MANAGING THE GENETIC DIVERSITY OF MICHIGAN PINES

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: MCINTIRE-STENNIS
• Reporting Frequency: Annual
• Accession No.: 0169429
• Project Start Date: Jul 1, 2006
• Project End Date: Jun 30, 2011
• Program Code: [(N/A)]- (N/A)

Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824

Performing Department
Forestry

Non Technical Summary
Forest management continually changes the natural landscape and structure of forested systems. Sustainable mangement necessitates modeling natural processes. This project provides essential information on natural levels of biodiversity in Michigan's native pine specis and will enable forest managers to more fully mimic natural systems. Our projects are having substantial impacts on furthering the field of plant population genetics, guiding genetic conservation efforts, and expanding and refining statistical methodology.

Animal Health Component

(N/A)

Research Effort Categories

Basic

(N/A)

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
123	0610	1080	50%
202	0610	1080	50%

Knowledge Area
202 - Plant Genetic Resources; 123 - Management and Sustainability of Forest Resources;

Subject Of Investigation
0610 - Conifer forests of the North;

Field Of Science
1080 - Genetics;

Keywords

red pine

starma

genetic diversity

cpssr haplotyping

molecular markers

biodiversity

Goals / Objectives
The proposed research would determine amounts of genetic diversity among red pine populations at the DNA level, so that we may: 1. identify the geographic distribution of genetic variation, by sampling a large number of populations, including previously uncharacterized populations that may contain unique genetic variation which could be sorely needed as new challenges arise; 2. better understand the historical genetic processes of this species and be better prepared for remedies, including use of breeding stock; and 3. begin to develop guidelines for deciding regional sources for seed stock to be used in plantations, and outreach and technology transfer services to red pine nurseries and plantation managers. Combined with spatial and geographical analyses, the molecular genetic information arising from the proposed work should allow us to better manage genetic diversity in silvicultural plantations and natural populations of red pine.

Project Methods
For the survey of the geographic pattern of genetic variation, we plan to use, in total, samples of bud tissue from 20 individuals from each of 20 populations located throughout the range of red pine (see figure 2), and to assay these for 6-10 nSSR loci and 5-9 cpSSR loci. We will use 20 (diploid genotypes) individuals (= 40 genes) for the nSSR assays, and 20 (haploid genotypes) individuals for the cpSSR assays. We already have access to enough trees from most of the 20 populations, in provenance trials managed by the MSU Department of Forest and MICHOTIP, and located near MSU. These accession sources by state include: 15 from Michigan; 9 from New York state; 5 from Minnesota; 21 from Wisconsin; 16 from New Brunswick; 12 from Ontario; 4 from three north-central counties of Pennsylvania, fairly near the Appalachian refugia; 1 from Vermont; 3 from Maine; 7 from Quebec; 3 from Nova Scotia; 11 from Manitoba; 36 from Petawa, Ontario; and 3 from New Hampshire. For most DNA isolations vegetative buds will be sampled using a modified the Guillemaut et al. (1992) protocol. For samples collected for testing Mendelian segregation, we will use seeds. For cpSSR haplotyping we will use existing markers. While there are 20 cpSSR primer pairs available, 15 have been identified as being most likely to generate polymorphic markers among conifers. For population genetic analyses, individual trees will be assayed for 9 cpSSR markers and 6 to 10 nSSR markers, giving 20 populations x 20 individuals x 9 markers or 3,600 chloroplast genotypes plus ca. 3,000 nuclear genotypes. PCR amplification of SSR markers will be done in 96-well plates, with multichannel pipettors. Individual PCR reactions using single primer pairs will be mixed to multiplex samples in single lanes on the gels. The number of loci analyzed per lane will vary from 4 to 6 or more, depending on the populational allele size ranges of individual loci. Thus for the entire survey we expect a total of 6,600 PCR reactions and about 1,500 lanes or approximately 50 sequencing gels. The statistics we will use include: 1. various spatial statistics (e.g., spatial autocorrelation statistics), which are powerful for quantifying geographic patterns of genetic variation and for identifying rates and patterns of dispersal events of the past; 2. probability of identity by descent measures, including the "coalescence" models and F-statistics; and 3. stochastic space-time models, and extensions to genotype by environment correlations, and connections to Geographic Information Systems (GIS). These methods will be applied to both cpDNA and nDNA variation. Spatial statistical analysis will proceed in a series of steps. The first step is to determine the overall degree of genetic isolation by distance, by calculating standard spatial autocorrelation statistics on the allele frequencies for both cpSSR and nSSR variation (and of haplotype frequencies of cpSSR variation). The next step is to fit these results to more detailed theoretical models. The most powerful of these is the STAR and STARMA models developed by the PI (Epperson 1993a, 1994), which can calculate the expected correlations for ANY migration model.

Progress 07/01/06 to 06/30/11

Outputs
OUTPUTS: Projects: 1. Research on theoretical population genetics, spatial and space-time models and statistics. 2. Research on the relationship of dispersal with spatial genetic structure. 3. Continuation of STARMA work, applying the computer program to datasets. 4. Interdisciplinary research projects in landscape genetics. 5. Theoretical modeling (computer simulations) of adaptation and gene flow. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: I recently began to re-enter the world of Linux. Years ago I did my own UNIX system administration, at a time when the OS was limited to terminal simulators for entering line commands only. Things have changed dramatically. Now very stable Linux operating systems can be obtained, free of charge, which have GUIs and even word processors, as well as spreadsheet programs that can be read by Excel, and a lot of other software. I decided to use an OS called Fedora, which is supported by thousands if not millions of computer scientists globally. Doing so allowed me to go from running simulations (in Fortran code) on a crippled old computer in my lab, to having it on an external hard drive that I can plug into a USB port on just about any computer and run the computer (and the simulations) on Fedora.

Impacts
The highly successful experience we had with the NCEAS working group put me squarely at the cutting edge of the new field of landscape genetics. I believe the papers we published have considerable likelihood of having major influences on how future research in the subject area is done. In particular, the paper I was lead on bridges computer simulation modeling in population genetics to future landscape genetics studies. I expect to continue to put some focus on forming collaborations and large multi-disciplinary projects. In addition, the interests of many of the working group members on climate change fit with my growing interest and knowledge about climate change and future population genetic modeling.

Publications

• Epperson BK 2012. The effects of some forms of microenvironmental selection on spatial autocorrelation of genetic variation within populations. Submitted to Theoretical Population Biology.
• Storfer A., Antolin MF, Rosenberg MS, Epperson BK, Scribner KT. 2012.More is not necessarily better: A bird's eye view of landscape genomics. (in preparation)
• M Murphy, M-J Fortin, M Dale, K Scribner, B McRae, S Spear, P Legendre, P James, B Epperson. 2012. Grappling with Graphs: A graph theoretic framework for hypothesis testing in landscape genetics

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: We have produced work that is pushing the envelop in landscape genetics, and have results that should lead to several publications, in addition to those listed elsewhere. Much of this is computer simulations. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
These results are forming the basis for how adaptative behaves and how populations may respond genetically to climate change.

Publications

• Epperson BK, McRae B, Scribner K et al. (2010) Utility of computer simulations in landscape genetics. Molecular Ecology 19, 3549-3564.
• Manel S, Joost J, Epperson BK, Holderegger H, Storfer A, Rosenberg MS, Scribner K, Bonin, A and Fortin MJ (2010) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology 19, 3760-3772.
• Anderson CD, Epperson BK, Fortin, M-J, Holdregger R, James PMA, Rosenberg MS,Scribner K, Spear S. (2010) Considering spatial and temporal scale in landscape-genetic studies of gene flow. Molecular Ecology 19, 3565-3575.
• Epperson BK (2010) Spatial correlations at different spatial scales are themselves highly correlated in isolation by distance processes Molecular Ecology Resources 10, 845-853.
• Segelbacher G, Cushman S, Epperson B, et al. (2010) Landscape Genetics: Concepts and Challenges in a Conservation Context. Conservation Genetics. 11, 375-385.

Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: We completed a number of manuscripts, initiated a new experimental project, sought funding and brought in a new doctoral student, all on the subject of adaptation and other population genetic response of pines to climate changes. PARTICIPANTS: Bryan K. Epperson (Professor), Paula Marquardt (doctoral student). TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Many of the new publications report new methodologies for making inferences about population genetic responses to climate changes.

Publications

• Bryan K. Epperson. 2010. Spatial correlations at different spatial scales are themselves highly correlated in isolation by distance processes. Molecular Ecology Resources (submitted).
• Stephanie Manel, Stephane Joost, Bryan K. Epperson, Rolf Holderegger, Andrew Storfer, Michael S. Rosenberg, Kim Scribner and Marie-Josee Fortin. 2010. Challenges in landscape genomics. Molecular Ecology (submitted).
• Corey Devin Anderson, Bryan K. Epperson, Marie-Josee Fortin, Rolf Holderegger,Patrick M. A. James, Michael S. Rosenberg, Kim T. Scribner, Stephen Spear. 2010. The importance of spatial and temporal scale in landscape genetics. Molecular Ecology (submitted).
• Epperson, B. K., F. W. Telewski and A. Willyard. 2009. Chloroplast diversity in a putative hybrid swarm of Ponderosae (Pinaceae). American Journal of Botany 96: 707-712.
• Segelbacher, G., S. A. Cushman, B. K. Epperson, et al. 2010. Landscape Genetics: concepts and challenges in a conservation context. Conservation Genetics (in press).
• Bryan K. Epperson, Brad McRae, Kim Scribner, Sam Cushman, Michael S. Rosenberg, Marie-Josee Fortin, Patrick M. A. James, Melanie Murphy, Stephanie Manel, Pierre Legendre, and Mark R. T. Dale. 2010. Utility of computer simulations in landscape genetics. Molecular Ecology (submitted).

Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: We took major steps towards coordinating our research on pine species in Michigan and elsewhere in the Great Lakes Region with the USFS Northern Research Station. We strengthened contacts and laid the groundwork for mutual research. We prepared a whitepaper on the population genetic response of pine species to climate change. We have also formed several collaborations with USFS personnel and others, and notified them about our recent findings (see publication list) regarding potentially discovering a new species of ponderosa pine. The PI (Epperson) has formed a working group through the National Center for Ecological Assesment and Synthesis on the subject of Landscape Genetics, a recently emerged field that combines environmental factors and spatial genetic structure, closely related to the population genetic response to climate change. PARTICIPANTS: the PI Epperson and graduate student Pan Yu-Wen Partner organizations: USFS Northern Research Station University of South Dakota Washington State University USFS Fire Lab, Idaho TARGET AUDIENCES: USFS NGOs Public Scientific Community PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Probably our most important finding is a potentially new species of ponderosa pine, using our molecular and population genetics analyses, combined with phylogenetic data. This species is limited to mountaintops in the desert southwest and could be endangered. Some forests have already been partially destroyed by wildfires. In addition to publishing our findings, we have notified NGOs and the USFS in the region, and this will certainly influence their choices regarding reforestation. Our fundamental works on spatial genetic structure continue to lead in that field, and for example major influence was made through the PI participating as a plenary speaker at the European Science Foundation-funded workshop "Landscape Genetics--A Conservation Approach," in Grenoble, France.

Publications

• Epperson, B.K., F.W. Telewski and A. Willyard. 2009. Chloroplast diversity in a putative hybrid swarm of Ponderosae. American Journal of Botany (in press).

Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: In addition to publications we have disseminated results on spatial genetic structure, statistical methods and applications to pines, through invited seminars and posters, including: Invited speaker, seminar "Spatial genetic structure of pines at multiple scales," Epperson, B.K., Washington State University, Pullman, October 15, 2007. Poster, "Genetic diversity in Ponderosae: challenges to management on mountain islands," Kilgore, J.S., F. Telewski and B.K. Epperson, Midwest Ecology and Evolution Conference, Kent State University, February 2007. PARTICIPANTS: Pan Yu-Wen

Impacts
Have been completing a much expanded survey of natural variation and are expanding to include the variation in both natural and managed stands of red pine and eastern white pine. Have isolated DNA, from the additional samples, and assayed them for chloroplast SSR and nuclear SSR loci. I have developed new spatial statistical methods for analying population genetics of forest trees. We have also completed collaborative works on spatial structure of many other species, including investigations of Pinus ponderosa and almond. The results from this study provide information about the natural population structure of Michigan's native conifers. This information is essential in designing management systems that preserve needed genetic variation for the future and which lead to the closest possible match with natural population dynamics and levels of biodiversity.

Publications

• Epperson, B.K. 2007. Plant dispersal, neighborhood size and isolation by distance. Molecular Ecology 16, 3854-3865.
• Luna, R. B.K. Epperson, and K. Oyama. 2007. High levels of population genetic variability and inbreeding in two Neotropical dioecious palms with contrasting life histories. Heredity 99,466-476.
• Sorkheh, K., B. Shiran, P. Martinez-Gomez, T. M. Gradziel, B.K. Epperson, and E. Asadi. 2007. Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm; genetic diversity among cultivated genotypes and related wild species of almond, and relationships with agronomic traits. Euphytica 156,327-344.
• Marquardt, P. E., C. S. Echt, B. K. Epperson and D. M. Pubanz. 2007. Genetic structure, diversity, and inbreeding of eastern white pine under different management conditions. Canadian Journal of Forest Research (in press).

Progress 01/01/06 to 12/31/06

Outputs
Have been completing a much expanded survey of natural variation and are expanding to include the variation in both natural and managed stands of red pine. Have collected the sample materials, and isolated DNA, from the additional samples, and assayed them for chloroplast SSR loci. Standard measures of heterozygosity and effective heterozygosity within populations, as well as the methods I have developed (spatial autocorrelation statistics) which describe the distribution of genetic diversity with much more power were used for the analysis. We have also completed collaborative works on spatial structure of many other species, including investigation of a hybrid zone in Pinus ponderosa. Recent information confirming self-pollination in red pine changes our overall understanding of the population's dynamics of this species and has forced us to reassess mating structure in these populations.

Impacts
The results from this study provide information about the natural population structure of Michigan's native conifers. This information is essential in designing management systems that preserve needed genetic variation for the future and which lead to the closest possible match with natural population dynamics and levels of biodiversity.

Publications

• No publications reported this period

Progress 01/01/05 to 12/31/05

Outputs
We analysed the high-throughput genotype data in studies the genetic structure of two populations of Pinus strobus in Hartwick Pines State Park. We isolated DNA from ca. 460 individuals (ca. 250 adult trees and ca. 210 seedlings), and genotyped them for five microsatellite loci, giving rise to three published refereed journal articles and an MS thesis. We analyzed data from a survey of chloroplast SSR loci, in Pinus resinosa, a species highly recalcitrant to identification of any polymorphic genetic markers, and published two papers on this work, with a third in progress. We also conducted studies on Ponderosa pine and its ecological genetic adaptation, having published another two papers. Among other production outpus, this work has raised several new theoretical and statistical issues, which have been addressed by the PI in a series of publications. Finally, We have also completed collaborative works on spatial structure of many other species, and published numerous articles.

Impacts
This project is defining the real basis of biodiversity such that forest management decisions for sustainable forest management will fully consider ecosystem dynamics and result in forests that reflect natural levels of biodiversity.

Publications

• Epperson, B. K. 2005. Mutation at high rates reduces spatial structure within populations. Molecular Ecology 14:703-710.
• Marquardt, P.E., and B. K. Epperson. 2004. Spatial and population genetic structure of microsatellites in white pine. Molecular Ecology 13: 3305-3315.
• Epperson, B. K., F. W. Telewski, A. Plovanich-Jones, and J. E. Grimes. 2001.Clinal differences and putative hybridization in a contact zone of Pinus ponderosa and P. arizonica (Pinaceae). American Journal of Botany 88:1052-1057.
• Walter, R., and B. K. Epperson. 2001. Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations. Molecular Ecology 10:103-111.
• Epperson, B. K. and M. G. Chung. 2001. Spatial genetic structure of allozyme polymorphisms within populations of Pinus strobus (Pinaceae). American Journal of Botany 88:1006-1010.
• Chung, M. G., M. Y. Chung, and B. K. Epperson. 2001. Conservation genetics of an endangered herb Hanabusaya asiatica (Campanulaceae). Plant Biology 3:42-49.
• Blanchong, J. A., K. T. Scribner, B. K. Epperson, and S. R. Winterstein. 2006. Changes in artificial feeding regulations impact white-tailed deer fine-scale spatial genetic structure. Journal of Wildlife Management (in press).
• Scribner, K. T., J. A. Blanchong, D. J. Bruggeman, B. K. Epperson, C.-Y. Lee, Y.-W. Pan, R. I. Shory, B. Williams, H. H. Prince, S. R. Winterstein, and D. R. Luukkonen. 2005. Geographical genetics: Conceptual foundations and empirical applications of spatial genetic data in wildlife management. Journal of Wildlife Management (in press).
• Epperson, B. K. 2005. Estimating dispersal from short distance spatial autocorrelation. Heredity 95:7-15.
• Walter, R., and B. K. Epperson. 2005. Geographic pattern of genetic diversity in Pinus resinosa: contact zone between descendants of glacial refugia. American Journal of Botany 92:92-100.
• Epperson, B. K. 2004. Multilocus estimation of genetic structure within populations. Theoretical Population Biology 65:227-237.
• Walter, R., and B. K. Epperson. 2004. Microsatellite analysis of spatial structure among seedlings in populations of Pinus strobus (Pinaceae). American Journal of Botany 91:549-557.
• Luna, R., B. K. Epperson, and K. Oyama. 2005. Spatial genetic structure of two sympatric neotropical palms with contrasting life histories. Heredity 95:298-305.
• Epperson, B. K. 2003. Covariances among join-count spatial autocorrelation measures. Theoretical Population Biology 64:81-87.
• Chung, M. Y., J. D. Nason, B. K. Epperson, and M. G. Chung. 2003. Temporal aspects of the fine-scale genetic structure in a population of Cinnamomum insularimontanum (Lauraceae). Heredity 90:98-106.
• Epperson, B. K. 2003. Geographical Genetics. Monographs in Population Biology 38. Princeton University Press. 356 pages.
• Epperson B. K., M. G. Chung, and F. W. Telewski. 2003. Spatial pattern of allozyme variation in a contact zone of Pinus ponderosa and P. arizonica (Pinaceae). American Journal of Botany 90:25-31.
• Epperson, B. K. 2003. Gustave Malecot, pp 792-793, in Nature Encyclopedia of the Human Genome Vol. 3, Nature Publishing Group, New York.
• Epperson, B. K. 2002. Spatial-temporal properties of gene genealogies in geographically structured populations,pp. 165-182 in (M. Slatkin and M. Veuille, eds.) Modern Developments in Theoretical Population Genetics. Oxford: Oxford University Press.
• Chung, M. Y., B. K. Epperson, and M. G. Chung. 2003. Genetic structure of age classes in Camellia japonica (Theaceae). Evolution 57:62-73.

Progress 01/01/04 to 12/31/04

Outputs
Graduate students = 2 We have made significant progress in finishing several published studies on experimental analyses of spatial structure of genetic variation in Pinus strobus, Pinus ponderosa, Pinus resinosa, and other species. We have completed several theoretical studies on spatial statistics. In addition, we have completed a statistical software package that conducts true space-time analyses and applied it to several datasets.

Impacts
Our projects are having substantial impacts on furthering the field of plant population genetics, guiding genetic conservation efforts, and expanding and refining statistical methodology.

Publications

• Epperson, B. K. 2004. Multilocus estimation of genetic structure within populations. Theoretical Population Biology 65:227-237.
• Walter R., and B. K. Epperson. 2004. Microsatellite analysis of spatial structure among seedlings in populations of Pinus strobus (Pinaceae). American Journal of Botany 91:549-557.
• Marquardt, P.E., and B. K. Epperson. 2004. Spatial and population genetic structure of microsatellites in white pine. Molecular Ecology 13: 3305-3315

Progress 01/01/03 to 12/31/03

Outputs
Graduate students = 2, and one postdoctoral student. We have made significant progress in finishing several published studies on experimental analyses of spatial structure of genetic variation in Pinus strobus, Pinus ponderosa, Pinus resinosa, and other species. We have completed several theoretical studies on spatial statistics. In addition, we have completed a statistical software package that conducts true space-time analyses.

Impacts
Our projects are having substantial impacts on furthering the field of plant population genetics, guiding genetic conservation efforts, and expanding and refining statistical methodology.

Publications

• Walter, R., and B. K. Epperson. 2003. Microsatellite analysis of spatial structure among seedling in populations of Pinus strobus (Pinaceae). American Journal of Botany (in press)
• Epperson, B. K. 2003. Covariances among join-count spatial autocorrelation measures. Theoretical Population Biology 64:81-87.
• Epperson, B. K. 2003. Geographical Genetics. Monographs in Population Biology 38. Princeton University Press. 356 pages.
• Epperson, B. K. 2003. Gustave Malecot. Nature Encyclopedia of the Human Genome, Nature Publishing Group, New York. (in press)

Progress 01/01/02 to 12/31/02

Outputs
Graduate Students = 2. We have published several articles (listed either as in print or in press below) on the spatial structure of genetic variation, particularly in Pinus species. Additional papers on the works on Pinus strobus have been submitted or are presently being written.

Impacts
This project is characterizing the actual genetic basis of diversity in important forest trees, and it aids management decisions for sustainability of natural levels of diversity.

Publications

• Epperson, B. K. 2002. Spatial-temporal properties of gene genealogies in geographically structured populations. Pages 165-182, in M. Slatkin and M. Veuille, eds., Modern Developments in Theoretical Population Genetics. Oxford: Oxford University Press.
• Epperson, B.K. 2003. Covariances among join count spatial autocorrelation measures. Theoretical Population Biology (in press)
• Chung, M. Y., B. K. Epperson, and M. G. Chung. 2003. Genetic structure of age classes in Camellia japonica (Theaceae). Evolution (in press)
• Chung, M. Y., J. D. Nason, B. K. Epperson, and M. G. Chung. 2003. Temporal aspects of the fine-scale genetic structure in a population of Cinnamomum insularimontanum (Lauraceae). Heredity (in press)
• Epperson B. K., M. G. Chung, and F. W. Telewski. 2003. Spatial pattern of allozyme variation in a contact zone of Pinus ponderosa and P. arizonica (Pinaceae). American Journal of Botany (in press).
• Epperson, B. K. 2003. Gustave Malecot. Encyclopedia of the Human Genome, Nature Publishing Group. (in press)

Progress 01/01/01 to 12/31/01

Outputs
Graduate Students = 2 We are writing several manuscripts for a study of the genetic structure of two populations of Pinus strobus in Hartwick Pines State Park. Both graduate students are presently writing there theses, based on these projects. We have also presented two posters at meetings. In addition, one postdoc has been funded on the project and is also preparing a publication, and we have another two papers already published.

Impacts
This project is defining the real basis of biodiversity such that forest management decisions for sustainable forest management will fully consider ecosystem dynamics and ersult in forests that reflect natural levels of biodiversity.

Publications

• No publications reported this period

Progress 01/01/00 to 12/31/00

Outputs
Graduate students = 3 We have completed the high-throughput genotyping for studying the genetic structure of two populations of Pinus strobus in Hartwick Pines State Park. We isolated DNA from ca. 460 individuals (ca. 250 adult trees and ca. 210 seedlings), and genotyped them for five microsatellite loci. We finished the analysis of the data from the adults and Ms. Paula Marquardt (an MS student) is preparing her thesis based on these data, has given two posters at meetings, and is also preparing a publication. We are just beginning to analyze the data for the seedlings, and will prepare at least one additional publication based on these. In addition, a collaborator and I conducted an isozyme analysis of the same populations, and the paper (Epperson and Chung 2001) was accepted without revisions by the American Journal of Botany. We completed a survey of chloroplast SSR loci, in Pinus resinosa, a species highly recalcitrant to identification of any polymorphic genetic markers. A paper (Walter and Epperson 2001) based on these results was accepted without revision in Molecular Ecology. We are presently conducting a much-expanded survey, and have already collected the sample materials, and isolated DNA, from more than 400 additional samples, and are presently assaying them for ten chloroplast SSR loci. We have also begun a study of insular populations of Pinus strobus in the Beaver Island Archipelago, the basis of a doctoral dissertation by Mr. Eric Myers. Eric has collected materials from over 400 individuals and almost finished isolating DNA from these, and is currently beginning to assay these for 6 chloroplast SSR loci, and has already analyzed them for isozyme loci. We have also completed collaborative works on spatial structure of many other species, including investigation of a hybrid zone in Pinus ponderosa. Again, the first paper from this study (Epperson et al. 2001) was accepted without revision by the American Journal of Botany.

Impacts
This project is defining the real basis of biodiversity such that forest management decisions for sustainable forest management will fully consider ecosystem dynamics and ersult in forests that reflect natural levels of biodiversity.

Publications

• Epperson, B. K. 2000. Spatial genetic structure and non-equilibrium demographics within plant populations. Plant Species Biology 15:269-279.
• M. G, Chung, and B. K. Epperson. 2000. Clonal and spatial genetic structure in Eurya emarginata (Theaceae). Heredity 84:170-177.
• Chung, M. G. and B. K. Epperson. 2000. Spatial genetic structure of allozyme polymorphisms in a population of Eurya japonica (Theaceae). Silvae Genetica 49:1-4.
• Chung, M. G., J. M. Chung, M. Y. Chung, and B. K. Epperson. 2000. Spatial distribution of allozyme polymorphisms following clonal and sexual reproduction in populations of Rhus javanica (Anacardiaceae). Heredity 84:178-185.
• Epperson, B. K. 2000. Spatial and space-time correlations in ecological models. Ecological Modeling 132:63-76.

Progress 01/01/99 to 12/31/99

Outputs
Graduate students =3 We have worked up all of the details and now have an efficient system for high-throughput genotyping for studying the genetic structure of populations of Pinus strobus. This includes DNA isolation, PCR-reactions and sequencing gels. We isolated DNA from ca. 460 individual, and finished the PCR and genotyping of one-half of these, for eight highly polymorphic microsatellite loci. We also collected cones this year for future analysis of the mating system. We finished preliminary analysis of nuclear SSR loci, and finished an initial survey of cholorplast SSR loci, in Pinus resinosa, a species highly recalcitrant to identification of any polymorphic genetic markers. We have also completed collaborative works on spatial structure of manyother species.

Impacts
This project will define the native vairiability in natural populations of pines in Michigan, help to more accurately quantify biodiversity, and will result in forest management systems that more closely model natural populations.

Publications

• Epperson, B. K. 1999. Gene genealogies in geographically structured populations. Genetics 152797-806.
• Epperson, B. K. 1999. Gustave Malecot, 1911-1998 Population genetics founding father. Genetics 15:477-484.
• Epperson, B. K., Z. Huang, and T.-Q. Li. 1999. Measures of spatial genetic structure of multiallelic loci. Genetical Research Cambridge 73:251-261.
• Chung, M. G. and B. K. Epperson. 1999. Spatial distribution of clonal and sexual reproduction in populations of Adenophora grandiflora (Campanulaceae). Evolution 53:1068-1078.

Progress 01/01/98 to 12/31/98

Outputs
Graduate students = 4 Sample collection was initiated and the best sample materials were identified. In addition we have set up the molecular capabilities of the lab, including allozymes and PCR, and we have begun to analyze the samples. Inaddition, we have been working on the first ever combination of genetic diversity and ecological diversity measures into a combined measure. We are presently also studying the mathematical and statistical properties of such measures. Allozyme diversity in jack pine is extensive, and will be assayed using well-established methods of seed extraction, storage and stratification. We will use standard measures of heterozygosity and effective heterozygosity within populations, as well as the methods I have developed (spatial autocorrelation statistics) which describe the distribution of genetic diversity with much more power. To examine the geographic distributions, rather than use the classic Nei's diversity measures (which require many questionable assumptions), we will use F-statistics, and spatial correlations statistics which I have developed.

Impacts
(N/A)

Publications

• Chung, M. Y., H. G. Chung, M. G. Chung, and B. K. Epperson. 1998. Spatial genetic structure in populations of Cymbidium goeringii. Genes and GeneticSystems. (in press).
• Epperson, B. K., Z. Huang, and T.-Q. Li . 1998. Spatial genetic structure of multiallelic loci. Genetical Research Cambridge (in press).
• Epperson, B. K. 1998. Spatial and space-time correlations in ecological models. Ecological Modelling (in press).

Progress 01/01/97 to 12/31/97

Outputs
number of grad students = 3 Using modern molecular genetic methods (for allozymes, RFLP's, and RAPD's) to reveal the basic genetics, and quantitative trait loci analyzes and spatial statistical analyzes to reveal the quantitative and population genetic basic of important traits. Studies were initiated on Michigan's native pine species, with a focus on identifying patterns of variation in red pine. Trees located in refugia outside the main body of the range were visited and sampled. PCR methodology was developed to enhance the power of the research methods. Microsatellite markers are being identified for red pine. Data will be used to better model patterns of gene flow and dispersal that produced the current geographic distribution of these species. Data will be collected from natural populations, managed populations and in germplasm collections. We will use this information to prescribe genetic aspects for managing Michigan's native pine resources.

Impacts
(N/A)

Publications

• Epperson, B.K. and T.-Q. Li. 1997. Gene dispersal and genetic structure. Evolution 51:672-681.
• Epperson, B.K. and E. Alvarez-Buylla. 1997. Spatial autocorrelation analysis of family structure in multiple life stages of Cecropia obtusifolia. Evolution 51:275-282.

Progress 01/01/96 to 12/30/96

Outputs
Using modern molecular genetic methods (for allozymes, RFLP's, and RAPD's) to reveal the basic genetics, and quantitative trait loci analyses and spatial statistical analyses to reveal the quantitative and population genetic basic of important traits. We will examine these aspects in natural populations, managed populations and in germplasm collections. We will use this information to prescribe genetic aspects for managing Michigan's native pine industry. Graduate students: 1.

Impacts
(N/A)

Publications