Phylogenetic relationships of Italian Bellevalia species (Asparagaceae), inferred from morphology,karyology and molecular systematics

The seven Bellevalia species and subspecies known from Italy, representing about 10% of the genus and three out of six sections, were studied. An integrated morphological, karyological and molecular approach was used to infer phylogenetic and systematic relationships among them. B. romana (the generitype) is the most distinctive species on karyotype asymmetry grounds. B. boissieri and B.dubia, usually considered as subspecies of one species (the latter endemic to Sicily), deserve specific status based on biparental nrDNA markers (internal transcribed spacer, ITS), since they do not form a single clade. The allotetraploid endemic B. pelagica, morphologically similar to B. romana, is sister to the latter under parsimony, both in morphological and ITS trees; it is also related with B. dubia, based on karyotype asymmetry and a uniparental cpDNA marker (trnL^(UAA)–trnF^(GAA) IGS (intergenic spacer)). A second allotetraploid endemic, B. webbiana, is closely related, on morphological, karyological and molecular grounds, with B. boissieri and B. ciliata, and also with B. trifoliata, three species that might all involved in its origin. B. sect. Conicae Feinbr. and sect. Nutantes Feinbr. are here typified, the former (type: B. ciliata) is most likely a synonym of the latter (type: B. trifoliata).     

A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences

The systematics of the mainly yellow flowered Gagea species complex (Liliaceae) has long been considered difficult because only a few phenotypic features within this genus and as a result of hypothesized interspecific hybridisation. A molecular phylogenetic study of seven Gagea species (G. bohemica, G. lutea, G. minima, G. pomeranica, G. pratenis, G. spathacea and G. villosa) from Germany has been undertaken, based on plastid DNA sequences (trnL(UAA)-trnF(GAA), psbA-trnH) and on the nuclear ribosomal internal transcribed spacer (ITS). Sequence divergence within the Gagea species ranges up to 15.5% for psbA-trnH, 22.0% for trnL-trnF and 23.7% for ITS (ITS1 + 5.8S rRNA + ITS2). Two subspecies of Gagea bohemica: G. bohemica subsp. saxatilis and G. bohemica subsp. bohemica are characterized by trnL-trnF data and morphological features. Analysis of the ITS region shows that G. pomeranica represents a hybrid of G. pratensis and G. lutea. Lloydia serotina was initially used as an outgroup species, but it was placed within the investigated Gagea species in the psbA-trnH and the trnL-trnF phylogenetic tree.     

Autecological traits determined two evolutionary strategies in Mediterranean plants during the Quaternary: low differentiation and range expansion versus geographical speciation in Linaria

The evolutionary patterns of the Mediterranean flora during the Quaternary have been relatively well documented based on phylogenetic and biogeographic analyses, but few studies have addressed the evolutionary traits that determined diversification and range expansion success during this period. We analysed previously published and newly generated sequences of three plastid noncoding regions (rpl32‐trnL^UAG, trnS‐trnG and trnL‐trnF), the nuclear ribosomal internal transcribed spacer (ITS) and a low‐copy nuclear gene intron (AGT1) of Linaria sect. Supinae, a group of angiosperms that diversified in the Quaternary. The origin and recent colonization dynamics of closely related lineages were inferred by biogeographic reconstruction and phylogeographic analyses, while breeding system experiments coupled with ecological and morphological data were used to test association with range expansion and diversification. A combination of traits, including selfing, short lifespan and the ability to tolerate a wide variety of substrates, were key factors underlying range expansion after long‐distance dispersal throughout the Mediterranean basin. By contrast, self‐incompatibility may have promoted higher diversification rates in narrow ranges of the Iberian Peninsula. We argue that a few traits contributed to the adoption of two contrasting strategies that may have been predominant in the evolution of Mediterranean angiosperms.     

Phylogenetic systematics of Sternbergia (Amaryllidaceae) based on plastid and ITS sequence data

The phylogenetics of Sternbergia (Amaryllidaceae) were studied using DNA sequences of the plastid ndhF and matK genes and nuclear internal transcribed spacer (ITS) ribosomal region for 38, 37 and 32 ingroup and outgroup accessions, respectively. All members of Sternbergia were represented by at least one accession, except S. minoica and S. schubertii, with additional taxa from Narcissus and Pancratium serving as principal outgroups. Sternbergia was resolved and supported as sister to Narcissus and composed of two primary subclades: S. colchiciflora sister to S. vernalis, S. candida and S. clusiana, with this clade in turn sister to S. lutea and its allies in both Bayesian and bootstrap analyses. A clear relationship between the two vernal flowering members of the genus was recovered, supporting the hypothesis of a single origin of vernal flowering in Sternbergia. However, in the S. lutea complex, the DNA markers examined did not offer sufficient resolving power to separate taxa, providing some support for the idea that S. sicula and S. greuteriana are conspecific with S. lutea. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 166 , 149–162.     

Unravelling the evolutionary history of the polyploid complex Ranunculus parnassiifolius (Ranunculaceae)

Ranunculus L. represents the largest genus within Ranunculaceae, comprising more than 600 species with a worldwide distribution. However, there are still many gaps in our knowledge of the infrageneric taxonomy and evolution of Ranunculus. In this regard, intraspecific variation of the polyploid complex Ranunculus parnassiifolius remains under discussion. To reconstruct the biogeographical history of the polyploid complex R. parnassiifolius, 20 populations distributed throughout the Cantabrian Mountains, Pyrenees, and Alps were investigated. Phylogenetic studies were based on nuclear internal transcribed spacers (ITS) and plastid (rpl32‐trnL, rps16‐trnQ) sequence data, analysed using Bayesian approaches as well as the evolution of morphological characters. Additionally, biogeographical patterns were conducted using statistical dispersal–vicariance analysis. The analyses presented here support the recognition of two evolutionary independent units: R. cabrerensis sensu lato (s.l.) and R. parnassiifolius s.l. Furthermore gradual speciation depending on the biogeographical territory is proposed, and optimal reconstructions have probably favoured the ancestor of Ranunculus parnassiifolius as originating in the Iberian Peninsula. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 477–493.     

Lack of trnL intron in the thermoacidophilic red alga Galdieria sulphuraria (Galdieri) Merola

Abstract

The plastid trnC‐trnL(UAA)‐ilvH region from Galdieria sulphuraria was cloned and sequenced with the aim of verifying the absence of the trnL intron. The sequence alignment shows both the absence of a trnL intron and the colinearity of the whole region of the plastidial DNA of G. sulphuraria with that of the other thermoacidophilic red algae.     

Evolution of trnF(GAA) pseudogenes in cruciferous plants

In several studies we used the 5′-trnL(UAA)–trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions, gene diversity calculations and phylogenetic analyses among the genera Arabidopsis and Boechera. Despite the fact that extensive gene duplications are rare within the chloroplast genome of higher plants, within several genera of the Brassicaceae the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with 1–12 tandemly repeated copies in close 5′-proximity of the functional gene. A recent re-examination and additional analysis of trnL(UAA)–trnF(GAA) regions from numerous cruciferous taxa not only reveal extensive trnF gene duplications, but also favour the hypothesis that in cruciferous taxa at least four independent phylogenetic lineages are characterized by these pseudogenes. Among these lineages there is one major clade of taxa carrying pseudogenes indicating an ancient split in crucifer evolution. In two case studies, Boechera and Arabidopsis, intra- and inter-molecular recombinations have been shown to be the reason for the reciprocal exchange of several similar motifs. However, functional constraints might favour two to three or five to six copies as shown for Arabidopsis and Boechera. Herein, we compare the occurrence and distribution of pseudogene copy number in the framework of a comprehensive survey of cpDNA haplotype variation in Boechera, the former genus Cardaminopsis and Arabidopsis thaliana and comment on the value of such kind of mutations in phylogenetic and evolutionary reconstructions.     

Bothriospermum longistylum sp. nov. (Boraginaceae) from north China

Based on field investigations as well as morphological and molecular systematic studies we found a new species of Bothriospermum which can be easily distinguished from all other known congeneric species by its unlobed faucal appendages and very long styles. We conducted molecular phylogenetic analyses based on a combined dataset from nrITS, plastid rps16, trnL‐trnF and trnG‐trnS regions. The results indicated that the new species indeed belongs in Bothriospermum and that it is well separated from other congeneric clusters, but that the genus Bothriospermum is paraphyletic with Nihon and Thyrocarpus clusetered within it. As a result, Bothriospermum longistylum sp. nov. is described and illustrated here. A revised key to species of Bothriospermum and a distributional map are also presented.     

New information for Ilex phylogenetics based on the plastid psbA‐trnH intergenic spacer (Aquifoliaceae)

The aim of the present work was to clarify the origin and phylogenetic position of the species belonging to the genus Ilex (Aquifoliaceae), especially the South American species. Phylogenetic relationships of the genus Ilex were investigated using the plastid psbA‐trnH intergenic spacer and parsimony and Bayesian analyses. The psbA‐trnH intergenic spacer was shown to evolve slowly within Ilex, but a major gap present in this region was useful in the phylogenetic study of the genus. To obtain more potentially parsimonious characters, atpB‐rbcL intergenic spacer data were combined with those for psbA‐trnH. Many gaps present in the psbA‐trnH region were useful in the phylogenetic study of the genus Ilex. The topology of the trees showed that, in general, the clades are strongly related to geographical areas, a fact especially evident in certain different Asian lineages. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 182–193.     

High mortality and female‐biased operational sex ratio result in low encounter rates and moderate polyandry in a spider

The taxonomy of the Old World bat genus Otomops (Chiroptera: Molossidae) has been the subject of considerable debate. The failure of classical morphological studies to provide consistent patterns regarding interspecific relationships within Otomops has limited any understanding of the evolutionary history of the genus. We used traditional and geometric morphometric approaches to establish the species limits of taxa from sub‐Saharan Africa, the Arabian Peninsula, and Madagascar. Morphometric data supported the recent recognition of three distinct Afrotropical taxa: Otomops madagascariensis from Madagascar; Otomops martiensseni s.s. from southern, eastern, central, and western Africa; and an undescribed taxon from north‐east Africa and the Arabian Peninsula. Analyses of craniodental measurements and landmark‐based data showed significant cranial size and shape divergence between the three taxa. Cranial size and shape variation within Afro‐Arabian Otomops were strongly influenced by altitude, seasonality of precipitation, and precipitation in the driest month. Based on morphometric patterns and molecular divergence estimates, we suggest that morphological evolution within Afro‐Arabian Otomops occurred in response to the fluctuating climate during the Pleistocene on the one hand, and the increasing aridity and seasonality over north‐eastern Africa on the other. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, •• , ••–••.     

Phylogenetics and classification of the pantropical fern family Lindsaeaceae

The classification and generic definition in the tropical–subtropical fern family Lindsaeaceae have been uncertain and have so far been based on morphological characters only. We have now studied the evolutionary history of the Lindsaeaceae by simultaneously optimizing 55 morphological characters, two plastid genes (rpoC1 and rps4) and three non‐coding plastid intergenic spacers (trnL‐F, rps4‐trnS and trnH‐psbA). Our data set included all genera associated with Lindsaeaceae, except Xyropteris, and c. 73% of the currently accepted species. The phylogenetic relationships of the lindsaeoid ferns with two enigmatic genera that have recently been included in the Lindsaeaceae, Cystodium and Lonchitis, remain ambiguous. Within the monophyletic lindsaeoids, we found six well‐supported and diagnostic clades that can be recognized as genera: Sphenomeris, Odontosoria, Osmolindsaea, Nesolindsaea, Tapeinidium and Lindsaea. Sphenomeris was shown to be monotypic; most taxa formerly placed in that genus belong to the Odontosoria clade. Ormoloma is embedded within Lindsaea and therefore does not merit recognition as a genus. Tapeinidium is sister to a clade with some species formerly placed in Lindsaea that are morphologically distinct from that genus and are transferred to Osmolindsaea and Nesolindsaea, proposed here as two new genera. We do not maintain the current subgeneric classification of Lindsaea itself, because neither of the two generally accepted subgenera (Lindsaea and Odontoloma) is monophyletic, and most of the sections also appear unnatural. Nesolindsaea shows an ancient biogeographical link between Sri Lanka and the Seychelles and many of the main clades within Lindsaea have geographically disjunct distributions. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 305–359.     

Molecular phylogenetics of Paphiopedilum (Cypripedioideae; Orchidaceae) based on nuclear ribosomal ITS and plastid sequences

Phylogenetic relationships in the genus Paphiopedilum were studied using nuclear ribosomal internal transcribed spacer (ITS) and plastid sequence data. The results confirm that the genus Paphiopedilum is monophyletic, and the division of the genus into three subgenera Parvisepalum, Brachypetalum and Paphiopedilum is well supported. Four sections of subgenus Paphiopedilum (Pardalopetalum, Cochlopetalum, Paphiopedilum and Barbata) are recovered as in a recent infrageneric treatment, with strong support. Section Coryopedilum is also recovered, with low bootstrap but high posterior probability values for support of monophyly. Relationships in section Barbata remain unresolved, and short branch lengths and the narrow geographical distribution of many species in the section suggest that it possibly underwent rapid radiation. Mapping chromosome and genome size data (including some new genome size measurements) onto the phylogenetic framework shows that there is no clear trend in increase in chromosome number in the genus. However, the diploid chromosome number of 2n = 26 in subgenera Parvisepalum and Brachypetalum suggests that this is the ancestral condition, and higher chromosome numbers in sections Cochlopetalum and Barbata suggest that centric fission has possibly occurred in parallel in these sections. The trend for genome size evolution is also unclear, although species in section Barbata have larger genome sizes than those in other sections. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 176–196.     

Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae,Allioideae) as inferred from nrDNA ITS,cpDNA rps16 and trnL–F sequences

Allium is a particularly species rich (more than 800 species) and economically important genus, with numerous taxonomic problems at all levels of classification. In this study, we try to uncover the phylogenetic relationships of the common leek Allium ampeloprasum based on selected samples of this species and its putative relatives in A. sect. Allium from Iran. The silica‐dried leaf samples of 56 accessions representing 23 species of Allium were sequenced; 53 sequences of nrDNA ITS, 35 sequences of plastid rps16 and 52 sequences of trnL–F were generated and additional accessions were extracted from GenBank in order to cover all recognized main lineages in the genus. Maximum Parsimony and Bayesian Inference generated similar trees, but the placement of A. ampeloprasum and its relatives differed slightly between the nuclear and the plastid phylogenies. In the nrITS tree, A. ampeloprasum is retrieved as a highly supported clade with A. iranicum, while in the combined plastid tree A. ampeloprasum formed a highly supported clade with A. vineale. This supports the hypothesis of a possible hybrid origin of A. ampeloprasum. Allium iranicum formed a clade in the plastid tree, but was resolved as paraphyletic in the nrITS tree, probably due to presence of multiple non‐concerted copies of nrITS. Close relationships are suggested between the following species: A. aznavense and A. wendelboi with A. talyschense, A. erubescens and A. rotundum with A. scorodoprasum and A. abbasii with A. phanerantherum.     

DNA sequences of tobacco chloroplast genes for tRNASer (GGA), tRNAThr (UGU), tRNALeu (UAA), tRNAPhe (GAA): the tRNALeu gene contains a 503 bp intron

Summary The location and nucleotide sequence of tobacco chloroplast genes for tRNA^Ser (GGA), tRNA^Thr (UGU), tRNA^Leu (UAA) and tRNA^Phe (GAA) (trnS-GGA, trnT-UGU, trnL-UAA and trnF-GAA, respectively) have been determined. These genes are located in the 10 kbp BamHI fragment which lies in the middle of the large single-copy region of the chloroplast DNA. The gene order is trnS-trnT-trnL-trnF. The trnS, trnL and trnF are encoded on the same strand while the trnT on the opposite strand. The trnL contains a 503 bp intron like maize and broad bean trnL-UAAs.     

Molecular phylogeny and divergence times of Onosma (Boraginaceae s.s.) based on nrDNA ITS and plastid rpl32‐trnL(UAG) and trnH–psbA sequences

We analysed 87 species of Onosma (Boraginaceae) from throughout its distribution range to investigate its evolutionary history. Using nrDNA ITS and two plastid (rpl32‐trnL_(UAG) and trnH–psbA) markers, we reconstructed phylogenetic relationships within Onosma by conducting maximum parsimony, maximum likelihood, Bayesian, and BEAST analyses. The analyses revealed that Onosma as currently circumscribed is not monophyletic. However, the vast majority of Onosma species appear to belong to a single clade, the so‐called Onosma s.s. Outside of this core clade is a clade containing O. rostellata, a subclade of Sino‐Indian species and Maharanga emodii. Podonosma orientalis (as O. orientalis) appear only distantly related to Onosma but is more closely related to Alkanna, as also suggested in previous molecular studies. The Onosma s.s. clade includes all representatives of O. sect. Onosma, and encompasses three subsections, i.e. Onosma, Haplotricha and Heterotricha, corresponding to asterotrichous, haplotrichous and heterotrichous groups, respectively, but none of these subsections was retrieved as monophyletic. We observed significant incongruence between nuclear and chloroplast phylogenies regarding the phylogenetic status of the heterotrichous group. A dozen of the Iranian haplotrichous species formed a lineage which may not hybridize with asterotrichous species. Divergence time estimates suggested that the early radiation of Onosma s.l. took place at the Oligocene‐Miocene boundary and the diversification within Onosma s.s. occurred during middle to late Miocene and Pliocene.     

Phylogenetics of Escallonia (Escalloniaceae) based on plastid DNA sequence data

Escallonia (Escalloniaceae) is a New World genus of c. 39 species distributed mainly in the South American highlands. Plastid DNA sequence data from the intergenic spacers trnS‐trnG and 3′ trnV‐ndhC and the ndhF gene for 32 species were used to examine the relationships among species and related genera and to analyse the relationship between phylogeny and the geographical distribution of the species. Maximum parsimony and Bayesian inference were employed to analyse the data. The sister relationship of Escallonia to Forgesia and Valdivia was corroborated. We recovered five strongly supported clades that are geographically structured, suggesting that the evolutionary history of the genus may be linked to historical processes, including the uplift of mountainous systems in South America. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 442–451.     

Phylogenetic analysis of Chloraeinae (Orchidaceae) based on plastid and nuclear DNA sequences

The phylogenetic relationships of subtribe Chloraeinae, a group of terrestrial orchids endemic to southern South America, have not been satisfactorily investigated. A previous molecular phylogenetic analysis based on plastid DNA supported the monophyly of Chloraeinae and Gavilea, but showed that Chloraea is non‐monophyletic and that the sole species of Bipinnula analysed is sister to Geoblasta. However, that analysis included only 18 of the 73 species belonging to this subtribe. Here, the phylogenetic relationships of Chloraeinae were assessed by analysing aproximately 7500 bp of nucleotide sequences from nuclear ribosomal internal transcribed spacer (ITS) and plastid DNA (rbcL, matK, trnL‐trnF, rpoB‐trnC) for 42 species representing all four currently accepted genera of Chloraeinae and appropriate outgroups. Nuclear and plastid data were analysed separately and in combination using two different methods, namely parsimony and Bayesian inference. Our analyses support the monophyly of Chloraeinae and their inclusion in an expanded concept of Cranichideae, but none of the genera of Chloraeinae that includes more than one species is monophyletic. Gavilea and Bipinnula are paraphyletic, with Chloraea chica nested in Gavilea and Geoblasta penicillata in Bipinnula. As currently delimited, Chloraea is polyphyletic. The taxonomic changes proposed recently are for the most part not justifiable on phylogenetic grounds, except for recognition of the monotypic genus Correorchis. The lack of resolution for the relationships among species of ‘core’Chloraea suggests a relatively recent diversification of this group. The current generic classification is in need or revision, but additional study is advisable before carrying out further taxonomic changes. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 258–277.     

Genetic polymorphism in Chondrilla (Asteraceae) in southern European Russia and the nature of Chondrilla juncea L

We studied genetic diversity in 54 populations of nine sexual and apomictic species of the genus Chondrilla (C. acantholepis, C. ambigua, C. brevirostris, C. canescens, C. graminea, C. juncea, C. laticoronata, C. latifolia and C. pauciflora) in SE European Russia and neighboring territories of NW Kazakhstan. We analysed the trnT–trnF region of plastid DNA and the internal transcribed spacer of ribosomal DNA (ITS1–5.8S–ITS2) using statistical parsimony, maximum likelihood and neighbor net methods. Two major evolutionary lineages, roughly corresponding to the two subgenera traditionally recognized in the region, were revealed. Within the first evolutionary lineage (subgenus Brachyrhynchus), the sexual diploid C. ambigua and its putatively hybrid apomictic derivatives C. brevirostris, C. laticoronata and C. pauciflora could be recognized. Their identity was also confirmed by analyses of ISSR markers. The second evolutionary lineage (subgenus Chondrilla) comprises C. juncea, C. acantholepis, C. canescens, C. graminea and C. latifolia in European Russia, but analyses of morphological variability and the genealogy of plastid and nuclear markers favor their treatment as the single facultatively apomictic species C. juncea. The results demonstrate that an apomictic mode of reproduction does not necessarily result in the formation of genetically separated microspecies.     

Molecular phylogenetics of Uvaria (Annonaceae): relationships with Balonga,Dasoclema and Australian species of Melodorum

An extended molecular phylogenetic analysis of Uvaria (Annonaceae) is presented, using maximum parsimony, maximum likelihood and Bayesian methods, based on sequences of four plastid DNA regions (matK, psbA‐trnH spacer, rbcL and trnL‐F). The additional taxa include the monotypic West African genus Balonga, the monotypic South‐East Asian genus Dasoclema and seven Australian representatives of the genus Melodorum. The results indicate that all of these taxa are nested within a well‐supported clade otherwise consisting of Uvaria species, indicating that their taxonomic treatment needs to be reassessed. The distinguishing morphological characteristics of the taxa are re‐evaluated and interpreted as specialized adaptations of the basic Uvaria structure. The genus Uvaria is accordingly extended following the transfer of these species, necessitating six new nomenclatural combinations and two replacement names. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 33–43.