Origin and evolution of the endemic Macaronesian Inuleae (Asteraceae): evidence from the internal transcribed spacers of nuclear ribosomal DNA

The tribe Inuleae (Asteraceae) has 10 species endemic to the Macaronesian islands, including the three endemic genera Allagopappus, Schizogyne, and Vierea. Phylogenetic analyses of DNA sequence data from the internal transcribed spacers (ITS) of the nuclear ribosomal DNA of 47 taxa were performed using all Macaronesian endemics and representative species from 21 of the 36 genera of the Inuleae. The resulting ITS phylogeny reveals that Allagopappus is sister to a large clade that contains all genera with a predominantly Mediterranean distribution. This finding suggests that Allagopappus may represent an ancient lineage that found refuge in the Canary Islands following the major climatic and/or geologic changes in the Mediterranean basin after the Tertiary. The Macaronesian endemic genus Schizogyne is sister to Limbarda from the Mediterranean. The third Macaronesian endemic genus, Vierea, is sister to Perralderia, which is restricted to Morocco and Algeria. Pulicaria canariensis is sister to P. mauritanica, a species endemic to Morocco and Algeria. In contrast, P. diffusa from the Cape Verde Islands is sister to a broadly distributed species, P. crispa, that occurs from North Africa to the Arabian peninsula. Based on the ITS data, the genera Blumea, Inula, and Pulicaria are not monophyletic. The ITS trees suggested that Blumea mollis belongs to the tribe Plucheeae, a finding that is congruent with recent morphological evidence. A possible southern African origin for the core of the Laurasian taxa of the Inuleae is also suggested.     

Phylogeny of firs (genus <Emphasis Type="Italic">Abies</Emphasis>, Pinaceae) based on multilocus nuclear markers (AFLP)

To study the phylogenetic relationships, evolutionary history, and molecular systematics of firs (genus Abies), the phylogenetic reconstruction, based on nuclear multilocus markers—amplified fragment length polymorphism (AFLP)—was conducted. Using seven combinations of selective primers, 84 samples of 39 taxa were genotyped for 553 polymorphic AFLP loci. A comparison with our earlier chloroplast and mitochondrial phylogenies of the genus (in 2014) shows that the nuclear phylogeny generally is more congruent to the chloroplast tree. Most of the clades resolved by the chloroplast phylogeny were supported also in the AFLP tree. Employing the nuclear DNA-based tree, we revealed the presence of new groups and the differences in the topology of several clades. AFLP confirmed the monophyly of Asian species of section Balsamea and their sister position in relation to the American group of species of this section. As shown by the tree of chloroplast DNA, Asian species of section Balsamea do not form a monophyletic group, but belong to the clade comprising the majority of Asian species. Phylogenetically mitochondrial DNA data to a large extent are not congruent to the nuclear and chloroplast DNA trees, and are more in line with geographical distribution of species. Conflicts between nuclear and cytoplasmic phylogeny were analyzed. Taking them into account, we consider the hypothesis of a hybrid origin of particular groups of firs, including ancient hybridization in section Balsamea. A comparison of molecular data with traditional taxonomy of the genus is discussed.     

Phylogeny of the genus Lophozia (Dumort.) Dumort. s. str. inferred from nuclear and chloroplast sequences ITS1-2 and TRNL-F

Maximum parsimony and maximum likelihood phylogenetic trees were constructed for 21 taxa of Lophozia s. str. and the related genera, Schistochilopsis (5 species), Protolophozia elongate, and Obtusifolium obtusum based on pooled nuclear ITS 1-2 and chloroplast trnL-F DNA sequences. The trees were characterized by similar topology. It was demonstrated that the genus Lophozia s. str. was monophyletic, excluding L. sudetica, which deserved isolation into a distinct cryptic genus. The species distribution among the clades disagreed with the sections distinguished based on anatomical and morphological data. The relationships within the genus Schistochilopsis were consistent with the sectioning of the genus, based on morphological characters. Analysis of molecular data provided more precise definition of the systematic position of a number of taxa. Small genetic divergence of geographically distant forms was demonstrated.     

Phylogeny of the genus <Emphasis Type="Italic">Lophozia</Emphasis> (Dumort.) Dumort. s. str. inferred from nuclear and chloroplast sequences ITS1-2 and TRNL-F

Maximum parsimony and maximum likelihood phylogenetic trees were constructed for 21 taxa of Lophozia s. str. and the related genera, Schistochilopsis (5 species), Protolophozia elongata, and Obtusifolium obtusum based on combined nuclear ITS1-2 and chloroplast trnL-F DNA sequences. The trees were characterized by similar topology. It was demonstrated that the genus Lophozia s. str. was monophyletic, excluding L. sudetica, which deserved isolation into a distinct cryptic genus. The species distribution among the clades disagreed with the sections distinguished based on anatomical and morphological data. The relationships within the genus Schistochilopsis were consistent with the sectioning of the genus, based on morphological characters. Analysis of molecular data provided more precise definition of the systematic position of a number of taxa. A low level of genetic divergence of geographically distant forms was demonstrated.     

Molecular phylogeny reveals the non-monophyly of tribe Yinshanieae(Brassicaceae) and description of a new tribe,Hillielleae

The taxonomic treatment within the unigeneric tribe Yinshanieae(Brassicaceae) is controversial, owing to differences in generic delimitation applied to its species. In this study, sequences from nuclear ITS and chloroplast trn L-F regions were used to test the monophyly of Yinshanieae, while two nuclear markers(ITS, ETS) and four chloroplast markers(trnL-F, trn H-psbA, rps16, rpL32-trnL) were used to elucidate the phylogenetic relationships within the tribe. Using maximum parsimony, maximum likelihood, and Bayesian inference methods, we reconstructed the phylogeny of Brassicaceae and Yinshanieae. The results show that Yinshanieae is not a monophyletic group, with the taxa splitting into two distantly related clades: one clade contains four taxa and falls in Lineage I, whereas the other includes all species previously placed in Hilliella and is embedded in the Expanded Lineage II. The tribe Yinshanieae is redefined, and a new tribe, Hillielleae, is proposed based on combined evidence from molecular phylogeny, morphology, and cytology.     

Evidence for the Polyphyly of Haworthia (Asphodelaceae Subfamily Alooideae; Asparagales) Inferred from Nucleotide Sequences of rbcL, matK, ITS1 and Genomic Fingerprinting with ISSR-PCR

Abstract: Four molecular markers have been studied to examine the phylogenetic position of the South African plant genus Haworthia Duval within the succulent Asphodelaceae. Sequence data of the chloroplast genes mat K and rbc L were compared to the nuclear markers ITS1 and ISSR (Inter Simple Sequence Repeat) analysis. Both lines of molecular data, chloroplast and nuclear DNA, indicate that Haworthia is polyphyletic, forming two distinct clades. Most taxa previously combined as Haworthia subgenus Haworthia branch off early in the alooid chloroplast trees forming a strongly monophyletic group, whereas subgenus Hexangulares forms a polyphyletic assemblage comprising other alooid genera. The nuclear markers ITS1 and ISSR fingerprinting support the two groups as distinctly different, therefore confirming the division seen in chloroplast DNA. The practical implication is that the generic concept of Haworthia may have to be restricted to H. subgenus Haworthia or alternatively, that the groups of Haworthia be treated as infrageneric taxa within a broadened (Linnaean) concept of Aloe.     

What is the phylogenetic placement of Dipteronia dyerana Henry? An example of plant species placement based on nucleotide sequences

Abstract

DNA sequence data have been widely used to evaluate species delimitations and examine infraspecific relationships. However, species placements inferred from different nucleotide sequences are frequently in conflict. As an example of plant species placement based on nucleotide sequences, the phylogenetic placement of Dipteronia dyerana Henry (Aceraceae) was analyzed in the present study. The study species included eight Acer species (from different sections of Acer), two Dipteronia species, and two outgroup taxa. Phylogenetic trees based on five datasets (ITS, trnL‐F, trnD‐trnT, psbM‐trnD, and rpl16 regions) as well as their combined datasets were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Further analyses were conducted to compare the strict consensus trees based on single regions and the combination of different regions. The results revealed a significant discrepancy among the phylogenetic placements of D. dyerana, inferred from various sequences. Phylogenetic trees using MP analysis based on trnD‐trnT, rpl16, and the four chloroplast combined sequences supported the genus Dipteronia as a monophyletic group, while in the other trees D. dyerana was positioned either in parallel with D. sinensis and Acer species or within the genus Acer. In ML analysis, only rpl16 and the four chloroplast combined sequence datasets supported the genus Dipteronia as a monophyletic group. We concluded that, although significant genetic differentiation occurred between D. dyerana and D. sinensis, D. dyerana was more advanced than D. sinensis. However, whether Dipteronia is monophyletic remains to be further investigated, e.g., by using more closely related taxa and more sequences. Furthermore, in addition to internal transcribed spacer sequences, more chloroplast gene sequences should be used for phylogenetic analyses of species.     

Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae)

Aim Vitis subg. Vitis provides an example of a plant disjunction occurring in the Northern Hemisphere. It shows broad morphological variation but is assumed to be a species complex with limited genetic differentiation. Based on a comprehensive sampling of taxa and polymorphism in both chloroplast and nuclear DNA, we assessed genetic variation within this subgenus. Our aims were to clarify the relationships among species and to examine their historical biogeography. Location Asia, Europe, North America. Methods We analysed a total of 30 species and putative hybrids from subgenus Vitis and examined the infra‐specific variation in some species. Polymorphism in chloroplast DNA was assessed in trnL and trnH–psbA–trnK sequences (c. 2170 bp) and in 15 microsatellite loci. We also obtained nuclear data for size variation at 24 microsatellite loci. Phylogenetic inference was performed with Bayesian analyses. A maximum parsimony network was constructed to depict the evolutionary relationships among haplotypes, and microsatellite data were also subjected to hierarchical clustering analysis using the Ward distance. In addition, we assessed size homoplasy by sequencing both chloroplast and nuclear microsatellite loci. Results Chloroplast polymorphisms resolved subgenus Vitis as a monophyletic group with limited genetic variation. The ancestral haplotypes were found in Eurasia. American taxa all harboured derived haplotypes. Most of them formed a monophyletic group that did not include Vitis californica. The four main haplotypes in Vitis vinifera corresponded to two different origins. Nuclear microsatellites indicated that genetic variation was especially large in North America. Asian species exhibited a lower level of nuclear divergence and the European V. vinifera corresponded to a differentiated nuclear lineage. Main conclusions We obtained some evidence that subgenus Vitis has an Asian origin and then dispersed to Europe and North America. Geographic separation was followed by diversification, presumably during the Pleistocene, resulting in phylogeographic patterns similar to other biota. In contrast to chloroplast DNA, nuclear DNA shows a larger than expected genetic variation. Our molecular data also highlight the need to re‐examine certain aspects of the current subgeneric classification.     

Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited

The family Brassicaceae comprises 3710 species in 338 genera, 25 recently delimited tribes, and three major lineages based on phylogenetic results from the chloroplast gene ndhF. To assess the credibility of the lineages and newly delimited tribes, we sequenced an approximately 1.8-kb region of the nuclear phytochrome A (PHYA) gene for taxa previously sampled for the chloroplast gene ndhF. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the approximately unbiased (AU) test to compare phylogenetic results from PHYA with findings from ndhF. We also combined ndhF and PHYA data and used a Bayesian mixed model approach to infer phylogeny. PHYA and combined analyses recovered the same three large lineages as those recovered in ndhF trees, increasing confidence in these lineages. The combined tree confirms the monophyly of most of the recently delimited tribes (only Alysseae, Anchonieae, and Descurainieae are not monophyletic), while 13 of the 23 sampled tribes are monophyletic in PHYA trees. In addition to phylogenetic results, we documented the trichome branching morphology of species across the phylogeny and explored the evolution of different trichome morphologies using the AU test. Our results indicate that dendritic, medifixed, and stellate trichomes likely evolved independently several times in the Brassicaceae.     

Phylogenetic analysis of Asian<Emphasis Type="Italic"> Symplocos</Emphasis> (Symplocaceae) based on nuclear and chloroplast DNA sequences

Thirty species and one variety of Symplocos (Symplocaceae), including all taxa distributed in Japan, were phylogenetically analyzed with DNA sequence data. The evolution of morphological characters is discussed on the basis of the phylogenetic relationships obtained. All species were Asian, except one, S. austromexicana, from Mexico. The nuclear ribosomal internal transcribed spacer (ITS) region and two intergenic spacer regions, between trnL and trnF, and between trnH and psbA of chloroplast DNA were used. The topologies of trees obtained from ITS and the chloroplast intergenic spacers are largely congruent. S. sonoharae, the representative of the subgenus Symplocos in Asia, was sister to all other species. The position of the American species, S. austromexicana, which also belongs to the subgenus Symplocos, was not well resolved. The phylogenetic tree based on combined sequence data largely supports the monophyletic origin of the infrageneric sections proposed earlier. However, the phylogenetic relationship between them is not well resolved, probably due to rapid diversification. The section Palura, a deciduous group, is well defined in the DNA analysis, suggesting its independent status in the genus Symplocos. In spite of their morphological divergence, the three endemic species of the Bonin Islands are monophyletic. The occurrence of curved seeds seems to be homoplastic, scattered over the phylogenetic tree without showing a particular infrageneric relationship.     

Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasets

Sideritis L. (Lamiaceae) comprises approximately 150 species of annuals and perennials distributed chiefly in the Mediterranean region. The majority of the species belong to the continental subgenus Sideritis which is divided into two perennial (Sideritis and Empedoclea) and two annual (Hesiodia and Burgsdorfia) sections. Twenty-three species are woody perennials endemic to the Macaronesian archipelagos of Madeira and the Canary Islands. In an effort to determine the continental origin of the insular group, we constructed independent phylogenies comprising sequence data from both chloroplast and nuclear markers. Sampling included 7 island taxa drawn from the Macaronesian subgenus Marrubiastrum and 25 continental taxa representing all four sections of subgenus Sideritis. Subgenus Marrubiastrum and the two continental perennial sections form well-supported monophyletic groups in both individual and combined analyses. The annual sections are not monophyletic in any analysis; further sampling of annual taxa is needed to resolve these relationships. All analyses identified Sideritis cossoniana, an annual species from Morocco, as the closest continental relative of the Macaronesian group. This contrasts with the hypothesis of earlier workers who suggested that the insular taxa were most closely related to eastern Mediterranean species of the genus. The phylogenies also demonstrate a distinct increase in woodiness among the Macaronesian species relative to their continental congeners, providing further support for the secondary nature of woodiness in island plants.     

Biogeography and floral evolution of baobabs (Adansonia,Bombacaceae) as inferred from multiple data sets

The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction sites, sequences of the chloroplast rpl16 intron, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, and morphology. We sampled each of the eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were largely concordant. The two chloroplast data sets showed concordance with one another but showed significant conflict with ITS and morphology. A possible explanation for the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum-likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and therefore involved overwater dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to pollination by mammals in the genus.     

Evolution of Lycopodiaceae Inferred from Spacer Sequencing of Chloroplast rRNA Genes

Nucleotide sequences of a chloroplast rDNA region including 8 bp from the 3" end of 23S rDNA–ITS2–4.5S rDNA–ITS3–5S rDNA–ITS4 (approximately 800 bp) were determined in 25 species of Lycopodiaceae and two species of the genus Isoetes. The rate of molecular evolution of spacers significantly varied in different Lycopsida taxa. A phylogenetic analysis by the neighbor-joining (NJ) method revealed that the family Lycopodiaceae is monophyletic. The topology of phylogenetic trees suggests the isolation of four or probably five genera in family Lycopodiaceae. For these genera, synapomorphic indels were detected. The obtained data were compared with the results of phylogenetic analysis of Lycopsida with regard to other sequences. The relationships of taxa within the family Lycopodiaceae is discussed.     

Phylogenetic Relationships of Extinct Cetartiodactyls: Results of Simultaneous Analyses of Molecular, Morphological, and Stratigraphic Data

Although some recent morphological and molecular studies agree that Cetacea is closely related to Hippopotamidae, there is little consensus on the phylogeny within Cetartiodactyla. We addressed this problem by conducting two analyses: (1) a simultaneous cladistic analysis of intrinsic data (morphology and molecules) and (2) a stratocladistic analysis, which included morphological, molecular, and stratigraphic data. Unlike previous simultaneous analyses, we had the opportunity to include data from the recently described hindlimbs of protocetid and pakicetid cetaceans. Our intrinsic dataset includes 73 taxa scored for 8,229 informative characters, of which 208 are morphological and 8,021 molecular. Both analyses supported the exclusion of Mesonychia from Cetartiodactyla and a close phylogenetic relationship between Hippopotamidae and Cetacea. Many polytomies in the strict consensus of the most parsimonious trees for the intrinsic dataset can be attributed to differing positions for Raoellidae, which in some trees is the sister-group to Cetacea. Pruning Raoellidae and 18 other taxa from all most parsimonious produced a fully resolved agreement subtree, which indicates that the Old World taxa Cebochoerus and Mixtotherium are successive stem taxa to Whippomorpha (i.e., Cetacea + Hippopotamidae). The main result of adding stratigraphic information to the intrinsic dataset was that we found fewer most parsimonious trees, which in most respects were congruent with a subset of the shortest trees for the intrinsic dataset. Our stratocladistic analysis supports species of Diacodexis as the most basal cetartiodactyls, a clade of suiform cetartiodactyls, a monophyletic Tylopoda that includes Protoceratidae, and a monophyletic Carnivora. We were unable to identify any pre-Miocene stem taxa to Hippopotamidae, thus its ghost lineage is still 39 million years long. The relatively low Bremer support for many nodes in our trees indicates that our phylogenetic hypotheses should be subjected to further testing.     

Phylogeny of Melaleuca, Callistemon, and Related Genera of the Beaufortia Suballiance (Myrtaceae) Based on 5S and ITS-1 Spacer Regions of nrDNA

A phylogenetic analysis of genera within the informal suballiance Beaufortia (family Myrtaceae), largely endemic to Australia and New Caledonia, is presented based on separate and combined data sets for 5S and ITS-1 spacer regions of nuclear ribosomal DNA. The two sets were not in conflict but the 5S data set was more informative. Data were analysed using conventional parsimony, jackknife parsimony, and three-item parsimony analyses. Three-item analysis gave more resolved trees than conventional parsimony analysis. The Beaufortia suballiance includes two major clades, with all Australian representatives of Callistemon (shown to be monophyletic) and most Australian representatives of Melaleuca forming one of these. The sister clade comprises a well-defined group of endemic New Caledonian taxa (classified as Callistemon and Melaleuca ), some Australian species of Melaleuca , a clade including the Western Australia/Northern Territory genera Beaufortia, Lamarchea , and Regelia , and a clade including the south-west Western Australian genera Calothamnus, Eremaea, Conothamnus , and Phymatocarpus . All molecular analyses sup port the monophyly of Conothamnus and of Regelia , genera for which a number of species were included. Three-item analysis of the combined data set supports the monophyly of Beaufortia . The findings have implications for both taxonomy and biogeography.     

紫乌头复合体nrDNA的ITS序列与系统发育分析

对乌头属 Aconitum L. 27个类群的nrDNA ITS序列进行了简约法与邻接法分析,两种方法得到的系统发育树基本一致。乌头亚属subgen. Aconitum 的蔓乌头系 ser. Volubilia 不是一个单系类群,显柱乌头系 ser. Stylosa 与兴安乌头系ser. Ambigua 各自作为单系类群也没有得到支持。特产于云南西北部横断山区的一些种之间存在非常近的系统发育关系,说明这些种可能是近期物种形成的产物。紫乌头 A. delavayi 复合体的不同类群在系统发育树上位     

An ITS phylogeny of Balsamorhiza and Wyethia (Asteraceae: Heliantheae)

The relationships among the species of Balsamorhiza and Wyethia (Asteraceae: Heliantheae) were examined using data from the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. The ITS sequences were obtained from nine species of Balsamorhiza and 14 species of Wyethia as well as seven outgroup genera. Five of the outgroup genera were members of the subtribe Engelmanniinae of the tribe Heliantheae, the subtribe that includes Balsamorhiza and Wyethia. The resulting trees show that Balsamorhiza and Wyethia together form a monophyletic group. Balsamorhiza alone is monophyletic, but neither of its two sections is monophyletic. Wyethia is paraphyletic. One group of Wyethia species, including all members of sections Alarconia and Wyethia as well as W. bolanderi from section Agnorhiza, is monophyletic and sister to Balsamorhiza. The other species of Wyethia (all placed in section Agnorhiza) are part of a polytomy along with the clade composed of Balsamorhiza plus the rest of Wyethia.     

Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae.

The internal transcribed spacer (ITS) region of 18-26S nuclear ribosomal DNA was sequenced in 12 representatives of the Compositae subtribe Madiinae and two outgroup species to assess its utility for phylogeny reconstruction. High sequence alignability and minimal length variation among ITS 1, 5.8S, and ITS 2 sequences facilitated determination of positional homology of nucleotide sites. In pairwise comparisons among Madiinae DNAs, sequence divergence at unambiguously aligned sites ranged from 0.4 to 19.2% of nucleotides in ITS 1 and from 0 to 12.9% of nucleotides in ITS 2. Phylogenetic relationships among ITS sequences of Hawaiian silversword alliance species (Argyroxiphium, Dubautia, and Wilkesia) and California tarweed taxa in Adenothamnus, Madia, Raillardella, and Raillardiopsis are highly concordant with a chloroplast DNA-based phylogeny of this group. Maximally parsimonious trees from ITS and chloroplast DNA data all suggest (a) origin of the monophyletic Hawaiian silversword alliance from a California tarweed ancestor, (b) closer relationship of the Hawaiian species to Madia and Raillardiopsis than to Adenothamnus or Raillardella, (c) paraphyly of Raillardiopsis, a segregate of Raillardella, and (d) closer relationship of Raillardiopsis to Madia and the silversword alliance than to Raillardella. These findings indicate that the ITS region in plants should be further explored as a promising source of nuclear phylogenetic markers.