New and earlier unnoted mealybugs and felt scale (Homoptera: Coccinea: Pseudococcidae,Eriococcidae) from Morocco

Two new species of mealybugs (Pseudococcidae), Puto (Ceroputo) chetverikovi n. sp. and Fonscolombia toubkalensis n. sp., are described and illustrated. Thirteen other species are noted for the first time to fauna of Morocco or to Africa as a whole. Additionally, one species of closely related family Eriococcidae, Acanthococcus ericae (Signoret, 1875), is also reported for the first time to Morocco.     

Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins

Highly diversified colorations among springtails (Collembola) have been widely used for species diagnosis, but their phylogenetic significance is poorly known. We addressed this issue in the largest Entomobryinae genus Entomobrya, which possesses variable color patterns among species. The relationships within the genus and to other genera have also rarely been studied. Based on material mainly from China, we have conducted a multilocus phylogeny and topology tests with likelihood and Bayesian algorithms, and accordingly demonstrated the non-monophyly of Chinese Entomobrya. The division of five clades, including Entomobrya and several related genera, coincided well with five types of colorations, respectively. Further analyses of divergence time and historical biogeography revealed that Chinese Entomobrya originated mainly from Palearctic (northern and western) China in the Paleocene and Eocene. This study highlights the great phylo? genetic values as well as taxonomic uses of coloration in Chinese Entomobrya. Multiple phylogenetic and biogeographic origins of Entomobrya imply its complicated relationships with both scaled and unsealed genera of Entomobryinae.     

Phylogeny of the families Pyuridae and Styelidae (Stolidobranchiata, Ascidiacea) inferred from mitochondrial and nuclear DNA sequences

The Order Stolidobranchiata comprises the families Pyuridae, Styelidae and Molgulidae. Early molecular data was consistent with monophyly of the Stolidobranchiata and also the Molgulidae. Internal phylogeny and relationships between Styelidae and Pyuridae were inconclusive however. In order to clarify these points we used mitochondrial and nuclear sequences from 31 species of Styelidae and 25 of Pyuridae. Phylogenetic trees recovered the Pyuridae as a monophyletic clade, and their genera appeared as monophyletic with the exception of Pyura. The Styelidae, on the other hand, appeared as a paraphyletic group split into several clades. One of them was formed by solitary oviparous species, of which the Pyuridae were a sister group. A second clade included the colonial genera Botryllus, Botrylloides and Symplegma. The remaining colonial and solitary genera formed several poorly resolved clades. One of the more species genus, Polycarpa, was shown to be polyphyletic, and the species Styela plicata grouped into two genetically distant clades suggesting the existence of two cryptic species. The internal phylogeny of Styelidae has bearings on the origin of coloniality in this family. We suggest to abandon the traditional division of colonial forms into social and compound species and use instead the categories of aggregated colonies that do not have common vascular systems, and integrated colonies, that do possess such systems. Our molecular results indicate that there have been several independent acquisitions of coloniality in the Styelidae, and that viviparity may be a pre-adaptation for a colonial life-style.     

Phylogeny of split‐footed lacewings (Neuroptera,Nymphidae), with descriptions of new Cretaceous fossil species from China

A phylogeny of the lacewing family Nymphidae based on morphology and DNA sequences is presented including representatives of all living genera and selected fossil genera. Widely distributed Jurassic and Cretaceous genera gave rise to recent taxa now restricted to Australasia. Two previously defined clades (i.e. Nymphinae and Myiodactylinae) were recovered and reflect the diverging adult and larval morphology of members of these two subfamilies. From Chinese Cretaceous deposits, a new genus (Spilonymphes gen. nov.) is described with one new species, as well as new species described in the genera Baissoleon Makarkin and Sialium Westwood.     

Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows

Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato (s.l.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis, Idesia, two genera of the Salicaceae sensu stricto (s.s.) (Populus and Salix). Five major subclades were recovered within the Populus clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the Salix clade. Molecular dating suggested that species diversification of the major subclades in the Populus and Salix clades occurred mainly within the recent Pliocene. In addition, we found that the rpl32 gene was lost and the rps7 gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae s.l. Compared with previous studies, our results provide a well‐resolved phylogeny from the perspective of the plastomes.     

Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation

Do phylogenies and branch lengths based on mitochondrial DNA (mtDNA) provide a reasonable approximation to those based on multiple nuclear loci? In the present study, we show widespread discordance between phylogenies based on mtDNA (two genes) and nuclear DNA (nucDNA; six loci) in a phylogenetic analysis of the turtle family Emydidae. We also find an unusual type of discordance involving the unexpected homogeneity of mtDNA sequences across species within genera. Of the 36 clades in the combined nucDNA phylogeny, 24 are contradicted by the mtDNA phylogeny, and six are strongly contested by each data set. Two genera (Graptemys, Pseudemys) show remarkably low mtDNA divergence among species, whereas the combined nuclear data show deep divergences and (for Pseudemys) strongly supported clades. These latter results suggest that the mitochondrial data alone are highly misleading about the rate of speciation in these genera and also about the species status of endangered Graptemys and Pseudemys species. In addition, despite a strongly supported phylogeny from the combined nuclear genes, we find extensive discordance between this tree and individual nuclear gene trees. Overall, the results obtained illustrate the potential dangers of making inferences about phylogeny, speciation, divergence times, and conservation from mtDNA data alone (or even from single nuclear genes), and suggest the benefits of using large numbers of unlinked nuclear loci. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 445–461.     

Molecular phylogeny of the Raphidiidae (Raphidioptera)*

We present a molecular phylogeny of the family Raphidiidae including representatives of 21 of the 26 genera. Sequences from the nuclear gene for the large subunit ribosomal RNA (28S rRNA) and the mitochondrial cytochrome c oxidase subunit 3 gene (cox3) were used. For the phylogenetic reconstructions we applied automated and manual approaches for sequence alignment and different evolutionary models and tree building algorithms. The trees based on the two alignment approaches were rather similar in their overall topology. A combination of both marker sequences increased the resolution of the trees. The six clades within the raphidiid family that emerged represent either single genera or groups of genera, namely: (i) the Nearctic genus Agulla Navás, (ii) the Nearctic/Central American genus Alena Navás, (iii) the Central Asiatic and Eastern Palaearctic genus Mongoloraphidia H. Aspöck & U. Aspöck, (iv) the Palaearctic Puncha clade, (v) the western Mediterranean Ohmella clade, and (vi) the Palaearctic Phaeostigma clade. The New World taxa Agulla and Alena are placed as successive out‐groups to a monophyletic Palaearctic clade. The Mongoloraphidia clade is distributed in the eastern Palearctic while the remaining three clades are exclusively (Ohmella clade) or mainly distributed in the western Palaearctic. The early radiation of extant Raphidiidae is interpreted based on the phylogenetic tree obtained in the present study, and the geological and palaeobiological processes around the K–T boundary.     

Genetic divergences and intraspecific variation in corvids of the genus Corvus (Aves: Passeriformes: Corvidae) – a first survey based on museum specimens

The first comprehensive overview of intra‐ and interspecific variation within the genus Corvus as well as first insights into the phylogenetic relationships of its species is presented. DNA sequences of the mitochondrial control region were obtained from 34 of the 40 described species (including subspecies: 56 taxa). As the study was based mainly on museum material, several specimens did not yield the full length marker sequence. In these cases, only a short section of the control region could be analysed. Nevertheless, even these individuals could be assigned tentatively to clades established on the full length marker sequence. Inclusion of sequences of other corvid genera as available in GenBank clearly confirmed the monophyly of the genus Corvus. Within the Corvus clade several distinct subclades can be distinguished. Some represent lineages of single species or species pairs while other clades are composed of many species. In general, the composition of the clades reflects geographical contiguousness and confirms earlier assumptions of a Palearctic origin of the genus Corvus with several independent colonizations of the Nearctic and the Aethiopis. The Australasian radiation seems to be derived from a single lineage. The distribution of plumage colour in the phylogenetic tree indicates that the pale markings evolved several times independently. The white/grey plumage colour pattern – which is found also in other genera of the family Corvidae, for example, in Pica– occurs already in the species pair representing the first split within the genus Corvus (Corvus monedula, Corvus dauuricus). Thus, reversal to full black colour seems to have occurred as well. The use of colour traits as a phylogenetic marker within Corvus should be considered with severe caution.     

Phylogeny,classification and divergence times of pygmy leaf‐mining moths (Lepidoptera: Nepticulidae): the earliest lepidopteran radiation on Angiosperms?

Nepticulidae represent one of the early diverging Lepidoptera lineages, and the family currently comprises over 850 described species. The larvae of the vast majority of the species are leaf miners on Angiosperms and highly monophagous, which has led to persistent ideas on coevolution with their plant hosts. We present here a molecular phylogeny based on eight gene fragments from 355 species, representing 20 out of 22 extant Nepticulidae genera. Using two fossil calibration points, we performed molecular dating to place the origin of the family in the Early Cretaceous, before the main Angiosperm diversification. Based on our results we propose a new classification, abandoning all ranks between family and genus, as well as subgenera to allow for a stable classification. The position of Enteucha Meyrick within Nepticulidae remains somewhat ambiguous, and the species‐rich cosmopolitan genus Stigmella Schrank, with nearly half of all described Nepticulidae, requires further study. Ectoedemia Busck, Zimmermannia Hering, Acalyptris Meyrick, Etainia Beirne, Parafomoria Borkowski, Muhabbetana Koçak & Kemal and Fomoria Beirne appear to have diversified in a relatively short evolutionary period, leading to short branches in the molecular phylogeny and unclear suprageneric relations. Otherwise support values throughout the phylogeny are mostly high and the species groups, genera and higher clades are discussed in respect of their supporting morphological and life‐history characters. Wing venation characters are confirmed to be mostly reliable and relevant for Nepticulidae classification, but some other previously used characters require reinterpretation. The species groups of most genera are recovered, but only partly so in the large genus Stigmella. The molecular dating results are compared with existing knowledge on the timing of the Angiosperm radiation and reveal that the diversification of Nepticulidae could largely have been contemporaneous with their hosts, although some of the genera restricted to a single plant family appear to have begun to diversify before their hosts.     

Phylogenies from genetic and morphological characters do not support a revision of Gigasporaceae (Glomeromycota) into four families and five genera

The family Gigasporaceae consisted of the two genera Gigaspora and Scutellospora when first erected. In a recent revision of this classification, Scutellospora was divided into three families and four genera based on two main lines of evidence: (1) phylogenetic patterns of coevolving small and large rRNA genes and (2) morphology of spore germination shields. The rRNA trees were assumed to accurately reflect species evolution, and shield characters were selected because they correlated with gene trees. These characters then were used selectively to support gene trees and validate the classification. To test this new classification, a phylogenetic tree was reconstructed from concatenated 25S rRNA and β-tubulin gene sequences using 35% of known species in Gigasporaceae. A tree also was reconstructed from 23 morphological characters represented in 71% of known species. Results from both datasets showed that the revised classification was untenable. The classification also failed to accurately represent sister group relationships amongst higher taxa. Only two clades were fully resolved and congruent among datasets: Gigaspora and Racocetra (a clade consisting of species with spores having one inner germinal wall). Other clades were unresolved, which was attributed in part to undersampling of species. Topology of the morphology-based phylogeny was incongruent with gene evolution. Five shield characters were reduced to three, of which two were phylogenetically uninformative because they were homoplastic. Therefore, most taxa erected in the new classification are rejected. The classification is revised to restore the family Gigasporaceae, within which are the three genera Gigaspora, Racocetra, and Scutellospora. This classification does not reflect strict topology of either gene or morphological evolution. Further revisions must await sampling of additional characters and taxa to better ascertain congruence between datasets and infer a more accurate phylogeny of this important group of fungi.     

Phylogenetic analyses of the isonychiid mayflies (Ephemeroptera: Isonychiidae) in the northeast palearctic region

We investigated the molecular phylogeny of isonychiid mayflies inhabiting the East Palearctic region, Isonychia (Isonychia) japonica, Isonychia (Isonychia) ignota, Isonychia (Isonychia) ussurica and Isonychia (Prinoides) shima. We discuss their genetic structures, phylogeny and phylogeography. We collected a total of 100 specimens of isonychiid mayfly species from 47 localities of the Northeast Palearctic region (the Japanese archipelago, the Korean peninsula, the Russian Far East and Mongolia). We analyzed the DNA sequences at the mtDNA COI and 16S rRNA regions, and the nuDNA Histone H3 region. As a result of our genetic analyses of the four Northeast Palearctic isonychiid mayflies, their monophyly at the species level was supported by both the mtDNA (COI and 16S rRNA regions) and the nuDNA (Histone H3 region). In addition, it also became clear that significantly large genetic differentiation exists at the inter‐species level; thus, the relationship of “shima + (japonica + (ignota + ussurica))” is supported. Among the four isonychiid mayflies of the Northeast Palearctic area, I. (P.) shima was shown to be a basal‐most linage within the included species     

Multi‐locus phylogeny of African pipits and longclaws (Aves: Motacillidae) highlights taxonomic inconsistencies

The globally distributed avian family Motacillidae consists of five to seven genera (Anthus, Dendronanthus, Tmetothylacus, Macronyx and Motacilla, and depending on the taxonomy followed, Amaurocichla and Madanga) and 66–68 recognized species, of which 32 species in four genera occur in sub‐Saharan Africa. The taxonomy of the Motacillidae has been contentious, with variable numbers of genera, species and subspecies proposed and some studies suggesting greater taxonomic diversity than currently recognized (five genera and 67 species). Using one nuclear (Mb) and two mitochondrial (cyt b and CO1) gene regions amplified from DNA extracted from contemporary and museum specimens, we investigated the taxonomic status of 56 of the currently recognized motacillid species and present the most taxonomically complete and expanded phylogeny of this family to date. Our results suggest that the family comprises six clades broadly reflecting continental distributions: sub‐Saharan Africa (two clades), the New World (one clade), Palaearctic (one clade), a widespread large‐bodied Anthus clade, and a sixth widespread genus, Motacilla. Within the Afrotropical region, our phylogeny further supports recognition of Wood Pipit Anthus nyassae as a valid species, and the treatment of Long‐tailed Pipit Anthus longicaudatus and Kimberley Pipit Anthus pseudosimilis as junior subjective synonyms of Buffy Pipit Anthus vaalensis and African Pipit Anthus cinnamomeus, respectively. As the disjunct populations of Long‐billed Pipit Anthus similis in southern and East Africa are genetically distinct and geographically separated, we propose a specific status for the southern African population under the earliest available name, Nicholson's Pipit Anthus nicholsoni. Further, as our analyses indicate that Yellow‐breasted Pipit Anthus chloris and Golden Pipit Tmetothylacus tenellus are both nested within the Macronyx longclaws, we propose transferring these species to the latter genus.     

Phylogeny and systematics of the Orycteropodidae (Mammalia,Tubulidentata)

The systematics of the order Tubulidentata is poorly known. Its phylogeny has never been thoroughly analysed and only a single review has ever been performed, which was over 30 years ago. This situation has hampered palaeoecological and palaeobiogeographical studies of these Neogene mammals. The present revision of the Orycteropodidae deals with the phylogeny and systematics of all African and Eurasian species over the last 20 Myr. The first comprehensive cladistic analysis of the family is presented here. The results of this analysis, based on 39 coded morphological characters, supplemented by non‐coded features taken from all over the skeleton, was used to reconstruct the phylogeny of the order Tubulidentata. Two distinct lineages within the genus Orycteropus are recognized and characterized. The new genus Amphiorycteropus is subsequently created, in order to harmonize taxonomy and phylogeny. The fossil genera Leptorycteropus and Myorycteropus are validated, bringing the number of genera in the order Tubulidentata to four. Moreover, within the family Orycteropodidae, the number of confirmed species is now 14. The outcome of this study allows us to propose a consistent palaeobiogeographical scenario for aardvarks. Finally, this revision represents the most comprehensive work on the evolutionary history of the order Tubulidentata to date, and provides a new framework for future studies. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 649–702.     

Phylogeny, Genome Evolution, and Host Specificity of Single-Stranded RNA Bacteriophage (Family Leviviridae)

Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species, such as Qβ and MS2, have been studied as model systems for replication, translation, and the role of secondary structure in gene regulation. Using nucleotide sequences from the coat and replicase genes we present the first statistical estimate of phylogeny for the family Leviviridae using maximum-likelihood and Bayesian estimation. Our analyses reveal that the coliphage species are a monophyletic group consisting of two clades representing the genera Levivirus and Allolevivirus. The Pseudomonas species PP7 diverged from its common ancestor with the coliphage prior to the ancient split between these genera and their subsequent diversification. Differences in genome size, gene composition, and gene expression are shown with a high probability to have changed along the lineage leading to the Allolevivirus through gene expansion. The change in genome size of the Allolevivirus ancestor may have catalyzed subsequent changes that led to their current genome organization and gene expression. Received: 3 March 2000 / Accepted: 17 October 2000     

Morphology‐based phylogenetic analysis and classification of the family Rhinocryptidae (Aves: Passeriformes)

The family Rhinocryptidae comprises an assemblage of 12 genera and 55 species confined to the Neotropical region. Here we present the first morphology‐based phylogenetic study of the Rhinocryptidae, using 90 anatomical characters (62 osteological, 28 syringeal) scored for all genera of the family and representatives of all families of the infraorder Furnariides. Parsimony analysis of this dataset recovered 7428 equally most‐parsimonious trees. The strict consensus of those trees was completely resolved at the genus level, with the topology (Liosceles (Psilorhamphus ((Eleoscytalopus + Merulaxis) (Acropternis ((Teledromas + Rhinocrypta) ((Pteroptochos + Scelorchilus) (Eugralla (Myornis + Scytalopus)))))))). The monophyly of the Rhinocryptidae as presently understood was recovered with strong support [eight synapomorphies and Bremer support (BS) = 6). Strongly supported internal arrangements included the basal position of the Amazonian genus Liosceles relative to the rest of the family (four synapomorphies, BS = 4), a clade containing Acropternis through Scytalopus (six synapomorphies, BS = 4), and other less inclusive nodes. The main points of congruence between the present morphological phylogeny and previous molecular phylogenetic work on the family were clades supported by six or more synapomorphies and Bremer values of 6–7: Eleoscytalopus + Merulaxis (eight synapomorphies, BS = 6), Scelorchilus + Pteroptochos (seven synapomorphies, BS = 7), Rhinocrypta + Teledromas (seven synapomorphies, BS = 7), and Eugralla + Myornis + Scytalopus (six synapomorphies, BS = 6). A classification derived from the morphological phylogeny is proposed, with new suprageneric taxa being named and diagnosed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 377–432.     

First phylogenetic analysis of the subfamily Pachydeminae (Coleoptera,Scarabaeoidea, Melolonthidae): the Palearctic Pachydeminae*

This paper presents the first phylogenetic analysis of Pachydeminae Reitter, 1902 ; one of the least known subfamilies of Melolonthidae, `leaf‐chafers' (Scarabaeoidea, Coleoptera). Some species of Pachydeminae have recently become agricultural pests in southern Spain. We analysed the phylogenetic relationships among 49 species belonging to 16 genera in the Palearctic region, based on a set of 63 morphological characters from the adult external morphology, wing anatomy, mouthparts and male and female genitalia. The last three sets of characters are described here for the first time. The phylogeny shows that the Palearctic Pachydeminae are monophyletic within the subfamily. Mouthparts and male and female genitalia provide the best synapomorphies for intergeneric relationships. In contrast, most of the external morphological characters used in the taxonomy of Pachydeminae are highly homoplastic. The phylogeny shows a basal split between the genera Hemictenius Reitter, 1897; Pachydema Castelnau, 1832, and the monospecific Peritryssus Reitter, 1918; and a second clade including the rest of genera. The remarkable Peritryssus is confirmed as a Pachydeminae, being the sister group to the monophyletic Hemictenius . Except for the position of P. rubripennis (Lucas, 1848) and P. zhora Normand, 1951, the phylogeny supports the monophyly of Pachydema but rejects the traditional division into species groups and the monophyly of the endemic Canarian species. In contrast, Tanyproctus Faldermann, 1835, must be rejected as polyphyletic. Otoclinius Brenske, 1896, is also probably polyphyletic (two new species synonymies), whereas Leptochristina Baraud and Branco, 1991 , is either mono‐ or paraphyletic. The two Mediterranean genera Ceramida Baraud, 1897, and Elaphocera Gené, 1836, form a monophyletic group, this clade being the best supported by the data set. Ceramida is clearly monophyletic, whereas Elaphocera is probably monophyletic except for E. barbara Rambur, 1843, which shares with Ceramida the character state for numerous mouthpart and genitalic characters. The phylogeny questions the generic status of the small and monospecific genera of Pachydeminae. The monotypic Alaia Petrovitz, 1980 , and Brenskiella Berg, 1898, are merged with Europtron Marseul, 1867, into one clade, whereas Atanyproctus Petrovitz, 1954, is grouped with some species of Tanyproctus , and the monotypic Pachydemocera Reitter, 1902 , is proposed as a junior synonym of Elaphocera .     

A review of Gammaridae (Crustacea: Amphipoda): the family extent,its evolutionary history,and taxonomic redefinition of genera

By molecular analysis of a high number of gammarids, including 29 out‐group genera, we could assure the monophyly of Gammaridae. To avoid the paraphyly of the family, we propose the omission of Pontogammaridae, Typhlogammaridae, and all Baikalian families. Similarly, the genera Fontogammarus, Sinogammarus, Lagunogammarus, Pephredo, Neogammarus, and Laurogammarus may be cancelled. But, tens of Baikal genera, nested within Gammarus, are so diverse that they must be retained, although rendering Gammarus paraphyletic. Besides we propose the polyphyletic Echinogammarus–Chaetogammarus group to be divided into monophyletic genera Echinogammarus s. str., Homoeogammarus, Parhomoeogammarus, Marinogammarus, R elictogammarus gen. nov. , Chaetogammarus, and T richogammarus gen. nov. These solutions made it possible to complete the first analysis of the family evolution in light of its phylogeny. Perimarine clades are mainly basally split clades, whereas in some ancient lakes extremely rich endemic faunas had developed polyphyletically. The troglobiotic Typhlogammarus group from Dinarides and Caucasus formed a monophylum, whereas the troglobiotic assemblage of Gammarus species is highly polyphyletic. Reduction of the uropod III endopodite, which classically distinguishes between the genera Gammarus and Echinogammarus, appeared to be highly polyphyletic. Protective dorsal pleonal projections occur scattered across the family and beyond, whereas lateral projections were limited to species of ancient lakes, so both structures were polyphyletic. The evolutionary history of Gammaridae was investigated with ten different calibration schemes, which produced incompatible results; however, the most probable scenario is a late rise of the family, which can only explain the absence of Gammaridae species around the Indo‐Pacific. © 2015 The Linnean Society of London