Phylogenetic relationships of the north-eastern Atlantic and Mediterranean blenniids

The phylogenetic relationships of 27 north-eastern Atlantic and Mediterranean blennioids are analysed based on a total of 1001 bp from a combined fragment of the 12S and 16S mitochondrial rDNA. The most relevant results with implications in current blenniid taxonomy are: (1) Lipophrys pholis and Lipophrys (=  Paralipophrys ) trigloides are included in a well-supported clade that by the rule of precedence must be named Lipophrys ; (2) the sister species of this clade are not the remaining species of the genus Lipophrys but instead a monotypic genus comprising Coryphoblennius galerita ; (3) the smaller species of Lipophrys were recovered in another well-supported and independent clade, which we propose to be recognized as Microlipophrys ; (4) although some authors included the genera Salaria and Lipophrys in a single group we have never recovered such a relationship. Instead, Salaria is more closely related to the genera Scartella and Parablennius ; (5) the genus Parablennius , which was never recovered as a monophyletic clade, is very diverse and may include several distinct lineages; (6) the relative position of Aidablennius sphynx casts some doubts on the currently recognized relationships between the different blenniid tribes. Meristic, morphological, behavioural and ecological characters support our results and are also discussed. The possible roles of the tropical West African coast and the Mediterranean in the diversification of blenniids are discussed.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 283–295.     

Phylogeography of the land snail Albinaria hippolyti (Pulmonata: Clausiliidae) from Crete, inferred from ITS-1 sequences

The polytypic Cretan land snail Albinaria hippolyti has a range that is partly fragmented and partly subdivided by hybrid zones. For this reason, it has served as a model species for investigating speciation and radiation in Mediterranean Clausiliidae. The first internal transcribed spacer ( ITS-1 ) of the nuclear ribosomal DNA was sequenced in 20 populations of A. hippolyti and phylogenetically analysed using maximum parsimony. We employed a novel method involving logarithmic weighting of gaps and topological constraints based on bootstrap values. The resulting phylogeography suggests that the species has undergone a recent cycle of range expansion and range reduction. Speciation cannot be linked to major geological vicariance events in the Miocene and Pliocene, as has been suggested previously. The subspecies A. h. arthuriana appears unrelated to other A. hippolyti subspecies, which supports recent suggestions, based on morphology, to regard it as a separate species.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 317–326.     

Molecular phylogeny of the western Atlantic species of the genus Portunus (Crustacea, Brachyura, Portunidae)

The genus Portunus encompasses a comparatively large number of species distributed worldwide in temperate to tropical waters. Although much has been reported about the biology of selected species, taxonomic identification of several species is problematic on the basis of strictly adult morphology. Relationships among species of the genus are also poorly understood, and systematic review of the group is long overdue. Prior to the present study, there had been no comprehensive attempt to resolve taxonomic questions or determine evolutionary relationships within this genus on the basis of molecular genetics. Phylogenetic relationships among 14 putative species of Portunus from the Gulf of Mexico and other waters of the western Atlantic were examined using 16S sequences of the rRNA gene. The resultant molecularly based phylogeny disagrees in several respects with current morphologically based classification of Portunus from this geographical region. Of the 14 species generally recognized, only 12 appear to be valid. We recommend that P. vossi be hereafter regarded as a junior synonym of P. spinimanus and that P. bahamensis be regarded as a junior synonym of P. depressifrons . Our analysis suggests that western Atlantic members of the genus can be subdivided into at least three well-defined clades. Pending further molecular analyses with a large subset of species, it appears that the genus is not monophyletic and that it warrants further taxonomic revision.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 211–220.     

A new species of Halisaurus from the Late Cretaceous phosphates of Morocco, and the phylogenetical relationships of the Halisaurinae (Squamata: Mosasauridae)

A new species of the basal mosasaurid Halisaurus from the Late Cretaceous (Late Maastrichtian) of the Oulad Abdoun Phosphate Basin of Morocco is described on the basis of both cranial and postcranial remains. H. arambourgi sp. nov. is characterized by unique features of the nares, frontal, parietal, girdle and limb bones. A phylogenetical analysis supports the monophyletic status of Halisaurus ; H. platyspondylus (Maastrichtian, New Jersey), H. ortliebi (Maastrichtian, Belgium) and H. arambourgi form an unresolved polytomy. This study does not support the attribution of ' Halisaurus ' sternbergii (Santonian, Kansas) to Halisaurus nor to any known genus. A new genus, Eonatator , is proposed for the reception of this species, Eonatator sternbergii comb. nov. The new taxon Halisaurinae ( Halisaurus  +  Eonatator ) is the sister-group of more advanced mosasaurids (Natantia). Halisaurines are defined by the shape of the lateral premaxilla–maxilla suture; an oblique contact plane between the parietal and the supratemporal; a preaxial ridge present on the distal two-thirds of the radius length; and tibia and fibula long and slender with slightly expanded extremities.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 447–472.     

Monophyly and phylogenetic placement of the spider genus Labulla Simon, 1884 (Araneae, Linyphiidae) and description of the new genus Pecado

The genus Labulla Simon is circumscribed in phylogenetic terms to include the species Labulla thoracica (Wider), L. flahaulti Simon and L. machadoi sp. nov. The genital anatomy of the genus is described in detail and the taxonomy of the genus is reviewed. The monophyly of Labulla is supported by numerous morphological apomorphies of the male palp and female epigynum. Based on a cladistic analysis, a new genus, Pecado gen. nov. , is erected to place Labulla impudica Denis, from Northern Africa. Lepthyphantes insularis Saito and ' Labulla ' nepula Tikader, both formerly included in Labulla , are not congeneric with the type species of Labulla .  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 359–404.     

Mitochondrial phylogeny of Arvicolinae using comprehensive taxonomic sampling yields new insights

Comprehensive taxonomic sampling can vastly improve the accuracy of phylogenetic reconstruction. Here, we present the most inclusive phylogenetic analysis of Arvicolinae (Mammalia, Rodentia) to date, combining all published cytochrome  b gene sequences of greater than 1097 bp and new sequences from two monotypic genera. Overall, the phylogenetic relationships between 69 species of voles and lemmings, representing 18 genera and 10 tribes, were studied. By applying powerful modern approaches to phylogenetic reconstruction, such as maximum likelihood and Bayesian analysis, we provide new information on the early pulse of evolution within the Arvicolinae. While the position of two highly divergent lineages, Phenacomys and Ondatra , could not be resolved, the tribe Lemmini, appeared as the most basal group of voles. The collared lemmings (Dicrostonychini) grouped together with all of the remaining tribes. The two previously unstudied monotypic genera Dinaromys and Prometheomys form a moderately well-supported monophyletic clade, possibly a sister group to Ellobius (Ellobiusini). Furthermore, with one exception, all tribes ( sensu Musser & Carleton, 2005) proved to be monophyletic and can thus be regarded as meaningful evolutionary entities. Only the tribe Arvicolini emerged as paraphyletic in both analyses because of the unresolved phylogenetic position of Arvicola terrestris . Steppe voles of the genus Lagurus were solidly supported as a sister group to the Microtus and allies clade.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 825–835.     

A molecular approach to the phylogenetic relationships of the western palaearctic Helicoidea (Gastropoda: Stylommatophora)

Molecular phylogenetic relationships among 45 members of the Helicoidea (Gastropoda: Stylommatophora) were examined using partial mitochondrial 16S rRNA sequences. Phylogenetic relationships were inferred using maximum parsimony, maximum likelihood and Bayesian methods. The reconstructed phylogenies showed a good degree of support for more recent branches, but gave little support to deeper nodes. Mitochondrial rDNA data further confirmed monophyletic status of helicids, recognized monachine hygromiid and bradybaenid clades and resolved a number of relationships in the helicelline hygromiids. With the respect to the latter assemblage, most of the anatomically based groups are confirmed, corroborating the diagnostic value of the dart-sac complex and a close affinity between Ichnusomunda sacchii and species of the genus Cernuella . Nevertheless, some well resolved branches challenge previous systematic arrangements, grouping species previously placed in different arrangements. In particular, support was not found for the monophyly of helicelline hygromiids with pedal penial innervation. Possible explanations for these incongruencies are suggested. 16S sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient radiations in the Helicoidea. It will be valuable to combine the 16S data with other gene sequences to estimate basal relationships.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 501–512.     

Systematics of African lowland rainforest Praomys (Rodentia, Muridae) based on molecular and craniometrical data

Representatives of the genus Praomys occur throughout the African intertropical zone. It is unclear how many species this genus contains, nor do we know the exact distribution ranges and phylogenetic relationships of these taxa. Using molecular (16S rRNA gene sequencing) and morphological (multivariate craniometry) analyses we clarify the taxonomy and phylogenetic relationships among the Praomys occurring in Africa's lowland tropical rainforests. We studied most species known from this area, based on specimens collected in seven countries (Guinea, Ivory Coast, Cameroon, Central African Republic, Gabon, Congo Republic and Democratic Republic of Congo). In our study, Praomys appears to be monophyletic. Our results identify two species complexes: the jacksoni complex includes at least two species ( P. jacksoni and P. mutoni ) and the tullbergi complex contains at least four species ( P. tullbergi , P. rostratus , P. misonnei , P. petteri ). Although the 16S rRNA gene appears insufficient to resolve the phylogenetic relationships among all the members of the tullbergi species complex, it is suitable for the identification of most of the studied species, and its use has allowed us to redefine the geographical limits of several species.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 145 , 539–553.     

Systematics and biogeography of the New World species of Trichadenotecnum Enderlein (Insecta: Psocodea: 'Psocoptera': Psocidae)

The taxonomy of the New World species of the genus Trichadenotecnum is revised. A total of 44 species, including 29 new species, were treated. These species are classified into 12 monophyletic species groups, eight of them newly proposed here. Two species previously assigned to Trichadenotecnum , T. pichincha New & Thornton and T. sylvaticum Turner, are recognized as not belonging to this genus. Phylogenetic relationships among 16 previously and presently proposed species groups are estimated based on a data matrix of 58 morphological characters. Trees from these analyses support monophyly of Trichadenotecnum and the proposed species groups. The New World species were divided into three major clades. Based on the phylogenetic hypothesis and distributional pattern of the species groups, the biogeographical history of the New World Trichadenotecnum is discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 651–723.     

Phylogeny and biogeography of Crinum L. (Amaryllidaceae) inferred from nuclear and limited plastid non-coding DNA sequences

The genus Crinum L. is the only pantropical genus of the Amaryllidaceae. Phylogenetic and biogeographical analyses of nrDNA ITS and plastid trnL-F sequences for all continental groups of the genus Crinum and related African genera are presented, with the genus Amaryllis used as outgroup. ITS indicates that C. baumii is more closely related to Ammocharis and Cybistetes than to Crinum sensu stricto . Three clades are resolved in Crinum s.s. One unites a monophyletic American group with tropical and North African species. The second includes all southern African species and the Australian endemic C. flaccidum . The third includes monophyletic Madagascar, Australasian and Sino-Himalayan clades, with southern African species. The trnL-F phylogeny resolves an American and an Asian/Madagscar clade, and confirms the relationship of C. flaccidum with species endemic to southern Africa. The salverform, actinomorphic perianths of subg. Crinum appear to have evolved several times in the genus from ancestors with zygomorphic perianths (subg. Codonocrinum ), thus neither subgenus is monophyletic. Biogeographical analyses place the origin of Crinum in southern Africa, as the region is optimized at all ancestral nodes in the tree topology, and in basal interior nodes of all but one of the major clades. The genus underwent three major waves of radiation corresponding to the three main clades resolved in our trees. Two entries into Australia for the genus are indicated, as are separate Sino-Himalayan and Australasian dispersal events.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 349–363.     

Evolution and phylogeny of the genus Natrix (Serpentes: Colubridae)

Some aspects of the natural history of snakes of the colubrid genus Natrix have been well studied. With their extensive European distribution and relative abundance, their ecology, reproduction and behaviour are well known. Yet other facets of their biology remain poorly understood. These include knowledge of Natrix phylogeny, hypotheses explaining the current distribution of the three extant members of the genus, and their evolution and relationships. In this study we used molecular data, the nucleotide sequences of four protein-coding mitochondrial genes (3806 bp total), to provide a well-supported phylogeny for the genus Natrix . With these molecular data, evidence from the fossil record, and knowledge of palaeogeological events, we used two approaches in designing a time scale which we used to date the major events in Natrix speciation and intraspecific variation. Our data strongly support a phylogeny for the genus in which N. maura is basal with N. natrix and N. tessellata being sister species. The calibrated molecular clock suggests that N. maura diverged from the common ancestor of the three species 18–27 mya and that N. natrix and N. tessellata diverged 13–22 mya. Although the ranges of these estimates are large they support an early Miocene to late Oligocene origin for the three species. Intraspecific divergence is estimated to have commenced 5.3, 6.0 and 6.7 mya with evolutionary rates of 1 : 1.25 : 1.35% per million years for N. maura, N. natrix and N. tessellata , respectively.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 127–143.     

Glass frogs (Centrolenidae) of Yanayacu Biological Station, Ecuador, with the description of a new species and comments on centrolenid systematics

We describe Centrolene bacatum , C. buckleyi , Cochranella posadae , and a new species of Cochranella from Yanayacu Biological Station on the Amazonian slopes of the Ecuadorian Andes. The new species differs from other species in Centrolenidae by a combination of characters, including reduced webbing between Fingers III and IV, and kidneys covered with white peritoneum. We summarize the current generic and infrageneric classification in Centrolenidae and discuss some of its problems. A phylogenetic analysis of morphological and behavioural data shows that the genera Centrolene and Cochranella might not be monophyletic; the genus Hyalinobatrachium and, in particular, the group H. fleischmanni seem to be monophyletic. However, an analysis with many more characters is needed to resolve the relationships of glass frogs.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 147 , 489–513.     

Relationships in Patagonian species of Berberis (Berberidaceae) based on the characterization of rDNA internal transcribed spacer sequences

Sequence analysis of the internal transcribed spacer (ITS) of the 18S(ITS1)-5.8S-26S(ITS2) rDNA region was performed in order to analyse the phylogenetic relationships between 13 Patagonian species of the genus Berberis (Berberidaceae). The divergence values between the pairwise sequence in the studied Patagonian species were in the range 2.9–22.9%. The lengths of the ITS1 and ITS2 sequences were in the range 227–231 bp and 220–224 bp, respectively, and the 5.8S sequence was 159 bp throughout all species . B. microphylla sensu Landrum does not appear to be monophyletic based on current sampling. Indeed, we suggest that B. microphylla should be distinguished from B. buxifolia , B. parodii , and B. heterophylla . ITS sequences, together with data obtained from morphological, biochemical, amplified fragment length polymorphism, and cytological characterizations, support the existence of diploid and polyploid hybrid speciation in the genus.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 321–328.     

A revision and phylogenetic analysis of Stapeliopsis (Apocynaceae)

A survey of morphological characters is carried out for Stapeliopsis . The information obtained from this is combined with molecular data from the plastid trn L-F DNA region and ITS1 of the nuclear encoded 18S−26S rRNA cistron, to obtain a hypothesis of the evolutionary relationships among the species. It is shown that Stapeliopsis is monophyletic in a combined molecular and morphological analysis. Stapeliopsis is sister to a clade containing Huernia , Orbea and Tromotriche . The species of Stapeliopsis group into two clades. One contains S. khamiesbergensis , S. neronis and S. urniflora , and this is highly supported. The remaining species fall into an unsupported clade in which S. exasperata is sister to the others. The genera Hermanschwartzia Plowes and Neopectinaria Plowes are rejected. It is shown that a synapomorphy for Stapeliopsis is the laterally flattened inner corona-lobes, which touch the anthers only at their bases. Eight species of Stapeliopsis are recognized, with no subgeneric divisions.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 125–155.     

Systematics and biogeography of the widespread Neotropical gekkonid genus Thecadactylus (Squamata), with the description of a new cryptic species

The systematics of the widespread neotropical gekkonid genus Thecadactylus is investigated using a combination of morphological, morphometric and mtDNA (cytochrome b ) sequence data, forming a total evidence dataset. The analysis tackles the common yet complex problem of a widespread taxon consisting of one or more cryptic species that are difficult to diagnose using morphology alone. The data are analysed using both maximum parsimony and Bayesian inference. Virtually all analyses resolve a well-supported south-western Amazonian clade distinct from the remainder of the recognized T. rapicauda . The south-western Amazonian clade is not only robustly supported, but also exclusive, geographically coherent and sufficiently distinct to warrant specific recognition. The new species is diagnosable on the basis of molecular sequences that are 23.0–26.9% divergent from those of T. rapicauda , and morphological evidence. Bayesian inference analysis robustly resolves meaningful and repeatable patterns of relationship. The biogeography of Thecadactylus is interpreted in the context of its two constituent species, and difficulties of resolving systematic and biogeographical patterns in widespread, cosmopolitan taxa are discussed. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 339–370.     

Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence

The genus Mus encompasses 38 species of mice divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . Each of these four taxa is characterized by discrete morphological as well as biochemical traits. We used two different molecular approaches to determine the relationships between these subgenera: DNA/DNA hybridization and 12S rRNA mitochondrial sequences. We compared the resulting phylogenies from each method and with phylogenies derived from morphological data. The degree of resolution of each molecular approach is discussed. The two molecular studies indicate that Mus , Pyromys , Nannomys and Coelomys are clearly distinct monophyletic groups, as previously indicated by morphological data and other biochemical and molecular approaches. There is one divergence between previous morphological and the molecular and morphological studies presented here: the position of the Indian species Mus famulus . This taxon, which was formerly included in the subgenus Coelomys , is demonstrated here to belong to the subgenus Mus. We also propose the following relationships within Mus sensu lato : Mus and Pyromys are the closest relatives, followed by Nannomys and Coelomys , whose relationships are still unclear. This arrangement is more robustly supported by DNA/DNA hybridization than by 12S rRNA data. A molecular time scale for the evolution within Mus sensu lato is proposed, using as a reference the Mus/Rattus divergence estimated by the fossil record at around 12 mya.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 137 , 385–401.     

Comparative morphology of the leaf epidermis in Schisandra (Schisandraceae)

The leaf epidermis of 127 samples representing ten species within Schisandra Michaux. and one species of the related genus, Kadsura Kaempf. ex Juss., was investigated using light and scanning electron microscopy. Many characters of the leaf epidermis in Schisandra , such as pattern of epidermal cells, type of stomata, shape of guard cell pairs and cuticular ornamentation, are usually constant within species and thus make good characters for studying the relationship between and within genera. A new character, rim number, of the outer stomatal rim in the genus is introduced. It is shown that double outer stomatal rims occur only in evergreen Schisandra species, whereas a single rim occurs in deciduous species. This character supports the classification of Schisandra into two subgenera based on habit and androecial organs. This classification is also supported by additional morphological and molecular taxonomic characters. Kadsura coccinea (Lem.) Smith A. C. is the most primitive taxon in the related genus Kadsura . The outer stomatal rim of this species also has double rims. Combined with morphological and molecular evidence, this suggests that Schisandra and Kadsura are closely related and may share a recent common ancestor.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 39–56.     

Genetic cohesion of Eresus walckenaeri (Araneae, Eresidae) in the eastern Mediterranean

The eresid spider genus Eresus is morphologically and ecologically conservative. At least three species occur in Europe. However, deep genetic divergence among geographical samples within two species, E. cinnaberinus and E. sandaliatus , may suggest more cryptic species. In the present study we investigate the genetic cohesion of the third species, Eresus walckenaeri , throughout its eastern Mediterranean distribution range, relative to the E. cinnaberinus–E. sandaliatus species complex. Eresus walckenaeri specimens were monophyletic. Genetic discreteness of E. walckenaeri in a region of sympatry with its sister species in Greece provides evidence for species integrity of E. walckenaeri within the European Eresus species complex. Eresus walckenaeri exhibited high concordance between geographical location and mtDNA genealogy. Two major phylogeographical clades were found in the Greek–Turkish and Syrian–Israel parts of the investigated area, respectively (∼6.5% sequence divergence). Concordance between geography and genetic divergence was further observed between Aegean island samples and their corresponding Greek and Turkish mainland samples, suggesting regional subdivision with gradual but potentially high dispersal propensity. Monophyly and limited regional distribution indicate Mediterranean endemic origin.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 1–9.     

Okeanomyces, a new genus to accommodate Halosphaeria cucullata (Halosphaeriales, Ascomycota)

The taxonomic affinity of Halosphaeria cucullata to Halosphaeria is reassessed based on a recent collection of this fungus. Halosphaeria cucullata is characterized by immersed, darkly coloured ascomata, clavate asci which deliquesce very early in development, and cylindrical ascospores with or without a polar cap-like appendage at one end. In a phylogenetic analysis of the LSU rDNA sequences from members of the Halosphaeriaceae, H. cucullata did not form a monophyletic clade with H. appendiculata , the type species of the genus. These results suggest that H. cucullata should not be included in Halosphaeria . Okeanomyces gen. nov. is proposed to accommodate this fungus.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 223–229.