Molecular Evolution and Phylogenetic Utility of the Chloroplastrpl16Intron inChusqueaand the Bambusoideae (Poaceae)

Phylogenetic relationships withinChusquea,a diverse genus of neotropical woody bamboos, and among selected members of the Bambusoideae were explored usingrpl16intron sequence data from the chloroplast genome. Mechanisms of mutation, including slipped-strand mispairing, secondary structure, minute inversions, and base substitutions, were examined within therpl16intron, and their effects on sequence alignment and phylogenetic analysis were investigated. Thirty-five bamboo sequences were generated and two separate matrices were analyzed using maximum parsimony. In the first, 23 sequences fromChusquea,1 ofNeurolepis,and 3 outgroups were included.Neurolepiswas supported as sister toChusquea, Chusqueawas strongly supported as a monophyletic lineage, and three species ofChusqueasubg.Rettbergiawere resolved as the most basal clade within the genus. In the second analysis, 15 sequences, 14 from across the subfamily and 1 outgroup, were included. A Bambusoideae clade was recovered with the Olyreae/Parianeae (herbaceous bamboos) and the Bambuseae (woody bamboos) each supported as monophyletic. Two clades corresponding to temperate and tropical woody bamboos were derived within the Bambuseae and the tropical taxa were further split into New World and Old World clades. Therpl16intron in bamboos was found to be susceptible to frequent length mutations of multiple origins, nonindependent character evolution, and regions of high mutability, all of which created difficulties in alignment and phylogenetic analysis; nonetheless therpl16intron is phylogenetically informative at the inter- and intrageneric levels in bamboos.     

Systematic positions of Lamiophiomis and Paraphlomis (Lamiaceae) based on nuclear and chloroplast sequences

Genera Lamiophlomis and Paraphlomis were originally separated from genus Phlomis s.l. on the basis of particular morphological characteristics. However, their relationship was highly contentious, as evidenced by the literature. In the present paper, the systematic positions of Lamiophlomis, Paraphlomis, and their related genera were assessed based on nuclear internal transcribed spacer (ITS) and chloroplast rpl16 and trnL-F sequence data using maximum parsimony (MP) and Bayesian methods. In total, 24 species representing six genera of the ingroup and outgroup were sampled. Analyses of both separate and combined sequence data were conducted to resolve the systematic relationships of these genera. The results reveal that Lamiophlomis is nested within Phlomis sect. Phlomoides and its genetic status is not supported. With the inclusion of Lamiophlomis rotata in sect. Phlomoides, sections Phlomis and Phlomoides of Phlomis were resolved as monophyletic. Paraphlomis was supported as an inde-pendent genus. However, the resolution of its monophyly conflicted between MP and Bayesian analyses, suggesting the need for expended sampling and further evidence.     

Phylogenetic relationships in Myrceugenia (Myrtaceae) based on plastid and nuclear DNA sequences

Myrceugenia is a genus endemic to South America with a disjunct distribution: 12 species occurring mainly in central Chile and approximately 25 in southeastern Brazil. Relationships are reconstructed within Myrceugenia from four plastid markers (partial trnK-matK, rpl32-trnL, trnQ-5'rps16 and rpl16) and two ribosomal nuclear regions (ETS and ITS) using maximum parsimony and Bayesian analyses. Relationships inferred previously from morphological data are not completely consistent with those from molecular data. All molecular analyses support the hypothesis that Myrceugenia is monophyletic, except for M. fernadeziana that falls outside the genus. Chilean species and Brazilian species form two separate lineages. Chilean species form three early diverging clades, whereas Brazilian species are a strongly supported monophyletic group in a terminal position. Least average evolutionary divergence, low resolution, short branches, and high species diversity found in the Brazilian clade suggest rapid radiation. Geographical distributions and phylogenetic reconstructions suggest that extant Myrceugenia species arose in northern Chile followed by colonization southward and finally to the Juan Fernández Islands and southeastern Brazil.     

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.     

Phylogeny of Camellia sects Longipedicellata,Chrysantha and Longissima (Theaceae) Based on Sequence Data of Four Chloroplast DNA Loci

We focused on the systematic positions and relationships of three sections of Camellia subgenThea of Theaceae, i.e., sect.Longipedicellata, sect.Chrysantha (golden camellias) and sect.Longissima by using four chloroplast DNA regions (rpl16, psbA trnH, trnL F & rpl32 trnL). We sampled 28 species representing four subgenus, 11 sections in Camellia and two outgroups. Combined analyses of chloroplast DNA sequence data sets are performed with the neighbor joining, maximum parsimony and Bayesian inference methods, and the gene trees are constructed. The topologies of gene trees revealed that: 1) sect. Chrysantha is paraphyletic or polyphyletic, containing three parallel lineages and Camellia longipedicellata (type of sectLongipedicellata) nested inside; 2) all four species from Vietnam, together with C. longipedicellata, forming a well supported monophyletic clade, which implies the close relationship between sect. Longipedicellata and sect.Chrysantha; and 3) sectLongissima is not monophyletic because C.hekouensis is the sister to the rest of Camellia species. The systematic position of C.longissima and the relationship between sect.Longissima and sect.Longipedicellata are unsolved.     

基于叶绿体四个DNA 片段联合分析探讨山茶属长柄山茶组、金花茶组和超长柄茶组的系统位置与亲缘关系

为探讨山茶属茶亚属 (Camellia subgenThea) 中长柄山茶组 (sectLongipedicellata)、金花茶组 (sectChrysantha)和超长柄茶组 (sectLongissima) 的系统位置和亲缘关系,本研究选取了该属4个亚属11组28个种及2个外类群的材料,对这些材料的叶绿体4个DNA片段 (rpl16、psbA trnH、trnL F和rpl32 trnL) 进行了测序,运用邻接法 (neighbor joining)、最大简约法 (maximum parsimony) 和贝叶斯推断 (Bayesian inference) 对获得的序列进行了联合矩阵分析,并构建基因树。基因树的拓扑结构显示：1) 金花茶组包括3个平行的支系,并且长柄山茶组的模式种长柄山茶 (Camellia longipedicellata) 嵌于其中一个支系,因而金花茶组可能是一个并系或多系类群;2) 长柄山茶与越南分布的金花茶组种类在分子系统树上构成一个单系支,暗示了长柄山茶组和金花茶组之间可能具有紧密的亲缘关系;3) 超长柄茶组不是一个单系类群,该组的河口超长柄茶 (C. hekouensis) 位于系统树的基部,与山茶属其余种构成姐妹群。由于缺乏更广泛取样的分析,超长柄茶在山茶属中的系统位置仍然不明确,超长柄茶组与长柄山茶组的亲缘关系问题也没有得到解决。     

Molecular phylogeny of the arthrostylidioid bamboos (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) and new genus Didymogonyx

We present the first multi-locus chloroplast phylogeny of Arthrostylidiinae, a subtribe of neotropical woody bamboos. The morphological diversity of Arthrostylidiinae makes its taxonomy difficult and prior molecular analyses of bamboos have lacked breadth of sampling within the subtribe, leaving internal relationships uncertain. We sampled 51 taxa, chosen to span the range of taxonomic diversity and morphology, and analyzed a combined chloroplast DNA dataset with six chloroplast regions: ndhF, trnD-trnT, trnC-rpoB, rps16-trnQ, trnT-trnL, and rpl16. A consensus of maximum parsimony and Bayesian inference analyses reveals monophyly of the Arthrostylidiinae and four moderately supported lineages within it. Six previously recognized genera were monophyletic, three polyphyletic, and two monotypic; Rhipidocladum sect. Didymogonyx is here raised to generic status. When mapped onto our topology, many of the morphological characters show homoplasy.     

Molecular phylogeny of the plant bugs (Heteroptera: Miridae) and the evolution of feeding habits

The first comprehensive cladistic analysis of Miridae, the plant bugs, is presented based on analysis of 3935 base pairs of mitochondrial (16S, COI) and nuclear (18S, 28SD3) DNA for 91 taxa in seven subfamilies. Data were analysed using maximum likelihood (ML), parsimony and Bayesian inference (BI) phylogenetic frameworks. The phylogenetic results are compared with previous hypotheses of higher relationships in the family using alternative hypothesis tests. A Bayesian relaxed molecular clock is used to examine divergence times, and ancestral feeding habits are reconstructed using parsimony and a Bayesian approach. Clades recovered in all analyses are as follows: Cimicomorpha, Miroidea and Miridae; Bryocorinae: Bryocorini; Stenodemini; Mirinae; Deraeocorinae (Clevinemini + Deraeocorini); Cylapinae; Isometopinae; Bryocorinae: Dicyphini; Orthotylini; Phylinae (Phylini + Pilophorini), and Phylinae as sister group to all the remaining mirid taxa. These results are largely congruent with former hypotheses based on morphological data with respect to the monophyly of various subfamilies and tribes; however, our results indicate that the subfamily Bryocorinae is not monophyletic, as the two tribes, Dicypini and Bryocorini, were separated in the phylogenetic results. Divergence time estimates indicate that the radiation of the Miridae began in the Permian; most genus‐level radiations within subfamilies began in the late Cretaceous, probably in response to the angiosperm radiation. Ancestral feeding state reconstructions based on Bayesian and parsimony inference were largely congruent and both reconstructed phytophagy as the ancestral state of the Miridae. Furthermore, the feeding habits of the common ancestors of Mirinae + Deraeocorinae, Bryocorinae + Cylapinae + Isometopinae + Orthotylinae, and the remaining taxa excluding Phylinae, were inferred as phytophagous. Therefore, at least three shifts from phytophagy or polyphagy to predation occurred within the Miridae. Additionally, based on the mirid host‐plant records, we discovered several trends, such as a strong relationship between host‐plant ranges and a facultative feeding habit. © The Willi Hennig Society 2011.     

Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data

DNA sequence data from the chloroplast noncoding rpl16 intron are used to address phylogenetic relationships among the major lineages of the grass family, with particular emphasis on the highly heterogeneous subfamily Bambusoideae and the basal lineages. Thirty-five grass sequences representing all six currently recognized major groups of the family and one outgroup sequence were analyzed using both parsimony and distance methods. The phylogenetic analyses indicated: (1) Puelia, a traditionally isolated bambusoid genus, is the most basal lineage in the BOP clade (Bambusoideae, Oryzoideae, and Pooideae); (2) the bambusoid clade is a sister group to the pooid clade; and (3) the monophyletic oryzoid clade is well separated from the bambusoid clade. The study further confirmed the recognition of two primary groups in the grass family: the BOP clade and the PACC clade (Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae); it also provided further evidence that the traditional subfamily Bambusoideae is highly heterogeneous and phylogenetically unacceptable. The data support Streptochaeteae, Anomochloeae, and Phareae as the most basal lineages among the extant grasses. Within the BOP clade, oryzoids and pooids are confirmed as two monophyletic clades, but the bambusoid clade, including only the woody bamboo tribe Bambuseae and the herbaceous bamboo tribe Olyreae, is relatively weakly supported. The study also indicated that the chloroplast noncoding region sequence data could be useful in phylogenetic analysis at relatively high taxonomic levels.     

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A>T, C>G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA.     

Molecular phylogenetic evidence for the monophyly of Fritillaria and Lilium (Liliaceae; Liliales) and the infrageneric classification of Fritillaria

We present phylogenetic analyses of 37 taxa of Fritillaria (Liliaceae), 15 species of Lilium, and several outgroup taxa from Liliaceae s.s. to investigate the generic delimitation of Fritillaria in relation to Lilium as well as infrageneric relationships within Fritillaria. We used DNA sequences from the maturase-coding plastid matK gene and the trnK intron, the intron of the ribosomal protein-coding rpl16 plastid gene, and the nuclear ribosomal internal transcribed spacers (ITS). Phylogenetic analysis using maximum parsimony defined Fritillaria and Lilium (the latter including Nomocharis) as sister taxa. Fritillaria sections Fritillaria and Liliorhiza are supported in part, and some of the most enigmatic species usually included in Fritillaria (sections Petilium and Theresia and the monotypic genus Korolkowia) are closely related. The results support the new classification of Fritillaria proposed by Rix. We postulate independent origins of the underground bulbils found in Fritillaria davidii and the remainder of subgenus Liliorhiza.     

Tribal and intergeneric relationships of Mesechiteae (Apocynoideae, Apocynaceae): evidence from three noncoding plastid DNA regions and morphology

The Neotropical tribe Mesechiteae (Apocynaceae) is currently considered to include nine genera: Allomarkgrafia, Galactophora, Macrosiphonia, Mandevilla, Mesechites, Quiotania, Secondatia, Telosiphonia, and Tintinnabularia. Tribal and intergeneric relationships, however, are in dispute. To test the monophyly of the tribe and evaluate intratribal relationships, a maximum parsimony analysis was conducted based on DNA sequences from the plastid rpl16 intron, rps16 intron, and trnS-G intergenic spacer region as well as morphological data for 23 taxa of Mesechiteae and 11 taxa from other tribes of Apocynoideae. Mesechiteae, as currently circumscribed, was found to be polyphyletic. Only removal of Secondatia and Galactophora and inclusion of Forsteronia rendered the tribe monophyletic. Thus defined, Mesechiteae forms a strongly supported clade including seven genera in three subclades: the Mesechites subclade (comprising Tintinnabularia, Allomarkgrafia, and Mesechites), the Forsteronia subclade (containing only Forsteronia) and the Mandevilla subclade (comprising Macrosiphonia, Mandevilla, and Telosiphonia). Allomarkgrafia is nested in Mesechites. Macrosiphonia and Telosiphonia form two distinct monophyletic clades. Both, however, are nested in Mandevilla. Results suggest upholding the following genera in Mesechiteae: Allomarkgrafia, Forsteronia, Mandevilla, Mesechites, and Tintinnabularia. The status of Quiotania could not be evaluated.     

A molecular phylogenetic study of Graptopetalum (Crassulaceae) based on ETS, ITS, RPL16, and TRNL-F nucleotide sequences

Nuclear ETS and ITS, as well as plastid rpl16 and trnL-F DNA sequences were used to determine relationships among species of Graptopetalum (Crassulaceae) and closely related genera. Graptopetalum is member of a group of taxa restricted to North America, one of the centers of diversity of Crassulaceae; however, their phylogenetic relationships are not yet understood. Nineteen species of Graptopetalum and 24 species from nine other genera of Crassulaceae were sampled for use in three separate parsimony analyses: ITS alone, ETS alone, and a combined nuclear + plastid DNA analysis using all four gene regions. The ETS data set had the highest number of parsimony-informative sites, about 30% more than in ITS, but the most fully resolved tree resulted when the four DNA regions were combined. Only four subclades of the tree received moderate to strong bootstrap support, one of which includes all species of Graptopetalum having a single whorl of stamens. However, Graptopetalum is not monophyletic. Instead, Tacitus bellus and select species of Cremnophila, Sedum, and Echeveria are interspersed among species of Graptopetalum and show evidence of grouping according to geographical range of distribution more so than habit or floral morphology.     

Novel relationships among hyloid frogs inferred from 12S and 16S mitochondrial DNA sequences

Advanced frogs (Neobatrachia) are usually divided into two taxa, Ranoidea (the firmisternal frogs) and Hyloidea (all other neobatrachians). We investigated phylogenetic relationships among several groups of Hyloidea using 12S and 16S rRNA mitochondrial gene sequences and tested explicit relationships of certain problematic hyloid taxa using a sample of 93 neobatrachians. Parsimony, maximum likelihood, and Bayesian inference methods suggest that both the Ranoidea and Hyloidea are well-supported monophyletic groups. We reject three hypotheses using parametric bootstrap simulation: (1) Dendrobatidae lies within the Ranoidea; (2) The group containing Hylidae, Pseudidae, and Centrolenidae is monophyletic; and (3) Brachycephalus is part of Bufonidae.     

An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference

The objective of this study was to obtain a quantitative assessment of the monophyly of morning glory taxa, specifically the genus Ipomoea and the tribe Argyreieae. Previous systematic studies of morning glories intimated the paraphyly of Ipomoea by suggesting that the genera within the tribe Argyreieae are derived from within Ipomoea; however, no quantitative estimates of statistical support were developed to address these questions. We applied a Bayesian analysis to provide quantitative estimates of monophyly in an investigation of morning glory relationships using DNA sequence data. We also explored various approaches for examining convergence of the Markov chain Monte Carlo (MCMC) simulation of the Bayesian analysis by running 18 separate analyses varying in length. We found convergence of the important components of the phylogenetic model (the tree with the maximum posterior probability, branch lengths, the parameter values from the DNA substitution model, and the posterior probabilities for clade support) for these data after one million generations of the MCMC simulations. In the process, we identified a run where the parameter values obtained were often outside the range of values obtained from the other runs, suggesting an aberrant result. In addition, we compared the Bayesian method of phylogenetic analysis to maximum likelihood and maximum parsimony. The results from the Bayesian analysis and the maximum likelihood analysis were similar for topology, branch lengths, and parameters of the DNA substitution model. Topologies also were similar in the comparison between the Bayesian analysis and maximum parsimony, although the posterior probabilities and the bootstrap proportions exhibited some striking differences. In a Bayesian analysis of three data sets (ITS sequences, waxy sequences, and ITS + waxy sequences) no supoort for the monophyly of the genus Ipomoea, or for the tribe Argyreieae, was observed, with the estimate of the probability of the monophyly of these taxa being less than 3.4 x 10(-7).     

Phylogenetic relationship among Libellula, Ladona and Plathemis (Odonata: Libellulidae) based on DNA sequence of mitochondrial 16S rRNA gene

Abstract. The type genus for the dragonfly family Libellulidae is Libellula. At present, Libellula s.l. includes twenty-nine species, whose distribution is largely Nearctic. Whether two other libellulid taxa, Ladona and Plathemis, should be considered synonyms of Libellula, subgenera of Libellula, or separate genera, has been a subject of intermittent debate for over a century. Earlier proposals concerning Ladona and Plathemis were based on a limited number of morphological characters and lacked rigorous phylogenetic analyses. Therefore, we used the DNA sequence of a portion of the mitochondrial 16S rRNA gene and parsimony, maximum likelihood and neighbour-joining analyses to explore whether Ladona and Plathemis are monophyletic lineages distinct from Libellula. We obtained ≈ 415 bp of DNA sequence from twenty-three taxa including thirteen species of Libellula s.s., all three recognized species of Ladona, the two species of Plathemis and representatives of four other libellulid genera. Tetragoneuria williamsoni (Odonata: Corduliidae) was included as the outgroup. Parsimony analysis suggested that Ladona and Plathemis are monophyletic lineages distinct from Libellula s.s. with a sister group relationship between Libellula and Ladona. The monophyly of Ladona, Plathemis and Libellula was supported in > 90% of bootstrap replications and in trees five to ten steps longer than the most parsimonious trees. Relationships inferred from maximum likelihood and neighbour-joining analyses also supported the monophyly of Ladona and Plathemis. The four other libellulid genera included in the study formed a monophyletic clade distinct from Libellula, Ladona and Plathemis. Based on our analysis, we propose that Ladona and Plathemis be considered either genera or subgenera within Libellulidae.     

A molecular phylogenetic study of the subtribe Glycininae (Leguminosae) derived from the chloroplast DNA rps16 intron sequences

Phylogenetic relationships among 13 genera of the subtribe Glycininae, two genera of the allied subtribe Diocleinae that were included within Glycininae by Polhill, and two genera of the subtribe Erythrininae as outgroups were inferred from chloroplast DNA rps16 intron sequence variation. Pairwise sequence divergence values ranged from identity between Teramnus mollis and T. micans and between T. flexilis and T. labialis to 7.89% between Pueraria wallichii and Pseudeminia comosa across all accessions. Phylogenies estimated using parsimony and neighbor-joining methods revealed that (1) Glycininae is monophyletic if Pachyrhizus and Calopogonium (both Diocleinae) are included within Glycininae; (2) the genus Teramnus is closely related to Glycine, and Amphicarpaea showed a sister relationship to the clade comprising Teramnus and Glycine; (3) the expanded Glycininae including two genera of Diocleinae is divided into three branches, temporarily named I (comprising the rest of the examined taxa), II (Pueraria wallichii), and III (Mastersia), but their relationships are equivocal; and (4) the genus Pueraria, regarded as a closely related genus to Glycine, is not monophyletic and should be divided into at least four genera (a hypothesis supported previously by Lackey).     

The phylogeny and classification of Embioptera (Insecta)

A phylogenetic analysis of the order Embioptera is presented with a revised classification based on results of the analysis. Eighty‐two species of Embioptera are included from all families except Paedembiidae Ross and Embonychidae Navás. Monophyly of each of the eight remaining currently recognized families is tested except Andesembiidae Ross, for which only a single species was included. Nine outgroup taxa are included from Blattaria, Grylloblattaria, Mantodea, Mantophasmatodea, Orthoptera, Phasmida and Plecoptera. Ninety‐six morphological characters were analysed along with DNA sequence data from the five genes 16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase I and histone III. Data were analysed in combined analyses of all data using parsimony and Bayesian optimality criteria, and combined molecular data were analysed using maximum likelihood. Several major conclusions about Embioptera relationships and classification are based on interpretation of these analyses. Of eight families for which monophyly was tested, four were found to be monophyletic under each optimality criterion: Clothodidae Davis, Anisembiidae Davis, Oligotomidae Enderlein and Teratembiidae Krauss. Australembiidae Ross was not recovered as monophyletic in the likelihood analysis in which one Australembia Ross species was recovered in a position distant from other australembiids. This analysis included only molecular data and the topology was not strongly supported. Given this, and because parsimony and the Bayesian analyses recovered a strongly supported clade including all Australembiidae, we regard this family also as monophyletic. Three other families – Notoligotomidae Davis, Archembiidae Ross and Embiidae Burmeister, as historically delimited – were not found to be monophyletic under any optimality criterion. Notoligotomidae is restricted here to include only the genus Notoligotoma Davis with a new family, Ptilocerembiidae Miller and Edgerly, new family, erected to include the genus Ptilocerembia Friederichs. Archembiidae is restricted here to include only the genera Archembia Ross and Calamoclostes Enderlein. The family group name Scelembiidae Ross is resurrected from synonymy with Archembiidae (new status) to include all other genera recently placed in Archembiidae. Embiidae is not demonstrably monophyletic with species currently placed in the family resolved in three separate clades under each optimality criterion. Because taxon sampling is not extensive within this family in this analysis, no changes are made to Embiidae classification. Relationships between families delimited herein are not strongly supported under any optimality criterion with a few exceptions. Either Clothodidae Davis (parsimony) or Australembiidae Ross (Bayesian) is the sister to the remaining Embioptera taxa. The Bayesian analysis includes Australembiidae as the sister to all other Embioptera except Clothididae, suggesting that each of these taxa is a relatively plesiomorphic representatative of the order. Oligotomidae and Teratembiidae are sister groups, and Archembiidae (sensu novum), Ptilocerembiidae, Andesembiidae and Anisembiidae form a monophyletic group under each optimality criterion. Each family is discussed in reference to this analysis, diagnostic combinations and taxon compositions are provided, and a key to families of Embioptera is included.     

Phylogenetic relationships in the Crassulaceae inferred from chloroplast DNA restriction-site variation

A restriction-site analysis of chloroplast DNA from 44 species, representing 19 genera and all six subfamilies of the Crassulaceae was conducted using 12 restriction endonucleases. A total of 969 variable sites was detected, 608 of which were phylogenetically informative and used in parsimony analysis. Estimated values of nucleotide sequence divergence were used to construct a distance tree by the neighbor-joining method. Maximum sequence divergence in the family was ~7%. Different tree inference methods yielded only moderately different topologies. The amount of support for the monophyletic groups obtained in the Wagner parsimony analysis was evaluated by bootstrap and decay analysis. There is very strong support for a basal division of the family, which separates the monophyletic subfamily Crassuloideae from all other taxa. Four of the six traditionally recognized subfamilies are indicated to be polyphyletic. These include the Cotyledonoideae, Sempervivoideae, Sedoideae, and Echeverioideae. The Kalanchoideae and the genera Cotyledon and Adromischus exhibit low levels of cpDNA sequence divergence relative to one another, suggesting a relatively recent radiation. The genera Sedum and Rosularia are indicated to be polyphyletic. Sedum comprises sister taxa of most of the other genera of the family.