Differences in patterns of species richness and taxonomic composition across continents are well documented. However, less is known about how these patterns originate from the fundamental processes that contribute to the assembly of continental biotas: speciation, extinction, immigration, and emigration. To truly decipher how these processes operate at a continental scale, it is crucial to understand how Earth-history events and environmental change shaped the biogeographical history of the taxa occurring in a region. The Pleistocene glacial cycles have been hypothesized to be a significant geological event which affected the Earth’s biota over the past three million years. During this period, multiple cycles, in which ice sheets covered a large portion of the Northern Hemisphere, have been hypothesized to facilitate allopatry and ecological differentiation. The central goal of this dissertation is to understand the assembly of continental biotas by integrating the role of Earth’s geological and environmental history and recent (late Quaternary) changes in distributions. Here, I studied the North American wood-warblers, which are passerine birds belonging to the family Parulidae. In the first chapter of this dissertation, I examined the extent to which recent diversification is underestimated by ignoring recently diverged taxa. To do so, I evaluated the effect of taxonomic delimitation on the inferred temporal patterns of diversification of wood-warblers in the genus Setophaga. My results show that species-level taxonomic delimitation in ecological and evolutionary studies is crucially important but is often ignored. Evaluating the effect of taxonomic delimitation in the genus Setophaga is particularly relevant because it has been widely cited as an ideal example of niche saturation, and previous studies suggested that lineages in this particular radiation exhibited an asymptotic accumulation of diversity through time. In this chapter, however, I demonstrate that this pattern was likely a consequence of the ways in which taxonomic diversity was sampled. In the second chapter, I examined how biotic and abiotic factors limit the distribution of species of the genus Oreothlypis at a continental scale. For most of the taxa examined, climatic- and biotic-based areas of suitability were equivalent, and therefore the relative importance of these factors could not be disentangled. However, in some cases, biotic variables limited the distribution in areas climatically suitable, and vice versa. The results of this chapter highlight the importance of considering potential effects of biotic interactions in the study of climate-driven range shifts. This paper is also an important methodological contribution to the general field of ecological niche modeling (ENM) by integrating climatic and palynological data to empirically estimate both abiotically and biotically suitable areas which that has only been done theoretically so far. In the third chapter, I integrated phylogenetic data, biotic and climatic ENMs, and reconstructions of environments during the LGM to test how cycles of fragmentation, differentiation, and expansion during the Pleistocene shaped the biogeographical patterns of the genus Oreothlypis in North America. Based on a time-calibrated phylogeny I identified two groups of taxa that diversified during the last million years and therefore were potentially affected by glacial cycles. My analyses suggest that there were rapid switches in the environmental conditions in which species of the genus occur and that glacial cycles resulted in dramatic range shifts from glacial maxima to interglacials. Distribution patterns during the LGM suggest that divergence in areas isolated by glaciers presumably contributed to the geographical structuring of Oreothlypis, as well as to their taxonomic and ecological diversity in the present. In summary, this work illustrates how wood-warblers are an ideal model system for examining the large-scale history of the North America biota and environment, particularly over the Pleistocene. They are highly diverse, have endemics in virtually all of North America's areas of endemism and ecosystems, and many of these patterns are repeated within and across clades. Furthermore, distributional patterns in warblers show high congruence with those of other organisms; thus inferences made about the history of this group likely have implications for understanding the biotic history of North America in general. In addition, many warblers have narrow ecological preferences in that they occupy forest environments with specific tree compositions. As a consequence, ecological models of their distributions, integrated with the North American pollen record of forest change, provide a new perspective on ecosystem change during glacial cycles, and its impact on the origin and maintenance of biodiversity in the continent.

Through common descent, closely-related taxa share many life history traits, some of which can influence extinction-proneness. Thus, examining historical and contemporary genetic patterns is valuable in accounting for evolutionary and ecological processes that may be critical to the successful conservation of threatened species. Unsustainable harvesting of monk seals (tribe Monachini) until the late nineteenth century caused the recent extinction of Caribbean monk seals (Neomonachus tropicalis) and critically low population sizes for Hawaiian and Mediterranean monk seals (Neomonachus schauinslandi and Monachus monachus, respectively). Having lost one branch of its evolutionary lineage, and with a second branch threatened by extinction, the genus Neomonachus can serve as a valuable case for examining evolutionary and ecological linkages that are sensitive to non-random anthropogenic selection pressure. An important foundation for such pursuits is the understanding of evolutionary sequences of speciation and diversification that gave rise to common traits shared by extinct and vulnerable species. Further consideration of the phylogenetic non-randomness of species vulnerability requires examination of genetic variation at the population level to infer the presence of fundamental processes (e.g., migration and reproduction) that directly influence population viability. This dissertation includes three individual studies that make use of molecular systematic and population genetic techniques to address these topics. First, a complete mitochondrial genome sequence of the extinct Caribbean monk seal (N. tropicalis) was assembled and used to resolve long-standing phylogenetic questions regarding the sequence of divergence among monk seal species and sister taxa. Second, novel microsatellite marker assays were developed and used to characterize the extent of population-level variation across 24 polymorphic microsatellite loci of 1192 endangered Hawaiian monk seals (N. schauinslandi) that were sampled during a longitudinal study spanning three decades. Third, resulting genotypes from a subset of individuals (N= 785) were integrated with previously reported genotypes consisting of 18 other loci for the largest ever population-level assessment of N. schauinslandi genetic diversity and population differentiation throughout the Hawaiian archipelago. The new microsatellite data will be of particular value for future individual-level assessment of parentage and relatedness in N. schauinslandi, which will help managers better infer the reproductive mechanisms that factor into population persistence and recovery. Results of this study expand understanding of the evolutionary and conservation genetic status of monk seals, as well as molecular genetic capacity, for future research regarding a unique and highly imperiled New World pinniped lineage.

No description available.

Frequency-dependent selection has long been a popular heuristic explanation for the maintenance of genetic diversity in natural populations. Indeed, a large body of theoretical and empirical work has already gone into elucidating the causes and consequences of frequency-dependent selection. Most theoretical work, to date, has focused either on the diallelic case, or dealt with only very specific forms of frequency-dependence. A general model of the maintenance of multiallelic genetic diversity has been lacking. Here we extend a flexible general model of frequency-dependent selection, the pairwise interaction model, to the case of multiple alleles. First, we investigate the potential for genetic variation under the pairwise interaction model using a parameter-space approach. This approach involves taking a large random sample of all possible fitness sets and initial allele-frequency vectors of the model, iterating each to equilibrium from each set of random initial conditions, and measuring how often variation is maintained, and by which parameter combinations. We find that frequency- dependent selection maintains full polymorphism more often than classic constant-selection models and produces more skewed equilibrium allele frequencies. Fitness sets with some degree of rare advantage maintained full polymorphism most often, but a variety of non-obvious fitness patterns were also found to have positive potential for polymorphism. Second, we further investigate some unusual dynamics uncovered by the parameter-space approach above. Long-period allele-frequency cycles and a small number of aperiodic trajectories were detected. We measured the number, length and domains of attraction of the various attractors produced by the model. The genetic cycles produced by the model did not have periods short enough to be observable on an ecological time scale. In a real world system, allele-frequency cycling is likely to be indistinguishable from stable equilibrium when observed over short time scales. Third, we use a construction approach to model frequency-dependent selection with mutation under the pairwise interaction model. This approach involves the construction of an allelic polymorphism by bombarding an initial monomorphism with mutant alleles over many generations. We find that frequency-dependent selection is able to generate large numbers of alleles at a single locus. The construction process generates a wide range of allele- frequency distributions and genotypic fitness relationships. We find that constructed polymorphisms remain permanently invasible to new mutants. Analysis of constructed fitness sets may even reveal a signature of positive frequency dependence. Finally, we examine the numbers and distributions of fitnesses and alleles produced by construction under the pairwise interaction model with mutation from existing alleles, using several different methods of generating mutant fitnesses. We find that, relative to more general construction models, generating mutants from existing alleles lowers the average number of alleles maintained by frequency-dependent selection. Nevertheless, while the overall numbers of alleles are lower, the polymorphisms produced are more stable, with more natural allele-frequency distributions. Overall, frequency-dependent selection remains a powerful mechanism for the maintenance of genetic variation, although it does not always work in intuitively obvious ways.

The mesoderm is the third germ layer, which is formed at gastrulation between the endoderm and the ectoderm in triploblastsc animals (Bilateria). The mesoderm differentiates into muscles, connective tissues and coelomic cavities. These structures have been key evolutionary innovations that prompted the enormous radiation of the bilaterians that at present make up for the 90% of animal species. As such, understanding the evolution of the mesoderm and its derivatives it is pivotal to understand the evolution of animals. In this thesis I have characterized the molecular patterning of the mesoderm and its derivatives (mainly muscles) in two different acoel species: Symsagittifera roscoffensis and Isodiametra pulchra. The acoels belong to the phylum Acoelomorpha (togheter with nemertodermatids and Xenoturbella). The phylogenetic placement of the Acoelomorpha is highly debated between a position basal to the bilaterians or nested inside the deuterostomes. The Acoelomorpha are morphologically simple animals and a trait sometimes considered a direct link to the cnidarians, the Bilateria sister group. With them they the acoelomorphs share a blind gut and a non centralized nervous system. Within the acoelomorphs, the acoels present the most derived body plan, however it is still rather simple if compared to other bilaterians. The nervous system for example is condensed anteriorly but not clear dorso ventral centralization exists as in most of the remaining bilaterians (the nerve cords are distributed circumferentially around the body). The mesoderm only develops from endodermal precursors, and this might be ancestral, since it is thought that the mesoderm evolved from the endoderm of a diploblastic, cnidarian-like ancestor. The muscles are the only mesodermal derivative in most basal acoelomorphs taxa, although in more advanced ones a parenchymal tissue, stem cells, and gonads also occupy the mesodermal space. The embryonic origins of the latter though, are at present still unknown. Thus acoelomorphs present most of traits considered to be eumetazoan ancestral traits (i.e. most of traits are also part of the cnidarians ground pattern), but still that the possibility that their body plan evolved in consequence of a secondary reduction must be considered as they could be more related to other deuterostomes than cnidarians. I have first investigated the molecular architecture of the muscles in the acoel Symsagittifera roscoffensis and found that although they have a smooth ultrastructural aspect they are molecularly more similar to the bilaterian striated muscles given that tey express key genes that control the contraction in the striated cells. This could be considered a first step into the evolution of the striated musculature without fully reaching it. Indeed, cnidarians have smooth epithelio muscular cells likely regulated by the same bilaterian smooth muscle proteins. However, the possibility of a secondary loss of the striation pattern cannot be discarded given that this already happened in some other bilaterians. Second, I have analyzed the expression of bilaterian mesodermal genes during embryogenesis and postembryonic development of Isodiametra pulchra and found that all but one (a FoxA ortholog) are expressed at the anterior pole, the site where the first myocytes start to differentiate. In juveniles and adults these genes are all expressed in muscles or at least a subset of them. Moreover the same genes are expressed in the gonads of I. pulchra and therefore it suggests that they could orginate in the endo-mesoderm of the worm. The cnidarians orthologues of these genes are expressed in the endoderm, which is moreover the site of the gametes differentation. The similarity between cnidarians endoderm and acoels mesoderm are astonishing, however before drawing conclusions we need a solid phylogenetic frame. / Los acelos son unos gusanos, principalmente marinos, de simetría bilateral y aplastados según el eje dorso ventral, que pertenecen al grupo de los acelomorfos (acelos +nemertodermatidos+xenoturbellidos), cuya posición filogenética es tema de debate entre los biólogos evolucionistas. Los acelomorfos carecen de cavidades corporales, su sistema digestivo es ciego y su sistema nervioso consiste de una concentración neuronal anterior y cuerda nerviosas no claramente desplazadas hacía el lado dorsal o ventral. La simplicidad morfológica de los acelos, entremedia entre la de cnidarios y bilaterales superiores, les hace buenos candidatos para el estudio de la transición de animales radiales-diploblastos a bilaterales-triploblastos. En esta tesis se presentan datos sobre el desarrollo e la especificación molecular del mesodermo, que ha sido una de las innovaciones claves para la radiación de los bilaterales. S. roscoffensis que como todos los acelos tiene exclusivamente musculatura de tipo liso, expresa un gen ortólogo a la troponina, un proteína clave para la regulación de los músculos estriados, y que no existe en cnidarios. La explicación más parsimoniosa es que las bases moleculares de evolución de músculos estriados se han implantado en los acelos, aunque estos no hayan alcanzado la condición completa (explicación favorecida si los acelomorfos son confirmados como grupo hermano de los demás bilaterales). Por otra parte se puede considerar esta condición como debida a una reducción secundaria (explicación favorecida en el caso que los acelos se confirmen ser deuteróstomos). Los ortólogos de genes endodermales de cnidarios y con clara expresión mesodermal en bilaterales se expresan en la músculatura del acelo l. pulchra. Estos datos concuerdan perfectamente con la evolución del mesodermo a partir del endodermo de animales diploblásticos. Aun así, es difícil proponer un modelo específico de evolución de miocitos hasta que la posición filogenética de los acelomorfos no esté resuelta.

Cichlid fishes from the East African Rift lakes Victoria, Tanganyika and Malawi represent a preeminent example of replicated and rapid evolutionary radiation. In this single natural system, numerous morphological (eg. jaw and tooth shape, color patterns, visual sensitivity), behavioral (eg. bower-building) and physiological (eg. development, neural patterning) phenotypes have emerged, much akin to a mutagenic screen. This dissertation encompasses three studies that seek to decipher the underpinnings of such rapid evolutionary diversification, investigated via the genetic variation in East African cichlids. We generated a valuable cichlid genomic resource of five low-coverage Lake Malawi cichlid genomes, from which the general properties of the genome were characterized. Nucleotide diversity of Malawi cichlids was low at 0.26%, and a sample genotyping study found that biallelic polymorphisms segregate widely throughout the Malawi species flock, making each species a mosaic of ancestrally polymorphic genomes. A second genotyping study expanded our evolutionary analysis to cover the entire East African cichlid radiation, where we found that more than 40% of single nucleotide polymorphisms (SNPs) were ancestral polymorphisms shared across multiple lakes. Bayesian analysis of genetic structure in the data supported the hypothesis that riverine species had contributed significantly to the genomes of Malawi cichlids and that Lake Malawi cichlids are not monophyletic. Both genotyping studies also identified interesting loci involved in important sensory as well as developmental pathways that were well differentiated between species and lineages. We also investigated cichlid genetic variation in relation to the evolution of microRNA regulation, and found that divergent selection on miRNA target sites may have led to differential gene expression, which contributed to the diversification of cichlid species. Overall, the patterns of cichlid genetic variation seem to be dominated by the phenomena of extensive sharing of ancestral polymorphisms. We thus believe that standing genetic variation in the form of ancestrally inherited polymorphisms, as opposed to variations arising from new mutations, provides much of the genetic diversity on which selection acts, allowing for the rapid and repeated adaptive radiation of East African cichlids.

The brain has been one of the central foci in studies of vertebrate evolution. Work in East African cichlids and other emerging fish models like the Mexican cavefish (Astyanax mexicanus) offer new insight on the role of patterning on brain evolution. These fish can be grouped into two major categories according to habitat; for cichlids it is rock-dwelling (known locally as mbuna) and sand-dwelling (non-mbuna) lineage. The brain development of mbuna versus non-mbuna is defined by changes in gene deployment working along the dorsal/ventral (DV) and anterior/posterior (AP) neuraxes, respectively. Comparison of disparate fish ecotypes offer a new perspective of the role of patterning on brain evolution; through the slight and early modification of signal pathways working across 3-D axes, and a subsequent magnifying effect across ontogeny, evolution can generate widespread changes in the brain. To illustrate this patterning model of brain evolution, two comparative studies were done between mbuna and non-mbuna, examining the action of gene pathways that work to pattern the cichlid forebrain. The first study found that non-mbuna cichlids have a more rapid AP expansion of a gene pathway (Wingless) into the presumptive midbrain and diencephalon versus mbuna. These forebrain structures are involved in sight processing and could be of ecological benefit to vision-focused non-mbuna. The second study described a difference within the developing telencephalon. The embryonic telencephalon is split into the pallium, which processes visual signals, and the subpallium, which develops into the olfactory bulbs. Mbuna possess a larger subpallium relative to non-mbuna, which have a larger pallium. This was correlated to a more rapid expansion of another gene pathway (Hedgehog) along the DV axis. The difference in size of the pallial vs. subpallialial comparments between cichlids can be correlated to expanded olfaction in mbuna and vision in non-mbuna adult brains. Overall, East African cichlids are an excellent system to investigate the role of patterning on brain evolution because they allow for the comparison of the earliest patterning events in brain ontogeny between distinct ecotypes. These fish systems link study in brain development to the brain morphology comparisons employed in classic studies of brain evolution.

Title from title page of PDF (University of Missouri--St. Louis, viewed February 10, 2010). Includes bibliographical references.

Thesis (Ph. D.)--University of Chicago, Department of Organismal Biology and Anatomy, June 2001. / Includes bibliographical references. Also available on the Internet.

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