trnL-F Spacer Research Articles

DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep.

Tubers of terrestrial orchids are harvested and traded from the eastern Mediterranean to the Caspian Sea for the traditional product Salep. Overexploitation of wild populations and increased middle-class prosperity have escalated prices for Salep, causing overharvesting, depletion of native populations and providing an incentive to expand harvesting to untapped areas in Iran. Limited morphological distinctiveness among traded Salep tubers renders species identification impossible, making it difficult to establish which species are targeted and affected the most. In this study, a reference database of 490 nrITS, trnL-F spacer and matK sequences of 133 taxa was used to identify 150 individual tubers from 31 batches purchased in 12 cities in Iran to assess species diversity in commerce. The sequence reference database consisted of 211 nrITS, 158 trnL-F and 121 matK sequences, including 238 new sequences from collections made for this study. The markers enabled unambiguous species identification with tree-based methods for nrITS in 67% of the tested tubers, 58% for trnL-F and 59% for matK. Species in the genera Orchis (34%), Anacamptis (27%) and Dactylorhiza (19%) were the most common in Salep. Our study shows that all tuberous orchid species in this area are threatened by this trade, and further stresses the urgency of controlling illegal harvesting and cross-border trade of Salep tubers.

Hemipilia galeata (Orchideae, Orchidaceae), a new species from Fujian Province, southeastern China

A new orchid species, Hemipilia galeata, is described and illustrated from Wuyi Mountains, Fujian Province, southeastern China, and included in a phylogenetic analysis using the nuclear ribosomal ITS and three plastid markers (matK, trnL intron and trnL-F spacer) DNA. This species is a member of H. section Hemipilia sensu Tang et al. and is distinguished from other species in Hemipilia by its hemispheric dorsal sepal. It is similar to H. hemipilioides, H. occidensichuanensis and H. thailandica, but H. galeata differs by its elliptic, purple-spotted leaf, suborbicular petals, oblong lateral lip lobes and an ovate midlobe.

Streptocarpus redefined to include all Afro‐Malagasy Gesneriaceae: Molecular phylogenies prove congruent with geographical distribution and basic chromosome numbers and uncover remarkable morphological homoplasies

AbstractThe taxonomy of the African, Madagascan and Comoro Island (Afro‐Malagasy) Gesneriaceae attracts a large amount of interest given the horticultural importance of Cape Primroses (Streptocarpus) and African Violets (Saintpaulia). Earlier studies indicated that the Afro‐Malagasy genera form a strongly supported clade, and recent classifications have included some of the genera within an expanded Streptocarpus. Given the global importance of this group, we carried out a comprehensive molecular phylogenetic analysis of all Afro‐Malagasy genera in subfamily Didymocarpoideae, tribe Trichosporeae, subtribe Streptocarpinae, to investigate species relationships in these genera as the basis for a new classification. Phylogenetic analyses of the nuclear ribosomal spacer (ITS, 5S NTS) and chloroplast intron and spacer regions (rpl20‐rps12 spacer, trnL intron, trnLF spacer) of 226 samples were performed, including all Streptocarpinae genera, except the monotypic Nodonema. The molecular phylogenies demonstrate that the genera with non‐twisted fruits are nested within Streptocarpus which has twisted fruits. Two main clades were found, one comprising herbaceous caulescent Streptocarpus that also included Saintpaulia, the caulescents Hovanella and Schizoboea, and the unifoliates Acanthonema and Trachystigma. The second clade comprises the woody caulescents and acaulescent Streptocarpus, Colpogyne and Linnaeopsis. Altogether, twelve well‐supported subclades can be recognized, each with a combination of distinct morphological characteristics. A new classification of tribe Streptocarpinae, de facto Streptocarpus, is presented, retaining the two subgenera, Streptocarpus and Streptocarpella, and dividing them into five and seven sections respectively. Nodonema is attributed to subg. Streptocarpus for morphological reasons. The former genus Saintpaulia is classified as Streptocarpus subg. Streptocarpella sect. Saintpaulia with ten species recognized.

Lacomucinaea, a new monotypic genus in Thesiaceae (Santalales)

A new monotypic genus from southern Africa is described based on Thesium lineatum. Lacomucinaea lineata has a number of vegetative and floral morphological features that differ from Thesium and other members of Thesiaceae. An apparently unique feature of the plant is the presence of succulent, fusiform, terete leaves that are caducous, eventually leaving a persistent petiolar stub. The stem surface shows striations formed by cortical fibers inside raised ridges. Anatomically, this type of primary phloem fiber bundle also occurs in Osyridicarpos. A molecular phylogenetic analysis using nuclear ribosomal ITS and the chloroplast trnLF spacer for representatives of all genera in Thesiaceae showed that Lacomucinaea is sister to Osyridicarpos, further supporting this relationship suggested by stem anatomy characters. Recognizing this taxon as a distinct genus results in the genus Thesium being monophyletic. A key to all genera in Thesiaceae is provided.

Phylogeny and biogeography of wild roses with specific attention to polyploids.

The genus Rosa (150-200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus. Phylogenetic relationships among 101 species of the genus Rosa were reconstructed using sequences from the plastid psbA-trnH spacer, trnL intron, trnL-F spacer, trnS-G spacer and trnG intron, as well as from nuclear glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which was used to identify putative allopolyploids and infer their possible origins. Chloroplast phylogeny was used to estimate divergence times and reconstruct ancestral areas. Most subgenera and sections defined by traditional taxonomy are not monophyletic. However, several clades are partly consistent with currently recognized sections. Allopolyploidy seems to have played an important role in stabilizing intersectional hybrids. Biogeographic analyses suggest that Asia played a central role as a genetic reservoir in the evolution of the genus Rosa. The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.

Conservation genetics of an endangered cycad, Dioon sonorense (Zamiaceae): implications from variation of chloroplast DNA

The endemic species Dioon sonorense comprises the northernmost group of populations of Dioon , in Sonora, Mexico. Although it is endangered, only the southern populations are protected within a preservation area, while the remaining populations have not been taken into account in management plans or genealogical studies. Describing the intraspecific genealogy and the geographical structure of the genetic variation of D. sonorense may help in the identification of units for further conservation. Therefore, the main objective of this study was to describe the intraspecific genealogy of populations throughout the range of distribution of the endangered species D. sonorense , using haplotypes of the trnL-F spacer of the cpDNA. In addition, the levels of diversity of the employed molecular marker were estimated. Low levels of variability were recorded and at least two evolutionary units, corresponding to each haplotype, were identified as components of the species. The inclusion of northern populations into conservation programs is recommended. In order to integrate these findings to the genealogy of genus Dioon , trnL-F sequences of all the remaining species were merged and analyzed. An ancestral haplotype with wide distribution was detected in several species and one haplotype in D. sonorense was found shared with its sister species, D. tomasellii . This work represents a first attempt to reconcile a genealogical approach in the identification of important centers of genetic diversity of Mexican cycads.

Taxonomic status and genetic differentiation of Hyrcanian Castanea based on noncoding chloroplast DNA sequences data

The taxonomy and phylogenetic relationships among Castanea species were investigated using sequence data from the chloroplast trnL-F and trnH-psbA intergenic spacer regions. Samples included Castanea specimens of uncertain taxonomic affinity that were collected in the Hyrcanian forest of northern Iran. The trnL-F data were more informative than trnH-psbA, having seven parsimony-informative sites. A low level of haplotype diversity was detected within Hyrcanian samples and the whole species of the genus Castanea. In the trnL-F dataset, Castanea sativa and Castanea mollissima have unique character states that differentiate them from other species of Castanea. The genus Castanea was recovered as a monophyletic with high to moderate support when inferred from combined trnH-psbA and trnL-F spacer data. Two main lineages received minimal support in the trnL-F analysis, whereas trnH-psbA could not distinguish different species of Castanea from each other. Finally, low levels of haplotype diversity was found within small remnant stands of Castanea in the Hyrcanian forest, indicating that genetic erosion may increase the extinction risk for these valuable trees.

Sibbaldia: a molecular phylogenetic study of a remarkably polyphyletic genus in Rosaceae

Using DNA sequence data from nuclear ribosomal ITS in combination with plastid trnLF spacer and trnL intron data, we show that Sibbaldia is a polyphyletic assemblage. It falls into five separate clades of Potentilleae, three within Fragariinae and two within Potentilla (Potentillinae sensu Sojak). To a large extent, our results are congruent with Sojak’s findings based on morphological characters such as anther structure. Four of the Sibbaldia species included in this study remain in Sibbaldia, while S. adpressa is classified in Sibbaldianthe, S. perpusilloides is considered to represent a new genus in Fragariinae, Chamaecallis Smedmark, S. micropetala is nested within the Potentilla anserina clade, and four species belong to a basal clade of Potentilla. The phylogenetic affinity of Sibbaldiopsis is still unsettled, but one of the three species that have been classified in the genus is found to belong inside Sibbaldia, and it should be named Sibbaldia retusa (O.F. Muller) T. Erikss. Further study will show whether the remaining two species, Potentillacuneifolia and P. miyabei, are more closely related to Sibbaldia, Sibbaldianthe, or if they make up a distinct lineage separate from either of these.

Phylogeny of Miliusa (Magnoliales: Annonaceae: Malmeoideae: Miliuseae), with descriptions of two new species from Malesia

The molecular phylogeny of Miliusa (Annonaceae) is reconstructed, with 27 (of ca. 50) species included, using a combination of seven plastid markers (rbcL exon, trnL intron, trnL-F spacer, matK exon, ndhF exon, psbA-trnH spacer, and ycf1 exon) constituting ca. 7 kb. In addition, two new species of Miliusa are described from the Malesian area: M. butonensis sp. nov. from Buton Island, Indonesia and M. viridiflora sp. nov. from Papua New Guinea. The former is included in the molecular phylogenetic analysis. The reconstructed phylogeny corresponds well to the informal morphological grouping proposed earlier. A revised key to 13 Austro-Malesian species of Miliusa is provided.

Integrative systematics supports the establishment of Winitia, a new genus of Annonaceae (Malmeoideae, Miliuseae) allied to Stelechocarpus and Sageraea

The generic circumscriptions of Stelechocarpus and Sageraea (Annonaceae) are assessed using molecular phylogenetic, macromorphological, and pollen morphological evidence. For molecular phylogenetic analysis the combined seven plastid markers: rbcL exon, trnL intron, trnL-F spacer, matK exon, ndhF exon, psbA-trnH spacer, and ycf1 exon constituting c. 7 kb are used. The results corroborate the recognition of a maximally supported clade as a new genus, Winitia. It is weakly to moderately supported as sister to Stelechocarpus burahol, the type and only species of Stelechocarpus. A clade consisting of Winitia and Stelechocarpus is strongly supported as sister to Sageraea, which is monophyletic with strong support. Winitia consists of two species, one of which (W. expansa) is proposed as a new species endemic to Thailand, whereas one new combination (W. cauliflora) is made. The new genus is primarily characterized by (1) multicolumellar stigmas (≥ 5 columns per stigma) and (2) pollen grains with a very thin tectum, a more or less columellate/coarsely granular infratectum, and a very distinct basal layer. The macromorphology and pollen morphology of the three genera (Stelechocarpus, Winitia, and Sageraea) are highlighted.

A new endemism for the Azores: the case of Centaurium scilloides (L. f.) Samp.

Centauriumscilloides is a very isolated taxon, taking into account morphological characteristics, chromosome number, and disjunct Atlantic distribution. Comparison of the Azorean plants with those living in mainland Europe reveals significant differences, which question their assimilation into a single taxon. Our molecular data inferred from sequences of nrDNA (internal transcribed spacer, ITS) and plastid regions (trnL intron and trnL-F spacer), confirmed the hypothesis that plants of C. scilloides from the Azores archipelago are different than those distributed on the Atlantic coasts of Europe, and both should, consequently, be treated as independent species. As a result, a new systematic treatment is proposed.

Abelia and relatives: phylogenetics of Linnaeeae (Dipsacales-Caprifoliaceae s.l.) and a new interpretation of their inflorescence morphology

We present a phylogenetic analysis with sampling from all taxonomic groups in the tribe Linnaeeae (Caprifoliaceae) and interpret the results in relation to inflorescence morphology. Characters from inflorescences are shown to be highly informative for the classification of Linnaeeae; however, they have been neglected in recent studies, possibly as a result of confusion between descriptive and typological views. The phylogenetic relationships of 27 taxa are investigated using the nuclear ribosomal internal transcribed spacer (ITS) region and multiple plastid regions (rbcL, ndhF, matK, trnL intron and trnL-F spacer). Two additional plastid regions, atpB-rbcL and the trnK intron, are also investigated for a subset of taxa. Results indicate that several taxonomic groups, including sections and genera, are not monophyletic. Several groups are supported, e.g. Zabelia, Vesalea and Abelia section Abelia, but Abelia series Serratae is not supported. A new hypothesis for inflorescence evolution in Dipsacales is proposed, and the distinctiveness of Abelia series Serratae is reinforced. The position of tribe Zabeliinae remains unclear within Caprifoliaceae.

An Expanded Plastid Phylogeny of Marsilea with Emphasis on North American Species

Abstract Ferns of the genus Marsilea (water clover) are potentially invasive aquatic and wetland plants. They are difficult to identify to species because of subtle diagnostic characters, the sterile condition of many specimens, and unresolved taxonomic problems. We sequenced four plastid regions (rbcL, rps4, rps4-trnS spacer, and trnL-F spacer) from 223 accessions across ca. 38 species. Our goals were to: 1) attempt to identify problematic Marsilea specimens from the southeastern U.S., and 2) assess species delimitation using molecular data. Florida specimens previously identified as M. aff. oligospora do not match true M. oligospora (native to the western USA), and might represent an undescribed native species. The molecular data fail to resolve many species as monophyletic within the New World Marsilea section Nodorhizae. The data reveal two strongly supported clades within section Nodorhizae: 1) A western U.S. /Mexican clade; and 2) A U.S. Gulf coastal plain/Florida/Caribbean clade. This DNA/morpholog...

Molecular circumscription and major evolutionary lineages of the fern genus Dryopteris (Dryopteridaceae).

BackgroundThe fern genus Dryopteris (Dryopteridaceae) is among the most common and species rich fern genera in temperate forests in the northern hemisphere containing 225–300 species worldwide. The circumscription of Dryopteris has been controversial and various related genera have, over the time, been included in and excluded from Dryopteris. The infrageneric phylogeny has largely remained unclear, and the placement of the majority of the supraspecific taxa of Dryopteris has never been tested using molecular data.ResultsIn this study, DNA sequences of four plastid loci (rbcL gene, rps4-trnS spacer, trnL intron, trnL-F spacer) were used to reconstruct the phylogeny of Dryopteris. A total of 122 accessions are sampled in our analysis and they represent 100 species of the expanded Dryopteris including Acrophorus, Acrorumohra, Diacalpe, Dryopsis, Nothoperanema, and Peranema. All four subgenera and 19 sections currently recognized in Dryopteris s.s. are included. One species each of Arachniodes, Leptorumohra, and Lithostegia of Dryopteridaceae are used as outgroups. Our study confirms the paraphyly of Dryopteris and provides the first strong molecular evidence on the monophyly of Acrophorus, Diacalpe, Dryopsis, Nothoperanema, and Peranema. However, all these monophyletic groups together with the paraphyletic Acrorumohra are suggested to be merged into Dryopteris based on both molecular and morphological evidence. Our analysis identified 13 well-supported monophyletic groups. Each of the 13 clades is additionally supported by morphological synapomophies and is inferred to represent a major evolutionary lineage in Dryopteris. In contrast, monophyly of the four subgenera and 15 out of 19 sections currently recognized in Dryopteris s.s is not supported by plastid data.ConclusionsThe genera, Acrophorus, Acrorumohra, Diacalpe, Dryopsis, Nothoperanema, and Peranema, should all be merged into Dryopteris. Most species of these genera share a short rhizome and catadromic arrangement of frond segments, unlike the sister genus of Dryopteris s.l., Arachniodes, which has anadromic arrangement of frond segments. The non-monophyly of the 19 out of the 21 supraspecific taxa (sections, subgenera) in Dryopteris strongly suggests that the current taxonomy of this genus is in need of revision. The disagreement between the previous taxonomy and molecular results in Dryopteris may be due partly to interspecific hybridization and polyplodization. More morphological studies and molecular data, especially from the nuclear genome, are needed to thoroughly elucidate the evolutionary history of Dryopteris. The 13 well-supported clades identified based on our data represent 13 major evolutionary lineages in Dryopteris that are also supported by morphological synapomophies.

Molecular phylogenetics of the juno irises, Iris subgenus Scorpiris (Iridaceae), based on six plastid markers

Relationships among the roughly 55 species of Iris subgenus Scorpiris have been studied. A matrix of six plastid DNA regions (matK, rpl14-rps8 spacer, infA-rpl36 spacer, trnE-trnT spacer, trnL intron and trnL-F spacer) was produced from 57 accessions (52 taxa) and analysed with both parsimony and Bayesian methods. Five major clades are identified, of which four have strong geographical correlations, whereas the fifth corresponds to Iris section Physocaulon. In our results, several species are placed with species not previously considered to be related, although, in some cases, there are morphological characters that suggest that these newly indicated relationships are reasonable. For some of the other oddly grouped species, we can only assume that remarkable parallelisms in morphology have occurred or hybridization is involved. Presently, with plastid DNA as our only comprehensive data resource, we are not able to evaluate more thoroughly these more puzzling associations of species. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 281–300.

Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) on the basis of plastid and nuclear DNA

The internal transcribed spacers (ITS) of nuclear ribosomal DNA (nrDNA) and plastid DNA, including the trnL intron, the trnL-F spacer, and the atpB-rbcL spacer, from most of the living species in the genus Phalaenopsis were sequenced. The monophyly of the genus described by Christenson (Christenson EA (2001) Phalaenopsis. Timber Press, Portland, p 330), that Doritis and Kingidium are synonyms of Phalaenopsis, was supported by these molecular data. Within the genus, subgenus Polychilos was monophyletic, and the species were divided into two subclades. The subgenus Phalaenopsis was shown to be non-monophyletic, because the sections Esmeralda and Deliciosae appeared separated the from sections Phalaenopsis and Stauroglottis. Meanwhile, subgenera Aphyllae and Parishianae were also shown to be non-monophyletic on the basis of the molecular data. Furthermore, the monotypic species of subgenus Proboscidioides, P. lowii, formed a clade with subgenus Aphyllae. In accordance with geographical distribution, the historical geography of Southeast Asia due to the periodic glacial epochs, and molecular phylogeny, two evolutionary trends of Phalaenopsis from the original center in South China to the Philippines, Indonesia, and Malaysia were suggested. First, using Indochina and some older parts of the Philippines (e.g., Mindoro and Palawan) as stepping stones, Phalaenopsis species dispersed from South China to the Philippines, where the sections Phalaenopsis and Stauroglottis of subgenus Phalaenopsis developed. Second, using the Malay Peninsula as a stepping stone, Phalaenopsis species dispersed from South China to Indonesia and Malaysia, where the subgenus Polychilos developed.

Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement.

The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250-300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and Trimelopter. Each of these has a particular syndrome of morphological characters. As a result, 105 new combinations are made and two new names are proposed to accommodate the taxa studied in the new arrangement. A short morphological diagnosis, synonymy, details of distribution and an identification key are presented.

Biogeography and Phylogeny of Cardamine (Brassicaceae)1

Abstract The biogeography and phylogeny of Cardamine L. were inferred based on sequences of the nuclear ribosomal ITS regions and the plastid trnL intron and trnL-F spacer regions. This genus is one of the largest and polyploid-rich genera of the Brassicaceae and has its center of diversity in Eurasia. Species were included from all populated continents, representing all sections except two monotypic ones. The results support a hypothesis of recent and rapid speciation in the genus. The traditional sectional classification was not supported. We found evidence for several extremely long-distance dispersal events. Colonization of the Southern Hemisphere and the Arctic has occurred repeatedly; we identified at least three phylogenetically distinct Arctic lineages, two distinct Oceanian lineages, and four distinct South American lineages. Polyploidization has occurred independently many times during the evolution of Cardamine. Recent divergence combined with widespread polyploidization offer an explanation fo...

Molecular systematics of Gagea and Lloydia (Liliaceae; Liliales): implications of analyses of nuclear ribosomal and plastid DNA sequences for infrageneric classification

Gagea is a Eurasian genus of petaloid monocots, with a few species in North Africa, comprising between 70 and approximately 275 species depending on the author. Lloydia (thought to be the closest relative of Gagea) consists of 12-20 species that have a mostly eastern Asian distribution. Delimitation of these genera and their subdivisions are unresolved questions in Liliaceae taxonomy. The objective of this study is to evaluate generic and infrageneric circumscription of Gagea and Lloydia using DNA sequence data. A phylogenetic study of Gagea and Lloydia (Liliaceae) was conducted using sequences of nuclear ribosomal internal transcribed spacer (ITS) and plastid (rpl16 intron, trnL intron, trnL-F spacer, matK and the psbA-trnH spacer) DNA regions. This included 149 accessions (seven as outgroups), with multiple accessions of some taxa; 552 sequences were included, of which 393 were generated as part of this research. A close relationship of Gagea and Lloydia was confirmed in analyses using different datasets, but neither Gagea nor Lloydia forms a monophyletic group as currently circumscribed; however, the ITS and plastid analyses did not produce congruent results for the placement of Lloydia relative to the major groups within Gagea. Gagea accessions formed five moderately to strongly supported clades in all trees, with most Lloydia taxa positioned at the basal nodes; in the strict consensus trees from the combined data a basal polytomy occurs. There is limited congruence between the classical, morphology-derived infrageneric taxonomy in Gagea (including Lloydia) and clades in the present phylogenetic analyses. The analyses support monophyly of Gagea/Lloydia collectively, and they clearly comprise a single lineage, as some previous authors have hypothesized. The results provide the basis for a new classification of Gagea that has support from some morphological features. Incongruence between plastid and nuclear ITS results is interpreted as potentially due to ancient hybridization and/or paralogy of ITS rDNA.

A phylogenetic study of Laeliinae (Orchidaceae) based on combined nuclear and plastid DNA sequences

Laeliinae are a neotropical orchid subtribe with approx. 1500 species in 50 genera. In this study, an attempt is made to assess generic alliances based on molecular phylogenetic analysis of DNA sequence data. Six DNA datasets were gathered: plastid trnL intron, trnL-F spacer, matK gene and trnK introns upstream and dowstream from matK and nuclear ITS rDNA. Data were analysed with maximum parsimony (MP) and Bayesian analysis with mixed models (BA). Although relationships between Laeliinae and outgroups are well supported, within the subtribe sequence variation is low considering the broad taxonomic range covered. Localized incongruence between the ITS and plastid trees was found. A combined tree followed the ITS trees more closely, but the levels of support obtained with MP were low. The Bayesian analysis recovered more well-supported nodes. The trees from combined MP and BA allowed eight generic alliances to be recognized within Laeliinae, all of which show trends in morphological characters but lack unambiguous synapomorphies. By using combined plastid and nuclear DNA data in conjunction with mixed-models Bayesian inference, it is possible to delimit smaller groups within Laeliinae and discuss general patterns of pollination and hybridization compatibility. Furthermore, these small groups can now be used for further detailed studies to explain morphological evolution and diversification patterns within the subtribe.