Genetic diversity and epidemiology of Tobacco streak virus and related subgroup 1 Ilarviruses

A quarter of Australia’s sunflower production is from the central highlands region of Queensland and is currently worth six million dollars ($AUD) annually. From the early 2000s a severe necrosis disorder of unknown aetiology was affecting large areas of sunflower crops in central Queensland, leading to annual losses of up to 20%. Other crops such as mung bean and cotton were also affected. This PhD study was undertaken to determine if the causal agent of the necrosis disorder was of viral origin and, if so, to characterise its genetic diversity, biology and disease cycle, and to develop effective control strategies. The research described in this thesis identified Tobacco streak virus (TSV; genus Ilarvirus, family Bromoviridae) as the causal agent of the previously unidentified necrosis disorder of sunflower in central Queensland. TSV was also the cause of commonly found diseases in a range of other crops in the same region including cotton, chickpea and mung bean. This was the first report from Australia of natural field infections of TSV from these four crops. TSV strains have previously been reported from other regions of Australia in several hosts based on serological and host range studies. In order to determine the relatedness of previously reported TSV strains with TSV from central Queensland, we characterised the genetic diversity of the known TSV strains from Australia. We identified two genetically distinct TSV strains from central Queensland and named them based on their major alternative hosts, TSV-parthenium from Parthenium hysterophorus and TSV-crownbeard from Verbesina encelioides. They share only 81 % total-genome nucleotide sequence identity. In addition to TSV-parthenium and TSV-crownbeard from central Queensland, we also described the complete genomes of two other ilarvirus species. This proved that previously reported TSV strains, TSV-S isolated from strawberry and TSV-Ag from Ageratum houstonianum, were actually the first record of Strawberry necrotic shock virus from Australia, and a new subgroup 1 ilarvirus, Ageratum latent virus. Our results confirmed that the TSV strains found in central Queensland were not related to previously described strains from Australia and may represent new incursions. This is the first report of the genetic diversity within subgroup 1 ilarviruses from Australia. Based on field observations we hypothesised that parthenium and crownbeard were acting as symptomless hosts of TSV-parthenium and TSV-crownbeard, respectively. We developed strain-specific multiplex PCRs for the three RNA segments to accurately characterise the range of naturally infected hosts across central Queensland. Results described in this thesis show compelling evidence that parthenium and crownbeard are the major (symptomless) alternative hosts of TSV-parthenium and TSV-crownbeard. While both TSV strains had wide natural host ranges, the geographical distribution of each strain was closely associated with the respective distribution of their major alternative hosts. Both TSV strains were commonly found across large areas of central Queensland, but we only found strong evidence for the TSV-parthenium strain being associated with major disease outbreaks in nearby crops. The findings from this study demonstrate that both TSV-parthenium and TSV-crownbeard have similar life cycles but some critical differences. We found both TSV strains to be highly seed transmitted from their respective major alternative hosts from naturally infected mother plants and survived in seed for more than 2 years. We conclusively demonstrated that both TSV strains were readily transmitted via virus-infected pollen taken from the major alternative hosts. This transmission was facilitated by the most commonly collected thrips species, Frankliniella schultzei and Microcephalothrips abdominalis. These results illustrate the importance of seed transmission and efficient thrips vector species for the effective survival of these TSV strains in an often harsh environment and enables the rapid development of TSV disease epidemics in surrounding crops. Results from field surveys and inoculation tests indicate that parthenium is a poor host of TSV-crownbeard. By contrast, crownbeard was naturally infected by, and an experimental host of TSV-parthenium. However, this infection combination resulted in non-viable crownbeard seed. These differences appear to be an effective biological barrier that largely restricts these two TSV strains to their respective major alternative hosts. Based on our field observations we hypothesised that there were differences in relative tolerance to TSV infection between different sunflower hybrids and that seasonal variation in disease levels was related to rainfall in the critical early crop stage. Results from our field trials conducted over multiple years conclusively demonstrated significant differences in tolerance to natural infections of TSV-parthenium in a wide range of sunflower hybrids. Glasshouse tests indicate the resistance to TSV-parthenium identified in the sunflower hybrids is also likely to be effective against TSV-crownbeard. We found a significant negative association between TSV disease incidence in sunflowers and accumulated rainfall in the months of March and April with increasing rainfall resulting in reduced levels of disease. Our results indicate that the use of tolerant sunflower germplasm will be a critical strategy to minimise the risk of TSV epidemics in sunflower.

Cryptic species and Miocene diversification of Palaearctic naked-toed geckos (Squamata: Gekkonidae) in the Indian dry zone

We sampled Palaearctic naked-toed geckos from across their range in India and used two mitochondrial and two nuclear genes to reconstruct relationships within a global phylogeny. Published sequences of Peninsular Indian Hemidactylus allow us to contrast these two groups in dating analyses - providing insights into the history of the Indian dry zone. Palaearctic naked-toed geckos first moved onto the Indian Plate in the Oligocene, with higher-level diversification probably linked to collision of the Indian and Eurasian plates, and subsequent dispersal into-India and diversification with increasing Miocene aridity. An independent gekkonid radiation with species in the dry zone, Hemidactylus diversified during the same period in Peninsular India. Our results demonstrate that dry zone taxa across India may date back to at least the Miocene, with a potential historical climatic barrier between the Indus and Peninsular Indian Divisions. `Cyrtopodion' aravallense is revealed to be a complex with seven genetically and environmentally divergent lineages that began diversifying in the late Miocene, congruent with increased aridity in north-western India. This discovery of cryptic diversity in the Indian dry zone represents the first terrestrial vertebrate radiation from north-western central India and highlights how little we understand of the regions' biodiversity, emphasizing the need for systematic geographic sampling and multiline evidence to reveal true patterns of diversity. The ancestor of `Cyrtopodion' aravallense came into the nascent Indian dry zone in the Miocene and has since diversified, potentially in the absence of any sympatric scansorial rupicolous geckos. Cyrtopodion scabrum represents a unique case of commensalism and shows phylogeographic structure in its presumed native range. The taxonomic implications of our study include a number of undescribed species, recognition of `Cyrtopodion' as a distinct lineage and the non-monophyly of Altiphylax.

Natural Suppression of the Aquatic Weed Salvinia molesta D.S. Mitchell, by Two Previously Unreported Fungal Pathogens

Salvinia molesta D. S. Mitchell (Salviniaceae), variously called giant salvinia, water fern or African payal, is a vegetatively reproducing, perennial, free-floating, aquatic weed, native to southeastern Brazil (Waterhouse and Norris 1987). It (hereafter called salvinia) is a very serious weed in most regions outside its native range (Harley and Mitchell 1981) including India. The purpose of this paper is to report on two fungal pathogens that were found to be the cause of a sudden decline in salvinia in Bangalore.(PDF has 4 pages.)

Silver King Creek Paiute cutthroat trout restoration, 1991 through 1993

Silver King Creek, Alpine County, is the native range of the Federally-threatened Paiute cutthroat trout, Oncorhynchus clarki seleniris. Paiute cutthroat currently inhabit Coyote Valley and Corral Valley creeks, which are tributaries to Silver King Creek below Llewellyn Falls, and also Silver King Creek and tributaries aboye Llewellyn Falls. Rainbow trout, O. mykiss, were introduced into the basin during 1949 and became hybridized with Paiute cutthroat. Chemical treatments attempted by the California Department of Fish and Game (CDFG) in 1964 and 1976 failed to eliminate hybrid trout. A chemical treatment project was again conducted by the CDFG from 1991 through 1993 to eliminate hybrid trout from within the range of Paiute cutthroat. This report presents a summary of events for the first two years of the Silver King Paiute Cutthroat Trout Restoration Project; a more thorough analysis is made of the third and final year of the project. (PDF contains 39 pages.)

Management of water hyacinth, Eichhornia crassipes, in Lake Victoria Basin

Water hyacinth is a free-floating waterweed native to the Amazon River Basin in South America. In its native range, water hyacinth is not an environmental problem, although the weed is one of the most invasive alien plants in freshwater environments. Water hyacinth has the potential to become invasive through fast vegetative reproduction and rapid growth to accumulate huge biomass and extensive cover in freshwater environments. Over the last 150 years water hyacinth has invaded most countries in the tropics and sub-tropics, introduced by man, mainly for ornamental purposes. Such introductions led to the infestation of most freshwater-ways in the southern United States of America, parts of Australia, the pacific islands, and most countries in Asia and Africa. The extensive tightly packed mats of water hyacinth are often associated with devastating socio-economic and environmental impacts. Invasion by the weed has, therefore, often generated urgent costly problems associated with the weed biomass and its management. A classic example of such problems was triggered by the invasion and proliferation of water hyacinth in the Lake Victoria Basin during the 1980s (Freilink 1989, Taylor 1993, Twongo et al., 1995). The weed infestation marked the beginning of a decade of intensive and systematic campaign by the three riparian states (Kenya, Tanzania and Uganda) to bring weed proliferation under control. The discussions in this Chapter span over ten years of dealing with the challenges paused by the imperative to manage infestations of water hyacinth in the Lake Victoria Basin. The challenges included the need to understand the dynamics of water hyacinth infestation; its distribution, proliferation and impact modalities; and the development and implementation of appropriate weed control strategies and options. Most specific examples were taken from the Ugandan experience (NARO, 2002).

Ecology of frontier populations of the invasive grey squirrel (Sciurus carolinensis) in Ireland

The rise in invasive species, together with habitat destruction, is associated with worldwide declines in biodiversity and ecosystem functioning. Management of invasive species, as well as amelioration of invasion impacts, provide challenges to species and ecosystem ecologists and conservation managers. Although any species can become invasive if it is transported to, establishes in and spreads in a new environment outside of its native range, rodents are a particularly frequent invader. Rodent introductions are often inadvertent but are also commonly intentional as these animals are traded and transported as pets and may escape from captivity. Tree squirrel species are attractive to humans and are able to establish populations with only a few founding individuals, making them a group well suited to performing the role of biological invaders. The eastern grey squirrel (Sciurus carolinensis) is the most commonly introduced squirrel species worldwide. This research addressed the grey squirrel invasion and frontier population biology. Novel results were generated through diverse research techniques. Public sighting surveys and hairtube surveys were used to locate the southern frontier of grey squirrel range expansion in Ireland. A 22-month intensive live trapping study of two frontier populations facilitated the collection of personality and demographic data from squirrels in increasing populations. A systematic literature search on grey squirrel demography provided context for the studied populations, among frontier and established introduced populations, as well as those in the native range. Advanced spatially explicit population modeling techniques predicted future range expansion and objectively compared the outcomes of 12 grey squirrel management strategies. The methods and results are discussed in both a basic scientific and applied invasion management context. An improved understanding of the behaviour, population dynamics, and future scenarios at the frontier of species invasions is crucial for managers worldwide and this is provided here for the grey squirrel in Ireland.

Tracking the invasive history of the green alga Codium fragile ssp. tomentosoides

The spread of nonindigenous species into new habitats is having a drastic effect on natural ecosystems and represents an increasing threat to global biodiversity. In the marine environment, where data on the movement of invasive species is scarce, the spread of alien seaweeds represents a particular problem. We have employed a combination of plastid microsatellite markers and DNA sequence data from three regions of the plastid genome to trace the invasive history of the green alga Codium fragile ssp. tomentosoides. Extremely low levels of genetic variation were detected, with only four haplotypes present in the species’ native range in Japan and only two of these found in introduced populations. These invasive populations displayed a high level of geographical structuring of haplotypes, with one haplotype localized in the Mediterranean and the other found in Northwest Atlantic, northern European and South Pacific populations. Consequently, we postulate that there have been at least two separate introductions of C. fragile ssp. tomentosoides from its native range in the North Pacific.

European hare (Lepus europaeus) invasion ecology: Implication for the conservation of the endemic Irish hare (Lepus timidus hibernicus)

European hare Lepus europaeus populations have undergone recent declines but the species has successfully naturalised in many countries outside its native range. It was introduced to Ireland during the mid-late nineteenth century for field sport and is now well established in Northern Ireland. The native Irish hare Lepus timidus hibernicus is an endemic subspecies of mountain hare L. timidus and has attracted major conservation concern following a long-term population decline during the twentieth century and is one of the highest priority species for conservation action in Ireland. Little is known about the European hare in Ireland or whether it poses a significant threat to the native mountain hare subspecies by compromising its ecological security or genetic integrity. We review the invasion ecology of the European hare and examine evidence for interspecific competition with the mountain hare for habitat space and food resources, interspecific hybridisation, disease and parasite transmission and possible impacts of climate change. We also examine the impact that introduced hares can have on native non-lagomorph species. We conclude that the European hare is an emerging and significant threat to the conservation status of the native Irish hare. Invasive mammal species have been successfully eradicated from Ireland before and immediate action is often the only opportunity for cost-effective eradication. An urgent call is issued for further research whilst the need for a European hare invasive Species Action Plan (iSAP) and Eradication strategy are discussed.

Polyopes lancifolius (Halymeniales, Rhodophyta), a new component of the Japanese marine flora introduced to Europe

Polyopes lancifolius (Harvey) S. Kawaguchi & H.W. Wang has been recorded for the first time in Europe, during the summer or 2008. A small population was discovered in the Gulf of Morbihan (northeast Atlantic, France). This is the first observation of P. lancifolius outside its native range. Vegetative and reproductive morphological features are compared with previous descriptions. rbcL sequences show no divergence from Japanese populations. Imports of Pacific oysters Crassostrea gigas (Thunberg 1793) are likely to be responsible for its accidental introduction into the Gulf of Morbihan, either directly from northwest Pacific regions or indirectly (secondary dispersal) by transfers from another European oyster farming site. The history of previous algal introductions from Japan suggests that if it becomes successfully established at Morbihan, the species is likely to spread to other European coastal areas.

Population genetics of C. Maenas : oceanography and larval dispersal

Decifrar a complexa interacção entre os ciclos de vida de espécies marinhas e a oceanografia revela-se fundamental para a compreensão do fluxo genético e da conectividade no meio marinho. Nas espécies marinhas com desenvolvimento indirecto o fluxo de genes entre populações depende da distância que separa as populações, bem como da interacção entre a duração do desenvolvimento larvar, do comportamento das larvas e dos padrões de circulação oceânica. A conectividade larvar influencia uma variedade de processos como a dinâmica de stocks e de populações, a distribuição e limites geográficos das espécies, a estrutura genética das populações e a dispersão de espécies invasivas e reveste-se consequentemente de uma importância fundamental na identificação das unidades populacionais evolucionariamente relevantes e para a gestão e conservação marinhas. Os marcadores genéticos e os Modelos Individuais Acoplados a Modelos Físico-Biológicos (“ICPBMs”) são actualmente ferramentas fundamentais para o estudo dos padrões de dispersão larvar e para avaliar o nível de conectividade populacional. A presente tese respeita à avaliação das escalas espaciais de conectividade de populações de uma espécie costeira, o caranguejo Carcinus maenas, e utiliza conjuntamente informação de marcadores genéticos, análise de séries temporais de fornecimento de larvas e um modelo numérico de circulação oceânica. O primeiro capítulo introduz a temática da conectividade em espécies marinhas e inclui algumas referências aos métodos moleculares, analíticos e de modelação seguidos ao longo da tese. Através da utilização de múltiplas ferramentas – avaliação da estrutura genética geográfica de C. maenas na sua distribuição nativa com recurso a marcadores de DNA (microssatélites) (Capítulo 2), avaliação da estrutura genética temporal das larvas que formam os eventos de fornecimento larvar à Ria de Aveiro, NW Portugal (Capítulo 3), descrição da variabilidade inter-anual do fornecimento larvar à Ria de Aveiro, NW Portugal (Capítulo 4) e validação de um modelo ICPBM que descreve os padrões observados de fornecimento (Capítulo 5) – esta tese espera poder contribuir para uma melhor compreensão dos mecanismos que regulam o fluxo de genes e a conectividade entre populações de organismos marinhos. No Capítulo 6 são apresentadas as principais conclusões da investigação. A análise genética com recurso a microssatélites indicou que as populações de C. maenas são geneticamente homogéneas ao longo de várias centenas de km, dentro da distribuição nativa da espécie. Paralelamente, não foram encontrados indícios da existência de reprodução por “sweepstakes” em C. maenas de populações da costa oeste da Península Ibérica, visto que não se obtiveram diferenças genéticas significativas entre os eventos larvares. Também não se encontrou qualquer estrutura familiar entre as larvas que formam cada episódio de fornecimento, e não houve nenhuma redução significativa da variabilidade genética das larvas quando comparada com a de caranguejos adultos. A análise de séries temporais de suprimento de larvas na Ria de Aveiro em cinco anos estudados indica que este é um fenómeno episódico e variável, sendo os maiores episódios de fornecimento coincidentes com as marés vivas e acentuados por fortes ventos de sul. O modelo ICPBM foi validado com sucesso e parece fornecer uma estimativa realística das escalas espaciais e temporais de dispersão larvar, de acordo com as observações da estrutura genética e da ausência de reprodução por “sweepstake” em C. maenas da costa oeste da Península Ibérica

Molecular variation at a candidate gene implicated in the regulation of fire ant social behavior

The fire ant Solenopsis invicta and its close relatives display an important social polymorphism involving differences in colony queen number. Colonies are headed by either a single reproductive queen (monogyne form) or multiple queens (polygyne form). This variation in social organization is associated with variation at the gene Gp-9, with monogyne colonies harboring only B-like allelic variants and polygyne colonies always containing b-like variants as well. We describe naturally occurring variation at Gp-9 in fire ants based on 185 full-length sequences, 136 of which were obtained from S. invicta collected over much of its native range. While there is little overall differentiation between most of the numerous alleles observed, a surprising amount is found in the coding regions of the gene, with such substitutions usually causing amino acid replacements. This elevated coding-region variation may result from a lack of negative selection acting to constrain amino acid replacements over much of the protein, different mutation rates or biases in coding and non-coding sequences, negative selection acting with greater strength on non-coding than coding regions, and/or positive selection acting on the protein. Formal selection analyses provide evidence that the latter force played an important role in the basal b-like lineages coincident with the emergence of polygyny. While our data set reveals considerable paraphyly and polyphyly of S. invicta sequences with respect to those of other fire ant species, the b-like alleles of the socially polymorphic species are monophyletic. An expanded analysis of colonies containing alleles of this clade confirmed the invariant link between their presence and expression of polygyny. Finally, our discovery of several unique alleles bearing various combinations of b-like and B-like codons allows us to conclude that no single b-like residue is completely predictive of polygyne behavior and, thus, potentially causally involved in its expression. Rather, all three typical b-like residues appear to be necessary.

Une approche interculturelle des relations entre les nations autochtones et non-autochtones au Canada : une porte ouverte sur le postcolonialisme?

La situation économique, sociale et politique des nations autochtones au Canada et leur relation avec les nations non-autochtones présentent des similarités avec les anciennes colonies européennes. Peut-on qualifier cette relation de « coloniale » ? Cette interrogation est primordiale, vu les aspects immoraux et illégaux que prit la colonisation. Nous parcourrons la pensée d’auteurs reliés au libéralisme, au nationalisme autochtone et à l’interculturalisme et nous choisirons ce dernier comme angle d’approche. Nous élaborerons ensuite le concept de colonisation interne et nous le confronterons au cas des autochtones. Puis, nous présenterons les motivations à la décolonisation ainsi que la composition d’un hypothétique État postcolonial canadien et de nations et communautés autochtones décolonisées. Finalement, nous analyserons la démarche judiciaire, la négociation d’ententes d’autonomie gouvernementale, la mobilisation des masses et l’approche des word warriors, l’objectif étant d’évaluer jusqu’à quel point ces moyens s’inscrivent dans un éventuel processus de décolonisation des nations autochtones.

Les enfants autochtones en protection de la jeunesse au Québec : leur réalité comparée à celle des autres enfants

Les populations autochtones canadiennes ont un passé difficile qui influence leur vécu actuel. Les recherches canadiennes et ailleurs dans le monde s’entendent sur la surreprésentation des enfants autochtones en protection de l’enfance. Au Canada, la surreprésentation s’explique présentement par la présence de conditions de vie dégradées plutôt qu’en raison d’un traitement différentiel des services de protection à l’égard des enfants autochtones. La présente étude ajoute aux connaissances sur les mauvais traitements et la réponse des services de protection de la jeunesse aux enfants autochtones québécois en s’intéressant à trois questions : leur surreprésentation, leurs différences par rapport aux autres enfants et les prédicteurs du placement. D’abord, à partir des données administratives de la protection de la jeunesse, la surreprésentation des enfants autochtones est évaluée à trois étapes des services : les signalements retenus, les situations fondées et les placements. Les enfants autochtones et les autres enfants sont comparés sur un ensemble de caractéristiques personnelles, familiales, parentales des signalements et des services rendus. Les prédicteurs du placement des enfants desservis par la protection de la jeunesse sont enfin vérifiés, en portant une attention particulière à l’importance du statut autochtone dans cette prédiction. Les résultats révèlent une augmentation de la surreprésentation des enfants autochtones d’une étape à l’autre des services de protection considérés. Ces enfants ont plus souvent des conditions de vie difficiles et sont confrontés à davantage de facteurs de risque que les autres enfants. Le statut autochtone est important dans la prédiction du placement, même après l’ajout d’un ensemble de caractéristiques pouvant contribuer à la prédiction. La complexité d’accès aux services de première ligne dans les communautés autochtones ou l’influence d’une variable non considérée, telle la pauvreté matérielle et économique, constituent de possibles explications. Les implications pour la recherche et la pratique sont discutées.

La situation socioéconomique des résidants des collectivités des Premières Nations et des collectivités environnantes du Québec : impact des facteurs de contexte et des facteurs individuels

Cette recherche se penche sur l’impact des facteurs de contexte et des facteurs individuels sur les conditions socioéconomiques des résidants des collectivités des Premières Nations du Québec et des résidants des communautés situées à proximité. Des régressions logistiques sur les données censitaires de 2001 ont été réalisées afin de répondre aux questions d’étude. Quatre dimensions, inspirées de l’indice de bien-être (IBC), ont été étudiées : l’activité, le logement, le revenu et la scolarité. Les résultats de recherche montrent que les deux types de facteurs contribuent à l’explication des inégalités sociales. Plus spécifiquement, les inégalités scolaires apparaissent principalement déterminées par les facteurs de contexte bien que les facteurs individuels, tel que l’âge et le genre, soient aussi déterminants. Ces dernières surviennent en amont des inégalités d’emploi et de revenu et expliquent celles-ci. De plus, les inégalités relatives au logement sont expliquées par l’emplacement spatial et le type de communauté de résidence. Par ailleurs, l’ethnicité des répondants ne joue pas un rôle de premier plan dans l’explication des disparités observées, une fois les autres caractéristiques contrôlées, ce qui ne signifie pas qu’il n’existe pas d’inégalités entre Amérindien et non-Amérindien. En fait, des chances différenciées persistent lorsque les autres caractéristiques sont contrôlées. Ainsi, les résultats mettent en évidence l’utilité de déplacer le point focal de la recherche quantitative sur les conditions autochtones du principal fait d’être Amérindien ou non vers un éventail plus large de déterminants.

Monáitaga úai – Palabra que se hace amanecer : el cambio en las formas de “gobierno propio” entre la Gente de Centro del medio río Caquetá, Amazonia colombiana

Depuis la fin du XIXe siècle, des dynamiques sociales diverses – holocauste du caoutchouc, colonie pénale, missions catholiques, présence d’institutions gouvernementales et non gouvernementales — ont reconfiguré les formes d’organisation sociale des habitants du moyen fleuve Caquetá, dénommés Gens de centre. Nous nous arrêterons en particulier sur l’effet de ces changements sur leurs formes d’autonomie. Avec la reconnaissance par l’État, au cours des années 1980 et 1990, des peuples indigènes en tant que minorités ethniques, surgit une dichotomie entre ce qui est « traditionnel » autochtone, par opposition à ce qui est « moderne », étant donné les processus d’acculturation et inclusion de ces groupes dans la société majoritaire. Dans le présent travail, on établit une comparaison des figures « d’autorité traditionnelle » et de « leader », une différenciation faite dans la région du moyen fleuve Caquetá. Dans un premier temps, on donne un aperçu théorique de la figure de chef dans les terres basses de l’Amérique du Sud et sa validité et pertinence dans la situation du moyen fleuve Caquetá. Puis, l’on présente comment se forme l’autorité traditionnelle et ses champs d’action. On montre, de la même façon, les différents processus qui ont donné lieu à l’apparition de la figure de leader et les espaces où celle-ci évolue. La relation entre les deux figures est à la fois contradictoire et complémentaire. Finalement, on expose, avec des exemples concrets, les rapports entre les Gens de centre et les institutions gouvernementales et la remise en question de l’autonomie accordée aux groupes minoritaires dans la Constitution politique de la Colombie de 1991.