Humans are generally having a strong, widespread, and negative impact on nature. Given the many ways we are impacting nature and the many ways nature is responding, it is useful to study responses in an integrative context. My thesis is focused largely (two out of the three data chapters) on butterfly species’ range shifts consistent with modern climate change in Canada. I employed a macroecological approach to my research, drawing on methods and findings from evolutionary biology, phylogenetics, conservation biology, and natural history. I answered three main research questions. First, is there a trade-off between population growth rate (rmax) and carrying capacity (K) at the mutation scale (Chapter 2)? I found rmax and K to not trade off, but in fact to positively co-vary at the mutation scale. This suggests trade-offs between these traits only emerge after selection removes mutants with low resource acquisition rates (i.e., unhealthy genotypes), revealing trade-offs between remaining genotypes with varied resource allocation strategies. Second, did butterfly species shift their northern range boundaries northward over the 1900s, consistent with climate warming (Chapter 3)? Leading a team of collaborators, we found that most butterfly species’ northern range boundaries did indeed shift northward over the 1900s. But range shift rates were slower than those documented in the literature for more recent time periods, likely reflecting the weaker warming experienced in the time period of my study. Third, were species’ rates of range shift related to their phylogeny (Chapter 3) or traits (Chapter 4)? I found no compelling relationships between rates of range shift and phylogeny or traits. If certain traits make some species more successful at northern boundary range expansion than others, their effect was not strong enough to emerge from the background noise inherent in the broad scale data set I used.

<p>Ecologists have long sought to uncover the mechanisms behind large-scale, macroecological patterns in the distribution and abundance of species. Macroecological patterns are often attributed to the dynamics of dispersal (e.g. dispersal limitation or widespread dispersal). However, few studies actually measure dispersal to determine if dispersal rates are commensurate with the observed macroecological patterns. In this dissertation, I use population genetic analyses across many species to obtain community-level estimates of dispersal rates for two different ecological systems: birds on islands and trees in tropical rainforests. These independent estimates of dispersal then allow me to determine if macroecological patterns in these two systems can be attributed to dispersal dynamics.</p><p>In chapter two, I explore the contrasting macroecological patterns of two groups of Lesser Antillean birds. The groups' differing macroecological patterns could be due to differences in dispersal, but other authors have advocated different mechanisms. Population genetic analyses show that the two groups do differ significantly in rates of inter-island dispersal, indicating that dispersal dynamics can explain their contrasting macroecological patterns. In chapter three, I turn my attention to tropical tree communities. In contrast to studies of birds on islands, studies of trees in tropical rainforests may suffer from misidentification of individuals in the field. Using a phylogenetic approach, I determine errors rates in identification, and then assess the effect of these errors on macroecological patterns and other ecological analyses of tropical tree communities. I find that error rates are substantial, but that they have little effect on macroecological patterns. In contrast, species-level ecological analyses can be dramatically affected by these errors.</p><p>In chapter four, I return to the influence of dispersal on macroecological patterns, this time in tropical tree communities. One notable macroecological pattern in Amazonian tree communities is a high correlation in the relative abundances of species shared across communities, which could indicate high rates of dispersal between communities. However, population genetic analyses show that dispersal is severely limited between communities. Thus, some factor besides dispersal, such as differences in competitive ability or susceptibility to disease, must be driving species to achieve similar relative abundances in geographically separated communities. In contrast, I show that dispersal limitation is the likely cause of another macroecological pattern frequently observed in tropical tree communities: the decline in the compositional similarity of communities with distance. However, this is not steady-state dispersal limitation in an equilibrium framework as is conventionally thought. Instead, the dispersal limitation appears to be historical in nature, which implies a heretofore unnoticed role for historical contingency in the assembly of Amazonian tree communities.</p> / Dissertation

The Lake Malawi cichlid fishes are a pre-eminent example of adaptive evolutionary radiation. The diversity of species (nearly 1000 extant) is mirrored by an array of variation in dozens of phenotypes (e.g. trophic morphology, tooth shape, color patterns, behavior, development). The unique characteristics of this system have produced unparalleled diversity with very little genetic differentiation between species. This dissertation is composed of four studies addressing different aspects of the variation in the LM cichlids and the mechanisms generating and maintaining this level of diversity at multiple biological levels. Community-level diversity is investigated using null model analysis of species co-occurrence data. We detect signals of non-random community assembly at only the broadest and finest spatial scales. Based on the unique ecological and evolutionary characteristics of this assemblage we suggest that different mechanisms are responsible for these patterns. A core‟ group of species is posited to act as a foundation on which these diverse communities are created as a result of fine-scale species interactions. We identify both positive and negative depth-based correlations between species and suggest these interactions play an important role in species diversity in these fish. The Lake Malawi cichlids exhibit an array of trophic morphologies which may play a role in the fine-scale species interactions described in chapter one. In the second chapter we build a genetic model to predict the evolution of jaw morphology and a complex functional jaw trait. We use a complex biomechanical system, the 4-bar jaw linkage, to simulate trait evolution during interspecific hybridizations. We find rampant transgression (trait values beyond parental distributions) in jaw function in a large proportion of potential crosses. This result is characterized by a lack of novel morphological components but rather is the result of recombinations of existing component traits thus producing functional novelty. In the third chapter we create a laboratory cross of one of the parental combinations suggested from the genetic model. The results of this study serve as a proof of principle to the simulations as we observe a large proportion of transgressive 4-bar function in the F2. As predicted this diversity is produced in the absence of transgressive morphology. We contrast these results between this complex system and data generated from several simple jaw lever traits and report differences in the patterns. Using quantitative trait locus (QTL) mapping approaches we examine the genetic basis for complex and simple jaw traits and discuss correlative patterns within and between systems. Finally we examine the genetic architecture of sex-determination and color morphs in this hybrid cross. We find both ZW and XY sex systems segregating as well as linkage to sex-specific color patterns. Several loci and epistatic interactions are associated with sex-determination and color morphs in this cross. The orange-blotch (OB) color is found associated with ZW as predicted from previous work but a previously undescribed (in these species) male nuptial color (blue) is found associated with both ZW and XY genetic systems as well as other loci segregating for sex-determination. These results are discussed in the context of models of sex chromosome evolution as a result of sexual conflict and the potential importance of sexual selection in the diversification of Lake Malawi cichlids. Overall we observe various mechanisms generating and maintaining diversity at different levels of biological organization. We use community co-occurrence analyses, genetic simulation, and QTL analysis of an F2 hybrid population to examine these mechanisms in this rapidly radiating assemblage. These results bolster our understanding of the origins of diversity and the interplay between variation and aspects of evolution in all biological systems.

Humans are generally having a strong, widespread, and negative impact on nature. Given the many ways we are impacting nature and the many ways nature is responding, it is useful to study responses in an integrative context. My thesis is focused largely (two out of the three data chapters) on butterfly species’ range shifts consistent with modern climate change in Canada. I employed a macroecological approach to my research, drawing on methods and findings from evolutionary biology, phylogenetics, conservation biology, and natural history. I answered three main research questions. First, is there a trade-off between population growth rate (rmax) and carrying capacity (K) at the mutation scale (Chapter 2)? I found rmax and K to not trade off, but in fact to positively co-vary at the mutation scale. This suggests trade-offs between these traits only emerge after selection removes mutants with low resource acquisition rates (i.e., unhealthy genotypes), revealing trade-offs between remaining genotypes with varied resource allocation strategies. Second, did butterfly species shift their northern range boundaries northward over the 1900s, consistent with climate warming (Chapter 3)? Leading a team of collaborators, we found that most butterfly species’ northern range boundaries did indeed shift northward over the 1900s. But range shift rates were slower than those documented in the literature for more recent time periods, likely reflecting the weaker warming experienced in the time period of my study. Third, were species’ rates of range shift related to their phylogeny (Chapter 3) or traits (Chapter 4)? I found no compelling relationships between rates of range shift and phylogeny or traits. If certain traits make some species more successful at northern boundary range expansion than others, their effect was not strong enough to emerge from the background noise inherent in the broad scale data set I used.

The Arctic region has experienced the largest degree of anthropogenic warming, causing rapid, yet variable sea-ice loss. The effects of this warming on the Canadian Beaufort Shelf have led to a longer ice-free season which has assisted the expansion of northern development, mainly in the oil and gas sector. Both these direct and indirect effects of climate change will likely impact the marine ecosystem of this region, in which benthic fauna play a key ecological role. The aim of this thesis was to expand the current baseline knowledge of benthic fauna in the interest of developing the capacity to identify, predict and manage benthic change. The distribution of benthic macro- and megafauna was characterized utilizing community data from two recent benthic surveys on the Canadian Beaufort shelf and slope. Fauna were collected from 63 stations using box core and trawl sampling gear over the summers of 2009 through 2012 between depths of 30 and 1,000 m. Spatial patterns of abundance, biomass and α and β diversity metrics were examined. Megafaunal abundance and α diversity were elevated on the shelf compared to the slope while the macrofauna did not vary significantly with depth. Multivariate analyses illustrated that both macro- and megafaunal community composition varied more across the depth gradient than from east to west along the shelf. However the change across the depth gradient was greater for the megafauna than for the macrofauna. I proposed that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appeared to be the main driver of megafaunal β diversity across the depth gradient. The lack of correlation between macro- and megafauna in abundance, biomass and α and β diversity suggests that these faunal components vary at different spatial scales. These results demonstrate how separately sampling the different benthic components can yield different spatial patterns, with implications for future benthic monitoring in the region. This work contributes to the current regional baselines by providing the first comprehensive description of megafaunal distribution on the Canadian Beaufort shelf and by extending our knowledge of benthic distribution patterns deeper on the slope. / Graduate / 0329

Les mammifères sont présents sur la surface terrestre depuis au moins le crétacé et ont colonisé l’ensemble des continents et des océans. Mon travail s’attache à comprendre la nature et l’importance relative des processus qui ont pu conduire à la répartition géographique actuelle des mammifères et notamment aux similarités faunistiques entre régions du globe. En décrivant les facettes phylogénétiques et fonctionnelles de la biodiversité des mammifères, j’adopte une approche résolument intégrative, à l’interface entre la biogéographie historique et la biogéographie fonctionnelle.À partir d’un travail de revue et de synthèse, la première partie de la thèse me permet de dégager un nombre limité de grandes lignes structurelles décrivant les facettes phylogénétiques et fonctionnelles de la biodiversité. En particulier, je mets en évidence comment la variation de l’échelle phylogénétique de travail peut permettre de mettre en lumière différents processus.La seconde partie de ma thèse s’attache à utiliser cette approche pour expliquer la répartition des mammifères sur le globe. Nous montrons ainsi que les compositions faunistiques à large échelle phylogénétique (p. ex. pour les familles) semblent expliquées par l’isolement géographique des masses continentales au cours du cénozoïque alors que les compositions à fine échelle phylogénétique (p. ex. pour les espèces) sont davantage conditionnées par les affinités climatiques. Nous montrons ensuite que les régions ayant développées des faunes mammaliennes indépendantes présentent en fait des similarités fonctionnelles exceptionnelles, résultat d’une évolution convergente.Comprendre les déterminants historiques et écologiques d’une telle répartition ne représente pourtant qu’un premier pas vers leur sauvegarde face aux multiples menaces anthropiques. La dernière partie de ma thèse entreprend de montrer l’importance d’une vision intégrative combinant les facettes phylogénétiques, fonctionnelles et taxonomiques pour la conservation de l’ensemble des dimensions de la diversité mammalienne. / Mammals inhabit the Earth since at least the Cretaceous and have colonised all continents and oceans. My work aims at understanding the nature and importance of the different processes leading to current geographical distributions of mammals and in particular faunal similarities between regions of the globe. By describing the phylogenetic and functional facets of mammalian diversity, I adopt an integrative approach, at the interface between historical and functional biogeography.First, I review and synthesize most of the published multifaceted diversity metrics to propose a limited number of structural dimensions that parsimoniously describe the phylogenetic and functional structure of species assemblages. In particular, I point out how a multi-phylogenetic scale approach might improve our understanding of the mechanisms shaping diversity patterns.Second, I use this approach to understand the geographical distribution of mammals worldwide. I show that at large phylogenetic scales (e.g. families) distributions seem to be driven by geographic isolation of the regions over the course of the Cenozoic Era, while at small phylogenetic scales (e.g. species), distributions are related to climatic affinities. In addition, I show that those regions having developed independent mammalian faunas show exceptional functional similarities due to evolutionary convergences.Understanding the historical and ecological drivers of mammal biodiversity only represents the first step toward their conservation in the face of anthropic threats. The last part of my thesis shows the importance of an integrative approach using phylogenetic, functional and taxonomic facets to protect all dimensions of mammal diversity.

Whilst the geographical range of species is a fundamental unit of macroecology and a leading predictor of extinction risk, the evolutionary dynamics of species’ ranges remain poorly understood. In some aquatic beetles, thermal niche has been shown to be related to both the relative range size and position of congeners but whether other physiological niche parameters play a role is unknown. Here, immunocompetence and metabolic plasticity were related to biogeography in these insects. Immunocompetence was first compared within a rare-common pair of Hydroporus species, finding species-specific immunity, which was affected by sex and acclimation time in the laboratory, with no clear relationship with rarity. This relationship was explored further in Deronectes species, whilst controlling for sex and acclimation time. Southern, narrow-ranging species had higher phenoloxidase (PO) activity, lower parasite load and antimicrobial peptide (AMP) activity that was stronger against Gram-negative Bacteria but weaker against Gram-positive Bacteria than their wider-ranging counterparts. As both of these studies found that PO activity did not positively correlate with encapsulation or AMP activity as reported in the literature, the pathway was investigated further in Tribolium castaneum. The data showed that the assumptions of the widely-used PO assay were violated, with differential activity between PO-driven reactions in melanin synthesis and different substrates used by larvae and adults. Future work should be wary of using the PO assay as a marker of potential melanin production and take into account the developmental requirements for melanin at different life stages. The relationship between metabolic plasticity and range was then assessed in Deronectes, finding that southerly species had more marked changes in glucose and protein content under elevated temperature stress than their northerly counterparts. Glucose content was also significantly positively correlated to lipid content, indicating that the energetics of species exhibiting differing range sizes may warrant future study. As the results from Hydroporus suggested that there may be trade-offs between immune defence and metabolism, the data on metabolic plasticity and immunocompetence in a sub-sample of Deronectes species were combined with thermal physiology, dispersal ability, body size and phylogenetic relatedness to assess which of these best explained variation in range size and position. Whilst variation in range extent and position were explained in part by thermal physiology, aspects of metabolic plasticity and immunocompetence also appeared to be important. This thesis provides one of the first indications that immunocompetence and metabolic plasticity may be related to geographical range and suggests parameters that may be worthy of exploration in other taxa.

Made available in DSpace on 2016-06-02T19:31:35Z (GMT). No. of bitstreams: 1 1022.pdf: 831752 bytes, checksum: 9e56fcd2ddeaa8d758e2e0c8baab175a (MD5) Previous issue date: 2006-04-28 / Universidade Federal de Sao Carlos / In this study we investigated the temporal dynamics of a chironomid assemblage in a forested stream located in southeastern Brazil. First, we analyzed some diversity patterns of this assemblage by describing two macroecological relationships (body size-species richness and body size-abundance) and by testing with they vary in an intra-annual scale. Second, we analyzed the emergence phenology using a time series of 48 weekly samples. In general, both species richness and abundance peaked on intermediate body sizes, moreover these relationships showed to be variable in this intra-annual scale; Chironomidae emergence was not seasonal, neither was related to any environmental variables measured; on the other hand, the most persistent species (Caladomyia sp. 1, Endotribelos sp. 4, Caladomyia sp. 2, and Corynoneura sp. 1) appeared to have some temporal structure on emergence, probably associated with photoperiod and minimum air temperature respectively; there was no synchrony in species emergence with most taxa emerging together through the year; species richness as taxonomic composition did not change over time. / Neste estudo nós investigamos a dinâmica temporal de Chironomidae em um córrego florestado localizado no sudeste do Brasil. Primeiro, nós analisamos alguns padrões de diversidade através da descrição de duas relações macroecológicas (tamanho do corpo-riqueza de espécies e tamanho do corpo-abundância) e também testamos se essas relações variavam na escala intra-anual. Segundo, nós analisamos a fenologia da emergência usando uma série temporal de 48 coletas semanais. De maneira geral, ambas a riqueza de espécies e a abundância apresentaram um pico nos tamanhos intermediários, além disso, estas relações mostraram ser variáveis nesta escala intra-anual; a emergência de Chironomidae não foi estacional, e também não foi relacionada a nenhuma variável ambiental medida; por outro lado, as espécies mais persistentes (Caladomyia sp. 1, Endotribelos sp. 4, Caladomyia sp. 2, e Corynoneura sp. 1) parecem apresentar alguma estrutura temporal na emergência, provavelmente relacionada ao fotoperíodo e a temperatura mínima do ar respectivamente; não houve sincronia na emergência das espécies, com a maioria dos taxa emergindo juntos ao longo do ano; a riqueza de espécies assim como a composição taxonômica não mudaram ao longo do tempo.

abstract: My dissertation contributes to a body of knowledge useful for understanding the evolution of subsistence economies based on agriculture from those based on hunting and gathering, as well as the development of formal rules and norms of territorial ownership in hunter-gatherer societies. My research specifically combines simple formal and conceptual models with the empirical analysis of large ethnographic and environmental data sets to study feedback processes in coupled forager-resource systems. I use the formal and conceptual models of forager-resource systems as tools that aid in the development of two alternative arguments that may explain the adoption of food production and formal territorial ownership among hunter-gatherers. I call these arguments the Uncertainty Reduction Hypothesis and the Social Opportunity Hypothesis. Based on the logic of these arguments, I develop expectations for patterns of food production and formal territorial ownership documented in the ethnographic record of hunter-gatherer societies and evaluate these expectations with large ethnographic and environmental data sets. My analysis suggests that the Uncertainty Reduction Hypothesis is more consistent with the data than the Social Opportunity Hypothesis. Overall, my approach combines the intellectual frameworks of evolutionary ecology and resilience thinking. The result is a theory of subsistence change that integrates elements of three classic models of economic development with deep intellectual roots in human ecology: The Malthusian, Boserupian and Weberian models. A final take home message of my study is that evolutionary ecology and resilience thinking are complementary frameworks for archaeologists who study the transition from hunting and gathering to farming. / Dissertation/Thesis / Ph.D. Anthropology 2014

Humans are generally having a strong, widespread, and negative impact on nature. Given the many ways we are impacting nature and the many ways nature is responding, it is useful to study responses in an integrative context. My thesis is focused largely (two out of the three data chapters) on butterfly species’ range shifts consistent with modern climate change in Canada. I employed a macroecological approach to my research, drawing on methods and findings from evolutionary biology, phylogenetics, conservation biology, and natural history. I answered three main research questions. First, is there a trade-off between population growth rate (rmax) and carrying capacity (K) at the mutation scale (Chapter 2)? I found rmax and K to not trade off, but in fact to positively co-vary at the mutation scale. This suggests trade-offs between these traits only emerge after selection removes mutants with low resource acquisition rates (i.e., unhealthy genotypes), revealing trade-offs between remaining genotypes with varied resource allocation strategies. Second, did butterfly species shift their northern range boundaries northward over the 1900s, consistent with climate warming (Chapter 3)? Leading a team of collaborators, we found that most butterfly species’ northern range boundaries did indeed shift northward over the 1900s. But range shift rates were slower than those documented in the literature for more recent time periods, likely reflecting the weaker warming experienced in the time period of my study. Third, were species’ rates of range shift related to their phylogeny (Chapter 3) or traits (Chapter 4)? I found no compelling relationships between rates of range shift and phylogeny or traits. If certain traits make some species more successful at northern boundary range expansion than others, their effect was not strong enough to emerge from the background noise inherent in the broad scale data set I used.