Richard Gerald Harrison, PhD - US grants

Most natural populations exhibit cycles of growth and decline. In addition, the number of individuals of a given species may increase in one area while it is decreasing in a neighboring locale. These local dynamics are tied together by individuals that move from one population to another, i.e. disperse, over the course of their lifetime. This research project focuses on two particular aspects of dispersal in animals. First, dispersal provides immigrants to areas from which a species has disappeared thus compensating for small scale extinctions which commonly occur in many species and ensuring long term persistence. Moreover, dispersal forms the basis for gene flow, one of the key factors that determine the genetic structure of populations. The following questions will be addressed. 1) How frequently should animals disperse in a given situation assuming that this strategy significantly influences their chances of survival and reproduction? 2) What are the critical factors that could trigger large scale extinction in this network of local extinction and recolonization? 3) How much genetic variation can be maintained in such a system of interconnected populations thereby providing the raw material for evolutionary change? The principal investigator will approach these questions by contrasting a computer simulation with a field study on the pond- dwelling water beetle Dineutus assimilis. The rate at which these beetles move from pond to pond will be measured in the field and genetic differences among the study populations will be quantified by analyzing mitochondrial DNA variants. This molecular technique is a powerful tool to describe small scale genetic variation in animals. The information obtained in the field will be used to check the assumptions on which the simulation is based. The computer model can then be used to extrapolate beyond this particular natural system to explore the consequences of dispersal over a wider range of conditions.

9423603 HAIRSTON The magnitude of dispersal between natural populations of organisms is known to affect a wide array of biological events, including speciation, extinction, and local adaptation. The genetic consequence of dispersal, termed gene flow, is commonly inferred from the geographic distribution of gene frequencies. However, the accuracy of such estimates is difficult to ascertain. Measuring gene flow in closely related species which vary in dispersal ability allows such indirect estimates to be evaluated. This proposal outlines a sampling regime for 19 species disperse of Arrenurus water mites across a range of spatial scales. The majority of these species disperse only once in their lifetime on the adult stages of aquatic insects, while a few do not disperse at all. Dispersal ability of the mite species can be ranked categorically based on known attributes of the host and the host-parasite relationship. Analyses of genetic population structure will be made for each mite species from allozyme data, as will the population structure of some insect hosts. Data regarding the insects will provide insight into the genetic consequences of the parasitic association to the parasites. For the water mites, correlations between dispersal and gene flow will be assessed statistically, and phylogenetic relationships will be considered. Because these mites are closely related, occur in similar habitats, and their dispersal potential is well understood, differences between them other than dispersal ability are minimized. This study will be the first attempt to assess population genetic structure in a large group of co-occurring, closely related species.

Long-term effects of population reductions on genetic diversity are well understood, but few studies have examined short-term changes in genetic diversity in populations immediately after they have been founded. The goal of this project is to compare changes in genetic diversity in three species of the grazing zooplankter Daphnia that recolonized a lake from a small number of founding individuals with a fourth population that was founded by a large number of individuals. Long-lived dormant Daphnia eggs in sediments record annual changes in populations that can be reconstructed from sediment cores. Genetic diversity of each of the four "populations" at several time points following recolonization will be measured to assess changes as the populations recovered in size.

Daphnia species are a key component of aquatic ecosystems, serving as a control on algae and a food source for fish. The ability of a population to respond to environmental changes depends on the level of genetic diversity present. This study will thus provide important insights into how Daphnia respond to environmental change and influence community and ecosystem processes. It will also provide empirical tests of theoretical models and contribute to our knowledge about how genetic diversity is maintained in natural populations, which in turn will foster more appropriate management or conservation plans.

This award provides partial support for purchase of a modern capillary DNA sequencer and supporting computer equipment for the Cornell Evolutionary Genetics Core Facility (EGCF). The instrument will be equipped for both sequence determination and fragment analysis. The facility supports research by evolutionary biologists, population biologists, behavioral ecologists, and systematists. Research in these areas increasingly depends on variation in the DNA sequences of individual organisms to provide information on mating systems, population structure, genealogy, and phylogeny. Automated DNA sequencing and genotyping are critical to studies employing such variation. The facility is used by 19 faculty in seven departments across the Cornell campus, and contributes significantly to their research programs and the educational experience of their graduate and undergraduate students. Their research programs address various aspects of biodiversity, including the origins and maintenance of plant and animal diversity, and the management of taxa of conservation concern or of economic importance. Aside from the impact of each individual user, the facility plays an important role in teaching and training on the Cornell campus. The new equipment will increase throughput and data quality for all users, improve the training of students, and catalyze interactions among evolutionary biologists and ecologists with diverse taxonomic and disciplinary interests.

While it is known that mutations in DNA are the source of genetic variation in natural populations, it is unclear how changes in genes translate into the diverse forms seen in nature. To address this, the proposed research focuses on a recently evolved unique trait, a reproductive foam produced by male Japanese quail. This study will characterize gene sequences and expression patterns for genes that encode foam proteins. Data will be obtained for multiple tissues from the Japanese quail and related species. The findings will address what types of genetic changes are responsible for unique traits and how genes underlying novel structures evolve.

The Japanese quail is an economically important domesticated poultry species raised globally for meat and eggs. It is important to understand the fertilization biology of poultry to design efficient and effective breeding programs. When foam is added to semen, it extends the life of sperm and simulates natural fertility levels. Characterizing foam genes will increase our knowledge of the fertilization biology of quail, provide targets for selection of more fertile males, and provide insight into improving sperm function across other poultry species. Additionally, understanding the evolution of reproductive proteins may inform us about the causes of infertility.

The long-term goal of the research is to understand the process of speciation, in which one species splits into two, often through the evolution of multiple forms of reproductive isolation. The project focuses on reproductive isolation that occurs because of differences in the timing of major life cycle events, a widespread and potentially major impetus for speciation when differences in time of reproduction restrict gene flow. In a multi-pronged approach that applies high-throughput DNA sequencing, genetic mapping, population genomic analysis, metabolic profiling and field experiments the research will examine the genetic basis of life cycle variation and temporal reproductive isolation in the European corn borer moth (Ostrinia nubilalis), and evaluate the consequence of these differences in preventing gene flow between populations in nature. These experiments will provide a rare glimpse into the role of temporal isolation in origin of new species.

Although a superb model for speciation, the European corn borer is also a major pest of corn and other crops, costing the United States ~$1B each year. By leveraging the moth as an organism of both scientific and economic interest, the research builds community partnerships to simultaneously promote basic scientific discovery, public understanding of the relevance of evolution in daily life, and sustainable agriculture.

Understanding the origins of evolutionary novelty is fundamental to the study of biological diversity. Many studies have focused on the role of selection in driving change. However, a complete picture of the evolutionary process must also account for the mechanisms that create variation. This project investigates genetic changes that produce variation in the jaws of a recently diverged group of fish, and will provide insight into the nature of genetic changes associated with evolution in wild populations. The work will train a graduate in genomic research, and provide research opportunities for undergraduate students interested in careers in science. The researchers will create materials designed for use in K-12 classrooms about fish evolution that highlight how evolutionary novelties arise.

The researchers will investigate the genetic and developmental basis of cranial modifications in recently diverged incipient species of Bahamian pupfish (Cyprinodon). The work addresses the role of gene regulation and sequence divergence in producing novel phenotypic change associated with speciation in three closely-related species that specialize on eating either the scales of other fish or hard-shelled prey or detritus. The project will identify whether the genes and regulatory changes producing pupfish jaw diversity are homologous to those identified in other classic radiations, thus informing our understanding of the extent to which similar genetic mechanisms underlie phenotypic change in disparate lineages. Importantly, the project also aims to identify previously unknown genes associated with evolutionary changes to jaw morphology. The researchers will use high throughput sequencing (RNA-seq) to characterize the extent of regulatory divergence and sequence divergence among the Bahamian forms and the widespread marine outgroup. They will investigate how patterns of transcriptional regulation have diverged among Bahamian forms and identify gene regulatory changes associated with the diversification of jaw morphology. These data will, furthermore, be used to identify sequence variation (SNPs) associated with phenotypic divergence and reproductive isolation in the system. This project will thus provide insight into the genetic changes associated with speciation and the evolution of morphological novelties during the early stages of diversification.

Populations of a single species that live in different geographic regions often diverge as natural selection drives adaptation to the local environment. Understanding the processes of divergence and local adaptation is of particular importance in this contemporary era of rapidly changing environments. The coastal salt marshes of North America provide excellent systems in which to study rapid adaptive divergence, given that these habitats have formed within the last 15,000 years and represent novel selective environments for their inhabitants. Within many independent lineages of birds, there is a strong pattern of evolving larger bills and darker plumage after colonizing coastal salt marshes, suggesting that these traits offer a selective advantage. This project will allow identification of the genetic basis of divergence in these traits, and provide a window into the evolutionary mechanisms underlying local adaptation. This project will also provide hands-on training for graduate and undergraduate students, and will provide useful information for the conservation of coastal bird populations.

Two locally adapted subspecies of the Swamp Sparrow exist in the northeastern US: A brown inland form with a small bill, and a dark grey coastal form with a large bill. Preliminary DNA sequence (ddRAD) data reveal that the two forms are very similar, but several regions of the genome are highly differentiated between them. The natural history of coastal Swamp Sparrows suggests that strong directional selection may have influenced sequence variation in these highly differentiated regions. To test this hypothesis, patterns of genome-wide divergence will be surveyed by generating additional DNA sequence data for each differentiated region; these will be statistically examined for molecular signatures of selective sweeps. This project provides an important test of this emerging statistical methodology.