David Lowry: Difference between revisions

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[[Image:Lowry_field_2.JPG|thumb|right|In the field]]
Michigan State University: Assistant Professor                        2014-Present


==About Me==
California State University, Monterey Bay: Assistant Professor          2014


The University of Texas at Austin: USDA NIFA Postdoctoral Fellow,    2010-2013


[[Image:Evolution_cover.jpg|thumb|left|Photo by David Lowry]]
Duke University:                         PhD,                        2004-2010


[http://web.me.com/davidbryantlowry/Site/Welcome.html I am a new postdoctoral researcher] at the [http://www.utexas.edu/ University of Texas at Austin] working on the genetics of adaptation and drought tolerance with the [[Texas Switchgrass Collaborative]] (''Panicum'').  The aims of this project are to understand the evolutionary genetic and genomic mechanisms responsible for abiotic stress tolerance in this group of grasses and to leverage this knowledge to eventually create higher yielding bioenergy crops that will require minimal water inputs.  This is an important goal, as there is often a [http://www.scientificamerican.com/article.cfm?id=the-future-of-fuel trade-off between alternative energy sources], such as biofuels, with ever diminishing water resources.
The University of California, Berkeley:   BS,                        1997-2001


The focus of my PhD dissertation research at Duke University was directed toward understanding the genetics of adaptation and speciation across the natural landscape.  To this end, I chose to study how divergent adaptation of the yellow monkey flower (''Mimulus guttatus''), to the coast versus inland habitat, contributes to reproductive isolation.  I used a combination of QTL mapping and candidate gene strategies to determine the genetic mechanisms that underlie the divergence of morphological and life-history traits between coast and inland ''Mimulus guttatus''.  Further, I carried out reciprocal transplant experiments and population genetic analysis to demonstrate that coast and inland ''Mimulus'' are locally adapted and reproductively isolated.  I also conducted a more recent reciprocal transplant experiment with near isogenic lines to test hypotheses of local adaptation and introgression between ecogeographic races.  In addition, I conducted genetic analysis of flowering time under different light conditions, anthocyanin production in vegetative tissues, and ion accumulation.  Finally, I was involved with multiple aspects of the ''Mimulus guttatus'' genome project.
==Research Interests==


==Publications==
[[Image:Perdenales.jpg|thumb|left|Switchgrass in its native riparian habitat in central Texas]]
[[Image:Lowry_field_2.JPG|thumb|right|Field experiment with ''Mimulus guttatus'']]
 
'''The genetics of adaptation and speciation'''


[[Image:PhilTransCover.jpg|thumb|right|Photo by David Lowry]]
Adaptation is the most fundamental way that the environment can change the phenotypes of organisms.  Adaptations can also lead to the formation of reproductive isolating barriers, which are the building blocks of new species.  I am very interested in understanding the genetic underpinnings of reproductive isolation at various stages in the speciation process.


Lowry, D. B. Ecotypes and the controversy over stages in the formation of new species. (2012) Biological Journal of the Linnean Society. ''Accepted''
Understanding adaptation is also crucial to predicting how organisms will respond to future global change and will help inform management decisions as well as guide future agricultural breeding.


Lowry, D. B., C. T. Purmal, E. Meyer, T. E. Juenger.  (2012) Microsatellite markers for the native Texas perennial grass,  ''Panicum hallii'' (Poaceae).  ''In press''
'''Landscape evolutionary genomics'''


Lowry, D. B., C. S. Sheng, Z. Zhu, T. E. Juenger, B. Lahner, D. E. Salt, J. H. Willis. (2012) Mapping of ionomic traits in ''Mimulus guttatus'' reveals Mo and Cd QTLs that colocalize with MOT1 homologues.  PLoS One. ''Accepted''
One of the core goals of my research program is to understand how the natural landscape molds the genomes of organisms through adaptation. To that end, I am using a combination of genetic mapping and genome sequencing approaches to identify genes involved with adaptation to the heterogeneity of the natural landscape. During my dissertation, I focused on how adaptive alleles in ''Mimulus guttatus'' are spread across the landscape and what phenotypic effects they have in different environments across western North America.  Currently, I am developing ''Panicum'' grasses as a model system to understand adaptation along a longitudinal soil moisture cline across Southwestern United States and a latitudinal temperature cline across the Great Plains. Our lab recently [http://www.utexas.edu/news/2012/08/02/biologist-grant-study-potential-biofuel-crops/ received funding from the Department of Energy] to develop ''Panicum hallii'' as a model system for local adaptation and bioenergy research. 


Lowry D. B., C.S. Sheng, J. R. Lasky, J.H. Willis. (2012) Five anthocyanin polymorphisms are associated with a R2R3-MYB cluster in ''Mimulus guttatus''. American Journal of Botany.  ''In press''
[[Image:Diversity.JPG|thumb|left|Phenotypic diversity of Switchgrass, ''Panicum virgatum'']]
[[Image:Field_2012.JPG|thumb|right|Field experiment with ''Panicum hallii'']]


Lowry, D. B., R. Hopkins. (2012) “Speciation and Natural Selection.” Invited book chapter in The Princeton Guide to Evolution, edited by Jonathan Losos.  Princeton, NJ: Princeton University Press.  ''In press''
'''Using evolutionary biology to improve bioenergy crops'''


[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000500 '''Lowry, D.B.,''' J. H. Willis. (2010) A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation.  PLoS Biology 8: e1000500]
Civilization is built on a foundation of domesticated grasses. Without those grasses (corn, wheat, rice, oats, barley, sorghum) there would be no ballet and human beings would never of landed on the moon.  Plant breeders have quietly worked in the shadows to increase the yield of crops and in turn maintain our modern world.


[http://www3.interscience.wiley.com/journal/123501089/abstract Hall M. C., '''D. B. Lowry''', J. H. Willis.  (2010).  Hall M. C., D. B. Lowry, J. H. Willis.  (2010)  Is local adaptation in ''Mimulus guttatus'' caused by trade-offs at individual loci?  Molecular Ecology. 19: 2739-2753]
Now, there may actually be potential to domesticate a new set of grass species to use to help combat the growing energy problem. My research is focused understanding the factors involved in local adaptation in the bioenergy crop switchgrass (''Panicum virgatum'').  Loci involved in local adaptation are likely to be of high value to crop breeders interested in improving drought, heat, cold, herbivore, and disease tolerance.


[http://rsbl.royalsocietypublishing.org/content/early/2010/01/22/rsbl.2009.0969.full '''Lowry, D. B.''' (2010) Landscape evolutionary genomics.  Biology Letters. 6: 502-504]
==Publications==


[http://www.springerlink.com/content/vm4456721023284g/ Wu, C. A., '''D. B. Lowry''', L. I. Nutter, J. H. Willis.  (2010)  Natural variation for drought response in the ''Mimulus guttatus'' species complex.  Oecologia 162: 23-33]  
'''PDFs for publications available through my''' [http://davidbryantlowry.wordpress.com/publications/ '''website''']


[http://www3.interscience.wiley.com/journal/122462935/abstract '''Lowry, D. B.''', M. C. Hall, D. E. Salt, J. H. Willis. (2009). Genetic and physiological basis of adaptive salt tolerance divergence between coastal and inland ''Mimulus guttatus.''  New Phytologist  183: 776-788]
==Important Things==


[http://rstb.royalsocietypublishing.org/content/363/1506/3009.long '''Lowry, D. B.''', J. L. Modliszewski, K. M. Wright, C. A. Wu, J. H. Willis.  (2008).  The strength and genetic basis of reproductive isolating barriers in flowering plants. Philosophical Transactions of the Royal Society B 363: 3009-3021]
*[http://davidbryantlowry.wordpress.com/ My website]


[http://www3.interscience.wiley.com/journal/120775240/abstract '''Lowry, D. B.''', R. C. Rockwood, J. H. Willis.  (2008).  Ecological reproductive isolation of coast and inland races of ''Mimulus guttatus''. Evolution 62: 2196-2214]
*[http://lowrylab.wordpress.com/david-lowry-cv/ David Lowry CV]


[http://www.nature.com/hdy/journal/v100/n2/abs/6801018a.html Wu, C. A., '''D. B. Lowry''', A. M. Cooley, K. M. Wright, Y. W. Lee, and J. H. Willis.  (2008).  ''Mimulus'' is an emerging model system for the integration of ecological and genomic studies.  Heredity 100: 220-230.]
*[http://scholar.google.com/citations?view_op=list_works&hl=en&user=yp5xdBEAAAAJ&gmla=AJsN-F6DFaPZ9A0TNBwOFnsWZf9Y9S7rGntDIzs1ZOqg52GhHzGJ090M-xxUubHEHF3dyXE6XlN-jmJ1uYNJiAULSHsEkKAaqniu606ZwKxaDjIwB3wfiIkspwU-gntSRaYs7bNl5Mmy Google Scholar Citations ]


==Important Things==
*[https://github.com/davidbryantlowry Programming Scripts on Github]


* [http://web.me.com/davidbryantlowry/Site/Welcome.html My Website]
*'''Contact Info:''' You can contact me at davidbryantlowry@gmail.com.
*'''Contact Info:''' You can contact me at davidbryantlowry@gmail.com.


*Make sure to check out the [[Mimulus Community]] and the [[Texas Switchgrass Collaborative]].
*Make sure to check out the [[Mimulus Community]] and the [[Texas Switchgrass Collaborative]].
==Bioinformatic/Statistical Software and Resources==
*[http://www.phytozome.net/ Phytozome]
*[http://home.clara.net/sisa/bonfer.htm Bonferroni Correction Calculator]
*[http://www.fruitfly.org/annot/apollo/ Apollo]
*[http://globin.cse.psu.edu/html/docs/sim4.html sim4]
*[http://genome.ucsc.edu/ BLAT]
*[http://www.ncbi.nlm.nih.gov/blast/mmtrace.shtml NCBI Trace Archives]
*[http://www.ebi.ac.uk/clustalw/ ClustalW]
*[http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Primer 3]
*[http://faculty.washington.edu/jstorey/qvalue/ Q-Value calculator]
*[http://labs.rajdye.com/how-to-install-mysql-server-on-osx-10-6-snow-leopard/ Install MySQL on a mac]
==Analysis of fitness data==
*[http://www.stat.umn.edu/geyer/aster/ ASTER]
==Other useful sites==
*[http://geography.about.com/library/blank/blxusx.htm Blank Outline Maps] that can be used to make figures.

Latest revision as of 07:10, 16 November 2014

Michigan State University: Assistant Professor 2014-Present

California State University, Monterey Bay: Assistant Professor 2014

The University of Texas at Austin: USDA NIFA Postdoctoral Fellow, 2010-2013

Duke University: PhD, 2004-2010

The University of California, Berkeley: BS, 1997-2001

Research Interests

Switchgrass in its native riparian habitat in central Texas
Field experiment with Mimulus guttatus

The genetics of adaptation and speciation

Adaptation is the most fundamental way that the environment can change the phenotypes of organisms. Adaptations can also lead to the formation of reproductive isolating barriers, which are the building blocks of new species. I am very interested in understanding the genetic underpinnings of reproductive isolation at various stages in the speciation process.

Understanding adaptation is also crucial to predicting how organisms will respond to future global change and will help inform management decisions as well as guide future agricultural breeding.

Landscape evolutionary genomics

One of the core goals of my research program is to understand how the natural landscape molds the genomes of organisms through adaptation. To that end, I am using a combination of genetic mapping and genome sequencing approaches to identify genes involved with adaptation to the heterogeneity of the natural landscape. During my dissertation, I focused on how adaptive alleles in Mimulus guttatus are spread across the landscape and what phenotypic effects they have in different environments across western North America. Currently, I am developing Panicum grasses as a model system to understand adaptation along a longitudinal soil moisture cline across Southwestern United States and a latitudinal temperature cline across the Great Plains. Our lab recently received funding from the Department of Energy to develop Panicum hallii as a model system for local adaptation and bioenergy research.

Phenotypic diversity of Switchgrass, Panicum virgatum
Field experiment with Panicum hallii

Using evolutionary biology to improve bioenergy crops

Civilization is built on a foundation of domesticated grasses. Without those grasses (corn, wheat, rice, oats, barley, sorghum) there would be no ballet and human beings would never of landed on the moon. Plant breeders have quietly worked in the shadows to increase the yield of crops and in turn maintain our modern world.

Now, there may actually be potential to domesticate a new set of grass species to use to help combat the growing energy problem. My research is focused understanding the factors involved in local adaptation in the bioenergy crop switchgrass (Panicum virgatum). Loci involved in local adaptation are likely to be of high value to crop breeders interested in improving drought, heat, cold, herbivore, and disease tolerance.

Publications

PDFs for publications available through my website

Important Things

  • Contact Info: You can contact me at davidbryantlowry@gmail.com.
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