Evolution is an historical process, and history greatly influences present- day observations. Genetic surveys using restriction mapping or DNA sequencing contain much historical information. Our general aim is to extract this historical information and use it in making evolutionary inferences on three interrelated problems in evolutionary genetics: population structure, founder and bottleneck events, and speciation. Population structure encompasses effective size, system of mating, and pattern of gene flow. Our first and primary aim is to develop phylogenetic techniques for the analysis of population structure by integrating cladistics (a methodology traditionally used to infer interspecific phylogenies) with coalescent theory (the subdiscipline of population genetics that deals with the genealogical structure of current genetic variants). These techniques will be applied to crayfishes, grasshoppers, and lizards. These species were chosen because biogeographical, behavioral, and/or habitat data indicate that this group covers a broad range of potential for restriction of gene flow on various geographical scales. The amount and distribution of genetic variation in a species today depends both upon its current population structure and upon past history (e.g., founder/bottleneck events). Our second specific aim is to develop phylogenetic methods of partitioning history from current population structure. We will use a nested cladistic analysis of geographical associations among haplotypes to detect recent historical events, use the branch length distribution of the cladogram (unrooted evolutionary tree) of the haplotypes to detect older historical events, and use recently evolved haplotypes to restrict inference to post-event gene flow patterns. To test these approaches, we will apply the techniques to several organisms for which we have excellent evidence of past historical events (either habitat fragmentation or colonization of new areas) on a known time scale that should cover a broad range in the predicted ease of detection of historical events. These species will also include crayfishes, grasshoppers and lizards, and broadly overlap with the organisms used for our first specific aim although the biogeographical scale differs. We will also test the validity of our assumptions by studying populations known to have undergone recent founder events; such as artificially released populations of collared lizards in the Ozarks and various captive zoo populations. The historical information encoded in the DNA extends beyond the existence of the species itself, and hence phylogenies of closely related species can be constructed from genetic data. We will construct such a phylogeny for a speciose and very diverse subgenus of crayfish and use the resulting phylogeny to test hypotheses about interactions among population structure, historical events, adaptative change, phenotypic change, geographical isolation, and speciation.
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