Chloroplast Gene Regions Research Articles

Closely related and sympatric but not all the same: genetic variation of Indo-West Pacific Rhizophora mangroves across the Malay Peninsula

Members of the mangrove genus Rhizophora represent the most commonly occurring and highly valued species in the Indo-West Pacific region. However, to date, few studies have been directed towards the understanding of their genetic variation. The levels and patterns of genetic variation at chloroplast and nuclear gene regions were studied in R. apiculata, R. mucronata, and R. stylosa sampled from Southeast Asia and Japan. All three species were characterized by low intraspecific genetic variation and a deficiency of heterozygotes in populations within the region, consistent with findings in studies on other mangrove species. Rhizophora mucronata and R. stylosa were also found to be more closely related than any of them with R. apiculata. During the Last Glacial Maximum, sea levels dropped to 120 m below the current levels, exposing part of the Sunda Shelf that became a barrier that limited gene flow between marine species living in the Pacific and Indian Oceans. Today, the Malay Peninsula is thought to still serve as a barrier to gene flow between populations occurring on its coasts. The pattern of genetic differentiation of R. apiculata supports the hypothesis of the land barrier effect of the Malay Peninsula, but such patterns were not found in R. mucronata and R. stylosa. Our findings suggest that R. apiculata, R. mucronata, and R. stylosa have different demographic histories despite being closely related and having sympatric distributions today. Furthermore, all three species appear to have high levels of inbreeding due to limited pollen and propagule dispersal, and that both these factors contributed to population differentiation.

Phylogeography and demographic history of Zamia paucijuga Wieland (Zamiaceae), a cycad species from the Mexican Pacific slope

We have investigated the phylogeographic structure and demographic history of Zamia paucijuga, based on 120 ITS2 and 117 psbK/I sequences from 13 populations distributed along the entire distribution range of the species. We have detected 15 ITS2 and four psbK/I haplotypes, for a total of 19. The genetic diversity estimated for psbK/I was relatively lower than the ITS2 diversity. These results imply that the average genetic diversity in Z. paucijuga is lower in comparison with other cycad species, but relatively higher than the diversity found in conifers. Non-hierarchical and hierarchical AMOVAs for ITS2 and psbK/I showed both low and high levels of genetic structure. This discrepancy likely reflects a decrease in gene flow intensity for seeds but high pollen gene flow, which correlates with the divergent inheritance processes in nuclear vis-a-vis organellar DNAs. SAMOVA tests for both loci (ITS2 and psbK/I) showed high correspondence with the regional geographic structure defined a priori, indicating that the use of both nuclear and chloroplast gene regions improves inferences concerning the evolutionary processes that affect population dynamics in Z. paucijuga. Furthermore, our results are consistent with the conclusions of other studies on the origin of the genus Zamia, which support locating the diversification times of Z. paucijuga populations in the Pleistocene.

Paraphyly of Section <I>Stygnanthe</I> (<I>Columnea,</I> Gesneriaceae) and a Revision of the Species of Section <I>Angustiflorae</I>, a New Section Inferred from ITS and Chloroplast DNA Data

Abstract Morphological data have produced conflicting results when analyzing evolutionary relationships within Gesneriaceae due to convergence of morphological characters. Columnea, the largest Neotropical genus in Gesneriaceae subfamily Gesnerioideae, has had a convoluted taxonomic history due to this convergence. Previously, the 200 + species of Columnea were placed in 14 genera, with up to nine sections in the genus; most recently classifying the species in a single genus with five sections. Phylogenetic analyses presented here included 129 accessions representing 90 species for five chloroplast gene regions (trnQ-rps16 spacer, rpl32-trnLUAG spacer, rps16 intron, trnS-G spacer, and trnH-psbA spacer) and nuclear ribosomal ITS to build a well-supported topology that can test the previously proposed subgeneric classifications. Our goal was to test the monophyly of section Stygnanthe, one of the five sections that encompasses 18 species based on floral morphology. Fifteen species of Stygnanthe and four spe...

Taxonomy and Systematic Analysis of the Two Genera Alpinia and Amomum of the Family Zingiberaceae in Sri Lanka

Alpinia and Amomum are the largest two genera that list the highest number of endemics offamily Zingiberaceae in Sri Lanka. The family is recognized as a least studied plant group inthe country, justifying the need for a thorough study. Hence, it is timely that the family istaken into consideration of molecular and systematic studies given new techniques areavailable. As a pioneering step, in this study, we addressed several taxonomic issues,phylogenetic relationships and conservational status of Alpinia and Amomum. In order tocollect more morphological data to address species boundaries with better insights, over 130morphological characters were studied and analysed using multivariate statistical methods.Molecular phylogenetic analysis was done using two Chloroplast gene regions (trnL-trnF andtrnS-trnfM). Results of the morphological analysis revealed the segregation of species ratherdepending on both vegetative and floral characters than only on floral characters. Study alsoidentified a group of Amomum with a new character combination which needs to berecognized as a new species or subspecies along with a new addition to genus Alpinia (A.zerumbet) in Sri Lanka. Furthermore, in our efforts to make a field key for easy identificationof species, results of this study also highlighted the difficulty in using only vegetativecharacters to differentiate species. Hence, the study has resulted in identifying a different andan easy set of morphological characters for species identification for Sri Lankan species.Evolutionary analysis of the two genera confirms that the Sri Lankan members of the twogenera Alpinia and Amomum have a monophyletic origin. Although the genus Alpinia has amonophyletic lineage, two members (A. abundiflora and A. fax) show a polytomy within thegenus. This was evident in both phylogenetic analysis and the morphological analysis.According to trnL-trnF and trnS-trnƒM data analysis, all the studied members of the genusAmomum have an exclusive monophyletic origin. Illumination of an immediate need forconservation efforts of these species is another important finding of the current study.

A phylogenetic hypothesis for the recently diversified Ruschieae (Aizoaceae) in southern Africa

The Ruschieae is a large tribe of about 1600 species of succulent perennials. They form a major component of the arid parts of the Greater Cape Floristic Region, both in numbers of species and in their density of coverage. So far phylogenetic relationships within the tribe have been unresolved, largely through the paucity of variable molecular characters and this is ascribed to the tribe’s recent and rapid radiation. Our phylogeny is based on 10 chloroplast gene regions and represents a nearly complete sampling of the 100 currently recognised genera of the Ruschieae. These chloroplast regions yielded relatively few phylogenetically informative characters, consequently providing only limited resolution in and poor support for many parts of the phylogeny. Nevertheless, for the first time, we provide well-supported evidence that taxa with mostly mesomorphic, often ephemeral leaves and weakly persistent fruits form a basal grade of lineages in the Ruschieae. These lineages subtend a large polytomy of taxa with almost exclusively xeromorphic, persistent leaves and strongly persisting fruits. Among the basal grade of lineages, those occurring within the winter-rainfall region typically shed their leaves or form (at least partly) a protective, dry sheath around the apical bud during the dry summer months, as a means of escaping the summer drought. This contrasts with taxa of the basal grade from outside the winter-rainfall region, in which the leaves persist. Our results show that, in both strongly and weakly persistent fruits, specialised characteristics of the fruit evolved repeatedly and so these structures are highly homoplasious. Perhaps as a consequence of repeated changes towards increased persistence and specialisation of leaves and fruits, several clades show little morphological cohesion. However, as in other groups in the Cape Flora, most clades in the Ruschieae represent regional groupings. Our analysis of sequences of the nuclear gene ‘chloroplast-expressed glutamine synthetase’ (ncpGS) revealed extensive paralogy within the Ruschieae, but found an intact reading frame in all its members. More data on the cytology of the Ruschieae is needed to evaluate whether the paralogy observed is due to gene duplication or polyploidy.

Morphological and molecular evidence supports the recognition of a new subspecies of the critically endangered Pityrodia scabra (Lamiaceae)

Taxonomic delineation of closely related taxa can be difficult, particularly in regions such as southern Western Australia where a highly diverse flora exhibits complex patterns of subtle morphological variation and genetic structuring and where some taxa have highly disjunct populations. A combined approach utilising highly variable, non-coding chloroplast gene regions and morphological data is used here to help delimit cryptic taxa in the rare Western Australian species Pityrodia scabra A.S.George. The species comprises disjunct populations over 400 km of the Western Australian wheatbelt from near Wyalkatchem, Southern Cross and Lake Lefroy. Morphological features such as leaf phyllotaxy, calyx size and indumentum vary among the populations and provide some evidence for cryptic taxa. Phylogenetic analyses based on cpDNA psbA–trnH and psbD–trnT and nuclear external transcribed spacer (ETS) sequences revealed genetic distinctiveness between the Wyalkatchem (type) population and the Southern Cross and Lake Lefroy populations. This evidence, when used in conjunction with the morphological differences, provides support for the recognition of the new subspecies described herein as Pityrodia scabra subsp. dendrotricha K.A.Sheph. subsp. nov. This new subspecies is of conservation concern because it is currently known only from a few, isolated populations; the typical subspecies remains Critically Endangered because it comprises one extant population. A description of both subspecies, a key and images are provided.

Plagiomnium floridanum sp. nov. (Mniaceae), a new moss from the southeastern United States

By most accounts, Plagiomnium cuspidatum is a typical bisexual, diploid species with n 5 12 throughout its wide range. Beginning with Lowry's (1948) chromosome count of n 5 6 for a collection from northern Florida, however, there have been sporadic reports of haploid or unisexual plants of this species. Unfortunately, none of these cases has been examined closely enough for sexuality, ploidy level, and possible morphological or other differences to be firmly established. Our studies of natural populations from Florida and Georgia reveal that there is a previously undescribed species that differs from P. cuspidatum in sexual condition, ploidy level, morphology, and ecology. This unisexual species has a chromosome number of n 5 6, elliptic leaves with teeth that extend more than halfway down the margin, leaf cells mostly , 25 mm, and a preference for circumneutral soils associated with limestone. Its closest relatives in sect. Plagiomnium are P. cuspidatum and P. acutum, but Nei's (1978) unbiased genetic identities of 0.669 and 0.705, respectively, show that it is strongly differentiated from both (Wyatt & Odrzykoski 1998). Independent evidence of the distinctiveness of these populations from the southeastern United States comes from phylogenetic reconstructions based on sequencing of chloroplast (rps4, rpL16) and nuclear (ITS2) gene regions by Harris (2008).

Studies on Lophocoleaceae. XIX. The systematic identity of Cyanolophocolea R.M. Schust., an intriguing liverwort from New Zealand and Australia, based on morphological and molecular evidence

Cyanolophocolea echinella R.M.Schust. is an intriguing species, possessing some character states characteristic of the genus Chiloscyphus, such as the ability to produce both male and female gametangia on leading shoots, while having other features that are generic characters of Heteroscyphus, namely presence of gametangia on short, abbreviated lateral-intercalary branches. Its systematic identity was here studied using morphological and DNA sequence data of the chloroplast gene regions of rbcL, rps4 and trnL-F. Thirty-seven exemplars including eight of Cyanolophocolea echinella, 27 of Lophocoleaceae and two of Plagiochilaceae were used for phylogenetic reconstruction using both maximum parsimony and Bayesian inference methods. Our analyses placed Cyanolophocolea echinella within Heteroscyphus with strong support. Heteroscyphus echinellus (Lindenb. & Gottsche) J.J.Engel & XiaoL.He is proposed and based on morphological variations two varieties, var. echinellus and var. hyalinus J.J.Engel, are recognized. A large indel (59 base pairs) and one substitution in the trnL intron region, and also one substitution in the intergenic spacer region were found in the trnL-F in two Cyanolophocolea echinella exemplars both with hyaline oil-bodies. This indicates rapid molecular evolution might have occurred within the species.

A New Lineage‐Based Tribal Classification of the Family Caryophyllaceae

Understanding the relationships within the Caryophyllaceae has been difficult, in part because of arbitrarily and poorly defined genera and difficulty in determining phylogenetically useful morphological characters. This study represents the most complete phylogenetic analysis of the family to date, with particular focus on the genera and relationships within the large subfamily Alsinoideae, using molecular characters to examine the monophyly of taxa and the validity of the current taxonomy as well as to resolve the obscure origins of divergent taxa such as the endemic Hawaiian Schiedea. Maximum parsimony and maximum likelihood analyses of three chloroplast gene regions (matK, trnL‐F, and rps16) from 81 newly sampled and 65 GenBank specimens reveal that several tribes and genera, especially within the Alsinoideae, are not monophyletic. Large genera such as Arenaria and Minuartia are polyphyletic, as are several smaller genera. The phylogenies reveal that the closest relatives to Schiedea are a pair of wid...

Genetic variation of chloroplast DNA in Zingiberaceae taxa from Myanmar assessed by PCR–restriction fragment length polymorphism analysis

AbstractWe examined genetic variation in 22 accessions belonging to 11 species in four genera of the Zingiberaceae, mainly from Myanmar, by PCR–restriction fragment length polymorphism analysis to investigate their relationships within this family. Two of 10 chloroplast gene regions (trnS‐trnfM and trnK2–trnQr) showed differential PCR amplification across the taxa. Restriction enzyme digestion of the PCR products revealed interspecific variability. The restriction patterns were used to classify the regions as either highly conserved or variable across the taxa. None of the regions was highly conserved across the four genera, and the level of conservation varied. The gene region trnS‐trnfM appeared to display interspecific variability among most of the species. However, the relative efficiency of different restriction enzymes depended on the gene regions and genera investigated. Cluster analysis revealed interspecific discrimination among the taxa. The two Curcuma species (Curcuma zedoaria and Curcuma xanthorrhiza) appeared to be identical, thus supporting their recent classification as synonyms. The results provide the basis for selecting specific combinations of restriction enzymes and gene regions of chloroplast DNA (cpDNA) to identify interspecific variation in the Zingiberaceae and to identify both highly conserved and variable regions. Overall, cpDNA depicted comparatively diverse genetic profile of the studied germplasm. The genetic information revealed here can be applied to the conservation and future breeding of Zingiber and Curcuma species.

Familial placement and relations of Rehmannia and Triaenophora (Scrophulariaceae s.l.) inferred from five gene regions

Accurate classification systems based on evolution are imperative for biological investigations. The recent explosion of molecular phylogenetics has resulted in a much improved classification of angiosperms. More than five phylogenetic lineages have been recognized from Scrophulariaceae sensu lato since the family was determined to be polyphyletic; however, questions remain about the genera that have not been assigned to one of the segregate families of Scrophulariaceae s.l. Rehmannia Liboschitz and Triaenophora Solereder are such genera with uncertain familial placement. There also is debate whether Triaenophora should be segregated from Rehmannia. To evaluate the phylogenetic relations between Rehmannia and Triaenophora, to find their closest relatives, and to verify their familial placement, we conducted phylogenetic analyses of the sequences of one nuclear DNA (ITS) region and four chloroplast DNA gene regions (trnL-F, rps16, rbcL, and rps2) individually and combined. The analyses showed that Rehmannia and Triaenophora are each strongly supported as monophyletic and together are sister to Orobanchaceae. This relation was corroborated by phytochemical and morphological data. Based on these data, we suggest that Rehmannia and Triaenophora represent the second nonparasitic branch sister to the remainder of Orobanchaceae (including Lindenbergia).

Phylogenetic Relationships of Gunnera based on Nuclear Ribosomal DNA ITS Region, rbcL and rps16 Intron Sequences

Abstract A previous analysis of two chloroplast gene regions, rbcL and the rps16 intron, showed a clear phylogenetic pattern in Gunnera. However, these regions were not informative enough to completely resolve the phylogeny. In this study the nuclear ITS region was sequenced for 24 specimens representing 22 species of Gunnera. 223 characters out of 819 were informative and supported the same monophyletic groups as the chloroplast gene regions. Because of its greater information content, the ITS region identified additional well-supported clades. In an analysis based on the three gene regions together, 272 characters out of 3154 were informative. The results show that the South American annual, G. herteri is sister to all other species. The African G. perpensa is well-supported as sister to the remaining species, which form two well-defined clades, one with the Malayan G. macrophylla as sister to subgenus Milligania from New Zealand and Tasmania. In the other clade, the South American subgenus Misandra is ...

The Hawaiian Archipelago is a stepping stone for dispersal in the Pacific: an example from the plant genus Melicope (Rutaceae)

AbstractAim Pacific biogeographical patterns in the widespread plant genus Melicope J.R. Forst. & G. Forst. (Rutaceae) were examined by generating phylogenetic hypotheses based on chloroplast and nuclear ribosomal sequence data. The aims of the study were to identify the number of colonization events of Melicope to the Hawaiian Islands and to reveal the relationship of Hawaiian Melicope to the Hawaiian endemic genus Platydesma H. Mann. The ultimate goal was to determine if the Hawaiian Islands served as a source area for the colonization of Polynesia.Location Nineteen accessions were sampled in this study, namely eight Melicope species from the Hawaiian Islands, four from the Marquesas Islands, one species each from Tahiti, Australia and Lord Howe Island, two Australian outgroups and two species of the Hawaiian endemic genus Platydesma. To place our results in a broader context, 19 sequences obtained from GenBank were included in an additional analysis, including samples from Australia, Papua New Guinea, New Zealand, Southeast Polynesia and Asia.Methods DNA sequences were generated across 19 accessions for one nuclear ribosomal and three chloroplast gene regions. Maximum parsimony analyses were conducted on separate and combined data sets, and a maximum likelihood analysis was conducted on the combined nuclear ribosomal and chloroplast data set. A broader nuclear ribosomal maximum parsimony analysis using sequences obtained from GenBank was also performed. Geographic areas were mapped onto the combined chloroplast and nuclear ribosomal tree, as well as onto the broader tree, using the parsimony criterion to determine the dispersal patterns.Results Phylogenetic analyses revealed that Platydesma is nested within Melicope and is sister to the Hawaiian members of Melicope. The Hawaiian Melicope + Platydesma lineage was a result of a single colonization event, probably from the Austral region. Finally, Marquesan Melicope descended from at least one, and possibly two, colonization events from the Hawaiian Islands.Main conclusions These data demonstrate a shifting paradigm of Pacific oceanic island biogeography, in which the patterns of long‐distance dispersal and colonization in the Pacific are more dynamic than previously thought, and suggest that the Hawaiian Islands may act as a stepping stone for dispersal throughout the Pacific.

Generic Circumscription in Menyanthaceae: A Phylogenetic Evaluation

Menyanthaceae consist of five genera of aquatic and wetland plants distributed worldwide. The three monotypic genera (Liparophyllum, Menyanthes, and Nephrophyllidium) are clearly differentiated morphologically, but the two larger genera (Nymphoides and Villarsia) contain several taxa of uncertain affinity. We undertook a phylogenetic analysis, using a combination of morphological and molecular data, to resolve relationships among species and to evaluate the current circumscription of genera. DNA sequence data for nuclear (ITS) and chloroplast (rbcL and trnK/matK) gene regions were largely congruent (by partition-homogeneity test), and a combined data phylogeny revealed several strongly supported relationships. Analyses using asterid outgroup taxa supported the monophyly of Menyanthaceae. Menyanthes trifoliata and Nephrophyllidium crista-galli comprised a clade sister to the remainder of the family. Species of Nymphoides, except N. exigua, resolved to a single, deeply-nested clade, indicating that the floating-leaved habit is derived evolutionarily within the family. The genus Villarsia comprised a paraphyletic grade toward Nymphoides, wherein the species resolved to three assemblages: (1) a shallowly nested clade containing V. albiflora, V. calthifolia, V. marchantii, V. parnassifolia, V. reniformis, and V. umbricola; (2) an isolated South African clade including V. manningiana and the type species, V. capensis; and (3) a heterogeneous clade of taxa from three genera, including V. exaltata, V. lasiosperma, and V. latifolia, plus the anomalous species V. capitata, V. congestiflora, Liparophyllum gunnii, and Nymphoides exigua. Our results indicate that the genera Menyanthes, Nephrophyllidium, and Nymphoides should be retained as circumscribed, with the exception that Nymphoides exigua should be restored to Villarsia. The genus Villarsia, however, eventually should be subdivided among monophyletic lineages, whereby in the strict sense Villarsia would contain only South African taxa.

Intercontinental dispersal prior to human translocation revealed in a cryptogenic invasive tree

In this study, complementary species-level and intraspecific phylogenies were used to better circumscribe the original native range and history of translocation of the invasive tree Parkinsonia aculeata. Species-level phylogenies were reconstructed using three chloroplast gene regions, and amplified fragment length polymorphism (AFLP) markers were used to reconstruct the intraspecific phylogeny. Together, these phylogenies revealed the timescale of transcontinental lineage divergence and the likely source of recent introductions of the invasive. The sequence data showed that divergence between North American and Argentinean P. aculeata occurred at least 5.7 million years ago, refuting previous hypotheses of recent dispersal between North and South America. AFLP phylogenies revealed the most likely sources of naturalized populations. The AFLP data also identified putatively introgressed plants, underlining the importance of wide sampling of AFLPs and of comparison with uniparentally inherited marker data when investigating hybridizing groups. Although P. aculeata has generally been considered North American, these data show that the original native range of P. aculeata included South America; recent introductions to Africa and Australia are most likely to have occurred from South American populations.

Phylogenetics of Cucumis (Cucurbitaceae)

Background: Melon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis. Results: Analyses of combined chloroplast sequences (4,375 aligned nucleotides) for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene. Conclusion: Based on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian/Asian clade and is phylogenetically far more distant from C. melo than implied by the current morphological classification.

Phylogenetics of Cucumis (Cucurbitaceae): Cucumber (C. sativus) belongs in an Asian/Australian clade far from melon (C. melo)

BackgroundMelon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis.ResultsAnalyses of combined chloroplast sequences (4,375 aligned nucleotides) for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene.ConclusionBased on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian/Asian clade and is phylogenetically far more distant from C. melo than implied by the current morphological classification.

Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions

BackgroundThe North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsections and sections). Previous presentations of relationships have been ambiguous and have not conformed to modern phylogenetic standards (e.g., were not presented as phylogenetic trees). Agalinis contains a large number of putatively rare taxa that have some degree of taxonomic uncertainty. We used DNA sequence data from three chloroplast genes to examine phylogenetic relationships among sections within the genus Agalinis Raf. (=Gerardia), and between Agalinis and closely related genera within Orobanchaceae.ResultsMaximum likelihood analysis of sequences data from rbcL, ndhF, and matK gene regions (total aligned length 7323 bp) yielded a phylogenetic tree with high bootstrap values for most branches. Likelihood ratio tests showed that all but a few branch lengths were significantly greater than zero, and an additional likelihood ratio test rejected the molecular clock hypothesis. Comparisons of substitution rates between gene regions based on linear models of pairwise distance estimates between taxa show both ndhF and matK evolve more rapidly than rbcL, although the there is substantial rate heterogeneity within gene regions due in part to rate differences among codon positions.ConclusionsPhylogenetic analysis supports the monophyly of Agalinis, including species formerly in Tomanthera, and this group is sister to a group formed by the genera Aureolaria, Brachystigma, Dasistoma, and Seymeria. Many of the previously described sections within Agalinis are polyphyletic, although many of the subsections appear to form natural groups. The analysis reveals a single evolutionary event leading to a reduction in chromosome number from n = 14 to n = 13 based on the sister group relationship of section Erectae and section Purpureae subsection Pedunculares. Our results establish the evolutionary distinctiveness of A. tenella from the more widespread and common A. obtusifolia. However, further data are required to clearly resolve the relationship between A. acuta and A. tenella.

PCR-RFLP analysis of chloroplast gene regions in Cajanus (Leguminosae) and allied genera.

Twenty-eight species belonging to five genera of the sub tribe Cajaninae; viz., Cajanus(15 species), Rhynchosia (10 species), Dunbaria, Flemingia and Paracalyx were analysed for variations in four chloroplast generegions, rbcL, trnS-psbC, 16S and trnL-UAA. The four chloroplast gene regions were amplified with specific primers and subsequently digested with 15 restriction enzymes. Rhynchosia did not show any inter-specific differences in the four gene regions for any of the enzymes used. In Cajanus, the inter-specific PCR-RFLP profile of the four gene regions for all the enzymes were similar except for the Pst I digests of trnS-psbC gene region. At inter-generic level, rbcL gene region did not show polymorphism with any of the enzymes used; while in trnS-psbC gene region polymorphism was observed only with Pst I and Hae III digestions. Inter-generic PCR-RFLP of 16S did not reveal any variation. The trnL-UAA gene region had restriction site only forEcoR I in which Cajanus and Rhynchosia showed similar profiles while Dunbaria showed a different profile. The trnL-UAA gene region in Paracalyx and Flemingia did not have restriction site for this enzyme. Despite the analyses of four gene regions using 15 restriction enzymes, differentiation at genus level could not be obtained. These observations indicated limited divergence of the chloroplast genome among the four genera of the sub-tribe Cajaninae suggesting close relationships of the taxa.