Chloroplast Non-coding Regions Research Articles

<i>Ranunculus dahlgreniae</i> (section <i>Batrachium</i>, Ranunculaceae), a new species from Crete, Greece, with remarks on taxonomy and phylogenetic relations within the section

A new species, <i>Ranunculus dahlgreniae</i>, is described from a seasonal lake at Omalos Plateau, Lefka Ori Mountains, western Crete, Greece. The heterophyllous species resembles <i>R. saniculifolius</i>, <i>R. peltatus</i>, and the Mediterranean forms of <i>R. baudotii</i>. It differs from the aforementioned species by a combination of characters not found in any of them, i.e., 5–6 mm long petals, up to 2.2 mm long, glabrous achenes with a partly persistent style, a densely pubescent, in fruit slightly elongating receptacle, and intermediate leaves with rigid filiform apical segments, being divided into two or three cuneate, shortly petiolate leaflets. A key to all similar East Mediterranean taxa is presented. DNA analyses based on the sequencing of nuclear, ribosomal Internal Transcribed Spacer (ITS), and two chloroplast noncoding regions (<i>rpl</i>32-<i>trn</i>L and <i>psb</i>E-<i>pet</i>L), complemented by the analysis of genome-wide polymorphism using double digest RAD Sequencing (ddRADseq) supported that <i>Ranunculus dahlgreniae</i> is a distinct lineage, clearly separated from <i>R. peltatus</i>, <i>R. baudotii</i>, and <i>R. saniculifolius</i>. The phylogeny based on ddRADseq resembles the topologies obtained from chloroplast and nrITS data but with increasing resolution and support of fine-scale relationships. Extensive sampling, including taxa from temperate Europe and the West Mediterranean area, as well as the application of reduced-representation sequencing, allowed to better understand the pattern of diversity in the section <i>Batrachium</i>.

Morphological and phylogenetic features of the Crimean population of Juniperus deltoides R.P. Adams.

Juniperus deltoides is a relict species from the Tertiary Period. It is a typical representative of the Mediterranean group of the section Juniperus. It is included in the Red Books of the Republic of Crimea and the city of Sevastopol. Until recently, it was believed that a population of J. oxycedrus grew in Crimea. Currently, J. deltoides is described as a cryptic species, morphologically difficult to distinguish from J. oxycedrus. As a result, it became necessary to conduct a series of detailed studies to determine the morphological and phylogenetic features of the Crimean cryptic population in order to identify it as being one of the species of the cryptic pair. The studies were carried out in two stages: at the first stage, the morphological features of the vegetative and generative organs and their difference from J. oxycedrus were determined; the second stage included genetic research. The length of the needles of the Crimean population is 12.94 ± 0.19 mm, which corresponds to the Eastern Italian population of J. deltoides. At the same time, the width of the needles is 1.39 ± 0.02 mm, which is typical of the Portuguese population of J. oxycedrus. The dimensions of the cones are d1 (conditional height) = 7.54 ± 0.14 mm, and d2 (conditional width) = 9.11 ± 0.09 mm, which is more in line with J. deltoides. The shapes of the cones are very diverse. Some individuals have cones, the covering scales of which are visually indistinguishable, and their tops are completely fused. A similar phenomenon is characteristic of the Western Mediterranean populations of J. oxycedrus. Morphological analysis of the vegetative and generative organs of J. deltoides showed that when these two traits are combined, it is not possible to reliably distinguish between J. deltoides and J. oxycedrus individuals. Nuclear (ITS internal transcribed spacer) and chloroplast (petN-psbM, trnS-trnG) non-coding regions of the genome were used for genetic analysis. Studies have shown that the nuclear regions of genes have greater variability than chloroplast regions. The sequences obtained in this work formed a clade with J. deltoides samples 9430 and 9431 (BAYLU) growing in Turkey, which makes it possible to assign the samples studied to J. deltoides.

Recircumscription of Utricularia leptorhyncha and U. lasiocaulis and three related new species for northern Australia

The Utricularia lasiocaulis F.Muell. complex (subg. Polypompholyx; sect. Lasiocaules) is a morphologically and ecologically variable group of closely related taxa with a mostly tropical distribution across northern Australia. A recent molecular phylogenetic study placed the recognised species U. kamienskii F.Muell. sister to a clade of accessions relegated to either U. leptorhyncha O. Schwarz or U. lasiocaulis, with the latter previously circumscribed as an assemblage of highly variable morphological forms. We have expanded the previous study to include populations representing the known distributions of all three species and have attempted to include all morphological variants; 55 ingroup accessions were used in the full phylogenetic analysis based on two non-coding chloroplast regions (rps16, trnD–T) and the nuclear ribosomal internal transcribed spacer (ITS). We found that the pink corolla form of the usually white flowered U. kamienskii is not sufficiently different, and we retain it under that species. We also found strong support for a paraphyletic U. leptorhyncha, with the smaller flowered accessions matching the type material placed sister to all other U. lasiocaulis forms, including a grouping previously assigned as a larger flowered U. leptorhyncha. Within the U. lasiocaulis clade we found that much of the variation sorts into well-supported clades that we find are sufficiently morphologically and genetically differentiated from the type clade for recognition at the specific rank, namely Utricularia brennanii R.W.Jobson & Baleeiro from Northern Territory and Queensland, Utricularia cowiei R.W.Jobson & Baleeiro from the Kimberley region of Western Australia, and U. disjuncta R.W.Jobson & Baleeiro restricted to the Darwin and Gulf region of the Northern Territory.

Identification of Apiaceae using ITS, ITS2 and psba-trnH barcodes.

Apiaceae plants are used as medicinal herbs, pesticides, spices, and vegetables; thus, accurately identifying Apiaceae species is important. The grassland ecosystem of Heilongjiang Province in northern China has huge reserves of wild Apiaceae plants, but few reports have systematically documented their diversity. In this study, 275 Apiaceae plants of 23 species in 18 genera were collected from this area. We identified Apiaceae species by using nuclear internal transcribed spacer (ITS/ITS2) and psbA-trnH (chloroplast non-coding region) sequences based on experimental data. The identification efficiency of ITS, ITS2 and psbA-trnH sequences was determined and evaluated by sequence alignment and analysis, intraspecific and interspecific genetic distance analyses, and phylogenetic tree construction. ITS, ITS2 could distinguish 21 species from 17 genera of Apiaceae with good identification effect. When identifying species in the Apiaceae family, ITS2 can be used as the core barcode and psbA-trnH can be used as the supplementary barcode. These results can enrich the reference Apiaceae DNA barcode database.

Chloroplast DNA insights into the phylogenetic position and anagenetic speciation of Phedimus takesimensis(Crassulaceae) on Ulleung and Dokdo Islands, Korea.

Phedimus takesimensis (Ulleungdo flat-leaved stonecrop) is endemic to Ulleung and Dokdo Islands off the east coast of the Korean Peninsula. It was suggested that P. takesimensis originated via anagenetic speciation from the continental progenitor species P. kamtchaticus or P. aizoon. However, little is known of the phylogenetic relationships and population genetic structure among species of Phedimus in the Korean Peninsula and Ulleung/Dokdo Islands. We inferred the phylogenetic relationships among congeneric species in Korea based on nuclear ribosomal DNA internal transcribed spacer and chloroplast noncoding regions. We also sampled extensively for P. takesimensis on Ulleung Island and the continental species, P. kamtschaticus and P. aizoon, to assess the genetic consequences of anagenetic speciation. We found (1) the monophyly of P. takesimensis, (2) no apparent reduction in genetic diversity in anagenetically derived P. takesimensis compared to the continental progenitor species, (3) apparent population genetic structuring of P. takesimensis, and (4) two separate colonization events for the origin of the Dokdo Island population. This study contributes to our understanding of the genetic consequences of anagenetic speciation on Ulleung Island.

Orostachys spinosa (Crassulaceae) origin and diversification: East Asia or South Siberian Mountains? Chloroplast DNA data

Limited data are available on genetic structures of the herbaceous plant species populations inhabiting mountainous areas of Siberia and Northeastern Asian (Russian Far East). Although this area was not directly impacted by the extensive ice-sheets during the Quaternary, it experienced significant climatic fluctuations that influenced rich local flora. Orostachys spinosa (Crassulaceae) lacks any adaptations for long-distance dispersal, yet the species is characterized by an unusually wide range spanning from the Urals to the coast of the Pacific Ocean. We studied O. spinosa phylogeography and genetic diversity across its range sampling 203 individuals from 21 natural populations. Using sequences from three chloroplast DNA non-coding regions, we revealed 82 haplotypes and observed high level of population differentiation indicating presence of the phylogeographic structure (GST = 0.501 and NST = 0.822 (p < 0.01)). In concordance with the previous phylogenetic analyses based on ITS rDNA data, parsimony network revealed two distinct cpDNA haplotype lineages deferring in their structure and characteristics of genetic diversity. The split between these haplotype groups can be dated to the Pliocene (ca. 3.6 Mya). According to our estimates diversification in the Western group of populations took place ca. 1 Mya earlier than in the Eastern group (3.1 Mya and 2.26 Mya, respectively). Apart from the generally accepted notion about East Asian origin of O. spinosa, our results indicated that the species could have originated in mountains of Southern Siberia (Altai). This region was colonized independently from O. thyrsiflora which has a largely overlapping distribution in this area.

Insights from Chloroplast DNA into the Progenitor-Derivative Relationship Between Campanula punctata and C. takesimana (Campanulaceae) in Korea

Of the nearly 40 endemics present on Ulleung Island, Campanula takesimana Nakai represents an anagenetically derived lineage of a continental progenitor, C. punctata Lam. Other than its low morphological divergence, little is known about the genetic diversity and population structure of the species pair or the geographical origin of C. takesimana. We sampled a total of 240 accessions in 22 populations, including one Dokdo Island population, of the two species, sequenced four noncoding chloroplast regions (rps16-trnK, trnQ-rps16, psbD-trnT, and psbM-trnD; 4482 bp), and assessed the genetic consequences of anagenetic speciation. Based on chloroplast DNA, we found substantially lower genetic diversity statistics for C. takesimana compared to its progenitor, significant population genetic structuring in insular derivative species, and significant molecular divergence between C. punctata and C. takesimana. Mutually exclusive haplotypes were found in the two species, and the haplotype network suggested that Ulleung Island haplotypes were derived from the Dokdo Island haplotype, which was originally derived from a C. punctata population in Bonghwa-gun, Gyeongsangbuk-do Province. This study pinpoints a very narrow geographical source area and suggests the potentially important role of Dokdo Island as an initial stepping stone for Ulleung Island endemics.

The molecular characterization of Indonesian Gonystylus species

The proper identification of a species is a very important factor for establishment of management and conservation strategies. This study aimed to confirm the identification of Gonystylus spp. using DNA markers. Twenty-four leaf samples of nine species of ramin were extracted using the modified CTAB method to obtain the template DNAs. Four primers were used to amplify ITS ribosomal DNA (partial of ITS2) and three chloroplast non-coding regions sequences. DNA sequences were analyzed using BLAST online software to identify the species. The phylogenetic tree was constructed to confirm species relationship. Based on the DNA markers, one sample of Aquilaria was misidentified as Gonystylus, and the other 23 samples were clustered into seven groups i.e. G. bancanus, G. brunescens, G. stenosepalus, G. forbesii, G. consanguineus, G. lucidulus and an unspecified Gonystylus. The clustering of those samples based on molecular characters was in disagreement with clustering based on morphological characters. This finding suggests that molecular characterization should be conducted to confirm the identification of species prior to establishing conservation areas.

&lt;p&gt;&lt;strong&gt;Genetic diversity and species limits in &lt;em&gt;Veltheimia&lt;/em&gt; (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data&lt;/strong&gt;&lt;/p&gt;

Veltheimia is a genus of two species of bulbous flowering angiosperms restricted to southern Africa. Both parsimony and Bayesian analysis of 1829 nucleotides of DNA sequence data, from three non-coding chloroplast regions from multiple samples of both species, indicates that specimens of V. bracteata form a monophyletic clade together with three specimens named as V. capensis. This clade receives low support and is embedded within a paraphyletic grade of specimens of V. capensis. A Median Joining Network analysis of a subset of samples revealed nine haplotypes, the relationships of which mirrored the relationships resolved by the Bayesian analysis. With the exception of the V. capensis members of the V. bracteata clade, the remaining specimens are from the summer rainfall thicket and coastal forests. The samples of the basal V. capensis grade are found in the winter rainfall regions of southern Africa. These results indicate that there is limited genetic diversity within the genus, and there is no clear distinction between these two species based on plastid non-coding DNA data. This may be due to their recent divergence and incomplete lineage sorting, or recent or ongoing hybridisation and / or introgression.

Radiations of fairy-aprons (Utricularia dichotoma, Lentibulariaceae) in Australia and New Zealand: molecular evidence and proposal of new subspecies

The Utricularia dichotoma Labill. complex is a morphologically and ecologically variable group of closely related taxa with a mostly temperate distribution across New Zealand, New Caledonia and Australia. Taxonomic boundaries within the complex have been the subject of speculation, with several previously recognised species being synonymised after a nomenclatural revision. We sampled 296 populations representing all known taxa; 223 accessions were used in the full phylogenetic analysis based on two non-coding chloroplast regions (rps16, trnD–T) and two nuclear ribosomal spacers (external transcribed spacer, ETS; internal transcribed spacer-1, ITS-1), whereas the remaining accessions were identified by using ITS-1 barcodes. We found strong support for a paraphyletic U. dichotoma, with accessions matching the type material of that name grouped within a polytomy that includes clades containing accessions of U. monanthos Hook.f and U. novae-zelandiae Hook.f. Specific statuses for five recently described species previously included in U. dichotoma s.l. do not fall within this polytomy, nor do the two species U. oppositiflora R.Br. and U. speciosa R.Br. resurrected from synonymy of U. dichotoma. All sampled accessions from New Zealand form a single clade within U. dichotoma as recognised here. We here propose that seven clades recovered here be recognised as subspecies, and describe eight new subspecies, including two new combinations. We also propose that the monophyletic clade sister to U. beaugleholei Gassin be assigned to subspecies rank under that name.

The speciation history of northern- and southern-sourced Eranthis (Ranunculaceae) species on the Korean peninsula and surrounding areas.

The temporal and spatial origins and evolution of the genus Eranthis have not been previously studied. We investigated the speciation and establishment histories of four Eranthis species: Eranthis byunsanensis, E. pungdoensis, E. stellata, and E. pinnatifida. The sampling localities were Korea, Japan, Jilin in China, and the area near Vladivostok in Primorskiy, Russia. We used 12 chloroplast microsatellite loci (n = 935 individuals) and two chloroplast noncoding regions (rpl16 intron, petL‐psbE intergenic spacer; n = 33 individuals). The genetic diversity, genetic structure, phylogenetic relationships of the four species were analyzed, and their ancestral areas were reconstructed. The high genetic diversity of the Jeju island population of E. byunsanensis and Russian populations of E. stellata indicated these species’ northward and southward dispersal, respectively. The genetic structure analyses suggest that the populations in these four species have limited geographical structure, except for the Chinese E. stellata population (SCP). The phylogenetic analyses suggest that E. byunsanensis and E. pinnatifida are sister species and that Chinese SCP may not belong to E. stellata. The ancestral area reconstruction revealed that the most recent common ancestor of the four species existed in the current Chinese habitat of E. stellata. This study shows that E. byunsanensis and E. pinnatifida originated from a southern Eranthis species and speciated into their current forms near Jeju island and near western regions of Japan, respectively, during the Miocene. E. stellata may have dispersed southward on and near the Korean peninsula, though its specific origin remains unclear. Interestingly, the Chinese E. stellata population SCP suggests that the Chinese population might be most ancient among all the four Eranthis species. E. pungdoensis may have allopatrically speciated from E. byunsanensis during the Holocene. The Korean peninsula and the surrounding areas can be considered interesting regions which provide the opportunity to observe both northern‐ and southern‐sourced Eranthis species.

Chloroplast diversity of giant buttercup (Ranunculus acris L., Ranunculaceae) in New Zealand and in its native range

ABSTRACTThe species Ranunculus acris L. (giant buttercup) is native to Europe but has a very large naturalised range in several countries. In New Zealand it is a serious weed of pasture, particularly in high rainfall areas. Biological control options are being sought as chemical control has proven insufficient and is leading to resistance. To find efficient pathogens or natural enemies the search needs to focus on areas of origin of the material present in New Zealand. The target range of biocontrol agents needs to be broad enough to include all R. acris haplotypes found in New Zealand but also host specific enough to not attack unintended targets. A previous study found that R. acris in New Zealand has very high chloroplast diversity, with mixed chloroplast haplotypes occurring in single populations. Haplotype-specific genetic data are therefore essential for the identification of the origin and for sourcing effective biocontrol agents. The aim of this study was to identify putative origins of the material found in New Zealand. We compared chloroplast diversity in New Zealand populations of R. acris to parts of the native and naturalised ranges, including areas of the putative origin of the New Zealand plants. The non-coding chloroplast regions trnK and psbJ-petA were sequenced to identify haplotypes. We found that the native range also had high chloroplast diversity, and that most New Zealand chloroplast haplotypes were common in northern Europe and the United Kingdom. Further sampling would be required to trace the remaining two New Zealand haplotypes to their origin, however the results suggest that R. acris was introduced from several regions in Europe.

Phylogeography of the moonwort fern Botrychium lunaria (Ophioglossaceae) based on chloroplast DNA in the Central-European Mountain System

Botrychium s.s. is a cosmopolitan fern genus comprising about 35 currently recognized species. Despite unexpected high genetic diversity recently highlighted within Botrychium lunaria in the circumboreal region, few studies have included representative samples from Central Europe. Therefore, the aim of this work was to study the phylogeography of B. lunaria in the Central-European Mountain System and to compare it with that of flowering plants. Two noncoding chloroplast regions (psbA-trnH and trnL-F) were sequenced (918 bp) from 87 individuals from 34 populations in the major European mountain chains (Sierra Nevada, Pyrenees, Massif Central, Jura, Vosges, Black Forest, Alps, Apennines, and Carpathians). Among the 24 haplotypes found in the B. lunaria aggregate in Europe, bayesian phylogeny and median-joining network support four main clades (LUN1, LUN2, LUN3, and TUN). NST and GST comparison as well as homogeneous groups indicated by SAMOVA indicate a clear phylogeographical pattern. However, unlinked to geographical distance, genetic diversity is greatest in the Prealps and highlights three main barriers to gene flow: S–N of Central Alps (Aosta-Lepontic Alps), and two separating E–W Alps (Lago di Como-Rhaetian Alps and Dolomites-Noric-Julian Alps). Our results indicate that alpine populations of the B. lunaria aggregate survived the Quaternary glaciations in situ in two main refugia, in the southern and eastern periphery of the Alps. Not only areas with higher values of genetic diversity, but also refugia and sites of geographical boundaries to gene flow, appear similar in both ferns and flowering plants.

Phylogenetic relationships of Vepris (Rutaceae) inferred from chloroplast, nuclear, and morphological data.

The tribe Toddalieae Hook. F. (Rutaceae) has been controversial since its inception by Bentham and Hooker. The nine taxa examined, Acronychia J.R. & G.Foster, Diphasia Pierre, Diphasiopsis Mendonca, Fagaropsis Mildbr.ex. Siebenl., Oricia Pierre, Teclea Delile, Toddaliopsis Engl., Toddalia Juss. and Vepris Comm. ex. A. Juss, have been recognized under the tribe Toddalieae or Tribes Acronychia, Phellodendron and Toddalia. More recently Araliopsis Engl., Diphasia, Diphasiopsis, Oricia, Teclea, and Toddaliopsis have been incorporated into the genus Vepris, while Toddalia and Fagaropsis have continued to be recognized as closely related. For this study, sequence data of one non-coding chloroplast region (trnL-F) and one nuclear region (ITS) and various morphological characters, based on Mziray’s taxonomic studies were examined to try to elucidate these relationships. This study found that the taxa Diphasia, Diphasiopsis, Oricia, Teclea, Toddaliopsis, Vepris, Toddalia eugeniifolia Engl. and Toddalia glomerata F. Hoffm. form a monophyletic group. Due to the amount of intrageneric and intraspecific variation, species delimitations were difficult to determine; however, these genera should be united into Vepris. The analyses also confirmed that Toddalia asiatica (L.) Lam., Zanthoxylon sp. and Fagaropsis angolensis (Engl.) H.M. Gardner are the closest relatives to this group.

Towards A Complete Species Level Phylogeny of Leptosiphon (Polemoniaceae)

Abstract Leptosiphon Benth. (Polemoniaceae) has 40 taxa, distributed mainly in western North America, with one species in Chile. Phylogenetic studies of Polemoniaceae have consistently supported recognition of Leptosiphon as a separate genus from Linanthus, and resolved an array of taxonomic problems; however, several issues remained unclear for Leptosiphon. In those studies, sampling of Leptosiphon was incomplete, and certain species having strikingly similar floral morphologies appeared non-monophyletic, while other species groups with divergent floral morphologies formed a clade. Our analyses use greater sampling across taxa in Leptosiphon and, in addition to nrITS, the non-coding chloroplast region trnS–trnG to help resolve the genus phylogeny. These results yielded a more complete phylogeny from which to base further research on floral evolution in this group. However, much work remains to be done in resolving species level relationships. Analyses of morphological character evolution suggest that sev...

Viola woosanensis, a recurrent spontaneous hybrid between V. ulleungdoensis and V. chaerophylloides (Violaceae) endemic to Ulleung Island, Korea.

Ulleung Island is an oceanic volcanic island in Korea, which has never been connected to the adjacent continent. Previous studies highlighted Ulleung Island as an excellent system to study the pattern and process of early stages of flowering plant evolutions on oceanic island. The predominant mode of speciation in flowering plants on Ulleung Island appears to be anagenesis. However, the potentially important role of hybrid speciation among incompletely reproductively isolated lineages cannot be ruled out. Viola woosanensis (Violaceae) is of purportedly hybrid origin between V. ulleungdoensis (i.e., formerly recognized as V. selkirkii in Ulleung Island) and V. chaerophylloides, based on morphology. To examine the origin of V. woosanensis, we sampled a total of 80 accessions, including V. woosanensis and its putative parental species and sequenced nrDNA ITS, and four highly variable chloroplast noncoding regions (trnL-trnF, rpl16 intron, atpF-atpH, and psbA-trnH). Representative species of Viola from Korea were also included in the phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference). Additive polymorphic sites in the nrDNA ITS regions were confirmed by cloning amplicons from representative species. The molecular data strongly supported the hybrid origin of V. woosanensis, and the maternal and paternal parent were determined to be V. ulleungdoensis and V. chaerophylloides, respectively. The presence of two parental ribotypes in V. woosanensis (with the exception in one population) was confirmed by cloning, suggesting V. woosanensis is primarily the F1 generation. No trace of backcrossing and introgression with its parents was detected due to low fertility of hybrid species. We found a multiple and unidirectional hybrid origin of V. woosanensis. Additional studies are required to determine which factors contribute to asymmetric gene flow of Viola species in Ulleung Island.

Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots.

BackgroundRoots of different plant species are typically morphologically indistinguishable. Of the DNA-based techniques, fluorescent amplified-fragment length polymorphisms (FAFLPs) are considered reliable, high throughput, inexpensive methods to identify roots from mixed species samples. False-negatives, however, are not uncommon and their underlying causes are poorly understood. We investigated several sources of potential biases originating in DNA extraction and amplification. Specifically, we examined the effects of sample storage, tissue, and species on DNA yield and purity, and the effects of DNA concentration and fragment size on amplification of three non-coding chloroplast regions (trnT-trnL intergenic spacer, trnL intron, and trnL-trnF intergenic spacer).ResultsWe found that sample condition, tissue and species all affected DNA yield. A single freeze–thaw reduces DNA yield, DNA yield is less for roots than shoots, and species vary in the amount of DNA yielded from extractions. The effects of template DNA concentration, species identity, and their interaction on amplicon yield differed across the three chloroplast regions tested. We found that the effect of species identity on amplicon production was generally more pronounced than that of DNA concentration. Though these factors influenced DNA yield, they likely do not have a pronounced effect on detection success of fragments and only underscore the restriction on the use of FAFLPs for measuring species presence rather than their abundance. However, for two of the regions tested—the trnT-trnL intergenic spacer and the trnL intron—size-based fragment competition occurred and the likelihood of detection was higher for smaller than larger fragments. This result reveals a methodological bias when using FAFLPs.ConclusionsTo avoid potential bias with the use of FAFLPs, we recommend users check for the disproportionate absence of species detected belowground versus aboveground as a function of fragment size, and explore other regions, aside from the trnT-trnL intergenic spacer and trnL intron, for amplification.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-015-0079-1) contains supplementary material, which is available to authorized users.

Phylogenetic relationships of Zieria (Rutaceae) inferred from chloroplast, nuclear, and morphological data.

Zieria Sm. (Rutaceae, Boronieae) is predominantly native to eastern Australia except for one species, which is endemic to New Caledonia. For this study, sequence data of two non-coding chloroplast regions (trnL-trnF, and rpl32-trnL), one nuclear region (ITS region) and various morphological characters, based on Armstrong’s (2002) taxonomic revision of Zieria, from 32 of the 42 described species of Zieria were selected to study the phylogenetic relationships within this genus. Zieria was supported as a monophyletic group in both independent and combined analyses herein (vs. Armstrong). On the basis of Armstrong’s (2002) non-molecular phylogenetic study, six major taxon groups were defined for Zieria. The Maximum-parsimony and the Bayesian analyses of the combined morphological and molecular datasets indicate a lack of support for any of these six major taxon groups. On the basis of the combined Bayesian analysis consisting of molecular and morphological characters, eight major taxon groups are described for Zieria: 1. Zieria cytisoides group, 2. Zieria granulata group, 3. Zieria laevigata group, 4. Zieria smithii group, 5. Zieria aspalathoides group, 6. Zieria furfuracea group, 7. Zieria montana group, and 8. Zieria robusta group. These informal groups, except for of the groups Zieria robusta and Zieria cytisoides, correspond to the clades with posterior probability values of 100.

The roles of history and ecology in chloroplast phylogeographic patterns of the bird‐dispersed plant parasite Phoradendron californicum (Viscaceae) in the Sonoran Desert

• A recurrent explanation for phylogeographic discontinuities in the Baja California Peninsula and the Sonoran Desert Region has been the association of vicariant events with Pliocene and Pleistocene seaway breaks. Nevertheless, despite its relevance for plant dispersal, other explanations such as ecological and paleoclimatic factors have received little attention. Here, we analyzed the role of several of these factors to describe the phylogeographic patterns of the desert mistletoe, Phoradendron californicum.• Using noncoding chloroplast regions, we assess the marginal probability of 19 a priori hypotheses related to geological and ecological factors to predict the cpDNA variation in P. californicum using a Bayesian coalescent framework. Complementarily, we used the macrofossil record and niche model projections on Last Glacial Maximum climatic conditions for hosts, mistletoe, and a bird specialist to interpret phylogeographic patterns.• Genealogical reconstructions revealed five clades, which suggest a combination of cryptic divergence, long-distance seed dispersal, and isolating postdivergence events. Bayesian hypothesis test favored a series of Pliocene and Pleistocene geological events related to the formation of the Baja California Peninsula and seaways across the peninsula as the most supported explanation for this genealogical pattern. However, age estimates, niche projections, and fossil records show dynamic host-mistletoe interactions and evidence of host races, indicating that ecological and geological factors have been interacting during the formation and structuring of phylogeographic divergence.• Variation in cpDNA across the species range results from the interplay of vicariant events, past climatic oscillations, and more dynamic factors related to ecological processes at finer temporal and spatial scales.

Phylogeography of Arabis serrata (Brassicaceae) in the Japanese Archipelago based on chloroplast DNA variations

AbstractArabis serrata (Brassicaceae), a perennial plant widely distributed along the Japanese Archipelago, occurs in various habitats: for example, limestone zones, serpentine barrens, volcanic soils, and roadsides. It likely survived by adapting to its surrounding environment, resulting in great morphological and ecological variation. In this study, we performed a phylogeographic analysis to examine past changes in the distribution of A. serrata following climate oscillations during the Pleistocene. To cover most of A. serrata's range, leaves were collected from eight to ten individuals randomly selected from each of 37 populations in the Japanese Archipelago. Two chloroplast noncoding regions of the samples were amplified and sequenced: trnT(GGU)‐psbD and trnH(GUG)‐psbA spacers. Twenty‐five haplotypes were detected and distinguished by 31 substitutions. Four main haplotypes were observed in many populations distributed throughout the Japanese Archipelago. According to the genetic boundaries detected using the Monmonier algorithm, A. serrata is clustered into four groups, each including several populations: Hokkaido Island, northern mainland Honshu, central Japan, and western Japan. The boundaries, however, were not robust because all genetic parameters did not support the differentiation among groups. These results indicate the absence of an obvious geographic structure in the distribution of A. serrata, suggesting that this species has experienced a rapid range expansion in postglacial times.