Browsing by Author "Yoder, Anne D"

A fundamental goal in the diverse field of evolutionary biology is reconstructing the historical processes that facilitated lineage diversification and the current geographic distribution of species diversity. Oceanic islands provide a view of evolutionary processes that may otherwise be obscured by the complex biogeographic histories of continental systems, and have thus provided evolutionary biology with some of its most lasting and significant theories. The Indian Ocean island of Madagascar is home to an extraordinarily diverse and endemic biota, and reconstructing the historical processes responsible for this diversity has consumed countless academic careers. While the flowering plant genus Coffea is but one lineage contributing to Madagascar's staggering floral diversity, it is representative of the common evolutionary theme of adaptive radiation and local endemism on the island. In this dissertation, I employ the genus Coffea as a model for understanding historical biogeographic processes in the Indian Ocean using methods of molecular phylogenetics and population genetics. In the molecular phylogenetic study of Coffea presented in chapter 2, I show that Madagascan Coffea diversity is likely the product of at least two independent colonization events from Africa, a result that contradicts current hypotheses for the single origin of this group.

Species of Coffea are known to exhibit self-incompatibly, which can have a dramatic affect on the geographic distribution of plant genetic diversity. In chapter 3, I identify the genetic mechanism of self-incompatibility in Coffea as homologous to the canonical eudicot S-RNase system. Baker's Rule suggests that self-incompatible lineages are very unlikely to colonize oceanic islands, and in chapter 4, I test this hypothesis by characterizing the strength of self-incompatibility and comparing S-RNase polymorphism in Coffea populations endemic to isolated Indian Ocean islands (Grande Comore and Mauritius) with that of Madagascan/African species. My findings suggest that while island populations show little evidence for genetic bottleneck in S-RNase allelic diversity, Mauritian endemic Coffea may have evolved a type of "leaky" self-incompatibility allowing self-fertilization at some unknown rate. Through the application of traditional phylogenetic methods and novel data from the self-incompatibly locus, my dissertation contributes a wealth of new information regarding the evolutionary and biogeographic history of Coffea in the Indian Ocean.

An organism's ability to detect and interpret chemical signals from the surrounding environment is vital to its survival. In mammals, the vomeronasal organ provides an integral part of this requirement as it allows for the detection of inter-individual chemical signals. Located within the vomeronasal epithelium is a group of highly specialized receptors called vomeronasal type-1 receptors (V1Rs). These receptors bind pheromones and kairomones, which are chemical cues from conspecifics and heterospecifics, respectively. Recently, V1Rs have been recognized as highly variable across mammalian taxa. One extraordinary example is the mouse lemur, in which ~83% of the estimated 259 genes are expected to be intact. This relatively young and cryptically diverse prosimian group has a controversial history of species delimitation and it is possible that patterns in the rapidly evolving and highly diverse V1R gene family may provide insight into species boundaries. This study generated broad and deep coverage of the two most diverse V1R subfamilies across multiple Microcebus species. By utilizing Pacific Bioscience's single molecule real time sequencing technology, this study produced sequences at a fraction of the time and cost of the traditional method of Sanger-sequenced clones. The results advance our understanding of the high diversity-at least 5.6% and 9.9% sequence divergence intra- and inter-individually for V1RIX and V1Rstrep, respectively-and rapid evolution of V1Rs in mouse lemurs. Comparing these results with draft genome mined sequences demonstrates the limited utility of low coverage genomes for identifying variation in this gene family. The patterns uncovered here provide no clear evidence for the role of these two characterized subfamilies in maintaining or generating species boundaries, but may instead point to an alternative mechanism of species recognition that is more complex and intricate than previously envisioned.

Host fitness is impacted by trillions of bacteria in the gastrointestinal tract (GIT) that facilitate development of the intestines and brain, digest fiber, and defend against pathogenic invasion. Gut microbes are closely tied to host development and, by extension, the components of life history. Yet, because microbes are capable of lateral gene transfer across vast phylogenetic distances, scientists have struggled to determine whether the taxonomic (microbiota) or genetic (microbiome) composition of a microbial community plays a greater role in its symbiosis with the host. The overarching theme of this dissertation is to explore the interplay between the phylogeny and phenotype of both host and its microbiome. By using 16S rRNA gene amplicon sequencing, metagenomic sequencing, and metabolomics to compare gut microbial communities associated with captive hosts, we are able to identify which microbial community features are correlated with specific host factors. First we compared gut colonization in infants across three lemur species with different diets and gut morphologies. Next we used metagenomic sequencing and nuclear magnetic resonance (NMR) spectroscopy to assess the suite of metabolic pathways and products associated with each host species. Both studies suggest that fiber is a critical dietary component associated with key features of microbial colonization in healthy infants. We next compared bacterial lineages shared between lemurs and bamboo specialists to assess which specific classes of microbial membership are impacted by host phylogeny versus diet. Finally, we compared secondary colonization trajectories to assess the impact of Cryptosporidium, an intestinal pathogen that seasonally infects captive sifakas at the Duke Lemur Center. We find that, while diet predictably shapes community structure and function during colonization, disease incurs age-related impacts on each individual’s microbiome uniquely.

Seasonal heterothermy—an orchestrated set of extreme physiological responses—is directly responsible for the over-winter survival of many mammalian groups living in seasonal environments. Historically, it was thought that the use of seasonal heterothermy (i.e. daily torpor and hibernation) was restricted to cold-adapted species; it is now known that such thermoregulatory strategies are used by more species than previously appreciated, including many tropical species. The dwarf and mouse lemurs (family Cheirogaleidae) are among the few primates known to use seasonal heterothermy to avoid Madagascar’s harsh and unpredictable environments. These primates provide an ideal study system for investigating a common mechanism of mammalian seasonal heterothermy. The overarching theme of this dissertation is to understand both the intrinsic and extrinsic drivers of heterothermy in three species of the family Cheirogaleidae. By using transcriptome sequencing to characterize gene expression in both captive and natural settings, we identify unique patterns of differential gene expression that are correlated with extreme changes in physiology in two species of dwarf lemurs: C. medius under captive conditions at the Duke Lemur Center and C. crossleyi studied under field conditions in Madagascar. Genes that are differentially expressed appear to be critical for maintaining the health of these animals when they undergo prolonged periods of metabolic depression concurrent with the hibernation phenotype. Further, a comparative analysis of previously studied mammalian heterotherms identifies shared genetic mechanisms underlying the hibernation phenotype across the phylogeny of mammals. Lastly, conducting a diet manipulation study with a captive colony of mouse lemurs (Microcebus murinus) at the Duke Lemur Center, we investigated the degree to which dietary effects influence torpor patterns. We find that tropical primate heterotherms may be exempt from the traditional paradigms governing cold-adapted heterothermy, having evolved different dietary strategies to tolerate circadian changes in body temperature.

Microbial communities associated with animals and plants (i.e., microbiomes) are implicated in the day-to-day functioning of their hosts, and there has been an explosion of research on them. Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these host-microbiome associations evolve. In this dissertation, we develop a computational agent-based frameworks for modelling the long-term evolution and short-term dynamics of microbiomes within a population of hosts. Our frameworks allow different ecological processes and evolutionary forces to directly or indirectly affect microbiome composition. By incorporating a Wright-Fisher or Moran genealogical population model, we combine host phylogeny with microbiome assembly to consider the shared evolutionary history between hosts and their microbes. We also incorporate how hosts acquire their microbiomes, and how the environmental microbial community available to the hosts is assembled under both neutrality and selection. Under the selective models, we allow selection to operate on both microbes and hosts and observe how microbial diversities are gradually shaped by this evolutionary feedback between hosts and microbes. Furthermore, host population division and dispersal limitation are taken into account for our short-term neutral models. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes over both long-term and short-term periods: with greater parental contribution, microbiome diversity within hosts tends to decline while microbiome diversity between hosts tends to increase. We also show that the implementation of selection further depresses microbial diversities and the comparison between host level and microbe level selection suggest that the evolutionary pressures directly acting on microbes is more dominant in shaping microbial diversity patterns. Finally, we show that host population division and dispersal limitation under high host contribution further shape the diversity patterns by elevating microbiome differences between hosts and depressing microbial diversity within hosts.

Anthropogenic effects on ecosystems have expanded in their scope and intensity, with significant consequences for global environmental, wildlife and human health. As human encroachment into wildlife habitat grows, habitat degradation and fragmentation intensify, leading to increased contact among wildlife, humans and domestic animals. Due to this increasing frequency of interaction, and the emergence of several high-profile diseases, global concern has grown over the risk of emerging infectious disease from zoonotic origins.

Due to Madagascar's rampant rate of human population growth and deforestation, its incredible species diversity, the widespread presence of domestic and invasive species, and its evolutionary isolation, it can be viewed as a high risk region for potential disease emergence. There is a need for assessment of the zoonotic and reverse zoonotic disease potential within this country.

To contribute to this assessment, consistent baseline health monitoring provides an effective tool for evaluating wildlife health and preparing for future disease occurrences. Limited, disconnected surveys of lemur health have occurred, yet there remained a need for more extensive, country-wide evaluations that also addresses invasive species, domestic animal and human health, as well shifting patterns of environmental and climatic change.

This research has investigated the connections among human, animal (both domestic and wildlife) and ecosystem health in Madagascar. I have examined current trends in anthropogenically-driven environmental change in Madagascar--including deforestation, illegal logging of precious hardwoods, mining, hunting, and agriculture--and evaluated how this change affects patterns of lemur, domestic animal and human health by evaluating a suite of health measures and parasite prevalence and richness. I have also examined how predicted global climate changes may influence the spatial patterns of lemur parasites and human infectious disease by assessing their shifts in distributions and geographic extent.

To assess the risk of disease transmission among lemur, domestic animal and human hosts, I have modeled the areas of geographic overlap among these parasites and their hosts and identified high-risk areas for disease emergence using geospatial analysis. This information can help to develop predictive statistical and spatial tools, which can inform both environmental management and public health planning.

Through this work, I have evaluated the severe loss of distribution that rosewood species have undergone, which highly qualifies them for international trade protection. We predicted areas of high risk for future logging, many of which occurred within protected areas in the biodiverse northeast.

Secondly, I have compiled the most comprehensive record of parasites of lemurs to date. Building upon the Prosimian Biomedical Survey Project data and the published literature, we have recorded 88 parasites that have been documented in lemurs. These are composed of helminths, bacteria, ectoparasites and protozoa. Of the 23 focal parasite species studied more in depth in this study, we noted high variability in prevalence measures for unique parasites at different sites. Parasite coinfection occurred quite commonly, with up to as many as 7 parasites concurrently. On average, lemur parasites tend to be less species-, genus-, or family-specific than other parasites across all primates.

Thirdly, I documented highly significant differences in health measures from two populations of Indri that exist under differing levels of anthropogenic pressure. Of note, the parasite richness, leukocyte count and differential, and nickel and cobalt levels were significantly higher in the more exposed population, while the total protein measures were significantly lower. These data suggest that the exposed population experiencing more anthropogenic pressure suffered from elevated health and nutritional stress.

Fourthly, I have documented strong correlations among environmental drivers (temperature, precipitation and landscape-scale features) and lemur parasite distributions. Striking shifts in their distributions are predicted to occur with projected climate change in Madagascar, including an expansion of helminth, virus and ectoparasite distributions, but a contraction of bacteria distributions due to warming and drying in the south.

Fifthly, I have examined 10 human and domestic animal parasites that hold great consequence for lemur, human and domestic animal health in Madagascar. I have similarly demonstrated strong correlations among environmental drivers (temperature, precipitation and landscape-scale features) and the distributions of these human parasites. Shifts in the distributions are also predicted to occur with projected climate change, including an expansion of helminth parasites, and a contraction of viruses and bacteria due to warming and drying in the south. I have identified areas of high risk for the transmission of parasites from human hosts to lemurs, as well as conversely from lemur hosts to humans. These risk indices will serve to highlight geographic areas at particular risk, and will also help to direct limited funds and staff to those areas most in need of attention.

Sixthly, I have demonstrated a need to train a growing cadre of One Health professionals from many different disciplines. I have offered several suggestions to integrate One Health training into graduate education, and have identified several geographic regions of potential to be a Center of One Health Excellence, of which the North Carolina Triangle area is one of great promise.

Mouse lemurs (genus Microcebus; Order Primates) are endemic to the island nation of Madagascar. These small, nocturnal primates offer a unique mammalian system ideally suited to study the patterns and processes of speciation, and the genomic revolution of the past decade has presented us with novel tools to test and understand these lineage-specific dynamics.

This thesis presents three independent projects on the speciation dynamics within mouse lemurs, interconnected by their utilization of the entire genome as a tool for reconstructing hidden evolutionary processes. Chapter 2 is an overview of the exploding field of speciation genomics and serves to ground these individual projects in evolutionary theory. In Chapter 3, we adopt a genome-wide approach to understand how the changing landscape of Madagascar has shaped the phylogeography of mouse lemurs while simultaneously leveraging the patterns derived from these species to discern clues about the ecology on the island in the distant past, and thus the impact of more recently arriving humans. The phylogenetic and population genetic patterns in a five-species clade of mouse lemurs suggest that longitudinal dispersal across the island occurred until approximately 500,000 ybp when a large ancestral population experienced rapid diversification, resulting in the present-day distributions of these species. However, the accuracy of the estimates of species ages from genetic data are limited primarily by our understanding of the mutation generation process in this non-model species. Thus, in Chapter 4, we improve these estimates by using high-coverage linked-read sequencing to estimate the generational de novo mutation rate within a family pedigree (n=8) of grey mouse lemurs (Microcebus murinus). We estimated a mutation rate of 1.64x10-8 mutations per basepair per generation, higher than nearly all mammals that have been previously characterized. Because estimates of these biological metrics critically affect estimates of divergence time we reanalyzed the results presented in the previous chapter and discover considerably more recent divergence times across the five-species clade. Finally, in Chapter 5, we utilize the knowledge of functional processes housed within genomic data to investigate the underlying causes of speciation in Microcebus. While many of the initial applications of genomic data in the genus have centered around understanding the phylogenetic relationships among the species rather than the mechanisms that underlie their diversification, we attempt to utilize genomic annotations to assess a putative mechanism driving speciation. We compared the rates of positive selection within sperm genes and a set of randomly drawn genes to look for the presence of positive selection. These comparisons reveal an elevated dN/dS, and thus evidence for positive selection, in sperm fertilization-related genes relative to sperm construction-related genes and a similarly-sized set of randomly-drawn genes. The results provide data that support our current knowledge of the behavior and natural history of these primates, highlighting what could be genomic mechanism of speciation among these highly speciose primates of Madagascar. In doing so we hope to have shown that detailed questions relating to both the extrinsic (e.g., inter- and intra- population and ecological interactions) and intrinsic (e.g., genome content and architecture) forces that drive speciation can be asked and answered, especially in non-model species.