京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21376号 / 農博第2300号 / 新制||農||1068(附属図書館) / 学位論文||H30||N5149(農学部図書室) / 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 神﨑 護, 教授 北島 薫 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

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Seed dispersal is crucial for plants to colonize new habitats and facilitate gene flow between populations. However, Pleistocene extinctions of large-bodied fruit-eating and seed-dispersing animals, known as ‘megafrugivores’, may have hindered the dispersal of plants with large fruits (> 4cm fruit length – ‘megafruits’). Plants with megafruits are common across the flora of Madagascar, especially within the palm (Arecaceae) family. This dissertation investigates the macro-ecological and micro-evolutionary consequences of dispersal limitation on palms with megafruits in Madagascar. Specifically, I investigated three key aspects: (i) turnover or beta-diversity of palms on Madagascar and the distribution of their dispersal-related traits, (ii) the genetic diversity and genetic structure of three palms with megafruits compared to one palm with small fruits, and (iii) population size and migration rate changes over time of several Malagasy palm species with different ecological characteristics. To address these questions, historical ranges of extinct megafrugivores were reconstructed based on fossil sites, and data on extant frugivores, human activities, and climate were collected. Fieldwork in Madagascar provided genetic data for 12 palm species across 46 populations, from which I generated double digest restriction-site associated DNA sequencing data. Various interdisciplinary methods were employed, including redundancy analyses, variation partitioning, linear mixed effect models, species distribution models, and demographic modelling. The findings indicate that the current turnover of palms in Madagascar is primarily influenced by extant frugivores and climate, with limited impact from extinct frugivores. Surprisingly, there is no evidence of decreased genetic diversity or increased genetic differentiation in megafruited palms due to the loss of their megafrugivore dispersers. Genetic diversity is positively associated with human population density but negatively influenced by road densities, possibly reflecting habitat fragmentation by humans. Connectivity between populations is linked to the number of shared extinct and extant (mega)frugivore species, for megafruited and small-fruited palm populations, respectively. This highlights the importance of past long-distance dispersal events by megafrugivores and human-mediated dispersal possibly maintaining connectivity for megafruited palms. Population declines are observed across palms since the Last Glacial Maximum, particularly in humid forest species rarely used by humans, while humid forest species with megafruits show recent migration disruption. In contrast, palm species with smaller fruits that are highly used by humans show less pronounced declines and more stable historical migration rates. Overall, this dissertation illustrates that while the role of megafrugivores as seed dispersers is still evident in the genome of megafruited palms, other factors such as human-mediated dispersal and climate have an influence over the distribution, genetics and demographic histories of palms in Madagascar. It further shows how integrating genetic data with ecological data on species distributions, climate, human activities, can provide novel insights into the drivers of different facets of biodiversity of such a diverse group of plants such as palms.:Chapter 1 - General introduction ....................................................................................... 7 Background and problem statement...................................................................................... 7 Plant seed dispersal, fleshy fruits and frugivory ............................................................ 7 Megafauna and megafruits ............................................................................................ 9 Thesis scope .......................................................................................................................... 12 Madagascar as a model system .................................................................................... 12 Palms as a model system .............................................................................................. 16 Thesis aims and importance ................................................................................................. 19 Overview of methodologies used ......................................................................................... 19 Field data collection ..................................................................................................... 19 Double digest restriction-site associated DNA (ddRAD) .............................................. 21 Outline of the thesis ............................................................................................................. 22 Chapter 2 - Megafrugivores as fading shadows of the past: extant frugivores and the abiotic environment as the most important determinants of the distribution of palms in Madagascar .................................................................................................................... 25 Chapter 3 - Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms ............................................................................................................................. 39 Chapter 4 - Insights into the demographic history of Malagasy palms: exploring the role of global change and species-specific characteristics ........................................................... 57 Chapter 5 – General discussion ....................................................................................... 73 Summary and key findings.................................................................................................... 73 The fate of megafruited plants in the post-megafrugivore era ........................................... 74 Vulnerability and resilience in megafruited plants .............................................................. 76 Understanding the complex role of humans in the distribution and genetics of megafruited plants ……………………………………………………………………………………………………………………………..77 The influence of abiotic factors over the distribution and genetics of Malagasy palms ..... 78 Outlook ................................................................................................................................. 79 References ...................................................................................................................... 83 Appendix ...................................................................................................................... 101 Appendix Chapter 2 ............................................................................................................ 101 Appendix Chapter 3 ............................................................................................................ 123 6 Appendix Chapter 4 ............................................................................................................ 145 Summary ...................................................................................................................... 159 Zusammenfassung ........................................................................................................ 163 Acknowledgments ........................................................................................................ 169 Curriculum Vitae ..................................................................................................................... 171 List of publications and scientific presentations .................................................................... 171 Selbstständigkeitserklärung……………………………………………………………………………………….……..168

Corvids are important seed and nut dispersers in North America. To date, the caching and recovery behaviors of four North American Corvids have been documented, n10st notably Clark1s Nutcracker (Nucifraga columbiana). Blue Jays (Cyanocitta cristata) are important dispersers of Quercus, Fagus, and Castanea nuts in eastern North America and their caching behavior in the wild has been well documented. Recovery of caches by the same individual Blue Jay that created the caches has not been demonstrated. In order to do this, I conducted a laboratory study in which I examined caching and recovery behaviors. I 'compared the performance of caching birds with noncaching birds and with a random foraging model. Blue Jays do return to their own caches with success rates higher than predicted by random searching and they also probe fewer sites than predicted by random. They also recover caches at success rates higher than non-caching birds searching for the same caches as well as probe fewer sites than the non-caching birds. There is a difference in probing patterns for recovered caches between caching birds and non-caching birds that suggests the use of spatial memory by caching birds and a difference in foraging strategies between the two groups. Cache recovery order does not exhibit either a primacy or recency effect and cache recovery order does not appear to correlate to nearest neighbor distance models. / Master of Science

Urbanization is an intensive form of habitat disturbance associated with detrimental effects on biodiversity. However, few studies have investigated its effects on the number, identity and structure of species interactions while considering seasonal fluctuations in communities. Avian seed dispersal is a vital ecosystem service, and the interplay of urbanization and seasonality may impact seed dispersal in ways not predicted by either factor alone. In this study, we evaluate the effects of urbanization and season on avian seed dispersal networks in the southern Appalachians. We found that the number and richness of interactions was unaffected, but the identity of interacting bird species differed based on landscape type. We also found that species strength was impacted by urbanization and season, but other network metrics were unaffected. These results suggest that species identity should be considered when making comparisons of seed dispersal networks, as it may reveal differences between networks with implications for dispersal quality and future plant communities.

The widespread threat of species extinctions caused by the destruction and degradation of tropical primary forest (PF) could potentially be mitigated by the expansion of regenerating secondary forest (SF). However, the conservation value of SF remains controversial, and is dependent on many site- and landscape-scale factors, such as habitat age and isolation. The aim of this thesis was to assess the role that SF can play in conserving forest bird communities in central Panama. We study a chronosequence of SF aged 20 – 120-years-old, with sites either isolated from or connected to extensive PF. Our results suggest that SF supports high levels of avian species diversity, and similar community composition to PF. Whilst forest age plays a small role in determining compositional similarity to PF, connectivity to extensive PF was the main determinant of community composition. However, despite high species richness and complex community composition, some specialist PF bird species were consistently absent from SF, and isolated PF. The functional diversity of bird communities did not vary substantially across the forest age and isolation gradient, although we did find some inter-guild differences; with distinct responses in communities of avian insectivores and frugivores. Isolation caused shifts in the trophic traits of insectivores, but resulted in alterations in the dispersal traits of frugivores. The response of bird and tree community composition to forest age and isolation was similar, although isolation had a stronger impact on bird communities. Bird diversity and composition tracked changes in forest structure over succession. When examining the role of birds in seed-dispersal networks, we found bird gape width was the key predictor of seed size consumed. Large-gaped birds consume a wider variety of seed-sizes than small-gaped birds, and small-seeded trees attract a greater number of bird species than large-seeded trees. These results imply high levels of redundancy among small-gaped avian frugivores and small-seeded plant species, but low levels of redundancy among large-seeded plant species and their avian dispersers. This suggests that large-seeded plants may be most at risk of dispersal failure following any change in avian frugivore assemblages. Together, these results suggest that SF can play a key role in sustaining most tropical biodiversity, and in maintaining ecosystem services. Our findings emphasise the importance of integrating SF into conservation strategies to support and buffer tropical PF habitats.

Introduction of invasive species can alter seed fate predictions made by the Janzen-Connell Escape Hypothesis (JCEH). The JCEH states that there is a suitable region around a plant that is ideal for seed germination, growth, and recruitment. Seeds dispersed too close to the maternal plant are subject to competition from the maternal individual and perhaps density-dependent predation, whereas seeds dispersed further away may end up in suboptimal habitats. Invasive species may change the amount of these suitable habitats for native plants by creating unsuitable light environments and as a result, may influence the size of the ideal recruitment zone surrounding a parent plant. This study examines the extent to which the invasive grass species, Microstegium vimineum, influences recruitment of the understory tree, Cornus florida. In general, M. vimineum was found to reduce both germination and early seedling success and may have significant consequences for future forest structure.

Endozoochory is an important part of plant-animal relationship. In model area of the Doupov Mountains large herbivore mammals, such as red deer, sika deer and wild boar, act as effective seed dispersers. Out of 282 dung samples 29 719 seedlings of 91 species emerged. The most common species was Urtica dioica (80 % of all seedlings). The amount of seeds in dung as well as species composition were highly dependent on dispersing animal, both showed strong seasonality and differences between two studied localities. Frequency of species in dung did not correspond to their frequency in vegetation suggesting strong preferences of herbivores as predators. However more research is needed to test this hypothesis. Given very high time demands for samples processing beforehand the emergence experiment, the influence of concentration by washing through on seedling emergence and species composition was tested. According to preliminary results more seedlings and species emerge from concentrated samples. However, concentration has no effect on emergence of U. dioica as the most common species. Concentration of samples by running water is recommended for faster emergence in greenhouse conditions. Preliminary results also suggest that the approximation of number of seedlings/species on weight of dry mass is not...

O papel do mico-leão-dourado ( Leontopithecus rosalia) como dispersor de sementes na Reserva Biológica União foi avaliado pelo acompanhamento mensal de dois grupos de micos, de dezembro de 1998 a dezembro de 2000, num total de 871,9h de observações no campo. No período de estudo os micos se alimentaram dos frutos de 57 espécies de árvores de pelo menos 17 famílias, ingerindo sementes de 39 espécies,das quais 23 foram colocadas para germinar em laboratório e/ou no campo. Leontopithecus rosalia pode ser considerado como agente dispersor legítimo para as espécies estadas, porque as sementes de todas as espécies germinaram, mesmo que em baixas porcentagens, após a ingestão. Também foi avaliada a velocidade de germinação das sementes. Estes primatas não apresentam um efeito consistente na germinação final de sementes, pois beneficiam algumas espécies, enquanto prejudicam a porcentagem e/ou velocidade da germinação de outras. Para as espécies de frutos mais consumidas foram anotados o tamanho e formato das sementes engolidas, o número de árvores visitadas, além dos hábitats de ocorrência das árvores e dos locais onde as fezes foram depositadas. O tempo de retenção das sementes no trato digestório e a distância de dispersão foram medidos, bem como foram procuradas sementes predadas e digeridas nas fezes. O tempo médio de passagem para as sementes das espécies ingeridas foi de 1,1 + 0,3h e a distância média de dispersão de 107,8 + 70,6m, sendo que de modo geral as sementes dispersadas por mamíferos não são depositadas próximo às árvores parentais. O hábitat de deposição das fezes foi adequado para a germinação das sementes para 88,9% das espécies testadas, estando de acordo com o ambiente das árvores visitadas pelos micos-leões. O mico-leãodourado é um dos primatas mais ameaçados de extinção do mundo, e estudos sobre seu comportamento e ecologia irão contribuir para a preservação da espécie, de seu hábitat, e da Reserva Biológica União, uma das últimas áreas de Mata Atlântica de Baixada Costeira do Estado do Rio de Janeiro. / The role of the golden lion tamarins (Leontopithecus rosalia) as a seed disperser was studied in União Biological Reserve. Two groups of golden lion tamarins were studied during 24 months from December 1988 to December 2000, on a total of 871.9h. During the study period the tamarins fed on fruits of 57 species of trees at least from 17 families. Seeds from 39 species were ingested, and of them, 23 were put to germinate in lab and/or in the field. Leontopithecus rosalia can be considered as a legitimate seed disperser for the tested species, because seeds of all species germinated after ingestion, even in low ercentages. It was still considered the seed germination velocity. These primates do not have a consistent effect on seed germination, since benefit the germination percentage and/or velocity of some species and decrease of others. It was noted the size and shape of swallowed seeds from most frequently eaten species, the total number of visited trees, the habitat where these trees occur and where the faeces were deposited. The retention time of the seeds in the gut and the dispersion distance was noted, and damage and digested seeds were searched in the faeces. The mean time of gut passage from seeds of ingested species was 1.1+0.3h and the mean distance of dispersion was 107.8 + 70.6m, and the seeds dispersed by mammals were not usually defecated near the parental trees. The habitats of faecal deposition and of visited trees were the same in 88.9% of tested species, being possibly appropriated for seed germination and establishment. The golden-liontamarin is one of the most threatened primates in the world, and studies on their behaviour and ecology will contribute to preserve the species the habitat, and the União Biological Reserve, one of the last areas of lowland Atlantic Forest of southeast Brazil.

A resposta da fauna à fragmentação e perda de hábitat pode variar amplamente segundo os requerimentos ecológicos, a configuração da paisagem, a conectividade e as pressões antrópicas. Os morcegos são bons candidatos para trabalhar os efeitos da fragmentação na fauna mas, mesmo assim, existem poucos estudos a respeito da diversidade dos morcegos frugívoros e sua dieta em áreas de cerrado do estado de São Paulo e nas demais áreas de cerrado do país, tendo em conta que este bioma vem sofrendo processos de mudança muito rápidos nas últimas décadas. Assim, vimos a importância de incorporar este grupo de fauna nos estudos que tem sido desenvolvidos na região. Durante 48 dias de coleta ao longo de um ano (2012), procurou-se inventariar a quiropterofauna de dois fragmentos de Cerrado correspondentes à Estação Ecológica de Jataí e ao Cerrado Pé-do-Gigante, nos municípios de Luiz Antônio e Santa Rita do Passa Quatro, localizados ao noroeste do Estado de São Paulo, sendo amostradas fisionomias diferentes: cerradão, cerrado sensu stricto, cerrado adensado e cerrado em estado de regeneração. Foram realizadas duas coletas mensais, de 4 horas cada, iniciadas após o pôr do sol, totalizando 24 amostragens em cada unidade de conservação. Os morcegos foram coletados com redes de neblina situadas a 50 cm do solo, em trilhas preexistentes e em áreas abertas, e identificados em nível de espécie. Outros dados ecológicos, como frequência, dominância, riqueza, constância, horário de atividade, dieta, dispersão de sementes através das fezes dos indivíduos capturados e a influência da luminosidade lunar foram analisados. Foram capturados e anilhados 195 indivíduos de 3 famílias e 7 subfamílias, pertencentes a 17 espécies diferentes, sendo 113 na estação chuvosa e 82 na estação seca. Na E.E. Jataí foram capturados 118 indivíduos de 15 espécies e, no Cerrado Pé-do-Gigante, 77 indivíduos, de 13 espécies, com um esforço amostral de de 31680 m². O índice de Shannon-Wiener apresentou uma diferencia sutil entre a diversidade de espécies em ambas as unidades de Conservação, constatada também pelo alto índice de similaridade de Sorensen (0,75). Obtiveram-se 5 recapturas, uma delas confirmando o fluxo entre unidades de conservação. As espécies dominantes foram: Artibeus lituratus, Anoura caudifer, Sturnira lilium, Glossophaga soricina e Carollia perspicillata. Com relação à dispersão de sementes, obtiveram-se 39 amostras de fezes, das quais 11 continham sementes que posteriormente foram germinadas em laboratório, obtendo-se assim 9 espécies de plantas petencentes a 4 gêneros, potencialmente dispersadas pela quiropterofauna local / The response of wildlife to fragmentation and habitat loss may vary widely according to the ecological requirements, landscape configuration, connectivity among landscape units, and anthropogenic pressures. Bats are ideal species to study fragmentation effects on wildlife, however, studies on the diversity of frugivore bats and their diet in savanna biomes are scarce, despite the intense changes linked to human pressures this biome has been recently submitted to. Therefore, we considered relevant to incorporate the evaluation of the regional bat assembly to fauna studies in Cerrado areas of São Paulo state. During a period of 48 days, representative of both rainy and dry seasons of 2012, we surveyed chiropterofauna in two Cerrado fragments, in the northwestern Sao Paulo state: Jataí Ecological Station (Luiz Antônio municipality) and Cerrado Pé-do-Gigante (Santa Rita de Passa-Quatro municipality). These units show different physiognomies: cerradão, cerrado sensu stricto, dense cerrado and cerrado in regeneration. The surveys were carried out under two nights per month in each conservation area. Bats were collected using mist nets located 50 cm above ground in existing trails in open areas. A total of 195 individuals belonging to 3 families, 7 subfamilies and 17 species were captured and ringed: 113 of these during the rainy season and the remaining 82 during dry season. In E.E. Jataí we registered 118 individuals belonging to 15 species, and in Cerrado Pé-do-Gigante, 77 individuals from 13 species (31680 m² of mist net in the two fragments of Cerrado). Most of the individuals recorded during the study belong to 5 species: Artibeuslituratus, Anoura caudifer, Sturnira Lilium, Glossophaga soricina and Carollia perspicillata. In relation to seed dispersion, 39 fecal samples were obtained, of these, 11 contained seeds that later were germinated in laboratory, obtaining nine species of plants of 4 geners potentiality dispersed by the local bats