京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19769号 / 農博第2165号 / 新制||農||1040(附属図書館) / 学位論文||H28||N4985(農学部図書室) / 32805 / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 井鷺 裕司, 教授 北山 兼弘, 教授 神﨑 護 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

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Understanding the disease transmission dynamics in wildlife species can be difficult and can prove more complicated if the population structure of a socially living species is shaped by territoriality. Understanding the connections and movements of individuals between groups is vital to documenting how a disease may be spread. The presence of a heterogeneous landscape can further complicate attempts to describe transmission of an infectious disease. Here, I sought to understand how dispersal patterns of individual banded mongooses (Mungos mungo) could potentially influence disease transmission. Banded mongooses are small fossorial mammals that live in social groups ranging from 5 to 75 individuals and defend their territories against rival troops. The focal population of mongooses for this study lives across a complex environment in the Chobe district of northern Botswana and is faced with a novel strain of tuberculosis, Mycobacterium mungi. To infer genetic structure and individual movements between troops, I utilized microsatellite genetic markers and population genetic analyses. I found moderately strong genetic structuring (FST = 0.086) among 12 troops of banded mongooses in the study area in 2017-18. The best supported number of genetic clusters was K = 7, with a considerable amount of admixture between troops in urban areas. Compared to the average pairwise differentiation values of troops residing in natural habitats (FST = 0.102), urban troops had a lower level of differentiation (FST = 0.081), which suggests more gene flow between these troops. Among 168 mongooses genotyped, 20 were identified as being likely dispersers, with the majority moving across anthropogenic environments, suggesting that dispersal is heightened in urbanized areas. To assess whether temporal variation had an effect on genetic structure and gene flow between troops, I compared population genetic results from 5 troops in 2008 to those from the same 5 troops in 2017. Genetic differentiation was lower between troops living in urban environments than in natural environments for both 2008 and 2017. This result suggests higher gene flow across the anthropogenic landscapes at both times steps. The overall genetic structuring of the troops persisted over almost a decade, with the exception of observing more mixture and admixture in 2017 than in 2008. The effective population sizes (Ne) of troops were larger in 2008, which would indicate that genetic variability declined as time progressed. For 11 individuals confirmed to have M. mungi, an assignment test suggested that 3 mongooses were likely dispersers. This finding would contradict that of previous work, which suggested that sick banded mongooses refrained from dispersing. Sequencing of the M. mungi strains would be needed to determine whether these dispersers moved while sick or became infected after entering their new troop. These findings suggest that emphasis should be placed on closely monitoring banded mongoose troops in areas with heavy human influence. Here we see lower pairwise differentiation, higher gene flow estimates, and more frequent dispersal events. Heightened dispersal potentially can result in elevated disease transmission between troops in urban habitats. With disease transmission being the result of complex interactions between environment, host, pathogen, and time, results from this study contribute to understanding of disease transmission dynamics. / MS / Understanding how groups of the same species are connected is important for assessing how wildlife diseases spread across a landscape. For social species, connections are established by the movements of individuals between different groups; however, these can prove difficult to observe. Further complicating our ability to infer connections and movements, groups often live under different environmental conditions, which can influence movement rates. I studied banded mongooses (Mungos mungo) living in northern Botswana to assess the role of individual movement on the potential for disease transmission. Banded mongooses are small ground-dwelling mammals that live in troops of 5-75 individuals and defend group home-ranges. In Botswana, some troops are infected with a species of tuberculosis (TB, caused by the bacterium Mycobacterium mungi) that is unique to banded mongooses. Using molecular genetic tools, I estimated how genetically similar troops were to one other and estimated the rates of movement of individuals between troops. I found that troops living in urban environments tended to be more genetically similar to one other compared to troops living in natural environments within nearby Chobe National Park. I also detected more cases of individuals moving between troops in urban settings, with little evidence of movement between troops living in natural areas. These results suggest that there is more genetic exchange and a higher degree of connection between troops living in areas heavily influenced by people. With more connections between town-dwelling troops, we would expect to see higher rates of disease transmission between these urban troops, and hence should monitor their movement and health status closely. I also assessed how genetic structure and connections between banded mongoose troops changed over time by comparing results for collections of samples made in 2008 and 2017. Although more movement was detected in 2017, the overall pattern of genetic connections remained similar over the ten-year period. In particular, there was greater genetic similarity between troops in town compared to troops in natural environments in both years. Additionally, I genetically assigned TB-positive individual mongooses to their troop of origin to determine whether sick individuals moved out of their original troops. I identified three sick individuals as probable dispersers, although it is difficult with the information available to know whether they moved while infected or became ill after joining a new troop.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Limited dispersal, territoriality and the occupation of patchy habitats; characters that typify most African rock-dwelling (saxicolous or rupicolous) species, often result in structured genetic patterns with little or no gene-flow among populations (e.g., velvet worms, net-winged midges, elephant shrews, red rock rabbits and a variety of lizards and agamas). In an attempt to deepen our understanding of taxa that inhabit these “terrestrial islands” the distribution of genetic variation was studied at several spatial scales in the rock hyrax, Procavia capensis. This species has a polygynous social system that is unusual among taxa with similar ecological requirements, and a morphology that would intuitively be associated with poor dispersal capabilities (short limbs and a squat, heavy body). Possibly as a consequence of these considerations, few studies have attempted to determine the distance of migration by rock hyraxes and the influence that their social system and the surrounding landscape has on dispersal success. This investigation therefore tests hypotheses of how the ecology, distribution, social structure and the connectivity of the surrounding landscape have contributed to shaping the structure of rock hyrax genetic variation across the Namaqualand and western Fynbos regions. To do so, mitochondrial and microsatellite markers were used to document gene-flow at a fine spatial scale (an isolated population comprising 5 koppies), an intermediate spatial scale (across known geographic barriers to saxicolous taxa - the Cape Flats and Knersvlakte), and a regional spatial scale (across the Namaqualand/western Fynbos regions of South Africa - regions exhibiting contrasting landscape connectivity). In addition the genetic diversity, spatial clustering, sex-biased dispersal and relatedness (fine-scale) of colonies is described and the major genetic breaks detected in the investigation dated using a relaxed molecular clock approach. Finally, these results were compared to other studies that identified the Cape Flats and Knersvlakte as phylogeographic disruptors. The genetic patterns at a fine spatial scale were complex: Gene-flow was restricted by the social structure of the rock hyrax rather than geographic distance, dispersal was female-biased and there was significant genetic structure. Genetic structure was also evident at the intermediate and regional spatial scales. In the Hottentots Holland Mountains and Cape Peninsula gene-flow was restricted (in both data sets) in comparison to localities that traversed the Cape Flats. In contrast, gene-flow across the Knersvlakte was restricted in the mitochondrial DNA data set but not so with microsatellites. A similar pattern was observed at a regional scale pointing to male-biased dispersal within this species - a result of its polygynous social structure. In addition to sex-biased dispersal, landscape connectivity also influenced gene-flow on a regional spatial scale as the Namaqualand region, which has greater intermediate suitable habitat compared to the western Fynbos region, displayed significantly higher levels of gene-flow between sampling localities. Consequently, colonies in Namaqualand were genetically more diverse compared to those of the western Fynbos region. Two major matrilineal clades were evident on both side of the Knersvlakte - one to the north of this biogeographic break (Namaqualand), and the other to the south (western Fynbos). This was not, however, evident from the microsatellite data (reflecting the influence of male dispersal) where seven nuclear clusters were found. In keeping with other studies on saxicolous vertebrate taxa straddling the same region, this area of low connectivity has acted (and probably still does) as a barrier to gene-flow. Importantly, unlike in many other (admittedly invertebrate) species, no evidence of a genetic break was detected among hyrax populations across the Cape Flats. Colonies across the Hottentots Holland Mountains and Cape Peninsula regions may have been subject to founder-events and breeding isolation. This investigation demonstrated the importance of using a well-structured sampling regime that included both mitochondrial and nuclear markers and it underscores the need to apply appropriate statistical programmes for inferring genetic patterns. It shows that landscape genetics may be useful in a conservation context and should be taken into account when planning conservation initiatives that include the implementation of corridors. In brief, the information contained in this study advances our knowledge of the dispersal capability and genetic diversity of contemporary rock hyrax populations. / AFRIKAANSE OPSOMMING: ‘n Beperkte spreidingsvermoë, territorialiteit en die bewoning van yl-verspreide habitat is kenmerkend van die meeste klip-bewonende spesies in Afrika en dit veroorsaak gereeld gestruktureerde genetiese patrone met min of geen genevloei tussen populasies (bv., die velvetwurms, net-vlerk muggies, klipklaasneuse, klipkonyne en ‘n verskeidenheid akkedisse en koggelmanders). In ‘n poging om kennis oor taksa wat hierdie “terrestriële eilande” bewoon te verdiep, het ons die die verspreiding van genetiese variasie bestudeer oor verskeie ruimtelike skale in die klipdassie, Procavia capensis. Hierdie spesie het ‘n veelwywige sosiale sisteem, wat vreemd is onder taksa met soortgelyke ekologiese vereistes, en ‘n morfologie wat intuïtief verbind kan word met swak spreidingsvermoëns (kort bene en ‘n kort, dik liggaam). As ‘n moontlike resultaat van hierdie oorwegings het min studies tot dusver daarop gefokus om die migrasie-afstand van klipdassies en die invloede van hulle sosiale sisteem en die omliggende landskap op spreidings-sukses te bepaal. Hierdie studie toets daarom hipoteses oor hoe die ekologie, verspreiding, sosiale struktuur en die konnektiwiteit (verbindheid) van die omliggende landskap bydra om die struktuur van genetiese variasie in klipdassies oor die Namakwaland en westelike Fynbos streke te beïnvloed. Derhalwe is mitochondriale en mikrosatelliet merkers gebruik om genevloei te bepaal op ‘n fyn ruimtelike skaal (‘n geïsoleerde populasie bestaande uit 5 koppies), ‘n gemiddelde ruimtelike skaal (oor bekende geografiese grense vir klipbewonende taksa - die Kaapse Vlakte en die Knersvlakte), en op ‘n streeks (groot) ruimtelike skaal (oor die Namakwaland/westelike Fynbos streke van Suid-Afrika - streke met kontrasterende konnektiwiteit van die landskap). Bykomend is die genetiese diversiteit, ruimtelike groepering, seksuele eensydigheid in spreiding en genetiese verwantskappe (fyn skaal) van kolonies beskryf en die hoof genetiese skeiding gedateer deur gebruik te maak van ‘n ontspanne molekulêre klok. Laastens het is die resultate van hierdie studie vergelyk met dié van ander studies wat die Kaapse Vlakte en Knersvlakte as filogeografiese skeidings gevind het. Die genetiese patrone op ‘n fyn ruimtelike skaal was kompleks: Genevloei is beperk deur die sosiale struktuur van die klipdassie eerder as geografiese afstand, migrasie was wyfie-spesifiek en daar was beduidende genetiese struktuur tussen kolonies. Genevloei was beperk in die Hottentots Holland berge en die Kaapse Skiereiland (in beide datastelle) in vergelyking met lokaliteite oor die Kaapse Vlakte. In kontras was genevloei oor die Knersvlakte beperk in die mitochondriale DNA, maar nie in die mikrosatelliete nie. ‘n Soortgelyke patroon is waargeneem op ‘n streeks skaal wat dui op mannetjie-spesifieke spreiding in hiérdie spesie - ‘n resultaat van die veelwywige sosiale struktuur. Bykomend, saam met geslag-spesifieke spreiding, het landskaps konnektiwiteit ook genevloei beïnvloed op ‘n streeks skaal omdat die Namakwaland streek, wat meer tussenleggende geskikte habitat bevat in vergelyking met die westelike Fynbos streek, beduidende hoër vlakke van genevloei tussen lokaliteite getoon het. Gevolglik was kolonies in Namakwaland geneties meer divers in vergelyking met dié van die westelike Fynbos streek. Twee hoof moederlike genetiese groepe is waargeneem op elke kant van die Knersvlakte - een aan die noorde van hierdie biogeografiese skeiding (Namakwaland) en een in die suide (westelike Fynbos). Dieselfde patroon was egter nie waarneembaar in die mikrosatelliet data nie (wat die invloed van mannetjie-spesifieke spreiding toon) waar sewe nukluêre groepe gevind is. In ag genome ander studies op klipbewonende gewerwelde taksa oor dieselfde verspreiding, het hierdie area van lae konnektiwiteit histories (en heelmoontlik ook huidiglik) as ‘n grens vir genevloei gedien. Belangrik, anders as in ander (hoewel ongewerwelde) spesies, kon ons geen bewyse verskaf van ‘n genetiese skeiding tussen klipdassie populasies oor die Kaapse Vlakte nie. Kolonies in die Hottentots Holland berge en Kaapse Skiereiland is dus onderhewig aan moontlike vestigings-effekte en telings-isolasie. Hiérdie studie demonstreer die belang van die gebruik van ‘n goed-gestruktureerde monsternemingskema, die insluiting van beide mitochondriale en nukluêre merkers en dit beklemtoon ook die noodsaaklikheid van die gebruik van toepaslike statistiese programme vir gevolgtrekkings oor genetiese patrone. Dit toon ook dat landskapsgenetika nuttig mag wees in ‘n bewaringskonteks en in ag geneem moet word in die beplanning van bewarings inisiatiewe wat die implementering van korridors insluit. Kortliks, die informasie in hierdie studie bevorder ons kennis oor die spreidingsvermoë en genetiese diversiteit van kontemporêre klipdassie populasies.

Στην παρούσα εργασία αξιολογήθηκε η χρήση των μικροδορυφορικών δεικτών για τη μελέτη της γενετικής δομής και των φυλογενετικών σχέσεων των φυσικών πληθυσμών της Atherina boyeri που προέρχονταν τόσο από θαλάσσιες όσο και λιμναίες/λιμνοθαλάσσιες περιοχές της Ελλάδας. Προηγούμενες μελέτες βασιζόμενες κυρίως σε μιτοχονδριακούς και RAPD δείκτες έχουν υποδείξει την πιθανή παρουσία τριών ομάδων πληθυσμών στην Atherina boyeri με τόσο υψηλές γενετικές αποστάσεις μεταξύ τους που θα μπορούσαν να τις καθιστούν ακόμα και διαφορετικά είδη. Οι ομάδες αυτές είναι: οι θαλάσσιοι πληθυσμοί τύπου Ι (μη εστιγμένοι),οι θαλάσσιοι πληθυσμοί τύπου ΙΙ (εστιγμένοι) και οι λιμναίοι/λιμνοθαλάσσιοι πληθυσμοί. Η ανάλυση στην παρούσα εργασία πραγματοποιήθηκε με χρήση 11 μικροδορυφορικών δεικτών που σχεδιάστηκαν από τους Milana et al. (2009). Οι μικροδορυφορικοί δείκτες θεωρούνται εξαιρετικό εργαλείο μελέτης των φυλογενετικών σχέσεων μεταξύ πρόσφατα διαχωρισμένων ειδών δεδομένου ότι είναι άφθονοι, πυρηνικοί, διάσπαρτοι στο γονιδίωμα, υψηλά πολυμορφικοί και ταχέως εξελισσόμενοι. Τα αποτελέσματα έδειξαν πολύ υψηλό βαθμό πολυμορφισμού στους υπό ανάλυση πληθυσμούς και μεγάλη γενετική διαφοροποίηση μεταξύ των ελληνικών πληθυσμών του είδους όπως αυτή εκφράζεται από τις διαφορές στις συχνότητες των αλληλομόρφων των μικροδορυφορικών δεικτών. Φαίνεται επίσης να επιβεβαιώνεται η διάκριση μεταξύ των δυο θαλάσσιων τύπων της Atherina boyeri, ωστόσο οι λιμναίοι/λιμνοθαλάσσιοι πληθυσμοί παρουσιάζουν τόσο διαφορετικό γενετικό πρότυπο που θεωρείται εξαιρετικά δύσκολο να συνιστούν μια ενιαία ομάδα πληθυσμών. Οι δείκτες αυτοί δεν ήταν δυνατό να χρησιμοποιηθούν στην ανάλυση όλων των διαθέσιμων πληθυσμών, κυρίως λόγω της παρουσίας μη ενισχυόμενων (null) αλληλομόρφων, καθώς επίσης και πολλαπλών ή/και ασθενών ζωνών, γεγονός που επίσης υποδεικνύει την ύπαρξη μεγάλων γενετικών διαφοροποιήσεων, που πιθανώς ξεπερνούν τα όρια του είδους. Προκείμενου να ξεπεραστούν τα ανωτέρω προβλήματα απαιτείται η βελτιστοποίησή τους ανά ομάδα πληθυσμών, μέσω α) αλλαγών στις συνθήκες των PCR αντιδράσεων και β) κλωνοποίησης και αλληλούχισης των δεικτών αυτών από άτομα των πληθυσμών στα οποία ήταν λειτουργικοί, ώστε να επιτευχθεί ο σχεδιασμός νέων ζευγών εκκινητών, ειδικών για επιμέρους ομάδες πληθυσμών. / The present study aims at the measure of the genetic differentiation and the resolution of the phylogenetic relationships among A.boyeri populations originating from lakes/lagoons and marine sites of Greece. Previously studies based on RAPD and mitochondrial markers suggest the existence of three forms of populations of A.boyeri which could represent three different species. These three types are: marine type I, which includes almost all marine populations (non-punctuated), excluding specimens collected from Preveza, Evoia and Kos, which form the marine type II (punctuated) and the “lagoon” type which consists of all the lagoon/lake populations. In the present study, eleven microsatellite markers designed by Milana et al. (2009), were used. Microsatellite markers are supposed to be great tools in phylogenetic studies among recently separated species because they are abundant, nuclear, dispersed around the genome, highly polymorphic and rapidly evolving. Our results showed very high degree of polymorphism in the analyzed populations and extended genetic differentiation among Greek populations of the species as expressed by differences in allele frequencies of the microsatellite markers. They also seems to confirm the distinction between the two marine types of A.boyeri, but the lagoon/lake populations present different allele paterns, pointing to the possible existence of differentiated groups among them. Some of the markers could not be used in the analysis of all the available populations. This is mainly attributed to the presence of null alleles for some of the populations and to scoring difficulties raising from the presence of multiple and/or weak amplicons. This also indicates the existence of great genetic variations, which possibly exceed species limit. To overcome the above difficulties, optimization per marker is required, including a) optimization of PCR conditions and b) cloning and sequencing of these markers from individuals of the population that were functional to achieve the design of new prime pairs, specific for each group of populations .

Dispersal is a fundamental process that shapes many aspects of population ecology and evolution. Dramatic local population declines brought about by anthropogenic-driven changes to ecological processes are unfortunately becoming ubiquitous and increasing the urgency to understand dispersal behaviour in many species. For species where direct methods of tracking movement and dispersal are unsuitable, other indirect methods need to be employed to understand and characterise these behaviours. The steep population decline, due to predation, at the largest EU population of Leach’s storm-petrels Oceanodroma leucorhoa (St Kilda, Scotland), and the potential part immigrant birds have in buffering this threat, highlighted the need to understand dispersal and connectivity of widely spaced colonies in this species. The implications for the persistence of local colonies and the wider population of Leach’s storm-petrels could then be assessed. A population genetic analysis of 9 colonies across the North Pacific and Atlantic distribution, using two DNA markers (mtDNA control region and microsatellites), revealed ocean basin differentiation (Global ST = 0.32 P <0.0001, Global FST = 0.04, P <0.0001) but also identified a migrant individual in the Pacific population (STRUCTURE migrant assignment). The Atlantic population was found to be genetically homogenous, with patterns of historical and contemporary gene flow, indicating that long-distance effective dispersal is prevalent in Leach’s storm-petrels within the ocean basin. Bayesian stable isotope analysis of carbon and nitrogen (13C & 15N) provides evidence for natal dispersal as an important dispersal mechanism, and reveals movement of immature birds between colonies during the breeding season as a likely mechanism to promote inter-colony exchange and gene flow. Stable isotope comparison also identified mixing on wintering grounds as another possible influence on dispersal. The potential for immigrant birds to offset the loss caused by predation at the St Kilda colony is supported by these studies, and will likely help the persistence of the colony in the short-term. However, future viability is debateable considering the evidence for both avian and mammalian predation. This research provides a better understanding of the extent and mechanism of dispersal in the Leach’s storm-petrel, which is important to predict the potential impact of environmental change and, where possible, implement effective population management for this species.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

La blennie fluviatile (Salaria fluviatilis) est une espèce qui a colonisé l'environnement dulcicole à partir d'un ancêtre marin et habite actuellement lacs et rivières situés autour de la Méditerranée. Comment un tel changement d'environnement peut avoir affecté la structure génétique et le phénotype de cette espèce ? C'est autour de cette question centrale que s'articulent les deux principaux volets de cette thèse. Le premier s'intéresse aux conséquences d'évènements géologiques historiques, affectant la structure génétique de S. fluviatilis. Nous y verrons, entre autres, qu'à l'intérieur du bassin occidental de la Méditerranée, les localisations les plus nordiques ont été colonisées à partir de deux refuges glaciaires. Le deuxième volet est centré sur l'adaptation et l'acclimatation que nécessite un tel changement d'environnement. Il y sera révélé que les réponses de la forme du corps et la longueur des nageoires face à la vitesse du courant sont contrôlées par un déterminisme environnemental chez la blennie fluviatile. Ensemble, ces deux volets permettent de mieux comprendre les processus derrière la différenciation des populations dans un contexte de colonisation d'un nouvel environnement. / The freshwater blenny (Salaria fluviatilis) colonised the freshwater environment from a marine ancestor and now inhabits lakes and rivers around the Mediterranean Sea. How this important environmental change affected the genetic structure and the phenotype of this species ? It is around this central question that two major axes will be developed in this thesis. The first axis focus on the consequences of historical geologic events that affected the genetic structure of S. fluviatilis. It will be show that the northern locations of the Occidental basin of the Mediterranean sea were colonised from two different glacial refuges. The second axis focus on the adaptation and acclimation required to colonise a new environment. It will be show that the reponses of body shape and fins length of S. fluviatilis to water velocity are controlled by an environmental determinism. Together, these two axes will allow for a better understanding of populations differentiation process following the colonisation of a new environment.

Understanding worldwide declines in reptiles due to factors such as habitat loss and emerging infectious disease has become an increasingly important focus in conservation biology. Here, I use novel approaches from the field of landscape genetics to combine spatial genetic data with landscape data at both regional and local spatial scales to explore natural and anthropogenic landscape features that shape population structure and gene flow in a federally threatened reptile, Gopherus polyphemus. I also utilize approaches from the field of spatial epidemiology to examine the extent to which environmental variables can be used to predict the seroprevalence of an associated pathogen Mycoplasma agassizzi in gopher tortoise populations. Using mitochondrial data, I find evidence of a historical barrier to gene flow that appears to coincide with the Apalachicola River. I also discover low genetic diversity and evidence of population bottlenecks in the western portion of the range. My evaluation at the regional scale shows that dispersal is limited by geographic distance, areas of low elevation and major roads ways. A finescale study reveals no evidence of spatial genetic structure within a 14 x 35 km area. However, soil type is significantly correlated with pairwise genetic distances between individuals, suggesting that this variable influences fine-scale population structure in the gopher tortoise. In addition to soil, high density canopy cover is an important factor impeding gene flow at the local level for females, while land cover type explains some of the genetic variance between males. Finally, temperature and precipitation appear to be important predictors of the seroprevalence of the pathogen Mycoplasma agassizii in gopher tortoises. The probability of an individual testing seropositive for exposure to this disease increased with high temperature and low precipitation values. The methods presented in this dissertation evaluate novel approaches for assessing the influence of environmental variables on population structure, dispersal and disease occurrence and could be applied in future studies of other threatened and endangered taxa.