cpDNA Regions Research Articles

Genetic diversity and differentiation in Prunus species (Rosaceae) using chloroplast and mitochondrial DNA CAPS markers.

Chloroplast (cpDNA) and mitochondrial DNA (mtDNA) were analyzed to establish genetic relationships among Tunisian plum cultivars using the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) technique. Two mtDNA regions (nad 1 b/c and nad 4 1/2) and a cpDNA region (trnL-trnF) were amplified and digested using restriction enzymes. Seventy and six polymorphic sites were revealed in cpDNA and mtDNA, respectively. As a consequence, cpDNA appears to be more polymorphic than mtDNA. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram showed that accessions were distributed independently of their geographical origin, and introduced and local cultivars appear to be closely related. Both UPGMA and principal component analysis grouped Tunisian plum accessions into similar clusters. The analysis of the pooled sequences allowed the detection of 17 chlorotypes and 12 mitotypes. The unique haplotypes detected for cultivars are valuable for management and preservation of the plum local resources. From this study, PCR-RFLP analysis appears to be a useful approach to detect and identify cytoplasmic variation in plum trees. Our results also provide useful information for the management of genetic resources and to establish a program to improve the genetic resources available for plums.

MOLECULAR PHYLOGENY OF MAIDENHAIR FERN GENUS ADIANTUM (PTERIDACEAE) FROM LESSER SUNDA ISLANDS INDONESIA BASED ON RBCL AND TRNL-F

The Lesser Sunda Islands of Indonesia are composed of small islands scattered from Bali to Timor Island. We analyzed a molecular phylogeny of Adiantum collected from Lesser Sunda Islands to reveal its phylogenetic relationships. A total of 12 species of Adiantum from this region and seven species from Java Island were collected and used in this study. Two cpDNA regions (rbcL and trnL-F) were chosen as markers and phylogenetic analyses were conducted using Neighbour-Joining (NJ) and Maximum Parsimony (MP) methods. The tree topologies reconstructed by NJ and MP from specimens used in this study and other species downloaded from GenBank are congruent in which trees are divided into five major clades. Adiantum species of Lesser Sunda Islands are not monophyletic and comprises three clades, i. e. Clade I composed of A. hispidulum group, Clade III composed of A. peruvianum group and Clade IV or A. caudatum group, each together with extra-Lesser Sunda samples. No sample from Lesser Sunda Islands examined is located in Clade II (A. tenerum group) and V (A. capillus-veneris group).

Phylogeography of the arid shrub Atraphaxis frutescens (Polygonaceae) in northwestern China: evidence from cpDNA sequences.

Climatic fluctuations during the Pleistocene are usually considered as a significant factor in shaping intraspecific genetic variation and influencing demographic histories. To well-understand these processes in desert northwest China, we selected arid adapted Atraphaxis frutescens as the study species. Two cpDNA regions (psbK-psbI, psbB-psbH) were sequenced in 272 individuals from 33 natural populations across the range of this shrub, and 10 haplotypes were identified. It was found to contain high levels of total gene diversity (H T = 0.858), and low levels of within-population diversity (H S = 0.092). Analysis of molecular variance (AMOVA) indicates that genetic differentiation primarily occurs among groups of populations. Based on BEAST (Bayesian Evolutionary Analysis Sampling Trees) analysis, we suggest that intraspecific differentiation of the species, resulting from isolated populations, accompanied enhanced desertification during the middle and late Pleistocene. The expansion of the Gurbantunggut and Kumtag deserts in this area appears to have triggered divergence among populations of the western, central, and eastern portions of the region and shaped genetic differentiation among them. Two possible independent glacial refugia were predicted, the Ili Valley and the northern Junggar Basin. Extensive development of arid habitats (desert margin and arid piedmont grassland) coupled with a more equable climate because the early Holocene are factors likely to have generated recent expansion of A. frutescens.

The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China

AbstractAimRapid and accurate species identification is the foundation for biodiversity assessment. DNA barcoding has been shown to be an effective tool to overcome the taxonomic impediment to facilitate biodiversity conservation in temperate forests. However, this tool has rarely been considered for use in tropical forests. This study aims to investigate the utility and species resolution of DNA barcoding in a subtropical region.LocationThe Dinghushan National Nature Reserve (DNNR) in China.MethodsA DNA barcoding database was constructed for 531 trees present in the DNNR. We used a phylogenetic method (neighbour‐joining trees) and sequence similarity (all‐to‐all BLASTn searches) to evaluate the utility and species resolution of five DNA barcode regions (rbcL, matK, ITS, ITS2 and trnH‐psbA), both singly and in combinations of two or three region.ResultsThe combination of rbcL + matK + ITS had the highest species resolution (94.19%). However, when considering the difficulty of sequence recoverability, rbcL + ITS2 performed best (64.64%). Species resolution for large genera containing more than two species was substantially lower than that for small genera with one and two species per genus. Local small spatial scales (1‐ha quadrats) resulted in moderately improved species resolution (70.82% for rbcL + ITS2) compared to larger spatial scales (20 and 1133 ha). We document incongruent signals between nuclear and cpDNA regions and the challenges associated with barcoding large genera inherent to subtropical floras.Main conclusionsThis study considerably expands the global DNA barcode database for subtropical trees. Based on cost‐effectiveness and the trade‐off between sequence recovery and species resolution, we suggest that the rbcL + ITS2 barcode combination is an effective tool for documenting plant diversity in the DNNR. This study also sheds some light on the limitations and challenges for the application of barcoding to conservation biogeography in subtropical forests.

Molecular and morphological data reveal hybrid origin of wild Prunus yedoensis (Rosaceae) from Jeju Island, Korea: implications for the origin of the flowering cherry.

The subgenus Cerasus of the genus Prunus includes several popular ornamental flowering cherries. Of the hundreds of cultivars, P. ×yedoensis ('Somei-yoshino') is the most popular and familiar cultivar in Korea and Japan and is considered to be of hybrid origin. However, the hybrid origin of P. ×yedoensis and its relationship to wild P. yedoensis, naturally occurring on Jeju Island, Korea, are highly controversial. We extensively sampled wild P. yedoensis, cultivated P. ×yedoensis, and numerous individuals from other species belonging to subgenus Cerasus on Jeju Island. Samples from 71 accessions, representing 13 species and one cultivar (P. ×yedoensis), were sequenced for nrDNA ITS/ETS (952 characters) and seven noncoding cpDNA regions (5421 characters) and subjected to maximum parsimony and maximum likelihood analysis. Additive polymorphisms in the ITS/ETS regions were confirmed by cloning amplicons from representative species. The nuclear (ITS/ETS and G3pdh) and cpDNA data, along with several morphological characteristics, provide the first convincing evidence for the hybrid origin of wild P. yedoensis. The maternal parent was determined to be P. spachiana f. ascendens, while the paternal parent was unresolved from the taxonomically complex P. serrulata/P. sargentii clade. The presence of two kinds of ribotypes was confirmed by cloning, and the possible origin of cultivated P. ×yedoensis from wild populations on Jeju Island was also suggested. Bidirectional and multiple hybridization events were responsible for the origin of wild P. yedoensis. Extensive gene flow was documented in this study, suggesting an important role of reticulate evolution in subgenus Cerasus.

Nuclear-cytoplasmic compatibility and the state of mitochondrial and chloroplast DNA regions in alloplasmic recombinant and introgressive lines (H. vulgare)-T. aestivum

Alloplasmic lines combining alien nuclear and cytoplasmic genomes are convenient models for studying the mechanisms of nuclear-cytoplasmic compatibility/incompatibility. In the.present study, we have investigated the correlation between the characters and state of mitochondrial (mt) and chloroplast (cp) DNA regions in alloplasmic recombinant common wheat lines with barley cytoplasm characterized by partial or total fertility. Fertility restoration in the studied lines (Hordeum vulgare)-Triticum aestivum is determined by different ratios of the genetic material of common wheat variety Pyrotrix 28, which is a fertility restorer in the cytoplasm of barley, and varietySaratovskaya 29, which is a fixer of sterility. In partially fertile lines with nuclear genomes dominated by the genetic material of Saratovskaya 29, plant growth and development are suppressed. In these lines we have identified the barley homoplasmy of cpDNA regions infA and rpoB and the heteroplasmy of the 18S/5S mt repeat and the cpDNA ycf5 region. Nuclear-cytoplasmic compatibility in lines with reduced fertility (the genetic material of Pyrotrix 28 predominates in their nuclear genomes) is associated with restoration of normal plant growth and development and the changes in thestate of the studied cpDNA and mtDNA regions towards the wheat type. Thus, in fertile lines, the cpDNA regions (infA, rpoB) and the 18S/5S mt repeat were identified in the homoplasmic wheat state; though the cpDNAycf5 region was in the heteroplasmic state, it was dominated by the wheat type of the copies. The nuclearicytoplasmic compatibility is not broken as a result of introgression of the alien genetic material into the nuclear genome of one of the fertile lines; the plants of introgressive lines are fertile and normally developed, and the states of the cpDNA and mtDNA regions correspond to their states in fertile recombinant lines.

Nuclear and Cytoplasmic DNA Sequence Data Further Illuminate the Genetic Composition of Leyland Cypresses

Leyland cypress [×Hesperotropsis leylandii (A.B. Jacks. & Dallim.) Garland & G. Moore, Cupressaceae] is a well-known horticultural evergreen conifer in the United Kingdom, United States, Australia, New Zealand, and other countries. As demonstrated by previous studies, this taxon is a hybrid between alaska (nootka) cypress [Callitropsis nootkatensis (D. Don) Oerst. ex D.P. Little] and monterey cypress [Hesperocyparis macrocarpa (Hartw. ex Gordon) Bartel]. However, the genetic background of leyland cypress cultivars is unclear. Are they F1 or F2 hybrids or backcrosses? In this study, six individuals that represent major leyland cypress cultivars and two individuals each of its two putative parental species were collected, and three nuclear DNA regions (internal transcribed spacer, leafy and needly), three mitochondrial (mt) DNA regions (coxI, atpA, and rps3), and two chloroplast (cp) DNA regions (matK and rbcL) were sequenced and analyzed. Sequencing results of nuclear DNA regions revealed that leyland cypress cultivars consist of putative F1 and F2 hybrids as well as backcrosses. Analysis of the cp and mt DNA from six cultivars of leyland cypress revealed that their cytoplasmic (cp and mt) genomes came from alaska cypress. Our findings will provide important instructions and background knowledge on the management of these major leyland cypress cultivars as well as future studies. Meanwhile, alaska cypress and monterey cypress may have diverged with each other ≈46 million years ago. The fact that they can produce fertile hybrids indicates that hybridization events may have played an important role in the evolutionary history of the cypress family (Cupressaceae).

Differences in population genetic structure of two ethnomedicinal herbs of the genus Phyllanthus from India: a consequence of anthropogenic intervention?

Phyllanthus amarus and Phyllanthus fraternus are important ethnomedicinal herbs used as traditional medicines in many parts of the world. The increasing popularity of these green medicines and almost no studies on structuring of genetic diversity in these herbs, led to this investigation. Keeping this in view, our main objective was to analyze the structuring of chloroplast DNA diversity in wild populations of the two herbs from Northern India, using chloroplast DNA (cpDNA) markers. PCR–RFLP of cpDNA regions was carried out to detect intraspecific polymorphisms. The study revealed differences in cpDNA diversity in the two ethnomedicinal herbs. Lower cpDNA diversity, lesser number of haplotypes and absence of correlation between phylogeny and geographical distribution of haplotypes were observed in P. amarus. Absence of phylogeographic structure in P. amarus may be attributed partly to higher anthropogenic intervention, owing to its commercialization for export and raw drug trade. The investigation identified populations with high haplotype diversity and unique haplotypes in both the herbs, which will be useful while formulating future conservation strategies. As there are comparatively less number of studies on structure of cpDNA diversity in annuals, the present analyses also add to the available data on population genetic structure in annual plants.

한약재 마늘(Allium sativum L.)의 식별을 위한 유전자 감식연구

ABSTRACT Objectives : This study was carried out to identify DNA markers of “Allium sativum” be circulated from Korea and China, which is difficult to discriminate from morpho logical characters because of fragmental materials of bulb. That is, all these studies focused on the di scrimination of Allium sativum L. But these day, Chinese A. sativum was in circulated Korean A. sativum in Korean medicine markets. Therefore, the purpose of our study was to develop molecular markers for discrimination between Korean A. sativum and imports from China.Methods : Materials were collected randomly from a markets in Korea and China and be analyzed with matK, ndhF and trnL-F regions of chloroplast DNA (cpDNA). We collected 45 A. sativum individuals from Korean and Chinese medicine markets, in 2013. Results : As a results, matK and ndhF regions of cpDNA was shown to be identify, Species that grow from warm place and cold place can divide as five SNP (Single nucleotide polymorphisms) markers in matK and ndhF genes. Also, in trnL-F regions, found one SNP that can divide Korean A. sativum and Chinese A. sativum.Conclusions : From the analysis of matK and ndhF regions of cpDNA, we presumed that three markers of cpDNA were found by useful marker that can distinguish Korean, Chinese, Warm place type, and Cold place type. Individual differences of Korean and Chinese was thought that appear in geographical difference and genetic difference by environment for long hour even if same sp ecies.Key words : DNA markers, Allium sativum L., SNP

Phylogeny of the restiid clade (Poales) and implications for the classification of Anarthriaceae, Centrolepidaceae and Australian Restionaceae

AbstractThree families, Anarthriaceae, Restionaceae and Centrolepidaceae, are generally recognised in the restiid clade of Poales. A new phylogeny is presented, with fuller sampling of Australian taxa, based on analyses of trnL‐F, trnK and rbcL data from the chloroplast genome. The findings agree with the major groups shown in previous molecular studies but provide a more substantial basis for reviewing the classification at family and generic levels. Anarthriaceae is sister to Restionaceae, with Anarthria sister to Lyginia+Hopkinsia. Centrolepidaceae, on an extremely long branch, appears embedded in Restionaceae in Bayesian trees; although it appears as sister to Restionaceae in analyses that are more subject to long‐branch attraction (in parsimony analyses and those of data from the less‐conserved trnL‐F cpDNA region). Accepting the embedded position, which would make this a subfamily of Restionaceae, the basal division in the Restionaceae separates the African subfamily Restionoideae from the Australasian clade (Sporadanthoideae, Centrolepidoideae, Leptocarpoideae). In subfamily Leptocarpoideae, Eurychorda forms the basal branch. At the next dichotomy the Leptocarpus clade, together with the Winifredia clade, is separated from a diverse assemblage including Loxocarya, Chordifex, Baloskion, Desmocladus, Lepidobolus and allied genera. The phylogeny indicates that several currently recognised genera are not monophyletic and that changes to the generic classification are required. A matrix of morphological characters was prepared and these were mapped onto the Bayesian consensus DNA tree to identify synapomorphies of the clades and genera. Observations on leaf laminae indicate that fully or partially unifacial leaf laminae are a synapomorphy of the restiid clade. The morphological characterisation of the following are considered: the restiid clade, Anarthriaceae, Restionaceae enlarged to include subfamily Centrolepidoideae, Leptocarpus s.l. (including as potential synonyms Meeboldina and Stenotalis) and Desmocladus s.l. (including potentially Harperia, Onychosepalum and Kulinia).

Species specific cpDNA markers useful for studies on the hybridisation between Pinus mugo and P. sylvestris

PCR-RFLP technique has been used to detect species-specific mutations of organelles DNA for closely related dwarf mountain pine (<em>Pinus mugo</em>) and Scots pine (<em>P. sylvestris</em>). Restriction fragment patterns have been compared of amplification products for <em>trn</em>L-<em>trn</em>F cpDNA and for <em>cox</em>I and <em>orf</em>25 genes of mtDNA. The difference has been found in the Dral and Hinfl restriction patterns of the amplification products for <em>trn</em>L-<em>trn</em>F region of cpDNA with two haplotypes detected. The haplotype M is characteristic for <em>P. mugo</em> and the haplotype S for <em>P. sylvestris</em>. These markers may be useful for the analysis of the natural hybridisation and introgression between these species postulated for some sympatric populations on the basis of morphological analysis. No differences have been disclosed in the studied mtDNA regions.

Identification of native Dendrobium species in Thailand by PCR-RFLP of rDNA-ITS and chloroplast DNA

The PCR-restriction fragment length polymorphism (PCR-RFLP) approach was successfully developed to identify 25 native Dendrobium species in Thailand. PCR-RFLP of the rDNA-ITS with six restriction enzymes and three chloroplast (cp) DNA regions with five primer-enzyme combinations produced 24 types of DNA patterns altogether. Twenty-three out of the 25 species determined in this study were found to belong to unique classes and were successfully differentiated. Two species, D. crumenatum and D. formosum, possessing the same DNA pattern, however, were identified after cutting the chloroplast DNA fragment amplified by psbC-trnS primer with MboI enzyme. An effective procedure for identifying each Dendrobium species was developed. PCR-RFLP of the rDNA-ITS with TaqI, which is the most informative enzyme, was used for the early detection of 16 Dendrobium species. To identify the remaining Dendrobium species, PCR- RFLP analysis was performed using one more primer-enzyme combination. Our study provides a rapid, simple, and reliable identification method for these Dendrobium species.

The chloroplast DNA locus psbZ-trnfM as a potential barcode marker in Phoenix L. (Arecaceae)

The genus Phoenix (Arecaceae) comprises 14 species distributed from Cape Verde Islands to SE Asia. It includes the economically important species Phoenix dactylifera. The paucity of differential morphological and anatomical useful characters, and interspecific hybridization, make identification of Phoenix species difficult. In this context, the development of reliable DNA markers for species and hybrid identification would be of great utility. Previous studies identified a 12 bp polymorphic chloroplast minisatellite in the trnG (GCC)-trnfM (CAU) spacer, and showed its potential for species identification in Phoenix. In this work, in order to develop an efficient DNA barcode marker for Phoenix, a longer cpDNA region (700 bp) comprising the mentioned minisatellite, and located between the psbZ and trnfM (CAU) genes, was sequenced. One hundred and thirty-six individuals, representing all Phoenix species except P. andamanensis,were analysed. The minisatellite showed 2-7 repetitions of the 12 bp motif, with 1-3 out of seven haplotypes per species. Phoenix reclinata and P. canariensis had species-specific haplotypes. Additional polymorphisms were found in the flanking regions of the minisatellite, including substitutions, indels and homopolymers. All this information allowed us to identify unambiguously eight out of the 13 species, and overall 80% of the individuals sampled. Phoenix rupicola and P. theophrasti had the same haplotype, and so had P. atlantica, P. dactylifera, and P. sylvestris (the “date palm complex” sensu Pintaud et al. 2013). For these species, additional molecular markers will be required for their unambiguous identification. The psbZ-trnfM (CAU) region therefore could be considered as a good basis for the establishment of a DNA barcoding system in Phoenix, and is potentially useful for the identification of the female parent in Phoenix hybrids.

DNA barcoding of Orchidaceae in Korea

Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK-psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF-atpH IGS (0.0648), trnH-psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH-psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.

Radiation and repeated transoceanic dispersal of Schoeneae (Cyperaceae) through the southern hemisphere

The broad austral distribution of Schoeneae is almost certainly a product of long-distance dispersal. Owing to the inadequacies of existing phylogenetic data and a lack of rigorous biogeographic analysis, relationships within the tribe remain poorly resolved and its pattern of radiation and dispersal uncertain. We employed an expanded sampling of taxa and markers and a rigorous analytic approach to address these limitations. We evaluated the roles of geography and ecology in stimulating the initial radiation of the group and its subsequent dispersal across the southern hemisphere. A dated tree was reconstructed using reversible-jump Markov chain Monte Carlo (MCMC) with a polytomy prior and molecular dating, applied to data from two nuclear and three cpDNA regions. Ancestral areas and habitats were inferred using dispersal-extinction-cladogenesis models. Schoeneae originated in Australia in the Paleocene. The existence of a "hard" polytomy at the base of the clade reflects the rapid divergence of six principal lineages ca. 50 Ma, within Australia. From this ancestral area, Schoeneae have traversed the austral oceans with remarkable frequency, a total of 29 distinct dispersal events being reported here. Dispersal rates between landmasses are not explicable in terms of the geographical distances separating them. Transoceanic dispersal generally involved habitat stasis. Although the role of dispersal in explaining global distribution patterns is now widely accepted, the apparent ease with which such dispersal may occur has perhaps been under-appreciated. In Schoeneae, transoceanic dispersal has been remarkably frequent, with ecological opportunity, rather than geography, being most important in dictating dispersal patterns.

Mapania multiflora, a distinctive new species of Cyperaceae (Mapanioideae) from Borneo

Mapania multiflora is described and illustrated. It is vegetatively similar to taxa with broad leaves and pseudopetioles, such as M. cuspidata. However, it is reproductively similar to sect. Thoractostachyum with a paniculate inflorescence and furrowed fruit. The DNA is similar to M. bancana in sect. Thoractostachyum, in the three sampled cpDNA regions: atpH-F, trnL-F and psbA-trnH. However, it is identical to none of these due to its unique combination of vegetative, reproductive and molecular characteristics.

Strong Accumulation of Chloroplast DNA in the Y Chromosomes of Rumex acetosa and Silene latifolia

Chloroplast DNA (cpDNA) sequences are often found in plant nuclear genomes, but patterns of their chromosomal distribution are not fully understood. The distribution of cpDNA on the sex chromosomes can only be studied in dioecious plant species possessing heteromorphic sex chromosomes. We reconstructed the whole chloroplast genome of Rumex acetosa (sorrel, XY₁Y₂ system) from next generation sequencing data. We systematically mapped the chromosomal localization of various regions of cpDNA in R. acetosa and in Silene latifolia (white campion, XY system) using fluorescence in situ hybridization. We found that cpDNA was accumulated on the Y chromosomes of both studied species. In R. acetosa, the entire Y chromosome gathered all parts of cpDNA equally. On the contrary, in S. latifolia, the majority of the cpDNA, corresponding to the single copy regions, was localized in the centromere of the Y chromosome, while the inverted repeat region was present also in other loci. We found a stronger accumulation of cpDNA on the more degenerated Y₁ and Y₂ chromosomes of R. acetosa than in evolutionary younger S. latifolia Y chromosome. Our data stressed the prominent role of the Y chromosome centromere in cpDNA accumulation.

A phylogeny of Bromeliaceae (Poales, Monocotyledoneae) derived from an evaluation of nine supertree methods

AbstractThere are 26 phylogenetic studies for Bromeliaceae based on different sources of evidence. Despite this broad phylogenetic coverage of Bromeliaceae, however, the available phylogenetic data display a scattered sampling, with little overlap among different types of evidence. The aim of this study is to integrate the available phylogenetic information of the Bromeliaceae in one hypothesis using a supertree. To test which of them integrates best the information for Bromeliaceae, nine supertree methods were employed: Avcon, MSS, MinFlip, MMC, MRP, PhySIC_IST, Robinson–Foulds Supertree, Sfit, and SuperFine. Supertrees were compared with a reference tree, generated from the maximum likelihood (ML) analysis of a supermatrix integrated by 120 taxa of Bromeliaceae and seven cpDNA regions. In order to select which method best reconstructs the most robust phylogeny, two different sets of source trees were used: (i) those generated from the analysis of each individual DNA regions; and (ii) four selected phylogenies (from the 26 published works). We used the consensus fork index, normalized partition metric, patristic distance coefficient, and the Shimodaira–Hasegawa test to compare supertrees with the reference tree. The best performing methods were used to construct a supertree using all phylogenies of Bromeliaceae. The SuperFine method generated the best supertree. The lack of overlapping among phylogenies was the major limiting factor for the integration of the phylogenetic information of Bromeliaceae. Nonetheless, supertree methods helped in the identification of poorly sampled groups, as well as to explore levels of agreement among published phylogenetic studies for Bromeliaceae.

Phylogeography of two closely related species of Nolana from the coastal Atacama Desert of Chile: post‐glacial population expansions in response to climate fluctuations

AbstractAimTo investigate the impact of Quaternary climate cycles on the coastal Atacama Desert flora by assessing phylogeographical patterns of the desert shrub Nolana crassulifolia (Solanaceae) and its congener Nolana incana.LocationThe latitudinal aridity gradient from the southern margin of the coastal Atacama Desert to the mediterranean semi‐arid region of Chile (25–33° S).MethodsTwo cpDNA regions were sequenced for 130 individuals in 15 populations of these two closely related species, covering their entire distribution range (1000 km) along the arid to semi‐arid Chilean coast. We explored haplotype relationships in a statistical parsimony network, and assessed population genetic diversity, population differentiation and phylogeographical structure. In addition, we conducted demographic analyses and spatial analysis of genetic variation, identified barriers to gene flow with Monmonier's algorithm, and used Bayesian phylogenetic reconstruction to estimate divergence dates between lineages.ResultsWe found a total of 14 haplotypes – four of them shared by both species – and high levels of genetic differentiation among populations, but no past distribution breaks that could account for major vicariant events. Genetic diversity decreased continuously from north to south, with loss of haplotypes and a greater number of monomorphic populations in the southern range. Landscape analysis revealed greater genetic differentiation in the northernmost populations of both species.Main conclusionsThe documented north–south gradient of declining genetic diversity, the origin and location of ancestral haplotypes in northern sites, and the loss of haplotypes from southern populations all support the hypothesis of post‐glacial range expansion of Nolana southwards during arid/warmer cycles in the Atacama. The higher genetic diversity and greater differentiation of northern populations of both Nolana species support the hypothesis that populations survived in northern arid sites during wetter/colder episodes of the glacial cycles. We suggest that Quaternary arid phases in the Atacama promoted southward expansion of the coastal desert vegetation.

Phylogenetic and phylogeographic evidence for a Pleistocene disjunction between Campanula jacobaea (Cape Verde Islands) and C. balfourii (Socotra)

Our understanding of processes that led to biogeographic disjunct patterns of plant lineages in Macaronesia, North Africa and Socotra remains poor. Here, we study a group of Campanula species distributed across these areas integrating morphological and reproductive traits with phylogenetic and phylogeographic data based on the obtention of sequences for 4 highly variable cpDNA regions and AFLP data. The phylogeny obtained shows a sister relationship between Campanula jacobaea (endemic to Cape Verde Islands) and C. balfourii (endemic to Socotra), thus revealing a striking disjunct pattern (8300km). These species diverged around 1.0Mya; AFLP and haplotype data suggest that no genetic interchange has occurred since then. Their closest taxon, C. hypocrateriformis, is endemic to SW Morocco. The archipelagos of Macaronesia and Socotra have probably acted as refugia for North-African species, leading to speciation through isolation. Although C. balfourii has a restricted distribution, its genetic variability suggests that its populations have suffered no bottlenecks. C. jacobaea is also genetically rich and its distribution across Cape Verde Islands seems to have been influenced by the NE–SW trade winds, which may also have favoured the admixture found among the populations of the three southern islands. Floral features of the morphologically hypervariable C. jacobaea were also measured to assess whether the taxon C. bravensis, described for some of the southeast populations of C. jacobaea, corresponds to a different evolutionary entity. We show that morphological variation in C. jacobaea does not correspond to any genetic or geographic group.