Phylogeny of the paleotropical fern genus Lepisorus (Polypodiaceae,Polypodiopsida) inferred from four chloroplast DNA regions

Phylogenetic relationships within the paleotropical genus Lepisorus (Polypodiaceae) were investigated using plastid DNA sequences from four regions: rbcL, rps4 and rps4-trnS IGS, trnL intron plus trnL-F IGS, rbcL-atpB IGS. Over 4000 nucleotides were sequenced for 77 specimens belonging to 54 species. Each cpDNA region was analyzed separately and combined into a single dataset. All phylogenetic analyses, maximum parsimony, maximum likelihood and Bayesian Inference of phylogeny, revealed the paraphyly of Lepisorus with the monotypic Drymotaenium miyoshianum and of the paleotropical genus Belvisia nested within the Lepisorus clade. Nine well-supported major clades were found. The phylogenetic results provided new evidence for the sectional classification of Lepisorus. The evolution of three morphological characters, clathrateness of rhizome scales, margin of rhizome scales and defoliated leaves, and the evolution of the karyotype, were reconstructed to identify lineage specific phenotypic character states or combination of characters. Unique character combinations, rather than synapomorphies, were found to be of systematic value in sectional delimitation. The variation of chromosome numbers is largely due to a single aneuploidy event instead of a stepwise reduction during the evolutionary history of this genus.     

Phylogeny and morphological evolution of tribe Menispermeae (Menispermaceae) inferred from chloroplast and nuclear sequences

The Menispermaceae family contains ca. 72 genera with 450 species that are almost entirely tropical. Its phylogeny at the tribal level has never been examined using molecular data. Here we used DNA sequences of the chloroplast matK gene and trnL-F regions, and the nuclear ITS region to study the delimitation and position of the tribe Menispermeae within the family and its subtribal monophyletic groups. Family-wide phylogenetic analyses of the chloroplast data produced two strongly supported clades. The first clade contains two subclades: Coscinieae including Arcangelisia and Anamirta, and Tinosporeae sensu lato including Fibraureae, supported by morphological characters, such as traits of the cotyledon, stylar scar and embryo. The second clade consists of the tribes Menispermeae sensu DC. and Tiliacoreae Miers. All our analyses surprisingly recognized that tribe Menispermeae is not monophyletic unless tribe Tiliacoreae is included, suggesting that characters of cotyledon and stylar scar are very important for the infrafamilial classification, and that endosperm presence vs. absence was over-emphasized in traditionally tribal division of the family. Our topologies indicate a secondary loss of endosperm. The monophyly of two subtribes of the tribe Menispermeae, Stephaniinae and Cissampelinae, is supported by the cpDNA and ITS data, as well as by morphological characters, including aperture types and shapes, and colpal membrane features of pollen grains, and sepal number of male flowers. The Cocculinae was recognized as a paraphyletic group containing the remaining genera of the tribe Menispermeae.     

Phylogeny of the genus Tordylium (Tordylineae,Apioideae, Apiaceae) inferred from morphological data

Tordylium is a medium‐sized genus characterized by an annual habit, 1–3‐pinnate leaves, dorsally compressed mericarps, and thickened mericarp margins. Eighteen Tordylium species occur in Turkey, of which seven are endemic. Although the morphology of the genus is well known, evolutionary relationships among its species have never been evaluated. In this study, phylogenetic relationships within Tordylium are investigated using parsimony analysis based on morphological data from 17 ingroup and 15 outgroup taxa from Turkey. The results indicate that Tordylium is paraphyletic due to the inclusion of Ormosciadium. Further, it suggests that Hasselquistia, Condylocarpus and Ainsworthia are nested within Tordylium, confirming their current taxonomic treatment as synonyms. Within the paraphyletic Tordylium, two major clades are apparent, but these clades are not compatible with the current sub‐generic classification. Tordylium lanatum, T. aegyptiacum and T. elegans, which have dimorphic mericarps, form a monophyletic subclade. In addition, it is suggested that T. aegaeum should be accepted as a distinct species rather than as a synonym of T. pestalozzae.     

Phylogeny ofTyphonium (Araceae) inferred from restriction fragment analysis of chloroplast DNA

The interrelationship of the ten species of the genusTyphonium and related genera in subtribe Arinae of the Araceae was inferred by chloroplast DNA restriction fragment analysis. A total of 42 site mutations were observed and 26 site mutations were shared by two or more species. A majority rule consensus tree was made by performing 100 bootstrap replicates using Wagner Parsimony. Two groups ofTyphonium were recognized significantly as monophyletic groups, i.e. 1)Typhonium larsenii andT. kunmingense, and 2)T. trilobatum, T. blumei andT. flagelliforme.     

Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from analyses of nuclear and chloroplast DNA regions

From a phylogenetic perspective, the genus Manihot can be considered as an orphan group of plants, and the scientific knowledge acquired has been mainly related to cassava, one of the most important crops in poor tropical countries. The goal of the majority of evolutionary studies in the genus has been to decipher the domestication process and identify the closest relatives of cassava. Few investigations have focused on wild Manihot species, and the phylogeny of the genus is still unclear. In this study the DNA sequence variation from two chloroplast regions, the nuclear DNA gene G3pdh and two nuclear sequences derived from the 3'-end of two cassava ESTs, were used in order to infer the phylogenetic relationships among a subset of wild Manihot species, including two species from Cnidoscolus as out-groups. Maximum parsimony and Bayesian analyses were conducted for each data set and for a combined matrix due to the low variation of each region when analyzed independently. A penalized likelihood analysis of the chloroplast region trnL-trnF, calibrated with various age estimates for genera in the Euphorbiaceae extracted from the literature was used to determine the ages of origin and diversification of the genus. The two Mesoamerican species sampled form a well-defined clade. The South American species can be grouped into clades of varying size, but the relationships amongst them cannot be established with the data available. The age of the crown node of Manihot was estimated at 6.6 million years ago. Manihot esculenta varieties do not form a monophyletic group that is consistent with the possibility of multiple introgressions of genes from other wild species. The low levels of variation observed in the DNA regions sampled suggest a recent and explosive diversification of the genus, which is confirmed by our age estimates.     

Phylogeny and evolution of Dyckia (Bromeliaceae) inferred from chloroplast and nuclear sequences

The genus Dyckia (Bromeliaceae) comprises more than 150 terrestrial or epilithic species with a strongly xeromorphic habit. Most of its members belong to the azonal rock vegetation of Neotropical savannas and forests of Brazil and adjacent countries. Dyckia is relatively species-rich compared with its closest relatives Encholirium (27 species) and Deuterocohnia (17 species). Here, we present the first molecular phylogenetic analysis of Dyckia using DNA sequence data from six plastid loci (matK gene, rps16 intron, petD intron, rpl32-trnL, rps16-trnK and trnD-trnT) and a portion of the nuclear gene phyC. A total of 124 accessions were included, corresponding to 79 taxa from six genera. Phylogenetic trees were generated using parsimony, likelihood and Bayesian methods. DNA sequence variation among Dyckia species turned out to be extremely low, and phylogenies were poorly resolved. The monophyly of Dyckia is supported, whereas evidence is provided that Encholirium is paraphyletic. Based on a dated plastid DNA tree, Dyckia experienced a recent radiation starting around 2.9 million years ago. Four major clades could be identified that roughly correspond to the geographic origin of the samples. A parsimony network based on plastid DNA haplotypes shows a star-like pattern, indicating recent range expansions. Our data are compatible with a scenario where Dyckia and Encholirium diverged in northeastern Brazil, whereas one lineage of Dyckia dispersed to southern Brazil from where a rapid colonization of suitable habitats was initiated. We discuss our results in relation to species delimitation in Dyckia.     

Phylogeny and evolution of the South African genus Metalasia (Asteraceae–Gnaphalieae) inferred from molecular and morphological data

Metalasia is a genus in tribe Gnaphalieae (Asteraceae), endemic to South Africa and with its main distribution in the Cape Floristic Region. The genus comprises 57 species and, with a number of closely related genera, it constitutes the ‘Metalasia clade’. A species‐level phylogenetic analysis is presented, based on DNA sequences from two nuclear (internal and external transcribed spacer: ITS, ETS) and two plastid (psbA‐trnH, trnL‐trnF) regions together with morphological data. Analyses combining molecular and morphological data attempt not only to resolve species interrelationships, but also to detect patterns in character evolution. Phylogenetic analyses corroborate our earlier study and demonstrate that Metalasia is formed of two equally sized, well‐supported sister groups, one of which is characterized by papillose cypselas. The results differ greatly from earlier hypotheses based on morphology alone, as few morphological characters support the phylogenetic patterns obtained. The two clades of Metalasia do, however, appear to differ in distribution, corresponding to the different rainfall regimes of South Africa. Analyses show a few taxa to be problematic; one example is the widely distributed M. densa which appears to be an intricate species complex. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 173–198.     

The evolution of growth-forms in the Macaronesian genus Aeonium (Crassulaceae) inferred from chloroplast DNA RFLPs and morphology

Phylogenetic relationships among species of Aeonium were studied using morphological characters and chloroplast DNA RFLPs. Cladistic analysis of weighted morphological data indicates that the small, herbaceous and least woody species are basal in the genus. Chloroplast DNA data gave similar results, supporting the separation of the herbaceous or small, woody species from the large, hapaxanth rosettes, rosette trees, and branched subshrubs with yellow, white or red flowers as well as the only (herbaceous) species with axillary inflorescences. The relationships among the species descending from a polytomy that comprises all species of the genus as well as a polytomy which comprises 18 of the 26 species studied, are only very incompletely resolved, except for two monophyletic clades that contain the branched subshrubs with yellow flowers ( A . sect. Aeonium ) and the branched subshrubs and rosette trees with white or red flowers ( A . sect. Leuconium ), respectively. Cladistic analysis of the combined morphological and chloroplast DNA data improved resolution considerably. Four monophyletic clades are distinguished, each of which, except for three species, comprises only one of the five main growth-form types. Although Aeonium is generally regarded as an outstanding example of adaptive radiation, this mode of speciation seems to have been of minor significance in the evolution of the genus, because each growth-form apparently evolved only once. Instead, island speciation in the absence of major ecological shifts, is probably more important in the evolution of the genus.     

Phylogeny and biogeography of Cedrus (Pinaceae) inferred from sequences of seven paternal chloroplast and maternal mitochondrial DNA regions

BACKGROUND AND AIMS: Cedrus (true cedars) is a very important horticultural plant group. It has a disjunct distribution in the Mediterranean region and western Himalaya. Its evolution and biogeography are of great interest to botanists. This study aims to investigate the phylogeny and biogeography of Cedrus based on sequence analyses of seven cytoplasmic DNA fragments. METHODS: The methods used were PCR amplification and sequencing of seven paternal cpDNA and maternal mtDNA fragments, parsimony and maximum likelihood analyses of the DNA dataset, and molecular clock estimate of divergence times of Cedrus species. KEY RESULTS: Phylogenies of Cedrus constructed from cpDNA, mtDNA and the combined cp- and mt-DNA dataset are identical in topology. It was found that the Himalayan cedar C. deodara diverged first, and then the North African species C. atlantica separated from the common ancestor of C. libani and C. brevifolia, two species from the eastern Mediterranean area. Molecular clock estimates suggest that the divergence between C. atlantica and the eastern Mediterranean clade at 23.49 +/- 3.55 to 18.81 +/- 1.25 Myr and the split between C. libani and C. brevifolia at 7.83 +/- 2.79 to 6.56 +/- 1.20 Myr. CONCLUSIONS: The results, combined with palaeogeographical and palaeoecological information, indicate that Cedrus could have an origin in the high latitude area of Eurasia, and its present distribution might result from vicariance of southerly migrated populations during climatic oscillations in the Tertiary and further fragmentation and dispersal of these populations. It is very likely that Cedrus migrated into North Africa in the very late Tertiary, while its arrival in the Himalayas would not have been before the Miocene, after which the phased or fast uplift of the Tibetan plateau happened.     

Phylogeny of the mud worm genus Marenzelleria (Polychaeta, Spionidae) inferred from mitochondrial DNA sequences

The taxonomy of the cryptic morphospecies of the mud worm genus Marenzelleria is particularly difficult and the phylogenetic relationship within the genus is unknown. Herein we reconstructed the phylogeny of all five species of this genus using sequence data of three mitochondrial genes (16SrDNA, cytochrome b, cytochrome oxidase subunit I) from 104 specimens out of 26 populations. For the three invasive species of the genus, Marenzelleria neglecta, M. viridis and M. arctia , individuals from native populations as well as from recently invaded populations were included. Nuclear 18S rDNA sequences were used to evaluate the appropriate outgroup taxon among several spionid polychaete species. The results supported the monophyly of Marenzelleria , and Malacoceros fuliginosus was found to be a suitable outgroup for the analysis of the mitochondrial gene segments. All phylogenetic reconstructions revealed a basal position of M. arctia and M. wireni , which have primarily Arctic distribution, with M. arctia obtaining the most basal position. Together with the present-day distribution of the species, this indicates an origin of the genus in the Arctic region. The relationship of the species M. neglecta , M. viridis and M. bastropi could not be resolved sufficiently due to genealogical discordance that might reflect relatively young cladogenetic events.     

Phylogeny of the genus Aphis Linnaeus, 1758 (Homoptera: Aphididae) inferred from mitochondrial DNA sequences

Aphis is the largest aphid genus in the world and contains several of the most injurious aphid pests. It is also the most reluctant aphid genus to any comprehensive taxonomic treatment: while most species are easily classified into "species groups" that form well defined entities, numerous species within these groups are difficult to tell apart morphologically and identification keys remain ambiguous and mostly rely on host plant affiliation. In this paper, we used partial sequences of COI/COII and CytB genes to reconstruct the first phylogeny of Aphis and discuss the present systematics. The monophyly of the subgenus Bursaphis and of the tree major species groups, Black aphid, Black backed aphid and frangulae-like species was recovered by all phylogenetic analyses. However our data suggested that the nominal subgenus was not monophyletic. Relationships between major species groups were often ambiguous but "Black" and "Black backed" species groups appeared as sister clades. The most striking result of this study was that our molecular data met the same limits as the morphological characters used in classifications: mitochondrial DNA did not allow the differentiation of species that are difficult to identify. Further, interspecies relationships within groups of species for which taxonomic treatment is difficult stayed unresolved. This suggests that species delineation in the genus Aphis is often ambiguous and that diversification might have been a rapid process.     

Phylogeny,biogeography, and morphological ancestral character reconstruction in the Mediterranean genus Fumana (Cistaceae)

Fumana is a diverse genus of the Cistaceae family, consisting of 21 currently accepted species. In this study, nuclear (ITS) and plastid (matK, trnT‐L) molecular markers were used to reconstruct the phylogeny and to estimate divergence times, including 19 species of Fumana. Phylogenetic analyses (Bayesian Inference, Maximum Parsimony and Maximum Likelihood) confirmed the monophyly of Fumana and did not support the infrageneric divisions previously established. The results support four main clades that group species that differ in vegetative and reproductive characters. Given the impossibility to define morphological characters common to all species within the clades, our proposal is to reject infrageneric divisions. Molecular dating and ancestral area analyses provide evidence for a Miocene diversification of the genus in the north‐western Mediterranean. Ancestral state reconstructions revealed ancestral character states for some traits related to xeric and arid habitats, suggesting a preadaptation to the Mediterranean climate.     

根据叶绿体ndhF和核核糖体DNA序列推断梓属(紫葳科)的系统发育

Phylogenetics of Chilopsis and Catalpa (Bignoniaceae) was elucidated based on sequences of chloroplast ndhF and the nrDNA ITS region. In Bignoniaceae, Chilopsis and Catalpa are most closely related as sister genera. Our data supported section Macrocatalpa of the West Indies and section Catalpa of eastern Asian and North American continents. Within section Catalpa, Catalpa ovata of eastern Asia form a clade with North American species, C. speciosa and C. bignonioides, while the other eastern Asian species comprise a clade where C. duclouxii is sister to the clade of C. bungei and C. fargesii. The Caribbean species of Catalpa diverged early from the continental species. More studies are needed to test whether the phylogenetic pattern is common in eastern Asian-North American disjunct genera with species in the West Indies.     

Phylogeny of magpies (genus Pica) inferred from mtDNA data

We investigated the phylogenetic relationships of species and subspecies of the cosmopolitan genus Pica using 813 bp of the mitochondrial genome (including portions of 16s rDNA, tRNA-Leu, and ND1). The phylogenetic relationships within the genus Pica revealed in our molecular analyses can be summarized as follows: (1). the Korean magpie (Pica pica sericea) appears basal within the genus Pica; (2). the European magpie (Pica pica pica) shows a close relationship to the Kamchatkan magpie (Pica pica camtschatica); (3). two North American species (Pica hudsonia and Pica nuttalli) shows a sister-group relationship; (4). most importantly, the European+Kamchatkan clade appears more closely related to the North American clade than to Korean magpies. Based on these results and genetic distance data, it is possible that members of an ancestral magpie lineage in East Asia initially moved north to form Kamchatkan magpies and then crossed the Bering land bridge to found North American taxa. At a later date, a group might have split off from Kamchatkan magpies and migrated west to form the Eurasian subspecies. The divergence between the two North American taxa appears to have happened no later than the divergence of Eurasian subspecies and both processes appear to have been relatively rapid. Rather than the formation of P. hudsonia by re-colonization from an Asian magpie ancestor, as suggested by, our data suggest a shared ancestry between P. hudsonia and P. nuttalli. Based on the above findings, including phylogenetic placement of P. hudsonia and P. nuttalli as nested within the larger Pica pica clade, and the lack of evidence suggesting reproductive isolation within the genus Pica, we believe that the current classification may be inaccurate. A more conservative classification would recognize one monophyletic species (i.e., P. pica) and treat P. nuttalli and P. hudsonia as subspecies (i.e., P. p. nuttalli and P. p. hudsonia). More extensive studies on the population genetics and biogeography of magpies should be conducted to better inform any taxonomic decisions.     

Phylogeny and biogeography of the genus Lycium (Solanaceae): inferences from chloroplast DNA sequences

Lycium comprises approximately 70 species and is disjunctly distributed in temperate to subtropical regions in South America, North America, southern Africa, Eurasia, and Australia. Among them, only Lycium sandwicense A. Gray sporadically occurs widely on oceanic islands in the Pacific Ocean. To investigate phylogenetic and biogeographic relationships of the genus with emphasis on L. sandwicense, the coding region of matK, the two intergenic spacers trnT (UGU)-trnL (UAA) and trnL (UAA)-trnF (GAA), and the trnL (UAA) intron of chloroplast DNA (cpDNA) were sequenced. A strict consensus tree resulting from the phylogenetic analysis indicates the following: (1) New World species comprise a potentially paraphyletic assemblage; (2) southern African, Australian, and Eurasian species together are monophyletic; (3) southern African species are a paraphyletic assemblage; and (4) L. sandwicense is in a clade with certain New World species. The estimated biogeographic events based on the cpDNA analysis indicate that (1) Lycium originated in the New World, (2) all southern African, Australian, and Eurasian species have a common ancestor from the New World, (3) Australian and Eurasian species originated once from a southern African progenitor, and (4) L. sandwicense differentiated from the New World species.     

Phylogeny and character evolution in the Indo-Pacific genus Ctenogobiops (Gobiiformes: Gobiidae)

Ctenogobiops is a genus of Indo-Pacific gobies that form obligate, mutualistic associations with shrimp in the genus Alpheus. This study provides a molecular phylogenetic analysis of eight Ctenogobiops species: C. aurocingulus, C. crocineus, C. feroculus, C. formosa, C. maculosus, C. mitodes, C. tangaroai, and C. tongaensis. We recover two clades within the genus, one consisting of C. feroculus and C. aurocingulus, the second including the remaining species arrayed as follows: (C. tongaensis (C. mitodes (C. formosa (C. maculosus (C. crocineus, C. tangaroai))))). Recovery of C. maculosus and C. crocineus as distinct taxa suggests that these species are not synonymous, although sampling in this study is limited. Species of Ctenogobiops are morphologically very similar to each other, with generally consistent meristic character states present throughout the genus. Recognition of species is based primarily on slight variations in color pattern, shape of the dorsal fin, and size of the gill opening. Comparison of our specimens of C. mitodes with accounts of C. pomastictus confirms that color pattern variations and lateral scale counts are more reliable indicators of species identity than relative dorsal fin spine length, particularly for smaller specimens. We evaluate the distribution of morphological characters in the context of the new phylogenetic hypothesis, and provide a summary of distinguishing characters for Ctenogobiops species. In this case, as in other instances of diverse reef-dwelling fish taxa, molecular data are ideal for inferring phylogenetic relationships, whereas morphological data remain the most expedient way to identify species.     

Phylogeny of the Malus (apple tree) species,inferred from its morphological traits and molecular DNA analysis

Some debated issues of the genus Malus (apple) taxonomy were examined using a variety of species from the collection of the Maikop Experimental Station, Vavilon Research Institute of Plant Industry (Krasnodar krai). Phylogenetic relationships among these species were studied using traditional analysis of morphological traits, RAPD, and complete sequencing of the 5'-internal transcribed spacer (ITS1), 5.8S rRNA, 3'-internal transcribed spacer (ITS2) (constituting a cluster of the rRNA genes), and the terminal fragment of the matK gene encoding chloroplast maturase. The results showed that the Sorbomalus section was polyphyletic; the American apple M. fusca was closely related to the species contributing to the East Asian center of the genus origin, and the American species M. angustifolia, M. coronaria, and M. ioensis were closely related to the M. trilobata relict species, whose assignment to the genus Malus is debated by some authors. Molecular analysis of the species relationships showed that the Middle Asian apple M. sieversii is the species from which apple domestication started.     

Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences

BACKGROUND AND AIMS: Rheum, a highly diversified genus with about 60 species, is mainly confined to the mountainous and desert regions of the Qinghai-Tibetan plateau and adjacent areas. This genus represents a good example of the extensive diversification of the temperate genera in the Qinghai-Tibetan plateau, in which the forces to drive diversification remain unknown. To date, the infrageneric classification of Rheum has been mainly based on morphological characters. However, it may have been subject to convergent evolution under habitat pressure, and the systematic position of some sections are unclear, especially Sect. Globulosa, which has globular inflorescences, and Sect. Nobilia, which has semi-translucent bracts. Recent palynological research has found substantial contradictions between exine patterns and the current classification of Rheum. Two specific objectives of this research were (1) to evaluate possible relationships of some ambiguous sections with a unique morphology, and (2) to examine possible occurrence of the radiative speciation with low genetic divergence across the total genus and the correlation between the extensive diversification time of Rheum and past geographical events, especially the recent large-scale uplifts of the Qinghai-Tibetan Plateau. METHODS: The chloroplast DNA trnL-F region of 29 individuals representing 26 species of Rheum, belonging to seven out of eight sections, was sequenced and compared. The phylogenetic relationships were further constructed based on the sequences obtained. KEY RESULTS: Despite the highly diversified morphology, the genetic variation in this DNA fragment is relatively low. The molecular phylogeny is highly inconsistent with gross morphology, pollen exine patterns and traditional classifications, except for identifying all samples of Sect. Palmata, three species of Sect. Spiciformia and a few species of Sect. Rheum as corresponding monophyletic groups. The monotypic Sect. Globulosa showed a tentative position within the clade comprising five species of Sect. Rheum. All of the analyses revealed the paraphyly of R. nobile and R. alexandrae, the only two species of Sect. Nobilia circumscribed by the possession of large bracts. The crude calibration of lineages based on trnL-F sequence differentiation implied an extensive diversification of Rheum within approx. 7 million years. CONCLUSIONS: Based on these results, it is suggested that the rich geological and ecological diversity caused by the recent large-scale uplifts of the Qinghai-Tibetan Plateau since the late Tertiary, coupled with the oscillating climate of the Quaternary stage, might have promoted rapid speciation in small and isolated populations, as well as allowing the fixation of unique or rare morphological characters in Rheum. Such a rapid radiation, combined with introgressive hybridization and reticulate evolution, may have caused the transfer of cpDNA haplotypes between morphologically dissimilar species, and might account for the inconsistency between morphological classification and molecular phylogeny reported here.     

Phylogeny of subfamily Epidendroideae (Orchidaceae) inferred from ndhF chloroplast gene sequences

This project undertakes the first molecular-based phylogenetic study of subfamily Epidendroideae (Orchidaceae). Approximately 1200 nucleotides (from the 3' half of the chloroplast gene ndhF for 34 orchid taxa and a lilioid monocot, Clivia miniata (Amaryllidaceae), were subjected to phylogenetic analysis using parsimony and maximum likelihood methods. Oryza sativa (Poaceae), a nonlilioid monocot, was designated as outgroup. Trees from both parsimony and maximum likelihood methods suggest that subfamily Epidendroideae is monophyletic, with Listera (Neottieae) as sister. Although subtribal relationships are typically well resolved and have strong branch support, intertribal relationships are generally poorly resolved. Perhaps this general lack of resolution among tribes reflects a rapid species radiation that coincided with anatomical, physiological, and anatomical adaptations that initiated large-scale epiphytism in the ancestral Epidendroideae. Six taxa in this study exhibit deletions that are not evenly divisible by three and result in extensive sequence frameshifts. For example, one deletion is 227 bp in length and is flanked by the short direct repeat sequence; TCAATAGGAATTTCTTTT. Multiple deletions and frameshifts suggest that ndhF may be a pseudogene, in at least some orchid taxa.