Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from trnK/ matK and trnL-trnF sequences

Cacti are a large and diverse group of stem succulents predominantly occurring in warm and arid North and South America. Chloroplast DNA sequences of the trnK intron, including the matK gene, were sequenced for 70 ingroup taxa and two outgroups from the Portulacaceae. In order to improve resolution in three major groups of Cactoideae, trnL-trnF sequences from members of these clades were added to a combined analysis. The three exemplars of Pereskia did not form a monophyletic group but a basal grade. The well-supported subfamilies Cactoideae and Opuntioideae and the genus Maihuenia formed a weakly supported clade sister to Pereskia. The parsimony analysis supported a sister group relationship of Maihuenia and Opuntioideae, although the likelihood analysis did not. Blossfeldia, a monotypic genus of morphologically modified and ecologically specialized cacti, was identified as the sister group to all other Cactoideae. The tribe Cacteae was found to be sister to a largely unresolved clade comprising the genera Calymmanthium, Copiapoa, and Frailea, as well as two large and well-supported clades. Browningia sensu stricto (excluding Castellanosia), the two tribes Cereeae and Trichocereeae, and parts of the tribes Notocacteae and Rhipsalideae formed one clade. The distribution of this group is largely restricted to South America. The other clade consists of the columnar cacti of Notocacteae, various genera of Browningieae, Echinocereeae, and Leptocereeae, the tribes Hylocereeae and Pachycereeae, and Pfeiffera. A large portion of this latter group occurs in Central and North America and the Caribbean.     

Phylogenetics and biogeography of the neotropical fern genera Jamesonia and Eriosorus (Pteridaceae)

Jamesonia and Eriosorus are two traditionally recognized fern genera in the Neotropics that together form a monophyletic group. Molecular phylogenetic analyses for this study suggest, however, that neither genus is itself monophyletic and that several independent lineages with the jamesonia morphotype have each undergone a fairly recent radiation in páramo ecosystems. A robust phylogeny was generated based on sequence data of the nuclear external transcribed spacer (ETS) of 18S-26S rDNA, the plastid gene rps4 and the intergenic spacer rps4-trnS. Several conclusions can be made concerning the evolutionary history and biogeographic patterns of the Jamesonia-Eriosorus complex: (1) "jamesonia" is polyphyletic, making "eriosorus" paraphyletic; (2) all analyses recover three major clades in the Andes; (3) two well-supported clades can be recognized, corresponding to the northern vs. central Andes; and (4) the sister taxon of the Andean radiation is the Brazilian taxon Eriosorus myriophyllus. Jamesonia is a potential example of a recent adaptive radiation because the group is characterized as being morphologically and ecologically diverse and its habitat is of recent origin.     

基于28S rRNA D2序列的内茧蜂亚科的分子系统发育

首次利用同源28S rRNA D2基因序列对内茧蜂亚科Rogadinae （昆虫纲Insecta：膜翅目Hymenoptera：茧蜂科Braconidae）进行了分子系统学研究。本研究从95%～100%乙醇浸渍保存的标本中提取基因组DNA并扩增了10种内群种类和5种外群种类的28S rDNA D2片段并测序（GenBank序列号AY167645-AY167659）,利用BLAST搜索相关的同源序列, 采用了GenBank中13个种类的28S rRNA D2同源序列,然后据此进行分子分析。利用3个外群（共8个种类）和3种建树方法 (距离邻近法distance based neighbor joining, NJ; 最大俭约法maximum parsimony, MP; 和最大似然法maximum likelihood, ML)分析了内茧蜂亚科内的分子系统发育关系。结果表明,由分子数据产生的不同的分子系统树均显示内茧蜂亚科是一个单系群。内茧蜂亚科内依据形态和生物学特征的分群（族和亚族）及其系统发育关系得到部分支持。NJ、MP和ML分析结果均表明内茧蜂族Rogadini不是一个单系,而是一个并系,其余3族则得到不同程度的支持。内茧蜂族可分成2个分支：“脊茧蜂属Aleiodes+弓脉茧蜂属Arcaleiodes”和“沟内茧蜂属Canalirogas+锥齿茧蜂属Conspinaria+刺茧蜂属Spinaria+内茧蜂属Rogas”,二者不是姐妹群。脊茧蜂属Aleiodes和弓脉茧蜂属Arcaleiodes始终是姐妹群。脊茧蜂属Aleiodes是一个单系,并可分成2个姐妹分支,这与依据形态和生物学特征的亚属分群相一致。弓脉茧蜂属Arcaleiodes Chen et He,1991是一个独立的属。分支“沟内茧蜂属Canalirogas+锥齿茧蜂属Conspinaria+刺茧蜂属Spinaria+内茧蜂属Rogas”的单系性仅得到部分分子数据的支持;因形态特异（腹部成甲壳状）而列为亚族级的刺茧蜂属Spinaria,分子分析没有证实这一点。横纹茧蜂族Clinocentrini是个单系,并在内茧蜂亚科的系统发育中处于基部（原始）的位置。我们研究结果还表明,阔跗茧蜂属Yelicones和潜蛾茧蜂属Stiropius相对应的阔跗茧蜂族Yeliconini和潜蛾茧蜂族Stiropiini为2个独立的分支, 与形态和生物学的结果一致,但它们在内茧蜂亚科的系统发育的位置不明,有待今后进一步研究。     

Inferring the diversification of the epiphytic fern genus Serpocaulon (Polypodiaceae) in South America using chloroplast sequences and amplified fragment length polymorphisms

In this study, we infer the phylogeny of the recently described epiphytic fern genus Serpocaulon. Four regions of the plastid genome were sequenced for 68 samples, representing 31 of ca. 40 currently accepted species of this genus. The reconstructed phylogeny supports most of the previously proposed clades, but more exhaustive studies are needed to improve species delimitation in several terminal clades. A further objective of this study was to determine the utility of amplified fragment length polymorphism (AFLP) data to study the diversification of species complexes. Independent analyses of data sets based on chloroplast DNA sequences or AFLPs resulted in phylogenetic trees with similar topologies, but showed also some notable differences. We present an explicit hypothesis of the biogeographic history of Serpocaulon. All reconstructed phylogenies suggest an origin of this genus in the Bolivian–Brazilian region and indicate a major role of the Bolivian Andes as a stepping-stone in the colonization of northern regions of the Andes. The majority of the extant species diversity of this almost exclusively epiphytic fern clade is likely the result of an adaptive radiation that was triggered by the colonization of Andean mountain forest habitats (above 2,000 m). This is the first report of a Bolivian origin of fern diversification in Andean mountain habitats using phylogenetic evidence.     

Evolution and trends in the Psychotrieae alliance (Rubiaceae)--a rarely reported evolutionary change of many-seeded carpels from one-seeded carpels

Bayesian and parsimony analyses of five plastid gene and nrITS regions from 58 Rubioideae (Rubiaceae) taxa further support the sister-group relationship between the African monotypic genus Schizocolea and the Psychotrieae alliance sensu Bremer & Manen. Our analyses show that the Psychotrieae alliance can be subdivided into in four well-supported clades: Schizocolea, (Schradereae(Gaertnereae(Mitchelleae-Morindeae s.s.))), Palicoureeae-Psychotrieae s.s., and Craterispermeae-Prismatomerideae. The relationships between the latter three clades remain unsettled. Our study further reveals much higher numbers of molecular autapomorphies of the tribes compared with those of molecular synapomorphies of two sister tribes or groups of tribes. Within the newly delimited Psychotrieae alliance a one-seeded carpel was inferred as ancestral and many- and two-seeded carpels evolved once each. We describe Mitchelleae to accommodate Damnacanthus and Mitchella and restrict Morindeae to include only Appunia, Coelospermum, Gynochthodes, Morinda, Pogonolobus, and Syphonandrium. Mitchelleae is characterized e.g., by placentae inserted near the top of the septum and a single campylotropous ovule per carpel, while Morindeae s.s. has massive and T-shaped placentae inserted in the middle of the septum and two anatropous ovules per carpel.     

Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.

Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing to (i) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae, and Cypereae; (ii) define the limits of Fuireneae s.s., and (iii) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognize as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr. nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub-Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognized tribes and genera are provided.     

Pereskia and the origin of the cactus life-form

The cactus life-form is cited as an example of a tight relationship between organism form and function: a succulent, long-lived, photosynthetic stem allows cacti to survive long periods of drought while maintaining a positive tissue water status. Pereskia (Cactaceae) comprises 17 species of leafy shrubs and trees that are thought to represent the original cactus condition. Recent phylogenetic work has shown that there are two separate clades of Pereskia species, which are basal and paraphyletic with respect to the rest of the cacti. We selected seven Pereskia species, representing both clades, and characterized their water relations by measuring a suite of physiological traits in wild populations. Additionally, we estimated basic climate parameters from collection localities for all 17 Pereskia species. Extant Pereskia species exhibit ecological water use patterns that are very similar to those of the leafless, stem-succulent cacti. Ancestral trait reconstruction for the physiological and environmental data provides a preliminary assessment of the ecology and water relations of the earliest cacti and suggests that several key elements of the cactus ecological niche were established before the evolution of the cactus life-form. We interpret these ecological traits as potentially important drivers of evolutionary innovation in the cacti.     

Species tree phylogeny,character evolution,and biogeography of the Patagonian genus <Emphasis Type="Italic">Anarthrophyllum</Emphasis> Benth. (Fabaceae)

Geologic events promoting the aridization of southern South America contributed to lineage divergences and species differentiation through geographic (allopatric divergence) and biotic and abiotic factors (ecological divergence). For the genus Anarthrophyllum, which is distributed in arid and semi-arid regions of Patagonia, we assessed how these factors affected species diversification and reconstructed its possible biogeographic history in South American arid environments. Sequences were obtained from two molecular markers: the ITS nuclear region and the trnS-trnG plastid region. Using Parsimony, Maximum likelihood and Bayesian inference individual gene trees were reconstructed, and a species tree was obtained using multi-species coalescent analysis. Divergence times among species were estimated using secondary calibrations. Flexible Bayesian models and stochastic character mapping were used to elucidate ancestral geographic distributions and the evolution of the floral and vegetative phenotypes in the genus. Gene trees and species tree analyses strongly support Anarthrophyllum as monophyletic; all analyses consistently retrieved three well-supported main clades: High Andean Clade, Patagonian Clade 1, and Patagonian Clade 2. Main diversification events occurred concomitant with the Andean uplift and steppe aridization; the Andean mountain range possibly acted as a species barrier for the High Andean Clade. Vegetative traits showed adaptations to harsh climates in some clades, while pollinator-related floral features were associated with independent diversification in bee- and bird-pollinated clades within both Patagonian Clades. In conclusion, evolutionary and biogeographic history of Anarthrophyllum resulted from the action of ecological, historical, and geographic factors that acted either alternatively or simultaneously.     

Panbiogeographical analysis of the genus Bomarea (Alstroemeriaceae)

Aim  A panbiogeographical analysis of the genus Bomarea was undertaken in order to determine generalized tracks and biogeographical nodes, and to evaluate the current distribution of the genus based on the available tectonic information and the biogeographical regionalization of Latin America.
Location  The Neotropical region from northern Mexico to northern Argentina, and the Nearctic and Andean regions.
Method  A total of 2205 records of 101 species were analysed, representing 95% of the species assigned to Bomarea . Localities were represented on maps and their individual tracks were drawn. Based on their comparison, generalized tracks were detected and mapped. Nodes were identified in the areas where different generalized tracks were superimposed.
Results  Five generalized tracks were recovered. One is located in the Eastern Central America and Western Panamanian Isthmus provinces (Caribbean subregion, Neotropical region), which was supported by three species of Central American distribution. The four remaining generalized tracks were located in South America, in the North Andean Paramo, Cauca and Puna biogeographical provinces. These tracks were supported by species of Bomarea with an Andean distribution. Biogeographical nodes were established in the Central Andean region of Colombia, central Ecuador and central Peru.
Main conclusions  The nodes obtained for Bomarea support a hybrid origin for the Andean region, which presents diverse components from both northern and southern South America. Likewise, the track recovered between Colombia and Ecuador includes Andean and Neotropical areas, providing further support for this hypothesis. The nodes obtained are coherent with vicariant elements evident for Bomarea. Species of three clades proposed for Bomarea are distributed in specific generalized tracks.     

The importance of shrub cover for four cactus species differing in growth form in an Andean semi‐desert

Question: Factors influencing seedling establishment are known to vary between open sites and those protected by plant cover. In many desert regions, protected microhabitats below shrubs are essential for establishment of many cactus species. Very little is known about these factors for Andean cacti and how the importance of vegetation cover varies with cactus species. Are Andean cacti associated more frequently to vegetation cover than to open ground? Are they associated to certain shrub species? Is the distributional pattern in relation to cover similar for different cactus species? In what microhabitat (below or away from shrubs) are cactus seeds more abundant? These questions are addressed for the case of an Andean semi‐desert. Location: Semi‐arid tropical Andes, La Paz department, Bolivia. Methods: We examined 132 isolated shrubs = 50 cm along a line across two microhabitats: areas below and away from shrubs/trees. Shrub crown size was measured. The among‐shrub samples were taken from open spaces contiguous to each of the sampled shrubs. In both microhabitats, all cactus species were recorded. The cardinal direction of the cacti was also registered. Correlation between canopy diameter and number of beneficiaries was evaluated for Prosopis flexuosa. The cactus seed bank in each microhabitat was also studied. Results and Conclusions: The four cactus species found behaved differently in relation to shrub canopies. These distributional differences could be due to differences in growth form. Columnar cacti apparently need the shade of shrubs. Only the columnar species is able to grow near the base of the tallest nurse species. The opuntioid cacti studied seem more facultative: although apparently preferring shrub un‐der‐canopies, they are able to establish in open ground. The globose cactus is the most indifferent to the presence of plant cover. These patterns parallel others found in North America. The capacity of different cacti to appear in open spaces could be related to vegetative propagation, and not necessarily to seedling tolerance of heat.     

Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. derived from mitochondrial DNA

Mitochondrial DNA sequences were used to reconstruct the phylogeny of the Penaeus s.l. genus of marine shrimp. This phylogeny was used to test the validity of hypotheses on the species groupings, in particular the subgenus/genus subdivision, and on the species' evolutionary history. Newly derived sequences of both 16S rRNA and COI genes from 19 species of Penaeus s.l. and one outgroup were combined with previous sequences from seven additional species to allow analysis of 26 of the 28 recognised (or nominated) species. Phylogenetic analyses do not support the validity of all the previously created six subgenera (or genera) but provide evidence for division of the genus into two previously unrecognised clades (Melicertus+Marsupenaeus and Penaeus s.s.+Fenneropenaeus+Farfantepenaeus+Litopenaeus). A key conclusion from a previous molecular study, that the subgenera Farfantepenaeus and Litopenaeus are paraphyletic, was rejected. The molecular data support an Indo-West Pacific origin of the genus, with a single relatively recent colonisation of the Western Hemisphere, and subsequent subdivision into two clades prior to the emergence of the Panamanian isthmus.     

Diversification patterns in the CES clade (Brassicaceae tribes Cremolobeae,Eudemeae, Schizopetaleae) in Andean South America

Dated molecular phylogenetic trees show that the Andean uplift had a major impact on South American biodiversity. For many Andean groups, accelerated diversification (radiation) has been documented. However, not all Andean lineages appear to have diversified following the model of rapid radiation, particularly in the central and southern Andes. Here, we investigated the diversification patterns for the largest South American‐endemic lineage of Brassicaceae, composed of tribes Cremolobeae, Eudemeae and Schizopetaleae (CES clade). Species of this group inhabit nearly all Andean biomes and adjacent areas including the Atacama–Sechura desert, the Chilean Matorral and the Patagonian Steppe. First, we studied diversification times and historical biogeography of the CES clade. Second, we analysed diversification rates through time, lineages and associated life forms. Results demonstrate that early diversification of the CES clade occurred in the early to mid‐Miocene (c. 12–19 Mya) and involved the central Andes, the southern Andes and the Patagonian Steppe, and the Atacama–Sechura desert. The Chilean Matorral and northern Andes were colonized subsequently in the early Pliocene (4–5 Mya). Diversification of the CES clade was recovered as a gradual process without any evidence for rate shifts or rapid radiation, in contrast to many other Andean groups analysed so far. Diversification time/rates and biogeographical patterns obtained for the CES clade are discussed and compared with patterns and conclusions reported for other Andean plant lineages.     

The phylogeny and a new classification of the gingers (Zingiberaceae): evidence from molecular data

The pantropical Zingiberaceae is the largest family in the order Zingiberales with 53 genera and over 1200 species. Classifications of the family first proposed in 1889 and refined by others since that time recognize four tribes (Globbeae, Hedychieae, Alpinieae, and Zingibereae) based on morphological features, such as number of locules and placentation in the ovary, development of staminodia, modifications of the fertile anther, and rhizome-shoot-leaf orientation. New phylogenetic analyses based on DNA sequences of the nuclear internal transcribed spacer (ITS) and plastid matK regions suggest that at least some of these morphological traits are homoplasious and three of the tribes are paraphyletic. The African genus Siphonochilus and Bornean genus Tamijia are basal clades. The former Alpinieae and Hedychieae for the most part are monophyletic taxa with the Globbeae and Zingibereae included within the latter. The results of these phylogenetic investigations are used to propose a new classification of the Zingiberaceae that recognizes four subfamilies and four tribes: Siphonochiloideae (Siphonochileae), Tamijioideae (Tamijieae), Alpinioideae (Alpinieae, Riedelieae), and Zingiberoideae (Zingibereae, Globbeae). Morphological features congruent with this classification and the taxonomic status of various monotypic genera are discussed.     

Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae)

All taxa endemic to the Qinghai-Tibet Plateau are hypothesized to have originated in situ or from immediately adjacent areas because of the relatively recent formation of the plateau since the Pliocene, followed by the large-scaled biota extinction and recession caused by the Quaternary ice sheet. However, identification of specific progenitors remains difficult for some endemics, especially some endemic genera. Nannoglottis, with about eight species endemic to this region, is one such genus. Past taxonomic treatments have suggested its relationships with four different tribes of Asteraceae. We intend to identify the closest relatives of Nannoglottis by evaluating the level of monophyly, tribal delimitation, and systematic position of the genus by using molecular data from ndhF gene, trnL-F, and ITS region sequences. We find that all sampled species of Nannoglottis are a well-defined monophyly. This supports all recent taxonomic treatments of Nannoglottis, in which all sampled species were placed in one broadly re-circumscribed genus. Nannoglottis is most closely related to the Astereae, but stands as an isolated genus as the first diverging lineage of the tribe, without close relatives. A tentative relationship was suggested for Nannoglottis and the next lineage of the tribe was based on the ITS topology, the "basal group," which consists of seven genera from the Southern Hemisphere. Such a relationship is supported by some commonly shared plesiomorphic morphological characters. Despite the very early divergence of Nannoglottis in the Astereae, the tribe must be regarded to have its origin in Southern Hemisphere rather than in Asia, because based on all morphological, molecular, biogeographical, and fossil data, the Asteraceae and its major lineages (tribes) are supposed to have originated in the former area. Long-distance dispersal using Southeast Asia as a steppingstone from Southern Hemisphere to the Qinghai-Tibet Plateau is the most likely explanation for this unusual biogeographic link of Nannoglottis. The 23-32-million-year divergence time between Nannoglottis and the other Astereae estimated by DNA sequences predated the formation of the plateau. This estimation is further favored by the fossil record of the Asteraceae and the possible time of origin of the Astereae. Nannoglottis seems to have reached the Qinghai-Tibet area in the Oligocene-Eocene and then re-diversified with the uplift of the plateau. The molecular infragenetic phylogeny of the genus identifies two distinct clades, which reject the earlier infrageneric classification based on the arrangement of the involucral bracts and the length of the ligules, but agree well with the habits and ecological preferences of its current species. The "alpine shrub" vs. "coniferous forest" divergence within Nannoglottis was estimated at about 3.4 million years ago when the plateau began its first large-scale uplifting and the coniferous vegetation began to appear. Most of the current species at the "coniferous forest" clade of the genus are estimated to have originated from 1.02 to 1.94 million years ago, when the second and third uprisings of the plateau occurred, the climate oscillated and the habitats were strongly changed. The assumed evolution, speciation diversity, and radiation of Nannoglottis based on molecular phylogeny and divergence times agree well with the known geological and paleobotanical histories of the Qinghai-Tibet Plateau.     

Phylogenetic Analyses of Aurantioideae (Rutaceae) Based on Non-Coding Plastid DNA Sequences and Phytochemical Features

Abstract: Sequences of the plastid DNA atp B/ rbc L intergenic spacer and rps16 intron from 23 genera and 47 species of Rutaceae were used to resolve phylogenetic relationships in subfamily Aurantioideae. According to these, the subfamily is monophyletic, but its classical subdivision into tribes Clauseneae and Citreae is only justified if the genus Murraya s.s. (exclusive of the species segregated as Bergera , e.g., Murraya koenigii and M. siamensis ) and Merrillia are transferred to Citreae s.l. This conclusion is also well supported by phytochemistry, demonstrating accumulation of carbazoles in Bergera and Clausena , and of 8-prenylated coumarins and polyoxygenated flavonoids in Murraya s.s. and Merrillia. Formation of both carbazoles, as well as 8-prenylated coumarins, and polyoxygenated flavonoids in Micromelum suggests relationships between Clauseneae s.s. and Citreae s.l. The monophyly of several larger genera in both tribes is supported by relatively high bootstrap percentages and specific chemical profiles for e.g., Clausena, Micromelum, Glycosmis and Atalantia. In contrast, molecular, chemical, and other data show that none of the subtribes recognized within Aurantioideae reflect phylogenetic relationships. Only the clades with Clausena + Bergera, Murraya s.s. + Merrillia, and Citrus + Clymenia + Eremocitrus + Fortunella + Poncirus ("true Citrus fruit trees") are well supported by such data. Among the outgroup genera, Zanthoxylum (Rutoideae) and Toddalia (Toddalioideae) are much closer to each other than to Ruta (Rutoideae).     

Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group

We present a revised molecular phylogeny of the Drosophila repleta group including 62 repleta group taxa and nine outgroup species based on four mitochondrial and six nuclear DNA sequence fragments. With ca. 100 species endemic to the New World, the repleta species group represents one of the major species radiations in the genus Drosophila. Most repleta group species are associated with cacti in arid or semiarid regions. Contrary to previous results, maximum likelihood and Bayesian phylogenies of the 10-gene dataset strongly support the monophyly of the repleta group. Several previously described subdivisions in the group were also recovered, despite poorly resolved relationships between these clades. Divergence time estimates suggested that the repleta group split from its sister group about 21millionyears ago (Mya), although diversification of the crown group began ca. 16Mya. Character mapping of patterns of host plant use showed that flat leaf Opuntia use is common throughout the phylogeny and that shifts in host use from Opuntia to the more chemically complex columnar cacti occurred several times independently during the history of this group. Although some species retained the use of Opuntia after acquiring the use of columnar cacti, there were multiple, phylogenetically independent instances of columnar cactus specialization with loss of Opuntia as a host. Concordant with our proposed timing of host use shifts, these dates are consistent with the suggested times when the Opuntioideae originated in South America. We discuss the generally accepted South American origin of the repleta group.     

Phylogenetic analysis of the Silurian Retiolitidae

A cladistic, phylogenetic analysis of the Retiolitidae, using 18 genera and parataxa and 23 characters, reveals that two distinct clades can be recognized within this family, as well as a primitive stem-group that includes the genus Pseudoretiolites . One of the derived clades includes Pseudo-plegmatograptus, Stomatograptus and Retiolites , which are assigned to the revised subfamily Retiolitinae. The other derived clade, the early part of which shows a paraphyletic relationship, includes the remaining known genera Rotaretiofites s.l., Paraplectograptus s.l., Sokolovograptus, Plectograptus, Agastograptus, Spinograptus, Gothograptus, Eisenackograptus, Neogothograptus, Semiplectograptus, Plectodinemagraptus and Holoretiolites . These genera are all included within an expanded Plectograptinae. The biostratigraphic distribution of these taxa suggests that these two clades diverged from a Pseudoretiolites-like ancestor in mid-Aeronian time.     

Molecular systematics of the Malagasy babblers (Passeriformes: timaliidae) and warblers (Passeriformes: sylviidae), based on cytochrome b and 16S rRNA sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy "babblers" are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy "babblers" are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Phylogenetic relationships and historical biogeography of tribes and genera in the subfamily Nymphalinae (Lepidoptera: Nymphalidae)

We infer for the first time the phylogenetic relationships of genera and tribes in the ecologically and evolutionarily well‐studied subfamily Nymphalinae using DNA sequence data from three genes: 1450 bp of cytochrome oxidase subunit I (COI) (in the mitochondrial genome), 1077 bp of elongation factor 1‐alpha (EF1‐α) and 400–403 bp of wingless (both in the nuclear genome). We explore the influence of each gene region on the support given to each node of the most parsimonious tree derived from a combined analysis of all three genes using Partitioned Bremer Support. We also explore the influence of assuming equal weights for all characters in the combined analysis by investigating the stability of clades to different transition/transversion weighting schemes. We find many strongly supported and stable clades in the Nymphalinae. We are also able to identify ‘rogue’ taxa whose positions are weakly supported (the different gene regions are in conflict with each other) and unstable. Our main conclusions are: (1) the tribe Coeini as currently constituted is untenable, and Smyrna, Colobura and Tigridia are part of Nymphalini; (2) ‘Kallimini’ is paraphyletic with regard to Melitaeini and should be split into three tribes: Kallimini s.s., Junoniini and Victorinini; (3) Junoniini, Victorinini, Melitaeini and the newly circumscribed Nymphalini are strongly supported monophyletic groups, and (4) Precis and Junonia are not synonymous or even sister groups. The species Junonia coenia, a model system in developmental biology, clearly belongs in the genus Junonia. A dispersal‐vicariance analysis suggests that dispersal has had a major effect on the distributions of extant species, and three biotic regions are identified as being centres of diversification of three major clades: the Palaearctic for the Nymphalis‐group, the Afrotropics for Junoniini and the Nearctic for Melitaeini. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86 , 227–251.