Cal Poly Biology Department

Effects of Recombination on Intraspecific Phylogenetic Analysis

Molecular Evolution and Phylogeography of the Cabezon (Scorpaenichthys marmoratus)

Population Genetic Structure of Cabezon (Scorpaenichthys marmoratus)

Temporal genetic variation and historic population genetic structure of the California Condor (Gymnogyps californianus)

Attend the annual meeting of the American Society of Cell Biologists - John Merriam

Developmental process by which a single cell, the fertilized egg, becomes a complex organism. This process at the cellular level is called differentiation. In order to study cell fate one can choose a specific step in the process and try to decipher the mechanisms, or one can choose a particular protein and find when it is involved. We have chosen the second path, and are looking at the role that tyrosine receptor kinases (Trks) play in sea urchin Strongylocentrotus purpuratus development. First degenerate primers will be constructed from consensus sequences of known Trks in other organisms such as human pig mouse, lymnaea, and chicken. These will be used to first probe the urchin genome and make specific primers. The new primers will then be used to probe cDNA libraries from a time course of developmental stages to find gene expression patterns. Parallel western blotting will be used to support transcriptional patterns with translational patterns. In this process we also hope to clone a complete copy of a S. purpuratus Trk that will be compared phylogenetically to other known Trks.

Science is not an individualistic endeavor, and so it is important to interact with other scientists, both in the same field of interest, and those from a broader or more distant branch of biology. Research conferences offer a perfect opportunity to meet new colleagues and learn of current research ideas and techniques outside of one’s immediate discipline. The annual meeting by the American Society of Cell Biologists offered just such an opportunity. Because of the ASCB’s reputation a large number, graduate students, post-docs, professors, and even world- renowned scientists, were in attendance. Symposiums discussed the state of our knowledge on topics such as cell signaling, trafficking, teaching techniques, and organelle production/inheritance to only name a few. Daily poster presentations also allowed me to see what current research is going on at other institutions as well as talk to the authors directly. This kind of first hand interaction cannot be replicated in the classroom and so justifies the need to travel to such a function.

The Effects of Recombination on Intraspecific Phylogenetic Analysis - Dan Berman

The advent of modern molecular laboratory techniques for sequencing has led to an explosion of interest in the fields of population genetics and molecular phylogenetic analysis. Phylogenetics uses the genetic variation in a set of aligned DNA sequences to <br>generate hypothesis about the ancestral relationships of the sampled taxa. A central assumption of most phylogenetic methods is that no recombination has occurred within the aligned sequences. This assumption is likely to be violated in intraspecific analysis, where recombination may in fact play a large role in generating the observed patterns of genetic diversity. The effects of violating the assumption of no recombination on the resulting phylogenetic analysis are poorly understood. Recent work using computer simulations indicates that recombination can lead to misleading phylogenetic tree topology, and skew estimates of evolutionary and demographic parameters that are commonly based on the phylogenetic tree. A number of new methods for detecting recombination and analyzing recombinant data sets are available, yet many currently published papers still do not address the issue of recombination. This research project will examine previously published analyses that did not consider recombination to determine if recombination is present in the sequence alignment, and if so, what effects, if any, it has on the resulting analyses and conclusions.

Assessment of the Molecular Evolution and Phylogeography of the Cabezon (Scorpaenichthys marmoratus) Based on mtDNA Control Region Sequence R. Todd Olive

The cabezon (Cottidae: Scorpaenichthys marmoratus) is the largest of the Pacific Coast sculpins. It has become a highly sought after species in the lucrative commercial live-fish fishery. From 1991 to 1998 commercial landings of cabezon rose from 7 to 170 metric tons in California. The intense fishing pressure was such that live cabezon landings were the highest in tonnage and dollar value in California’s live-finfish fishery during 1998 and 1999. Because of this and the gaps in scientific information for this species, this study was established to determine the population genetic structure of the cabezon over a large portion of its geographic range. Our initial efforts have focused on sequencing the mtDNA control region for some of the 500 tissue samples have been collected from northern Washington to San Diego, California. We have developed primers for the amplification of the control region and sequence data have been obtained for some of the samples from various locations. The work accomplished thus far indicates that there is a degree of genetic variability over a portion of the range of this species. Once the data collection is completed, a combination of models and software packages will be used to gain further understanding of the population genetic structure, gene flow, dispersal distance, and the possible effects of fishing pressure on cabezon populations.

Population Genetic Structure of Cabezon (Scorpaenichthys marmoratus) Along the California Coast Based on Microsatellite Loci - Aaron Floyd

With the recent trend in nearshore live-fish markets escalating rapidly the California Department of Fish and Game has set out strict guidelines and moratoria on cabezon (Scorpaenichthys marmoratus) harvests for both commercial and recreational fishers. As this regulation is put into effect, it is done so as a precautionary method as the overall scientific knowledge available on cabezon is still very limited. The intent of this project is to look for possible population genetic structure among cabezon along the California coast. The overall study area will be divided up into three relatively similar sized areas. The southern area will extend from Point Conception south to the Mexico-California border, the central region will extend from Point Conception north to San Francisco Bay, and the northern region will extend from San Francisco Bay north to the California-Oregon border. Fifty samples will be used from each of the three areas. The method for detection of structure will be achieved by the use of five polymorphic microsatellite loci. The results of this project will be used to determine if the current closures and management techniques in use along California will be effective in maintaining cabezon numbers along the state, or if the fish exhibits site fidelity throughout its life history stages and would therefore be better managed in the three unique areas. Similar studies on rockfish have shown this to be an effective method for determining population structure. This work is intended to supplement the work on cabezon using mtDNA being conducted by Todd Olive at Cal Poly.

Temporal genetic variation and historic population genetic structure of the California Condor (Gymnogyps californianus) - Neil Clipperton

When a historically large population has a severe reduction in population size it is exposed to genetic factors which may result in a less fit population. An increased level of genetic drift in small populations may result in a loss of diversity. In large populations, this loss is opposed by factors such as mutation and selection. A small population is also more likely to experience inbreeding. As heterozygosity is lost in an inbreeding population the population becomes susceptible to deleterious recessive alleles. The severity of inbreeding depression is proportional to the rate at which a population decreases in size. The California Condor has recently passed through a severe bottleneck with only 22 individuals surviving in 1982. It is not clear whether the condor’s decline was gradual or rapid. It is also unclear if genetic drift and inbreeding have had significant effects on the population’s fitness. A portion of the mitochondrial genome will be sequenced from archival specimens of California Condors. These DNA sequences will allow a direct comparison between sequences already available on the 1982 bottlenecked population and a historic population representing pre-bottleneck diversity levels. Two historic populations will be sampled. One population will come from a range equal to that of the most recent condor population. The other population will be composed of birds outside of the most recent range. Several analyses will be performed in order to evaluate genetic changes through the bottleneck. Estimates of historic Ne will allow extent and timing of past declines to be determined.

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