Fragmentation of forest habitat by urban and rural development has had profound effects on the distribution and abundance of many native species; however, little is known about the ecological processes driving patterns in community structure (species richness and composition) of host-specialised herbivores in modified habitats. I examined patterns in community structure of 9 specialist and 19 generalist invertebrate herbivores of cabbage trees (Cordyline australis Laxmanniaceae) across a highly-modified landscape. I found that, although species richness of specialists was highest in forest sites, the majority of host-specialised species were not restricted to forest habitats and were as widespread as many generalists. In terms of site occupancy, only two specialist and four generalist species were rare. I show that patterns of species occupancy and abundance reflect differing susceptibility to habitat modification, with landscape-level variation an important predictor of abundance for nearly all species. When species occurrences and life history traits were considered I did not find strong evidence for the importance of dispersal ability, which suggests that habitat variability had a stronger organising effect on the community. In a replicated common garden experiment, I found distinct regional patterns in the community structure of the specialist invertebrates occurring on different phylogenetic groups of C. australis. In contrast, community structure of generalist herbivores did not differ significantly among host genotypes. I speculate these patterns are due to historical changes in the distribution of cabbage trees in the Southern phylogenetic region that caused specialised herbivores to become locally adapted on populations of low genetic diversity following expansion after the last glacial maximum. However, this consistent selection pressure did not occur in the Northern region where C. australis habitat has been more consistently available over the past tens of thousands of years, reflected in higher host genetic diversity. This study has advanced our understanding of the patterns in community structure of an indigenous, host-specialised fauna in a highly modified and fragmented urban and rural landscapes.

Comparer les structures génétiques des populations d’un couple hôte-parasite permet d’évaluer les facteurs qui façonnent la dispersion ainsi que la potentialité d’adaptation locale de ces espèces. Le modèle étudié est le crabe ectoparasite Dissodactylus primitivus et son oursin-hôte Meoma ventricosa, endémiques des Caraïbes et des côtes américaines voisines. <p>En étudiant des populations le long de l’arc antillais et de la côte panaméenne, ce travail a mis en évidence que la structure génétique des populations du parasite D. primitivus diffère fortement de celle de son hôte M. ventricosa (microsatellites et cytochrome oxydase I). En effet, alors que les populations du parasite présentent une différenciation au sein de cette région, celles de l’hôte sont génétiquement homogènes. Ce contraste peut être expliqué par des caractères biologiques et écologiques (fécondité, habilité à la nage, disponibilité de l’habitat) et suggère des potentialités d’adaptation locale distinctes. La distance géographique semble être importante dans la structuration des populations du crabe mais la courantologie ou encore des évènements passés (glaciations) jouent également un rôle. A l’échelle d’une même île, les crabes ne présentent pas de différenciation entre des sites distincts. En outre, nous avons pu montrer que des crabes issus d’hôtes d’espèces différentes ne sont pas différenciés génétiquement ce qui pourrait être liée à la mobilité des crabes adultes. Par des analyses de paternité, nous avons souligné cette mobilité, démontrant que le mode de reproduction du crabe est de la polygamie mais aussi que des accouplements pouvaient avoir lieu entre crabes d’espèces hôtes distinctes.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

La phylogéographie intègre l’information géographique et génétique pour inférer l’histoire démographique et les processus évolutifs des espèces. La présente étude recherche à travers les patrons de différenciation de l’ADN chloroplastique (ADNcp) au sein de Santiria trimera (Oliv.) H.J.LAM ex AUBR. [Emend. ONANA] la reconstitution d’une histoire des végétations des écosystèmes de forêts tropicales humides d’Afrique. Le modèle S. trimera est un arbre dioïque endémique des forêts humides d’Afrique dont les drupes sont dispersées par les primates et les oiseaux. Les formes morphologiques de ce modèle sont très variables et suscitent la délicate question de délimitation des espèces.<p>\ / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The dispersal of freshwater fishes in the Cape Floristic Region of South Africa has been attributed to river capture events and confluence of rivers during sea level regression. The role of low drainage divides and inter-basin water transfers have received less attention. A unique lineage of Galaxias zebratus (hereafter the Joubertina galaxias) occurs in two currently isolated river systems, the Gamtoos and Krom. The present study mapped the distribution of the Joubertina galaxias and used mitochondrial and nuclear DNA sequences to assess the processes that could have influenced its current distribution pattern. Analyses of both mitochondrial cytochrome ♭ and nuclear (S7) sequences revealed that observed genetic differentiation cannot be explained by isolation between the Gamtoos and Krom River systems. No genetic differentiation was found between the Krom River System and the Twee River (a tributary of the Gamtoos River System). Shallow genetic differentiation (0.4% for cytochrome ♭ and 0.3% for S7) was found between the Krom and the remaining populations in the Gamtoos River System. High levels of genetic structuring were observed within the Gamtoos River System with most tributaries having one or more unique alleles. Inter-basin dispersal during pluvial periods or recent human mediated translocation seems to be the most plausible explanations for presence of the Joubertina galaxias in the Krom River System. The present study also assessed the threats and habitat preferences of the Joubertina galaxias, and an evaluation of the conservation status of this lineage was done. The Joubertina galaxias is threatened mainly by alien fish invasion, habitat loss and loss of genetic diversity due to fragmentation of its populations. Due to its very restricted geographic range, small known population sizes and the intensity of threats to this lineage’s survival, this lineage has been assessed as Endangered. The lineage has a restricted Area of Occupancy (AOO) and Extent of Occurrence (EOO). The extent of occurrence has declined in all tributaries and is continuing to decline in all except two tributaries that are secure. The lineage may have had natural fragmentation among its populations, but recent threats have completely isolated the populations. The threats affect the lineage’s survival potential in the four tributaries which have small populations that are not presently viable. The densities observed for the Joubertina galaxias ranged from 0.16 - 1.3 fish /m² and the number of mature individuals for the whole population seems to be less than 2500 mature individuals. There is therefore a need for specific conservation actions to ensure the long-term survival of this unique lineage.

Subspecific taxonomic designations solely based on morphological characters can often lead to erroneous assumptions about the evolutionary history of populations. This study sought to investigate evolutionary questions and conservation implications associated with morphological subspecific designations of island populations. To this end, I focused my attention on the Lower Keys of Florida, a unique chain of islands with well-known geologic history and rich in endemic, endangered subspecies. I employed genetic analyses to evaluate historical variation and contemporary restriction of gene flow between the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) and its sister mainland taxa. A Bayesian phylogeny using 1063 base pairs of the mitochondrial cytochrome b gene did not recover reciprocal monophyly of the three named subspecies, and a 95% statistical parsimony haplotype network showed haplotypes being shared among subspecies. Furthermore, clustering analyses using 10 microsatellite loci identified a break within the Lower Keys, separating the western Lower Keys from the island of Big Pine Key. Surprisingly, Big Pine Key grouped with mainland populations and exhibits higher genetic diversity than the western Lower Keys islands. These unexpected findings suggest either a stepping-stone colonization pattern or recent gene flow between the mainland and Big Pine Key via natural dispersal or undocumented man-mediated transfers. Although these results suggest that subspecies designations within S. palustris are unwarranted, this study supports the designation western Lower Keys population as a discrete unit of conservation with regard to both DPS and ESU criteria. The importance of using several lines of evidence to uncover the evolutionary history of populations and implications for the conservation of island populations are discussed.

<p>Eastern black walnut (<i>Juglans nigra</i> L.) ranks among the most highly valued timber species in the central hardwood forest and across the world. This valuable tree fills a critical role in native ecosystems as a mast bearing pioneer on mesic sites. Along with other <i>Juglans</i> spp. (Juglandaceae), <i>J. nigra</i> is threatened by thousand cankers disease (TCD), an insect-vectored disease first described in 2009. TCD is caused by the bark beetle <i>Pityophthorus juglandis</i> Blackman (Corthylini) and the phytopathogenic fungus <i>Geosmithia morbida</i> Kol. Free. Ut. & Tiss. (Bionectriaceae). Together, the <i>P. juglandis</i>-<i>G. morbida</i> complex has expanded from its historical range in southwest North America throughout the western United States (U.S.) and Europe. This range expansion has led to widespread mortality among naïve hosts <i>J. nigra</i> and <i>J. regia</i> planted outside their native distributions.</p> <p> The severity of TCD was previously observed to be highest in urban and plantation environments and outside of the host native range. Therefore, the objective of this work was to provide information on biotic and abiotic environmental factors that influence the severity and impact of TCD across the native and non-native range of <i>J. nigra</i> and across different climatic and management regimes. This knowledge would enable a better assessment of the risk posed by TCD and a basis for developing management activities that impart resilience to natural systems. Through a series of greenhouse-, laboratory- and field-based experiments, environmental factors that affect the pathogenicity and/or survival of <i>G. morbida</i> in <i>J. nigra</i> were identified, with a focus on the microbiome, climate, and opportunistic pathogens. A number of potentially important interactions among host, vector, pathogen and the rest of the holobiont of TCD were characterized. The <i>holobiont</i> is defined as the whole multitrophic community of organisms—including <i>J. nigra</i>, microinvertebrates, fungi and bacteria—that interact with one another and with the host.</p> <p>Our findings indicate that interactions among host, vector, pathogen, secondary pathogens, novel microbial communities, and novel abiotic environments modulate the severity of TCD in native, non-native, and managed and unmanaged contexts. Prevailing climatic conditions favor reproduction and spread of <i>G. morbida</i> in the western United States due to the effect of wood moisture content on fungal competition. The microbiome of soils, roots, and stems of trees and seedlings grown outside the host native range harbor distinct, lower-diversity communities of bacteria and fungi compared to the native range, including different communities of beneficial or pathogenic functional groups of fungi. The pathogen <i>G. morbida</i> was also associated with a distinct community of microbes in stems compared to <i>G. morbida</i>-negative trees. The soil microbiome from intensively-managed plantations facilitated positive feedback between <i>G. morbida</i> and a disease-promomting endophytic <i>Fusarium solani</i> species complex sp. in roots of <i>J. nigra</i> seedlings. Finally, the nematode species <i>Bursaphelenchus juglandis</i> associated with <i>P. juglandis</i> synergizes with <i>G. morbida</i> to cause foliar symptoms in seedlings in a shadehouse; conversely, experiments and observations indicated that the nematode species <i>Panagrolaimus</i> sp. and cf. <i>Ektaphelenchus</i> sp. could suppress WTB populations and/or TCD outbreaks.</p> <p>In conclusion, the composition, function, and interactions within the <i>P. juglandis</i> and <i>J. nigra</i> holobiont play important roles in the TCD pathosystem. Managers and conservationists should be aware that novel associations outside the host native range, or in monocultures, intensive nursery production, and urban and low-humidity environments may favor progression of the disease through the effects of associated phytobiomes, nematodes, and climatic conditions on disease etiology. Trees in higher diversity, less intensively managed growing environments within their native range may be more resilient to disease. Moreover, expatriated, susceptible host species (<i>i.e.</i>, <i>J. nigra</i>) growing in environments that are favorable to novel pests or pest complexes (<i>i.e.</i>, the western U.S.) may provide connectivity between emergent forest health threats (<i>i.e.</i>, TCD) and native host populations (<i>i.e.</i>, <i>J. nigra</i> in its native range).</p>

[ES] Esta tesis investiga las oportunidades, desafíos y limitaciones para la investigación en el campo de la ecología vegetal, en el contexto de los acantilados mediterráneos. En concreto, las especies casmofiticas, cuyos hábitats naturales se caracterizan por su acusada pendiente. Las laderas de las montañas de piedra caliza en la proximidad del mar, en la parte central y occidental del área mediterránea se consideran objetos de estudio. Los estudios se llevaron a cabo en los cinturones costeros de montaña de las costas del noroeste de Sicilia y la costa diánica en la Comunidad Valenciana. El primer capítulo, titulado "The complexity of environmental factors: cliff microclimate", investiga la variabilidad del microclima del acantilado en tres áreas diferentes en Sicilia y España, analizando las condiciones ambientales creadas por el acantilado en una escala muy estrecha. Se recopilaron seis conjuntos de datos independientes y comparables que recogen las principales variables meteorológicas a lo largo de un período total de 18 meses. La gama resultante de condiciones ambientales se compara por pares a lo largo de dos gradientes ambientales principales: la orientación del acantilado Norte/Sur y la proximidad al mar. Además, los rasgos foliares intraespecíficos se utilizan para estudiar la variación en la respuesta funcional de las plantas que viven en las orientaciónes opuestas en una misma área de investigación. La variación resultante se correlaciona con la influencia de las condiciones microclimáticas creadas por la pendiente y el aspecto en los rasgos de la planta antes mencionados. El segundo capítulo, titulado "Compositional data and analyses of areas and plant communities in the coastal cliffs of the Valencian Community (Spain)", presenta una ordenación de los sitios de estudio y de las especies vegetales que habitan en las zonas de acantilados del cinturón montañoso a lo largo de las costas de la región diánica en el este de España. El estudio reveló correlaciones significativas entre las unidades de vegetación y los sitios con referencia a la amplia orientación geográfica Norte/Sur. Sin embargo, fue poco informativo con respecto a revelar las principales diferencias observadas en la estructura del conjunto de plantas relacionadas con laa variaciones microtopográficas registradas en el conjunto de datos. En el tercer capítulo, titulado "UAV (drone) surveys for the study of plant- microtopography relationships and for the conservation of rare species", se describe la metodología propuesta para investigar entornos verticales poco accesibles. También se analizaron los desafíos y las oportunidades de la investigación ecológica vegetal en estas áreas tipicamente inaccesibles. Un primer conjunto de datos comprende un censo visual parcial y total de dos especies endémicas de acantilados estrechos en las áreas de estudio españolas e italianas. Mediante el uso de la fotogrametría aérea de corto alcance y el modelado 3D, fue posible estudiar los efectos de la micro topografía en la segregación de nichos, tanto a nivel de comunidad como de especie. Se utilizaron métodos de ordenación para correlacionar las especies endémicas seleccionadas y conjuntos de plantas con factores ambientales como el aspecto local y global, la pendiente y la distancia desde los bordes de los acantilados. En el cuarto capítulo, titulado "Distribution, ecology, conservation status and phylogeography of Pseudoscabiosa limonifolia, a paleo-endemic chasmophytic species from Sicily (Italy)", se analiza en detalle la estructura filogeográfica de una especie endémica de acantilados, Pseudoscabiosa limonifolia (Caprifoliaceae, subfamilia Dipsacaceae), también considerando las relaciones filogeográficas con sus taxones más próximos. Además, su distribución total se determinó mediante observaciones de campo, caracterizando su hábitat y evaluando su estado de conservación como Vulnerable de acuerdo con las / [CA] Aquesta tesi va investigar les oportunitats, reptes i limitacions per a la investigació en el camp de l'ecologia vegetal, en el context dels penya-segats mediterranis. En concret, les espècies casmofitiques, amb hàbitats naturals que es caracteritzen pel seu acusat pendent. Les vessants de les muntanyes de pedra calcària en la proximitat del mar, a la part central i occidental de l'àrea mediterrània són considerats objectes d'estudi. Els estudis es portaren a terme als cinturons costers de muntanya de les costes del nord de Sicília i la costa diànica a la Comunitat Valenciana. El primer capítol, titulat "The complexity of environmental factors: cliff microclimate", investiga la variabilitat del microclima del penya-segat en tres àrees diferents de Sicília i Espanya, analitzant les condicions ambientals creades pel penya-segat a una escala molt estreta. Es recopilen sis conjunts de dades independents i comparables que reconeixen les principals variables meteorològiques a llarg termini durant un període total de 18 mesos. Les dades resultants de les condicions ambientals es comparen per parells al llarg de dos gradients ambientals principals: l'orientació del penya-segat Nord/Sud i la proximitat a la mar. A més, els trests foliars intraespecífics s'utilitzen per estudiar la variació en la resposta funcional de les plantes que habiten orientacions oposades dins d'un àrea d' investigació. La variació resultant es correlaciona amb la influència de les condicions microclimàtiques creades pel vessant i els aspectos funcionals dels trets vegetals esmentats. El segon capítol, titulat "Compositional data and analyses of areas and plant communities in the coastal cliffs of the Valencian Community (Spain)", presenta una ordenació dels llocs d'estudi i de les espècies de plantes que habiten a les zones de penya- segats del cinturó de muntanya al llarg de les costes de la regió diànica de España. L'estudi va a revelar correlacions significatives entre les unitats de vegetació i els llocs amb referència a l'amplias orientació geogràfica Nord/Sud. No obstant aixó, va ser poc informatiu per poder revelar les diferències observades en l'estructura del conjunt de plantes relacionades amb les variacions microtopogràfiques registrades al conjunt de dades Al tercer capítol, titulat "UAV (drone) surveys for the study of plant-microtopography relationships and for the conservation of rare species", es descriu la metodologia proposada per a investigar entorns verticals poc accessibles. També es van analitzar els reptes i les oportunitats de la investigació ecològica vegetal en aquestes àrees normalment inaccesibles. Un primer conjunt de dades inclou el cens visual parcial i el total de dues espècies endèmiques de penya-segats a les àrees d'estudi espanyoles i italianes. Mitjançant la fotogrametria aèrea a curt abast i el modelat 3D, va ser possible estudiar els efectes de la microtopografia en la segregació de nínxols, tant a nivell comunitari com d'espècies. Es van utilitzar mètodes d'ordenació per a correlacionar les espècies endèmiques seleccionades i conjunts vegetals sencers amb factors ambientals com ara l'aspecte local i global, el pendent i la distància de les vores dels penya-segats. En el quart capítol, titulat "Distribution, ecology, conservation status and phylogeography of Pseudoscabiosa limonifolia, a paleo-endemic chasmophytic species from Sicily (Italy)", que s'analitza en detall l'estructura filogeográfica d'una espècie endèmica de penya-segats, Pseudoscabiosa limonifolia (Caprifoliaceae, subfamilia Dipsacaceae), considerant tambè les relacions filogeogràfiques amb els seus taxons més propers. A més, la seva distribució total es va determinar mitjançant observacions de camp, caracteritzant el seu hàbitat i avaluant el seu estat de conservació com a Vulnerable, d'acord amb les directrius de la llista roja de la UICN. / [EN] This thesis investigated opportunities, challenges and limitations for plant ecological research in the context of Mediterranean cliffs. In particular, chasmophytic species, whose natural habitats are very steep, limestone mountain slopes in the proximity of the sea, in the Central and Western part of the Mediterranean area are considered as study objects. Studies were carried out in the coastal mountain belts of both North-western Sicily and Dianic coasts in the Valencian Community (Spain). The first chapter, entitled "The complexity of environmental factors: cliff microclimate", investigates the variability of cliff microclimate in three different areas in Sicily and Spain, analysing the environmental conditions created by the cliff at very fine scale. Six independent and comparable datasets including the main meteorological variables were compiled in a total period of 18 months. The resulting spectra of environmental conditions are compared pairwise along two key environmental gradients: North/South cliff orientation and proximity to the sea. Intraspecific leaf traits are used in order to investigate variations in the functional response of plants living on opposite orientations. The resulting variation is then correlated with the influence of microclimatic conditions created by slope and functional aspects of the aforementioned plant traits. The second chapter, entitled "Compositional data and analyses of areas and plant communities in the coastal cliffs of the Valencian Community (Spain)", presents an ordination of the study sites and of the plant species inhabiting the cliff zones of the mountain belt along the coasts of the Dianic region in Eastern Spain. The study revealed significant correlations between the vegetation units and the sites with reference to the broad North/South geographical orientation. However, it was poorly informative in respect to reveal the major differences observed in the structure of the plant assemblage related to the micro- topographic variations recorded in the dataset. In the third chapter, entitled "UAV (drone) surveys for the study of plant- microtopography relationships and for the conservation of rare species", a proposed survey methodology for investigating inaccessible vertical environments is described. Challenges and opportunities of plant ecological research in these typically inaccessible areas were also analysed. A first set of data is comprised of partial and total visual census of two narrow endemic cliff species in the Spanish and Italian study areas. Through the use of aerial close- range photogrammetry and 3D modelling, it was possible to study the effects of micro-topography on niche segregation, both at community and species level. Ordination methods were used to correlate selected endemic species and entire plant assemblages to environmental factors such as local and global aspect, slope and distance from cliff edges. The fourth chapter, entitled "Distribution, ecology, conservation status and phylogeography of Pseudoscabiosa limonifolia, a paleo-endemic chasmophytic species from Sicily (Italy)", is addressed to analyse in details the phylogeographic structure of a cliff narrow endemic species, Pseudoscabiosa limonifolia (VAHL) DEVESA (Caprifoliaceae, subfamily Dipsacaceae), also taking in consideration its closest sister taxa. Furthermore, its total distribution was determined by field surveys, characterizing its habitat, and assessing its conservation status as Vulnerable according to IUCN red list guidelines. / De Simone, L. (2020). Ecological aspects of plants inhabiting Mediterranean cliffs. Challenges and prospects of life in vertical environments [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/159877

The sap beetle genus Carpophilus Stephens (Coleoptera: Nitidulidae) is a large genus consisting of over 200 species and are found worldwide. Several species are important pests of crops and stored products, and are frequently intercepted as part of biosecurity operations. The genus is poorly known taxonomically, and there are several species groups that are challenging to identify by morphological methods. In particular, two species found across the Pacific, C. maculatus Murray and C. oculatus Murray are frequently confused with each other. These two species are similar in size and colour, but differ primarily by the shape of the colour pattern on their elytra. However, this colour pattern is highly variable within both species, leading to ambiguity in the indentification of these species. Within C. oculatus, three subspecies have been described based on differences in the male genitalia and pronotal punctation: C. o. oculatus and C. o. gilloglyi Dobson are distributed widely across the Pacific, while C. o. cheesmani Dobson is known only from Vanuatu. A search of literature records and specimen collections revealed 32 species of Carpophilus recorded from the Pacific region. In addition there remain several unidentified specimens representing at least four species, two of which will be described subsequent to this research. A number of species recorded in the literature may have been misidentified, and these require further field collections and inspection of museum specimens to confirm their presence in the Pacific. To test the validity of the subspecies of C. oculatus, and its distinctiveness from C. maculatus, a phylogeny of available specimens of Carpophilus was inferred from one mitochondrial gene (cytochrome c oxidase subunit I (COI)), and two nuclear genes (28S ribsomal RNA (28S) and the internal transcribed spacer 2 (ITS2)). These data show large genetic distances between the three subspecies of C. oculatus of 7-12%. Given these distances are similar to those between other species in the genus, this indicates these subspecies may be elevated to full species. The data also consistently support a monophyletic relationship between C. o. oculatus and C. o. gilloglyi. Nuclear genes also support C. o. cheesmani as part of a clade with the other subspecies, but these relationships are unresolved in COI. Carpophilus maculatus was not supported as being the sister taxon of the C. o. oculatus and C. o. gilloglyi clade. Other relationships within Carpophilus were unresolved, possibly due to a combination of incomplete taxon sampling, and saturation of substitutions within the COI gene. Phylogeographic analysis of specimens collected from several localities within the range of C. oculatus showed that, with only one exception, there were no shared haplotypes between archipelagoes. This result suggests it may be possible to determine the provenence of intercepted specimens, providing further information regarding potential invasion pathways. A degree of geographic structuring was also present within C. o. gilloglyi, being separated into a western clade found in Fiji and Rotuma and an eastern clade distributed from the Kermadec Islands and Tonga to French Polynesia. This separation was most profound in COI data, with a mean pairwise distance between the clades of 7%. ITS2 data also demonstrates a degree of differentiation between the two clades, based on differences in the insertions and deletions between the clades. The variability in the shape and colour of the elytral pattern of C. oculatus was also investigated. Colour was quantified using a method based on Red-Green-Blue (RGB) colour values derived from digital photographs, while an outline analysis of the elytral pattern was conducted using elliptic Fourier analysis (EFA). Principal Components Analysis of the RGB values and EFA coefficients showed no clear separation between subspecies, nor were any trends correlated with host fruit or collection localities. Variation at all levels and all measures studied in this thesis show that this geographic region and this genus of beetles offer intruiging insights into speciation, biogeography and biological invasions. There is much scope for further research on the causes and consequences of this variation and the lives of these interesting insects.