Molecular phylogeny of Vipera Laurenti, 1768 and the related genera Macrovipera (Reuss, 1927) and Daboia (Gray, 1842), with comments about neurotoxic Vipera aspis aspis populations

We used mtDNA sequences (cytochrome b and NADH dehydrogenase subunit 2) to reconstruct molecular phylogenies of Vipera sensu lato, Vipera sensu stricto, and Vipera aspis. Three major clades were identified within the Vipera s.l. group: (1) the European vipers, (2) the oriental vipers, consisting of Montivipera (Vipera 2) plus Macrovipera lebetina, and (3) a group of Asian and North African vipers consisting of Daboia russelii, V. palaestinae, and Macrovipera mauritanica. We also distinguished three clades within the monophyletic European Vipera group: V. ammodytes, V. aspis, and V. latastei, and Pelias with monophyly of Vipera 1 uncertain. Within V. aspis, the specimens collected in France formed the sister group of an Italian clade. The "neurotoxic" French population of V. aspis, which has a specific venom profile, separated from other French V. aspis early in the history of this group.     

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.     

CLOSTERIUM MONILIFERUM-EHRENBERGII (CHAROPHYCEAE, CHLOROPHYTA) SPECIES COMPLEX VIEWED FROM THE 1506 GROUP I INTRON AND ITS2 OF NUCLEAR rDNA

To assess phylogenetic relationships and speciation modes in Closterium , we sequenced two noncoding regions of the nuclear ribosomal cistron, the 1506 group I intron in small subunit and the internal transcribed spacer 2, for a total of 58 strains of the Closterium moniliferum-ehrenbergii species complex. These include both homothallic and heterothallic C. moniliferum Erenberg ex Ralfs v. moniliferum , heterothallic C. moniliferum v. submoniliferum (Woronichin) Krieger, and heterothallic C. ehrenbergii Meneghini ex Ralfs that can be divided into several mating groups. We found no or very little sequence divergence within single mating groups of C. ehrenbergii and among all heterothallic strains of C. moniliferum v. moniliferum or C. moniliferum v. submoniliferum. Nevertheless, sequence divergence was much greater between those mating groups of C. ehrenbergii and also among the three traditional taxa . Maximum parsimony and maximum likelihood analyses showed that the taxon C. ehrenbergii was not monophyletic. The two varieties of C. moniliferum appeared as a sister clade to certain mating groups of C. ehrenbergii . Among the clades that were recovered in different trees by maximum parsimony and maximum likelihood analyses, we consistently found two large conspicuous clades: clade I consisted of mating groups A, B, C, H, K, and L of C. ehrenbergii whose zygospores have smooth-walls, and clade II contained the mating groups D, E, I, J, and S whose zygospores are scrobiculate. Phylogenetic incongruences observed are discussed from the viewpoints of the different molecular nature of the group I intron and internal transcribed spacer 2, as well as putative rapid diversification of the mating groups and probable ancient ancestral hybridization.     

Evolutionary insight into the Peripatopsis balfouri sensu lato species complex (Onychophora: Peripatopsidae) reveals novel lineages and zoogeographic patterning

Evolutionary relationships in the widely distributed velvet worm Peripatopsis balfouri sensu lato species complex were examined using DNA sequence data, gross and SEM morphology. Sequence data were generated for the COI mtDNA and the 18S rRNA loci and analysed using a Bayesian inference approach, maximum likelihood and maximum parsimony. Phylogenetic analyses of the combined DNA sequence data revealed that Peripatopsis clavigera specimens from the southern Cape (clade 1) was sister to P. balfouri sensu lato specimens from the Cederberg Mountains (clade 2). Within the main P. balfouri sensu lato species complex, three addition clades could be discerned (clades 3, 4 and 5). The obligatory troglobitic species Peripatopsis alba was equidistant between the Cape Peninsula and adjacent interior (clade 3) and the two Boland and Hottentots Holland Mountains (clades 4 and 5). On the Cape Peninsula, P. stelliporata specimens nested among the sympatric P. balfouri sensu lato specimens. The Cape Peninsula specimens were sister to specimens from Jonkershoek site 1, Kogelberg and Simonsberg. Two Boland clades were retrieved, comprising Du Toit's Kloof, Bain's Kloof and Mitchell's Pass and sister (in clade 4) to specimens from the Boland and adjacent Hottentots Holland Mountains in clade 5. These results revealed complex biogeographic patterning in the P. balfouri sensu lato species complex. The presence of sympatric, yet genetically discrete species pairs at six of the sample localities (Du Toit's Kloof, Simonsberg, Jonkershoek sites 1 and 2, Kogelberg and Landroskop) suggests that there is reproductive isolation between the lineages. Divergence time estimations suggest a Miocene/Pliocene/Pleistocene cladogenesis. A taxonomic revision of the P. balfouri sensu lato species complex was undertaken to stabilize the taxonomy. P. clavigera is monophyletic and retained for the southern Cape specimens, P. balfouri sensu stricto is now confined to the Cape Peninsula and adjacent interior, while P. stelliporata is regarded as a junior synonym of the latter taxon, P. alba is endemic to the Wynberg Cave systems on the Cape Peninsula. Three novel species (Peripatopsis cederbergiensis, sp. n., Peripatopsis bolandi sp. n. and Peripatopsis purpureus, sp. n.) are described.     

Molecular phylogenetics and taxonomy of the African mole-rats, genus Cryptomys and the new genus Coetomys Gray, 1864

Cryptomys represents the most speciose and widely distributed genus of the Bathyergidae (Mammalia; Rodentia), a family of mole-rats endemic to sub-Saharan Africa. Throughout its range in southern, central, and western Africa, Cryptomys displays diversity in terms of morphology, patterns of behavior, and chromosome number, thus complicating the systematics of the group. A molecular phylogeny was obtained by separate and combined analyses of the mitochondrial 12S rRNA and intron I of the nuclear transthyretin gene for chromosomally and geographically diverse populations of Cryptomys. Our results show that Cryptomys sensu lato is comprised of two distinct and divergent monophyletic clades: hottentotus and mechowi. Based on our analyses, we propose the elevation of the mechowi clade to the genus Coetomys, retaining Cryptomys as the generic epithet of the South African hottentotus clade. This is supported by: (1) reciprocal monophyly of the two lineages based on independent datasets, (2) the level of sequence divergence observed between these lineages relative to other genera (i.e., Bathyergus and Georychus), and (3) different patterns of chromosomal evolution, with Cryptomys sensu stricto being karyotypically conserved (2N=54) and Coetomys exhibiting high karyotypic diversity (2N=40-78).     

Phylogenetic relationships in Disa based on non-coding trnL-trnF chloroplast sequences: evidence of numerous repeat regions

Sequence data from the intron and spacer of the trnL-F chloroplast region elucidate the phylogenetic relationships of the tribe Diseae (Orchidoideae: Orchidaceae). Within Diseae, 41 species of Disa, two of Brownleea, three of Satyrium, and two of Corycium were included, with five species of Habenaria sensu lato (Orchideae) and one epidendroid as outgroups. The sequences revealed substitutions and considerable length variation, due mainly to the presence of repeat motifs. Phylogenetic analysis using parsimony revealed five distinct clades. The branching order of the five weakly supported the paraphyly of Diseae, with the successive divergence of Brownleea, Corycium, Habenaria, Satyrium, and Disa. Within the monophyletic Disa, three main groupings appeared, two strongly supported clades representing sect. Racemosae and sect. Coryphaea and the third grouping containing several clades currently grouped into sections based on morphological phylogenies. Some discrepancies between the molecular phylogeny and the phylogeny based on morphological characters may require reevaluation of some of the morphological characters. The presence of different numbers of repeat motifs, both among different taxa and within taxa, indicates that these characters may be phylogenetically informative at the population level.     

Molecular phylogeny of the yellow peach moth,Conogethes punctiferalis (Lepidoptera: Crambidae): distribution of two genetic lineages across Japan

Mating disruption using synthetic sex pheromones is an effective pest-control method to prevent the evolution of insecticide resistance. Although the sex pheromone of the yellow peach moth Conogethes punctiferalis (Guenée) (Lepidoptera, Crambidae) has already been identified and artificially synthesized, mating disruption in the field has been less successful than expected. Such ineffectiveness may be caused by genetic variation in the attractiveness of the sex pheromone across moth populations. To evaluate this possibility, we evaluated the genetic population structure of this species across 10 populations in Japan. We found that two clades were present at the mtDNA COI region, each clade was sympatrically distributed, and no genetic structure was detected among the populations. In addition, the frequencies of the two clades did not differ between the samples in pheromone traps using two types of blend and those hand collected from infested fruit. Our mating experiment revealed random mating between the two clades. Our results strongly suggest that the genetic variation in the attractiveness of the sex pheromone is minimal and symmetrical gene flow likely occurs between the clades in the field.

     

Re-evaluation of the enigmatic species complex Saprolegnia diclina-Saprolegnia parasitica based on morphological, physiological and molecular data

The phylogenetic relationships among isolates of the Saprolegnia diclina-Saprolegnia parasitica complex were investigated based on ITS rDNA sequences, and correlated with morphological and physiological characters. The isolates studied belong to five phylogenetically separate clades. The majority of presumed parasitic isolates, mostly isolated from fish lesions, fell within a clade that comprises isolates which has been variously named as S. diclina Type 1, S. parasitica, Saprolegnia salmonis or just as unnamed Saprolegnia sp. Presence of bundles of long-hooked hairs on secondary cysts, high frequency of retracted germination, and oogonia production at 7 degrees C (when occurring) were characteristic of this clade. A single isolate identified as S. diclina Type 2 clustered in a clade along with Saprolegnia ferax isolates. The isolates identified as S. diclina s. str. (S. diclina Type 3) distributed in two clades and appeared closely related to Saprolegnia multispora and to a number of Chilean isolates identified as Saprolegnia australis. The ITS sequences of clade I were almost identical even though the isolates were of diverse geographical origins and showed physiological and morphological differences and variations in their pathogenicity. This suggest these species reproduces clonally even in apparently sexually competent isolates. Adaptation to parasitism in Saprolegnia might have occurred at spore level by the development of long-hooked hairs to facilitate host attachment and selection of a retracting germination. The use of the name S. parasitica should be assigned to isolates of clade I that contained isolates forming cysts with bundles of long-hooked hairs.     

Phylogenetic analysis of Petunia sensu Jussieu (Solanaceae) using chloroplast DNA RFLP

BACKGROUND AND AIMS: The phylogenetic relationships of Petunia sensu Jussieu (Petunia sensu Wijsman plus Calibrachoa) are unclear. This study aimed to resolve this uncertainty using molecular evidence. METHODS: Phylogenetic trees of 52 taxa of Petunia sensu Jussieu were constructed using restriction fragment length polymorphism (RFLP) of chloroplast DNA digested with 19 restriction enzymes and hybridized with 12 cloned Nicotiana chloroplast DNA fragments as probes. KEY RESULTS: In all, 89 phylogenetically informative RFLPs were detected and one 50 % majority consensus tree was obtained, using the maximum parsimony method, and one distance matrix tree, using the neighbour joining method. Petunia sensu Wijsman and Calibrachoa were monophyletic sister clades in both trees. Calibrachoa parviflora and C. pygmaea, previously thought to differ from the other species in terms of their cross-compatibility, seed morphology, and nuclear DNA content, formed a basal clade that was sister to the remainder of Calibrachoa. Several clades found in the phylogenetic trees corresponded to their distribution ranges, suggesting that recent speciation in the genus Petunia sensu Jussieu occurred independently in several different regions. CONCLUSIONS: The separation of Petunia sensu Wijsman and Calibrachoa was supported by chloroplast DNA analysis. Two groups in the Calibrachoa were also recognized with a high degree of confidence.     

Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences

We examined intra-specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Interpopulation sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out-group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.     

Horizontal Transfer of Genetic Material among Saccharomyces Yeasts

The genus Saccharomyces consists of several species divided into the sensu stricto and the sensu lato groups. The genomes of these species differ in the number and organization of nuclear chromosomes and in the size and organization of mitochondrial DNA (mtDNA). In the present experiments we examined whether these yeasts can exchange DNA and thereby create novel combinations of genetic material. Several putative haploid, heterothallic yeast strains were isolated from different Saccharomyces species. All of these strains secreted an a- or alpha-like pheromone recognized by S. cerevisiae tester strains. When interspecific crosses were performed by mass mating between these strains, hybrid zygotes were often detected. In general, the less related the two parental species were, the fewer hybrids they gave. For some crosses, viable hybrids could be obtained by selection on minimal medium and their nuclear chromosomes and mtDNA were examined. Often the frequency of viable hybrids was very low. Sometimes putative hybrids could not be propagated at all. In the case of sensu stricto yeasts, stable viable hybrids were obtained. These contained both parental sets of chromosomes but mtDNA from only one parent. In the case of sensu lato hybrids, during genetic stabilization one set of the parental chromosomes was partially or completely lost and the stable mtDNA originated from the same parent as the majority of the nuclear chromosomes. Apparently, the interspecific hybrid genome was genetically more or less stable when the genetic material originated from phylogenetically relatively closely related parents; both sets of nuclear genetic material could be transmitted and preserved in the progeny. In the case of more distantly related parents, only one parental set, and perhaps some fragments of the other one, could be found in genetically stabilized hybrid lines. The results obtained indicate that Saccharomyces yeasts have a potential to exchange genetic material. If Saccharomyces isolates could mate freely in nature, horizontal transfer of genetic material could have occurred during the evolution of modern yeast species.     

Oogonial biometry and phylogenetic analyses of the Pythium vexans species group from woody agricultural hosts in South Africa reveal distinct groups within this taxon

Pythium vexans fits into the internal transcribed spacer (ITS) clade K sensu Lévesque & De Cock (2004). Within clade K, P. vexans forms a distinct clade containing two enigmatic species, Pythium indigoferae and Pythium cucurbitacearum of which no ex-type strains are available. In South Africa, as well as in other regions of the world, P. vexans isolates are known to be heterogeneous in their ITS sequences and may consist of more than one species. This study aimed to investigate the diversity of South African P. vexans isolates, mainly from grapevines, but also citrus and apple using (i) phylogenetic analyses of the ITS, cytochrome c oxidase (cox) I, cox II, and β-tubulin regions and (ii) seven biometric oogonial parameters. Each of the phylogenies clustered P. vexans isolates into a single well-supported clade, distinct from other clade K species. The β-tubulin region was phylogenetically uninformative regarding the P. vexans group. The ITS phylogeny and combined cox I and II phylogenies, although each revealing several P. vexans subclades, were incongruent. One of the most striking incongruences was the presence of one cox subclade that contained two distinct ITS subclades (Ib and IV). Three groups (A-C) were subjectively identified among South African P. vexans isolates using (i) phylogenetic clades (ITS and cox), (ii) univariate analysis of oogonial diameters, and (iii) multivariate analyses of biometric oogonial parameters. Group A is considered to be P. vexans s. str. since it contained the P. vexans CBS reference strain from Van der Plaats-Niterink (1981). This group had significantly smaller oogonial diameters than group B and C isolates. Group B contained the isolates from ITS subclades Ib and IV, which formed a single cox subclade. The ITS subclade IV isolates were all sexually sterile or produced mainly abortive oospores, as opposed to the sexually fertile subclade Ib isolates, and may thus represent a distinct assemblage within group B. Although ITS subclade Ib included the P. indigoferae ex-type sequence, this group was considered to be P. vexans since South African isolates in this clade produced globose sporangia. Group C contained four apple isolates that were related to, but distinct from P. cucurbitacearum. Although P. vexans groups A-C might be distinct species, they are not described here as such due to (i) these groups only representing some of the known diversity in P. vexans, (ii) conflicting gene tree phylogenies preventing phylogenetic species identification, and (iii) sexually sterile isolates preventing the broad application of biometrical data.     

Higher‐level phylogeny of diving beetles (Coleoptera: Dytiscidae) based on larval characters

A comprehensive higher‐level phylogeny of diving beetles (Dytiscidae) based on larval characters is presented. Larval morphology and chaetotaxy of a broad range of genera and species was studied, covering all currently recognized subfamilies and tribes except for the small and geographically restricted Hydrodytinae, where the larva is unknown. The results suggest several significant conclusions with respect to the systematics of Dytiscidae including the following: monophyly of all currently recognized subfamilies, although Dytiscinae when considered in a broad context is rendered paraphyletic by Cybistrinae; currently recognized tribes are monophyletic except for Agabini, Hydroporini and Laccornellini; inter‐subfamily and inter‐tribe relationships generally show weak support, except for a few well supported clades; three distinct clades are recognized within Dytiscinae [Dytiscini sensu lato (i.e. including the genera Dytiscus Linnaeus and Hyderodes Hope), Hydaticini sensu lato, and Cybistrini]; and recognition of Pachydrini as a distinct tribe. Other less robust results include: Methlini sister to the rest of Hydroporinae; relative basal position of Laccornini, Hydrovatini and Laccornellini within Hydroporinae; close relationship of Agabinae and Copelatinae; Matinae nested deep within Dytiscidae, as sister to a large clade including Colymbetinae, Coptotominae, Lancetinae and Dytiscinae sensu lato; the sister‐group relationship of Agabetini and Laccophilini is confirmed. The results presented here are discussed and compared with previous phylogenetic hypotheses based on different datasets, and the evolution of some significant morphological features is discussed in light of the proposed phylogeny. All suprageneric taxa are diagnosed, including illustrations of all relevant synapomorphies, and a key to separate subfamilies and tribes is presented, both in traditional (paper) format and as an online Lucid interactive identification key.     

Test of the monophyly of Odostomiinae and Turbonilliinae (Gastropoda, Heterobranchia, Pyramidellidae) based on 16S mtDNA sequences

Schander, C., Halanych, K. M., Dahlgren, T. & Sundberg, P. (2003) Test of the monophyly of Odostomiinae and Turbonilliinae (Gastropoda, Heterobranchia, Pyramidellidae) based on 16S mtDNA sequences. — Zoologica Scripta, 32 , 243−254.
While gastropod phylogeny has received much recent attention, relationships within some major gastropod clades have still not been studied. The Pyramidellidae is one such group, comprising more than 6000 named species in more than 350 genera. We sequenced part of the mitochondrial 16S gene from 32 species in an attempt to clarify pyramidellid phylogeny and employed a successive alignment approach that allowed us to maximize the phylogenetic signal of the data. Neighbour-joining, maximum parsimony and likelihood analyses recovered two distinct clades. One clade consisted of Noemiamea which nested within Odostomia ( sensu stricto ) . The inclusion of Brachystomia , Megastomia , Jordaniella and Liostomia within Odostomia is not supported. The second clade comprised Spiralinella , Brachystomia , Boonea , Jordaniella , Liostomia and Parthenina . Our results further suggest that Turbonilla, as interpreted by most authors, is polyphyletic. This study shows that the 16S gene is useful in unravelling pyramidellid phylogeny but needs to be combined with other data (including molecular, morphological and developmental) to fully clarify the evolutionary relationships.     

Phylogenetics and biogeography of Mascarene angraecoid orchids (Vandeae, Orchidaceae)

The large angraecoid orchid clade (subtribe Angraecinae sensu lato) has undergone extensive radiation in the western Indian Ocean, which includes Africa, Madagascar, and a number of Indian Ocean islands, such as the Mascarene Archipelago. To investigate systematics and biogeography of these Mascarene orchids, phylogenetic relationships were inferred from four plastid DNA regions, trnL intron, trnL-F intergenic spacer, matK gene, and rps16 intron. Parsimony and Bayesian analyses provided identical sets of relationships within the subtribe; the large genus Angraecum as currently circumscribed does not form an exclusive clade. Bonniera, an endemic genus to Reunion, is shown to be embedded in part of Angraecum. Evidence from our research supports the main origin of Mascarene Angraecinae from Madagascar, and although there were many independent colonizations, only a few of the lineages radiated within the Mascarene Archipelago.     

Molecular systematics of the neotropical shovelnose catfish genus Pseudoplatystoma Bleeker 1862 based on nuclear and mtDNA markers

Pseudoplatystoma is a commercially important genus of Neotropical migratory catfishes widely distributed in all major river basins of South America. Historically, only three species were recognized, but a recent revision proposed eight putative morphospecies for the genus. A molecular study based on mitochondria DNA (mtDNA) provided support for recognition of only some of the species and raised questions about species boundaries in this group. We present a more encompassing analysis based on mtDNA (cytochrome b, 818bp) and nuclear DNA-based phylogenies (Rag1 intron 1, 664bp and S7 intron 1, 635bp) for a more extensive sampling (279 individuals from 42 localities) of all putative species in all major river basins. Patterns generated by individual gene genealogies and a multispecies coalescent analysis provided evidence to suggest recognition of only four distinct species in this genus: Pseudoplatystoma magdaleniatum, Pseudoplatystoma corruscans, Pseudoplatystoma tigrimun (sensu lato) and Pseudoplatystoma fasciatum (sensu lato). The species phylogeny places P. magdaleniatum as the sister group to all the other species in the genus, but the relationships among P. fasciatum s.l, P. tigrimum s.l., and P. corruscans could not be resolved with confidence.     

Random interbreeding between cryptic lineages of the Common Raven: evidence for speciation in reverse

DNA sequence studies frequently reveal evidence of cryptic lineages in morphologically uniform species, many of which turn out to be evolutionarily distinct species. The Common Raven (Corvus corax) includes two deeply divergent mtDNA lineages: one lineage seems restricted to western North America and the other is Holarctic in distribution. These deep clades hint of the possibility of cryptic species in the western United States. We tested this hypothesis in a population consisting of an equal proportion of both mtDNA clades, by quantifying mating patterns and associated fitness consequences with respect to mtDNA. We also tested for morphological, behavioural and ecological correlates of sex and mtDNA clade membership. Mate pairings were random with respect to mtDNA clades, and there were no differences in reproductive success between assortatively and nonassortatively mated pairs. We found no differences in survival or resource use between clades. There were no differences in morphological or behavioural characters between mtDNA clades, except one clade trended towards greater mobility. These results suggest there are no barriers to gene flow between mtDNA clades and argue that the mtDNA clades have remerged in this population, likely due to a lack of ecological or signal differentiation between individuals in each lineage. Hence, in Common Ravens, phylogeographic structure in mtDNA is a reflection of likely past isolation rather than currently differentiated species.