Browsing by Subject "Phylogeography"

Islands have been the inspiration for some of evolutionary biology's most important advances. This is largely due to the unique properties of islands that promote the differentiation of island species from their mainland counterparts. Rodents are widely distributed across even the most remote islands, a rarity among mammals, making them uniquely suited to study the factors leading to the divergence of insular species. In this dissertation, I use two case studies to examine the morphological and genetic divergences that take place in an insular environment.

In chapters one and two, I examine how different factors influence insular body size change in rodents. In chapter one, I examine factors influencing the direction of island body size change using classification tree and random forest (CART) analyses. I observe strong consistency in the direction of size change within islands and within species, but little consistency at broader taxonomic scales. Including island and species traits in the CART analyses, I find mainland body mass to be the most important factor influencing size change. Other variables are significant, though their roles seem to be context-dependent.

In chapter two, I use the distributions of mainland rodent population body sizes to identify `extreme' insular rodent populations and compare traits associated with those populations and their islands with those island populations of a more typical size. I find that althought there is no trend among all insular rodents towards a larger or smaller size, `extreme' populations are more likely to increase in size. Using CART methods, I develop a predictive model for insular size change that identifies resource limitations as the main driver when insular rodent populations become `extremely small'.

Chapters three and four shift their focus to a single rodent species, the deer mouse Peromyscus maniculatus, as they examine the genetic differentiation of deer mice across the California Channel Islands and the nearby mainland. In chapter three, I sequence a region of the mitochondrial control region for individuals from 8 populations across the northern Channel Islands and two mainland sites, and I analyze these sequences by calculating population genetics parameters and creating a Bayesian inference tree and a statistical parsimony haplotype network. All of these analyses reveal significant divergences between island and mainland populations. Among the islands, Santa Barbara and Anacapa islands both display unique genetic signatures, but the other northern islands remain relatively undifferentiated.

In chapter four, I genotype individuals from the previous chapter at 5 microsatellite loci, I calculate additional population genetics parameters and I utilize a Bayesian clustering algorithm to examine the similarities and differences between nuclear and mitochondrial analyses. I find the nuclear data to be largely congruent with the mitochondrial analyses; there are significant differences between island and mainland populations, and Anacapa Island is significantly differentiated from the other islands. Unlike the previous analyses, Santa Barbara Island is not significantly different from the northern islands, yet San Miguel Island has a unique genetic signature.

These studies underscore the importance of ecological processes and historical biogeography in the generation of diversity, and they highlight the role of islands as drivers of evolutionary divergence.

Morphological characters from the gametophyte and sporophyte generations have been used in land plants to infer relationships and construct classifications, but sporophytes provide the vast majority of data for the systematics of vascular plants. In bryophytes both generations are well developed and characters from both are commonly used to classify these organisms. However, because morphological traits of gametophytes and sporophytes can have different genetic bases and experience different selective pressures, taxonomic emphasis on one generation or the other may yield incongruent classifications. The moss order Hookeriales has a controversial taxonomic history because previous classifications have focused almost exclusively on either gametophytes or sporophytes. The Hookeriales provide a model for comparing morphological evolution in gametophytes and sporophytes, and its impact on alternative classification systems. Sometimes, placement of certain groups within Hookeriales remains challenging even at the molecular level. That is the case of the genus Calyptrochaeta. We study diversification dynamics in this genus to elucidate possible mechanisms obscuring its placement and we address biogeographic questions using the Tropical Conservatism scenario as our null hypothesis. Furthermore, to better understand biogeographic patterns in the Southern Hemisphere, infraspecific molecular patterns are compared in two species of the genus Calyptrochaeta (i.e., C. apiculata and C. asplenioides) and vicariance and recent long distance dispersal are tested to explain the disjunct distributions observed in these species.

In this study we reconstruct relationships among pleurocarpous mosses in or associated to the Hookeriales, in Calyptrochaeta, and within Calyptrochaeta. Six molecular markers are explored in total from all three genome compartments to reconstruct the evolution of morphological characters and habitat preferences in our phylogenies. Divergence times are estimated in a Bayesian framework using a relaxed molecular clock, and diversification rates are calculated on the chronograms resulting from these estimations.

As a result, we found that the Hookeriales, as currently circumscribed, are monophyletic and that both sporophyte and gametophyte characters are labile. We documented parallel changes and reversals in traits from both generations. We show that diversification rates in Calyptrochaeta have changed through its history. Also, though we lack support to clearly reject the tropical conservatism hypothesis, our data point to a more complex scenario where both temperate and tropical species can be ancient and give rise to one another, since shifts between tropical and temperate regions seem to be possible in any direction. Finally, we have show that recent long distance dispersal best explains the distribution of both C. apiculata and C. asplenioides in the Southern Hemisphere.

This dissertation is an investigation of the systematics, phylogeography, and ecology of a globally distributed fungal family, the Elaphomycetaceae. In Chapter 1, we assess the literature on fungal phylogeography, reviewing large-scale phylogenetics studies and performing a meta-data analysis of fungal population genetics. In particular, we examined the possible effects of asexuality, trophic niche, dispersal method, and ocean barriers on population structure. In Chapter 2, we examine the systematics and phylogeography of the Elaphomycetaceae, a family consisting of the truffle genus Elaphomyces and the stalked genus Pseudotulostoma, hypothesizing that the mammal-dispersed truffle would show evidence of dispersal limitation. Using DNA sequence data, we determined that Pseudotulostoma is derived from a lineage of Elaphomyces, indicating that Elaphomyces as currently defined is paraphyletic. The distribution of each subgenus of Elaphomyces is nearly global; representative species have been found on every continent save Africa and Antarctica. This biogeographic pattern does not follow the pattern expected by a scenario of continental vicariance. Dating analysis in BEAST confirmed that broadly distributed clades are, in most cases, too young for this pattern to be explained by continental vicariance, indicating that occasional long-distance dispersal has been a significant component in the biogeographic history of the Elaphomycetaceae. This finding contradicts our initial hypothesis that the mammal-dispersed truffles would be dispersal- limited. In Chapter 3, we investigate the role of Elaphomyces as a host for the fungal parasite Elaphocordyceps, a parasite derived from insect pathogens that attacks both insect larvae and Elaphomyces, its only fungal host. We examined the biogeography of Elaphocordyceps isolated from Elaphomyces specimens in order to test whether it, like its host, showed recent connections between the Southern and Northern Hemispheres. We also evaluated the pathogenicity of infection as determined by a visual rubric for the truffle gleba, the phylogenetic distribution of Elaphocordyceps species on its host, testing for seasonal, climate, and host-parasite effects. In Chapter 4, based on the phylogeographic pattern seen in Elaphomyces that resembles that of some air-dispersed fungi, we used theoretical and experimental methods to test whether Elaphomyces could be dispersed by air. We tested the capacity for air dispersal with an experimental test of passive air dispersal on the powdery spores of Elaphomyces morettii and found that these large spores could disperse over a short distance (10 m) in comparable numbers with the spores of the giant puffball Calvatia cyathiformis, which is known to be air-dispersed. The major findings of this thesis are that 1) fungi in general show high dispersal ability, but that trophic niche and dispersal mode may affect population structure, 2) that Pseudotulostoma, a stalked genus, is derived from the truffle Elaphomyces, 3) that the Elaphomycetaceae have experienced frequent long-distance dispersal despite 4) that the fitness of Elaphomyces as indicated by glebal development varies with host-parasite interactions based on species identity, but not with climate or season, and that 5) Elaphomyces spores, should they be released into the air, can remain in the air long enough to be dispersed long distances by the wind. The overall conclusion of this thesis is that, while Elaphomyces is clearly reliant on animal vectors for excavation and dispersal, its past history of long-distance dispersal and current spore trajectories indicate it can be passively air-dispersed as well.

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.