Multi-gene analysis provides a well-supported phylogeny of Rosales

Despite many attempts to resolve evolutionary relationships among the major clades of Rosales, some nodes have been extremely problematic and have remained unresolved. In this study, we use two nuclear and 10 plastid loci to infer phylogenetic relationships among all nine families of Rosales. Rosales were strongly supported as monophyletic; within Rosales all family relationships are well-supported with Rosaceae sister to all other members of the order. Remaining Rosales can be divided into two subclades: (1) Ulmaceae are sister to Cannabaceae plus (Urticaceae+Moraceae); (2) Rhamnaceae are sister to Elaeagnaceae plus (Barbeyaceae+Dirachmaceae). One noteworthy result is that we recover the first strong support for a sister relationship between the enigmatic Dirachmaceae and Barbeyaceae. These two small families have distinct morphologies and potential synapomorphies remain unclear. Future studies should try to identify nonDNA synapomorphies uniting Barbeyaceae with Dirachmaceae.     

A molecular phylogeny of celtidaceae and ulmaceae (Urticales) based onrbcL Nucleotide sequences

On the basis of 1,290 bp sequences of the chloroplast generbcL, a molecular phylogeny of seven of nine genera of the Celtidaceae and four of six genera of the Ulmaceae was produced. These data were analyzed together with some other urticalean genera using three methods (i.e., maximum parsimony, maximum likelihood, and neighbor joining methods). Maximum likelihood topology among 18 trees obtained indicated that the Urticales are monophyletic with its common clade splitting basally into two: one leading to a line comprisingAmpelocera (traditionally placed in Celtidaceae) and Ulmaceae, and the other leading to a line comprising the remaining genera of Celtidaceae, Moraceae, and other Urticales. Ulmaceae, to whichAmpelocera is a sister group, are monophyletic, as supported by many lines of morphological evidence. In contrast to Ulmaceae, the monophyly of Celtidaceae (excludingAmpelocera) was not supported, and resolution of relationships of Celtidaceae with other Urticales, as well as of those within the family, is left for future study.     

Gynoecial vascular anatomy and its systematic implications in Celtidaceae and Ulmaceae (Urticales)

Vasculature in the bicarpellate, pseudomonomerous gynoecium with two distinct styles is examined and compared in all of 15 genera of Celtidaceae and Ulmaceae (Urticales). Gynoecial vasculature is diversified in the families but consistet in a genus or a group of genera. Our observations corroborate the earlier suggestion that Ulmaceae (six genera) basically have three-bundled styles, while Celtidaceae (nine genera) always have one-bundled styles. Comparisons with other Urticales and with Eucommiaceae as an outgroup of Urticales indicate that Celtidaceae are more closely related to Moraceae in sharing one-bundled style (a synapomorphy), rather than to Ulmaceae. This supports a separation of Celtidaceae as a distinct family from Ulmaceaesensu lato. Based on the degree of fusion of major vascular bundles running in the gynoecium, we further distinguish three types of gynoecial vasculature in Ulmaceae and, likewise, three types in Celtidaceae, and discuss evolutionary trends of gynoecial vasculature as well as some generic relationships within the families.     

Book Reviews

Book reviewed in this article:
Plant Collectors in Madagascar and the Comoro islands , by Laurence J. Dorr.
Plant Life Histories: Ecology, Phylogeny and Evolution , edited by Jonathan Silvertown, Miguel Franco and John L. Harper.
Flore de la Polynésie Française. Vol. 1., Cannabaceae, Cecropiaceae, Euphorbiaceae, Moraceae, Piperaceae, Ulmaceae, Urticaceae , by Jacques Florence     

Circumscription of the Malvales and relationships to other Rosidae: evidence from rbcL sequence data

The order Malvales remains poorly circumscribed, despite its seemingly indisputable core constituents: Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae. We conducted a two-step parsimony analysis on 125 rbcL sequences to clarify the composition of Malvales, to determine the relationships of some controversial families, and to identify the placement of the Malvales within Rosidae. We sampled taxa that have been previously suggested to be within, or close to, Malvales (83 sequences), plus additional rosids (26 sequences) and nonrosid eudicots (16 sequences) to provide a broader framework for the analysis. The resulting trees strongly support the monophyly of the core malvalean families, listed above. In addition, these data serve to identify a broader group of taxa that are closely associated with the core families. This expanded malvalean clade is composed of four major subclades: (1) the core families (Bombacaceae, Malvaceae, Sterculiaceae, Tiliaceae); (2) Bixaceae, Cochlospermaceae, and Sphaerosepalaceae (Rhopalocarpaceae); (3) Thymelaeaceae sensu lato (s.l.); and (4) Cistaceae, Dipterocarpaceae s.l., Sarcolaenaceae (Chlaenaceae), and Muntingia. In addition, Neurada (Neuradaceae or Rosaceae) falls in the expanded malvalean clade but not clearly within any of the four major subclades. This expanded malvalean clade is sister to either the expanded capparalean clade of Rodman et al. or the sapindalean clade of Gadek et al. Members of Elaeocarpaceae, hypothesized by most authors as a sister group to the four core malvalean families, are shown to not fall close to these taxa. Also excluded as members of, or sister groups to, the expanded malvalean clade were the families Aextoxicaceae, Barbeyaceae, Cannabinaceae, Cecropiaceae, Dichapetalaceae, Elaeagnaceae, Euphorbiaceae s.l., Huaceae, Lecythidaceae, Moraceae s.l., Pandaceae, Plagiopteraceae, Rhamnaceae, Scytopetalaceae, Ulmaceae, and Urticaceae.     

Phylogenetic relationships of the enigmatic angiosperm family Podostemaceae inferred from 18S rDNA and rbcL sequence data

The phylogenetic relationships of some angiosperm families have remained enigmatic despite broad phylogenetic analyses of rbcL sequences. One example is the aquatic family Podostemaceae, the relationships of which have long been controversial because of major morphological modifications associated with their aquatic habit. Podostemaceae have variously been associated with Piperaceae, Nepenthaceae, Polygonaceae, Caryophyllaceae, Scrophulariaceae, Rosaceae, Crassulaceae, and Saxifragaceae. Two recent analyses of rbcL sequences suggest a possible sister-group relationship of Podostemaceae to Crassulaceae (Saxifragales). However, the branch leading to Podostemaceae was long, and use of different outgroups resulted in alternative placements. We explored the phylogenetic relationships of Podostemaceae using 18S rDNA sequences and a combined rbcL + 18S rDNA matrix representing over 250 angiosperms. In analyses based on 18S rDNA data, Podostemaceae are not characterized by a long branch; the family consistently appears as part of a Malpighiales clade that also includes Malpighiaceae, Turneraceae, Passifloraceae, Salicaceae, Euphorbiaceae, Violaceae, Linaceae, Chrysobalanaceae, Trigoniaceae, Humiriaceae, and Ochnaceae. Phylogenetic analyses based on a combined 18S rDNA + rbcL data set (223 ingroup taxa) with basal angiosperms as the outgroup also suggest that Podostemaceae are part of a Malpighiales clade. These searches swapped to completion, and the shortest trees showed enhanced resolution and increased internal support compared to those based on 18S rDNA or rbcL alone. However, when Gnetales are used as the outgroup, Podostemaceae appear with members of the nitrogen fixing clade (e.g., Elaeagnaceae, Ulmaceae, Rhamnaceae, Cannabaceae, Moraceae, and Urticaceae). None of the relationships suggested here for Podostemaceae receives strong bootstrap support. Our analyses indicate that Podostemaceae are not closely allied with Crassulaceae or with other members of the Saxifragales clade; their closest relatives, although still uncertain, appear to lie elsewhere in the rosids.     

Seed coat morphology and evolution in Celtidaceae and Ulmaceae (Urticales)

The seed coat surface morphology of Celtidaceae and Ulmaceae (Urticales) indicates a significant evolutionary diversity.Celtis, Chaetachme andPteroceltis (Celtidaceae) have a unique sculpturing with many crateriform holes; such holes occasionally sparsely occur in seeds ofAphananthe, Gironniera (Celtidaceae) andPlanera (Ulmaceae), but not in those of the nine remaining genera of the two families. The perforated seed coat further occurs in at least some genera of all other urticalean families. A pattern of its occurrence in families and genera suggest that the perforation represents a common archaic feature of all Urticales, rather than a feature derived many times independently within the order. The seed coat of Celtidaceae and Ulmaceae seems to have lately lost the holes probably by a neotenic evolution: one or more times within Celtidaceae, and one time in an ancestral line leading to all Ulmaceae. The derived reticulate seed coat surface sculpturing, which is shared byGironniera (Celtidaceae) and some Ulmaceae, is probably the result of parallel evolution. On the basis of evidence from seed coat morphology and other sources, close relationships ofLozanella, Parasponia andTrema within Celtidaceae, as well as variously distinct positions ofAmpelocera, Aphananthe andGironniera, are also discussed.     

THE MORPHOLOGY AND RELATIONSHIPS OF BARBEYA OLEOIDES

Barbeya, a monotypic genus of dioecious, arborescent dicotyledonous plants from northeast Africa and adjacent Arabia, is usually regarded as having affinities within the Urticales. It is placed either in the Ulmaceae or segregated as a closely related, monotypic family. Leaves are opposite, exstipulate, and vascularized by a single, crescent-shaped trace from a unilacunar node. Wood anatomy indicates specialization at about the same level as other Urticales. Sieve tube elements of the secondary phloem exhibit highly oblique, compound sieve plates which indicate a low level of evolutionary advancement. The vascularity of the flower is described and compared with other Urticales. Pollen is tricolporate. The relationships of the genus to Moraceae, Ulmaceae, Urticaceae, and Eucommiaceae are discussed. The totality of anatomical and morphological evidence supports the retention of the family Barbeyaceae.     

Vernation patterns in Celtidaceae and Ulmaceae (Urticales), and their evolutionary and systematic implications

In two associated families, Celtidaceae and Ulmaceae, vernation pattern (represented by spatial relationships between leaf lamina and stipules, the presence or absence of stipular fusion, lamina orientation, and lamina folding pattern) is consistent within a genus but shows a significant diversity within a family. Six vernation types are distinguishable and tentatively named: 1) Celtis type (Aphananthe, Celtis, Lozanella, Parasponia, Pteroceltis, Trema), 2) Chaetachme type (Chaetachme), 3) Gironniera type (Gironniera), 4) Holoptelea type (Ampelocera, Holoptelea, Phyllostylon), 5) Zelkova type (Hemiptelea, Planera, Zelkova), and 6) Ulmus type (Ulmus). The former three types (found in most of celtidaceous genera) possess free or fused stipules inside of the lamina; in contrast, the latter three types (found in all six ulmaceous genera andAmpelocera) are characterized by having the free stipules outside of the lamina. Within Celtidaceae, Celtis type is probably primitive in having free stipules and an ordinarily oriented lamina; Chaetachme type (with fused, convolute stipules and obliquely oriented laminas) and Gironniera type (with laterally oriented laminas) are the derived. Likewise, within Ulmaceae, both Zelkova and Ulmus types (with laterally oriented laminas) are the derived, while Holoptelea type (with ordinarily oriented laminas) is primitive. Comparisons in vernation pattern suggest the distinctness of Celtidaceae from Ulmaceae and the isolated position ofAmpelocera.     

Karyomorphology of some Moraceae and Cecropiaceae (Urticales)

The karyomorphology of 16 species in 13 genera representing Moraceae and Cecropiaceae was investigated in an effort to contribute to a better understanding of chromosome features and evolution in the families. All genera investigated have similar karyomorphology, but differences are found in (1) chromosome features of Interphase nucleus (simple, simple-complex, or complex chromocenter type), (2) basic chromosome number (x=13 or 14), (3) size variation (mono-or bimodial), and (4) frequencies of chromosomes with median centromeres (m-chromosome) (25–85%) and those with subterminal (or terminal) centromeres (st-chromosome) (14–69%). Comparisons with Ulmaceae as an outgroup of the remainder of Urticales suggest that the simple chromocenter type,x=14 comprising bothm- andst-chromosomes, and the monomodial karyotype are plesiomorphies in Moraceae and Cecropiaceae. Most of Moraceae and Cecropiaceae retain generalized chromosome features of the order, but have involved a few evolutionary changes in karyomorphology. Based on some detailed karyomorphological data, inter- and infrafamilial relationships are also briefly discussed.     

TheUlmaceae, one family or two? Evidence from chloroplast DNA restriction site mapping

The Ulmaceae is usually split into two subgroups, referred to as either tribes or more commonly subfamilies (Ulmoideae andCeltidoideae). The two groups are separated, with some exceptions, on the basis of leaf venation, fruit type, seed morphology, wood anatomy, palynology, chemistry, and chromosome number. Propositions to separate the two groups as distinct families have never gained general acceptance. Recent morphological and anatomical data have suggested, however, that not only is family status warranted but thatCeltidaceae are more closely related toMoraceae and otherUrticales than toUlmaceae. In order to test these alternative sets of relationships, restriction site mapping of the entire cpDNA was done with nine rare cutting enzymes using 11 genera ofUlmaceae s. l., three other families of theUrticales, and an outgroup family from theHamamelidae. Cladistic analysis of the data indicates thatUlmaceae s. l. is not monophyletic and that distinct families (Ulmaceae andCeltidaceae) are warranted; thatUlmaceae is the sister group toCeltidaceae plus all other families in the order; and thatCannabaceae might be nested withinCeltidaceae. Familial placements of various problematic genera (e.g.Ampelocera, Aphananthe) are resolved and character evolution of key morphological, anatomical, chemical, and chromosomal features are discussed.     

Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids

Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an “expanded” malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.     

Ancestral State Reconstruction Reveals Rampant Homoplasy of Diagnostic Morphological Characters in Urticaceae,Conflicting with Current Classification Schemes

Urticaceae is a family with more than 2000 species, which contains remarkable morphological diversity. It has undergone many taxonomic reorganizations, and is currently the subject of further systematic studies. To gain more resolution in systematic studies and to better understand the general patterns of character evolution in Urticaceae, based on our previous phylogeny including 169 accessions comprising 122 species across 47 Urticaceae genera, we examined 19 diagnostic characters, and analysed these employing both maximum-parsimony and maximum-likelihood approaches. Our results revealed that 16 characters exhibited multiple state changes within the family, with ten exhibiting >eight changes and three exhibiting between 28 and 40. Morphological synapomorphies were identified for many clades, but the diagnostic value of these was often limited due to reversals within the clade and/or homoplasies elsewhere. Recognition of the four clades comprising the family at subfamily level can be supported by a small number carefully chosen defining traits for each. Several non-monophyletic genera appear to be defined only by characters that are plesiomorphic within their clades, and more detailed work would be valuable to find defining traits for monophyletic clades within these. Some character evolution may be attributed to adaptive evolution in Urticaceae due to shifts in habitat or vegetation type. This study demonstrated the value of using phylogeny to trace character evolution, and determine the relative importance of morphological traits for classification.     

Karyomorphology and relationships of Celtidaceae and Ulmaceae (Urticales)

Based on karyomorphological features, six (examined in this study) of nine genera of Celtidaceae are divided into three groups: 1)Celtis, Parasponia, Pteroceltis andTrema; 2)Aphananthe; 3)Gironniera, and six genera of Ulmaceae into two: 1)Holoptelea andPhyllostylon; 2)Hemiptelea, Planera, Ulmus andZelkova. The first four genera share the simple chromocenter type at the resting stage andx-10, with all chromosomes with submedian or median centromeres (frequency of chromosomes with subterminal or terminal centromeres 0%, although uncertain inTrema).Aphananthe hasx=13, but resembles the above four genera in other features.Gironniera is distinct from all other Celtidaceae in having the diffuse-complex chromocenter type andx=14, features which occur in Ulmaceae. InGironniera the frequency of chromosomes with subterminal or terminal centromeres is 43%, a proportion similar to those inHoloptelea (36%) andPhyllostylon (58%) of Ulmaceae. All six genera of Ulmaceae havex=14, yetHemiptelea, Planera, Ulmus andZelkova are distinct fromHoloptelea andPhyllostylon (with the simple chromocenter type) in having the diffuse-complex chromocenter type and in predominantly possessing chromosomes with subterminal or terminal centromeres (93%). Evidence from karyomorphology, as well as from other sources, suggests 1) thatAphananthe (x=13) is most distantly related to all genera withx=10 within Celtidaceae, 2) thatGironniera may have a key role for understanding evolutionary relationships between Celtidaceae and Ulmaceae, and 3) thatHoloptelea andPhyllostylon represent derivatives of a line that diverged early from a common ancestor or all Ulmaceae. On the basis of comparisons with other Urticales and the putative outgroups of the order, it is also suggested that the chromosome morphology of Ulmaceae represents the more derived state in Urticales.     

Craniodental characters and the relationships of Procyonidae (Mammalia: Carnivora)

Recent phylogenies of Procyonidae based on molecular data differ significantly from previous morphology‐based phylogenies in all generic sister taxon relationships. I have compiled the most comprehensive dataset of craniodental morphology that incorporates previous morphological characters, and with the aid of high‐resolution X‐ray computed tomography, new characters. This expanded craniodental analysis is based on 78 characters and yields new phylogenetic results regarding the ingroup relationships of Procyonidae. These results include Bassariscus astutus as the least derived member of Procyonidae and Ailurus fulgens nested well within the clade. Additionally, there are some similarities to previous morphological analyses of Procyonidae. Although the characters used to unite and diagnose Procyonidae vary depending on the phylogenetic analysis and have ambiguous taxonomic distribution amongst both Procyonidae and Musteloidea, there is significant morphological support for clades within Procyonidae. In addition to the strength of the morphological support within the clade, the disparate topographical regions of the skull from which the characters are derived may indicate that these synapomorphies are indeed the result of homology rather than adaptive convergence, as suggested by analyses based on molecular data. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 669–713.     

The utility of trnK intron 5′ region in phylogenetic analysis of Ulmaceae s. l.

The sequences of chloroplast trn K intron 5' region were determined for seven genera of Ulmaceae s.l. ( 12 species), two genera of Cannabaceae, two of Moraceae and one genus from each of the three families, i.e. , Urticaceae, Eucommiaceae and Malvaceae. The aligned sequences used in PAUP analyses were 805 bp, and the maximum parsimony analysis resulted in a single most parsimonious tree with tree length = 665, CI = 0.7714 and RI = 0.7965. The topology of the tree is relatively strongly supported by the bootstrap test and congruent with those generated from rbc L sequence analysis and cpDNA restriction site analysis. The phylogenetic tree indicated that Ulmaceae s. l. is polyphyletic, and that the monophyletic Ulmaceae s. str. is sister to the other Urticales taxa. Cannabaceae, represented by Humulus and Cannabis, is nested within Celtidaceae, revealing that Celtidaceae is a paraphyletic group. Gironniera and Aphananthe are both clades of Celtidaceae. 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The phylogenetic relationships of the suborder Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence

Fragments of 12S and 16S mitochondrial DNA genes were sequenced for 14 acanthuroid taxa (representing all six families) and seven outgroup taxa. The combined data set contained 1399 bp after removal of all ambiguously aligned positions. Examination of site saturation indicated that loop regions of both genes are saturated for transitions, which led to a weighted parsimony analysis of the data set. The resulting tree topology generally agreed with previous morphological hypotheses, most notably placing the Luvaridae within the Acanthuroidei, but it also differed in several areas. The putative sister group of Acanthuroidei, Drepane, was recovered within the suborder, and the sister group of the family Acanthuridae, Zanclus, was likewise recovered within the family. Morphological characters were included to produce a combined data set of 1585 characters for 14 acanthuroid taxa and a single outgroup taxon. An analysis of the same 15 taxa was performed with only the DNA data for comparison. The total-evidence analysis supports the monophyly of the Acanthuridae. A parametric bootstrap suggests the possibility that the paraphyly of Acanthuridae indicated by the molecular analyses is the result of long-branch attraction. The disagreement between molecular and morphological data on the relationships of the basal acanthuroids and its putative sister taxon is unresolved.     

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.