Evolution in the Genus Geum

Even though the alpine landscape is naturally fragmented and vegetative reproduction is important in Geum reptans, I conclude that gene flow and repeated seedling recruitment during succession might be more frequent than commonly suggested and is similar at different altitudes. Random genetic drift plays an important role in population differentiation and is suggested to account for the high variation in growth and reproduction among populations. Gene flow may additionally counteract selective forces in alpine plants from contrasting habitats: plants performed similar in most traits within the same environmental treatment irrespective of origin. This indicates limited adaptation to different habitats and a high phenotypic plasticity in G. reptans. Despite of the overall low competition strength and susceptibility to warm temperature, great size-dependent plasticity in the proportion of sexual vs. clonal reproduction ensures population peristence and reproduction in a lrage range of habitat conditions. Selection for larger seeds along the altitudinal trajectory can be confirmed in a majority of alpine species, but is not generally operating. My results suggest that seed weight only rarely changes as a single trait, but rather evolves as an element of a correlated set of characters involving taxonomic differentiation at the species or at least infra-specific level. In contrary to the findings with G. reptans in the naturally fragmented alpine landscape, Scabiosa columbaria from recently created habitat remnants is affected by habitat fragmentation more severely. Local extinction risk of S. columbaria is suggested to be increased as a consequence of a decreased viability and of reduced phenotypic plasticity due to genetic erosion. However, there is only weak indirect evidence for a poorer plant performance of small populations, indicating that population size is not always the best indicator for population viability and genetic diversity. Restoration efforts should therefore not only tend towards increasing local population sizes, but should also consider genetic diversity by itself accounting for possible interactions between genetic and non-genetic effects on population viability. My results suggest, that plants from naturally fragmented habitats are clearly less affected by isolation than plants in recently fragmented habitats. From the results with Geum reptans it can be concluded that phenotypic plasticity may be a successful strategy to cope with contrasting habitat conditions in the alpine landscape and probably also buffers against possible effects of natural fragmentation.

The spider infraorder Mygalomorphae includes the funnel-web spiders, tarantulas, trapdoor spiders and their kin. Because of their particular life history characteristics, systematic revisions of mygalomorph taxa are fundamentally informative and of broader biological interest, but also a matter of conservation priority. Mygalomorph spiders are relatively long-lived, usually with limited dispersal abilities, high habitat specificity, and a long historical presence in areas relative to landscape processes. These characteristics lead to high levels of speciation and local endemism in many mygalomorph lineages, and a build-up of genetic structure between and within species at fine spatial scales. From the perspective of a researcher, high levels of genetic structure and speciation make mygalomorph lineages ideal for investigating biogeographic history and speciation processes. From a conservation perspective, local endemism, habitat specificity and low dispersal ability mean that mygalomorph populations (and potentially species) are sensitive to habitat modification, and have little ability to disperse from, or recolonise, affected areas. In the context of a biodiversity crisis, and hindered by ‘impediments’ to systematics and taxonomy, systematists must allocate their time and efforts carefully. Given their inherent vulnerability and the value of research on mygalomorph taxa, revisions of poorly known elements of this fauna are both urgent and of evolutionary importance. Intergeneric relationships within the spiny trapdoor spiders of Australasia (Idiopidae: Arbanitinae) were recently stabilised. This provided a foundation for targeted work into genera within the subfamily, many of which had never received substantial systematic attention. Prior to my project, only seven species of golden trapdoor spider (tribe Euoplini, previously all in the genus Euoplos) had been described from eastern Australia, despite the genus spanning the length and breadth of the eastern mesic zone. The genus was seen as a conservation priority because it is highly diverse in south-eastern Queensland, Australia, a region where urban development (sub-coastal) and agricultural development (inland) threaten to encroach on the natural remnants where undescribed species occur. Furthermore, undocumented variability in morphology and burrow entrance structure in the genus presented a valuable opportunity to study morphology and behavioural evolution in mygalomorph spiders. In this thesis, I compare and integrate morphological data, behavioural data (burrow entrance type) and molecular data in order to: infer the first robust phylogeny of the genus Euoplos; investigate the phylogenetic signal of morphology and burrow entrance architecture to generate evolutionary hypotheses of broader relevance to mygalomorph systematics; and revise select lineages in the genus based on their conservation priority. In Chapter 2, I use morphological data to guide targeted sampling of Euoplos from eastern Australia, before generating the first comprehensive molecular phylogeny for the genus. Male morphology and burrow entrance architecture are then compared with the molecular phylogeny to reveal the existence of two widespread, sympatric lineages which differ in their burrow entrance structure and male morphology: the ‘wafer-door’ lineage and the ‘plug-door/palisade’ lineage. I also identify a taxonomic error in the literature, where males belonging to a wafer-door species were incorrectly linked with females belonging to a sympatric species in the plug-door/palisade lineage. In chapter 3, I present a systematic revision of a group of Euoplos which were recovered as a clade in Chapter 2, and which construct remarkable ‘palisade’ type burrow entrances. Revision of the group was seen as urgent because all species have very small natural ranges and occur in remnant rainforest habitats within heavily modified landscapes. This revision results in the description of four new species, and I was also able to identify species-specific differences in burrow entrance architecture, providing a means of non-intrusive species identification. In Chapter 4, all available data are integrated into a total-evidence phylogenetic analysis of the entire tribe Euoplini. Ancestral state reconstruction is used to demonstrate how morphological and behavioural (burrow entrance architecture) characters relate to topology. This chapter results in the reclassification of the tribe, with two new genera erected: Cryptoforis (wafer-door lineage) and Narellea (a single, divergent species). This chapter also highlights the utility of both male and female morphology for phylogenetic and taxonomic studies on mygalomorph spiders, and provides morphological characters and a phylogenetic framework for future integrative phylogenetics/taxonomy on the Idiopidae and other mygalomorph groups. Chapter 5 consists of a complete taxonomic synopsis of the newly-recognised genus Cryptoforis. Revision of this new genus was seen as a priority due to the cryptic nature of the wafer-door burrows they create, and due to the fact that they were previously undocumented from mainland Australia. Numerous species also appear to be short-range endemics, restricted to remnant or relictual habitats in eastern Australia. In total, 16 species are described in the genus. In summary, my project is a comprehensive systematic treatment of the golden trapdoor spiders (tribe Euoplini) of Australia, revealing a diverse assemblage of mygalomorph spiders in multiple evolutionary lineages. It presents new data on phylogenetic relationships, morphology, and behaviour in the tribe. Immediate practical outcomes include a new generic classification of the tribe which more accurately represents the diversity contained within it, a full revision of the new genus Cryptoforis, and a targeted revision of the short-range endemic palisade-building Euoplos from south-eastern Queensland. My thesis demonstrates the strength of a ‘holistic’ total-evidence systematic approach, whereby different data types are iteratively compared and integrated, and in particular, the utility of this approach to understanding the taxonomy and evolution of poorly known mygalomorph taxa.

Since the 18th century, the Lower Jurassic-Middle Jurassic transition Brachiopods from the Lusitanian Basin have been studied, there being a number of references dealing with partial aspects of Systematics, geographic distribution or chronological framework for this fauna. The present study includes a global approach to the brachiopods recorded in this basin within the stratigraphic interval ranging from the Upper Toarcian to the Lower Bajocian. For this purpose, an exhaustive sampling was carried out at different stratigraphic sections, representing the different environments developed during this time in the basin. As a result, a high number of specimens were collected, which were later prepared, studied and described, considering both external and internal morphology. During the Lower Jurassic-Middle Jurassic transition, the Lusitanian Basin developed an extensive, slightly sloping, open ramp. At the West of the basin, a submarine fan sequence is preserved related to the Berlengas Horst. In the ramp and the submarine fan, different sedimentary environments are recorded, representing different palaeoecological conditions and yielding different brachiopod fauna. The proximal, bioclastic sediments are observed in the Tomar area. The different parts of the carbonated ramp, where the lateral variation of facies indicate its orientation, opening towards the west, are represented by the sediments of Porto de Mos, Rabacal, Coimbra and Cabo Mondego regions. The sediments of the submarine fan sequence can be observed in the Peniche region. A total of 24 brachiopod species belonging to 14 genera have been identified in the interval late Toarcian-early Bajocian of the Lusitanian Basin. As a result of the systematic study, twelve new species have been described as well as four new genera. The Order Rhynchonellida is represented in the Lower-Middle Jurassic transition of the Lusitanian Basin by 11 species. Three of these species belong to the genus Soaresirhynchia ALMERAS: the Toarcian species S. renzi (CHOFFAT in ALMERAS), and two new Aalenian species, S. minor sp. nov., characterised by its small size, and S. murtinheirensis sp. nov., which extends the distribution of the genus to the Bajocian. Another new species from the upper Toarcian, P.? jorali sp. nov., has been tentatively included in the genus Pamirorhynchia OVCHARENKO, which had a record up to now limited to the Pamir region. The genus Pseudogibbirhynchia AGER, was also recognised in the basin: P. bothenhamptonensis (WALKER) from the Upper Toarcian, and P. mutans (ROTHPLETZ) from the Aalenian. A new genus, Mondegia, is defined to include a new species: M. limica, a rhynchonellid from the lower Bajocian limestones of the Cape Mondego region. Another new species from the Toarcian, C. alcariensis sp. nov., is assigned to the genus Choffatirhynchia GARCIA JORAL & GOY. Finally, the Superfamily Norelloidea is represented in the basin by two Toarcian genera; Praemonticlarella GARCIA JORAL, with a new species, P. conimbrigensis sp. nov., and Nannirhynchia BUCKMAN, with two local species, N. cotteri (CHOFFAT in ALMERAS et al.) and N. delgadoi (CHOFFAT in ALMERAS et al.). Regarding the Order Terebratulida, 13 different species are represented in the basin within the referred chronological interval. Two species belong to the genus Stroudithyris BUCKMAN: S. stephanoides ALMERAS & MOULAN, common in the Upper Toarcian and lower Aalenian in the Mediterranean area, and S. choffati sp. nov., recorded in the lower Bajocian of the Cape Mondego region. A peculiar group of terebratulids recorded in the lower Bajocian of the Cape Mondego region has been described as a new species and a new genus: Lusothyris atlantica gen. nov., sp. nov. Two frequent taxa in nearby basins, Lophrothyris withingtonensis (BUCKMAN) from the middle-upper Aalenian, and Loboidothyris perovalis (SOWERBY) from the lower Bajocian, were also recognised in the Lusitanian Basin. Another widely distributed genus, Sphaeroidothyris BUCKMAN, is represented in the basin by three species; S. vari (ROLLIER), common in the middle-upper Toarcian of the “Spanish Bioprovince of Brachiopods”; S. uretae GARCIA JORAL, a species known from the Aalenian of the Iberian basin, and a new species present only in the Aalenian- Lower Bajocian of the basin: S. henriquesae sp. nov. As for the Zeilleroidea, four species were included into the genus Neozeilleria gen. nov., described to group the small-sized zeillerids which appear after the mass extinction that takes place in the lower Toarcian. Two of these species were previously included in the genus Zeilleria BAYLE: N. anglica (OPPEL), a well-known species from the European Aalenian, and N. sharpei (CHOFFAT), only known from the Lusitanian and Iberian basins. The other two species, N. duartei sp. nov. and N. nuskae sp. nov., are typical from the upper Toarcian of the Lusitanian Basin. Finally, a new Laqueoidea from the lower Bajocian was described; Lusitanina bituminis gen. nov., sp. nov., a small brachiopod recorded at rich in organic matter marls from the Cape Mondego region. The stratigraphic distribution of the different taxa of brachiopods from the Lusitanian Basin is established for the niddle Toarcian – lower Bajocian interval. A biozonation based on these distributions is proposed, and compared with those established for the neighbouring basins. The paleobiogeographic relationships of the brachiopod fauna of the Lusitanian Basin and those of other basins, from the Protoatlantic to the Pamir, are analysed and discussed, leading to a proposal of a dispersion model for the brachiopod groups along the North Tethyan coast. The relevant differences observed in the brachiopod assemblages, related to the various sedimentary and palaeoecological environments, have been used to reconstruct a pattern relating the distribution of these assemblages with distinct areas of the carbonate ramp and the submarine fan sequence of Peniche in the Lusitanian Basin. The evolution of brachiopod assemblages along the upper Toarcian-lower Bajocian interval shows three distinct episodes: starting from the lower Toarcian typical fauna of the “Spanish Bioprovince of Brachiopods”, a decline both in diversity and abundance is observed at the end of the Toarcian, with relatively poor and endemic assemblages. After a faunistic turnover in the Opalinum Zone, new assemblages appear, including new species that frequently belong to the same genera present in the assemblages previous to the turnover.

Amphibian diversity, distribution and conservation in the Ethiopian highlands : morphological, molecular and biogeographic investigation on Leptopelis and Ptychadena (Anura)

Sexual selection in hermaphrodites is thought to result in conflict over mating roles, where individuals will be eager to act as the (sperm) donor but hesitant to act as the (sperm) recipient. Likely due to this conflict, some species engage in elaborate reciprocal mating behaviours such as egg trading or reciprocal copulation, often followed by intense postcopulatory conflict, to control the fate of the received ejaculates (e.g. sperm digestion or mechanical sperm removal). Besides reciprocal mating, another possible solution to the conflict about mating roles is hypodermic insemination, where the male copulatory organ is used to inject ejaculate directly into the tissue of the recipient. Such mating behaviour allows the donor to minimise the recipient’s ability to control the fate of the received ejaculate, which potentially leads to a paternity benefit. Hypodermic insemination appears to be common in hermaphrodites, but it is unclear how frequently it evolves and through what routes it originates. In this thesis, I conducted a large-scale comparative analysis of the flatworm genus Macrostomum, to investigate the origins and the consequences of hypodermic insemination. I have conducted field collections to expand both taxon-sampling and the geographic representation of the genus. By combining detailed morphological documentation and the first phylogenomic analysis of the genus, I documented 89 species that are new to science and present here three taxonomic descriptions that resulted from this work. I, therefore, showed that Macrostomum harbours large undiscovered biodiversity. Analysis of sperm and genital morphology, as well as the location of received sperm, shows that hypodermic insemination has evolved up to 13 times within the genus, thereby almost doubling the number of documented origins of this mating strategy across all hermaphrodites. These origins of hypodermic insemination are associated with consistent changes in the morphology of the male copulatory organ, the female sperm storage organ, and the sperm design. Such consistent correlations imply that these changes are adaptations to hypodermic insemination. I further show that hypodermic insemination likely evolved via initial internal wounding during copulation, leading to internal traumatic insemination and subsequently to the complete loss of copulation. Since hypodermic insemination by-passes several processes that can decrease the level of sperm competition (e.g. cryptic female choice or sperm displacement), its evolution has been proposed to increase the proportion of reproductive resources allocated to sperm production. Contrary to this prediction, my work shows that in Macrostomum, hypodermic insemination is associated with reduced allocation towards sperm production. Most likely, this mating strategy is associated with the ability to self or other factors reducing the intensity of sperm competition. While no data on such a relationship exists in animals, this supports findings in plants, where selfing is associated with reduced investment into pollen production. Finally, I here present evidence that reproduction-related genes evolve at an accelerated rate across the genus, as indicated both by sequence divergence and a decreased probability of identifying homologs with phylogenetic distance. This is the first documented case of such rapid evolution in hermaphrodites and supports a growing body of evidence that sexual selection can drive rapid gene evolution.

Objectives To identified the strain 1012 from the National Center of Clinical Laboratory of China for microbe inter-laboratory quality assessment in 2010, and study the taxonomic status of strain 1012 and related species in the genus Actinomyces. Methods The bacterial traditional morphological characteristics, commercial API systems, and 16S rRNA gene sequence analysis were applied to identify the problematic culture of strain 1012. The phylogenetic tree based on the remote information of the prokaryotes systems was constructed to study the taxonomic status and evolutionary relationship of the genus Actinomyces and related species in the family Actinomycetaceae. Results Strain 1012 was determined as a kind of facuhative anaerobic, non-spot-forming, Gram-positive coryneform bacteria, which was identified to Actinomyces turicensis for the phenotypic biochemical characteristics of more than 60 items, The comparative study of 16S rRNA gene showed the strain 1012 with 99. 8％ similarities to Actinomyces turicensis, but only 90. 6％ to the type species of Actinomyces bovis in the genus Actinomyces. However, the comparative study of 16S rRNA gene showed the strain 1012 with only 90. 6％ homology to the type species of Actinomyces bovis in the genus Actinomyces. Further phylogenetic analysis showed that nine independent clusters were grouped in the family Actinomycetaceae, of which four clusters were separately represented the genera Varibaculum,Mobiluncus, Actinobaculum and Arcanobacterium, while other five clusters all were designated to the genus Actinomyces. The study showed strain 1012 was located in genus Ⅲ of Actinomyces, yet with a relatively long genetic distance to Actinomyces bovis. Conclusion The genus Actinomyces may be reclassified as one genus Actinomyces sensu stricto and several new genera for the genotypic characteristics. Key words: Actinomycetaceae; RNA, ribosomal, 16S; Sequence analysis, RNA; Evaluation studies

Implications of homoplasy: explanations of homoplasy at different levels of biological organization, D.R. Brooks, homoplasy connections and disconnections - genes and species, molecules and morphology, J.J. Doyle, the relationship be-tween homoplasy and confidence in a phylogenetic tree, M.J. Sanderson and M.J. Donoghue, nonfloral homoplasy and evolutionary scenarios in living and fossil land plants, R.M. Bateman, behavioural characters and homoplasy - perception versus practice, H.C.Proctor measures of homoplasy: measures of homoplasy, J.W. Archie, the measurement of homoplasy - a stochastic view, J.T. Chang and J. Kim gen-eration of homoplasy: complexity and homoplasy, D.W. McShea, exaptation, adaptation, and homoplasy - evolution of ecological traits in dalechampia vines, W.S. Armbruster, patterns of homoplasy in behavioural evolution, S.A. Foster, W.A. Cresko, K.P. Johnson, M.U. Tlusty, and H.E. Willmott, ontogenetic evolution, clade diversification, and homoplasy, L. Hufford, homoplasy in angiosperm flowers, P.K. Endress Appendices: families and genera with completely trimerous flowers families and genera with flowers that are trimerous except for the gynoecium families and genera with flowers that are trimerous except for the adnorecium, which is polymerous families and genera with flowers that are trimerous except for the calyx, which is pentamerous homoplasy and the evolutionary process - an afterword, M.J. Sanderson and L. Hufford.

Coevolution or cospeciation of phytophagous insects and plants is assumed to be a major driver of evolution leading to the present enormous insect diversity. However, an increasing number of insect–plant studies suggest that speciation is driven by geographical vicariance, and host switching to related plant taxa also occurs frequently in insects. Despite a number of studies on global patterns of insect–plant associations, there are notable gaps in the interpretation of evolutionary processes leading to insect speciation. This thesis consists of four studies in five papers (three published papers and two are to be submitted) conducted to investigate the biodiversity of a poorly known group of insects, the psyllids or jumping plant-lice, and their associations with host-plants. The studies were focused on areas from which few information were available: western Palaearctic (Belarus) and south temperate Neotropical regions. Most psyllids are mono- or oligophagous on a restricted number of plant taxa. The first study examined the plausibility of polyphagy of the Neotropical potato pest Russelliana solanicola Tuthill by means of multivariate analyses of morphological characters. The results showed an unexpectedly high polyphagy of the species on a number of economically important crops and its very likely introduction from the native Andean region into eastern South America. Considering its high potential of a successful invasion into non-native regions, it is extremely important to prevent spread and invasion of R. solanicola in the incipient stages. The second project assessed and predicted the potential occurrence of R. solanicola worldwide using species distribution models (SDMs), based on environmental variables derived from its natural range of distribution. We also investigated the similarities between geographical, environmental and morphological characteristics of R. solanicola and its related Solanaceae-feeders, and their tolerance to a range of environmental conditions by contrast to non-Solanaceae feeding species from the same genus. The third study investigated and described the diversity of Russelliana species in order to understand patterns of psyllid speciation and explain the evolutionary processes leading to the species diversity in the genus. The Neotropical genus Russelliana is an excellent and interesting model group for host-plant and biogeographical studies, considering its high species-richness and wide host associations with species from a number of plant families. The revision of Russelliana included the descriptions of 24 new psyllid species and the redescriptions of 19 previously described ones. A phylogenetic analysis suggested that the psyllid speciation in Russelliana is better explained by geographical vicariance rather than by cospeciation with plants, and host switching has occurred relatively frequently in the genus. The fourth study is reflected in two publications on the fauna of Belarusian psyllids. The psyllid fauna of the west Palaearctic region is relatively well known, with Belarus being a notable exception. Based on the literature records and recently collected material, an updated checklist of psyllids of Belarus is provided. The checklist is supplemented with an illustrated identification key for the psyllid species confirmed from and likely to occur in Belarus. To my knowledge, the results of this thesis provide important taxonomic information on the biodiversity and host-plant associations of a poorly studied group of insects from the western Palaearctic (Belarus) and south temperate Neotropical regions. These findings may contribute to studies on global patterns of insect–plant associations helping to interpret the evolutionary processes leading to insect speciation and its current huge diversity on the planet. Moreover, the studies on the polyphagy and potential distribution of pest species in new regions can predict the establishment of invasive populations and provide the pest management with all necessary information before the species is recognised as a serious threat. In addition, the developed illustrated identification keys for the psyllid species will be of help to applied entomologists dealing with agricultural, forestry and ornamental pests.

THE PLIO-HOLOCENE LARGE MAMMALS OF THE WESTERN EURASIA: MACROECOLOGICAL AND EVOLUTIONARY ANALYSES OF THE FAUNAS

Fil: Salariato, Diego Leonel. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Botanica Darwinion. Academia Nacional de Ciencias Exactas, Fisicas y Naturales. Instituto de Botanica Darwinion; Argentina

INTRODUCTION Bacteriophage containing RNA have been found for three genera of eubacteria: Escherichia, Pseudomonas and Caulobacter. Several phage groups for each genera have been established, based on serological variation (Miyake et al. 1971; Bradley 1966; Schmidt and Stanier 1965), and in the case of the coliphage, on the template specificity of the replicase (Mikaye et al. 1971). The data indicate, however, that all the known RNA phage, irrespective of the genus and species of the host, are strikingly similar in size, structure and mode of infection, thus placing RNA containing phage in a unique evolutionary position. Accordingly, we will present in this chapter the physical and biochemical parameters of the known RNA phage, their interaction with host cells, factors contributing to host specificity, and a discussion of a plausible basis for the apparent evolutionary constancy displayed by the RNA bacteriophage. PROPERTIES OF RNA PHAGE OF SEVERAL GENERA Classification The parameters of RNA bacteriophage infecting three bacterial genera are presented in Table 14.1. Bacteriophage specific for the Caulobacter genus have been shown to comprise three groups, based on serological distinctions and host specificity. Each group infects only one of the following Caulobacter species: crescentus, bacteroides or fuseformis (Schmidt and Stanier 1965). In the case of Pseudomonas RNA phage, two serologically similar isolates have been shown to be specific for Pseudomonas aeruginosa: 7s and PP7 (Feary, Fisher and Fisher 1963; Bradley 1966); and phage φ 6 has been shown to specifically infect Pseudomonas phaseolicola (Vidaver, Koski and Van Etten 1973). E. coli, whose...

The Poxviruses are a family of double stranded DNA (dsDNA) viruses that cause disease in many species, both vertebrate and invertebrate. Their genomes range in size from 135 to 365 kbp and show conservation in both organization and content. In particular, the central genomic regions of the chordopoxvirus subfamily (those capable of infecting vertebrates) contain 88 genes which are present in all the virus species characterised to date and which mostly occur in the same order and orientation. In contrast, however, the terminal regions of the genomes frequently contain genes that are species or genera-specific and that are not essential for the growth of the virus in vitro but instead often encode factors with important roles in vivo including modulation of the host immune response to infection and determination of the host range of the virus. The Parapoxviruses (PPV), of which Orf virus is the prototypic species, represent a genus within the chordopoxvirus subfamily of Poxviridae and are characterised by their ability to infect ruminants and humans. The genus currently contains four recognised species of virus, bovine papular stomatitis virus (BPSV) and pseudocowpox virus (PCPV) both of which infect cattle, orf virus (OV) that infects sheep and goats, and parapoxvirus of red deer in New Zealand (PVNZ). The ORFV genome has been fully sequenced, as has that of BPSV, and is ~138 kb in length encoding ~132 genes. The vast majority of these genes allow the virus to replicate in the cytoplasm of the infected host cell and therefore encode proteins involved in replication, transcription and metabolism of nucleic acids. These genes are well conserved between all known genera of poxviruses. There is however another class of genes, located at either end of the linear dsDNA genome, that encode proteins which are non-essential for replication and generally dictate host range and virulence of the virus. The non-essential genes are often the most variable within and between species of virus and therefore are potentially useful for diagnostic purposes. Given their role in subverting the host-immune response to infection they are also targets for novel therapeutics. The function of only a relatively small number of these proteins has been elucidated and there are several genes whose function still remains obscure principally because there is little similarity between them and proteins of known function in current sequence databases. It is thought that by selectively removing some of the virulence genes, or at least neutralising the proteins in some way, current vaccines could be improved. The evolution of poxviruses has been proposed to be an adaptive process involving frequent events of gene gain and loss, such that the virus co-evolves with its specific host. Gene capture or horizontal gene transfer from the host to the virus is considered an important source of new viral genes including those likely to be involved in host range and those enabling the virus to interfere with the host immune response to infection. Given the low rate of nucleotide substitution, recombination can be seen as an essential evolutionary driving force although it is likely underestimated. Recombination in poxviruses is intimately linked to DNA replication with both viral and cellular proteins participate in this recombination-dependent replication. It has been shown, in other poxvirus genera, that recombination between isolates and perhaps even between species does occur, thereby providing another mechanism for the acquisition of new genes and for the rapid evolution of viruses. Such events may result in viruses that have a selective advantage over others, for example in re-infections (a characteristic of the PPV), or in viruses that are able to jump the species barrier and infect new hosts. Sequence data related to viral strains isolated from goats suggest that possible recombination events may have occurred between OV and PCPV (Ueda et al. 2003). The recombination events are frequent during poxvirus replication and comparative genomic analysis of several poxvirus species has revealed that recombinations occur frequently on the right terminal region. Intraspecific recombination can occur between strains of the same PPV species, but also interspecific recombination can happen depending on enough sequence similarity to enable recombination between distinct PPV species. The most important pre-requisite for a successful recombination is the coinfection of the individual host by different virus strains or species. Consequently, the following factors affecting the distribution of different viruses to shared target cells need to be considered: dose of inoculated virus, time interval between inoculation of the first and the second virus, distance between the marker mutations, genetic homology. At present there are no available data on the replication dynamics of PPV in permissive and non permissive hosts and reguarding co-infetions there are no information on the interference mechanisms occurring during the simultaneous replication of viruses of different species. This work has been carried out to set up permissive substrates allowing the replication of different PPV species, in particular keratinocytes monolayers and organotypic skin cultures. Furthermore a method to isolate and expand ovine skin stem cells was has been set up to indeep further aspects of viral cellular tropism during natural infection. The study produced important data to elucidate the replication dynamics of OV and PCPV virus in vitro as well as the mechanisms of interference that can arise during co-infection with different viral species. Moreover, the analysis carried on the genomic right terminal region of PCPV 1303/05 contributed to a better knowledge of the viral genes involved in host interaction and pathogenesis as well as to locate recombination breakpoints and genetic homologies between PPV species. Taken together these data filled several crucial gaps for the study of interspecific recombinations of PPVs which are thought to be important for a better understanding of the viral evolution and to improve the biosafety of antiviral therapy and PPV-based vectors.

Eighty-eight chromosome number counts representing 62 species in nine genera of the Lythraceae are presented based primarily on meiotic figures from pollen mother cells. Included are first reports for 47 species and the first count for the monotypic genus Koehneria. Numbers for 40 species of Cuphea from Brazil and Bolivia are reported, significantly increasing representation of chromosome number data for South American sections of the genus. Comparisons of the new counts are made to previously published numbers for each genus. Basic numbers for 24 of the 31 genera are provided. Eight genera retain the apparent original diploid number of x = 8; 12 are functional diploids of paleopolyploid origin with secondary basic numbers of x = 15, 16, 24, 28, or 32. Polyploid events are hypothesized to have occurred early in the evolution of the family so that the majority of monotypic or ditypic genera, which today constitute 65% of the family, are relictual polyploids. The most chromosomally diverse and actively speciating genera are the herbaceous perennials Ammannia, Nesaea, Cuphea, and Lythrum. In contrast, the woody genera Diplusodon, Ginoria, and Lafoensia, are species-rich but speciation has not involved chromosome number changes. Further understanding of chromosomal evolution in Lythraceae will depend on production of well-supported phylogenies for the family and cytological investigations in the genera where many different chromosome numbers occur. Communicating Editor: John V. Freudenstein

Recently, it has been shown that the stem nematode, Ditylenchus dipsaci (Nematoda: Anguinidae), is genetically more related to the gall-forming nematodes from genera Anguina , Heteroanguina , and Mesoanguina than to other members of the genus Ditylenchus . This finding was provided by molecular data written in the evolutionary variable, non-coding internal transcribed spacers (ITS1 and ITS2) of the ribosomal DNA (rDNA). In the current paper, we analyze the nucleotide sequences and predict the secondary structures of two expansion segments (D2, D3) of the 28S ribosomal RNA (rRNA)-coding gene for the plant-parasitic nematodes from the genus Ditylenchus and their related anguinids. In general, the expansion segment D2 appeared to be more variable than the segment D3 illustrating their different evolutionary constraints. Comparative analysis of the aligned sequences and predicted secondary structures revealed similar trend showing the tight relationships between the stem nematodes ( D. dipsaci , D. gigas , D. weischeri ) and gall-forming nematodes from the subfamily Anguininae. Phylogeny reconstructions disjoined the family Anguinidae into two monophyletic clusters (Clade 1 and 2). Clade 1 constitutes the stem nematodes ( D. dipsaci , D. gigas , etc) and gall-forming nematodes from the genera Anguina , Heteroanguina , Subanguina and Mesoanguina , while clade 2 includes other Ditylenchus species like D. destructor and D. halictus . Collectively, deciphering the exact phylogenetic relationships within the family Anguinidae (Nematoda: Tylenchida) with respect to our results should provide a framework for a taxonomic revision in order to reflect biological history of these nematodes. In addition, we provide novel molecular data, which may be exploited in diagnostic tools for phytosanitary control of these economically important plant parasites.

The present thesis deals with aspects of biogeography, phylogenetics, systematics, and evolution. Its goal was to investigate patterns of biotic assembly in the Mediterranean region, with special emphasis on the effect of earth processes on species origins and distribution, the origin of species endemic to islands, and the biogeographic links between the Mediterranean and Irano-Turanian regions. To address these issues, two genera of Rutaceae (citrus family) that met several requirements were selected as model systems: Ruta and Haplophyllum. The former, the type genus of the family, is restricted to the Mediterranean region and comprises species endemic to both continental fragment (Corsica and Sardinia) and oceanic (Canary Islands) islands. The latter, one of the most species-rich genera of the family, has been used to characterize the flora of the Irano-Turanian region, where it reaches maximum species diversity, but also includes species endemic to the Mediterranean region. In Chapter I we generated molecular phylogenies for Ruta and closely related taxa, essential to provide a robust framework for subsequent biogeographic analyses. Moreover, we tested conflicting taxonomic treatments of Ruta and affiliated taxa based on different classes of characters. The analyses supported the current circumscription of Ruta and showed that the genus can only be diagnosed by using a suite of homoplasious, plesiomorphic, and autapomorphic morphological character states. Conflict between molecular and phytochemical datasets was ascribed to convergence in secondary chemical compounds. In Chapter II we carried out biogeographic analyses of Ruta aimed at elucidating the time frame and sequence of range expansion events associated with its origin and diversification, focusing mainly on the island endemics. Biogeographic scenarios were proposed by integrating information from phylogeny, molecular dating, and ancestral range reconstruction methods that incorporate palaeo-geographic models. The analyses showed that Ruta invaded the Mediterranean region from the north before the onset of the current Mediterranean climate. Land migration through a temporary connection between the Corso- Sardinian and Apulian microplates, followed by vicariance, was inferred as the process underlying the origin of the Corso-Sardinian endemic lineage. The origin and diversification of the clade restricted to the Canary Islands was explained by means of a single colonization event of the archipelago, driven by long-distance dispersal from North Africa, followed by inter-island speciation and parallel invasion of similar ecological zones. In Chapter III we carried out molecular phylogenetic analyses of Haplophyllum in order to explore the biogeographic links between the Mediterranean and Irano-Turanian regions. The analyses identified many instances of species non-monophyly, but also cases of strongly-supported species monophyly. Optimization of morphological characters on the molecular phylogeny indicated that several species of the genus, especially those with a widespread distribution, can only be diagnosed by combinations of homoplasious character states. Preliminary biogeographic patterns suggested that the Mediterranean representatives of the genus arrived from the east multiple times, corroborating the hypothesis that the Irano- Turanian region served as a key source for the colonization of the Mediterranean region.