Submitted by Valquíria Barbieri (kikibarbi@hotmail.com) on 2018-04-25T22:37:17Z No. of bitstreams: 1 DISS_2014_Alexandre Ebert.pdf: 1748514 bytes, checksum: d9c571963613083829534e6c841c99ff (MD5) / Approved for entry into archive by Jordan (jordanbiblio@gmail.com) on 2018-05-16T14:25:20Z (GMT) No. of bitstreams: 1 DISS_2014_Alexandre Ebert.pdf: 1748514 bytes, checksum: d9c571963613083829534e6c841c99ff (MD5) / Made available in DSpace on 2018-05-16T14:25:20Z (GMT). No. of bitstreams: 1 DISS_2014_Alexandre Ebert.pdf: 1748514 bytes, checksum: d9c571963613083829534e6c841c99ff (MD5) Previous issue date: 2014-02-25 / CAPES / Os distúrbios causados pela antropização de áreas naturais causam fortes alterações na estrutura original da floresta, aumentam o grau de isolamento entre indivíduos afetando o sistema reprodutivo das populações. Diversos processos estão relacionados à distribuição espacial dos indivíduos de uma população, sendo que estes processos refletem na diversidade genética da população. Do ponto de vista genético qualquer alteração no ambiente poderá influenciar nos padrões da estrutura genética, sendo que a extinção de uma espécie é etapa final de um longo processo de declínio ecológico que passa pela perda da diversidade genética. No presente estudo avaliaram-se os padrões espaciais pontuais não homogêneos e a diversidade genética dentro de uma população natural fragmentada de Mezilaurus itauba, buscou-se estabelecer os objetivos de modo que se conclui com a afirmação da hipótese de que as alterações dos padrões de distribuição espacial de indivíduos exercem influência direta na estrutura genética da população. A avaliação dos padrões de distribuição espacial para a espécie foi testada através da função K proposta por Ripley e buscou-se associar a diversidade genética através de análise de agrupamentos estatísticos. Os resultados indicam que a população estudada apresenta padrões de distribuição aleatório com tendência a agregado para as árvores adultas, e de completa aleatoriedade espacial para as árvores jovens. Na análise genética verificou-se uma distribuição da diversidade entre os indivíduos jovens e adultos, porém alelos observados entre as árvores adultas não foram observados entre as árvores jovens, o que indica que na exploração das espécies adultas alelos importantes poderão ser perdidos. O trabalho conclui a afirmação de que estudos da diversidade genética de população são de suma importância para a definição de estratégias de conservação das espécies exploradas economicamente na Amazônia meridional brasileira. / The disturbances caused by human disturbance of natural areas cause strong changes in the original structure of a forest, increase the degree of isolation between individuals affecting the reproductive system of populations. Several processes are related to the spatial distribution of individuals in a population, and that these processes reflect the genetic diversity of the population. From a genetic perspective any changes in the environment may influence the patterns of genetic structure, and the extinction of a species is the final step in a long process of ecological decline that passes through the loss of genetic diversity. In the present study evaluated the inhomogeneous spatial point patterns and genetic diversity within a natural population of fragmented Mezilaurus itauba, we sought to establish the objectives so that concludes with the statement of the hypothesis that changes in the patterns of spatial distribution individuals exert direct influence on the genetic structure of the population . The evaluation of the spatial distribution of the species was tested by K function proposed by Ripley and sought to associate genetic diversity through analysis of statistical groupings. The results indicate that the studied population presents patterns of random distribution with a tendency to aggregate for adult trees, and complete spatial randomness for the young trees. In genetic analysis showed a distribution of diversity among young people and adults, but alleles observed among adult trees were not observed between the young trees, which indicate that the operation of adult species important alleles may be lost. The paper concludes the statement that studies the genetic diversity of the population is of paramount importance for the development of strategies for the conservation of species exploited economically in the southern Brazilian Amazon.

Orientador: Eliana Morielle Versute / Banca: Fabrício Rodrigues dos Santos / Banca: Luciana Bolsoni Lourenço / Banca: Cláudia Marcia Aparecida Carareto / Banca: Lilian Ricco Medeiros / Resumo: A destruição e a modificação do hábitat são aceitas, entre os biólogos conservacionistas, como as causas primárias da perda da biodiversidade, e a situação para os anfíbios não é exceção. Diversos processos antropogênicos contribuem para a deterioração das paisagens, podendo afetar negativamente as populações de anfíbios, por alterar fisicamente os ambientes aquáticos e terrestres, reduzindo a conectividade dos hábitats e estruturando as populações. Contudo, poucos dados existem sobre os efeitos do cultivo agrícola para as populações de anfíbios. Os programas de preservação atuam na recuperação de populações ameaçadas e, em geral, estão baseados na manutenção da máxima quantidade de diversidade genética, de tal forma que, a primeira etapa de um programa conservacionista, consiste na avaliação da variabilidade genética e distribuição desta entre as populações. A estruturação gênica populacional dos organismos, estimada a partir de técnicas de biologia molecular é um aspecto fundamental na caracterização da aptidão das espécies aos ambientes. Particularmente os marcadores moleculares do tipo microssatélite tem acessado com êxito a variabilidade gênica das populações. Assim, foram desenvolvidos loci microssatélites polimórficos para as espécies Hypsiboas raniceps, Leptodactylus chaquensis e Rhinella schneideri e avaliada a variabilidade genética de populações provenientes de hábitats com diferentes tipos de perturbação antrópica (práticas agrícolas, pastagem), com o intuito de relacionar o impacto de diferentes matrizes sobre a diversidade genética. A espécie generalista R. schneideri exibiu um estoque uniforme de variabilidade genética, baixa estruturação e reduzido nível de endogamia em todas as populações, sugerindo um elevado potencial de dispersão, responsável pela homogeneização das populações... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The destruction and modification of habitat are accepted between conservation biologists as the primary causes of biodiversity loss, and the situation for amphibians is no exception. Several anthropogenic processes contribute to the deterioration in the landscape, which can adversely affect amphibian populations by physically altering the aquatic and terrestrial environments, reducing the connectivity of habitats and structuring populations. However, few data exist on the effects of the crop for the populations of amphibians. The conservation programs act in the recovery of threatened populations, and generally are based on maintaining the maximum amount of genetic diversity, therefore, the first step in a conservationist program, is to assess the genetic variability and distribution of this among the populations. Population structure of organisms, estimated from molecular biology techniques is fundamental to characterize the fitness of species to environments. Particularly the molecular markers microsatellite has successfully accessed the genetic variability of populations. Therefore, we developed polymorphic microsatellite loci in the Hypsiboas raniceps, Leptodactylus chaquensis and Rhinella schneideri species and evaluated the genetic variability of populations from habitats with different types of anthropogenic disturbance (agricultural practices, pasture), in order to relate the impact of different matrix on genetic diversity. R. schneideri generalist species showed an even amount of genetic variability, low structure and low level of inbreeding in all populations, suggesting a high potential for dispersal, responsible for the homogenization of populations. However, in L. chaquensis and H. raniceps, the populations located in regions with strong agricultural impact (Tietê Batalha) showed genetically depauperate and strong population structure. It can be concluded... (Complete abstract click electronic access below) / Doutor

Estudos em genética de paisagem, das espécies zootécnicas, podem impulsionar o entendimento dos processos adaptativos, bem como, a maneira que o ambiente afeta o sucesso destas populações. O objetivo principal do projeto foi identificar assinaturas de seleção no genoma populações de suínos naturalizados brasileiros. Procurando obter a maior representatividade da variabilidade genética e ambiental dos suínos dentro do território brasileiros, amostras de DNA de pelo menos um animal e de pelo menos um grupo genético foram obtidas dentro do Banco de Germopalsma da EMBRAPA, totalizando 191 animais de 18 grupos genéticos suínos brasileiras que foram genotipadas, e classificadas de acordo com sua origem dentro de raça ou grupo genético, estado bioma, bacia hidrográfica, tipo de solo, ecoregião e tipo de vegetação. Após um controle de qualidade os genótipos resultantes foram utilizados no calculo das estatísticas F de Wright, equilíbrio de Hardy-Weinberg. Análise de componentes principais, coeficiente de endogamia, analise da variância molecular, testes de Mantel, e a determinação do número ideal de populações. Os dados ambientais foram convertidos em layers através do Qgis e utilizados na detecção de assinaturas de seleção através do BayeScan v2.1 (Foll & Gaggiotti 2008) e do Samβada (Stucki et al. 2014) Os resultados obtidos mostram que as populações estudadas têm uma estrutura variada entre e dentre si. A maior parte da variabilidade genética esta presente nos indivíduos dentro de grupos genéticos, e indivíduos dentro de estados. Existe diferenciação genética dos suínos dentro das variáveis ambientais classificatórias. As raças Monteiro e Marajó foram as que mostraram maiores níveis de estruturação. Os componentes principais mostram proximidade entre as raças comerciais, assim como o elevado grau de variação na composição genéticas das demais raças, com marcante separação dos animais Monteiro e Marajó. Níveis elevados de endogamia foram encontrados. Foram encontrados pelo menos 8 assinaturas de seleção no genoma das raças suínas localmente adaptadas. A freqüência dos genótipos destes marcadores divide o território brasileiro em duas regiões latitudinais distintas. Os níveis de estruturação das populações demonstram uma grande variabilidade genética entre e dentre as raças. As marcas de seleção encontradas demonstram a influência do meio ambiente no sucesso adaptativo destes animais ao território brasileiro. / Study of landscape genetics in livestock species can help understand the adaptive processes and the way that the environment affects the success of these populations. The main objective was the identification of genetic signatures of selection in the Brazilian autochthone swine breeds. We aim the higher representation of genetic and environmental variability from Brazilian territory sampling at least one animal from one genetic group per sampling point. The samples were obtained on CENARGEN-EMBRAPA Germplasm Bank in a total of 191 DNA samples from 19 Brazilian locally adapted swine genetic groups, classified into state, region, biome, hydrological basins, soil type, ecoregion and vegetation type. These samples were genotyped and after a quality control, we calculated Wright’ F-statistics, individual inbreeding coefficient, Hardy-Weinberg equilibrium, Principal components, IBD, Mantel test, an ideal number of subpopulations and an analysis of molecular variance. Environmental data was converted in layers through Qgis and used to detect signatures of selection by BayeScan v2.1 (Foll & Gaggiotti 2008) and Samβada ((Stucki et al. 2014) Population studied had genetic structure among different subpopulations, in a same category. The biggest part of genetic variability is the individual within breed and in individual within state. We found different intensity of population structure in the categories studied, been the he Monteiro and Marajó breeds that ones with highest values from population genetic structure. Principal component analyses showed proximity between commercial breeds, as well as the high degree of genetic variation among other breeds, with great detachment of Monteiro and Marajó animals from others. High inbreeding levels were found. Signatures of selection were found on the genome of Brazilian locally adapted swine pig. The genotypic frequency of these signatures of selection divides the Brazilian territory into two distinct latitudinal regions. The population structure levels demonstrate a wide genetic variability inside and among races. The signatures of natural selection found demonstrate the influence of the environment to successful adaptation of swine in Brazil.

Cariniana legalis Mart. O. Kuntze (Lecidiaceae) is the largest tree of the Atlantic Forest. To contribute to in situ and ex situ genetic conservation programs for the species, herein we investigate the genetic diversity, inbreeding, intrapopulation spatial genetic structure (SGS), mating system and contemporary pollen flow in three fragmented populations of this species. We found 65 adult trees in the Ibicatu population, 22 in MGI, and four in MGII. Seeds were hierarchically sampled among and within fruits directly from the canopy of 15 seed-trees in Ibicatu (n= 40), five seed-trees in MGI (n= 50), and two seed-trees in MGII (n= 100). Thirteen specific microsatellite loci were developed and validated for 51 C. legalis trees. Eleven loci were polymorphic, revealing a maximum of two to 15 alleles per locus. Using the progeny arrays and seed-tree genotypes, we investigated the Mendelian inheritance, genetic linkage and genotypic disequilibrium of seven microsatellite loci specifically isolated for C. legalis and two previously developed heterologous microsatellite loci. No notable deviations from the expected Mendelian segregation, linkage, or genotypic disequilibrium were detected. The average allelic richness in the adult cohort of Ibicatu was 11.65 and 14.29 for MGI-II and for seeds it was 14.18 in Ibicatu and 10.85 in MGI-II; the average observed heterozygosity for adults of Ibicatu was 0.811 and 0.838 for MGI-II and for seeds it was 0.793 in Ibicatu and 0.786 in MGI-II; the average expected heterozygosity for adults of Ibicatu was 0.860 and 0.900 for MGI-II and for seeds it was 0.856 in Ibicatu and 0.853 in MGI-II. The average fixation index was significantly greater than zero for adults and seeds from both populations. Multilocus outcrossing rate ( m t ) in the three populations was significantly lower than unity (1.0), especially in MGII ( m t = 0.830). The rate of mating among relatives was significant when compared to zero only for Ibicatu ( ????0.266) m s t t . Paternity correlation is substantially higher within than among fruits. The average coancestry coefficient ( ??) was higher and variance effective size ( e N ) was lower than expected for halfsib progenies in all three populations. The number of seed-trees necessary for seed collection to obtain progeny arrays with an effective size of 150 was estimated between 54 to 58 seedtrees. The pollen immigration rate was low, especially for the small stands (maximum of 0.4% for MGI), indicating significant genetic isolation of MGI and MGII. The effective pollination radius was also low in MGI (68 m) and MGII (191 m). For MGII, we also found higher levels of selfing (18%) than for Ibicatu (6%) and MGI (6.4%). The substantial genetic isolation of these stands suggest that we can expect an increase in SGS in the future and strategies to increase gene flow and effective population size, such as transplanting individuals among the populations, are desirable for long term in situ conservation. In conclusion, this study produced valuable information for the management of fragmented populations of C. legalis, contributing to breeding programs and providing guidelines for seed collection aimed at conservation and reforestation programs. / Cariniana legalis Mart. O. Kuntze (Lecidiaceae) é a maior árvore da Mata Atlântica. Para contribuir com a conservação in e ex situ nós investigamos a diversidade genética, endogamia, estrutura genética espacial intrapopulacional (EGE), sistema de reprodução e fluxo contemporâneo de pólen em três populações fragmentadas da espécie. Encontrámos 65 árvores adultas na população Ibicatu, 22 em MGI, e quatro em MGII. As sementes foram colhidas e amostradas hierarquicamente entre e dentro de frutos diretamente da copa de 15 árvores matrizes em Ibicatu (n = 40), cinco em MGI (n = 50), e duas em MGII (n = 100). Treze locos microssatélites foram desenvolvidos e validados em 51 indivíduos de C. legalis. Onze deles foram polimórficos, revelando um máximo de dois a 15 alelos por loco. Usando os genótipos das progênies e matrizes, foi investigada a herança mendeliana, ligação genética e desequilíbrio genotípico de sete locos isolados de C. legalis e dois heterólogos. Não foram detectados desvios notáveis da segregação mendeliana, de ligação, ou desequilíbrio genotípico. A riqueza alélica média de adultos de Ibicatu foi 11,65 e 14,29 para MGI-II e para as sementes foi de 14,18 em Ibicatu e 10,85 na MGI-II, a heterozigosidade média observada para adultos em Ibicatu foi 0,811 e 0,838 para MGI-II, para as sementes foi de 0,793 em Ibicatu e 0,786 em MGI-II, a heterozigosidade média esperada para adultos de Ibicatu foi 0,860 e 0,900 para MGI-II, para as sementes foi de 0,856 em Ibicatu e 0,853 em MGI-II. O índice médio de fixação foi significativamente maior do que zero para adultos e sementes de ambas as populações. A taxa de cruzamento Multilocus (? ) nas três populações foi significativamente menor do que a unidade (1,0), especialmente para MGII ( = 0,830). A taxa de acasalamento entre parentes foi significativa apenas para Ibicatu ( . A correleção de paternidade foi substancialmente maior dentro do que entre os frutos. O coeficiente médio de coancestria (?) foi maior e variação de tamanho efetivo (Ne ) foi menor do que o esperado para progênies de meio-irmãos em todas as populações. O número estimado de árvores matrizes necessárias para a coleta de sementes para se obter um tamanho efetivo de 150 foi de 54-58 árvores. A taxa de imigração de pólen foi baixa, especialmente para os fragmentos menores (máximo de 0,4% para MGI), indicando isolamento genético significativo. O raio efetivo de polinização foi baixo em MGI (68 m) e MGII (191 m). Para MGII também encontramos níveis mais elevados de autofecundação (18%) do que para Ibicatu (6%) e MGI (6,4%). O isolamento genético substancial desses estandes sugerem que podemos esperar um aumento na EGE e que estratégias para aumentar o fluxo gênico e tamanho efetivo da população, como o transplante de indivíduos nas populações, são desejáveis para o longo prazo. Em conclusão, este estudo gerou informações valiosas para a gestão de populações fragmentadas de C. legalis, contribuindo para programas de melhoramento e fornecendo orientações para a coleta de sementes destinadas a programas de conservação e reflorestamento.

Abstract Many species and populations have perished as a consequence of human actions. During the last ~200 years, large carnivores have been almost completely extirpated from Western Europe. Large-scale wolf hunting started in Finland around the 1850s, and the population size quickly collapsed. The population was very small until the mid-1990s, when wolves started to regularly reproduce in Finland again. The wolf is an endangered species in Finland, and the biggest threat to the species’ survival is excessive hunting. In this doctoral thesis study, I inspected the genetic structure and diversity of the Finnish wolf population using neutral genetic markers. Almost 300 wolves from the contemporary Finnish population and over 50 wolves from the north-western Russia were analyzed with genetic methods. Additionally, the genetic history of the population was examined with the help of over 100 museum samples. The modern Finnish wolf population proved to be genetically as diverse as the non-endangered Eastern European and North American wolf populations. However, the genetic diversity decreased significantly during the study period (1995–2009), and was at its lowest level in the final phase of the examination. In tandem, the inbreeding coefficient rose to a relatively high level. Genetic sub-structures were observed due to social structures within wolf packs. The mean dispersal distances of wolves were approximately only 100 km. The Finnish wolf population is divided into neighbourhoods of related individuals, and their size substantially decreased during the study period. This pattern, together with the growth of the inbreeding coefficient, suggests that lost alpha individuals in wolf packs are replaced by their offspring. This study demonstrated that Russian and Finnish wolf populations are nowadays genetically differentiated. Gene flow between the populations is low, despite the geographic interconnection. Only a few possible immigrants from Russia into Finland were detected in the study. The effective size of the Finnish wolf population proved to be small, and was mainly below the often-considered critical size of 50. Historical analysis revealed that the Finnish wolf population was formerly genetically more diverse, more continuous with the Russian wolf population, and had a more than 90% larger effective size. On the basis of this study, the genetic status of the Finnish wolf population is worrying and needs to be monitored. The population should be substantially larger than today and/or the amount of gene flow higher, so that the population viability could be considered secured even in the short term. / Tiivistelmä Ihmisen toiminnan seurauksena lukuisat eliölajit ja –populaatiot ovat hävinneet. Viimeisten noin 200 vuoden aikana suurpedot hävitettiin lähes koko Länsi-Euroopasta. Laajamittainen sudenmetsästys alkoi Suomessa 1850-luvun paikkeilla ja kanta romahti nopeasti. Populaatio oli hyvin pieni lähes koko 1900-luvun, ja sudet ovat jälleen lisääntyneet yhtäjaksoisesti Suomessa vasta 1990-luvun puolivälistä. Susi on erittäin uhanalainen Suomessa ja merkittävin uhka lajin säilymiselle on liiallinen metsästys. Tarkastelen tässä väitöskirjatyössäni Suomen susipopulaation geneettistä rakennetta ja monimuotoisuutta neutraaleja geenimerkkejä käyttäen. Tutkimuksessa analysoitiin geneettisin menetelmin lähes 300 sutta nyky-Suomesta sekä yli 50 sutta Luoteis-Venäjältä. Lisäksi populaation geneettistä historiaa selvitettiin yli 100 museonäytteen avulla. Nykyinen Suomen susipopulaatio osoittautui tutkimuksessa geneettisesti yhtä monimuotoiseksi kuin ei-uhanalaiset susipopulaatiot Itä-Euroopassa ja Pohjois-Amerikassa. Geneettisen muuntelun määrä kuitenkin laski tutkimusajanjaksolla (1995–2009) merkitsevästi ollen matalin tarkastelujakson lopussa. Samanaikaisesti populaation sukusiitoskerroin nousi verrattain korkeaksi. Susipopulaatiossa havaittiin sosiaalisista rakenteista johtuvia geneettisiä alarakenteita. Susien dispersaalimatkat olivat keskimäärin vain noin 100 km. Suomen susipopulaatio on jakautunut toisilleen sukua olevien yksilöiden naapurustoiksi, joiden koko pieneni huomattavasti tutkimusajanjaksolla. Tämä yhdessä sukusiitoskertoimen kasvun kanssa viittaa susilaumojen menetettyjen alfayksilöiden korvautumiseen jälkeläisillään. Tutkimus osoitti, että Venäjän ja Suomen susipopulaatiot ovat nykyisin geneettisesti erilaistuneet. Geenivirta populaatioiden välillä on maantieteellisestä yhteydestä huolimatta vähäistä. Tutkimuksessa havaittiin vain muutamia todennäköisiä immigrantteja Venäjältä Suomeen. Suomen susipopulaation efektiivinen koko osoittautui pieneksi ollen pääosin alle kriittisenä rajana pidetyn 50:en. Historiallinen tarkastelu osoitti Suomen susipopulaation olleen aiemmin geneettisesti monimuotoisempi, yhtenäisempi Venäjän susipopulaation kanssa ja efektiiviseltä kooltaan yli 90 % nykyistä suurempi. Tutkimuksen perusteella Suomen susipopulaation geneettinen tila on huolestuttava ja tarvitsee seurantaa. Populaation tulisi olla nykyistä huomattavasti suurempi ja/tai geenivirran määrän korkeampi, jotta populaation elinvoimaisuuden voitaisiin katsoa olevan turvattu edes lyhyellä aikavälillä.

Abstract The protection of endangered species requires knowledge about the habitat requirements and the genetic issues related to the population viability. In this doctoral thesis, I defined the breeding habitat features of the Finnish populations of the Golden Eagle (Aquila chrysaetos) and the Peregrine Falcon (Falco peregrinus) by applying habitat suitability modelling. Secondly, I studied the conservation genetic issues of the Finnish population of the White-tailed Eagle (Haliaeetus albicilla) and the two Reed Bunting subspecies Emberiza schoeniclus witherbyi and E.s. lusitanica met in the Iberian Peninsula. All study populations are classified as threatened according to IUCN classification and they have experienced declines in population sizes in recent history. My results from habitat suitability models showed that human-induced changes in habitat threaten the Golden Eagle in Finland. The relative suitability for the species presence dropped to zero when the proportion of human altered landscape (agricultural or urbanized areas) in the core of the breeding habitat (4 km2) was more than 5%. Models further showed that habitat structure influences breeding habitat selection of the Peregrine Falcon, as it favours well-connected areas of open peatlands. Therefore, fragmentation (i.e., decreasing the connectivity) of open peatlands decreases the habitat quality for the species. The White-tailed Eagle has recovered mainly through local growth, but my results suggest that gene flow from neighbouring populations has had an impact as well, and has enhanced the genetic viability of the Finnish population. The current structure of the two subpopulations (one along the Baltic Sea coast line and another inland in Northern Finland) results mainly from the species’ ecology (i.e., philopatric behaviour), not from the recent population bottlenecks. The effective population size estimate of the coastal subpopulation of White-tailed Eagle was below the critical size needed to maintain evolutionary potential. The estimates of the effective population sizes for E.s. lusitanica and E.s. witherbyi and inland subpopulation of White-tailed Eagle were close or below the critical level of 50, which makes them prone to losing fitness due to inbreeding depression in the short term. Therefore, these study populations need to increase in size in order to secure population viability in the future. / Tiivistelmä Ihmisen aiheuttamat elinympäristöjen muutokset uhkaavat biodiversiteettiä kasvattamalla yhä useampien eliölajien sukupuuttoriskiä. Tehokkaat suojelutoimenpiteet edellyttävät tietoa uhanalaisten lajien elinympäristövaatimuksista sekä populaation elinkyvylle keskeisistä geneettisistä tekijöistä. Tarkastelen väitöskirjatyössäni maakotkan (Aquila chrysaetos) sekä muuttohaukan (Falco peregrinus) Suomen populaatioiden pesimäympäristön piirteitä maisemaekologisen mallinnuksen avulla. Toiseksi tarkastelen Suomen merikotkapopulaation (Haliaeetus albicilla) sekä Iberian niemimaalla esiintyvien pajusirkun alalajien Emberiza schoeniclus witherbyin ja E.s. lusitanican suojelun kannalta tärkeitä geneettisiä tekijöitä. Kaikki tutkimuspopulaatiot ovat uhanalaisia ja ne ovat kärsineet voimakkaista kannan pienenemisistä. Maisemaekologiset mallit osoittivat maakotkan välttävän ihmisen muokkaamaa ympäristöä (maatalousalueet ja rakennetut alueet). Lajin esiintymistodennäköisyys laski nopeasti nollaan, kun ihmisen muokkaaman ympäristön osuus nousi yli 5 prosenttiin pesimäympäristön ydinalueella (4 km2). Mallit osoittivat maiseman rakenteen vaikuttavan muuttohaukan habitaatinvalintaan, sillä se suosi pesimäympäristönään kytkeytyneitä avosoita. Avosoiden pirstoutuminen (l. kytkeytyneisyyden väheneminen) vähentää näin ollen muuttohaukan pesimäympäristön laatua. Merikotkapopulaatio on toipunut pääosin paikallisen kasvun myötä, mutta tulokseni viittaavat myös siihen, että geenivirta naapurimaiden populaatioista on lisännyt Suomen populaation geneettistä muuntelua. Nykyinen rakenne (rannikon ja Lapin alapopulaatiot) on seurausta lajin synnyinpaikkauskollisuudesta, ei niinkään populaatiokoon romahduksista. Rannikon merikotkapopulaation efektiivinen koko jäi alle kriittisen rajan, joka tarvitaan evolutiivisen potentiaalin säilymiselle. Pajusirkun alalajien sekä Lapin merikotkapopulaation efektiiviset populaatiokoot olivat lähellä kriittisenä pidettyä 50:tä tai jäivät alle, joten ne ovat vaarassa menettää kelpoisuutta sukusiitosdepression seurauksena lyhyellä aikavälillä. Sekä pajusirkun alalajien että merikotkapopulaatioiden tulee sen vuoksi kasvaa säilyäkseen elinvoimaisina tulevaisuudessa.

No description available.

No description available.

Tigers (Panthera tigris tigris) can be viewed as a proxy for intact and healthy ecosystems. Their wild populations have plummeted to fewer than 3,200 individuals in the last four decades and threats to these apex predators are mounting rather than diminishing. Global conservation bodies (Global Tiger Initiative, World Wildlife Fund, Wildlife Conservation Society, Panthera etc.) have recently called for solidarity and scaling up of conservation efforts to save tigers from extinction. In South Asia, tiger habitat ranges from tropical evergreen forests, dry arid regions and sub-tropical alluvial floodplains, to temperate mixed deciduous forest. The churia habitat is relatively unstudied and is considered a young and geologically fragile mountain range in Nepal. The contribution of the churia habitat to tiger conservation has not been considered, since modern conservation started in 1970's. This study focuses on the ecology of the tiger with respect to population density, habitat use, and prey occupancy and density, in the churia habitat of Chitwan National Park. This study also includes the first assessment of genetic diversity, genetic structure, and gene flow of tigers across the Terai Arc Landscape- Nepal. The Terai Arc Landscape harbors the only remaining tiger population found across the foothills of the Himalayas in Nepal and northwest India. I used a combination of camera-trapping techniques, which have been a popular and robust method for monitoring tiger populations across the landscape, combined with a noninvasive genetic approach to gain information on tigers, thus adding new information relevant to global tiger conservation. I investigated tiger, leopard (Panthera pardus fusca), and prey densities, and predicted the tiger density across the Churia habitat in Chitwan National Park. I used a camera-trap grid with 161 locations accumulating 2,097 trap-nights in a 60 day survey period during the winter season of 2010-2011. Additionally, I used distance sampling techniques for estimating prey density in the churia habitat by walking 136 km over 81 different line transects. The team photographed 31 individual tigers and 28 individual leopards along with 25 mammalian species from a sampling area of 536 km² comprising Churia and surrounding areas. Density estimates of tigers and leopards were 2.2 (SE 0.42) tigers and 4.0 (SE 1.00) leopards per 100 km². Prey density was estimated at 62.7 prey animals per 100 km² with contributions from forest ungulates to be 47% (sambar Rusa unicolor, chital Axis axis, barking deer Muntiacus muntjak, and wild pigs Sus scrofa). Churia habitat within Chitwan National Park is capable of supporting 5.86 tigers per 100 km² based on applying models developed to predict tiger density from prey density. My density estimates from camera-traps are lower than that predicted based on prey availability, which indicates that the tiger population may be below the carrying capacity. Nonetheless, the churia habitat supports 9 to 36 tigers, increasing estimates of current population size in Chitwan National Park. Based on my finding, the Churia habitat should no longer remain ignored because it has great potential to harbor tigers. Conservation efforts should focus on reducing human disturbance to boost prey populations to potentially support higher predator numbers in Churia. I used sign surveys within a rigorous occupancy framework to estimate probability of occupancy for 5 focal prey species of the tiger (gaur Bos gaurus, sambar, chital, wild pig, and barking deer); as well as probability of tiger habitat use within 537 km² of churia habitat in Chitwan National Park. Multi-season, auto-correlation models allowed me to make seasonal (winter versus summer) inferences regarding changes in occupancy or habitat use based on covariates influencing occupancy and detection. Sambar had the greatest spatial distribution across both seasons, occupying 431-437 km² of the churia habitat, while chital had the lowest distribution, occupying only 100-158 km². The gaur population showed the most seasonal variation from 318- 413 km² of area occupied, with changes in occupancy suggesting their migration out of the lowland areas in the summer and into the churia in the winter. Wild pigs showed the opposite, moving into the churia in the summer (444 km² area occupied) and having lower occupancy in the winter (383 km²). Barking deer were widespread in both seasons (329 - 349 km²). Tiger probability of habitat use Ψ SE(Ψ) was only slightly higher in winter 0.63 (SE 0.11) than in summer 0.54 (SE 0.21), but confidence intervals overlapped and area used was very similar across seasons, from 337 - 291 km². Fine-scale variation in tiger habitat use showed that tigers intensively use certain areas more often than others across the seasons. The proportion of available habitat positively influenced occupancy for the majority of prey species and tigers. Human disturbance had a strong negative influence on the distribution of the majority of prey species but was positively related to tiger habitat use. Tigers appear to live in areas with high disturbance, thus increasing the risk of human-tiger conflict in the churia habitat. Thus, efforts to reduce human disturbance would be beneficial to reducing human wildlife conflict, enriching prey populations, and would potentially support more tigers in churia habitat of Nepal. Overall, I found high prey occupancy and tiger habitat use, suggesting that the churia is highly valuable habitat for tigers and should no longer be neglected or forgotten in tiger conservation planning. Thirdly, I assessed genetic variation, genetic structure, and gene flow of the tigers in the Terai Arc Landscape, Nepal. I opportunistically collected 770 scat samples from 4 protected areas and 5 hypothesized corridors across the Terai Arc Landscape. Historical landuse change in the Terai Arc was extracted from Anthrome data sets to relate landuse change to potential barriers and subsequent hypothesized bottleneck events in the landscape. I used standard genetic metrics (allelic diversity and heterozygosity) to estimate genetic variation in the tiger population. Using program Structure (non-spatial) and TESS (spatial), I defined the putative genetic clusters present in the landscape. Migrant analysis was carried out in Geneclass and Bayesass for estimating contemporary gene flow. I tested for a recent population bottleneck with the heterozygosity test using program Bottleneck. Of the 700 samples, 396 were positive for tiger (57% success). Using an 8 multilocus microsatellite assay, I identified 78 individual tigers. I found large scale landuse changes across the Terai Arc Landscape due to conversion of forest into agriculture in last two centuries and I identified areas of suspected barriers. I found low levels of genetic variation (expected heterozygosity = 0.61) and moderate genetic differentiation (F_ST = 0.14) across the landscape, indicative of sub-population structure and potential isolation of sub-populations. I detected three genetic clusters across the landscape consistent with three demographic tiger sub-populations occurring in Chitwan-Parsa, Bardia, and Suklaphanta protected areas. I detected 10 migrants across all study sites confirming there is still some dispersal mediated gene flow across the landscape. I found evidence of a bottleneck signature, especially around the lowland forests in the Terai, likely caused by large scale landuse change in last two centuries, which could explain the low levels of genetic variation detected at the sub-population level. These findings are highly relevant to tiger conservation indicating that efforts to protect source sites and to improve connectivity are needed to augment gene flow and genetic diversity across the landscape. Finally, I compared the abundance and density of tigers obtained using two non-invasive sampling techniques: camera-trapping and fecal DNA sampling. For cameras: I pooled the 2009 camera-trap data from the core tiger population across the lowland areas of Chitwan National Park. I sampled 359 km² of the core area with 187 camera-trap locations spending 2,821 trap-nights of effort. I obtained 264 identifiable photographs and identified a total of 41 individual tigers. For genetics, I sampled 325 km² of the core area along three spatial routes, walking a total of 1,173 km, collecting a total of 420 tiger fecal samples in 2011. I identified 36 tigers using the assay of 8 multilocus genotypes and captured them 42 times. I analyzed both data types separately for estimating density and jointly in an integrated model using both traditional, and spatial, capture-recapture frameworks. Using Program MARK and the model averaged results, my abundance estimates were 46 (SE 1.86) and 44 (SE 9.83) individuals from camera and genetic data, respectively. Density estimates (tigers per 100 km²) via traditional buffer strip methods using half of the Mean Maximum Distance Moved (½ MMDM) as the buffer surrounding survey grids, were 4.01 (SE 0.64) for camera data and 3.49 (SE 1.04) for genetic data. Spatially explicit capture recapture models resulted in lower density estimates both in the likelihood based program DENSITY at 2.55 (SE 0.59) for camera-trap data and 2.57 (SE 0.88) for genetic data, while the Bayesian based program SPACECAP estimates were 2.44 (SE 0.30) for camera-trap data and 2.23 (SE 0.46) for genetic data. Using a spatially explicit, integrated model that combines data from both cameras and genetics, density estimates were 1.47 (SD 0.20) tigers per 100 km² for camera-trap data and 1.89 (SD 0.36) tigers per 100 km² for genetic data. I found that the addition of camera-trap data improved precision in genetic capture-recapture estimates, but not visa-versa, likely due to low numbers of recaptures in the genetic data. While a non-invasive genetic approach can be used as a stand-alone capture-recapture method, it may be necessary to increase sample size to obtain more recaptures. Camera-trap data may provide a more precise estimates, but genetic data returns more information on other aspect of genetic health and connectivity. Combining data sets in an integrated modeling framework, aiding in pinpointing strengths and weaknesses in data sets, thus ultimately improving modeling inference. / Ph. D.

La gorgone rouge, Paramuricea clavata (Cnidaire, Octocoralliaire), est une espèce sessile, longévive à faible croissance dont les populations présentent une lente dynamique. Cette espèce est caractérisée par une phase larvaire pélagique qui représente l’unique phase de dispersion potentielle au cours du cycle de vie de cette espèce. P. clavata est une espèce clé des assemblages à coralligène de Méditerranée, qui subit les effets combinés des activités de plongée sous-marine et du changement climatique. Dans ce contexte, il était donc fondamental d’approfondir les connaissances sur les traits d’histoire de vie, la biologie et l’écologie de cette espèce. L’objectif de ce travail était d’étudier, à l’aide d’une approche génétique, les facteurs biologiques et écologiques clés qui devraient être importants pour la réponse de l’espèce aux changements environnementaux. Parmi ces facteurs, la dispersion larvaire joue un rôle fondamental dans la dynamique et la connectivité des populations marines. Dans le contexte actuel des fortes pressions anthropiques, la compréhension des degrés de connectivité entre les populations est primordiale pour évaluer le devenir des populations, face au changement climatique, et pour mettre en place des plans de conservation et des réseaux d’aires marines protégées. / The red gorgonian, Paramuricea clavata (Cnidaria, Octocorallia), is a sessile, long-lived and slow growing species which displays slow population dynamics. This species is characterized by a pelagic larval phase that represents the sole potential phase of dispersal during the life cycle of this species. P. clavata is a key species of coralligenous assemblages of the Mediterranean Sea which undergoes the combined effects of diving activities and climate change. In this context, extending the knowledge about life history traits, biology and ecology of the red gorgonian was of fundamental importance. Using a genetic approach, the goal of this work was to study some key biological and ecological factors which should be important for the response of this species to environmental changes. Among these factors, larval dispersal plays a major role in driving marine population dynamics and connectivity. In the current context of strong anthropic pressures, understanding the level of population connectivity is primordial to evaluate population outcome, facing climate change, and to develop conservation plans as well as to design marine reservenetworks.