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.     

Cytochrome b-based phylogeny of the Praomys group (Rodentia,Murinae): a new African radiation?Phylogénie du groupe Praomys (Rodentia,Murinae) basée sur le cytochrome b : une nouvelle radiation africaine ?

Complete cytochrome b gene sequences allows, for the first time, establishing a nearly complete phylogeny among the Praomys group sensu lato. The genera Praomys, Mastomys and Stenocephalemys appear paraphyletic. Myomys is polyphyletic and this genus name probably needs to be restricted to its type species, M. verreauxii. The genera Zelotomys and Colomys appear as sister groups. Mastomys pernanus and Malacomys verschureni nest within the Praomys group, but their generic assignation must be further clarified. The genus Heimyscus appears closest to Praomys than to Hylomyscus. The different lineages probably result from an adaptive radiation at the end of the Miocene.     

Molecular phylogeny of Myomys/Stenocephalemys complex and its relationships with related African genera

Partial 16S rRNA mitochondrial gene sequences were used to infer the phylogenetic relationships among Stenocephalemys albocaudata, S. griseicauda and Myomys albipes, three closely related Ethiopian endemic murines and a selection of related species (Myomys daltoni, Praomys delectorum, Mastomys natalensis, Hylomyscus kaimosae, and Colomys goslingi) from other African regions. The obtained phylogeny confirms the close relationship between M. albipes and the two Stenocephalemys species, but it also suggests that both the genera Myomys and Stenocephalemys are paraphyletic, as M. albipes is closer to Stenocephalemys than to M. daltoni and S. griseicauda is more closely related to M. albipes than to S. albocaudata. These data, if confirmed, would argue that M. albipes should be renamed S. albipes. In conclusion, our study suggests that morphological similarity is not always a reliable measure for close genetic relationship in murines. Morphological similarity among species that evolved under similar ecological conditions can be the result of convergent evolution rather than a consequence of recent common ancestry.     

Chromosomal phylogeny of Muridae: a study of 10 genera

The karyotypes of 10 different species of the family Muridae (Acomys airensis, Arvicanthis niloticus, Hylomyscus stella, Malacomys longipes, Mastomys huberti, Myomys daltoni, Mus musculus, Rattus norvegicus, Thamnomys gazellae, and Uranomys ruddi) are compared by different banding techniques. From a reconstruction of the presumed ancestral karyotype of the Muridae the sequence of the various rearrangements leading to the present karyotypes is proposed in order to determine their phylogenetic relationships. In particular, the present karyotypes of the mouse and rat differ from the ancestral one by at least 12 and 7 rearrangements, respectively. A clear tendency for accumulation of a specific type of rearrangement in a given branch of the cladogram is observed. In regard to the mouse, a large number of translocations, with break points situated in the proximal part of the long arms, have occurred, which conserved the acrocentric form of the ancestral chromosomes but led to multiple recombinations of the bands.     

Diversity and distribution of murid rodent populations between forest and derived savanna sites within south western Nigeria

Southward encroachment of the derived savanna zone with its attendant denudation of the rainforest in Nigeria adversely affects the diversity and distribution of mammals, particularly murid rodents. This study was carried out to establish the identities of murid rodent populations and to compare their diversity between forest and derived savanna sites within south western Nigeria. Identification of captured specimens was carried out by multivariate statistics of body and skull measurements, and also by analysis of certain discrete characters. Six species were identified: Praomys tullbergi, Hylomyscus stella, Mastomys natalensis, Arvicanthis rufinus, Lemniscomys striatus and Lophuromys sikapusi. Forest sites possessed a higher Shannon’s diversity index (1.685) than the derived savanna sites (0.978), containing a higher number of taxa and larger abundance of murid rodents. This underscores the negative impact that encroachment of the derived savanna has upon diversity of animals in areas that were once forest.     

Small mammal diversity and dynamics within Nigeria,with emphasis on reservoirs of the lassa virus

Nigeria has a rich small mammal community, with several species implicated as carriers of zoonotic microbes such as the Lassa virus (LASV). We sought to elucidate the diversity and distribution of these animals (including known LASV reservoirs) geographically, habitat-wise and seasonally. Our DNA-assisted survey detected at least 19 small mammal species amongst 790 specimens. Diversity indices were similar between ecological zones and also between endemic and non-endemic areas for Lassa fever. Mastomys natalensis, the most renowned LASV host, was present in eight out of nine localities sampled. We also described the spatial occurrence of other known LASV hosts such as M. erythroleucus and Hylomyscus pamfi, including carriers of LASV-like arenaviruses such as Mus (Nannomys) spp. The most numerous rodents (Mastomys natalensis, M. erythroleucus, and Praomys daltoni) were captured mainly inside human dwellings. Reproductive activity occurred throughout the year, but led to population peaks for M. natalensis in the dry season and for M. erythroleucus and P. daltoni in the rainy season. Extensive geographic distribution of LASV rodent reservoirs, with population peaks in different seasons, shows that the risk of rodent-to-human transmission of LASV is greater than currently realized.     

Phylogeny of the scathophagidae (Diptera, calyptratae) based on mitochondrial DNA sequences

The family Scathophagidae constitutes, together with members of the families Muscidae, Fannidae, and Anthomyiidae, the Muscoidea superfamily. The species Scathophaga stercoraria has been used extensively to investigate questions in animal ecology and evolution, particularly as a model system for studies of sperm competition and life history evolution. However, no phylogenetic studies have ever been performed on the Scathophagidae and the relationships within this family remain unclear. This study represents a molecular approach aimed at uncovering the phylogenetic relationships among 61 species representing 22 genera of Scathophagidae. A fragment of the terminal region of the mitochondrial gene COI (subunit I of the cytochrome oxidase gene) was sequenced in scathophagid species covering a wide geographic area, as well as a diverse spectrum of ecological habitats. Several clades grouping different genera and species have been identified, but the resolution power of the COI was insufficient to establish the exact relationships between these clades. The molecular data confirm the existence of a group consisting of the genera Delina, Chylizosoma, and Americina, which could represent the subfamily Delinae. Concerning the controversial position of the genus Phrosia, our data clearly suggest that it should be removed from the Delinae and placed within the genus Cordilura. Monophyly of most genera was confirmed, except for the genus Scathophaga, which should be divided into several different taxa.     

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.     

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)     

Phylogenetic relationships of the Clavelinidae and Pycnoclavellidae (Ascidiacea) inferred from mtDNA data

Abstract. The phylogenetic relationships within the Order Aplousobranchiata (Ascidiacea) are largely unexplored. In this work, we study the phylogenetic status of the genera Clavelina and Pycnoclavella. Traditionally, both genera had been included in the family Clavelinidae, until the new family Pycnoclavellidae was defined, removing the genus Pycnoclavella from Clavelinidae. Not all authors accept the validity of Clavelina and Pycnoclavella as distinct genera, let alone their belonging to different families. In addition, the assignment of species to these genera, as well as to the genus Archidistoma , has been controversial. We analyzed sequences of the mitochondrial gene cytochrome c oxidase subunit I belonging to ten species of Pycnoclavella (including several formerly assigned to Archidistoma and Clavelina ), 11 species of Clavelinidae, and ten species of other aplousobranch genera belonging to seven families, plus two outgroups. Two different tree construction methods (maximum likelihood and Bayesian inference) showed similar results. Pycnoclavella and Clavelina appeared in distinct clades but formed a monophyletic group relative to representatives of the main families of the order Aplousobranchiata. Our phylogenetic results indicate that both genera are valid but should be included within a single family, with the name Clavelinidae having precedence. The monotypic clavelinid genus Nephtheis branches in our trees within the clade of the genus Clavelina. Our results also confirm that some forms assigned to Archidistoma and Clavelina have been misplaced and belong to the genus Pycnoclavella. Pycnoclavella martae n.sp. is described.     

Comparative seed morphology of <Emphasis Type="Italic">Leandra</Emphasis> (Miconieae,Melastomataceae)

The seed morphology of 79 species of neotropical Miconieae (Melastomataceae) is presented. These species have been chosen, in majority, from the polyphyletic genus Leandra. A few other species from the polyphyletic genera Miconia, Ossaea, and Clidemia were also sampled, because of potential similarities. Sixteen morphological seed types are defined after analysis through light microscopy and scanning electron microscopy. The seed morphology appears to possess a great deal of variability on the level of the overall shape as well as the structure and the surface of the testa. The different types defined here do not match with genera or sections, but rather are composed of species coming from different genera. In comparison with a preliminary molecular phylogeny study done on Leandra, some types of seeds are related to well supported clades. In some cases seed morphology corresponds with natural groups of species, thus being of high phylogenetic importance.     

New polymorphic microsatellite loci for rodents of the genus Mastomys using PCR multiplexing,and cross‐species amplification in Myomys and Praomys

The Praomys complex contains some of the most important agricultural pests of Africa, including Mastomys species. We describe the development of nine supplementary microsatellite markers isolated from Mastomys huberti. We show the potential utility of M. huberti microsatellites as population markers for two other species of Mastomys, and two other species of the Praomys complex, Myomys daltoni and Praomys cf. rostratus.     

Host range of Cercospora apii and C. beticola and description of C. apiicola, a novel species from celery

The genus Cercospora is one of the largest and most heterogeneous genera of hyphomycetes. Cercospora species are distributed worldwide and cause Cercospora leaf spot on most of the major plant families. Numerous species described from diverse hosts and locations are morphologically indistinguishable from C. apii and subsequently are referred to as C. apii sensu lato. The importance and ecological role that different hosts play in taxon delimitation and recognition within this complex remains unclear. It has been shown that Cercospora leaf spot on celery and sugar beet are caused respectively by C. apii and C. beticola, both of which are part of the C. apii complex. During this study we characterized a new Cercospora species, C. apiicola, which was isolated from celery in Venezuela, Korea and Greece. The phylogenetic relationship between C. apiicola and other closely related Cercospora species was studied with five different gene areas. These analyses revealed that the C. apiicola isolates cluster together in a well defined clade. Both C. apii and C. beticola sensu stricto form well defined clades and are shown to have wider host ranges and to represent distinct species.     

Mitochondrial phylogeny of African wood mice, genus Hylomyscus (Rodentia, Muridae): implications for their taxonomy and biogeography

This paper investigates the usefulness of two mitochondrial genes (16S rRNA and cytochrome b) to solve taxonomical difficulties within the genus Hylomyscus and to infer its evolutionary history. Both genes proved to be suitable molecular markers for diagnosis of Hylomyscus species. Nevertheless the resolving powers of these two genes differ, and with both markers (either analyzed singly or in combination), some nodes remain unresolved. This is probably related to the fact that the species emerged during a rapid diversification event that occurred 2-6 Myr ago (4-5 Myr ago for most divergence events). Our molecular data support the recognition of an "aeta" group, while the "alleni" and "parvus" groups are not fully supported. Based on tree topology and genetic divergence, two taxa generally recognized as subspecies should be elevated at the species level (H. simus and H. cf kaimosae). H. stella populations exhibit ancient haplotype segregation that may represent currently unrecognized allopatric species. The existence of cryptic species within H. parvus is questioned. Finally, three potentially new species may occur in West Central Africa. The Congo and Oubangui Rivers, as well as the Volta and Niger Rivers and/or the Dahomey gap could have formed effective barriers to Hylomyscus species dispersal, favoring their speciation in allopatry. The pronounced shifts in African climate during the late Pliocene and Miocene, which resulted in major changes in the distribution and composition of the vegetation, could have promoted speciation within the genus (refuge theory). Future reports should focus on the geographic distribution of Hylomyscus species in order to get a better understanding of the evolutionary history of the genus.     

基于线粒体Cyt b基因的线蛱蝶亚科的系统发育

基于线粒体Cytb基因部分序列,以波蛱蝶为外群,采用邻接法、最大简约法和贝叶斯法分别构建了中国线蛱蝶亚科10属25种蝶类的系统发育树,探讨了各主要类群间的系统发育关系。其结果表明,所有线蛱蝶亚科聚为两大枝:第一枝包括环蛱蝶属、菲蛱蝶属、蟠蛱蝶属和缕蛱蝶属,其中缕蛱蝶属与环蛱蝶族亲缘关系较近;第二枝包括丽蛱蝶属、穆蛱蝶属、线蛱蝶属、带蛱蝶属、律蛱蝶属和翠蛱蝶属,其中线蛱蝶属为非单系群,翠蛱蝶属和律蛱蝶属则为单系发生,并构成姐妹群。     

Speciation,phenotypic plasticity,or ontogeny,the case of the genus Galkinius (Pyrgomatidae,Cirripedia, Crustacea)

Barnacles of the genus Galkinius occupy a large spectrum of host corals, making it one of the least host‐specific genera within the Pyrgomatidae. Molecular analyses show that within the genus Galkinius there are highly supported clades, suggesting that the genus Galkinius is a complex of evolutionarily significant units (ESUs). The morphology of the opercular valves has been used as the basis for the separation of species of Galkinius. In this study, morphological variability was found both between specimens within ESUs extracted from different host species and between specimens extracted from the same colony. Identifications based on the opercular valves cannot therefore be assigned to different species despite being genetically distinguishable. It is proposed that in many cases the differences between valve morphology of different species of Galkinius are the outcome of ontogeny. Allometric growth of the valves has resulted in differences in the proportions of the parts of the valve. © 2015 The Linnean Society of London     

Phylogenetic Relationships within the Excavating Hadromerida (Porifera), with a Systematic Revision

This study was performed to ascertain the relationships among clionid and spirastrellid species from the Mediterranean Sea, based on phylogenetic criteria. A matrix of 34 taxa and 20 characters was analysed. Cladistic analysis using PAUP produced 12 equally parsimonious trees of 54 steps (CI=0.648, RI=0.865). Resolution was high in all parts of the strict consensus tree except in those which involved relationships among the most characteristic clionid species: those having only tylostyles as megascleres and, if microscleres are present, these being spirasters. Six monophyletic groups, three of them represented by monospecific clades, appear in the totally resolved part of the trees, which supports their separation into different genera. On the basis of the results obtained, the species at present within the genus Cliona have been allocated to five different genera: Scantilletta, Pione, Volzia, Bernatia and Cliona , while Dotona and Cliothosa are maintained as separate genera. Scantilletta and Pione are genera erected by de Laubenfels (1936 Pap. Tortugas Lab. 30 , 1–225) and Gray (1867 Proc. Zool. Soc. Lond. XXXII , 492–558) respectively, and whose diagnoses are amended here. Volzia and Bernatia are proposed as new genera to include Cliona albicans and Cliona rovignensis , and Cliona vermifera , respectively. Thus, the genus Cliona clearly appears in our analysis as a polyphyletic group. It is only maintained provisionally to harbour species whose position cannot be clearly ascertained from the information at hand. Skeletal characters such as spicule types and skeletal arrangement have proven to be useful in discriminating some genera and families but they do not completely resolve the phylogeny of this group of species. Biochemical, genetic, cytological or reproductive information, when available, may help in the resolution of the phylogenetic tree.     

Phylogeny of the Spiny African Daisies (Compositae, tribe Arctotideae, subtribe Gorteriinae) based on trnL-F, ndhF, and ITS sequence data

The tribe Arctotideae (African Daisies), of the flowering plant family Compositae (Asteraceae), is a diverse and interesting group with a primarily southern African distribution (ca. 13 genera, 215 species) and many species in the Cape Floristic Region. It is divided into two subtribes: Arctotidinae (ca. 5 genera, 85 species) and Gorteriinae (ca. 8 genera, 130 species). The monophyly of the genera within the subtribe Gorteriinae and their relationship to one another was investigated using 71 samples/212 sequences including 64/141 of which are newly reported from three phylogenetic markers, two from chloroplast DNA (trnL-F and ndhF) and one from the nuclear genome (ITS). The outgroup was composed of seven members from the sister subtribe. Results show the subtribe Gorteriinae to be divided into three monophyletic groups, the Gazania-Hirpicium-Gorteria group, the Didelta group, and the Berkheya-Cullumia group. Within these three groups are 13 sub-groups, one of which has sub-clades. The genus Berkheya Ehrh. is paraphyletic, falling into five different sub-groups. The two monotypic genera, Cuspidia and Heterorhachis are not nested within any of the Berkheya clades. Hirpicium and Cullumia each have most of their taxa in a monophyletic group, but they also have one or two taxa associated with other clades. Four of the five sub-groups of Berkheya have morphologically recognizable shared characters, such as habit and spines that have been recognized by past studies. However, the grouping of one species with Didelta is difficult to explain. Support for the major clades and most of the sub-groups is strong but the relationships among some of the terminal taxa are variable.     

Patterns of karyotype evolution in complexes of sibling species within three genera of African murid rodents inferred from the comparison of cytogenetic and molecular data

Here we report on the analysis of three rodent sibling species complexes belonging to the African genera Arvicanthis, Acomys and Mastomys. Using cytogenetic and molecular approaches we set out to investigate how karyotype and molecular evolution are linked in these muroid sibling species and, in particular, to what extent chromosomal changes are relevant to cladogenic events inferred from molecular data. The study revealed that each complex is characterized by a distinct pattern of karyotype evolution (karyotypic orthoselection), and a specific mutation rate. However we found that the general pattern may be considerably modified in the course of evolution within the same species complex (Arvicanthis, Acomys). This observation suggests that karyotypic orthoselection documented in numerous groups is not so much a reflection of selection of a definite type of chromosomal mutation, as suggested by the classical concept, but is due to genome structure of a given species. In particular, karyotypic change appears related to the quantity and chromosomal location of repeated sequences. The congruence between the chromosomal and molecular data shows that chromosomal changes are often valuable phylogenetic characters (Arvicanthis and Mastomys, but not Acomys). However, most importantly the approach underscores the value of incorporating both in order to gain a better understanding of complex patterns of evolution. Moreover, the fact that every cladogenetic event in Mastomys is supported by two pericentric inversions allowed us to hypothesize that genetic differentiation is initiated by the suppression of recombination within inverted segments, and that the accumulation of multiple pericentric inversions reinforces genetic isolation leading to subsequent speciation. Finally, the low sequence divergences distinguishing karyotypically distinct sibling species within Arvicanthis and Mastomys emphasizes the power of combining cytogenetic and molecular approaches for the characterization of unrecognized components of biodiversity.     

SPECIES PHYLOGENY OF COSMARIUM AND STAURASTRUM (DESMIDIACEAE) BASED ON RBC L SEQUENCES

Cosmarium and Staurastrum are the two most diverse genera of placoderm desmids (Family Desmidiaceae), with approximately 1100 and 800 species, respectively. Phylogenetic analysis of relationships of species has been extremely difficult. In a monograph of North American placoderm desmids, Prescott et al. described early phylogenetic work that concluded Staurastrum to be polyphyletic and certainly polymorphic. Likewise, Cosmarium has also been viewed as polyphyletic, and a number of workers have proposed splitting these genera. The classical view of West and West grouped species within each genus into two divisions and 6–8 sections based on wall features and semicell shape. We sequenced rbc L from 18 species of Cosmarium (2 divisions, 7 sections) and 12 species of Staurastrum (2 divisions and 7 sections) and performed a phylogenetic analysis (parsimony, maximum likelihood, bootstrap) using other placoderm desmids and Zygnematales as outgroups. The results exhibit little support for the monophyly of sections or divisions of the two genera. Furthermore, although there is support for the monophyly of clades within each genus, there is also support for a separate clade containing species from both genera.