has been inferred. It needs to be tested and further resolved using other molecular data. Nonetheless, the genus clearly has two clades that have distinct biogeographic patterns.     

Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota)

Research on the molecular systematics of Cortinarius, a species-rich mushroom genus with nearly global distribution, is just beginning. The present study explores infrageneric relationships using rDNA ITS and LSU sequence data. One large dataset of 132 rDNA ITS sequences and one combined da-taset with 54 rDNA ITS and LSU sequences were generated. Hebeloma was used as outgroup. Bayesian analyses and maximum-likelihood (ML) analyses were carried out. Bayesian phylogenetic inference performed equally well or better than ML, especially in large datasets. The phylogenetic analysis of the combined dataset with species representing all currently recognized subgenera recovered seven well-supported clades (Bayesian posterior probabilities BPP > 90%). These major clades are: /Myxacium s.l., /subg. Cortinarius, the /phlegmacioid clade (including the subclades /Phlegmacium and /Delibuti), the /calochroid clade (/Calochroi, /Ochroleuci and /Allutus), the /telamonioid clade (/Telamonia, /Orellani, /Anomali), /Dermocybe s.l. and /Myxotelamonia. Our results show that Cortinarius consists of many lineages, but the relationships among these clades could not be elucidated. On one hand, the low divergence in rDNA sequences can be held responsible for this; on the other hand, taxon sampling is problematic in Cortinarius phylogeny. Because of the incredibly high diversity (~2000 Cortinarius species), our sampling included <5% of the known species. By choosing type species of subgenera and sections, our sampling is strongly biased toward Northern Hemisphere taxa. More extensive taxon sampling, especially of species from the Southern Hemisphere, is essential to resolve the phylogeny of this important genus of ectomycorrhizal fungi.     

Phylogenetic relationships,molecular taxonomy,biogeography of <Emphasis Type="Italic">Betula</Emphasis>, with emphasis on phylogenetic position of Iranian populations

Birch trees inhabiting the high-altitude Hyrcanian forest (the southern shores of the Caspian Sea of Iran and Azerbaijan) are classified in the EN (endangered) category of the International Union for Conservation of Nature (IUCN). Taxonomic status and phylogenetic relationship of Iranian populations, molecular taxonomy, and biogeography of the genus Betula in the world have been considered. Four remnant populations of Betula were selected from north and northwestern parts of Iran. The internal ITS and trnH-psbA intergenic spacer regions were sequenced. Based on the trnH-psbA and ITS, Iranian birch and white birch were placed in a clade, but based on trnH-psbA divided into two subclades. Phylogenetic trees based on ITS and trnH-psbA data did not completely support the morphological classification. Network analysis confirms a close relationship of B. pendula with B. platyphylla and B. papyrifera with B. humilis, and B. ermanii were in a group with the other tetraploid species of the subgenus Neurobetula. Divergence time analysis showed that about 75 Ma ago the Betula genus separated from the other genus of Betulaceae and then divided into two main clades in Oligocene. Our divergence analysis supports that two subgenera of Betulenta and Betulaster are the oldest subgenera in the genus Betula and they date back to Eocene. The ancestral reconstruction suggests that ancestors of the genus Betula originated from Southeast Asia.     

Chromosome and breeding system evolution of the genus Mercurialis (Euphorbiaceae): implications of ITS molecular phylogeny

 The internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were amplified and sequenced from 19 samples representing all species of the genus Mercurialis and two outgroup species, Ricinus communis and Acalypha hispida. The length of ITS1 in the ingroups ranged from 223 to 246 bp and ITS2 from 210 to 218 bp. Sequence divergence between pairs of species ranged from 1.15% to 25.88% among the ingroup species in the combined data of ITS1 and ITS2. Heuristic phylogenetic analyses using Fitch parsimony on the combined data of ITS1 and ITS2 with gaps treated as missing generated 45 equally parsimonious trees. The strict consensus tree was principally concordant with morphological classification. Within the genus, the ITS sequences recognised two main infrageneric clades: the M. perennis complex including three Eurasian stoloniferous species (M.␣leiocarpa, M. ovata and M. perennis) and the western Mediterranean group including eight both annual and perennial species. Of the western Mediterranean clade, the annual and perennial species grouped respectively into two different groups, and the annual life form is revealed as a synapomorphic character derived from perennial, whereas in the Eurasian clade ITS phylogeny suggested M. leiocarpa as basal clade sister to M.␣perennis and M. ovata. ITS phylogeny failed to resolve the relationships among the different cytotypes of M. ovata and M. perennis. ITS phylogeny also suggested rapid karyotypic evolution for the genus. The karyotypic divergence among the perennial species of western Mediterranean region did not corroborate the nucleotide sequence divergence among the species. Optimisation of chromosome numbers onto the ITS phylogeny suggested x=8 to be the ancestral basic chromosome number of the genus. ITS phylogeny confirmed that the androdioecy of M. ambigua is derived from dioecy. The nucleotide heterozygosity and additivity in ITS sequences clearly confirm the interspecific hybridisation in the genus Mercurialis. Received December 22, 2001; accepted May 21, 2002?Published online: November 14, 2002 Address of the authors: Martin Kr?henbühl, Yong-Ming Yuan (correspondence) and Philippe Küpfer, Institut de Botanique, Laboratoire de botanique évolutive, Université de Neuchatel, Emile-Argand 11, CH-2007 Neuchatel, Suisse. (e-mail: yong-ming.yuan@unine.ch)     

Phylogeny of Rubus (rosaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences

We used nuclear ribosomal DNA internal transcribed spacer region (ITS 1 - 5.8S - ITS 2; ITS) sequences to generate the first phylogeny of Rubus based on a large, molecular data set. We sampled 57 taxa including 20 species of subgenus Rubus (blackberries), one to seven species from each of the remaining 11 subgenera, and the monotypic and closely related Dalibarda. In Rubus, ITS sequences are most informative among subgenera, and variability is low between closely related species. Parsimony analysis indicates that Rubus plus Dalibarda form a strongly supported clade, and D. repens may nest within Rubus. Of the subgenera with more than one species sampled, only subgenus Orobatus appears monophyletic. Three large clades are strongly supported: one contains all sampled species of nine of the 12 subgenera; another includes extreme Southern Hemisphere species of subgenera Comaropsis, Dalibarda, and Lampobatus; and a third clade consists of subgenus Rubus plus R. alpinus of subgenus Lampobatus. Rubus ursinus appears to be a hybrid between a close relative of R. macraei (subgenus Idaeobatus, raspberries) and an unidentified subgenus Rubus species. ITS sequences are generally consistent with biogeography and ploidy, but traditionally important morphological characters, such as stem armature and leaf type, appear to have limited phylogenetic value in Rubus.     

An expanded phylogeny of Cuphea (Lythraceae) and a North American monophyly

A phylogenetic analysis of the New World genus Cuphea was conducted employing sequences from the nuclear rDNA internal transcribed spacer (ITS) and chloroplast trnL-trnF spacer and rpl16 intron. The analysis expands the number of Cuphea species from 53 in an earlier ITS study to 70 and adds two chloroplast data sets in order to generate a more complete and robust phylogeny and to test a previous result that suggested the presence of a large North American clade. Results reaffirm the monophyly of Cuphea with Pleurophora as the sister genus and recover a basal divergence event that mirrors the two subgenera of the current classification. Phylogenies of the two chloroplast regions are largely unresolved beyond the initial dichotomy and some resolution at the terminal and subterminal nodes. Based on the ITS phylogeny, five major clades are recognized. Subgenus Cuphea (Clade 1), defined morphologically by the synapomorphic loss of bracteoles, is sister to the much larger subg. Bracteolatae (Clades 2–5). Clades 2–4, comprising the South American and Caribbean species, grade successively to Clade 5, an exclusively North American lineage of 29 species. Among the 12 sections included in the study, only section Trispermum, a subclade of Clade 4, is monophyletic. Section Pseudocircaea is nested within Clade 3, which is largely equivalent to section Euandra. The North American endemic clade includes four sections, of which none are recovered as monophyletic in this study.     

Phylogenetic relationships of Pterocarya (Juglandaceae) with an emphasis on the taxonomic status of Iranian populations using ITS and trnH-psbA sequence data

Pterocarya fraxinifolia (Lam.) Spach., a relict tree species of the Juglandaceae family, is native to the Great Caucasus, Anatolia, and to the Hyrcanian forests of the southern Azerbaijan and Northern Iran. In this study, the phylogenetic relationship of the species, sampled in selected Iranian populations, and the global biogeography of the genus Pterocarya were addressed. Leaves were collected from 8 to 10 trees from three geographically isolated habitats. The samples were analyzed with nuclear (internal transcribed spacer [ITS] regions) and chloroplast (trnH-psbA) DNA markers. The obtained results were compared and analyzed with the data registered in NCBI GenBank. It is reported that the ITS regions varied from 644 to 652 for Pterocarya genus, but we did not observe polymorphisms for Iranian Pterocarya. The phylogenetic tree divided the Pterocarya genus in three clades: clade 1 grouping exclusively the samples P. fraxinifolia, clearly separated from the East Asiatic taxa; clade 2 that includes the species P. hupehensis and P. macroptera; clade 3 clustering P. stenoptera and P. tonkinensis. Although the Iranian Pterocarya samples and P. fraxinifolia from the Caucasus were in the same clade, they presented two different secondary structures. The Iranian populations showed the maximum genetic distance with P. stenoptera and P. tonkinensis. Our analysis demonstrates that the traditional division of all the six species sampled throughout their distribution area as well as the phylogeny of the genus Pterocarya needs to be reviewed.     

The phylogenetic utility of nucleotide sequences of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae)

Sequences from s6pdh, a gene that encodes sorbitol-6-phosphate dehydrogenase in the Rosaceae, are used to reconstruct the phylogeny of 22 species of Prunus. The s6pdh sequences alone and in combination with previously published sequences of the internal transcribed spacer (ITS) and the cpDNA trnL-trnF spacer are analyzed using parsimony and maximum likelihood methods. Both methods reconstructed the same phylogeny when s6pdh sequences are used alone and in combination with ITS and trnL-trnF, and the topology is in agreement with previous studies that used a larger sample size. The s6pdh sequences have about twice as many informative sites as ITS. A molecular clock is rejected for s6pdh, most likely due to greater rates of evolution in subgenera Padus and Laurocerasus than in the rest of the genus. Phylogenetic reconstruction of Prunus as determined by analysis of the combined data set suggests an early split into two clades. One is composed of subgenera Cerasus, Laurocerasus, and Padus. The second includes subgenera Amygdalus, Emplectocladus, and Prunus. Species of section Microcerasus (formerly in subgenus Cerasus) are nested within subgenus Prunus. The order of branching and relationships among early diverging lineages is weakly supported, as a result of very short branches that may indicate rapid radiation.     

Teleomorph-anamorph relationships and reclassification of <Emphasis Type="Italic">Cordyceps cuboidea</Emphasis> and its allied species

Based on morphological characteristics and molecular phylogeny, we reclassified Cordyceps cuboidea and allied species C. alboperitheciata, C. prolifica, and Ophiocordyceps ryogamiensis. We investigated their teleomorph-anamorph relationships and revealed that these four species have Hirsutella-like anamorphs with morphological differences between them. By analyzing their molecular phylogeny, inferred from DNA sequences of internal transcribed spacer (ITS) and large subunit (LSU) D1/D2 region of rDNA, they were separated into four close-knit clades. Although C. prolifica and O. ryogamiensis formed their own clades, isolates of C. cuboidea separated into two clades, i.e., a true C. cuboidea clade and one resembling a new species, the O. paracuboidea clade. The latter two species are distinguished by the fruiting region of the stroma. In addition, C. alboperitheciata is regarded as a synonym of C. cuboidea. From the morphology, teleomorph-anamorph relationships, and molecular phylogeny, we concluded these species should be assigned to the genus Ophiocordyceps.     

Isolation of the symbiotic fungus of Acromyrmex pubescens and phylogeny of Leucoagaricus gongylophorus from leaf-cutting ants

Leaf-cutting ants live in an obligate symbiosis with a Leucoagaricus species, a basidiomycete that serves as a food source to the larvae and queen. The aim of this work was to isolate, identify and complete the phylogenetic study of Leucoagaricus gongylophorus species of Acromyrmex pubescens. Macroscopic and microscopic features were used to identify the fungal symbiont of the ants. The ITS1-5.8S-ITS2 region was used as molecular marker for the molecular identification and to evaluate the phylogeny within the Leucoagaricus genus. One fungal symbiont associated with A. pubescens was isolated and identified as L. gongylophorus. The phylogeny of Leucoagaricus obtained using the ITS molecular marker revealed three well established monophyletic groups. It was possible to recognize one clade of Leucoagaricus associated with phylogenetically derived leaf-cutting ants (Acromyrmex and Atta). A second clade of free living forms of Leucoagaricus (non-cultivated), and a third clade of Leucoagaricus associated with phylogenetically basal genera of ants were also recognized. The clades corresponded to traditional taxonomic groups, and were differentiated by ecological habitats of different species.     

Systematics of North American Froelichia (Amaranthaceae subfam. Gomphrenoideae) II: Phylogeny and biogeographic speciation patterns inferred from nrITS sequence data

Molecular phylogenetic analyses of the nuclear ribosomal DNA internal transcribed spacer (ITS 1 and ITS 2) and the 5.8S gene were used to infer a phylogeny among the ten recognized taxa of Froelichia in North America. Analyses using both maximum parsimony (MP) and maximum-likelihood (ML) depicted a low level of sequence divergence though it was sufficient in most cases to differentiate taxa. Froelichia xantusii, a species restricted to southern Baja California was shown to be the basalmost member of the group subtending three clades. Two of the clades received good bootstrap support in the MP analysis and corresponded to a genetically homogeneous F. interrupta, and a clade comprising the two species F. latifolia and F. texana. A third clade receiving low bootstrap support contained F. floridana, F. gracilis, F. arizonica, and F. drummondii. Species diversity within the genus was centered within the Tamaulipan Brushland region of north-east Mexico and the southern portion of the US state of Texas where taxa from two of the three principal clades occurred, indicating a region of high speciation and diversification within the genus.     

A molecular phylogenetic study of Hemsleya (Cucurbitaceae) based on ITS, rpl16, trnH-psbA, and trnL DNA sequences

This paper presents the first molecular phylogeny of the genus Hemsleya using nuclear ITS and plastid trnH-psbA, rpl16, and trnL DNA sequences to examine the relationships among Hemsleya species. Phylogenetic relationships were elucidated using a combined analysis of all four datasets, however, the number of parsimony-informative characters was still insufficient to resolve all relationships. Parsimony and Bayesian trees were highly congruent. Twenty-three species of Hemsleya split into two major clades corresponding to two subgenera, i.e., subg. Graciliflorae and subg. Hemsleya. These results are partly in agreement with Li’s sectional classification. However, the molecular data are inconsistent with Li’s classification at the subsectional level. The molecular phylogeny revealed a striking overall correlation between the phylogenetic relationships of the species and their geographical distribution. The Kangdian ancient landmass could be the center of origin of the genus.     

Molecular phylogeny of the genus Ceanothus (Rhamnaceae) using rbc L and ndh F sequences

 Intrageneric phylogeny among ten representative Ceanothus species was investigated using DNA sequences of the chloroplast encoded ndhF and rbcL genes. Parsimony analysis of the ndhF sequences identified two main clades corresponding to two subgenera Ceanothus and Cerastes. The phylogenetic results suggest that three monophyletic clades within the subgenus Ceanothus can be delimited on the basis of (1) evergreen or (2) deciduous leaves and (3) thorn presence within the evergreen clade. The estimated divergence time based on rbcL sequences suggests that the two subgenera diverged 18–39 million years ago whereas species within each subgenus diverged more recently. Taken together, the results support the division of Ceanothus into two monophyletic subgenera and are consistent with the postulated recent divergence of many species within each subgenus. Received: 25 September 1996/Accepted: 8 November 1996     

A first approach to the molecular phylogeny of the genusEchinops (Asteraceae): Sectional delimitation and relationships with the genusAcantholepis

A first attempt to establish the phylogeny of the generaEchinops andAcantholepis has been carried out using the analysis of the internal transcribed spacers (ITS) sequences of the nuclear ribosomal DNA including 30Echinops species and the only species of the monotypicAcantholepis. The results of this analysis are discussed in the light of morphological and cytogenetic characters. The genusAcantholepis is placed in a robust clade withEchinops nanus, and together they appear in a basal position to other members ofEchinops. The ITS phylogeny and several other characters, such as chromosome number and nuclear DNA amount, do not agree with the sections currently recognized withinEchinops. Some groups are defined in the present approach, but further studies are necessary to reach a complete, stable and natural infrageneric classification of this genus.     

Multiple reproductive strategies of a spring ephemeral plant,Fritillaria maximowiczii,enable its adaptation to harsh environments

Spring ephemeral plants that experience harsh environments have developed specific reproductive characteristics. These characteristics are of great importance to the survival and reproduction of these species, particularly for rare and endangered plants. Fritillaria is a genus consisting of spring ephemeral plants with significant medicinal and ornamental value whose wild resources are highly threatened and whose reproductive characteristics and adaptative evolutionary mechanisms are still not well understood. Fritillaria maximowiczii is positioned at the most basal clade on the Fritillaria phylogenetic tree, whose reproductive characteristics remain obscure. In this study, we report the flowering dynamics, pollination biology and breeding system of F. maximowiczii. The flowering process of F. maximowiczii can be divided into seven stages. Based on the pollen/ovule ratio, the outcrossing index and a field pollination experiment on a natural population, F. maximowiczii showed high levels of outcrossing and self-compatibility. Three types of pollinators were observed: two kinds of bumblebees, and spiders. Diverse herkogamy and dichogamy may have considerably improved its reproductive success rate. Furthermore, a special reproductive mode not previously reported in wild populations of Fritillaria, apomixis, was strongly suspected based on a high fruit setting rate (36.84%). Our study suggests F. maximowiczii has developed multiple reproductive strategies to adapt to harsh environments and ensure population reproduction, and the diverse reproductive mechanisms may be related to its primitive phylogenetic position in the genus. This study not only broadens our understanding of mechanisms of ecological adaptation in spring ephemeral plants but also provides key data for the conservation of Fritillaria.     

Molecular phylogeny of black flies (Diptera: Simuliidae) from Thailand, using ITS2 rDNA

The sequences of the second internal transcribed spacer (ITS2) of ribosomal DNA (rDNA) were determined for 40 black fly species from Thailand, belonging to 4 subgenera of the genus Simulium, namely Gomphostilbia (12 species), Nevermannia (5 species), Montisimulium (1 species), Simulium sensu stricto (21 species), and an unknown subgenus with one species (Simulium baimaii). The length of the ITS2 ranged from 247 to 308 bp. All black fly species had high AT content, ranging from 71 to 83.8%. Intraindividual variation (clonal variation) occurred in 13 species, ranging from 0.3 to 1.1%. Large intrapopulation and interpopulation heterogeneities exist in S. feuerboni from the same and different locations in Doi Inthanon National Park, northern Thailand. Phylogenetic relationships among 40 black fly species were examined using PAUP (version 4.0b10) and MrBAYS (version 3.0B4). The topology of the trees revealed two major monophyletic clades. The subgenus Simulium and Simulium baimaii were placed in the first monophyletic clade, whereas the subgenera Nevermannia + Montisimulium were placed as the sister group to the subgenus Gomphostilbia in the second monophyletic clade. Our results suggest that S. baimaii belongs to the malyschevi-group or variegatum-group in the subgenus Simulium. The molecular phylogeny generally agrees with existing morphology-based phylogenies.     

Phylogeny and infrageneric classification of Correa Andrews (Rutaceae) on the basis of nuclear and chloroplast DNA

This paper presents phylogenies of the small but ecologically and horticulturally important Australian genus Correa (Rutaceae). Consensus phylogenies generated using parsimony were congruent with their counterparts generated by Bayesian analysis, although usually less well resolved. The phylogeny generated from the second internal transcribed spacer region of the nuclear ribosomal DNA supported the monophyly of Correa and identified two well supported clades (one comprising C. lawrenceana and C. baeuerlenii and the other containing all other species of the genus). Phylogenetic reconstructions based on the combined trnL-trnF spacer and the trnK intron (including the matK gene) regions of chloroplast DNA also supported the monophyly of Correa and of the C. lawrenceana/C. baeuerlenii clade, but the topology among the other species differed markedly from that in the ITS-based phylogeny. The major clades identified in the chloroplast phylogenies seemed to follow geographic patterns rather than species boundaries, with different samples of C. glabra bearing chloroplast genotypes from different clades. These patterns are likely to be because of independent evolution of the chloroplast and nuclear genomes, and are typical of cases of introgressive hybridisation among species or incomplete lineage sorting of chloroplast genomes leading to incongruence between chloroplast and nuclear phylogenies. Thus, the phylogenies based on nuclear DNA should reflect species relations better than the chloroplast phylogeny in Correa, and we propose a new subgeneric classification of the genus on the basis of the ITS-based phylogeny and morphology. Correa subgenus Persistens Othman, Duretto and G.J. Jord., containing C. lawrenceana and C. baeuerlenii, is formally described.