Chloroplast Intergenic Spacers Research Articles

An updated infrageneric classification of the pantropical species-rich genus Garcinia L. (Clusiaceae) and some insights into the systematics of New Caledonian species, based on molecular and morphological evidence.

Garcinia L. is a pantropically distributed genus comprised of at least 250 species of shrubs and trees and has centers of diversity located in Africa/Madagascar, Australasia, and Southeast Asia. The genus is notable due to its extreme diversity of floral form, common presence in lowland tropical rainforests worldwide, and potential pharmacological value. Across its entire geographic range, Garcinia lacks a recent taxonomic revision, with the last genus-level taxonomic treatment of Garcinia conducted over 40 years ago. In order to provide an evolutionary-based framework for a revised infrageneric classification of the genus and to investigate in more detail the systematics of New Caledonian species, we conducted molecular phylogenetic analyses using DNA sequence data for the nuclear ITS region on all samples, and for three chloroplast intergenic spacers (psbM-trnD, trnQ-rps16 and rps16-trnK) on a subset of our overall sampling. Our phylogenetic analyses are the most comprehensive to date for the genus, containing 111 biogeographically and morphologically diverse Garcinia species. The analyses support a broad circumscription of Garcinia, including several previously segregated genera (e.g. Allanblackia, Clusianthemum, Ochrocarpos p.p., Pentaphalangium, Rheedia, and Tripetalum). We recovered nine major clades falling within two major lineages, and we delimit 11 sections. We discuss each of the clades, assign them sectional names, discuss their distinguishing morphological features, compare our taxonomic treatment with the most recent sectional treatment, list representative species, note geographic distribution, and highlight some questions that deserve future investigations. We propose nine new nomenclatural combinations, four new names, and three new lectotypes. In New Caledonia (NC), a total of ten, all endemic, species are recognized and were included in our phylogenetic analyses, with several replicates per species (with the exception of G.virgata and G.urceolata, represented by a single accession each). New Caledonian species were retrieved within three separate clades, respectively including 1) G.balansae; 2) G.comptonii, G.neglecta, G.urceolata, G.virgata; and 3) G.amplexicaulis, G.densiflora, G.pedicellata, G.puat, G.vieillardii. Within NC, the phylogenies did not support the distinction between a putative undescribed species and G.balansae. However, it confirmed the distinction between NC species and both G.vitiensis (found in Fiji and Vanuatu) and G.adinantha (found in Fiji), suggesting that all NC species should be considered as endemics.

Extraordinary genetic diversity in Uzbekistan wild roses (Rosa)

We have studied a population of Rosa kokanica from slopes of the Greater Chimgan Mt. in Tashkent Region of Uzbekistan. We reconstructed a statistical parsimony network of ndhC-trnV chloroplast intergenic spacer for 34 samples from three subpopulations found in valleys of the northern, southern and south-western macro slopes of the mountain. The study revealed 19 haplotypes, one of which, the basal internal haplotype 1, was shared between the northern and southern subpopulations, while 13 unique haplotypes were found in the south-western subpopulation. We suppose that such a kind of genetic structure could arise during long lasting isolation of the subpopulations in glacial times.

Differentiation of Centella asiatica (L.) Urb. from Hydrocotyle umbellata L. using the trnH-psbA region, species-specific bands and anisocytic stomata as markers for quality control of raw materials and their products

Centella asiatica (L.) Urb. has been confused with Hydrocotyle umbellata L. in Thailand. The plants grow in the same habitat and look alike, making H. umbellata a potential adulterant species for C. asiatica. This study aimed to (i) establish reference markers of authentic C. asiatica and H. umbellata using DNA barcoding, thin-layer chromatography (TLC) and microscopic methods and (ii) determine whether H. umbellata adulterants are present in C. asiatica products in Thailand. Ribulose-bisphosphate carboxylase (rbcL), maturase K (matK), internal transcribed spacer (ITS) and chloroplast intergenic spacer (trnH-psbA) were identified as core DNA barcode regions that can be used to differentiate C. asiatica and H. umbellata. The trnH-psbA region showed the highest nucleotide variation between C. asiatica and H. umbellata and had distinct amplicon sizes of approximately 506 and 398 bp, respectively. TLC analysis revealed three distinct bands at Rf 0.20, 0.30 and 0.32 that could be used to differentiate C. asiatica and H. umbellata. Anisocytic stomata were present only in C. asiatica and were purposed as a microscopic marker. The trnH-psbA amplicon, TLC species-specific markers and anisocytic stomata were utilized to examine six Bua Bok products traded in Thailand. Agarose gel electrophoresis showed PCR amplicons at approximately 500 bp, TLC showed species-specific bands at Rf 0.20, 0.30 and 0.32, and anisocytic stomata were found in all products, confirming that all tested products were C. asiatica. These markers will benefit the herbal industry and other end users by allowing the detection of the adulterant species H. umbellata in C. asiatica raw materials and products.

Genetic diversity of the Rhododendron subsection Ledum species in Sakhalin Island: data from chloroplast DNA markers variability

A high genetic variability was revealed in the populations of the Rhododendron subsection Ledum species complex in Sakhalin. In total, 94 individuals from natural populations of the four sympatric species of Labrador tea (R. tomentosum, R. subarcticum, R. tolmachevii and R. hypoleucum) were analyzed to evaluate the genetic variation in the territory of the Sakhalin Island and in two mainland populations. The haplotype diversity of five chloroplast intergenic spacers (trnH–psbA, petB–petD, 3’trnV (UAC)–ndhC, K2R–K707, atpB–rbcL) was quite high. There were 16 haplotypes (h1–h16) identified; h1, h2 and h4 are the most common, the rest were rare and no species-specific ones were found. Analysis of Molecular Variance (AMOVA) indicate that about 37 % of the genetic diversity is due to among population differences (FST = 0.37, p < 0.001). Molecular phylogenetic analysis based on chloroplast DNA data did not reveal a clear species structure, but revealed a trend towards the isolation of two genetic groups: including a group of samples from the southern and the middle parts of Sakhalin Island.

Clear phylogeographical structures shed light on the origin and dispersal of the aquatic boreal plant Hippuris vulgaris.

Aquatic plants are an important ecological group in the arctic flora; however, their evolutionary histories remain largely unknown. In order to deepen our understanding of the evolution of these plants, we explored the phylogeographical structure of an aquatic boreal plant Hippuris vulgaris in a broad geographical sampling from Eurasia and North America using the chloroplast intergenic spacer psbA-trnH and seven nuclear microsatellite loci. Two closely-related species H. lanceolata and H. tetraphylla were also included because of their taxonomic controversy. Both chloroplast DNA sequences and nuclear microsatellite data revealed three genetic lineages with distinct distribution ranges. Incongruence between nuclear and chloroplast DNA lineages occurred in 14 samples from Russian Far East and Europe caused by inter-lineage hybridization. No private haplotypes or independent genetic clusters were evident in H. lanceolata or H. tetraphylla, suggesting that these two species should be considered conspecific ecotypes of H. vulgaris. Analysis using Approximate Bayesian Computation-Random Forest approach suggests that Hippuris vulgaris originated in China, followed by dispersal into Russia plus Northeast China, then successively westwards into Europe and North America, and finally into the Russian Far East from both North America and Russia plus Northeast China. This study is the first to elucidate the historical dispersal processes of a circumarctic aquatic plant across the entirety of its range.

Initial Stage of Formation of Spontaneous Invasive Populations of Garden Lupine (Lupinus polyphyllus Lindl.) at the Northern Limit of Its Secondary Distribution Range in the Veps Forest Nature Park

A weed plant of the species Lupinus polyphyllus was found in settlements located on the territory of the natural park “Vepssky forest” of the Leningrad region. The plant is known as a transforming species in the southern regions of Russia. The distribution of L. polyphyllus within the Vepsian forest occurs not due to the migration of the species to the north along transport routes, as one might assume, but due to flight from gardens and the formation of spontaneous invasive populations. The goal of the study was to identify the molecular and biochemical characteristics of garden lupine at the northern borders of its secondary range. To interpret the obtained data, the task of the study also included a comparison of intraspecific variability between the “old” invasive populations (in Finland and Central Russia, studied by us earlier) and the “new” naturalizing population of L. polyphyllus in the Vepsian forest. The search for L. polyphyllus localities in the territory of the Vepssky Les natural park was carried out by the route method with geobotanical descriptions of experimental sites (5 m × 5 m). DNA was isolated from eight herbarium specimens of L. polyphyllus (MHA, LE) and fifteen specimens collected in the territory of the natural park “Vepssky Les”. To reveal the internal structure and phylogenetic relationships in lupine populations, networks of nuclear and chloroplast haplotypes and cluster analysis (UPGMA) with the SplitsTree program were used. The total content of polyphenols and flavonoids in the leaves was determined spectrophotometrically. The low inter-locality variability of ITS indicates that the populations of L. polyphyllus in Central Russia and in the North of Russia (St. Petersburg and Vepsskaya Pushcha) have the same origin. Analysis of the chloroplast intergenic spacer (rpl32–trnL) indicates intrapopulation diversity and suggests the presence of microevolutionary processes near the northern limits of the secondary distribution range of L. polyphyllus. The high content of polyphenols and flavonoids in the leaves reveals the adaptive capabilities of lupine in the studied area. Evidence suggests that a neglected species may soon become invasive, as has already happened in other regions.

The Phylogeography of Rhizophora in Peninsular Malaysia: High Genetic Variation between West and East

Geographic history of Rhizophora species and hybrid is effect on their genetic structure. In addition, determining population genetic variation is essential for phylogeography research. For this phylogeography investigation, Four natural population of Rhizophora were collected from five different regions in peninsular Malaysia for this phylogeography study. This study aims to evaluate the genetic diversity of Rhizophora species namely Rhizophora apiculata , Rhizophora mucronata , Rhizophora stylosa and hybrid R. × lamarcki and clarify their genetic structure of its populations using Nucleotide polymorphism in chloroplast intergenic spacer between trnL and trnF genes was studied.The populations of Rhizophora species and hybrids were divided into two groups: the east coast populations, which were represented by samples collected from Mersing, Tanjang Piai, and Sedili; and the west coast populations, which were represented by samples collected from Mersing, Tanjang Piai, and Sedili. The population of the west coast was the second cluster. This result was supported by UPGMA analysis using MEGA5 software.

The Phylogeography of Rhizophora in Peninsular Malaysia: High Genetic Variation between West and East

Geographic history of Rhizophora species and hybrid is effect on their genetic structure. In addition, determining population genetic variation is essential for phylogeography research. For this phylogeography investigation, Four natural population of Rhizophora were collected from five different regions in peninsular Malaysia for this phylogeography study. This study aims to evaluate the genetic diversity of Rhizophora species namely Rhizophora apiculata , Rhizophora mucronata , Rhizophora stylosa and hybrid R. × lamarcki and clarify their genetic structure of its populations using Nucleotide polymorphism in chloroplast intergenic spacer between trnL and trnF genes was studied.The populations of Rhizophora species and hybrids were divided into two groups: the east coast populations, which were represented by samples collected from Mersing, Tanjang Piai, and Sedili; and the west coast populations, which were represented by samples collected from Mersing, Tanjang Piai, and Sedili. The population of the west coast was the second cluster. This result was supported by UPGMA analysis using MEGA5 software.

Chloroplast DNA polymorphism and morphometric characteristics of Carpinus betulus in the Lithuania forests

The European hornbeam (Carpinus betulus L.) is a medium-sized deciduous tree that spreads northeast of the middle of Lithuania. Carpinus betulus L. is a native tree in Poland, and its branch is migrated by two Pleistocene refugia. We hypothesised that its branches had spread to Lithuania. In this study, we selected 10 populations of hornbeam that were chosen from their distribution location. We sequenced the chloroplast intergenic spacer psbA-trnH of 70 individuals. We found 24 bp deletion in chloroplast DNA (cpDNA) individuals of two populations in the southeastern part of Lithuania. In the seven forest populations, we examined the morphological variability of hornbeam seed involucres and nuts variations of 30 morphometric characteristics. Initial genetic population studies were conducted over a wider area; when differences were detected, morphological studies were conducted in the contact zone. Morphometric differences between the study populations were significant. The existence of two haplotypes of cpDNA supports the hypothesis of two migration refugia in C. betulus populations. This study contributes to significant novel knowledge about the morphological and cpDNA variability of European hornbeam populations in Lithuania and Europe.

Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China.

Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.

Chromosome and Molecular Analyses Reveal Significant Karyotype Diversity and Provide New Evidence on the Origin of Aegilops columnaris.

Aegilops columnaris Zhuk. is tetraploid grass species (2n = 4x = 28, UcUcXcXc) closely related to Ae. neglecta and growing in Western Asia and a western part of the Fertile Crescent. Genetic diversity of Ae. columnaris was assessed using C-banding, FISH, nuclear and chloroplast (cp) DNA analyses, and gliadin electrophoresis. Cytogenetically Ae. columnaris was subdivided into two groups, C-I and C-II, showing different karyotype structure, C-banding, and FISH patterns. C-I group was more similar to Ae. neglecta. All types of markers revealed significant heterogeneity in C-II group, although group C-I was also polymorphic. Two chromosomal groups were consistent with plastogroups identified in a current study based on sequencing of three chloroplast intergenic spacer regions. The similarity of group C-I of Ae. columnaris with Ae. neglecta and their distinctness from C-II indicate that divergence of the C-I group was associated with minor genome modifications. Group C-II could emerge from C-I relatively recently, probably due to introgression from another Aegilops species followed by a reorganization of the parental genomes. Most C-II accessions were collected from a very narrow geographic region, and they might originate from a common ancestor. We suggest that the C-II group is at the initial stage of species divergence and undergoing an extensive speciation process.

DNA barcoding aids in identification of adulterants of Trillium govanianum Wall. ex D. Don

The correct scientific identification of the plant material is crucial to the safety and efficacy of herbal products. Trillium govanianum Wall. ex D. Don, a pharmaceutically prized medicinal plant species endemic to the Himalaya, has been recently subjected to large-scale extraction in the wild due to increasing market demand. Consequently, adulteration and/or substitution of the traded material of T. govanianum with closely-related plants such as Paris polyphylla Sm. has become a quality control problem for the herbal industry. Therefore the present study aimed to (i) develop a reference DNA barcode of T. govanianum and its potent adulterant P. polyphylla for correct identification, (ii) and check adulteration of market samples of T. govanianum. Reference DNA barcode library of T. govanianum and P. polyphylla was successfully established, using Internal transcribed spacer (ITS), Maturase K (matK), chloroplast intergenic spacer (trnH-psbA), and ribulose-bisphosphate carboxylase (rbcL) regions. The ITS, matK and trnH-psbA were found to be ideal reference barcodes for T. govanianum, while ITS and trnH-psbA were suitable for P. polyphylla. All the trade samples (i.e. dried rhizomes), investigated during the present study, got putatively identified with the respective reference barcodes; and thereby indicating the ITS and trnH-psbA regions as the potential DNA barcodes for the identification of the trade samples/adulterants. The ITS region showed the highest mean intra- and inter-specific distances, which proves its high efficiency in differentiating closely related species. Phylogenetic trees were also constructed following the neighbor-joining (NJ) method, based on ITS, rbcL, and trnH-PsbA regions of Trillium and Paris species, which distinguished Trillium species from those of Paris. The availability of a novel DNA barcode for this important medicinal plant species will be helpful for correct identification of its raw plant material, checking illegal trade, and to regulate its sustainable collection from the natural habitats.

Natural hybridization between two butterfly bushes in Tibet: dominance of F1 hybrids promotes strong reproductive isolation

BackgroundIt has been recognized that a certain amount of habitat disturbance is a facilitating factor for the occurrence of natural hybridization, yet to date we are unaware of any studies exploring hybridization and reproductive barriers in those plants preferentially occupying disturbed habitats. Buddleja plants (also called butterfly bush) generally do grow in disturbed habitats, and several species with hybrid origin have been proposed, based solely on morphological evidence.ResultsIn the present study, we test the hypothesis that B. × wardii is of natural hybridization origin in two sympatric populations of three taxa including B. × wardii and its parents (B. alternifolia and B. crispa) plus 4 referenced parental populations, using four nuclear genes and three chloroplast intergenic spacers, as well as with 10 morphological characters. Our results suggest that at both sites B. × wardii is likely to be a hybrid between B. alternifolia and B. crispa, and moreover, we confirm that most of the hybrids examined are F1s. That these plants are F1s is further supported by morphology, as no transgressive characters were detected. B. crispa was found to be the maternal parent in the Bahe (BH) population, from cpDNA evidence. However, in the Taji (TJ) population, the direction of hybridization was difficult to establish due to the shared cpDNA haplotypes between B. alternifolia and B. crispa, however we still predicted a similar unidirectional hybridization pattern due to results from cross-specific pollination treatments which supported the “SI × SC rule”.ConclusionsThe presence of mainly F1 hybrids can successfully impede gene flow and thus maintain species boundaries in parental species in a typical distribution of Buddleja, i.e. in disturbed habitats.

Chloroplast DNA-based genetic variation of Rosa roxburghii in Southwest China: Phylogeography and conservation implications

Rosa roxburghii Tratt. is a well-known commercial horticultural crop in China with nutritional and medicinal value. Wild germplasms of this species are mainly distributed in Southwest China but the population is decreasing due to continuous exploitation, habitat destruction, and fragmentation. Therefore, assessing the genetic diversity and phylogeography is essential for efficient conservation. Herein, two chloroplast intergenic spacers (trnL-trnF and accD-psaI) were investigated in 255 individuals from 29 R. roxburghii populations and 18 haplotypes (H1–H18) were identified. High levels of haplotype diversity (Hd = 0.829) and nucleotide diversity (π = 1.3 × 10−3) were detected in these populations. Also, the genetic variation representing 86.4% of the total variation was detected by an analysis of molecular variance. A significant correlation was established between genetic divergence and geographic distance by the Mantel test (r = 0.204, P = 0.04, 9 999 permutations), suggesting the isolation-by-distance model. A significantly higher Nst than Gst (Nst = 0.257, Gst = 0.136, P < 0.05) indicated the phylogeographic structure of R. roxburghii. Further phylogeographic analysis revealed rapid range expansion in the population, probably between 647 073 and 217 848 years ago. The primary processes shaping the genetic patterns of the R. roxburghii populations included restricted gene flow with isolation distance within clades 1-8, 2-3, and overall, contiguous expansion within clades 1-3 and 3-2, past fragmentation, and/or long-distance colonization within clades 1-9 and 2-2. Conservation priority should be given to the core populations GZ, FQ, DF, DS, xy, AL, LC, PB, and XY in the Yunnan-Guizhou Plateau, NZ and MX in the Qingling-Bashan mountains, and MN in the Hengduan mountains, where an in situ preservation and management strategy should be applied.

&lt;p&gt;&lt;strong&gt;&lt;em&gt;Allium gilanense&lt;/em&gt;, a new species of &lt;em&gt;Allium&lt;/em&gt; sect. &lt;em&gt;Codonoprasum&lt;/em&gt; (Amaryllidaceae) from Iran: evidence from morphological and molecular data&lt;/strong&gt;&lt;/p&gt;

As a result of recent botanical expeditions to the north of Iran, we describe here a new endemic Allium species from Gilan province named Allium gilanense. Molecular and morphological data indicate that it belongs to Allium sect. Codonoprasum. We provide a morphological description, comparing Allium gilanense with the closest relative taxa A. lenkoranicum and A. paniculatum, the preliminary karyotype of the new species, and molecular phylogenetic data derived from the nuclear ribosomal DNA internal transcribed spacers (ITS) and the chloroplast intergenic spacer trnH-psbA. The chromosome number of the new species is 2n = 16 with 0-3 B chromosomes.

Phylogeny of Aconitum Subgenus Aconitum in Europe

&lt;p&gt;Phylogenetic relations within &lt;em&gt;Aconitum &lt;/em&gt;subgen. &lt;em&gt;Aconitum &lt;/em&gt;(Ranunculaceae) in Europe are still unclear. To infer the phylogeny of the nuclear (ITS) region and chloroplast intergenic spacer &lt;em&gt;trn&lt;/em&gt;L&lt;sup&gt;(UAG)&lt;/sup&gt;-&lt;em&gt;ndh&lt;/em&gt;F of the chloroplast DNA (cpDNA), we analyzed 64 accessions within this taxon, 58 from Europe and six from the Caucasus Mts. Nuclear ITS sequences were identical in 51 European and two Caucasian accessions, whereas the remaining sequences were unique. cpDNA sequences could be categorized into five haplotypes, i.e., &lt;em&gt;A–E&lt;/em&gt;, including a European-Caucasian &lt;em&gt;Aconitum &lt;/em&gt;haplotype &lt;em&gt;B&lt;/em&gt;. Ten cpDNA sequences were unique. A 5-bp indel distinguished the diploids from the tetraploids. None of the extant European diploids were basal to the tetraploid local group. A phylogenetic tree based on combined ITS and cpDNA sequences (bayesian inference, maximum likelihood, minimal parsimony) placed &lt;em&gt;Aconitum&lt;/em&gt;&lt;em&gt; &lt;/em&gt;&lt;em&gt;burnatii &lt;/em&gt;(Maritime Alps, Massif Central) and &lt;em&gt;A. nevadense &lt;/em&gt;(Sierra Nevada, Pyrenees) in a sister group to all other European species. A Bayesian relaxed clock model estimated the earliest split of the Caucasian species during the Late Miocene [ca. 7 million years ago (Mya)], and the divergence of &lt;em&gt;A. burnatii &lt;/em&gt;and &lt;em&gt;A. nevadense &lt;/em&gt;from the European genetic stock during the Miocene/Pliocene (ca. 4.4 Mya). Diploids in Europe are likely to be descendants of the Miocene European-Caucasian flora linked with the ancient Asian (arctiotertiary) genetic stock. The origins of the tetraploids remain unclear, and it is possible that some tetraploids originated from local, now extinct diploids. Both the diploids and tetraploids underwent rapid differentiation in the Late Pliocene – Quaternary period.&lt;/p&gt;

Looking Inside Non-coding Chloroplast Regions of Calophyllum brasiliense (Calophyllaceae) to Understand Its Southernmost Population Distribution

In recent years the growing interest in the conservation of Parana River’s riparian forest led to the discovery of botanical novelties for Argentina. Populations of Calophyllum brasiliense Camb. (Calophyllaceae), a typically flooded lowlands species, were identified in the remaining hygrophile forest of northeast Argentina and southeast Paraguay. Deforestation and flooding, due to the construction of dams, have caused these populations to suffer intensive fragmentation. The aim of this work was to infer phylogeographic relationships among five populations of C. brasiliense, three from Argentina and two from Paraguay, which represent the southernmost points of species’ distribution. We also compared them with samples of a C. brasiliense population from Mexico, the northernmost edge of the species distribution. The chloroplast intergenic spacers petG-trnP, psbJ-petA and the trnL-UAA chloroplast intron were amplified from leaves’ DNA. A total of 2234 bp were characterized once the three regions were analyzed. The three chloroplast regions showed nucleotide differences, represented by InDels, inversions and a few SNPs; however, only the trnL intron was selected for further phylogeographic analysis due to the amount of the information obtained for all populations. Based on trnL intron, it was possible to estimate nucleotide and haplotype diversity (π = 0.00237 and Hd = 0.29600, respectively). Three haplotypes were identified, which allowed Argentinean, Paraguayan and Mexican populations to be differentiated. Based on the three haplotypes found, we discuss and propose a model for a C. brasiliense’ geographic dispersion and historical colonization routes, including an alternative new one to the well-known of the Parana River.

Phylogeography and genetic structure of an iconic tree of the Sonoran Desert, the Cirio (Fouquieria columnaris), based on chloroplast DNA

AbstractWe have examined the phylogeographical distribution of chloroplast DNA (cpDNA) lineages of Fouquieria columnaris (Kellogg) Kellogg ex Curran (Fouquieriaceae) in the Sonoran Desert, to understand how historical climatic and/or geological changes have influenced genetic patterns in the species. Using two chloroplast intergenic DNA spacers (psbJ-petA and ndhF-rpl32), we found low levels of nucleotide diversity (π = 0.0025) but high levels of haplotype diversity (h = 0.9339). Analysis of 28 haplotypes revealed four lineages, one belonging to the continental massif and three to the peninsula of Baja California. This structure may be explained and dated by three events: (1) formation of the Gulf of California during the late Miocene (7.24 Mya), (2) activity of the Tres Vírgenes volcanic field (1.20 Mya) and (3) opening of the mid-peninsula seaway during the late Pleistocene (1.53 Mya). Furthermore, the cpDNA lineages show evidence for population contraction during the Last Glacial Maximum, with a subsequent population expansion in the Holocene.

Molecular and elemental characterizations and taxonomic notes of three endemic Lathyrus L. species

In this study, the morphological, genetical (molecular) and elemental compositions of morphologically similar three endemic Lathyrus L. species such as L. phaselitanus Hub.-Mor. & Davis, L. lycicus Boiss. and L. belinensis N. Maxted & D. J. Goyder belong to genus Lathyrus in Turkey were investigated. In the morphological part, some important parameters such as stem shape, plant height, leaflet number, leaflet length, leaflet width, stipule shape, stipule length, stipule width, fruit length, fruit width, fruit shape, number of flowers and standard were investigated. In the genetical part of the study, chloroplast intergenic spacer trnH-psbA was used to reveal the genetic diversity and phylogenetic relationship among the three endemic Lathyrus species to decide whether they were systematically similar or not. Additionally, the concentration of some elements such as Nickel (Ni), Iron (Fe), Copper(Cu), Cadmium (Cd), Chromium (Cr), Manganese (Mn), Magnesium (Mg), Zinc (Zn), Sodium (Na) and Potassium (K) were also determined by flame atomic absorption spectrometry to observe the similarities and/or differences among these three endemic Lathyrus species based on elemental composition. The results revealed that there was also a genetic similarity of 99% between morphologically similar L. belinensis and L. lycicus species but they were previously placed in different sections.

Volcanism rather than climatic oscillations explains the shared phylogeographic patterns among ecologically distinct plant species in the southernmost areas of the South American Arid Diagonal

Shared genetic patterns within a community of ecologically distinct species may reflect the role of past geoclimatic events imprinting species evolutionary history. Although Pleistocene glaciations are the most important processes evoked as drivers of these shared patterns, in some regions Quaternary volcanic activity should also be considered as a potential process shaping genetic diversity distribution. Additionally, phenotypic attributes related to dispersal and persistence may affect the time and manner in which species respond to geoclimatic changes. We performed a comparative phylogeographical study within a plant community of the South American Arid Diagonal to assess whether genetic patterns are better explained by climatic changes or volcanisms, taking into account the possible influence of life form and dispersal syndromes of the focal species. Chloroplast intergenic spacers were sequenced for five plant species. Genealogy, divergence time estimates, demographic and range expansion analyses were performed. Approximate Bayesian computation was used to test plausible shared phylogeographic scenarios. Climatically stable areas during the last glacial period were inferred with distribution modeling. Results showed that most species were split into northern and southern lineages separated by a phylogeographic break at around 37.5 °S, with the northern populations being genetically less diverse, inhabiting both climatically stable and unstable areas, but being severely affected by intense Plio-Pleistocene magmatic activity; the southern populations, less influenced by volcanism, appeared to be genetically more diverse and occupied climatically stable areas through time. Most recent range expansions and effective population size increases occurred after most of the volcanic episodes, before and during the Last Glacial Maximum. All species shared the same geographic origin of the detected spatial expansion. Overall, our results suggest a preponderant effect of Quaternary volcanism rather than climatic oscillations on the evolutionary history of this xerophytic community. Additionally, we found evidence that autecological traits would have modulated the community historical responses.