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SDSU Nepal Lab


Molecular Phylogenetics and Evolutionary Genetics

SNP213, McFadden Biostress Laboratory

Department of Biology and Microbiology
South Dakota State University
Brookings, SD 57007

Ethan by his poster

Ph.D. student Ethan Andersen joined Nepal lab in 2014 as an undergraduate researcher. His undergraduate research poster received the best poster award at the 100th Annual Meeting of the South Dakota Academy of Science.

Surendra Neupane in Nepal Lab

This photo was taken when Ph.D. student Surendra Neupane was setting up the PCR reactions.  Surendra joined SDSU Nepal Lab in  2016 after his BS degree in Biotechnology  from Tribhuvan University (Nepal). Surendra was in the top five in his School Leaving Certificate (SLC) board exam attended by over 200,000 students in Nepal that year.

Surendra Neupane in Green House

Ph.D. student Surendra Neupane studying Soybean-Soybean Aphid interaction in greenhouse  

Lauren Lindsey collecting DNA samples from the native relatives of wheat

 Freshman biology major Lauren Lindsey collecting DNA samples for her undergraduate research project 

    Publications

    *Corresponding author, +Undergraduate author 

    1. Neupane, S., E.J. Andersen, Q. Ma, F. Mathew, A. Varenhorst and *M.P. Nepal. Accepted.  Evolutionary Divergence of TNL Disease Resistance Proteins in Soybean and Common Bean. Biochemical Genetics.
    2. *Nepal, M.P., E.J. Andersen, S. Neupane  and B.V. Benson. 2017. Comparative Genomics of non-TNL Disease Resistance Genes from Six Plant  Species. Genes. doi:10.3390/genes8100249 
    3. Andersen, E.J. and *M.P. Nepal. 2017. Genetic Diversity of Disease Resistance Genes in Foxtail millet (Setaria italica[L.] P. Beauv.). Plant Gene. 10: 8–16  
    4. NandaKafle, G., T. Seale, T. Flint, M.P. Nepal, S.N. Venter and  V. S. Brözel. 2017. Distribution of Diverse Escherichiacoli between Cattle and Pasture. Microbes and Environments, 32(3): 226–233 
    5. Andersen E.J. and *M.P. Nepal. In press. Corrigendum to “Genetic Diversity of Disease Resistance Genes in Foxtail millet (Setaria italica [L.] P. Beauv.)” [Plant Gene 10 (2017) 8–16] 
    6. Andersen E.J. and *M.P. Nepal. 2017.  Data on Genome-wide Identification of CNL R-genes in Setaria italica (L.) P. Beauv. Data in Brief. 13: 259–273
    7. Andersen, E.J., S. Ali, R.N. Reese, Y. Yen, S. Neupane and *M.P. Nepal. 2016. Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.)Evolutionary Bioinformatics.12:99-108 
    8. *Nepal, M.P.  and B.V. Benson. 2015.  Soybean Disease Resistance Genes and Their Evolutionary DivergenceEvolutionary Bioinformatics11: 49–63 
    9. +Andersen, E.J., +S.R. Shaw and *M.P. Nepal. 2015. Genome-wide Identification of Disease Resistance Genes in Aegilops tauschii Coss. (Poaceae). PSDAOS. 94:281-295
    10. *Nepal, M.P., M.H. Mayfield and C.J. Ferguson. 2015. Breeding System and Sex ratio Variation in MulberriesJBRIT. 9(2):383–395
    11. Benson, B.V., *M.P. Nepal, +L.G. Davison, +P. B. Duwadi  and B.G. Moore. 2014. In Silico Analysis of Cis-Regulatory Elements of Disease Resistance Genes across Six Plant SpeciesProceedings of the South Dakota Academy of Science. 93: 133–144
    12. Piya, S., *M.P. Nepal, J.L. Butler, G.E. Larson and A. Neupane. 2014. Genetic Diversity and Population Structure of Sickleweed (Falcaria vulgaris;Apiaceae) in the Upper Midwest USABiological Invasions 16(10): 2115–2125 
    13. Neupane A., *M.P. Nepal, B.V. Benson, +K.J. MacArthur and S. Piya. 2013. Evolutionary History of Mitogen-activated Protein Kinase (MAPK) Genes in Lotus, Medicago and Phaseolus. Plant Signaling & Behavior  8 (11): e27189 
    14. *Nepal, M.P. and +D.J. Wichern. 2013. Taxonomic Status of Red Mulberry (Morus rubra, Moraceae) at Its Northwestern BoundaryProceedings of the South Dakota Academy of Science. 92: 19–29  
    15. Piya, S., and M.P. Nepal.  2013. Characterization of nuclear and chloroplast microsatellite markers for Falcaria vulgaris (Apiaceae)American Journal of Plant Sciences4(03), 590-595
    16. Neupane, A., *M.P. Nepal, S. Piya, S. Subramanian, J.S. Rohila, R.N. Reese and B.V. Benson. 2013. Identification, Nomenclature, and Evolutionary Relationships of Mitogen-Activated Protein Kinase (MAPK) Genes in SoybeanEvolutionary Bioinformatics. 9: 363–386  (IF = 1.5)
    17. *Nepal, M.P. and C.J. Ferguson. 2012. . Phylogenetics of Morus (Moraceae) Inferred from ITS and trnL-trnF Sequence DataSystematic Botany. 37(2): 442–450 
    18. Piya, S., *M.P. Nepal,  A. Neupane, G.E. Larson and J.L. Butler. 2012. Introduction History and Spread of Falcaria vulgaris Bernh. (Apiaceae) in the United States Based on Herbarium RecordsProceedings of South Dakota Academy of Science. 91:113–129
    19. *Nepal, M.P. and C.J. Ferguson. 2012. . Phylogenetics of Morus (Moraceae) Inferred from ITS and trnL-trnF Sequence DataSystematic Botany. 37(2): 442–450 
    20. *Nepal, M.P., M.H. Mayfield and C.J. Ferguson. 2012. Identification of Eastern North American Morus(Moraceae):Taxonomic Status of M. murrayanaPhytoneuron 26:1–6 
    21. *Mathew, F., P. Okello, J. Kleinjan, S. Osborne, M.P. Nepal, A. Varenhorst, and E. Byamukama. 2017Understanding the Relationship between Soybean Cyst Nematode and Fusarium on Soybean.  South Dakota Soybean Leader. May-June: 19
    22. *Nepal, M.P. and B.V. Benson. 2014. Understanding Plant's Disease Surveillance. "iGrow" Book.
    23. Wake, C.M, and M.P. Nepal. 2011. General Botany Laboratory Manual. South Dakota State University. 112 p. 
    24. *Nepal, M.P. 2006. Is White Mulberry a threat to Red Mulberry on KonzaTallgrass Gazette, Spring 2006: 1-2 
    25. Woods, T.M., S.C. Strakosh, M.P. Nepal, S. Chakrabarti, N.B. Simpson, M.H. Mayfield, and C.J. Ferguson. 2005. Introduced species in Kansas: Floristic changes and patterns of collection based on an historical herbariumSIDA Contributions to Botany  21: 1695–1725 
    26. Chaudhary, R.P., M.P. Nepal, V.N.P. Gupta and O.R. Vetaas. 2002. Traditional use of plants by the indigenous peoples of Makalu-Barun Buffer zone, Eastern Nepal. In: Chaudhary, R.P., B.P Subedi, O.R. Vetaas, and T.H. Aase (eds). Vegetation and Society: Their Interaction in the Himalayas. Tribhuvan University, Nepal and Bergen University, Norway. Pp. 83–97 
    27. *Nepal, M.P., V.N.P. Gupta, O.R. Vetaas, and R.P. Chaudhary. 1999. Utilization of Plant Resources of Makalu-Barun Buffer zone, Eastern Nepal by the Rais and the Sherpa Communities. Proceedings of Royal Nepal Academy of Science and Technology (RONAST), Pp. 1359–1370 

     

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    Conference Presentations  (Regional/National only) 

    Teaching Related 

    1. *Nepal, M.P.,M. Orth and D. York. 2017. Honors in Herbarium: Course-Based Undergraduate Research Experiences (CUREs) for Freshman Biology Students. Paper presented at the Annual Conference of Botanical Society of America- Botany 2017, June 24-28. Fort Worth TX, USA

    2. *Nepal, M.P., M. Miller and L.B. Browning. 2016. Integrative Lesson Plans Centered on Vertical Hydroponic System (VHS): Immersive Professional Development Workshops for Science Teachers in a Rural Setting. Paper presented at the Annual Conference of Botanical Society of America- Botany 2016, July 30 –August 3. Savannah, Georgia, USA.

    3. Nepal, M.P. 2016. Scopes and Challenges of Incorporating Active Learning in a Large Section Introductory Botany Course. Poster presented at the Annual Conference of Botanical Society of America- Botany 2016, July 30 –August 3. Savannah, Georgia, USA.

    4. Vestal S., L.B. Browning, M. Miller, M.P. Nepal and P. White. 2016. Factors that Influence Recruitment and Retention of STEM Teachers in Rural Areas. Poster presented at the 2016 Noyce Summit (National Science Foundation). July 20-22, 2016. Washington DC, USA.

    5. *Nepal, M.P., R. Turner and P.A. Shea. 2015. Helping Transfer Students: Drafting Passport Learning Outcomes and Proficiency Criteria for Natural Science General Education Courses. Paper presented at the Annual Conference of Botanical Society of America- Botany 2015, July 25 -29. Edmonton, Alberta, Canada.

    6. *Nepal, M.P., M. Miller and L.B. Browning. 2015. From Plant Press to Bioinformatics: Professional Development
      Workshops for Science Teachers in a Rural Setting. Paper presented at the Annual Conference of Botanical Society of America- Botany 2015, July 25 -29. Edmonton, Alberta, Canada.

    7. Browning, L.B., M. Miller, M.P. Nepal and *S. Vestal. 2015. REMAST Phase II: Studying Our Phase I Project. Paper presented at the Midwest Regional Noyce Conference. October 29-30, Omaha, Nebraska, USA

    8. *Nepal, M.P. 2014. Collaborative Reading, Writing & Sharing(CREWS) When Combined with Project-Based Learning & Write Like a Scientist (PBL-WLS) Assignments Improved Student Learning Experience in Evolution Course. Paper presented at the Annual Conference of Botanical Society of America- Botany 2014, July 27-30. Boise, ID, USA.

    9. *Nepal, M.P. 2014. Traditional Note-taking Integrated with Instructional Technology Enhanced Student Learning in a Large Section Botany Course. Paper presented at the Annual Conference of Botanical Society of America- Botany 2014, July 27-30. Boise, ID, USA.

    10. *Nepal, M.P. 2013. Effectiveness of Multiple Instructional Delivery Methods in a Large Section Botany Course. 2013. Paper presented at the Annual Conference of Botanical Society of America- Botany 2013, July 27-31. New Orleans, LA, USA.

    11. Nepal, *M. P. and C. Wake.2012. Student Engagement and Assessment Tools (SEATs) for Large Section Botany Course. Paper presented at the Annual Conference of Botanical Society of America- Botany 2012, July 7 -11, 2012. Columbus, OH, USA.

    12. *Nepal, M.P. and L. Browning. 2014. Quadrat to Query Plants and Prairies. Paper presented at the 22nd Annual Joint Conference of South Dakota Science Teachers Association/Council of Teachers of Mathematics. February 2-8, 2014. Huron, SD.

    13. *Nepal, M.P. and L. Browning. 2014. Plant Press Make and Take. Paper presented at the 22nd Annual Joint Conference of South Dakota Science Teachers Association/Council of Teachers of Mathematics. February 2-8, 2014. Huron, SD.

    14. *Nepal, M.P. and L. Browning. 2014. Bioinformtaics in South Dakota High School Classrooms. Paper presented at the22nd Annual Joint Conference of South Dakota Science Teachers Association/Council of Teachers of Mathematics. February 2-8, 2014. Huron, SD.

    15. *Nepal, M. P., R. Stecher and A. Perry. Pre-and-Post-Chapter Tests (PAPCTs) as an instructional assessment tool for teachers. Poster presented at the American Society of Plant Biologists (ASPB) Midwestern Section Meeting 2012, March 24-25. Lincoln, NE, USA. (Also presented at the Faculty Showcase, Faculty Excellence Day)

    Research Related

    1. Andersen, E.J. and *M.P. Nepal. 2017. Evolution of the NB-ARC protein domain as a major signaling component of plant defense response. Poster presented at theAnnual Conference of Botanical Society of America- Botany 2017, June 24-28. Fort Worth TX, USA
    2. Andersen, E.J., *M.P. Nepal, S. Ali, Y. Yen, and S. Neupane. 2017. Genome-wide identification of disease resistant genes in wheat (Triticum aestivum L.; Poaceae). Poster presented at the Annual Conference of Botanical Society of America- Botany 2017, June 24-28. Fort Worth TX, USA
    3. Neupane, S., *M.P. Nepal,Q. Ma, F. Mathew and A. Varenhorst. 2017.Quantifying induced susceptibility effects in soybean-aphid interaction. Paper presented at the Annual Conference of Botanical Society of America- Botany 2017, June 24-28. Fort Worth TX, USA
    4. Andersen, E.J., *M.P. Nepal, S. Ali, Y. Yen, R.N. Reese, S. Neupane. 2016. Genome-wide identification of the CNL Disease Resistance enes in barley (Hordeum vulgare L.) and Their Evolutionary Divergence. Paper presented at the Annual Conference of Botanical Society of America- Botany 2016, July 30 –August 3. Savannah, Georgia, USA.
    5. Andersen, E., *M.P. Nepal, R. N. Reese, S. Ali, S. Neupane. 2016. Evolutionary divergence of disease resistance genes in six monocot species. Paper presented at the Annual Conference of Botanical Society of America- Botany 2016, July 30 –August 3. Savannah, Georgia, USA.
    6. *Nepal, M.P., S. Neupane, F. Mathew, Q. Ma, A. Varenhorst, E.J Andersen, R.N. Reese. 2016. Comparative Genomics of Disease Resistance Genes in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris). Poster presented at the Annual Conference of Botanical Society of America- Botany 2016, July 30 –August 3. Savannah, Georgia, USA.
    7. Hummel, M.J. and *M.P. Nepal. 2016. Assessing Phylogenetic Relationships among Anseriformes Based on Nuclear and Mitochondrial DNA Sequences. Paper presented at the 101st Annual Meeting of South Dakota Academy of Sciences. April 8-9, University of Sioux Falls. Sioux Falls, SD, USA.
    8. *Nepal, M.P., S.R. Shaw, E.J. Andersen. 2015. Tracking Disease Resistance in Wheat through Identification of R-gene Orthologs in Aegilops tauschii Coss. (Poaceae). Poster presented at the Annual Conference of Botanical Society of America- Botany 2015, July 25 -29. Edmonton, Alberta, Canada
    9. *Nepal, M.P., E.J. Andersen, S.R. Shaw, J.L. Gonzalez, Y. Yen, and R.N. Reese. 2015. Comparative Genomics of CNL Disease Resistance Genes in Six Grass Species. Poster presented at the Annual Conference of Botanical Society of America- Botany 2015, July 25 -29. Edmonton, Alberta, Canada.
    10. Andersen, E.J.., S.R. Shaw and *M.P. Nepal. 2015. Genome-wide Identification of Disease Resistance Genes in Aegilops tauschii. Poster presented at the 100th Annual Meeting of South Dakota Academy of Sciences. April 10-11, Cedar Shore, SD, USA
    11. Adhikari S., K. Acharya, R. Chowdhary, A. Charif, E. Byamukama, X. Gu, W. Li, J.S. Rohila, M.P. Nepal and S. Subramanian. 2015. Efficient and economical molecular diagnostic tools for soybean stresses. Poster presented at the 11th Annual AgOutlook Conference and Tradeshow. December 10th; Sioux Falls, SD, USA. (Second place prize winner poster)
    12. Benson, B.V., *M.P. Nepal, S. Subramanian and S. Ali. 2014. Soybean Disease Resistance Genes and Their Evolutionary Divergence. Paper presented at the Annual Conference of Botanical Society of America-Botany 2014, 27-30 July, 2014. Boise, ID, USA.
    13. Andersen, E.J, *M.P Nepal, B.V. Benson and E.A Opitz. 2014. Undergraduate Research Project on Genome-wide Identification of Disease Resistance Genes in Cultivated Barley (Hordeum vulgare, Poaceae). Paper presented at the Annual Conference of Botanical Society of America. Botany 2014, 27-30 July, 2014. Boise, ID, USA.
    14. Opitz, E.A, *M.P Nepal, B.V. Benson and E. J. Andersen. 2014. Undergraduate Research Project on Identification of Disease Resistance Genes in Foxtail Millet (Seteria italica, Poaceae. Poster presented at the Annual Conference of Botanical Society of America. Botany 2014, 27-30 July, 2014. Boise, ID, USA.
    15. Benson, B.V. and *M.P. Nepal. 2013. Diversity and Evolutionary Divergence of Resistant Genes (R Genes) in Legumes. Poster presented at the Annual Conference of Botanical Society of America-Botany 2013, July 27-31. New Orleans, LA, USA.
    16. *Nepal, M.P. 2013. Effectiveness of Multiple Instructional Delivery Methods in a Large Section Botany Course. 2013. Paper presented at the Annual Conference of Botanical Society of America- Botany 2013, July 27-31. New Orleans, LA, USA.
    17. MacArthur, K.J., K. Murray, A. Neupane, B.V. Benson, S. Piya and *M.P. Nepal. 2013. Evolution of Mitogen Activated Protein Kinase Kinase (MAPKK) Gene Family in Plants. Poster presented at the Annual Conference of Botanical Society of America- Botany 2013, July 27-31. New Orleans, LA, USA.
    18. Schreier, S., S. Piya and *M.P.Nepal. 2013. Postglacial Founder Effect Detected in Endangered Populations of Native Red Mulberry at its Northwestern Boundary. Poster presented at the Annual Conference of Botanical Society of America- Botany 2013, July 27-31. New Orleans, LA, USA.
    19. Piya S., *M.P. Nepal, J.L. Butler and GE. Larson. 2013. Exploring genetic basis of Sickleweed (Falcaria vulgaris) invasion in the United States. Poster presented at the 98th Annual Meeting of Ecological Society of America. 4-9 August, Minneapolis, MN, USA.
    20. *Nepal, M.P. and C. Wake. 2012. Student Engagement and Assessment Tools (SEATs) for Large Section Botany Course. Poster presented at the Annual Conference of Botanical Society of America-Botany 2012, July 7 -11 , 2012. Columbus, OH, USA.
    21. Neupane, A., S. Piya, N. Reese, J. Rohila, S. Subramanian and *M. P. Nepal. 2012. Identification of Mitogen Activated Protein Kinase Family Members in Soybean. Poster presented at the Annual Conference of Botanical Society of America-Botany 2012, July 7 -11, 2012. Columbus, OH, USA.
    22. Piya, Sarbottam, G.E Larson, J.L. Butler, A. Neupane and *M.P. Nepal. 2012. Population Genetics of Falcaria vulgaris (Sickleweed) in North America. Paper presented at the Annual Conference of Botanical Society of America-Botany 2012, July 7 -11, 2012. Columbus, OH, USA.
    23. Piya, Sarbottam, G.E. Larson, J.L. Butler, A. Neupane and *M.P. Nepal. 2012. Introduction history and spread of Falcaria vulgaris Bernh. (Apiaceae) in the United States based on herbarium records. Paper presented at the Annual Meeting of South Dakota Academy of Science. April, 13-14 2012. Vermillion, SD, USA.
    24. Neupane, A., S. Piya, N. Reese, J. Rohila,S. Subramanian and *M. P. Nepal. 2012. Identification of Mitogen Activated Protein Kinase Family Members in Soybean. BOTANY 2012, 7 -11July, 2012. Columbus, OH, USA.
    25. *Nepal, M.P., L. Browning, K. Emo, M. Miller and K. Russow and S.Vestal. 2011. Summary of Rural Enhancement of Math And Science Teachers (REMAST) Summer Conference 2011 at South Dakota State University. NSF Robert Noyce Teacher Scholarship Program Conference. July 6-8, 2011. Washington DC, USA.
    26. Emo K., L. Browning, M. Miller, M.P. Nepal, K. Russow and S. Vestal. 2011. K-12 Connections: Creating a Community of STEM Educators. The 20th Annual SDSTA/SDCTM Joint Conference. February 2-4, 2011. Huron, SD, USA.
    27. *Nepal, M. P., and G.E. Larson. 2010. Natural hybridization in Morus: Is an exotic mulberry threatening the native one? Paper presented at the Annual Conference of Botanical Society of America -Botany 2010, July 31 - August 4 , 2010. Providence, RI, USA.
    28. Korman, B. L., G.E. Larson, J.L. Butler, and M. P. Nepal. 2010. Sickleweed, an Emerging Problem in the Northern Mixed Grass Prairie. Poster presented at the Annual Conference of Botanical Society of America- Botany 2010, 31 July–4 August. Providence, RI, USA.
    29. *Nepal, M.P., S.D. Fehlberg and C.J. Ferguson.2009. Developing and applying low-copy nuclear regions for phylogenetic study in the genus Phlox (Polemoniaceae). Paper presented at Botany and Mycology Joint Congress 2009, July 25-29. Snowbird, UT, USA.
    30. Fehlberg, S.D., M.P. Nepal and C.J. Ferguson. The importance of genetic and cytotype variation in conservation: an example from Phlox (Polemoniaceae). Paper presented at Botany and Mycology Joint Congress 2009, July 25-29. Snowbird, UT, USA.
    31. Fehlberg, S.D., M.P Nepal, M.C. Ty, and C.J. Ferguson. 2008. Evolutionary history and ecological significance of polyploidy in the Phlox woodhousei complex in the arid southwest. 14 - 16 November 2008. Paper presented at Ecological Genomics: sixth annual symposium. Kansas City, MO, USA.
    32. *Nepal, M.P., C.J. Ferguson and M.H. Mayfield. 2007. Exploring A.S. Hitchcock's herbarium: historical botanical findings from computerization of the Kansas State University Herbarium. Paper presented at Botany and Plant Biology Joint Congress 2007, July 7-11. Chicago, IL, USA
    33. *Nepal, M.P., M.H. Mayfield and C.J. Ferguson. 2007. Phylogenetic relationships of Morus L. (Moraceae) inferred from nuclear and chloroplast DNA sequences. Paper presented at Botany and Plant Biology Joint Congress 2007, July 7-11. Chicago, IL, USA.
    34. Nepal, M.P., M.H Mayfield, and C.J. Ferguson. 2006. Systematics and reproductive biology of the genus Morus (Moraceae). Poster presented at the Annual Conference of Botanical Society of America- Botany 2006, July 28 - August 2. California State University, Chico, California, USA.
    35. Woods, T.M., S.C. Strakosh, M.P. Nepal, S. Chakrabarti, N.B. Simpson, M.H. Mayfield, and C.J. Ferguson. 2004. Floristic changes documented by historical herbarium specimens: plant species introduced to Kansas. Paper presented at the Annual Conference of Botanical Society of America- Botany 2004, July 31 - August 5, Snowbird, Salt Lake City, UT, USA.
    36. *Nepal, M.P. and V.S. Berg. 2004. Photosynthetic gas exchange in Potentilla gracilis. Poster presented at the Annual conference ofPlant Biology 2004. July 24-28. Lake Buena Vista, Florida, USA.