A phylogenetic analysis of the nursery-web spider family Pisauridae, with emphasis on the genera Architis and Staberius (Araneae: Lycosoidea)

This study presents a general cladistic analysis of pisaurid genera, with emphasis on the Neotropical genera Architis Simon and Staberius Simon. The analysis was based on a matrix with 21 terminal taxa: eight species of Architis , Staberius spinipes (Taczanowski), seven exemplars of other pisaurid genera and five outgroup taxa. These terminals were scored for 59 morphological and three behavioural characters. An analysis with all characters equally weighted resulted in two most parsimonious trees, differing only in the position of Architis colombo Santos. In both trees Pisauridae arouse as a monophyletic group, and the exemplars of Architis composed a clade with S. spinipes . Contrary to hypotheses from the literature, Thalassius Simon emerged as sister-group of all remaining pisaurids, not as a close relative of Dolomedes Latreille. The genera Tinus F.O.P. -Cambridge and Thaumasia Perty appeared in the trees as the closest relatives of Architis and Staberius Simon. The analysis strongly supported S. spinipes as the sister-group of A. helveola (Simon), indicating that Architis as currently delimited is paraphyletic. Based on these results, Staberius is considered a subjective junior synonym of Architis . Additionally, the genus Mimicosa Petrunkevitch, originally described in Tetragnathidae, is transferred to Pisauridae and considered a junior synonym of Architis . Two species are proposed as junior synonyms of A. spinipes comb.n. Mimicosa spinosa Petrunkevitch and Staberius lemoulti Caporiacco.     

A phylogenetic appraisal of Sigmodontinae (Rodentia,Cricetidae) with emphasis on phyllotine genera: systematics and biogeography

Here, we present a comprehensive phylogenetic analysis based on nuclear and mitochondrial DNA sequences of rodents of the subfamily Sigmodontinae. The emphasis is placed on the large tribe Phyllotini; sampling includes for the first time in any molecular‐based phylogenetic analysis representatives of several genera traditionally considered to be phyllotines. Given the broad taxonomic sampling, results provide substantial improvements in our knowledge on both the structure of the sigmodontine radiation and of phyllotine phylogenetic relationships. For instance, the tribe Ichthyomyini was not recovered monophyletic. Similarly, in a novel hypothesis on the contents of the tribe Phyllotini, it is shown that unlike Galenomys, the genera Chinchillula, Neotomys and Punomys are not phyllotines. The later genera together with Andinomys, Euneomys, Irenomys and Juliomys form part of novel generic clades of mostly Andean sigmodontine rodents. More in general, results strongly suggest the occurrence of several instances of putative morphological convergence among distinct sigmodontine lineages (e.g. among now considered to be ichthyomyines; between Phyllotini and some Andean taxa; among Euneomys‐Neotomys and Reithrodon). Finally, we suggest that the historical biogeography of the sigmodontine rodents is far more complex than earlier envisioned.     

A molecular phylogenetic study of southern African Apiaceae

It has been suggested that southern Africa is the origin of the predominantly herbaceous Apiaceae subfamily Apioideae and that the woody habit is plesiomorphic. We expand previous molecular phylogenetic analyses of the family by considering all but three of the approximately 38 genera native to southern Africa, including all genera whose members, save one, have a woody habit. Representatives of five other genera are included because they may be closely related to these southern African taxa. Chloroplast DNA rps16 intron and/or nuclear rDNA ITS sequences for 154 accessions are analyzed using maximum parsimony, Bayesian, and maximum likelihood methods. Within Apioideae, two major clades hitherto unrecognized in the subfamily are inferred. The monogeneric Lichtensteinia clade is sister group to all other members of the subfamily, whereas the Annesorhiza clade (Annesorhiza, Chamarea, and Itasina) plus Molopospermum (and Astydamia in the ITS trees) are the successive sister group to all Apioideae except Lichtensteinia. Tribe Heteromorpheae is expanded to include Pseudocarum, "Oreofraga" ined., and five genera endemic to Madagascar. The southern African origin of subfamily Apioideae is corroborated (with subsequent migration northward into Eurasia along two dispersal routes), and the positions of the herbaceous Lichtensteinia and Annesorhiza clades within the subfamily suggest, surprisingly, that its ancestor was herbaceous, not woody.     

A phylogenetic analysis of relationships among genera of Conopidae (Diptera) based on molecular and morphological data

Members of the family Conopidae (Diptera) have been the focus of little targeted phylogenetic research. The most comprehensive test of phylogenetic support for the present subfamily classification of Conopidae is presented here using 66 specimens, including 59 species of Conopidae and seven outgroup taxa. Relationships among subfamily clades are also explored. A total of 6824 bp of DNA sequence data from five gene regions (12S ribosomal DNA, cytochrome c oxidase subunit I, cytochrome b, 28S ribosomal DNA and alanyl‐tRNA synthetase) are combined with 111 morphological characters in a combined analysis using both parsimony and Bayesian methods. Parsimony analysis recovers three shortest trees. Bayesian analysis recovers a nearly identical tree. Five monophyletic subfamilies of Conopidae are recovered. The rarely acknowledged Zodioninae is restored, including the genera Zodion and Parazodion. The genus Sicus is removed from Myopinae. Morphological synapomorphies are discussed for each subfamily and inter‐subfamily clade, including a comprehensive review of the character interpretaions of previous authors. Included are detailed comparative illustrations of male and female genitalia of representatives of all five subfamilies with new morphological interpretation.     

A phylogenetic analysis of the family Dermatophilaceae

The comparative analysis of the 16S ribosomal ribonucleic acid (rRNA) of Geodermatophilus obscurus DSM 43060 and Dermatophilus congolensis DSM 43037 revealed that these members of the family Dermatophilaceae were only remotely related. While G. obscurus represented an individual and separate line of descent within the phylogenetically defined order Actinomycetales, D. congolensis was closely related to representatives of Arthrobacter, Micrococcus, Cellulomonas, Brevibacterium, Promicromonospora and Microbacterium.     

A phylogenetic analysis of the genera of Lejeuneaceae (Hepaticae)

The Lejeuneaceae are the largest family of the liverworts (Hepaticae), with almost a thousand species in 91 currently accepted genera. We analysed phylogenetic relationships of 69 genera, representing all major subfamilies and tribes recognized in the family, by using 49 informative morphological characters (31 gametophytic, 18 sporophytic), one chemical character, and applying equal and successive weighting of characters and parsimony analysis. In all trees recovered, the Lejeuneaceae were monophyletic with Nipponolejeunea (subfam. Nipponolejeuneoideae) forming the basalmost lineage. The remaining genera clustered in two major groups, the monophyletic Lejeuneoideae (52 genera) and the paraphyletic Ptychanthoideae (16 genera). Within each, several multigeneric lineages corresponding in part to previously described taxa were recovered: the Acrolejeuneinae and Ptychanthinae clades in the Ptychanthoideae, and the Brachiolejeuneinae, Lejeuneeae and Tuyamaella–Cololejeunea clades in the Lejeuneoideae. Bryopteris , a genus sometimes treated as a separate family, was nested in the Ptychanthinae clade. The Tuyamaella–Cololejeunea lineage corresponded with three previously recognized subfamilies (Cololejeuneoideae, Myriocoleoideae and Tuyamaelloideae) and contained genera with neotenic features, in two subclades. These features seemed to have originated by multiple heterochronic events: single origins were detected for 'protonemal neoteny' and 'primary neoteny', whereas 'secondary neoteny' probably evolved twice. Relationships within the large Lejeuneeae clade (43 genera) remained largely unresolved, although several putative lineages were detected in majority rule trees. Additional characters such as DNA sequences may provide better phylogenetic resolution in this group.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 391–410.     

A molecular phylogenetic assessment of the advanced Asiatic and Malesian didymocarpoid Gesneriaceae with focus on non-monophyletic and monotypic genera

Based on a considerably enlarged sampling, a phylogenetic analysis of the largest group of didymocarpoid Gesneriaceae, the ??advanced Asiatic and Malesian genera??, was performed, covering all but 3 of the 60 genera presently recognised in this group (20 of these, mostly from China, are monotypic). The results suggest that no fewer than 17 out of the 57 genera examined are poly- (or rarely para-)phyletic. Highly polyphyletic are Briggsia, Chirita, Henckelia and Raphiocarpus. Only a dozen of the non-monotypic genera (including the three species-richest genera, Cyrtandra, Aeschynanthus and Agalmyla) are confirmed as monophyletic entities, though some exhibit considerable genetic variation. For eight genera, no statement can be made, as only one (of two or several) species was included in the analysis. For a dozen of the (particularly Chinese) monotypic genera a close relationship (or possible congenerity) with other genera was found. In China, only Allostigma, Cathayanthe, Conandron and Metapetrocosmea seem to have no strong affinities to other genera, indicating that they represent phylogenetically isolated lineages or represent remnants of previously larger and earlier diversified groups. The present study forms the foundation for targeted molecular, morphological and phytogeographic studies of the polyphyletic and monotypic genera and particular of clades of genera with interrelations uncovered here for the first time.     

A phylogenetic analysis of the lipocalin protein family

The lipocalins are a family of extracellular proteins that bind and transport small hydrophobic molecules. They are found in eubacteria and a great variety of eukaryotic cells, in which they play diverse physiological roles. We report here the detection of two new eukaryotic lipocalins and a phylogenetic analysis of 113 lipocalin family members performed with maximum-likelihood and parsimony methods on their amino acid sequences. Lipocalins segregate into 13 monophyletic clades, some of which are grouped in well-supported superclades. An examination of the G + C content of the bacterial lipocalin genes and the detection of four new conceptual lipocalins in other eubacterial species argue against a recent horizontal transfer as the origin of prokaryotic lipocalins. Therefore, we rooted our lipocalin tree using the clade containing the prokaryotic lipocalins. The topology of the rooted lipocalin tree is in general agreement with the currently accepted view of the organismal phylogeny of arthropods and chordates. The rooted tree allows us to assign polarity to character changes and suggests a plausible scenario for the evolution of important lipocalin properties. More recently evolved lipocalins tend to (1) show greater rates of amino acid substitutions, (2) have more flexible protein structures, (3) bind smaller hydrophobic ligands, and (4) increase the efficiency of their ligand-binding contacts. Finally, we found that the family of fatty-acid-binding proteins originated from the more derived lipocalins and therefore cannot be considered a sister group of the lipocalin family.     

A molecular phylogeny of apple snails (Gastropoda, Caenogastropoda, Ampullariidae) with an emphasis on African species

Ampullariids are widespread in Africa, Asia, South- and Central America, and the Caribbean Islands. Basal phylogenetic relationships of the African genera Afropomus and Saulea have been inferred based on anatomical evidence. Until recently the Viviparidae was regarded as the sister-group of Ampullariidae, but recent molecular data infer a sister-group relationship with Campanilidae. We have used members of both families as outgroups in the present investigation on ampullariid phylogeny. We have used data from portions of five molecular loci, that is, the nuclear genes 18S rRNA, 28S rRNA and H3, and the mitochondrial genes 16S rRNA and COI. Our data most often infer a basal position of Afropomus . The West African species Saulea is inferred as the basal member of a clade including the South American Marisa and Pomacea . We hypothesize that evolutionary lineages leading to Saulea and the American genera were isolated from each other by vicariance events (Gondwanaland break-up 130–110 Mya). Our individual gene analyses inferred two major clades of the African Lanistes . However, in some analyses they were not inferred as sister-groups making Lanistes paraphyletic. The African and Asian genus Pila is most often inferred to be monophyletic (except for the generally unresolved 28S). Our analyses most often inferred a sister-group relationship between Lanistes and Pila . The very low genetic diversity of the endemic radiation of Lanistes in Lake Malawi suggests that the morphological divergence has happened much faster than the molecular divergence as is also evidenced from the cichlid radiations.     

A phylogenetic analysis of Sciomyzidae (Diptera) and some related genera

Sciomyzidae is a family of acalyptrate flies with 546 species in 61 genera that is among the most extensively studied groups of higher Diptera. Most of the known larvae are obligate enemies of Gastropoda. Hundreds of studies published over the past 50 years have resulted in detailed information concerning morphology of adults and immature stages, biology, development, behaviour, phenology and distribution. However, studies of phylogenetic relationships are based almost exclusively on morphological characters of adults, and no comprehensive molecular analysis across the family has been published. Here we fill this void by generating and analysing molecular data for 54 species of Sciomyzidae (22 genera), including Phaeomyiidae (one genus), and seven representative species of five other families of Sciomyzoidea (Coelopidae, Dryomyzidae, Helcomyzidae, Heteromyzidae and Huttoninidae) as outgroups. The reconstruction is based on morphological characters as well as nucleotide sequences for genes from the mitochondrial (12S, 16S, COI, COII, Cytb) and nuclear genome (28S, EF1α). The results are compared with recent morphological analyses. Our analyses support the monophyly of Sciomyzidae + Phaeomyiidae, and place Phaeomyiinae as a unique lineage within Sciomyzidae. A modified classification comprising three subfamilies is proposed. The major subfamily, Sciomyzinae, consists of two monophyletic and well separated groups, the tribes Sciomyzini and Tetanocerini.     

Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhacophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were performed in combination with already published mitochondrial 12S and 16S sequences of Rhacophorinae frogs. In all cases, Philautus romeri Smith, 1953 is recovered as the sister taxon to all other Rhacophorinae, although the support values are weak. Chirixalus doriae Boulenger, 1893 is closer to Chiromantis [ Chiromantis rufescens (Günther, 1868) and Chiromantis xerampelina Peters, 1854] than to Chirixalus vittatus (Boulenger, 1887). The clade { Philautus odontotarsus Ye & Fei, 1993, [ Philautus idiootocus (Kuramoto & Wang, 1987), Kurixalus eiffingeri (Boettger, 1895)]} is recovered with strong support. The monophyly of Theloderma and Rhacophorus rhodopus Liu & Hu, 1959 is not supported. It is suggested that Philautus albopunctatus Liu & Hu, 1962 should be placed into the synonymy of Theloderma asperum (Boulenger, 1886), and that Philautus rhododiscus Liu & Hu, 1962 should be assigned to Theloderma , so as to correct the paraphyly. Additionally, the monophyly of ' Aquixalus ' is not supported, and this requires further examination. Results also indicate that the Rhacophorus leucomystax (Gravenhorst, 1829)/ Rhacophorus megacephalus (Hallowell, 1861) complex needs further revision. Studies employing broader sampling and more molecular markers will be needed to resolve the deep relationships within the subfamily Rhacophorinae.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 733–749.     

A phylogenetic analysis of the Gruiformes (Aves) based on morphological characters,with an emphasis on the rails (Rallidae)

The order Gruiformes, for which even familial composition remains controversial, is perhaps the least well understood avian order from a phylogenetic perspective. The history of the systematics of the order is presented, and the ecological and biogeographic characteristics of its members are summarized. Using cladistic techniques, phylogenetic relationships among fossil and modern genera of the Gruiformes were estimated based on 381 primarily osteological characters; relationships among modern species of Grues (Psophiidae, Aramidae, Gruidae, Heliornithidae and Rallidae) were assessed based on these characters augmented by 189 characters of the definitive integument. A strict consensus tree for 20,000 shortest trees compiled for the matrix of gruiform genera (length = 967, CI = 0.517) revealed a number of nodes common to the solution set, many of which were robust to bootstrapping and had substantial support (Bremer) indices. Robust nodes included those supporting: a sister relationship between the Pedionomidae and Turnicidae; monophyly of the Gruiformes exclusive of the Pedionomidae and Turnicidae; a sister relationship between the Cariamidae and Phorusrhacoidea; a sister relationship between a clade comprising Eurypyga and Messelornis and one comprising Rhynochetos and Aptornis; monophyly of the Grues (Psophiidae, Aramidae, Gruidae, Heliornithidae and Rallidae); monophyly of a clade (Gruoidea) comprising (in order of increasingly close relationship) Psophia, Aramus, Balearica and other Gruidae, with monophyly of each member in this series confirmed; a sister relationship between the Heliornithidae and Rallidae; and monophyly of the Rallidae exclusive of Himantornis. Autapomorphic divergence was comparatively high for Pedionomus, Eurypyga, Psophia, Himantornis and Fulica; extreme autapomorphy, much of which is unique for the order, characterized the extinct, flightless Aptornis. In the species-level analysis of modern Grues, special efforts were made to limit the analytical impacts of homoplasy related to flightlessness in a number of rallid lineages. A strict consensus tree of 20,000 shortest trees compiled (length = 1232, CI = 0.463) confirmed the interfamilial relationships resolved in the ordinal analysis and established a number of other, variably supported groups within the Rallidae. Groupings within the Rallidae included: monophyly of Rallidae exclusive of Himantornis and a clade comprising Porphyrio (including Notornis) and Porphyrula; a poorly resolved, basal group of genera including Gymnocrex, Habroptila, Eulabeornis, Aramides, Canirallus and Mentocrex; an intermediate grade comprising Anurolimnas, Amaurolimnas, and Rougetius; monophyly of two major subdivisions of remaining rallids, one comprising Rallina (paraphyletic), Rallicula, and Sarothrura, and the other comprising the apparently paraphyletic ''long-billed'' rails (e.g. Pardirallus, Cyanolimnas, Rallus, Gallirallus and Cabalus and a variably resolved clade comprising ''crakes'' (e.g. Atlantisia, Laterallus and Porzana, waterhens (Amaurornis), moorhens (Gallinula and allied genera) and coots (Fulica). Relationships among ''crakes'' remain poorly resolved; Laterallus may be paraphyletic, and Porzana is evidently polyphyletic and poses substantial challenges for reconciliation with current taxonomy. Relationships among the species of waterhens, moorhens and coots, however, were comparatively well resolved, and exhaustive, fine-scale analyses of several genera (Grus, Porphyrio, Aramides, Rallus, Laterallus and Fulica) and species complexes (Porphyrio porphyrio -group,Gallirallus philippensis -group and Fulica americana -group) revealed additional topological likelihoods. Many nodes shared by a majority of the shortest trees under equal weighting were common to all shortest trees found following one or two iterations of successive weighting of characters. Provisional placements of selected subfossil rallids (e.g. Diaphorapteryx, Aphanapteryx and Capellirallus ) were based on separate heuristic searches using the strict consensus tree for modern rallids as a backbone constraint. These analyses were considered with respect to assessments of robustness, homoplasy related to flightlessness, challenges and importance of fossils in cladistic analysis, previously published studies and biogeography, and an annotated phylogenetic classification of the Gruiformes is proposed.     

Preliminary study on phylogenetic position and delimitation of the ciliate arthrodontous genera of the moss family Mniaceae

The history of the generic and sectional concepts in the traditional moss family Mniaceae is summarised. The division of the Mniaceae into nine genera has been generally accepted. A phylogenetic analysis, based on 35 Mniaceae samples as ingroup and one Leptostomataceae and three Bryaceae samples as outgroups was completed. A total of 113 new sequences were obtained and 4139 aligned characters were included in the combined dataset. Bayesian inferences based on the combined data set showed five well supported clades, which, as a whole, form the monophyletic family Mniaceae. The number of genera in the traditional Mniaceae is 9 and the number of species is 74. All the genera appear monophyletic except Plagiomnium; accepting Orthomnion at the generic level makes Plagiomnium paraphyletic. The principle that only monophyletic taxa are allowed and may be named necessitates the uniting of Plagiomnium and Orthomnion. The necessary combinations are made. The taxonomy of the genera and sections is discussed. Rhizomnium section Macromnium T.J.Kop. & Y.Sun, sect. nov. is described and the new combination Rhizomnium chlorophyllosum (Kindb.) T.J.Kop. is made. The controversy of paraphyly – monophyly in accepting and naming taxa is discussed and Plagiomnium versus Orthomnion given as an example. All the present genera and species seem to have diverged in the area of the Laurasian supercontinent and the speciation of most genera took place in the temperate forested areas of western and eastern North America, Europe and south-eastern Asia.     

A phylogenetic analysis of 100+ genera and 50+ families of euasterids based on morphological and molecular data with notes on possible higher level morphological synapomorphies

 A data matrix of 143 morphological and chemical characters for 142 genera of euasterids according to the APG system was compiled and complemented with rbcL and ndhF sequences for most of the genera. The data were subjected to parsimony analysis and support was assessed by bootstrapping. Strict consensus trees from analyses of morphology alone and morphology + rbcL + ndhF are presented. The morphological data recover several groups supported by molecular data but at the level of orders and above relationships are only superficially in agreement with molecular studies. The analyses provide support for monophyly of Gentianales, Aquifoliales, Apiales, Asterales, and Dipsacales. All data indicate that Adoxaceae are closely related to Dipsacales and hence they should be included in that order. The trees were used to assess some possible morphological synapomorphies for euasterids I and II and for the orders of the APG system. Euasterids I are generally characterised by opposite leaves, entire leaf margins, hypogynous flowers, “early sympetaly” with a ring-shaped corolla primordium, fusion of stamen filaments with the corolla tube, and capsular fruits. Euasterids II often have alternate leaves, serrate-dentate leaf margins, epigynous flowers, “late sympetaly” with distinct petal primordia, free stamen filaments, and indehiscent fruits. It is unclear which of these characters represent synapomorphies and symplesiomorphies for the two groups, respectively, and there are numerous expections to be interpreted as reversals and parallelisms. Received August 28, 2000 Accepted August 7, 2001     

A molecular phylogenetic investigation of Opisthonecta and related genera (Ciliophora, Peritrichia, Sessilida)

The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs.     

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed.     

Seed plant genera endemic to the Caribbean Island biodiversity hotspot: A review and a molecular phylogenetic perspective

The Caribbean Island Biodiversity Hotspot is composed primarily of the Bahamas and Greater and Lesser Antilles. A total of 180 genera (727 spp., ca. 9% of the species endemic to the Antilles) are restricted to this hotspot. Most of these genera are unispecific (51%), a pattern that is also found on other islands of the world. The majority of the endemic genera belong to the “Core Eudicot” clade, and they were published in two time periods (1854–1878 and 1904–1928). There are molecular phylogenies available for 63 of the endemic genera. However, phylogenetic reconstructions of only 21 genera are based on more than one independent DNA region and have well-supported clades and good taxonomic sampling. Six of the endemic genera form part of early-branching groups. We could not infer biogeographical conclusions from the molecular phylogenies of most of the endemic genera (43: 68%). There is an urgent need for (1) additional field studies to learn the conservation status of these genera, (2) effective protection of the habitats where the most endangered genera occur, and (3) additional biological and systematic studies of the least understood genera.     

Molecular phylogenetic analysis of Tulipa (Liliaceae) based on noncoding plastid and nuclear DNA sequences with an emphasis on Turkey

We investigated the phylogenetic relationships in Tulipa in Turkey using DNA sequences from the plastid trnL‐trnF region and the internal transcribed spacer (ITS) of nuclear ribosomal DNA. We generated trnL‐trnF and nuclear ITS sequences for 11 Tulipa spp. from Turkey and compared the utility of trnL‐trnF and ITS sequences for phylogenetic analysis. Neighbor‐joining, Bayesian and maximum parsimony methods were implemented using the same matrices. Our study of Tulipa based on molecular data revealed congruent results with previous studies. Despite the relatively lower resolution of trnL‐trnF than that of ITS, both sequence matrices generated similar results. Three clades were clearly distinguished, corresponding to subgenera Tulipa, Eriostemones and Orithyia. It is not fully resolved whether Clusianae should be recognized as a separate section of subgenus Tulipa or a distinct subgenus. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 270–279.     

A molecular phylogenetic analysis of the bloodroot and kangaroo paw family, Haemodoraceae: taxonomic, biogeographic and conservation implications

A phylogenetic analysis of plastid DNA sequences from the trn L-F region corroborates the hypothesis that Haemodoraceae, a small monocotyledonous family centred in southwestern Australia, are monophyletic with relationships to Philydraceae, Pontederiaceae and Comme–linaceae. It also supports the long-standing recognition of two subfamilies. In Conostylidoideae Tribonanthes falls in an isolated position, thus supporting its segregation as a recently recognized monogeneric tribe. Tribal status for Phlebocarya is not supported as this taxon is unexpectedly placed in Conostylideae as sister to Conostylis–Blancoa. Macropidia falls as sister to Anigozanthos . The DNA tree permits continued recognition of Macropidia and Blancoa as distinct genera, contrary to a recent morphological cladistic analysis. Haemodoroideae fall into two clades: ( Dilatris(Lachnanthes+Haemodorum )) and ( Xiphidium(Schiekia+Wachendofia )). It is unlikely that Haemodoraceae are of Gondwanan origin, and the phylogenetic pattern indicates a largely relictual distribution with a recent radiation in Western Australia.