Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA

Sequence data of the trnL group I intron, the petD group II intron, the trnL-F and petB-D spacers, and the rapidly evolving matK gene were analysed from all families of the basal eudicot grade and from representatives of 19 core eudicot orders. The dataset comprised 5654 positions of aligned sequence plus a matrix of 1087 binary indel characters. Mutational hotspots correspond in number and extension to hotspots already known from basal angiosperms and, with respect to secondary structure, are generally located in terminal parts of stem-loop regions. Parsimony, Bayesian, and likelihood analyses depict Ranunculales as sister to all remaining eudicots with maximum support. The branching order in the basal eudicot grade is further resolved as Sabiales, Proteales, Trochodendrales, and Buxales. Nearly all of the backbone nodes gain high confidence, except for the node showing Proteales diverging before Trochodendrales, which is only moderately supported (83% JK). In Ranunculales, the woody Eupteleaceae are first-branching, with Papaveraceae plus Fumariaceae coming next. Within Proteales, Nelumbo is clearly resolved as sister to a Platanaceae–Proteaceae clade. Gunnerales are found as the first branch in core eudicots, with maximum support in the combined analysis. This node is also resolved with matK alone, but unsupported. It appears that the combined analysis of sequence data from rapidly evolving and non-coding genomic regions leads to significantly improved statistical support values in comparison to earlier studies of basal eudicots using multiple conserved genes.See also Electronic Supplement at doi:10.1016/j.ode.2006.08.001     

Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points

A molecular dating of the phylogenetically basal eudicots (Ranunculales, Proteales, Sabiales, Buxales and Trochodendrales sensu Angiosperm Phylogeny Group II) has been performed using several fossils as minimum age constraints. All rbcL sequences available in GenBank were sampled for the taxa in focus. Dating was performed using penalized likelihood, and results were compared with nonparametric rate smoothing. Fourteen eudicot fossils, all with a Cretaceous record, were included in this study for age constraints. Nine of these are assigned to basal eudicots and the remaining five taxa represent core eudicots. Our study shows that the choice of methods and fossil constraints has a great impact on the age estimates, and that removing one single fossil change the results in the magnitude of tens of million years. The use of several fossil constraints increase the probability of approaching the true ages. Our results suggest a rapid diversification during the late Early Cretaceous, with all the lineages of basal eudicots emerging during the latest part of the Early Cretaceous. The age of Ranunculales was estimated to 120 my, Proteales to 119 my, Sabiales to 118 my, Buxales to 117 my, and Trochodendrales to 116 my.     

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atpl, matR, had5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales-Oxalidales-Malpighiales) clade is sister to malvids (or rosid Ⅱ), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. This study shows that the mitochondrial genes are informative markers for resolving relationships among genera, families, or higher rank taxa across angiosperms. The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes, as found in this study, make them particularly useful for reconstructing ancient phylogenetic relationships. A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes, nuclear genes, and non-molecular data to reconstruct the underlying organismal phylogeny.     

Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots), but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ∼4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8) that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.     

Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early‐branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schi‐sandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well‐supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well‐supported eudicot clade, the early‐diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise six well‐supported subclades: (1) Berberidopsidaceae/Aextoxicaceae; (2) Myrothamnaceae/ Gunneraceae; (3) Saxifragales, which are the sister to Vitaceae (including Leea) plus a strongly supported eurosid clade; (4) Santalales; (5) Caryophyllales, to which Dilleniaceae are sister; and (6) an asterid clade. The relationships among these six subclades of core eudicots do not receive strong support. This large data set has also helped place a number of enigmatic angiosperm families, including Podostemaceae, Aphloiaceae, and Ixerbaceae. This analysis further illustrates the tractability of large data sets and supports a recent, phylogenetically based, ordinal‐level reclassification of the angiosperms based largely, but not exclusively, on molecular (DNA sequence) data.     

Out of Africa: molecular phylogenetics and biogeography of Wolffiella (Lemnaceae)

The monophyletic genus Wolffiella (Lemnaceae) comprises 10 species divided taxonomically into three sections. Relative to other genera of Lemnaceae, Wolffiella has a restricted range, with species distributed in warm temperate to tropical areas of Africa and the Americas, with only one species occurring in both areas. Sequence data from coding (rbcL and matK) and non‐coding (trnK and rpl16 introns) regions of cpDNA were analyzed phylogenetically to resolve relationships within Wolffiella, and these results were compared to earlier allozyme and morphological studies. Allozymes, cpDNA and morphology all supported the recognition of three sections. Relationships among species were similar in most respects between the allozyme and cpDNA trees, as well as among the different plastid partitions. In Wolffiella, both non‐synonymous and synonymous substitutions were greater in matK than in rbcL, as observed in other taxa. The synonymous substitution rate in matK was similar to the substitution rate of the non‐coding regions. All partitions, including coding regions, exhibited some homoplasy. Biogeographical reconstructions from a combination of cpDNA partitions indicated that Wolffiella originated in Africa with early movement to and radiation in the Americas. The one species found in both Africa and the Americas, W. welwitschii, likely originated in the Americas and subsequently dispersed to Africa. Using the SOWH test, the cpDNA data could reject two alternative biogeographical hypotheses suggested from analyses of morphological and allozyme data. The present distribution of Wolffiella can be explained by two major dispersal events and this contrasts with the more complex species distributions in other Lemnaceae genera. Limited dispersal in Wolffiella relative to other Lemnaceae genera may be due to more recent origins of species, lower dispersibility and poorer colonizing ability. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 79 , 565–576.     

A phylogenetic analysis of palm subtribe Archontophoenicinae (Arecaceae) based on 14 DNA regions

Subtribe Archontophoenicinae belongs to Areceae, the largest of all palm tribes. It includes 15 species distributed in five genera, all found in the south‐western Pacific Region. Archontophoenicinae are rather homogeneous in morphology, making phylogenetic relationships problematic to reconstruct using morphological characters. In this study we investigated phylogenetic relationships in Archontophoenicinae based on all 15 species of the subtribe, using a combination of nine plastid and five nuclear DNA sequence markers. The plastid regions used were the coding rbcL, matK, ndhF and rpoC1 (exon 2) and the non‐coding rps16 intron, atpF‐atpH, psbK‐psbI, trnL‐trnF and trnQ‐rps16. The nuclear regions used were AG1, BRSC, ITS2, PRK and RPB2, which have all proved useful in palm systematics. We compared the phylogenetic hypotheses resulting from the plastid versus nuclear datasets, and combined both datasets to retrieve as much phylogenetic information as possible. Our results strongly support a clade composed of all species of Archontophoenix, Actinokentia, Chambeyronia and Kentiopsis, but raise the question of whether Actinorhytis, the fifth genus, should remain in Archontophoenicinae. Interspecific relationships in ‘core Archontophoenicinae’ still remain incompletely resolved, despite the gene and taxon sampling being substantially greater than in previous studies, and question the monophyly of the New Caledonian genera Chambeyronia and Kentiopsis. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 469–481.     

Dynamic diversification history with rate upshifts in Holarctic bell‐flowers (Campanula and allies)

Campanula s.l. is one of the most speciose flowering plant lineages of the Holarctic (ca. 600 species). In the present study we sequenced three regions of the plastid genome (petD, rpl16 and trnK/matK) across a broad sample of Campanula s.l., which markedly improved phylogenetic resolution and statistical support compared to previous studies. Based on this robust phylogenetic hypothesis we estimated divergence times using BEAST, diversification rate shifts using Bayesian Analysis of Macroevolutionary Mixture (BAMM) and TreePar, and ancestral ranges using Biogeography with Bayesian (and likelihood) Evolutionary Analyses in R. Campanula s.l. is estimated to have originated during the Early Eocene but the major diversification events occurred between the Late Oligocene and Middle Miocene. Two upward diversification rate shifts were revealed by BAMM, specific to the crown nodes of two Campanula clades: CAM17, a mostly South European‐SW Asian lineage originating during the Middle Miocene and containing nearly half of all known Campanula species; and CAM15B, a SW Asian–Sino‐Himalayan lineage of nine species originating in the early Pleistocene. The dynamic diversification history of Campanula and the inferred rate shifts are discussed in a geo‐historical context.     

Phylogenetic signal in matK vs. trnK: a case study in early diverging eudicots (angiosperms)

The matK gene has been among the most useful loci for resolving plant phylogenetic relationships at different evolutionary time-scales, but much less is known about the phylogenetic utility of the flanking trnK intron, especially for deep level phylogenetics. We compared the relative performance of matK and trnK intron regions for resolving the relationships of the early diverging eudicots (angiosperms). The two regions display similar nucleotide compositions and distributions of rate variation among sites. The trnK intron sequences also provide similar levels of phylogenetic information per-site as matK. Combining the trnK intron sequences with matK increases overall bootstrap support for the early diverging eudicots compared to analyses of matK alone. MP, ML and Bayesian analyses provide strong support for eudicots, the sister group relationship of Ranunculales to remaining eudicots, and a Buxales+Trochodendraceae+core eudicots clade. matK and the trnK intron support conflicting positions for Buxales and Trochodendrales in relation to the core eudicots.     

A multi-locus plastid phylogenetic analysis of the pantropical genus Diospyros (Ebenaceae), with an emphasis on the radiation and biogeographic origins of the New Caledonian endemic species

We aimed to clarify phylogenetic relationships within the pantropical genus Diospyros (Ebenaceae sensu lato), and ascertain biogeographical patterns in the New Caledonian endemic species. We used DNA sequences from eight plastid regions (rbcL, atpB, matK, ndhF, trnK intron, trnL intron, trnL-trnF spacer, and trnS-trnG spacer) and included 149 accessions representing 119 Diospyros species in our analysis. Results from this study confirmed the monophyly of Diospyros with good support and provided a clearer picture of the relationships within the genus than in previous studies. Evidence from phylogenetic analyses suggests that Diospyros colonized New Caledonia multiple times. The four lineages of Diospyros in New Caledonia also differ in their degree of diversification. The molecular data indicate that one lineage is paleoendemic and derived from an ancient Australian species. The other three lineages are more closely related to several Southeast Asian species; two of them are neoendemics, and one has radiated rapidly and recently.     

Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales

The familial placements of Cyrtandromoea Zoll. and Wightia Wall., two small and enigmatic South‐East Asian genera, have long been controversial in Lamiales. Here we adopt a two‐step approach to resolve their phylogenetic relationships. We initially reconstructed a large‐scale phylogeny of Lamiales using six chloroplast markers (atpB, matK, ndhF, psbBTNH, rbcL, and rps4). The results showed that both Cyrtandromoea and Wightia emerged in the LMPO clade, including Lamiaceae, Mazaceae, Phrymaceae, Paulowniaceae, and Orobanchaceae. Based on the second set of six chloroplast markers (atpB, matK, ndhF, rbcL, rps16, and trnL‐F) and two nuclear ribosomal regions (external transcribed spacer and internal transcribed spacer) for the analyses focusing on the LMPO clade, our results revealed that Cyrtandromoea was consistently nested within Phrymaceae, whereas Wightia was supported as sister to Phrymaceae by the chloroplast DNA dataset or sister to Paulowniaceae by the nuclear ribosomal DNA dataset. Morphological and anatomical evidence fully supports the inclusion of Cyrtandromoea in Phrymaceae, and an updated tribal classification is done for Phrymaceae with five tribes, that is, Cyrtandromoeeae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Diplaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Leucocarpeae, Mimuleae, and Phrymeae. The conflicting phylogenetic position of Wightia indicated by different genome markers results in difficulty placing the genus in either Phrymaceae or Paulowniaceae. Considering the distinct morphological differences between Wightia and other families in the LMPO clade, we here propose a new family, Wightiaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, fam. nov., to accommodate it, which is the 26th family recognized in Lamiales.     

Differential diversifications of South American and Eastern Asian disjunct genera Bocconia and Macleaya (Papaveraceae)

Bocconia (10 species) and Macleaya (2 species) are two disjunct genera between South America and eastern Asia (EAS) in the Papaveraceae offering an opportunity to compare its biogeographic history with that of the well‐known disjunction between EAS and eastern North American (ENA). Our phylogenetic analyses of the chloroplast matK and rbcL gene sequences of Ranunculales including two species of Macleaya and six species of Bocconia supported the monophyly of Bocconia, Macleaya, and Chelidonioideae to which Bocconia and Macleaya belong. Nucleotide sequences of matK, rbcL, and nrDNA ITS supported the sister relationship of Bocconia and Macleaya. Biogeographic analyses of Chelidonioideae using S‐DIVA (statistical dispersal vicariance analysis) and DEC (dispersal extinction cladogenesis) methods inferred Eurasia as the most likely ancestral area of Bocconia and Macleaya and suggested no extinction events in either Bocconia or Macleaya. This agrees with the “Out‐of‐Asia” pattern of the EAS‐ENA disjunction. Molecular dating of Ranunculales with fossil‐based calibrations showed that Bocconia and Macleaya diverged in the late Eocene and early Oligocene, which is much earlier than most EAS‐ENA disjunct taxa. The disjunction may have formed via long distance dispersal or boreotropical connections via the North Atlantic and Bering land bridges. Both Bocconia and Macleaya diversified in the late mid‐Miocene, but Bocconia has apparently experienced a greater diversification probably aided by the evolution of the bird dispersal syndrome in fruit and seed after migration to South America. The greater diversification of Bocconia is also evidenced by the diverse leaf morphology and growth habit in response to colonization in various local habitats in South America.     

A molecular phylogeny and a revised classification of tribe Lepisoreae (Polypodiaceae) based on an analysis of four plastid DNA regions

Phylogenetic relationships within the palaeotropical tribe Lepisoroideae (Polypodiaceae) were investigated by studying sequence variation of four plastid DNA regions: rbcL, rps4 plus rps4‐trnS IGS, trnL intron plus trnL‐F IGS, rbcL‐atpB IGS plus part of atpB. In total, over 4000 nucleotides were sequenced for 39 species. Seven well‐supported clades were found in the analyses of the combined data set. We provide a new classification of Lepisoroideae by integrating phylogenetic results and known variation of morphological characters. The two small genera Neocheiropteris and Tricholepidium are supported as monophyletic, the genus Paragramma is resurrected and the genera Lepisorus, Neolepisorus, Lemmaphyllum and Lepidomicrosorium are re‐circumscribed. We proposed 14 new combinations, among which Caobangia is treated as a synonym of Lemmaphyllum. A key for identifying the recognized genera is presented. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 28–38.     

Phylogenetic analysis of the Malvadendrina clade (Malvaceae s.l.) based on plastid DNA sequences

Phylogenetic relationships within Malvaceae s.l., a clade that includes the traditional families Bombacaceae, Malvaceae s.str., Sterculiaceae, and Tiliaceae, have become greatly clarified thanks to recent molecular systematic research. In this paper, we use DNA sequences of four plastid regions (atpB, matK, ndhF, and rbcL) to study relationships within Malvadendrina, one of the two major clades of Malvaceae s.l. The four data sets were generally in agreement, but five terminal taxa manifested highly unexpected affinities in the rbcL partition, and the non-coding sequences of the trnK intron were found to provide limited phylogenetic information for resolving relationships at the base of Malvadendrina. The remaining data strongly support the existence of six major clades within Malvadendrina: Brownlowioideae, Dombeyoideae, Helicteroideae, Malvatheca (comprising Bombacoideae and Malvoideae), Sterculioideae, and Tilioideae. These data also resolve the placement of two problematic taxa: Nesogordonia (in Dombeyoideae) and Mortoniodendron (in Tilioideae). The relationships among the six clades are not definitively resolved, but the best-supported topology has Dombeyoideae as sister to the remainder of Malvadendrina (posterior probability PP=80%) and Sterculioideae as sister to Malvatheca (PP=86%). This early branching position of Dombeyoideae is supported by similarities in floral characters between members of that clade and outgroup taxa in Byttnerioideae. Similarly, the sister-group relationship of Sterculioideae and Malvatheca receives support from androecial characteristics, like subsessile or sessile anthers and an absence of staminodes, shared by these two clades.     

Diversification of lindsaeoid ferns and phylogenetic uncertainty of early polypod relationships

We analysed one nuclear gene (18S) and seven plastid markers [five protein coding (atpA, atpB, rbcL, rpoC1, rps4) and two non‐coding (trnH‐psbA, trnL‐trnF] for 31 members of Polypodiales and four outgroup taxa. We focused our sampling on the lindsaeoids and associated ferns in order to obtain a better understanding of the diversification of the early polypods. However, the exact phylogenetic position of Saccoloma and Cystodium remained uncertain. Based on relaxed molecular clock analyses, it appears that the crown group lindsaeoids diversified in the Caenozoic, more or less simultaneously with the main radiation of other Polypodiales, even though the original divergence between the lindsaeoid and non‐lindsaeoid polypods occurred before the end of the Jurassic. The current pantropical distribution of lindsaeoids can be explained by either long‐distance dispersal across the oceans or vicariance caused by the retreat of previously widely distributed tropical forests from higher to lower latitudes. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 489–503.     

Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

We first report the complete chloroplast (cp) genome of Fritillaria taipaiensis and determine its characteristics, sequence divergence and phylogenetic relationships by comparing it with complete cp genomes of Liliaceae s.l. (including e.g. Nartheciaceae, Amaryllidaceae and Asparagaceae) species obtained from NCBI Genbank. We show that the ycf1, ycf15 and infA genes have become pseudogenes or are lost in some of the seventeen Liliaceae species, and that dispersed repeats are prevailing among the four types of repeats (dispersed, palindromic, complement and tandem repeats). The number of simple sequence repeats ranged from 53 to 84 in the seventeen species, with mononucleotide repeats being the most abundant, followed by dinucleotides. A total of nine genes with positive selection sites were identified (atpB, atpE, ndhF, ndhH, petB, rpl2, rpl20, rpl22 and ycf2). Furthermore, we examined 19 mutational hotspot regions, including three coding regions (rps16, infA and rpl22) and sixteen non-coding regions. A phylogenetic analysis of the complete cp genomes and protein-coding sequences showed that Fritillaria is most closely related to Lilium. Moreover, Asparagus and Polygonatum, Hosta and Yucca are closely related to the Liliaceae. These results will contribute to further study of evolutionary patterns and phylogenetic relationships in Liliaceae s.l.     

Study of molecular genetic diversity and evolutionary history of medicinally important endangered genus Chlorophytum using DNA barcodes

This study was aimed to authenticate and present phylogenetic relationship among 19 species of genus Chlorophytum using DNA barcoding. In all, 107 accessions were analyzed with eight plastid (matK, rbcL, trnH-psbA, rpoC1, ycf5, rpoB, atp and psbK-psbI) and six nuclear (ITS) markers. The matK and rbcL were found to be ideal markers for identification and discrimination of Chlorophytum species. Phylogenetic analysis based on matK and rbcL sequences resolved the species in two major clades. All markers, except matK and rbcL, showed ambiguous reads and paralogy in analysis. DGGE analysis showed the presence of pseudogenes and/or co-amplification in these markers, which caused poor sequence quality. Phylogeny and probable evolution of genus Chlorophytum was proposed on the basis of cytological, morphological and genetic information.