Three groups of species in Petunia sensu Jussieu (Solanaceae) inferred from the intact seed

The intact seed surface morphology in 45 taxa of Petunia sensu Jussieu native to South America (Petunia sensu Wijsman plus Calibrachoa) was compared under scanning electron microscopy. The existence of three groups of species, differentiated in terms of seed morphology, was revealed as follows: (1) all species of Petunia sensu Wijsman, having coarse wavy middle lamellae and anticlinal walls; (2) Calibrachoa parviflora and C. pygmaea, having fine wavy middle lamellae embedded in straight anticlinal walls; and (3) the other species of Calibrachoa, having straight middle lamellae and anticlinal walls. Close relationships between seed morphology and the other characteristics observable in the groups of species are discussed.     

Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B

Phylogenetic analyses of partial phytochrome B (PHYB) nuclear DNA sequences provide unambiguous resolution of evolutionary relationships within Poaceae. Analysis of PHYB nucleotides from 51 taxa representing seven traditionally recognized subfamilies clearly distinguishes three early-diverging herbaceous "bambusoid" lineages. First and most basal are Anomochloa and Streptochaeta, second is Pharus, and third is Puelia. The remaining grasses occur in two principal, highly supported clades. The first comprises bambusoid, oryzoid, and pooid genera (the BOP clade); the second comprises panicoid, arundinoid, chloridoid, and centothecoid genera (the PACC clade). The PHYB phylogeny is the first nuclear gene tree to address comprehensively phylogenetic relationships among grasses. It corroborates several inferences made from chloroplast gene trees, including the PACC clade, and the basal position of the herbaceous bamboos Anomochloa, Streptochaeta, and Pharus. However, the clear resolution of the sister group relationship among bambusoids, oryzoids, and pooids in the PHYB tree is novel; the relationship is only weakly supported in ndhF trees and is nonexistent in rbcL and plastid restriction site trees. Nuclear PHYB data support Anomochlooideae, Pharoideae, Pooideae sensu lato, Oryzoideae, Panicoideae, and Chloridoideae, and concur in the polyphyly of both Arundinoideae and Bambusoideae.     

Molecular phylogeny of grouse: individual and combined performance of W-linked,autosomal, and mitochondrial loci

The phylogeny of grouse (Aves: Tetraoninae) was reconstructed using four noncoding loci: two were W-linked, one was autosomal, and one was the mitochondrial control region (CR). The rapidly evolving CR provided resolution throughout the tree, whereas the slowly evolving nuclear loci failed to resolve deeper nodes. The tree based on all four loci combined was almost identical to the CR tree and did not improve resolution or bootstrap support. The stemminess and imbalance of the trees were good determinants of the quality of the phylogenetic signal. The skewness of the tree score distribution (g(1)) behaved contrary to prediction; loci that had a more symmetric tree score distribution produced trees that had greater stemminess and balance. The quality of the phylogenetic signal was related to the evolutionary rate. Four clades of grouse were discovered. Two of these clades corresponded to currently recognized genera Bonasa and Lagopus. Bonasa was the sister to other grouse and Lagopus was the sister to the other two non-Bonasa clades. The third clade included Falcipennis, Tetrao, and Lyrurus. The fourth clade included the genera Centrocercus, Dendragapus, and Tympanuchus. The data support recognition of Falcipennis canadensis franklinii and Dendragapus obscurus fuliginosus as species.     

Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages

Phylogenetic studies based on different types and treatment of data provide substantially conflicting hypotheses of relationships among seed plants. We conducted phylogenetic analyses of sequences of two highly conserved chloroplast genes, psaA and psbB, for a comprehensive taxonomic sample of seed plants and land plants. Parsimony analyses of two different codon position partitions resulted in well-supported, but significantly conflicting, phylogenetic trees. First and second codon positions place angiosperms and gymnosperms as sister clades and Gnetales as sister to Pinaceae. Third positions place Gnetales as sister to all other seed plants. Maximum likelihood trees for the two partitions are also in conflict. Relationships among the main seed plant clades according to first and second positions are similar to those found in parsimony analysis for the same data, but the third position maximum likelihood tree is substantially different from the corresponding parsimony tree, although it agrees partially with the first and second position trees in placing Gnetales as the sister group of Pinaceae. Our results document high rate heterogeneity among lineages, which, together with the greater average rate of substitution for third positions, may reduce phylogenetic signal due to long-branch attraction in parsimony reconstructions. Whereas resolution of relationships among major seed plant clades remains pending, this study provides increased support for relationships within major seed plant clades.     

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.     

Phylogenetic congruence and discordance among one morphological and three molecular data sets from Pontederiaceae

A morphological data set and three sources of data from the chloroplast genome (two genes and a restriction site survey) were used to reconstruct the phylogenetic history of the pickerelweed family Pontederiaceae. The chloroplast data converged towards a single tree, presumably the true chloroplast phylogeny of the family. Unrooted trees estimated from each of the three chloroplast data sets were identical or extremely similar in shape to each other and mostly robustly supported. There was no evidence of significant heterogeneity among the data sets, and the few topological differences seen among unrooted trees from each chloroplast data set are probably artifacts of sampling error on short branches. Despite well-documented differences in rates of evolution for different characters in individual data sets, equally weighted parsimony permits accurate reconstructions of chloroplast relationships in Pontederiaceae. A separate morphology-based data set yielded trees that were very different from the chloroplast trees. Although there was substantial support from the morphological evidence for several major clades supported by chloroplast trees, most of the conflicting phylogenetic structure on the morphology trees was not robust. Nonetheless, several statistical tests of incongruence indicate significant heterogeneity between molecules and morphology. The source of this apparent incongruence appears to be a low ratio of phylogenetic signal to noise in the morphological data.     

The phylogeny of Schistidium (Bryophyta, Grimmiaceae) based on primary and secondary structure study of nuclear rDNA internal transcribed spacers

The phylogeny of Schistidium (Bryophyta, Grimmiaceae) was studied on the basis of nucleotide sequences of internal transcribed spacers ITS1-2 of nuclear DNA and trnT-trnD region of chloroplast DNA. The consistency of phylogenetic trees constructed from nuclear and chloroplast sequences was shown. A basal grade and two large clades were resolved on the phylogenetic trees. Morphological characteristics specific for these clades were described. ITS1 and ITS2 secondary structures of Schistidium species were modeled using thermodynamic criteria. Four different structures of the longest ITS1 hairpin were identified. Possible paths of Schistidium evolution were considered based on the four types of ITS1 secondary structure and phylogenetic trees.     

Nuclear DNA Content as an Index Character Discriminating Taxa in the Genus Petunia sensu Jussieu (Solanaceae)

Nuclear DNA contents over the total range of the genus Petuniasensu Jussieu comprising 20 taxa of Petunia sensu Wijsman (2n = 2 x = 14) and 32 taxa of Calibrachoa(2 n = 2 x = 18) wereestimated by flow cytometry after staining the nuclei with propidiumiodide (PI) or 4',6-diamidino-2-phenylindole (DAPI). With respectto nuclear DNA content, taxa of Petunia sensu Wijsman seemedto be homogeneous (2C = 2.60 to 3.41 pg), but Calibrachoa taxawere clearly separated into two groups: (1)C. parviflora andC. pygmaea(1.56 to 1.91 pg); and (2) remaining members of Calibrachoa(2.84to 3.26 pg). Taxa of Petunia sensu Wijsman exhibited largerPI/DAPI ratios (relative fluorescence intensity with PI stainingto that with DAPI staining) than Calibrachoa species exceptC.parviflora and C. pygmaea. This suggests that Petunia sensuWijsman has nuclear DNA with more adenine-thymine rich regionsthan Calibrachoa. Copyright 2000 Annals of Botany Company Calibrachoa, 4',6-diamidino-2-phenylindole (DAPI), flow cytometry, nuclear DNA content,Petunia , PI/DAPI ratio, propidium iodide (PI), Solanaceae     

Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae).

Quercus is one of the most abundant and economically important genera of woody plants in the Northern Hemisphere. To infer phylogenetic relationships within Quercus subgenus Quercus, chloroplast DNA (cpDNA) restriction sites and nucleotide sequences of the internal transcribed spacers (ITS) and the 5.8S coding region of the nuclear ribosomal DNA repeat were obtained for 44 individuals, including 25 species, intraspecific samples, and three outgroups. Separate parsimony analyses of each data set showed that individual gene trees were congruent and often complementary in supporting clades that generally corresponded to previously recognized taxonomic groups. Only one instance of strongly supported gene tree incongruence was detected and this anomalous pattern was explained best by ancient introgression of cpDNA across sectional boundaries. Simultaneous parsimony analysis of the pruned data sets supported the recognition of the strictly Eurasian section Cerris and resolved a novel hypothesis for the major infrageneric groups (Cerris- (Lobatae- (Protobalanus + Quercus sensu stricto))). The biogeographic hypothesis that all major oak lineages evolved locally at middle latitudes within the general distribution of their fossil ancestors was fully supported. This set of relationships also suggested a New World origin for the widespread white oaks of the Northern Hemisphere (section Quercus s. s.). For both data sets, inter- and intraspecific sampling within section Protobalanus showed little correspondence to morphological species. Greater cladistic structure among the samples was obtained by cpDNA restriction sites and two well-delimited plastomes types comprising a total of 15 distinct haplotypes were resolved. Haplotypes of 2 of the peripheral species in this species complex occupy terminal portions of one of the plastome clades, suggesting a more recent origin relative to those of more widespread species. The phylogeography of the two divergent plastome types suggested a north-south pattern, consistent with a Late Tertiary disjunction in the ancestral distribution of section Protobalanus.     

The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences

A phylogenetic study of Asteridae sensu lato was conducted based on chloroplast ndhF gene sequences for 116 ingroup and 13 outgroup species. Prior molecular studies based on rbcL sequences identified terminal groups corresponding to families, but were unable to resolve relationships among them. These results are largely consistent with earlier rbcL studies, but provide much greater resolution and stronger bootstrap support throughout the tree. The parsimony analysis found eight equally parsimonious trees, all of which recognize four major clades with the following relationship: (Cornales (Ericales (Euasterids I, Euasterids II))). Euasterids I includes (Garryales ((Solanales, Boraginaceae) (Gentianales, Lamiales))), although with weak support for relationships among the named clades. Euasterids II includes (Aquifoliales (Asterales (Apiales, Dipsacales))) with strong support for these relationships. Relationships within Ericales are weakly supported and merit further attention.     

基于广义形态学性状对木通科的分支系统学分析

基于43个广义的形态学性状,对木通科进行了分支系统学分析。经过简约性分析,得到了68个同等简约的分支树。50％多数规则一致树的分支结构与以前建立的族划分系统基本一致。外类群大血藤属与木通科的勃奎拉藤属形成姐妹群,与以前的分支分析结果一致,但在分子系统发育树中,大血藤属却是整个木通科的姐妹群;除此之外,形态分支树的结构与分子树的结构差别不大,但一致性指数、保持性指数和各分支内部支持率均较低。单型的猫儿屎族和串果藤族位于分支树的基部,拉氏藤族与木通族是姐妹群,在木通族内,长萼木通属和木通属是姐妹群,作为一个分支;另一分支是PHS（牛藤果属、八月瓜属和野木瓜属）复合群,牛藤果属位于八月瓜属和野木瓜属各类群的基部。但八月瓜属和野木瓜属的属内系统发育关系仍有待进一步研究。     

CHLOROPLAST DNA EVOLUTION AND PHYLOGENETIC RELATIONSHIPS IN CLARKIA SECT. PERIPETASMA (ONAGRACEAE)

Restriction-site analysis of chloroplast DNA in Clarkia sect. Peripetasma (Onagraceae) was done to test previously proposed phylogenetic models. One hundred nineteen restriction-site mutations were identified among the nine species using 29 restriction enzymes, and these were used to construct rooted most parsimonious trees (Wagner and Dollo). A chloroplast DNA evolutionary clock could not be statistically rejected. Branch points of this tree were statistically tested by Felsenstein's bootstrap method. This tree 1) provided an unambiguous and detailed genealogical history for the section, 2) verified a previous partial phylogenetic model for the section based on gene duplications and differential silencing, 3) provided details of the phylogenetic model not inferred or expected based on morphology and reproductive isolation, and 4) indicated that morphology evolves at markedly different rates within and between lineages in the section.     

Phylogenetic analysis of the genus <Emphasis Type="Italic">Petunia</Emphasis> (Solanaceae) based on the sequence of the <Emphasis Type="Italic">Hf1</Emphasis> gene

Polymerase chain reaction fragment length polymorphisms and nucleotide sequences for a cytochrome P450 gene encoding flavonoid-3',5'-hydroxylase, Hf1, were studied in 19 natural taxa of Petunia. Natural Petunia taxa were classified into six groups based on major insertion or deletion events that occurred only in intron II of the locus. The maximum parsimony method was used to calculate strict consensus trees based on nucleotide sequences in selected regions of the Hf1 locus. Petunia taxa were divided into two major clades in the phylogenetic trees. Petunia axillaris (including three subspecies), P. exserta, and P. occidentalis formed a clade with 100% bootstrap support. This clade is associated with a consistently inflexed pedicel, self-compatibility in most taxa, and geographical distribution in southern and western portions of the genus range. The other clade, which comprised the remainder of the genus is, however, less supported (up to 71% bootstrap); it is characterized by a deflexed pedicel in the fruiting state (except P. inflata), self-incompatibility, and a northeastern distribution. A nuclear gene, Hf1, seems to be a useful molecular marker for elucidating the phylogeny of the genus Petunia when compared with the nucleotide sequence of trnK intron of chloroplast DNA.     

Infrafamilial Phylogeny of the Aquatic Angiosperm Podostemaceae Inferred from the Nucleotide Sequences of the matK Gene

Abstract: The infrafamilial relationships of Podostemaceae were deduced from nucleotide sequences of the chloroplast matK gene. The matK phylogenetic analyses show that Podostemaceae are composed of two major clades that correspond to the subfamily Tristichoideae sensu stricto and Weddellina and the subfamily Podostemoideae. Weddellina, which has long been recognized as a member of the Tristichoideae, is sister to the Podostemoideae, supporting the classification that recognized a third subfamily Weddellinoideae. Malaccotristicha malayana and Terniopsis sessilis form a basal clade in Tristichoideae sensu stricto. Tristichoideae show a high morphological diversity and, surprisingly, a close relationship exists between Dalzellia zeylanica and Indotristicha ramosissima, which remarkably differ in their body plans. A few genera defined by particular characters, such as Synstylis and Torrenticola, merge into clades of other larger genera. The Podostemoideae taxa studied are composed of two American clades, an Asian-Australian clade and a Madagascan clade, and may suggest that the subfamily perhaps originated in America and migrated to the Old World.     

Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data

Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto . The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the β-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.     

DNA似近距离及进化时间的估算

在似近分析和Ｎｅｉ氏遗传距离的基础上,给出了ＤＮＡ似近距离计算公式,并以ＤＮＡ似近距离估算类群间的分歧时间（进化时间）,应用１０种限制内切酶对猕猴属（ｇｅｎｕｓ Ｍａｃａｃａ）内５个种ｍｔＤＮＡ的切点数据计算了这５个种的ＤＮＡ似近距离和进化时间,比较由ＤＮＡ似近距,遗传距离构建的歧化树和Ｆｏｏｄｅｎ及Ｄｅｌｓｏｎ的形态歧化树表明,除遗传距离的歧化树外,其它三种歧化树都有一个共同点,就是熊猴（Ｍ．ａ     

Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci

This study represents the first phylogenetic analysis of the molluscan class Polyplacophora using DNA sequence data. We employed DNA from a nuclear protein-coding gene (histone H3), two nuclear ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), one mitochondrial protein-coding gene (cytochrome c oxidase subunit I), and one mitochondrial ribosomal gene (16S rRNA). A series of analyses were performed on independent and combined data sets. All these analyses were executed using direct optimization with parsimony as the optimality criterion, and analyses were repeated for nine combinations of parameters affecting indel and transversion/transition cost ratios. Maximum likelihood was also explored for the combined molecular data set, also using the direct optimization method, with a model equivalent to GTR + I + Γ that accommodates gaps. The results of all nine parameter sets for the combined parsimony analysis of all molecular data (as well as ribosomal data) and the maximum-likelihood analysis of all molecular data support monophyly of Polyplacophora. The resulting topologies mostly agree with a division of Polyplacophora into two major lineages: Lepidopleuridae and Chitonida (sensu Sirenko 1993). In our analyses the genus Callochiton is positioned as the sister group to Lepidopleuridae, and not as sister group to the remaining Chitonida (sensu Buckland-Nicks & Hodgson 2000), nor as the sister group to the remaining Chitonina (sensu Buckland-Nicks 1995). Chitonida (excluding Callochiton) is monophyletic, but conventional subgroupings of Chitonida are not supported. Acanthochitonina (sensu Sirenko 1993) is paraphyletic, or alternatively monophyletic, and is split into two clades, both with abanal gills only and cupules in the egg hull, but one has simple cupules whereas the other has more strongly hexagonal cupules. Sister to the Acanthochitonina clades is Chitonina, including taxa with adanal gills and a spiny egg hull. Schizochiton, the only genus with adanal gills that has an egg hull with cupules, is the sister-taxon to one of the Acanthochitonina clades plus Chitonina, or alternatively basal to Chitonina. Support values for either position are low, leaving this relationship unsettled. Our results refute several aspects of conventional classifications of chitons that are based primarily on shell characters, reinforcing the idea that chiton classification should be revised using additional characters.     

Higher Level Phylogeny of Curculionidae (Coleoptera: Curculionoidea) based mainly on Larval Characters, with Special Reference to Broad-Nosed Weevils

A cladistic analysis of Curculionidae was performed using 49 characters (41 from larvae, three from pupae, and five from adults). Illustrations of characters of immatures are provided. The analysis involved 19 terminal units and a hypothetical ancestor determined by the outgroup comparison method used to root the tree. One most parsimonious cladogram was obtained based on the complete data set and the following phylogenetic hypothesis is proposed: Ithycerinae, Microcerinae, and Brachycrinae sensu stricto are broad-nosed weevils placed sequentially at the base of the cladogram. The remaining weevil subfamilies form two major natural groups: one constituted by the sister taxa Rhynchophorinae—Platypodinae; the other with Erirhininae at the base, as sister taxon of the "Curculionidae sensu stricto " which show an unresolved trichotomy involving Curculioninae, Cossoninae—Scolytinae, and the clade including the Entiminae and allied subfamilies. This latter clade of broad-nosed weevils has Thecesterninae at the base; the next branch is Amycterinae, the sister taxon of the clade comprising two groups: one constituted by Aterpinae, Rhytirrhininae, and Gonipterinae; the other is Entiminae whose units form two main clades: one constituted by the sister tribes Pachyrhynchini—Ectemnorhinini, and the other by Alophini, Sitonini, and Entimini. When the analysis was done using only immature characters, results congruent with those based on the complete data set were obtained, except for the placement of Erirhininae. According to the results the hypothesis of monophyly of broad-nosed weevils is not accepted; the Entiminae are justified as monophyletic and their natural classification into tribes is proposed and the phylogenetic position and relationships of higher taxa of Curculionidae are discussed. This paper shows the importance of immature characters in recognition of natural groups and relationships in Curculionidae.     

A molecular phylogeny of scaly tree ferns (Cyatheaceae)

Tree ferns recently were identified as the closest sister group to the hyperdiverse clade of ferns, the polypods. Although most of the 600 species of tree ferns are arborescent, the group encompasses a wide range of morphological variability, from diminutive members to the giant scaly tree ferns, Cyatheaceae. This well-known family comprises most of the tree fern diversity (～500 species) and is widespread in tropical, subtropical, and south temperate regions of the world. Here we investigate the phylogenetic relationships of scaly tree ferns based on DNA sequence data from five plastid regions (rbcL, rbcL-accD IGS, rbcL-atpB IGS, trnG-trnR, and trnL-trnF). A basal dichotomy resolves Sphaeropteris as sister to all other taxa and scale features support these two clades: Sphaeropteris has conform scales, whereas all other taxa have marginate scales. The marginate-scaled clade consists of a basal trichotomy, with the three groups here termed (1) Cyathea (including Cnemidaria, Hymenophyllopsis, Trichipteris), (2) Alsophila sensu stricto, and (3) Gymnosphaera (previously recognized as a section within Alsophila) + A. capensis. Scaly tree ferns display a wide range of indusial structures, and although indusium shape is homoplastic it does contain useful phylogenetic information that supports some of the larger clades recognised.