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A primary goal of evolutionary biology is to elucidate the factors necessary for a single interbreeding species to become two independent species. Observations and data collected and recorded since the 6th century B.C. have added to our comprehension of the "the origin of species--that mystery of mysteries" (DARWIN 1859). To continue to add to our knowledge of how speciation occurs and how species interact, it is crucial to determine 1) how different categories of genes evolve as species diverge, 2) what happens to hybrids of two species, and 3) if genetic exchange is allowed between species, where it is located. In the first research aim of my dissertation, I look for population genetic trends and signatures of gene flow in a minimally studied set of Drosophila sister species using sequences of 26 nuclear and mitochondrial regions in 29 isofemale lines of D. subobscura and D. madierensis. Standard population genetic tests revealed that the X chromosome evolves faster than the autosomes in these species. We also find evidence of genetic exchange for some autosomal genes while both the sex chromosomes and mitochondrial genomes remain distinct between species. In the second research aim of my dissertation, I assess the rates of gene expression evolution for sex-biased genes located on the X chromosome and autosomes. We find that gene expression evolves faster in males than females and find evidence of faster-X evolution that is exclusive to genes expressed at higher levels in males. The X chromosome has previously been shown to have a disproportionately large influence on hybrid male sterility compared to autosomes. I investigate this trend and find that the sex chromosomes have a large influence on autosomal expression levels in hybrid males and hybrid females. Specifically, uniparental inheritance of the X chromosome results in greater differences between reciprocal hybrids and higher levels of hybrid misexpression.
Over evolutionary time genomes diverge by acquiring new mutations, some of which isolate species by erecting reproductive barriers. The study of such genes sheds light on how fundamental developmental processes diverge and result in new species. Hybrid incompatibility (HI) genes contribute to speciation by causing the sterility and inviability of interspecific offspring. The Hmr (Hybrid male rescue) and Lhr (Lethal hybrid rescue) genes are a major cause of hybrid lethality between Drosophila melanogaster and its sibling species D. simulans. Hybrid sons from this cross are normally inviable; however by mutating either the D. melanogaster ortholog of Hmr or the D. simulans ortholog of Lhr, viable adult hybrid sons are recovered. Like other HI genes, both Lhr and Hmr are rapidly evolving under selection. In the first study, I asked whether the evolutionary history of selection for Hmr is confined to the hybridizing lineages. I conducted a population genetic survey of Hmr alleles from two sister species D. yakuba and D. santomea, whose common ancestor diverged from the common ancestor of D. melanogaster and D. simulans approximately 10 Myrs ago. I found that Hmr has diverged recurrently under positive selection in multiple independent speciation events, suggesting that Hmr is likely to be functionally diverging in multiple species. In the second study, I examined the molecular nature of functional divergence for the HI gene, Lhr. Strikingly, I found that despite rapid evolution of the Lhr coding sequence, hybrid lethal activity is not a derived function specific to one lineage, but instead a conserved function shared by both Lhr orthologs. Examination of the heterochromatic localization patterns of Lhr orthologs also failed to reveal any evidence of functional divergence. Instead I discovered that regulatory divergence underlies the asymmetric hybrid lethal activities of Lhr orthologs. In the last study, I identified Lhr2, a D. simulans Lhr allele with a highly unusual coding sequence, as a hybrid rescue mutation. I used it to identify a conserved region in the C-terminus of the LHR protein that is critical for hybrid incompatibility. Using the Lhr2 allele I was able to assay the effect of an indel polymorphism that was segregating in the common ancestor of D. melanogaster and D. simulans on hybrid incompatibility. Notably, I found that this indel polymorphism contributes significantly to the functional divergence of Lhr.
Identifying ecological and genetic mechanisms driving the formation of species barriers is central to understanding the process of speciation; however dissecting these factors in diverse wild systems remains challenging. My dissertation features a set of complementary experiments that evaluate how variation in environmental context, physiology, and genetics influence evolutionary divergence and the emergence of prezygotic isolation, using a diverse set of Drosophila species. In Chapter 1, I evaluate whether sympatry with heterospecifics has led to "reinforcement" of female remating behaviors so as to reduce the fitness costs of hybridization. I find no evidence for altered female remating rates in sympatry; instead observed remating behaviors are consistent with postcopulatory manipulation by unfamiliar (con- or hetero-specific) males, not reinforcement. In Chapter 2, I evaluate how trait variation among three allopatric Drosophila species has been shaped by divergence in abiotic habitat. I find that species differences in both desiccation resistance and pigmentation are consistent with differential natural selection imposed by variation in environmental water availability. To better understand the role of plasticity in this desiccation resistance variation, Chapter 3 examines gene expression in the same species under ambient and stressed conditions and finds only a modest number of genes have species-specificity in plastic or constitutive expression. Finally, in Chapter 4, I assess mating patterns and cuticular hydrocarbon (CHC) variation among these species. I find evidence for strong prezygotic isolation between two species, based on female preference for male CHC profiles, and identify a CHC elongase gene whose patterns of expression and sequence variation are consistent with a role in CHC divergence. Together, these studies identify several ecological and genetic factors that are critical for shaping patterns of trait divergence, and that have direct consequences for the early emergence of prezygotic barriers among closely related, ecologically diverse species.
The nature of populations, races, subspecies, and species. Genetic basis of isolation. Origin of isolation - theoretical. Origin of isolation - experimental. The nature of the speciation process.
The origin of biological diversity, via the formation of new species, can be inextricably linked to adaptation to the ecological environment. Specifically, ecological processes are central to the formation of new species when barriers to gene flow (reproductive isolation) evolve between populations as a result of ecologically-based divergent natural selection. This process of 'ecological speciation' has seen a large body of particularly focused research in the last 10-15 years, and a review and synthesis of the theoretical and empirical literature is now timely. The book begins by clarifying what ecological speciation is, its alternatives, and the predictions that can be used to test for it. It then reviews the three components of ecological speciation and discusses the geography and genomic basis of the process. A final chapter highlights future research directions, describing the approaches and experiments which might be used to conduct that future work. The ecological and genetic literature is integrated throughout the text with the goal of shedding new insight into the speciation process, particularly when the empirical data is then further integrated with theory.
Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.
Hybrid zones--geographical areas in which the hybrids of two races are found--have attracted the attention of evolutionary biologists for many years, both because they are windows on the evolutionary process and because the patterns of animals and plant variation seen in hybrid zones do notfit the traditional classification schemes of taxonomists. Hybrid zones provide insights into the nature of the species, the way barriers to gene exchange function, the genetic basis of those barriers, the dynamics of the speciation process. Hybrid Zones and the Evolutionary Process synthesizes theextensive research literature in this field and points to new directions in research. It will be read with interest by evolutionary biologists, geneticists, and biogeographers.
The second volume in a series dedicated to fossil discoveries made in the Afar region of Ethiopia, this work contains the definitive description of the geological context and paleoenvironment of the early hominid Ardipithecus kadabba. This research by an international team describes Middle Awash late Miocene faunal assemblages recovered from sediments firmly dated to between 5.2 and 5.8 million years ago. Compared to other assemblages of similar age, the Middle Awash record is unparalleled in taxonomic diversity, composed of 2,760 specimens representing at least sixty five mammalian genera. This comprehensive evaluation of the vertebrates from the end of the Miocene in Africa provides detailed morphological and taxonomic descriptions of dozens of taxa, including species new to science. It also incorporates results from analyses of paleoenvironment, paleobiogeography, biochronology, and faunal turnover around the Pliocene-Miocene boundary, opening a new window on the evolution of mammals, African fauna, and its environments.
The average person can name more bird species than they think, but do we really know what a bird “species” is? This open access book takes up several fascinating aspects of bird life to elucidate this basic concept in biology. From genetic and physiological basics to the phenomena of bird song and bird migration, it analyzes various interactions of birds – with their environment and other birds. Lastly, it shows imminent threats to birds in the Anthropocene, the era of global human impact. Although it seemed to be easy to define bird species, the advent of modern methods has challenged species definition and led to a multidisciplinary approach to classifying birds. One outstanding new toolbox comes with the more and more reasonably priced acquisition of whole-genome sequences that allow causative analyses of how bird species diversify. Speciation has reached a final stage when daughter species are reproductively isolated, but this stage is not easily detectable from the phenotype we observe. Culturally transmitted traits such as bird song seem to speed up speciation processes, while another behavioral trait, migration, helps birds to find food resources, and also coincides with higher chances of reaching new, inhabitable areas. In general, distribution is a major key to understanding speciation in birds. Examples of ecological speciation can be found in birds, and the constant interaction of birds with their biotic environment also contributes to evolutionary changes. In the Anthropocene, birds are confronted with rapid changes that are highly threatening for some species. Climate change forces birds to move their ranges, but may also disrupt well-established interactions between climate, vegetation, and food sources. This book brings together various disciplines involved in observing bird species come into existence, modify, and vanish. It is a rich resource for bird enthusiasts who want to understand various processes at the cutting edge of current research in more detail. At the same time it offers students the opportunity to see primarily unconnected, but booming big-data approaches such as genomics and biogeography meet in a topic of broad interest. Lastly, the book enables conservationists to better understand the uncertainties surrounding “species” as entities of protection.