Peter Breslin

Peter Breslin

Nov 30, 2017

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Visualizing Population Genetic Structure

Another aspect of the research I'm doing is a population genetics approach to Cochemiea halei, the cactus species I am studying, to determine the within population and between population genetic diversity, the landscape effects on gene flow and the overall genetic differentiation between the most widely separated populations across the range of the species. If there isn't much population genetic structure, that would mean, most likely, that the hummingbird that is probably the main pollinator of the species ( Basilinna xantusii ) has a wide range and isn't daunted by geographical barriers between islands or in the mountainous island landscape.

I've collected 96 samples of tissue from 10 populations, as shown in this map:

Although some populations are close together, they are separated either by habitat type (bayside versus ridgetop) or by a significant geographical feature.

The methods used to analyze the genetic aspects of this species include DNA extraction, restriction site associated DNA sequencing (RADseq) and a powerful analytical software program called Structure, that produces very clear visualizations of subpopulations broken down by allele frequencies or other measures of variation.

An example of an analysis of between-population genetic diversity for a Brazilian rodent species, Ctenomys minutus (the minor tuco-tuco), in a hybrid zone. The x-axis is position along the chromosome and the y-axis is relative allele frequency. Separate colors represent separate populations. (Casthilo et al. 2012)

Another example of a strong visualization from Structure of a wide variety of New York City populations of the white-footed mouse ( Peromyscus leucopus) http://nycevolution.org/research/urban-landscape-genetics-of-white-footed-mice/

I am hoping that the population genetics analysis of my study organism will provide crucial insight into the genetic diversity of this species across its range as well as between subpopulations. The population genetic structure informs questions of evolution, biogeography, proper maintenance of genetic health, maximizing fitness, preserving maximum diversity and many other issues. This information is crucial to management of endangered plant populations, but is often by-passed.

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About This Project

I am developing and applying innovative population genetics data analysis with habitat suitability modeling to solve longstanding challenges in the effort to save endangered plant species. Combining high throughput RADseq data analysis with species distribution models, I am exploring relatively inexpensive, feasible methods to generate powerful population viability assessments, estimates of threshold population size and the constraints on the habitats of rare plants.

Blast off!

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