Phylogenetic relationships of African microhylid frogs inferred from DNA sequences of mitochondrial 12S and 16S rRNA genes

The phylogenetic relationships of microhylid frogs are poorly understood. The first molecular phylogeny for continental African microhylids is presented, including representatives of all subfamilies, six of the eight genera, and the enigmatic hemisotid Hemisus. Mitochondrial 12S and 16S rRNA sequence data were analysed using parsimony, likelihood and Bayesian methods. Analyses of the data are consistent with the monophyly of all sampled subfamilies and genera. Hemisus does not nest within either brevicipitines or non-brevicipitines. It is possibly the sister group to brevicipitines, in which case brevicipitines might not be microhylids. Phrynomantis and Hoplophryne potentially group with non-African, non-brevicipitine microhylids, in agreement with recent morphological and molecular data. Within brevicipitines, Breviceps is recovered as the sister group to a clade of Callulina+Spelaeophryne+Probreviceps. The relationships among the genera within this latter clade are unclear, being sensitive to the method of analysis. Optimal trees suggest the Probreviceps macrodactylus subspecies complex might be paraphyletic with respect to P. uluguruensis, corroborating preliminary morphological studies indicating that P. m. rungwensis may be a distinct species. P. m. loveridgei may be paraphyletic with respect to P. m. macrodactylus, though this is not strongly supported. Some biogeographic hypotheses are examined in light of these findings.     

Molecular analysis of the biting midges (Diptera: Ceratopogonidae), based on mitochondrial cytochrome oxidase subunit 2

Sequences from the mitochondrial cytochrome oxidase subunit 2 gene (cox2) were determined for 14 species from the family Ceratopogonidae, representing 12 genera and all five subfamilies, along with six representatives of other nematoceran families. The purpose was to develop a molecular phylogeny of the Ceratopogonidae, and interpret the phylogenetic position of the family within the infraorder Culicomorpha. These taxa have been analysed using cladistic methodology which, in combination with an excellent fossil record, provides a well established morphological phylogeny. Sequence analysis of cox2 revealed a high degree of sequence divergence among the species, reflecting in part the antiquity of the family, but also a significant acceleration of sequence evolution in the ceratopogonids compared to other nematoceran Diptera. Phylogenetic reconstruction by neighbor-joining and maximum parsimony gave strong support for an early separation of an ancient lineage that includes the two genera, Austroconops and Leptoconops, from the remainder of the family. The results support the existence of a clade that includes two subfamilies, Dasyheleinae and Forcipomyiinae, and this clade appears as sister to the remaining subfamily, Ceratopogoninae. The molecular phylogeny also supports monophyly of the Ceratopogonidae, and either a sister or paraphyletic relationship of this family with the Chironomidae.     

Phylogeny and classification of Marantaceae

Relationships of Marantaceae were estimated from nucleotide sequence variation in the rps16 intron (plastid DNA) and from morphological characters. Fifty-nine species (21 genera) formed the ingroup, and 12 species (12 genera) of other Zingiberales formed the outgroup. There is no support for the traditional subdivision of Marantaceae into a triovulate and a uniovulate tribe or the informal groups previously proposed. The so-called Donax group forms a paraphyletic grade that is basal within Marantaceae. Thalia appears as the distal branch of this grade, but its position is not supported in jackknife analysis. The so-called Calathea group is monophyletic in all shortest trees but not supported with greater than 50% jackknife. The genus Calathea appears to be paraphyletic. The Maranta and Phrynium groups are clearly polyphyletic. Maranta, Koernickanthe , and genera of the Mymsma group, all neotropical, form a strongly supported monophyletic group. The sister of this group is the palaeotropical genus Halopegia. Koernickanthe is nested within Maranta , as this genus is traditionally circumscribed. The African genera Ataenidia and Marantochloa form a strongly supported clade in which Ataenidia is the sister group to Marantochloa . Based on phylogeny it is concluded that Africa, in spite of being much poorer in species, is the most likely ancestral area of Marantaceae     

Nuclear and mtDNA-based phylogeny of southern African sand lizards, Pedioplanis (Sauria: Lacertidae)

The diversity of lacertid lizards in Africa is highest in the southern African subcontinent, where over two-thirds of the species are endemic. With eleven currently recognized species, Pedioplanis is the most diverse among the southern African genera. In this study we use 2200 nucleotide positions derived from two mitochondrial markers (ND2 and 16S rRNA) and one nuclear gene (RAG-1) to (i) assess the phylogeny of Pedioplanis and (ii) estimate divergence time among lineages using the relaxed molecular clock method. Individual analyses of each gene separately supported different nodes in the phylogeny and the combined analysis yielded more well supported relationships. We present the first, well-resolved gene tree for the genus Pedioplanis and this is largely congruent with a phylogeny derived from morphology. Contrary to previous suggestions Heliobolus/Nucras are sister to Pedioplanis. The genus Pedioplanis is monophyletic, with P. burchelli/P. laticeps forming a clade that is sister to all the remaining congeners. Two distinct geographic lineages can be identified within the widespread P. namaquensis; one occurs in Namibia, while the other occurs in South Africa. The P. undata species complex is monophyletic, but one of its constituent species, P. inornata, is paraphyletic. Relationships among the subspecies of P. lineoocellata are much more complex than previously documented. An isolated population previously assigned to P. l. pulchella is paraphyletic and sister to the three named subspecies. The phylogeny identifies two biogeographical clades that probably diverged during the mid-Miocene, after the development of the Benguella Current. This probably led to habitat changes associated with climate and, in conjunction with physical barriers (Great Escarpment), contributed towards speciation within the genus Pedioplanis.     

Reconstructing the evolutionary history of the Lorisidae using morphological, molecular, and geological data

Major aspects of lorisid phylogeny and systematics remain unresolved, despite several studies (involving morphology, histology, karyology, immunology, and DNA sequencing) aimed at elucidating them. Our study is the first to investigate the evolution of this enigmatic group using molecular and morphological data for all four well-established genera: Arctocebus, Loris, Nycticebus, and Perodicticus. Data sets consisting of 386 bp of 12S rRNA, 535 bp of 16S rRNA, and 36 craniodental characters were analyzed separately and in combination, using maximum parsimony and maximum likelihood. Outgroups, consisting of two galagid taxa (Otolemur and Galagoides) and a lemuroid (Microcebus), were also varied. The morphological data set yielded a paraphyletic lorisid clade with the robust Nycticebus and Perodicticus grouped as sister taxa, and the galagids allied with Arctocebus. All molecular analyses maximum parsimony (MP) or maximum likelihood (ML) which included Microcebus as an outgroup rendered a paraphyletic lorisid clade, with one exception: the 12S + 16S data set analyzed with ML. The position of the galagids in these paraphyletic topologies was inconsistent, however, and bootstrap values were low. Exclusion of Microcebus generated a monophyletic Lorisidae with Asian and African subclades; bootstrap values for all three clades in the total evidence tree were over 90%. We estimated mean genetic distances for lemuroids vs. lorisoids, lorisids vs. galagids, and Asian vs. African lorisids as a guide to relative divergence times. We present information regarding a temporary land bridge that linked the two now widely separated regions inhabited by lorisids that may explain their distribution. Finally, we make taxonomic recommendations based on our results.     

Molecular phylogeny reveals the non-monophyly of tribe Yinshanieae(Brassicaceae) and description of a new tribe,Hillielleae

The taxonomic treatment within the unigeneric tribe Yinshanieae(Brassicaceae) is controversial, owing to differences in generic delimitation applied to its species. In this study, sequences from nuclear ITS and chloroplast trn L-F regions were used to test the monophyly of Yinshanieae, while two nuclear markers(ITS, ETS) and four chloroplast markers(trnL-F, trn H-psbA, rps16, rpL32-trnL) were used to elucidate the phylogenetic relationships within the tribe. Using maximum parsimony, maximum likelihood, and Bayesian inference methods, we reconstructed the phylogeny of Brassicaceae and Yinshanieae. The results show that Yinshanieae is not a monophyletic group, with the taxa splitting into two distantly related clades: one clade contains four taxa and falls in Lineage I, whereas the other includes all species previously placed in Hilliella and is embedded in the Expanded Lineage II. The tribe Yinshanieae is redefined, and a new tribe, Hillielleae, is proposed based on combined evidence from molecular phylogeny, morphology, and cytology.     

Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)

Melocanninae is sister to other subtribes of Paleotropical woody bamboos with some 90 species mainly concentrated in Asia. However, phylogenetic relationships within the subtribe are poorly known. Here, we filled the gaps in complete plastome data of Melocanninae, reconstructed the phylogeny of Melocanninae, and further estimated divergence time and ancestral distribution range. Our results showed that the two major genera, Cephalostachyum Munro and Schizostachyum Nees, were paraphyletic. Species of Cephalostachyum were resolved in two successive basal clades, whereas Annamocalamus H. N. Nguyen, N. H. Xia, & V. T. Tran was embedded in the Schizostachyum clade. Different plastid regions provided inconsistent signals for the relationship of Melocanna and Pseudostachyum. Conservative loci supported a successive divergence rather than sister relationship between them and the difference may be caused by long-branch attraction. We infer that Melocanninae originated in the East Himalaya to northern Myanmar in the early Miocene. Three routes were revealed in forming its present biogeographic pattern: in situ diversification on the Asian mainland, dispersing southwest to Sri Lanka and to the Western Ghats in South India, and spreading southeast to Malesia and Oceania by way of the Indo-China Peninsula. The rapid uplift of the Tibetan Plateau and the intensification of Asian monsoons since the Miocene and the sea level fall events since the Late Miocene might be potential driving forces for diversification of Melocanninae and, particularly the latter event, for the species radiation of Schizostachyum.     

Molecular phylogeny of Nyctaginaceae: taxonomy, biogeography, and characters associated with a radiation of xerophytic genera in North America

The four o'clock family (Nyctaginaceae) has a number of genera with unusual morphological and ecological characters, several of which appear to have a "tendency" to evolve repeatedly in Nyctaginaceae. Despite this, the Nyctaginaceae have attracted little attention from botanists. To produce a phylogeny for the Nyctaginaceae, we sampled 51 species representing 25 genera (of 28-31) for three chloroplast loci (ndhF, rps16, rpl16, and nrITS) and included all genera from North America. Parsimony, likelihood, and Bayesian methods were used to reconstruct the phylogeny for the family. The family is neotropical in origin. A radiation of woody taxa unites Pisonia and Pisoniella with the difficult tropical genera Neea and Guapira, which also form a clade, though neither appears to be monophyletic. This group is sister to a clade containing Bougainvillea, Belemia, and Phaeoptilum. A dramatic radiation of genera occurred in the deserts of North America. The tribe Nyctagineae and its subtribes are paraphyletic, due to over-reliance on a few homoplasious characters, i.e., pollen morphology and involucre presence. Two notable characters associated with the desert radiation are cleistogamy and edaphic endemism on gypsum soils. We discuss evolutionary trends in these traits in light of available data about self-incompatibility and gypsum tolerance in Nyctaginaceae.     

Phylogenetic analysis of the grape family (Vitaceae) based on three chloroplast markers

Seventy-nine species representing 12 genera of Vitaceae were sequenced for the trnL-F spacer, 37 of which were subsequently sequenced for the atpB-rbcL spacer and the rps16 intron. Phylogenetic analysis of the combined data provided a fairly robust phylogeny for Vitaceae. Cayratia, Tetrastigma, and Cyphostemma form a clade. Cyphostemma and Tetrastigma are each monophyletic, and Cayratia may be paraphyletic. Ampelopsis is paraphyletic with the African Rhoicissus and the South American Cissus striata nested within it. The pinnately leaved Ampelopsis form a subclade, and the simple and palmately leaved Ameplopsis constitutes another with both subclades containing Asian and American species. Species of Cissus from Asia and Central America are monophyletic, but the South American C. striata does not group with other Cissus species. The Asian endemic Nothocissus and Pterisanthes form a clade with Asian Ampelocissus, and A. javalensis from Central America is sister to this clade. Vitis is monophyletic and forms a larger clade with Ampelocissus, Pterisanthes, and Nothocissus. The eastern Asian and North American disjunct Parthenocissus forms a clade with Yua austro-orientalis, a species of a small newly recognized genus from China to eastern Himalaya. Vitaceae show complex multiple intercontinental relationships within the northern hemisphere and between northern and southern hemispheres.     

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.     

基于孢子形态和分子证据探讨鳞盖蕨属(碗蕨科)系统分类

孢粉学是解决植物分类中疑难类群物种微形态分化的重要方法, 随着分子系统学的发展, 结合这两门学科的优势可以更加有效地解决疑难类群的分类学问题。鳞盖蕨属(Microlepia)是一个分类困难的疑难类群, 采用孢粉学与分子系统学一一对应的方法, 以及居群取样方式, 选取280份样本, 联合4个叶绿体片段(rbcL、trnL-F、psbA-trnH和rps4), 采用最大似然法和贝叶斯法构建该属的系统发生关系, 在此基础上对凭证标本中100份材料的孢子进行观察和分析。综合分子系统学和孢粉学的研究结果, 得出结论: (1) 在形态学研究中广泛被接受的15个物种得到了单系支持, 并厘清了分类困难的复合群; (2) 发现边缘鳞盖蕨(M. marginata)可能存在隐性种; (3) 建议恢复过去归并处理为异名的瑶山鳞盖蕨(M. yaoshanica)、罗浮鳞盖蕨(M. lofoushanensis)、四川鳞盖蕨(M. szechuanica)以及滇西鳞盖蕨(M. subspeluncae); (4) 提出鳞盖蕨属可能存在杂交现象; (5) 提出鳞盖蕨属完整的属下分类建议。     

Evolutionary morphology of whip spiders: towards a phylogenetic system (Chelicerata: Arachnida: Amblypygi)*

The aim of this study is to present a cladogram and phylogenetic system and to use this to discuss the phylogeny and biogeography of the Amblypygi. A total of 29 morphological structures were studied, their plesiomorphic and apomorphic characters or character states were identified, and the resulting data matrix was analysed. As a result, the ‘old’Charontidae or Pulvillata emerge as a paraphyletic group; the genus Paracharon is the sister group of all other amblypygids, which are now termed Euamblypygi. The ‘new’Charontidae (sensu Quintero: the genera Stygophrynus and Charon) are the sister group of the Phrynida or Apulvillata; together they form the Neoamblypygi. The relationships of the genera of the Charinidae cannot be resolved with the available data. They may be a paraphyletic group. The genus Catageus is a possible candidate for being the sister group of the Neoamblypygi. The new system allows a discussion of the phylogeny and biogeography of whip spiders. It also points to unresolved taxa and thus indicates the questions future research should address.     

A molecular phylogeny of fleas (Insecta: Siphonaptera): origins and host associations

Siphonaptera (fleas) is a highly specialized order of holometabolous insects comprising ～2500 species placed in 16 families. Despite a long history of extensive work on flea classification and biology, phylogenetic relationships among fleas are virtually unknown. We present the first formal analysis of flea relationships based on a molecular matrix of four loci (18S ribosomal DNA, 28S ribosomal DNA, Cytochrome Oxidase II, and Elongation Factor 1‐alpha) for 128 flea taxa from around the world representing 16 families, 25 subfamilies, 26 tribes, and 83 flea genera with eight outgroups. Trees were reconstructed using direct optimization and maximum likelihood techniques. Our analysis supports Tungidae as the most basal flea lineage, sister group to the remainder of the extant fleas. Pygiopsyllomorpha is monophyletic, as are the constituent families Lycopsyllidae, Pygiopsyllidae, and Stivaliidae, with a sister group relationship between the latter two families. Macropsyllidae is resolved as sister group to Coptopsyllidae with moderate nodal support. Stephanociricidae is monophyletic, as are the two constituent subfamilies Stephanocircinae and Craneopsyllinae. Vermipsyllidae is placed as sister group to Jordanopsylla. Rhopalopsyllidae is monophyletic as are the two constituent subfamilies Rhopalopsyllinae and Parapsyllinae. Hystrichopsyllidae is paraphyletic with Hystrichopsyllini placed as sister to some species of Anomiopsyllini and Ctenopariini placed as sister to Carterettini. Ctenophthalmidae is grossly paraphyletic with the family broken into seven lineages dispersed on the tree. Most notably, Anomiopsyllini is paraphyletic. Pulicidae and Chimaeropsyllidae are both monophyletic and these families are sister groups. Ceratophyllomorpha is monophyletic and includes Ischnopsyllidae, Ceratophyllidae, and Leptopsyllidae. Leptopsyllidae is paraphyletic as are its constituent subfamilies Amphipsyllinae and Leptopsyllinae and the tribes Amphipsyllini and Leptopsyllini. Ischnopsyllidae is monophyletic. Ceratophyllidae is monophyletic, with a monophyletic Dactypsyllinae nested within Ceratophyllinae, rendering the latter group paraphyletic. Mapping of general host associations on our topology reveals an early association with mammals with four independent shifts to birds. © The Willi Hennig Society 2008.     

Phylogenetic analysis of a polyphyletic African genus of Caesalpinioideae (Leguminosae): Monopetalanthus Harms

 To assess the new taxonomy of Monopetalanthus proposed by Wieringa, a phylogenetic study was performed using the chloroplast trnL intron and psbA-trnH spacer, and the nuclear ITS region of the 18-26S rDNA. The phylogeny clearly indicates the polyphyletic nature of Monopetalanthus. The molecular data support the transfer of M. longiracemosus to Tetraberlinia and the newly defined Aphanocalyx, which now includes all the previous Monopetalanthus species having leaflets with a marginal vein. Our analyses do not support the monophyly of the newly described genus Bikinia, which includes four new species and six species transferred from Monopetalanthus. Bikinia occurs either as paraphyletic with Tetraberlinia (chloroplast DNA data) or as a monophyletic group that also includes the new monotypic genus Icuria sister to Tetraberlinia (ITS data). Nonetheless, the molecular phylogeny generally supports the taxonomy of Wieringa in subdividing the genus Monopetalanthus into distinct groups, none of which retains the name Monopetalanthus. Received May 28, 2001; accepted July 6, 2002 Published online: November 20, 2002 Address of the authors: G. Y. Fannie Gervais, Anne Bruneau (e-mail: bruneaua@irbv.umontreal. ca), Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke est, Montréal, Québec, Canada, H1X2B2.     

Evolution and biogeography of Alectryon (Sapindaceae).

Phylogenetic analysis of nucleotide sequences from four plastid loci (matK, partial trnK-matK introns, rps16 intron) and one nuclear locus (the internal transcribed spacer of rDNA; ITS-1) was conducted for 14 species of Alectryon and five related genera in Sapindaceae. Both matK and rps16 intron provide few informative characters within Alectryon, whereas ITS-1 provides the largest number of parsimony-informative characters and has the greatest sequence divergence between taxa. Support for branches in cladograms produced in PAUP increased markedly upon inclusion of ITS-1 data to matK and rps16 intron data. Analyses of each region alone or combined produced congruent results, suggesting that the regions are complementary. Phylogenetic analysis indicates that there are two main lineages within Alectryon, with A. subcinereus sister to the remaining sampled Alectryon taxa. Two morphological characters, presence/absence of petals and aril patterning, are congruent with the molecular phylogeny. One robustly supported clade is characterized by smooth arils and petals, in contrast to the taxa in the other major clade which have patterned arils and an absence of petals. These analyses also support a number of revised subgeneric groupings for Alectryon. The decision to submerge Heterodendrum in Alectryon is supported, although taxa belonging to Heterodendrum do not form a clade. The majority of the Australian Alectryon appear to belong to the tropical monsoonal/arid flora with species from both lineages being found in representative vine thickets across northern Australia. It appears that the seasonally dry rainforest communities comprise a number of elements that do not share common evolutionary histories within this genus.     

Evolution of feeding habits of sap beetles (Coleoptera: Nitidulidae) and placement of Calonecrinae

Nitidulidae includes some 4500 species under 350 genera in ten subfamilies, making it the most species-rich family in Cucujoidea. In this study, we present a phylogeny of the family based on five gene regions (COI, 28s, CAD, H3, Wingless) for 73 ingroup taxa representing nine of the ten currently recognized subfamilies of Nitidulidae, including the enigmatic subfamily Calonecrinae. Our results are consistent with a prior molecular study that recovered (i) paraphyletic Nitidulinae with the inclusion of Meligethinae and Cillaeinae and (ii) subfamilial status of Prometopiinae. The molecular phylogenetic position of Calonecrinae is recovered for the first time, as a sister taxon to Epuraeinae. Ancestral state reconstruction of feeding behaviour indicates that the stem group nitidulids were largely mycophagous with transitions to other feeding types independently derived.     

高茎紫菀(菊科)形态描述补充及细胞学和分子系统学研究北大核心CSCD

结合在模式产地采集的高茎紫菀(Aster procerus Hemsley)以及查阅文献资料,发现原始文献对其形态描述不充分且缺乏细胞学和分子系统学方面的报道。本研究对高茎紫菀的形态特征进行了补充描述以及核型特征和系统位置分析,为紫菀属的修订提供资料。结果表明:(1)依据观察结果,补充了高茎紫菀新的形态特征:基生叶羽状分裂,成熟的基生叶较大,长可达26 cm,宽可达8 cm;花序托圆锥状。(2)高茎紫菀的染色体数目为2n=18;核型公式为2n=2x=16 m+2 M,核型属于1 A。(3)基于ITS和ETS标记的分子系统发育树分析表明,高茎紫菀不同居群的2个个体在同一进化支上(LP=100,PP=1.00),且位于核心紫菀属(LP=100,PP=1.00),与女菀[Turczaninovia fastigiata(Fischer)Candolle]构成姐妹类群(LP=52,PP=0.99)。研究认为,高茎紫菀基生叶和花序托的特征可为紫菀属的分类提供新的证据,支持高茎紫菀位于紫菀属(Aster L.)内,建议将女菀并入紫菀属。