This thesis aims to explore distributional patterns of tree species in the neotropical lowland rain forest biome based on diversity analyses, dated phylogenies and species distribution models, using the family Sapotaceae as a case study. Sapotaceae is an abundant and diverse group in the neotropical lowland rain forest and its distributional patterns are representative of other tree clades in this biome. These characteristics make this family a good model to test ecological and biogeographic hypothesis in neotropical rain forests. An analysis of beta-diversity measured by the number of shared species was used as a test of biotic homogeneity of Morrone's (2001) widely used system of neotropical biogeographic units. Biotic homogeneity was generally low, and Morrone's (2001) biogeographic regionalisation was found not to coincide with the distributional patterns of Sapotaceae species. Divergence times of Sapotaceae species were estimated using a dated phylogeny based on DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS) to explore the effects of Andean uplift, closure of the Isthmus of Panama and Pleistocene climatic changes on the evolutionary history of lowland rain forests in northern South America. The Andean uplift was found to have affected patterns of distribution by creating new habitats and altering hydrologic systems in northern South America, and in some cases by isolating lineages to the east and west of the Eastern Cordillera of the Andes. The closure of the Panama Isthmus and Pleistocene climatic changes do not seem to have strongly affected patterns of distribution or diversification in Sapotaceae. In general, the lack of congruent dates for many repeated biogeographic splits in the phylogeny (e.g., Amazon-Choco) suggests that idiosyncratic dispersal events have had a substantial effects on Sapotaceae's biogeography. Finally, species distribution models generated for Sapotaceae in the Neotropics were used to identify areas of high predicted species richness in Colombia. The highest diversity of Sapotaceae species was predicted for the inter-Andean valleys and northern Amazon. These results were compared to the current system of Protected Areas in this country, demonstrating that areas of high conservation value based on predicted species richness have a low coverage of Protected Areas. Such gaps highlight the potential need for new systems for the delimitation of basic units for conservation at national levels in Colombia.

Background: Coastal ecosystems in Mexico remain understudied in spite of their ecological, economic and conservation value and are being impacted by human activities along the coast. Knowledge on spatial patterns of plant species distribution that helps preserve these fragile ecosystems is crucial. Aims: We evaluated differences in species richness, species diversity and species dominance patterns in 16 plant communities as well as the degree to which differences were driven by climatic conditions in sandy dunes in Yucatán. We evaluated the importance of invasive species in mediating patterns of species diversity and species dominance patterns. Results: We found wide variation in plant species richness, species diversity and species dominance patterns among communities that stems from broad climatic differences along dune systems. Invasive plants represent almost one-third of total species richness and seem to be drastically changing the species dominance patterns in these communities. Conclusions: Regional climatic differences along the Yucatán north coast seems to be a major driver of plant diversity and species composition. Our findings suggest that invasive plants have successfully colonised and spread along the coast over the past 30 years. Even though invasive species do not alter spatial patterns of species diversity, they are becoming more dominant with potential detrimental consequences for native plants.

Researchers have learned much about the biological assemblages that form around hydrothermal vents. However, identities of species in these assemblages and their basic ecological features are often lacking. In 2015, the first leg of the Hydrothermal Hunt expedition identified likely new vent sites in the Mariana Back-arc Spreading Center (BASC). In 2016, the second leg of the expedition used a remotely operated vehicle (ROV) to confirm and sample two new sites and two previously known sites. My first objective is to identify the animals collected from these four vent sites. In these samples, I identify 42 animal taxa, including the discovery of four new vent-associated species, five potentially new species and six taxa not previously reported in the Mariana BASC vents. My second objective is to combine these new data with previous studies and examine the species distributions among all known vent sites in the Mariana BASC using the α-, β-, and γ-diversity framework. I present updated species absence-presence lists for all eight Mariana BASC vent sites, which begin to resolve some of the issues with species identification. In this thesis, my approach to assessing β-diversity is novel in the field of hydrothermal vent ecology. My work also provides the first intra-regional scale assessments of β-diversity that include all sites known in a vent system. My third objective is to explore environmental factors driving these species distribution patterns. The α-diversity of BASC vent sites gradually increases with latitude, and the β-diversity calculated using the Raup-Crick index correlates with distance to nearby vent sites. Stochastic assembly processes likely shape the diversity patterns throughout the Mariana BASC as few environmental variables are known to correlate with these patterns. My fourth objective is to compare the β-diversity patterns between the Mariana BASC vent sites and those in two other vent systems: the Mariana Arc and the Juan de Fuca Ridge. The γ- and average α-diversity values for the BASC vents are relatively low compared to the other two systems. The Jaccard index revealed that the average number of shared species among the Arc vent sites is much lower than those of the BASC and the Juan de Fuca Ridge. The Raup-Crick index indicates that stochastic processes explain the average β-diversity of the Mariana BASC vents better than those of the Mariana Arc and Juan de Fuca Ridge. / Graduate / 2021-04-17