Molecular phylogeny of the Praomys complex (Rodentia: Murinae): a study based on DNA/DNA hybridization experiments.

Within the Murinae (Muridae: Rodentia), the African rats of the Praomys group, whose systematics has been studied through different approaches, have raised numerous taxonomic problems. Different taxa related to Praomys have successively been described, among which Mastomys, Myomys and Hylomyscus were considered either as separate genera or subgenera of Praomys. In order to clarify the relationships within the Praomys group, we conducted a series of DNA/DNA hybridization experiments involving different species of Praomys, Mastomys, Myomys and Hylomyscus plus other Murinae and a Cricetomyinae. This study indicates that the Praomys complex is a monophyletic entity clearly separated from the other African and Asian Murinae. If Mastomys and Hylomyscus appeared to be independent genera, the taxonomic situation of Praomys and Myomys is more difficult to ascertain. Indeed, Praomys tullbergi appears more closely related to Myomys daltoni than to another species of Praomys , namely P. jacksoni , suggesting paraphyly for Praomys. Furthermore, P. jacksoni is as distant from P. tullbergi as from any species of Mastomys. Additional species of Praomys and, especially, of Myomys , are needed for reaching a definitive conclusion on these latter taxa. The Praomys group is more related to Mus than to Rattus. To calibrate our molecular distances with geological time, we used a dating of 10 Myr for the Musi Rattus dichotomy. The inferred rate of molecular evolution suggests a dating of c. 8 Myr for the separation of the Praomys group from the Mus lineage.     

The phylogeny of the Praomys complex (Rodentia: Muridae) and its phylogeographic implications

Among the African Murinae (Rodentia, Muridae), the Praomys complex, whose systematics has been studied by different approaches, has raised numerous taxonomic problems. Different taxa, namely Praomys, Mastomys , Myomys and Hylomyscus have been considered either as separate genera or subgenera of Praomys . In order to understand the relationships within the Praomys complex and to test the monophyly of the genus Praomys , a cladistic analysis was conducted, based on morpho-anatomical factors involving different species of Praomys , Mastomys , Myomys and Hylomyscus. The results indicate that the Praomys complex is monophyletic, as are the genera Hylomyscus , Mastomys and Myomys , whereas the genus Praomys appears paraphyletic. Indeed, a group of species including Praomys jacksoni was found to be more closely related to the genera Mastomys and Myomys than to a Praomys tullbergi -group. The biotopes and the distribution areas of the species were mapped on the phylogeny. It appears that the different clades each present a relative ecological cohesion and are arranged according to a gradient from closed to open habitats. From there, an evolutionary scenario is proposed for the emergence of the different clades and species of the genus Praomys sensu stricto.     

Chromosomal and protein evolution in morphologically similar species of Praomys sensu lato (Rodentia, Muridae)

Evidence of extensive chromosomal evolution in a biologically and economically important group of African murids of the Praomys/Mastomys complex was provided by examination of G- and C-band chromosomal data on P. coucha (2n = 32), P. fumatus (2n = 38), P. hildebrandti (2n = 32), P. jacksoni (2n = 28), P. misonnei (2n = 36), and P. cf. tullbergi (2n = 35). A coding system was developed for the chromosomal characters, and analyses were performed by a computer program to find the shortest tree with a minimum of 35 autosomal rearrangements (pericentric inversions, complex translocations, centric fusions, centric fissions, tandem fusions, euchromatic additions, and heterochromatic additions). The resulting phylogenetic hypothesis differs from traditionally accepted hypotheses regarding this complex group of rodents. The cytogenetic data show that 1) there is no support for the dichotomy of Mastomys/Praomys previously based on morphology, 2) the 2n = 32 species from eastern Africa (P. hildebrandti) is distinct from the 2n = 32 species from southern Africa (P. natalensis), and 3) there is a close association between P. jacksoni and P. cf. tullbergi. Polyacrylamide gel electrophoresis of liver membrane proteins demonstrated few differences in protein mobilities between species and even fewer between individuals of the same species taken from different habitats and localities in Kenya. Monoclonal antibodies produced against liver proteins of one species and tested for reactivity to other species confirmed the evolutionary similarity of species of this complex. This immunologic approach may provide a robust data set for future phylogenetic studies of muroid rodents.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular evidence suggests an ancient radiation for the fairy shrimp genus Streptocephalus (Branchiopoda: Anostraca)

Phylogenetic relationships among assumed Gondwanan aquatic inland invertebrate fauna are generally largely neglected, and biogeographical hypotheses for these organisms are generally inferred from historic (palaeogeographical) and contemporary distribution patterns. The distribution of the monogeneric thermophilic freshwater fairy shrimp family Streptocephalidae ( Streptocephalus ) provides a particularly useful framework to test the three contrasting biogeographical scenarios proposed for the evolution of this group: (1) the genus evolved in Laurasia and subsequently dispersed into Africa and North America; (2) the genus evolved and dispersed out of Africa and (3) the current distribution of the genus is the result of vicariance following the fragmentation of Gondwana. In the present study, the phylogenetic relationships of species in this genus are examined with the use of two mitochondrial genes (12S rRNA and COI mtDNA), while the phylogenetic relationships among the North American species and selected African taxa was investigated using the nuclear fragment (5.8S-ITS-1-18S). Phylogenetic results indicate that Streptocephalus probably evolved in Gondwana and that the current distribution patterns are a consequence of a combination of vicariance and limited dispersal. The implications for the evolution of continental freshwater crustaceans are discussed.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 313–327.     

The impact of the Congo River and its tributaries on the rodent genus Praomys: speciation origin or range expansion limit?

We studied the taxonomy, distribution, and ecology of species within Praomys, a common rodent genus present in rainforests and montane forests in sub‐Saharan Africa. The taxonomy of the group is problematic, and for the sampled region of Kisangani (Democratic Republic of Congo) no prior genetic study has been published. We used a combination of molecular (cyt b sequencing) and craniometric techniques (canonical analyses of skull measurements) for the species identification of a total of 654 specimens. We confirm the presence of Praomys minor in the region, up to now only known from the type and paratype specimens. At least seven species are present in the Kisangani region, and two clades occur along both banks of the Congo River. The present‐day distribution of the genus seems to be influenced by large‐scale rainforest fragmentation related to drier periods in geological history. The Congo River could in this case constitute a modern barrier to gene flow when the climate enabled rainforest expansion. The tributaries of the Congo River play no role in limiting Praomys species distribution, apart from the Aruwimi River for Praomys jacksoni s.l. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 983–1002.     

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.     

The taxonomic status and relationships of bracken ferns (Pteridium: Dennstaedtiaceae) from sub-Saharan Africa

Two morphotypes of bracken fern in the genus Pteridium Gled. ex Scop. occur in sub-Saharan Africa. The more common and widespread of these is assigned in contemporary systematic treatments to the European subspecies, P. aquilinum (L.) Kuhn ssp. aquilinum . We show that this African form is separable morphometrically and genomically from the European subspecies, and reinstate its earlier name P. aquilinum ssp. capense (Thunb.) C.Chr. The second African bracken, with a more localized tropical distribution mainly in the drainage basins of the Congo and Zambezi River systems, is confirmed as P. aquilinum ssp. centrali-africanum Hieron. ex R.E. Fr. We reject suggestions that this taxon be treated as a full species. Phenetic cluster analysis based on use of Arbitrarily Primed Polymerase Chain Reaction (A-P PCR) and Inter Simple Sequence Repeat (ISSR) fingerprinting of the nuclear genome provides evidence that the two African brackens are more closely related to each other than to other taxa, and sister to a grouping of the European sspp. aquilinum and pinetorum . The two African subspecies share solely with ssp. aquilinum a distinctive chloroplast haplotype carrying a 5-base direct repeat in the rps 4 –trn S region, confirming the close phyletic relationship between sspp. aquilinum , capense and centrali-africanum .  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 311–321.     

Southern African pholcid spiders: revision and cladistic analysis of Quamtana gen. nov. and Spermophora Hentz (Araneae: Pholcidae), with notes on male−female covariation

The southern African pholcid spiders previously assigned to Pholcus and Spermophora are revised and their phylogenetic position within Pholcidae is analysed cladistically. Two distinct groups are recognized: the first is restricted to the Cape region and probably correctly placed in Spermophora ; it includes Spermophora peninsulae Lawrence and four new species. The second is more widely distributed in southern and eastern South Africa, and reaches as far north as Cameroon, Congo (Democratic Republic) and Uganda; it is assigned generic status ( Quamtana gen. nov .), and includes two species transferred from Pholcus [ Q. leptopholcica (Strand), Q. ciliata (Lawrence)] as well as 23 new species. A key to the pholcid spiders of South Africa is presented. A close correlation between a male character (distance between cheliceral apophyses) and a female character (distance between pockets on epigynum) is documented in Quamtana .  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 139 , 477−527.     

Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

The phylogenetic relationships of orbiniid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA and nuclear 18S rRNA genes. Both genes were analysed separately and in combination using maximum likelihood, Bayesian inference and maximum parsimony. Regardless of the method used, a clade consisting of the investigated Orbiniidae, Methanoaricia dendrobranchiata and Questa was strongly supported by the 18S dataset. The analysis of the combined dataset suggests inclusion of M. dendrobranchiata within the Orbiniidae with close relationships to species of Orbinia and Phylo, rather than as a sister taxon to all other orbiniids. Evidence is given for the paraphyletic status of Leitoscoloplos , Naineris , Orbinia , Phylo and Scoloplos , which represent the most species-rich genera of the Orbiniidae. It is thus reasoned that the morphological characters presently used for genus diagnosis are not informative for cladistic analysis. No support is found for the hypothesis that taxa of the Protoariciinae represent juveniles of Orbiniinae. Instead, in the case of Protoaricia oerstedi , strong support for a progenetic origin is found.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 59−73.     

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.     

Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data

The genus Mus encompasses at least 38 species divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . The subgenus Mus , which comprises the house mouse and related species, is by far the most extensively studied, although the subgenus Nannomys is the most speciose. Although the relationships within the subgenus Mus are rather well characterized, those between subgenera are still unclear. In the present study, phylogenetic analyses of the whole genus were performed using a larger species sample of Nannomys than in previous studies, and a nuclear gene (IRBP) in addition to mitochondrial data (cytochrome b and 12S rRNA). Members of the Acomyinae and Murinae were used as outgroups. Separate and combined analyses were performed with maximum parsimony, maximum likelihood and Bayesian methods, and divergence times were estimated. The results showed that the monophyly of the genus Mus and of each subgenus was strongly supported by the three genes and the combined analysis. The phylogenies derived from the three genes were on the whole congruent; however, several conflicting topologies were observed such as the relationships between the three Asian species of the subgenus Mus ( caroli , cervicolor and cookii ). Increasing the taxonomic sampling of Nannomys did not satisfactorily improve the resolution of relationships between the four subgenera. In addition, molecular calibrations indicate that the Mus and Nannomys radiation coincided with major environmental changes.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 417–427.     

Geographical diversification of the genus Cicer (Leguminosae: Papilionoideae) inferred from molecular phylogenetic analyses of chloroplast and nuclear DNA sequences

Cicer L. (Leguminosae: Papilionoideae) consists of 42 species of herbaceous or semi-shrubby annuals and perennials distributed throughout the temperate zones of the Northern Hemisphere. The origin and geographical relationships of the genus are poorly understood. We studied the geographical diversification and phylogenetic relationships of Cicer using DNA sequence data sampled from two plastid regions, trnK / matK and trnS - trnG , and two nuclear regions, the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of nuclear ribosomal DNA, from 30 species. The results from the phylogenetic analyses of combined nuclear and chloroplast sequence data revealed four well-supported geographical groups: a Middle Eastern group, a West-Central Asian group, an Aegean–Mediterranean group, and an African group. Age estimates for Cicer based on methods that do not assume a molecular clock (for example, penalized likelihood) demonstrate that the genus has a Mediterranean origin with considerable diversification in the Miocene/Pliocene epochs. Geological events, such as mountain orogenesis and environmental changes, are major factors for the dispersal of Cicer species. The early divergence of African species and their geographically distinct region in the genus suggest a broader distribution pattern of the genus in the past than at present.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 175–186.     

Morphological character evolution and molecular trees in sepiids (Mollusca: Cephalopoda): is the cuttlebone a robust phylogenetic marker?

The sepiids are characterized by their cuttlebone or sepion, an internal shell resulting from secondary mineralization of a chitinous 'gladius'. The various species are identified using a combination of shell criteria and 'soft-part' characters. Using mitochondrial genes, we established phylogenetic relationships of sepiids including the three accepted genera ( Sepia , Sepiella , Metasepia ) and a species complex of uncertain status ( Doratosepion ). We showed the Sepia genus to be paraphyletic and found no direct correlation between geographical distribution and systematics. We mapped, on the molecular tree, shell characteristics commonly used as reliable diagnostic criteria for taxonomy. Due to the plasticity of the shell, these characters did not appear phylogenetically informative. In an attempt to define systematic categories related to phylogenetic relationships, new clear synapomorphies need to be established for each genus, necessitating a revision of the genus Sepia .  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 139–150.     

Delimiting species in the hoplonemertean genus Tetrastemma (phylum Nemertea): morphology is not concordant with phylogeny as evidenced from mtDNA sequences

The marine genus Tetrastemma contains monostiliferous hoplonemertean (phylum Nemertea) species which mostly undergo direct development with no free-swimming stages of larvae. The lack of a pelagic phase, and the fact that many benthic species lay eggs attached to the bottom substrate, are obvious restrictions on dispersal and gene flow. Nevertheless, some of the species, for example T. candidum and T. melanocephalum , are described as ubiquitous and are reported from waters all over the world. We studied genetic variation and evolutionary relationships in order to assess whether they are concordant with external characters in samples of nine morphologically distinct forms formally named as different Tetrastemma species, from different geographical localities. We estimated the phylogeny and species network based on 539 base pairs of the mitochondrial protein-coding gene cytochrome oxidase-1 (CO1) for 30 ingroup specimens. From this, we assessed the evolutionary history and phylogenetic relationships between these forms. We conclude that in most cases there was no correspondence between evolutionary lineage and morphotype. Our results thus indicate that morphological species delimitation in nemerteans may be questionable, and that this in turn may have a profound effect upon estimates of species diversity within the phylum.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 86 , 201–212.     

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.     

On the systematic status of the desert plated lizard (Angolosaurus skoogi): phylogenetic inference from DNA sequence analysis of the African Gerrhosauridae

The desert plated lizard ( Angolosaurus skoogi ), a 'sand sea' endemic of the northern Namib Desert, exhibits remarkable morphological convergence with other dune-dwelling lizards worldwide. This distinct ecomorphic condition sets Angolosaurus apart from the remaining genera in the family Gerrhosauridae. Indeed, a morphological phylogeny addressing generic relationships within the Cordyliformes (Cordylidae + Gerrhosauridae) identified Angolosaurus as the earliest diverging taxon among African gerrhosaurids. We re-evaluated the basal status of Angolosaurus , conducting a molecular phylogenetic analysis of the African and Madagascan gerrhosaurid genera. Our survey involved a comprehensive species-level comparison among the four nominal genera of mainland Africa ( Angolosaurus , Cordylosaurus , Tetradactylus and Gerrhosaurus ). Mitochondrial DNA sequence data from the cytochrome b , ND2, 12S and 16S rRNA genes were combined for analysis using both parsimony and maximum likelihood procedures. In contrast to the morphological hypothesis, our results do not depict Angolosaurus as the sister taxon to other African gerrhosaurids. Rather, the molecular analyses consistently place Angolosaurus within Gerrhosaurus , rendering the latter genus paraphyletic.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78 , 253–261.     

Chromosome variation in the genus Pinellia (Araceae) in China and Japan

The chromosome numbers of 23 populations belonging to seven species of Pinellia Tenore were counted. The basic chromosome number of all the species studied was x  = 13, and the previously reported basic numbers x  = 9 and x  = 14 in P. ternata and P. cordata were not confirmed. Chromosome numbers of 2 n  = 26 in P. polyphylla and 2 n  = 78 in P. integrifolia are reported for the first time. Heptaploid (7 x ) and nonuploid (9 x ) are new ploidy levels reported for P. ternata , and hexaploid for P. cordata. Taxonomic, phylogenetic and phytogeographical inferences are made for the genus. Particular attention was given to P. ternata , the most widely distributed species in the genus, and considerable variation of chromosome number was found in its different populations. Based on chromosome studies of 11 populations of P. ternata , together with 12 populations reported in previous studies, the lower reaches of the Yangze River are identified as its centre of origin. From there it dispersed, with generation of hexaploid, heptaploid, octoploid and nonuploid forms.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 449–455.     

A new Dryopteris (Pteropsida: Dryopteridaceae) species from south-central Africa

Dryopteris katangaensis , a new species endemic to the Katango–Zambian centre of endemism (Congo-Zambezi watershed) in Zambia and the Democratic Republic of Congo is described and illustrated. The morphological differences between the new species and D. schimperiana are discussed, and the ferns endemic to the Katango–Zambian Centre are reviewed.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 237–242.