Molecular phylogeny of the genus Ceanothus (Rhamnaceae) using rbc L and ndh F sequences

 Intrageneric phylogeny among ten representative Ceanothus species was investigated using DNA sequences of the chloroplast encoded ndhF and rbcL genes. Parsimony analysis of the ndhF sequences identified two main clades corresponding to two subgenera Ceanothus and Cerastes. The phylogenetic results suggest that three monophyletic clades within the subgenus Ceanothus can be delimited on the basis of (1) evergreen or (2) deciduous leaves and (3) thorn presence within the evergreen clade. The estimated divergence time based on rbcL sequences suggests that the two subgenera diverged 18–39 million years ago whereas species within each subgenus diverged more recently. Taken together, the results support the division of Ceanothus into two monophyletic subgenera and are consistent with the postulated recent divergence of many species within each subgenus. Received: 25 September 1996/Accepted: 8 November 1996     

A phylogenetic analysis of 100+ genera and 50+ families of euasterids based on morphological and molecular data with notes on possible higher level morphological synapomorphies

 A data matrix of 143 morphological and chemical characters for 142 genera of euasterids according to the APG system was compiled and complemented with rbcL and ndhF sequences for most of the genera. The data were subjected to parsimony analysis and support was assessed by bootstrapping. Strict consensus trees from analyses of morphology alone and morphology + rbcL + ndhF are presented. The morphological data recover several groups supported by molecular data but at the level of orders and above relationships are only superficially in agreement with molecular studies. The analyses provide support for monophyly of Gentianales, Aquifoliales, Apiales, Asterales, and Dipsacales. All data indicate that Adoxaceae are closely related to Dipsacales and hence they should be included in that order. The trees were used to assess some possible morphological synapomorphies for euasterids I and II and for the orders of the APG system. Euasterids I are generally characterised by opposite leaves, entire leaf margins, hypogynous flowers, “early sympetaly” with a ring-shaped corolla primordium, fusion of stamen filaments with the corolla tube, and capsular fruits. Euasterids II often have alternate leaves, serrate-dentate leaf margins, epigynous flowers, “late sympetaly” with distinct petal primordia, free stamen filaments, and indehiscent fruits. It is unclear which of these characters represent synapomorphies and symplesiomorphies for the two groups, respectively, and there are numerous expections to be interpreted as reversals and parallelisms. Received August 28, 2000 Accepted August 7, 2001     

Phylogeny of extant genera in the family Characeae (Charales,Charophyceae) based on rbcL,sequences and morphology

Extant genera of Characeae have been assigned to two tribes: Chareae (Chara, Lamprothamnium, Nitellopsis, and Lychnothamnus) and Nitelleae (Nitella and Tolypella), based on morphology of the thallus and reproductive structures. Character analysis of fossil and extant oogonia suggest that Tolypella is polyphyletic, the genus comprising two sections, one in each of the two tribes. Eleven morphological characters and sequence data for the Rubisco large subunit (rbcL) were used to reconstruct the phylogeny of genera, including the two sections of Tolypella. Parsimony analysis of the rbcL data, with all positions and changes weighted equally, strongly supports the monophyly of the Characeae. The two Tolypella sections form a robust monophyletic group basal to the family. Transversion weighting yielded the same tree but with a paraphyletic Tolypella. The rbcL data strongly support monophyly of tribe Chareae but tribe Nitelleae is paraphyletic. Parsimony analysis of morphological data produced one unrooted tree consistent with monophyly of the two tribes; on this tree the Tolypella sections were paraphyletic. Combining morphological with rbcL data did not change the results derived from rbcL sequences alone. The rbcL data support the monophyly of the Characeae and Coleochaete, which together form a monophyletic sister group to embryophytes.     

Higher-level systematics of Acanthaceae determined by chloroplast DNA sequences

Parsimony analyses of ndhF chloroplast gene sequences were undertaken for 15 species of Acanthaceae and nine representative outgroup species. In addition, parsimony analyses of rbcL sequences were undertaken for 12 species of Acanthaceae and the same nine outgroup species as for ndhF. The results indicate that ndhF provides more informative characters and greater systematic resolution at this hierarchical level than rbcL. The ndhF analyses demonstrate that Elytraria and Thunbergia are successive sister taxa to all Acanthaceae taxa that have retinacula and explosive fruits. These data also demonstrate that taxa with both retinacula and explosive fruits can be subdivided further into two monophyletic groups that correspond to taxa with and without cystoliths. Within the group with cystoliths three putatively monophyletic groups correspond to taxa possessing quincuncial, left contort, and ascending-cochlear corolla aestivation patterns. The results of the rbcL analysis provide less systematic resolution than ndhF but do contain several congruent arrangements of taxa within Acanthaceae.     

A search for the phylogenetic position of the seven-son flower (Heptacodium, Dipsacales): Combining molecular and morphological evidence

A first report on the problematic phylogenetic position ofHeptacodium (2 spp.; China) using molecular data from chloroplast DNA is presented. Amplification of ORF2280 homolog region was executed in a number of representative taxa in order to determine ifHeptacodium shows similar structural rearrangements as other Dipsacales. DNA sequences ofndhF were generated to clarify the phylogenetic position ofHeptacodium among Caprifoliaceae (s.l.). Six outgroup taxa and fifteen representatives of Dipsacales were sampled and more than 2100 basepairs ofndhF sequence were used in a cladistic analysis. Parsimony analysis produced two shortest trees and showedHeptacodium as sister to all members of Caprifoliaceae (s.str.), although weakly supported. Additionally, trees were constructed withndhF data supplemented with availablerbcL sequences and a morphological data set. Results of all analyses support an unresolved basal position forHeptacodium among Caprifoliaceae (s.l.), which in part explains the difficulty experienced previously in classifying the genus.     

Morphological and genetic evidence of contemporary intersectional hybridisation in Mediterranean Helichrysum (Asteraceae,Gnaphalieae)

Hybridisation is considered an important evolutionary phenomenon in Gnaphalieae, but contemporary hybridisation has been little explored within the tribe. Here, hybridisation between Helichrysum orientale and Helichrysum stoechas is studied at two different localities in the islands of Crete and Rhodes (Greece). Using three different types of molecular data (AFLP, nrDNA ITS sequences and cpDNA ndhF sequences) and morphological data, the aim is to provide simultaneous and direct comparisons between molecular and morphological variation among the parental species and the studied hybrid populations. AFLP profiles, ITS sequences and morphological data support the existence of hybrids at the two localities studied, shown as morphological and genetic intermediates between the parental species. Chloroplast DNA sequences show that both parental species can act either as pollen donor or as maternal parent. Fertility of hybrids is demonstrated by the viability of seeds produced by hybrids from both localities, and the detection of a backcross specimen to H. orientale. Although there is general congruence of morphological and molecular data, the analysis of morphology and ITS sequences can fail to detect backcross hybrids.     

DNA Sequence Evidence for Placement of the Ground Cuscus, Phalanger gymnotis, in the Tribe Phalangerini (Marsupialia: Phalangeridae)

A region of mitochondrial DNA, including the 3 end of tRNA phenylalanine, the complete 12S rRNA and tRNA valine genes, and the 5 end of 16S rRNA, was sequenced for four phalangerids and one burramyid; additional marsupial sequences were extracted from GenBank. Parsimony, minimum evolution, and maximum likelihood analyses show that the ground cuscus, Phalanger gymnotis, groups with the tribe Phalangerini, not with the tribe Trichosurini as had been suggested on the basis of certain morphological characters. This result is in agreement with an earlier study using DNA hybridization and is supported by some morphological evidence as well. We conclude that the character states that link the ground cuscus with the Trichosurini are the result of convergence, and therefore the placement of several other species in the trichosurin genus Strigocuscus based on the same characters should be reconsidered. The hypothesized close relationship of two fossil taxa, Strigocuscus reidi and S. notialis, to Phalanger gymnotis is also questionable because the fossils do not share morphological synapomorphies that link the ground cuscus to the Phalangerini.     

Functional analysis of <Emphasis Type="Italic">Antirrhinum kelloggii</Emphasis> flavonoid 3′-hydroxylase and flavonoid 3′,5′-hydroxylase genes; critical role in flower color and evolution in the genus <Emphasis Type="Italic">Antirrhinum</Emphasis>

The enzymes flavonoid 3′-hydroxylase (F3′H) and flavonoid 3′,5′-hydroxylase (F3′5′H) play an important role in flower color by determining the B-ring hydroxylation pattern of anthocyanins, the major floral pigments. F3′5′H is necessary for biosynthesis of the delphinidin-based anthocyanins that confer a violet or blue color to most plants. Antirrhinum majus does not produce delphinidin and lacks violet flower colour while A. kelloggii produces violet flowers containing delphinidin. To understand the cause of this inter-specific difference in the Antirrhinum genus, we isolated one F3′H and two F3′5′H homologues from the A. kelloggii petal cDNA library. Their amino acid sequences showed high identities to F3′Hs and F3′5′Hs of closely related species. Transgenic petunia expressing these genes had elevated amounts of cyanidin and delphinidin respectively, and flower color changes in the transgenics reflected the type of accumulated anthocyanidins. The results indicate that the homologs encode F3′H and F3′5′H, respectively, and that the ancestor of A. majus lost F3′5′H activity after its speciation from the ancestor of A. kelloggii.     

Molecular phylogenetics of Hippophae L. (Elaeagnaceae) based on the internal transcribed spacer (ITS) sequences of nrDNA

 The genus Hippophae comprises 7 species and 8 subspecies according to the latest classification, and has shown enormous ecological, nutrient and medicinal values. Here we analyzed the phylogenetic relationships among 15 taxa of the genus by comparing sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA). ITS sequences in Hippophae varied in length from 651 bp to 666 bp. The aligned sequences were 690 bp in length and 269 (39.0%) were variable sites with 150 being parsimony-informative. The amount of polymorphism observed within a taxon was extremely low in most taxa except for two putative hybrid species. The aligned sequences were analyzed by maximum parsimony (MP) and neighbor-joining (NJ) methods. In the strict consensus trees of parsimony analysis, the monophyly of Hippophae was supported by 100% bootstrap value. H. tibetana was at the basal position of the genus, and the remaining taxa formed two clades with high bootstrap support. The first clade included subspecies of H.␣rhamnoides and the other one consisted of remaining species. Parsimony analysis also suggested that the species H. tibetana, H. neurocarpa and H.␣salicifolia were all distinct. Although the sequence divergence among subspecies of H. rhamnoides was also remarkably high, the molecular data supported the monophyly of H. rhamnoides when H. rhamnoides subsp. gyantsensis Rousi was excxluded. The NJ trees showed essentially the same topology. The taxonomical arrangement that divided the genus into two sections was not supported based on the ITS sequences. However, the hybrid origin of H. goniocarpa and H. litangensis proposed previously was supported by the present ITS data. Received January 7, 2002; accepted May 10, 2002 Published online: November 22, 2002 Addresses of the authors: Kun Sun, Xuelin Chen, Ruijun Ma, Qin Wang, Institute of Botany, Northwest Normal University, Lanzhou 730070, China. Changbao Li, Song Ge (e-mail: gesong@ns.ibcas.ac.cn or song_ge@hotmail.com), Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.     

Sectional relationships in the genus Rhododendron (Ericaceae): evidence from matK and trnK intron sequences

 Phylogenetic relationships among all eight subgenera and 12 sections in Rhododendron as well as its related genera were inferred from matK and trnK intron sequences. The results of this study provided the following insights: (1) Rhododendron is paraphyletic because Menziesia is nested within Rhododendron. (2) Subgenus Therorhodion forms a basal lineage of tribe Rhodoreae. (3) Subgenera Hymenanthes and Tsutsusi are monophyletic. (4) Subgenera Azaleastrum and Pentanthera are polyphyletic. (5) Subgenus Rhododendron is monophyletic, if section Rhododendron subsection Ledum is excluded. Received January 8, 1999, in definite form December 22, 2000 Accepted April 12, 2001     

Region-specific rates of molecular evolution: A fourfold reduction in the rate of accumulation of “Silent” mutations in transcribed versus nontranscribed regions of homologous DNA fragments derived from two closely related mouse species

Summary We have sequenced homologous DNA fragments of 2.7 and 2.8 kbp derived from the closely related mouse speciesMus musculus domesticus (M. domesticus) andMus musculus musculus (M. musculus), respectively. These two species diverged approximately 1 million years ago. Each DNA fragment contains 1.35 kbp of the 3′ end of the constitutively expressed 2.2-kbpaprt (adenine phosphoribosyltransferase) gene and a similarly sized nontranscribed region downstream of theaprt gene. Theaprt gene region contains protein coding sequences (0.35 kbp), intronic sequences (0.75 kbp), and a 3′ nontranslated sequence (0.25 kbp). Both theM. domesticus andM. musculus downstream regions share three partial copies of the B1 repetitive element with theM. musculus downstream region containing an additional complete copy of this element. A comparison of the 2.7-and 2.8-kbp DNA fragments revealed a total of 63 molecular alterations (i.e., mutations) that were approximately fourfold more abundant in the nontranscribed downstream region than in the transcribedaprt gene. Of the 11 mutations observed in the transcribed region, 7 were found in introns, 3 in the 3′ untranslated sequence, and 1 was a synonymous change in an exon. A comparison of the human andM. domesticus aprt genes has previously revealed no homology in either the intronic or 3′ nontranslated regions with the exception of a 26-bp sequence in intron 3 and sequences at the exon/intron boundaries necessary for correct mRNA splicing (Broderick et al.,Proc. Natl. Acad. Sci. USA, 84:3349, 1987). Therefore, there does not appear to be selective pressure for sequences within these regions. We conclude that there is a lower rate of accumulation of “silent” mutations in the transcribed mouseaprt gene than in a contiguous nontranscribed downstream region. A possible molecular mechanism involving preferential DNA repair for the transcribed region is discussed.     

Phylogenetic reconstruction of the genusBrachypodium P. Beauv. (Poaceae) from combined sequences of chloroplastndhF gene and nuclear ITS

A phylogenetic reconstruction of eight species of the genusBrachypodium P. Beauv. (Poaceae) has been obtained combining sequence data from the chloroplastndhF gene and the nuclear ITS, and using five representatives of tribes Triticeae (Secale), Poeae (Lolium), Meliceae (Melica, Glyceria) and Oryzeae (Oryza) as out-groups. Similar numbers of informative substitutions for the ingroup species were provided by both the 3 region of the chloroplastndhF gene and the nuclear ITS region. The Mediterranean annualBrachypodium distachyon appears to be the basal lineage, followed by the divergence of the New World non-rhizomatousB. mexicanum, which antedates the separation of a core of six European and Eurosiberian rhizomatous perennials (Brachypodium arbuscula, B. retusum, B. rupestre, B. phoenicoides, B. pinnatum, andB. sylvaticum). The evolutionary reconstruction based on sequences of the chloroplast and the nuclear genomes is congruent with topologies obtained from analysis of RAPD data.     

A series of repetitive DNA sequences are associated with human core and H1 histone genes

Summary Repetitive DNA sequences, derived from the human β-globin gene cluster, were mapped within a series of human genomic DNA segments containing core (H2A, H2B, H3 and H4) and H1 histone genes. Cloned recombinant λCH4A phage with human histone gene inserts were analyzed by Southern blot analysis using the following³²P-labeled (nick translated) repetitive sequences as probes:Alu I,Kpn I and LTR-like. A cloned DNA designated RS002-5′C6 containing (i)a (TG)₁₆ simple repeat, (ii) an (ATTTT)n repeat and (iii)a 52 base pair alternating purine and pyrimidine sequence was also used as a radiolabelled hybridization probe. Analysis of 12 recombinant phage, containing 6 arrangements of core histone genes, indicated the presence ofAlu I,Kpn and RS002-5′C6 repetitive sequences. In contrast, analysis of 4 human genomic DNA segments, containing both core and H1 histone genes, indicated the presence of onlyAlu I family sequences. LTR-like sequences were not detected in association with any of the core or H1 histone genes examined. These results suggest that human histone and β-globin genes share certain aspects of sequence organization in flanking regions despite marked differences in their overall structure and pattern of expression.     

Revisiting the phylogeny of Dipsacales: New insights from phylogenomic analyses of complete plastomic sequences

Phylogenetic relationships in Dipsacales have long been a major challenge. Although considerable progress has been made during the past two decades, questions remain; the uncertain systematic positions of Heptacodium, Triplostegia, and Zabelia, in particular, impede our understanding of Dipsacales evolution. Here we use 75 complete plastomic sequences to reconstruct the phylogeny of Dipsacales, of which 28 were newly generated. Two primary clades were recovered that form the phylogenetic backbone of Dipsacales. Seven of the primary clades correspond to the recognized families Adoxaceae, Caprifoliaceae s. str., Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae, and Valerianaceae, and one corresponds to Zabelia, which was found to be the closest relative of Morinaceae in all analyses. Additionally, our results, with greatly increased confidence in most branches, show that Heptacodium and Triplostegia are members of Caprifoliaceae s. str. and Dipsacaceae, respectively. The results of our study indicate that the complete plastomic sequences provide a fully‐resolved and well‐supported representation of the phylogenetic relationships within Dipsacales.     

Phylogenetic analysis of eastern Asian and eastern North American disjunct Lespedeza (Fabaceae) inferred from nuclear ribosomal ITS and plastid region sequences

Lespedeza (tribe Desmodieae, Fabaceae) follows a disjunct distribution in eastern Asia and eastern North America. Phylogenetic relationships among its species and related taxa were inferred from nuclear ribosomal internal transcribed spacer (ITS) and plastid sequences (trnH‐psbA, psbK‐psbI, trnK‐matK and rpoC1). We examined 35 species of Lespedeza, two of Kummerowia and one of Campylotropis, the sole constituents of the Lespedeza group. An analysis of these data revealed that the genus Campylotropis is sister to the other two genera. However, we were unable to resolve the relationships between Kummerowia and Lespedeza in the strict consensus trees of parsimony analyses based on plastid and combined DNA data. In the genus Lespedeza, the Old World subgenus Macrolespedeza is monophyletic, whereas the transcontinental subgenus Lespedeza is paraphyletic. Monophyly of eastern Asian species and of North American species is strongly supported. Although inconsistent with the traditional classification, this phylogenetic finding is consistent with seedling morphology. Three subgroups recognized in subgenus Macrolespedeza were unresolved in our phylogenetic trees. An incongruence length difference (ILD) test indicated that the two partitions (nuclear ITS and plastid sequences) were significantly incongruent, perhaps because of hybridization between species in Lespedeza. Most of the primary clades of tribe Desmodieae are Asian, implying that the relatively few New World ones, such as those in Lespedeza, are more recently derived from Asia. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 221–235.     

Identification and characterization of plastid trnF(GAA) pseudogenes in four species of Solanum (Solanaceae)

Non-functional trnF pseudogenes that rarely occur in embryophytes have been found in Solanaceae. We have sequenced the trnL-F intergenic spacer of four species of Solanum, and found duplicated regions of the original trnF gene. These repeats were 94–260 bp long causing large length variation in the trnL-F intergenic spacer resulting from differences in pseudogene copy number (2–4). The duplicated trnF regions are comprised of several highly structured motifs, which were partial residues, or entire parts of the Anticodon, T- and D-domains of the original gene, but all lacked the acceptor stems at the 5′- or 3′-end. Pseudogenes included several transitions and transversions in their sequences compared to the original trnF gene. Among pseudogene copies, T-domains were more frequent and fragmented than D-domain elements. Our results demonstrate that although chloroplast evolution is uniform such structural duplications in the sequences used for phylogenetic reconstructions should be treated with great caution.     

Systematics of the tribe Trematocarini (Perciformes: Cichlidae) from Lake Tanganyika, Africa

 Phylogenetic relationships among eight Trematocara species and a single Telotrematocara species included in the Tanganyikan cichlid tribe Trematocarini were investigated on the basis of morphological features. The monophyly of the tribe is supported by the presence of hypertrophied sensory pores on the head, tendon “c” of adductor mandibulae section 1, a single scale row between the upper lateral line and body axis, great depth of the anteriormost infraorbital (reversed in Trematocara caparti and T. stigmaticum), and the absence of a lower lateral line. Trematocara is paraphyletic unless Telotrematocara is treated as a junior synonym. Received: December 10, 2001 / Revised: March 18, 2002 / Accepted: April 4, 2002