Quotes of the Month

"It is easy without any very profound logical analysis to perceive the difference between a succession of favorable deviations from the laws of chance, and on the other hand, the continuous and cumulative action of these laws. It is on the latter that the principle of natural selection relies." - R. A. Fisher (1958). The Genetical Theory of Natural Selection.

"Far better an approximate answer to the right question, which is often vague, than an exact answer to the wrong question, which can always be made precise." - J. W. Tukey (1962). Ann. Math. Stat. 33: 1-67.
Academic Pedigree

I grew up in Napa, California and attended Humboldt State University where I graduated with a Bachelor of Science in Biology and minors in Biometry, Botany and Geography. In 2001, I joined the laboratory of Benjamin Hall in the Department of Biology located at the University of Washington. I completed my Ph.D. in 2006 and moved to a Postdoctoral Fellow position in the laboratories of David Neale and Charles Langley in the Section of Evolution and Ecology located at the University of California - Davis. I joined the Department of Biology at Virginia Commonwealth University as an Assistant Professor during August of 2011.
Research Interests

Biological systems are complex and continuous hierarchies ranging from molecules to collections of species. This statement is found in almost every biological textbook published during the last half century. Only recently, however, have biologists been able to form testable hypotheses that span the link between genotypes, phenotypes and the ecological and evolutionary contexts in which those links occur. Such multilevel analyses are based upon the integration of several traditional fields of biological enquiry – genetics, molecular biology, population genetics, population biology, ecology and phylogenetics.

My research addresses several fundamental questions in population genetics and phylogeography: (1) How does genetic diversity within plant populations vary in time and space? (2) What is the extent and distribution of adaptive genetic variation within plant genomes? (3) What are the historical factors affecting floristic development of North America? Often answering these questions requires novel uses of existing methodologies or creation of new methods, which also is a research interest of mine. Additional musings about the nature of biological groups and how they are studied and used in biological inference can be found here.
Available Positions

I am looking for graduate students (M.S. or Ph.D.) and postdoctoral associates. If you are interested in opportunities at the graduate student level, please visit the website for the Department of Biology at Virginia Commonwealth University or click on one of the following links: M.S. or Ph.D.

If you are interested in a position at the postdoctoral level, please e-mail me directly at aeckert2@vcu.edu. At this time, I have no funding for postdoctoral associates, but am happy to help write grant applications to obtain funding or to sponsor those with funding.

Potential students or postdoctoral associates should read my research interests as well as the following statements about my approach to mentoring and my expectations for students and postdoctoral associates.
Publications

Submitted

Baker, P. A., Fritz, S. C., C. W. Dick, A. J. Eckert, B. K. Horton, S. Manzoni, C. C. Ribas, C. N. Garzione, and D. S. Battisti. The emerging field of geogenomics: constraining geological problems with genetic data.

Eckert, A. J., P. E. Maloney, D. R. Vogler, C. E. Jensen, A. Delfino Mix, and D. B. Neale. Ecological genetics of sugar pine (Pinus lambertiana, Pinaceae) populations located in the Lake Tahoe Basin, USA.

In Press or Print

DeGiorgio, M., J. Syring, A. J. Eckert, A. I. Liston, R. Cronn, D. B. Neale, and N. A. Rosenberg. 2014. An empirical evaluation of species tree inference strategies using a multilocus data set from North American pines. BMC Evolutionary Biology. In Press.

Eckert, A. J., J. L. Wegrzyn, J. D. Liechty, J. M. Lee, W. P. Cumbie, J. M. Davis, B. Goldfarb, C. A. Loopstra, S. R. Palle, T. Quesada, C. H. Langley, and D. B. Neale. 2013. The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics 195: 1353-1372. Cover Highlight.

Bashalkhanov, S., A. J. Eckert, and O. P. Rajora. 2013. Genetic signatures of natural selection in response to air pollution in red spruce (Picea rubens, Pinaceae). Molecular Ecology 22: 5877-5889.

Eckert, A. J., A. D. Bower, K. D. Jermstad, J. L. Wegrzyn, B. J. Knauss, J. V. Syring, and D. B. Neale. 2013. Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus). Molecular Ecology 22: 5635-5650.

Palle, S. R., C. M. Seeve, A. J. Eckert, J. L. Wegrzyn, D. B. Neale, C. A. Loopstra. 2013. Association of loblolly pine xylem development gene expression with single nucleotide polymorphisms. Tree Physiology 33: 763-774.

Sork, V. L., S. N. Aitken, R. J. Dyer, A. J. Eckert, P. Legendre, and D. B. Neale. 2013. Putting the landscape into the genomics of forest trees: Approaches for understanding local adaptation and population responses to a changing climate. Tree Genetics and Genomes 9: 901-911.

Mosca, E., A. J. Eckert, E. Di Pierro, D. Rocchini, N. La Porta, P. Belletti, and D. B. Neale. 2012. The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps. Molecular Ecology 21: 5530-5545.

Eckert, A. J., H. Shahi, S. L. Datwyler, and D. B. Neale. 2012. Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae). American Journal of Botany 99: 1323-1334.

Chen, J., T. Kallman, X. Ma, N. Gyllenstrand, G. Zaina, M. Morgante, J. Bousquet, A. Eckert, J. Wegrzyn, D. Neale, U. Lagercrantz and M. Lascoux. 2012. Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression for photoperiodic genes in Norway spruce (Picea abies). Genetics 191: 865-881.

Eckert, A. J. and R. J. Dyer. 2012. Defining the landscape of adaptive genetic diversity. Molecular Ecology 21: 2836-2838. (commentary).

Mosca, E., A. J. Eckert, J. D. Liechty, J. L. Wegrzyn, N. La Porta, G. G. Vendramin, and D. B. Neale. 2012. Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests. Evolutionary Applications 5: 762-775.

Eckert, A. J., J. L. Wegrzyn, W. P. Cumbie, B. Goldfarb, D. A. Huber, V. Tolstikov, O. Fiehn, and D. B. Neale. 2012. Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome. New Phytologist 193: 890-902.

Chancerel, E., C. Lepoittevin, G. Le Provost, Y. C. Lin, J. P. Jaramillo-Correa, A. J. Eckert, J. L. Wegrzyn, D. Zelenika, A. Boland, J. M. Frigerio, P. Chaumeil, P. Garnier-Géré, C. Boury, D. Grivet, S. C. González-Martínez, P. Rouzé, Y. Van de Peer, D. B. Neale, M. T. Cervera, A. Kremer, and C. Plomion. 2011. Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine. BMC Genomics 12: 368.

Maloney, P. E., D. R. Vogler, A. J. Eckert, C. E. Jensen, and D. B. Neale. 2011. Population biology of sugar pine (Pinus lambertiana Dougl.) with reference to historical disturbances in the Lake Tahoe Basin: Implications for restoration. Forest Ecology and Management 262: 770-779.

Cumbie, W. P., A. J. Eckert, J. L. Wegrzyn, R. Whetten, D. B. Neale and B. Goldfarb. 2011. Association genetics of carbon isotope discrimination, height, and foliar nitrogen in a natural population of Pinus taeda L. Heredity 107: 105-114.

Jermstad, K. D., A. J. Eckert, J. L. Wegrzyn, A. D. Mix, D. A. Davis, D. C. Burton and D. B. Neale. 2011. Comparative mapping in Pinus: Sugar pine (Pinus lambertiana Dougl.) and loblolly pine (Pinus taeda). Tree Genetics and Genomes 7: 457-468.

Eckert, A. J. 2011. Seeing the forest for the trees: Statistical phylogeography in a changing world. New Phytologist 189: 894-897. (Commentary).

Palle, S. R., C. M. Seeve, A. J. Eckert, W. P. Cumbie, B. Goldfarb and C. A. Loopstra. 2011. Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.). Tree Genetics and Genomes 7: 193-206.

Quesada, T., V. Gopal, W. P. Cumbie, A. J. Eckert, J. L. Wegrzyn, D. B. Neale, B. Goldfarb, D. A. Huber, G. Casella and J. M. Davis. 2010. Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.). Genetics 186: 677–686.

Wegrzyn, J. L., A. J. Eckert, M. Choi, J. M. Lee, B. J. Stanton, R. Sykes, M. Davis, C. J. Tsai and D. B. Neale. 2010. Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytologist 188: 515-532.

Eckert, A. J., A. D. Bower, S. C. González-Martínez, J. L. Wegrzyn, G. Coop and D. B. Neale. 2010. Back to nature: Ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Molecular Ecology 19: 3789-3805.

Eckert, A. J., J. van Heerwaarden, J. L. Wegrzyn, C. D. Nelson, J. Ross-Ibarra, S. C. González-Martínez and D. B. Neale. 2010. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.

Eckert, A. J., M. L. Eckert and B. D. Hall. 2010. Effects of historical demography and ecological context on spatial patterns of genetic diversity within foxtail pine (Pinus balfouriana, Pinaceae) stands located in the Klamath Mountains, California. American Journal of Botany 97: 650-659.

Eckert, A. J., J. D. Liechty, B. R. Tearse, B. Pande and D. B. Neale. 2010. DnaSAM: Software to perform neutrality testing for large datasets with complex null models. Molecular Ecology Resources 10: 542-545.

Eckert, A. J., J. L. Wegrzyn, B. Pande, K. D. Jermstad, J. M. Lee, J. D. Liechty, B. R. Tearse, K. V. Krutovsky and D. B. Neale. 2009. Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold-hardiness in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii). Genetics 183: 289-298.

Olmstead, R. G., M. L. Zjhra, L. G. Lohmann, S. O. Grose and A. J. Eckert. 2009. A molecular phylogeny and classification of Bignoniaceae. American Journal of Botany 96: 1731-1743.

Eckert, A. J., A. D. Bower, B. Pande, K. D. Jermstad, K. V. Krutovsky, J. B. St. Clair and D. B. Neale. 2009. Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182: 1289-1302.

Eckert, A. J., B. Pande, E. S. Ersoz, M. H. Wright, V. K. Rashbrook, C. M. Nicolet and D. B. Neale. 2009. High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genetics and Genomes 5: 225-234.

Eckert, A. J. and B. C. Carstens. 2008. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating a species phylogeny in the presence of gene flow. Molecular Phylogenetics and Evolution 49: 832-842.

Eckert, A. J., B. R. Tearse, and B. D. Hall. 2008. A phylogeographical analysis of the range disjunction for foxtail pine (Pinus balfouriana, Pinaceae): the role of Pleistocene glaciation. Molecular Ecology 17: 1983-1997.

Eckert, A. J. and M. L. Eckert. 2007. Effects of aspect, elevation, and substrate type on size class distributions of foxtail pine (Pinus balfouriana, Pinaceae) in the Klamath Mountains, California. Madroño 54: 117-125.

Eckert, A. J. 2006. Influence of substrate type and microsite availability on the persistence of foxtail pine (Pinus balfouriana, Pinaceae) in the Klamath Mountains, California. American Journal of Botany 93: 1615-1624.

Eckert, A. J. and B. D. Hall. 2006. Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae) – Phylogenetic tests of fossil-based hypotheses. Molecular Phylogenetics and Evolution 40: 166-182.

del Moral, R. and A. J. Eckert. 2005. Colonization of volcanic deserts from productive patches. American Journal of Botany 92: 27-36.

Goetsch, L., A. J. Eckert, and B. D. Hall. 2005. The molecular systematics of Rhododendron (Ericaceae): A phylogeny based upon RPB2 gene sequences. Systematic Botany 30: 616-626.

Eckert, A. J. and J. O. Sawyer. 2002. Foxtail pine importance and conifer diversity in the Klamath Mountains and southern Sierra Nevada, California. Madroño 49: 33-45.

Book Chapters and Technical Reports

Jermstad, K. D., A. J. Eckert, J. L. Wegrzyn, B. B. Kinloch, A. D. Mix, D. A. Davis, D. C. Burton and D. B. Neale. 2011. A sugar pine consensus map: Comparative mapping between the Pinus subgenus Pinus and the subgenus Strobus. USDA National Forest Service, Rocky Mountain Research Station Proceedings Publication.

Bower, A. D., S. C. McLane, A. J. Eckert, S. Jorgensen, A. Schoettle, S. Aitken. (in press). Conservation genetics of high elevation five-needle pines. USDA National Forest Service, Rocky Mountain Research Station Proceedings Publication.

González-Martínez S. C., S. Dillon, P. Garnier-Géré, K. Krutovsky, R. Alía, C. Burgarella, A. J. Eckert, M. R. García-Gil, D. Grivet, M. Heuertz, J. P. Jaramillo-Correa, M. Lascoux, D. B. Neale, O. Savolainen, Y. Tsumura and G. G. Vendramin. 2011. Patterns of nucleotide diversity and association mapping. In: "Conifers" (Eds. C. Plomion & J. Bousquet). Series on "Genomics of Industrial Crops" (Ed. C. Kole). Science Publishers, Inc., New Hampshire; Edenbridge Ltd., British Isles.

Published abstracts and Popular Articles

Eckert, A. J. 2011. Population and conservation genomics of forest trees: seeing the forest for the trees. BMC Proceedings 5(Suppl 7): I2. Not peer reviewed.

Eckert, A. J. 2010. Landscape genomics – Is it landscape genetics on steroids or something novel? Conifer Translational Genomics Network Newsletter. Issue 03, 06/2010, pgs. 7-8.

Li, X. B., B. Kahn, R. Sykes, J. L. Wegrzyn, A. Eckert, V. Gopal, D. A. Huber, J. M. Davis, G. Casella, and D. B. Neale. 2009. Association and Quantitative Genetics of Wood Properties in Loblolly Pine. 30th Southern Forest Tree Improvement Conference Proceedings. Not peer reviewed.

Eckert, A. J., J. L. Wegrzyn, J. M. Lee, J. D. Liechty, K. Stevens, K. D. Jermstad, C. D. Nelson, S. C. Gonzalez-Martinez, C. H. Langley, and D. B. Neale. 2009. The Integration of Resequencing, Genotyping and Population Structure Data Reveals Patterns of Adaptive Genetic Diversity in Loblolly Pine (Pinus taeda L.). 30th Southern Forest Tree Improvement Conference Proceedings. Not peer reviewed.

Tsang, K., A. J. Eckert, J. L. Wegrzyn, J. M. Lee, W. P. Cumbie, V. Tolstikov, B. Goldfarb, and D. B. Neale. 2009. Association Genetics of the Loblolly Pine Metabolome. 30th Southern Forest Tree Improvement Conference Proceedings. Not peer reviewed.

Stambolia-Kovach, A., J. L. Wegrzyn, I. Korf, A. J. Eckert, M. Yandell, C. Holt, G. E. Bruening, D. R. Cook, C. H. Langley, and D. B. Neale. 2009. Sequencing and Annotation of 10 Loblolly Pine BACs. 30th Southern Forest Tree Improvement Conference Proceedings. Not peer reviewed.

Palle, S., C. Seeve, A. Eckert, J. Wegrzyn, W. P. Cumbie, B. Goldfarb, D. B. Neale, and C. Loopstra. 2009. Association Studies of Wood Development and Stress Response Genes in Loblolly Pine. 30th Southern Forest Tree Improvement Conference Proceedings. Not peer reviewed.

Pande, B., B. Tearse, J. Wegrzyn, J. Lee, A. Eckert, K. V. Krutovsky, and D. B. Neale. 2007. Nucleotide diversity and neutrality testing in genes involved in adaptation in Douglas-fir. 29th Southern Forest Tree Improvement Conference Proceedings. Not peer reviewed.

Eckert, A. J., J. M. Lee, J. L. Wegrzyn, K. Stevens, C. H. Langley, and D. B. Neale. 2007. ADEPT2: Resequencing, SNP Discovery, and Association Studies for Loblolly Pine. 29th Southern Forest Tree Improvement Conference Proceedings. Not peer reviewed.

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