David Lowry: Difference between revisions

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[[Image:David_field_2009.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|right|Photo by David Lowry]]
Duke University:                         PhD,                        2004-2010


I am a fifth year graduate student in the [http://upg.duke.edu/ Duke University Program in Genetics and Genomics], who hails from the redwood empire and wine country of Northern California.  I spent 4.5 years of long latte-drinking nights at UC Berkeley during the thrilling boom and crash of the dot-com era.  After college, I set out to explore the finer delights of world cultures and wildlife before joining the grind of graduate school.  Alas, my time at [http://www.duke.edu Duke] has been good to me thanks to many fantastic people and my amazingly optimistic leader/advisor, [http://www.biology.duke.edu/willislab/ Dr. Johh Willis].
The University of California, Berkeley:   BS,                         1997-2001


The focus of my research is directed toward understanding the genetics of adaptation and speciation.  To this end, I have chosen to study how divergent adaptation of the yellow monkey flower (''Mimulus guttatus''), to the coast versus inland habitat, contributes to reproductive isolation.  I am using 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 have carried out reciprocal transplant experiments and population genetic analysis to demonstrate that coast and inland ''Mimulus'' are locally adapted and reproductively isolated.  I am currently conducting a new reciprocal transplant experiment with near isogenic lines to test hypotheses of adaptation and ecogeographic reproductive isolation.  In addition, I am conducting studies on the evolution of flowering time, anthocyanin production in vegetative tissue, ion accumulation, and working on the assembly of the ''Mimulus guttatus'' genome.
==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'']]


[[Image:PhilTransCover.jpg|thumb|right|Photo by David Lowry]]
'''The genetics of adaptation and speciation'''


Lowry, D. B., J.H. Willis.  Rearranged and colinear chromosomal regions confer adaptive divergence between widespread races of ''Mimulus guttatus.''  ''In prep''
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., M. C. Hall, J. H. Willis. Genetic and physiological basis of adaptive salt tolerance divergence between coastal and inland ''Mimulus guttatus.''  ''in revision''
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.


Wu, C. A., D. B. Lowry, L. I. Nutter, J. H. Willis.  Natural variation for drought response in the ''Mimulus guttatus'' species complex.  ''in review''
'''Landscape evolutionary genomics'''


[http://journals.royalsociety.org/content/5h3j39kkwr338675/?p=fb43d599f16f4102a053e1d4e420e09a&pi=4 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]
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.   


[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]
[[Image:Diversity.JPG|thumb|left|Phenotypic diversity of Switchgrass, ''Panicum virgatum'']]
[[Image:Field_2012.JPG|thumb|right|Field experiment with ''Panicum hallii'']]


[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.]
'''Using evolutionary biology to improve bioenergy crops'''


==Important Things==
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.


*'''Contact Info:''' You can contact me at david.lowry@duke.edu.
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.


*[[Media:David_Lowry_CV7.doc|Curriculum Vitae]]
==Publications==


*Make sure to check out the [[Mimulus Community]].
'''PDFs for publications available through my''' [http://davidbryantlowry.wordpress.com/publications/ '''website''']


*See the [[:Image:Pop_graph.pdf|relationship of coast and inland populations]] as determined by neutral microsatellite loci.
==Important Things==
 
*Treat your fears with [http://www.bachcentre.com/centre/38/mimulus.htm Mimulus].
 
==Field Sites==
 
[[Image:coast_lowry.jpg|thumb|right|Habitat of coastal ''Mimulus'']]
 
[[Image:inland_lowry.jpg|thumb|right|Habitat of inland ''Mimulus'']]
 
===United States===
*[http://www.parks.ca.gov/default.asp?page_id=592 Copperopolis]
*[http://www.parks.ca.gov/default.asp?page_id=592 Montana de Oro State Park]
*[http://www.redshift.com/~bigcreek/ Big Creek Reserve]
*[http://www-bml.ucdavis.edu/ Bodega Marine Lab]
*[http://nrs.ucop.edu/Reserves/Angelo/Angelolinkingpage.html Angelo Reserve]
*[http://www.nps.gov/redw/ Redwood National Park]
*[http://www.oregonstateparks.org/park_197.php Saddle Mountain]
 
===Canada===
*[http://www.portrenfrew.com/botbeach.htm Botanical Beach]
*[http://www.pc.gc.ca/pn-np/bc/gwaiihaanas/index_e.asp Gwaii Haanas]
*[http://www.bms.bc.ca/ Bamfield Marine Science Center]
*[http://www.pc.gc.ca/pn-np/bc/pacificrim/index_e.asp Pacific Rim National Park]
 
 
 
==Bioinformatic/Statistical Software and Resources==
*[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]


==Population Genetic Software==
*[http://davidbryantlowry.wordpress.com/ My website]
*[http://www-timc.imag.fr/Olivier.Francois/tess.html TESS]
*[http://www2.unil.ch/popgen/softwares/fstat.htm FSTAT]
*[http://www.maizegenetics.net/index.php?page=bioinformatics/tassel/index.html Tassel]
*[http://anthro.unige.ch/arlequin/ Arlequin]
*[http://pritch.bsd.uchicago.edu/structure.html Structure]
*[http://www.rubic.rdg.ac.uk/~mab/home.html Mark Beaumont]
*[http://geospatial.amnh.org/open_source/gdmg/index.html Geographic distance matrix generator]
*[http://wbiomed.curtin.edu.au/genepop/ Genepop (web)]
*[http://dyerlab.bio.vcu.edu/wiki/index.php/Software Dyerlab (Population Graphs)]
*[http://ibdws.sdsu.edu/ Isolation by Distance]
*[http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php Genetic Data Analysis]
*[http://www.biology.lsu.edu/general/software.html Software for Populaiton Genetic Analysis]
*[http://www.mas.ncl.ac.uk/~nijw/ Ian Wilson (Batwing)]
*[http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm Jody Hey (SITES)]
*[http://www.structurama.org/index.html Structurama]
*[http://www.ub.es/dnasp/ DNASP]
*[http://www.cals.ncsu.edu/plantpath/people/faculty/carbone/workbench.html SNAP]


==Analysis of fitness data==
*[http://lowrylab.wordpress.com/david-lowry-cv/ David Lowry CV]
*[http://www.stat.umn.edu/geyer/aster/ ASTER]


==Abiotic Stress Websites==
*[http://scholar.google.com/citations?view_op=list_works&hl=en&user=yp5xdBEAAAAJ&gmla=AJsN-F6DFaPZ9A0TNBwOFnsWZf9Y9S7rGntDIzs1ZOqg52GhHzGJ090M-xxUubHEHF3dyXE6XlN-jmJ1uYNJiAULSHsEkKAaqniu606ZwKxaDjIwB3wfiIkspwU-gntSRaYs7bNl5Mmy Google Scholar Citations ]
*[http://www.inra.fr/internet/Produits/vast/projects.htm Drought Tolerance Arabidopsis]
*[http://www.knowledgebank.irri.org/TsunamisAndRice/How_Do_You_Measure_Soil_Salinity_.htm How to measure soil salinity]


==Other useful sites==
*[https://github.com/davidbryantlowry Programming Scripts on Github]
*[http://geography.about.com/library/blank/blxusx.htm Blank Outline Maps] that can be used to make figures.


==Friends on OWW==
*'''Contact Info:''' You can contact me at davidbryantlowry@gmail.com.


*[[Sri Kosuri|Sri Kosuri]]
*Make sure to check out the [[Mimulus Community]] and the [[Texas Switchgrass Collaborative]].
*[[Kevin Wright|Kevin Wright]]
*[http://www.openwetware.org/wiki/User:Bdilkes Brian Dilkes]

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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