Mark P. Simmons
Colorado State
University
Fort Collins,
Colorado 80523-1878
970-491-2154
Positions held
Associate professor and curator
of the herbarium, Department of Biology, Colorado State University, 2007 –
present
Assistant professor and
curator of the herbarium, Department of Biology, Colorado State University,
2001 – 2007
Postdoctoral fellow,
Department of Evolution, Ecology, and Organismal Biology; Ohio State
University, 2000 – 01
Ph.D. (Plant Biology) L.H. Bailey
Hortorium, Cornell University, 2000
B.A. (Biology) University of
Richmond, 1994
Teaching experience
Introduction to Evolution
(co-taught; BZ220), 2002, -03, -04, -05, -06, -07
Plant Systematics (BZ325), 2002,
-04, -06, -08
Independent Study – Undergraduate
Research (BZ495), 2004, -05, -06, -07, -08
Advanced Systematics (co-taught;
BZ520), 2002, -04, -06, -08
Independent Study – Readings in Systematics
(BZ594), 2003
Evolution Seminar (BZ692G), 2002,
-04 (x2), -06
Departmental Seminar (BZ692H), 2003,
-04
National Science Foundation – REU
Supplement, 2008
National Science Foundation – Systematic
Biology and Biodiversity Inventories
“Phylogeny and
diversification of the aril in the Celastraceae,” 2007 – 10
National Geographic Society
“Biogeography and
Systematics of the Madagascan Celastraceae,” 2006 – 07
National Science Foundation – REU
Supplement, 2005
Bureau of Land Management, Plant
Information Network II, 2004 – 05
National Science Foundation – REU
Supplement, 2004
National Science Foundation –
Biological Research Collections
“Collaborative
Research: Linked Databases and an Interactive Key for the Vascular Flora of the
Southern Rocky Mountain Region,” 2003 – 07
Bureau of Land Management, Plant
Information Network II, 2003
Colorado State University, Career
Enhancement Grant, 2002
Cornell University, Mellon
Foundation Fellowship, 1995 – 99
American Society of Plant Taxonomists,
Graduate Student Research Grant, 1998
Cornell University, Graduate School
Travel Grant, 1997
L.H. Bailey Hortorium, Moore/Mellon
Foundation Travel Grant, 1997
Cornell University, Sage Graduate
Fellowship, 1994 – 95
University of Richmond, Summer
fellowship, 1993
University of Richmond,
Undergraduate research grants, 1991, 1993
Systematic
Biology Publisher’s Award for Excellence, 2000
Golden Key National Honor Society,
1993 – 94, 2005 (honorary member)
Magna Cum Laude, 1994
Phi Beta Kappa, 1994
Biology
Department Honors Program, 1992 – 94
2.
Simmons, M.P., W.J. Hayden, and D.M.E. Ware. 1995. The vascular flora of
the Potomac River watershed of King George County, Virginia. Castanea 60:
179-209.
3.
Simmons, M.P. and W.J. Hayden. 1997. Revision of the cerrado hemicryptophytic
Chamaesyce of Boissier's Pleiadeniae (Euphorbiaceae). Brittonia
49: 155-180.
4.
Davis, J.I., M.P. Simmons, D.W. Stevenson, and J.F. Wendel. 1998. Data
decisiveness and data quality in phylogenetic analysis: an example from the
monocots using mitochondrial atpA
sequences. Systematic Biology 47:
282-310.
5. Simmons, M.P. and J.P. Hedin. 1999.
Relationships and morphological character change among genera of the
Celastraceae sensu lato (including Hippocrateaceae). Annals of the Missouri
Botanical Garden 86: 723-757.
6.
Stevenson, D.W., J.I. Davis, J.V. Freudenstein, C.R. Hardy, M.P. Simmons,
and C.D. Specht. 2000. A phylogenetic analysis of the monocotyledons based on
morphological and molecular character sets, with comments on the placement of Acorus and Hydatellaceae. Pages 17-24 in
Monocots systematics and evolution (K. L. Wilson and D. A. Morrison, eds.).
CSIRO Publishing, Sydney.
7.
Simmons, M.P. 2000. A fundamental problem with amino-acid-sequence
characters for phylogenetic analyses. Cladistics 16: 274-282.
8.
Simmons, M.P. and H. Ochoterena. 2000. Gaps as characters in
sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
9.
Simmons, M.P., C.D. Bailey, and K.C. Nixon. 2000. Phylogeny reconstruction
using duplicate genes. Molecular Biology and Evolution 17: 469-473.
11.
Simmons, M.P., C.C. Clevinger, V. Savolainen, R.H. Archer, S. Mathews,
and J.J. Doyle. 2001. Phylogeny of the Celastraceae inferred from phytochrome B
gene sequence and morphology. American Journal of Botany 88: 313-325.
12.
Simmons, M.P., V. Savolainen, C.C. Clevinger, R.H. Archer, and J.I.
Davis. 2001. Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal
DNA, phytochrome B, rbcL, atpB, and
morphology. Molecular Phylogenetics and Evolution 19: 353-366.
13. Simmons, M.P., H. Ochoterena, and
T. Carr. 2001. Incorporation, relative homoplasy, and effect of gap characters
in sequence-based phylogenetic analyses. Systematic Biology 50: 454-462.
14. Simmons,
M.P. and J.V. Freudenstein. 2002. Uninode coding vs. gene-tree parsimony
for phylogenetic reconstruction using duplicate genes. Molecular Phylogenetics
and Evolution 23: 481-498.
15. Simmons,
M.P. and J.V. Freudenstein. 2002. Artifacts of coding amino acids and other
composite characters for phylogenetic analysis. Cladistics 18: 354-365.
16. Simmons,
M.P., C. Randle, J.V. Freudenstein, and J.W. Wenzel. 2002. Limitations of
Relative Apparent Synapomorphy Analysis (RASA) for measuring phylogenetic
signal. Molecular Biology and Evolution 19: 14-23.
17. Simmons,
M.P., H. Ochoterena and J.V. Freudenstein. 2002. Conflict between amino
acid and nucleotide characters. Cladistics 18: 200-206.
18. Simmons, M.P., H. Ochoterena and J.V. Freudenstein. 2002. Amino acid vs.
nucleotide characters: challenging preconceived notions. Molecular
Phylogenetics and Evolution 24: 78-90.
19. Simmons,
M.P. and J.V. Freudenstein. 2003. The effects of increasing genetic
distance on alignment of, and tree construction from, rDNA internal transcribed
spacer sequences. Molecular Phylogenetics and Evolution 26: 444-451.
20.
Baumberger, N., B. Doesseger, R. Guyot, A. Diet, R.L. Parsons, M.A. Clark, M.P.
Simmons, P.A Bedinger, S.A. Goff, C. Ringli, and B. Keller. 2003.
Whole-genome comparison of LRR-extensins (LRXs) in Arabidopsis thaliana
and Oryza sativa: a conserved family of cell wall proteins form a
vegetative and a reproductive clade. Plant Physiology 131: 1313-1326.
21. Freudenstein, J.V., K.M. Pickett, M.P. Simmons, and J.W.
Wenzel. 2003. From basepairs to bird songs: phylogenetic data in the age of
genomics. Cladistics 19: 333-347.
22.
Simmons, M.P. 2004. Celastraceae. Pages 29-64 in The families and
genera of vascular plants, volume 6 (K. Kubitzki, ed.). Springer, Berlin.
23.
Simmons, M.P. 2004. Parnassiaceae. Pages 291-296 in The families
and genera of vascular plants, volume 6 (K. Kubitzki, ed.). Springer, Berlin.
24. Simmons,
M.P. 2004. Independence of alignment and tree search. Molecular Phylogenetics
and Evolution 31: 874-879.
25. Simmons, M.P.
2004. Hippocrateaceae. Pages 3-19 in
Flore de la Nouvelle-Calédonie, volume 25 (P. Morat, ed.). Muséum National
d’Histoire Naturelle, Laboratoire de Phanérogramie, Paris.
26. Simmons, M.P.
and M. Miya. 2004. Efficiently resolving the basal clades of a phylogenetic
tree using Bayesian and parsimony approaches. Molecular Phylogenetics and
Evolution 31: 351-362.
27.
Simmons, M.P., K.M. Pickett and M. Miya. 2004. How meaningful are
Bayesian posterior probabilities? Molecular Biology and Evolution 21: 188-199.
28.
Simmons, M.P., A. Reeves and J.I. Davis. 2004. Character-state space
versus rate of evolution for phylogenetic inference. Cladistics 20: 191-204.
29.
Simmons, M.P., T.G. Carr and K. O’Neill. 2004. Relative character-state
space, amount of potential phylogenetic information, and heterogeneity of
nucleotide and amino acid characters. Molecular Phylogenetics and Evolution 32:
913-926.
30.
Davis, J.I., D.W. Stevenson, G. Petersen, O. Seberg, L.M. Campbell, J.V.
Freudenstein, D.H. Goldman, C.R. Hardy, F.A. Michelangeli, M.P. Simmons,
C.D. Specht, F. Vergara-Silva, and M.A. Gandolfo. 2004. A phylogeny of the
monocots, as inferred from rbcL and atpA sequence variation, and
a comparison of methods for calculating jackknife and bootstrap values.
Systematic Botany 29: 467-510.
31.
Simmons, M.P. 2005. Amino acid versus nucleotide characters for
phylogenetic inference of the "basal" angiosperms. Pages 1-27 in Plant genome biodiversity and
evolution, volume 1B: phanerogams (A.K. Sharma and A. Sharma, eds.). Science
Publishers, Inc., Enfield, New Hampshire.
32.
Abdel-Ghany, S.E., I.S. Day, M.P. Simmons, P. Kugrens and A.S.N. Reddy.
2005. Origin and evolution of kinesin-like calmodulin-binding proteins. Plant
Physiology 138: 1711-1722.
33.
Simmons, M.P. and C.T. Webb. 2006. Quantification of the success of
phylogenetic inference in simulations. Cladistics 22: 249-255.
34.
Simmons, M.P., L.-B. Zhang, C.T. Webb and A. Reeves. 2006. How can third
codon positions outperform first and second codon positions in phylogenetic
inference? An empirical example from the seed plants. Systematic Biology 55:
245-258.
35.
Simmons, M.P., L.-B. Zhang, C.T. Webb, A. Reeves and J.A. Miller. 2006.
The relative performance of Bayesian and parsimony approaches when sampling
characters evolving under homogeneous and heterogeneous sets of parameters.
Cladistics 22: 171-185.
36.
Davis, J.I., G. Petersen, O. Seberg, D.W. Stevenson, C.R. Hardy, M.P.
Simmons, F.A. Michelangeli, D.H. Goldman, L.M. Campbell, C.D. Specht and
J.I. Cohen. 2006. Are mitochondrial genes useful for the analysis of monocot
relationships? Taxon 55: 857-870.
37.
Islam, M.B. and M.P. Simmons. 2006. A thorny dilemma: testing
alternative intrageneric classifications within Ziziphus (Rhamnaceae).
Systematic Botany 31: 826-842.
38.
Islam, M.B., M.P. Simmons and R.H. Archer. 2006. Phylogeny of the Elaeodendron
group (Celastraceae) inferred from morphological characters and nuclear and
plastid genes. Systematic Botany 31: 512-524.
39. Petersen,
G., O. Seberg, J.I. Davis, D.H. Goldman, D.W. Stevenson, L.M. Campbell, F.A.
Michelangeli, C.D. Specht, M.W. Chase, M.F. Fay, J.C. Pires, J.V. Freudenstein,
C.R. Hardy and M.P. Simmons. 2006. Mitochondrial DNA in monocot
phylogenetics. Aliso 22: 52-62.
40.
Poff, N.L., J.D. Olden, N.K.M. Vieira, D.S. Finn, M.P. Simmons and B.C.
Kondratieff. 2006. Functional trait niches of North American lotic insects:
evolutionary constraints on trait-based ecological applications. Journal of the
North American Benthological Society 25: 730-755.
41.
Richardson, D., M.P. Simmons and A.S.N. Reddy. 2006. Comprehensive
comparative analysis of kinesins in photosynthetic eukaryotes. BMC Genomics 7:
18.
42.
Zhang, L.-B. and M.P. Simmons. 2006. Phylogeny and delimitation of the
Celastrales inferred from nuclear and plastid genes. Systematic Botany 31:
122-137.
43. Zhang,
L.-B., M.P. Simmons, A. Kocyan, and S.S. Renner. 2006. Phylogeny of the
Cucurbitales based on DNA sequences of nine loci from three genomes:
implications for morphological and sexual system evolution. Molecular
Phylogenetics and Evolution 39: 305-322.
44.
Simmons, M.P., K. Müller and A.P. Norton. 2007. The relative performance
of indel-coding methods in simulations. Molecular Phylogenetics and Evolution
44: 724-740.
45.
Simmons, M.P., L.-B. Zhang, C.T. Webb and K. Müller. 2007. A penalty of
using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic
inference. Molecular Phylogenetics and Evolution 42: 528-542.
46. Zhang, L.-B., M.P. Simmons and S.S.
Renner. 2007. A phylogeny of Anisophyllaceae based on six nuclear and plastid
loci: ancient disjunctions and recent dispersal between South America, Africa,
and Asia. Molecular Phylogenetics and Evolution 44: 1057-1067.
47.
Poon, W.-S., P.-C. Shaw, M.P. Simmons and P.P.-H. But. 2007. Congruence
of molecular, morphological, and biochemical profiles in Rutaceae: a cladistic
analysis of the subfamilies Rutoideae and Toddalioideae. Systematic Botany 32:
837-846.
48.
Simmons, M.P., D. Richardson and A.S.N. Reddy. 2008. Incorporation of
gap characters and lineage-specific regions into phylogenetic analyses of gene
families from divergent clades: an example from the kinesin superfamily across
eukaryotes. Cladistics 24: 372-384.
49.
Simmons, M.P., J.J. Cappa, R.H. Archer, A.J. Ford, D. Eichstedt and C.C.
Clevinger. 2008. Phylogeny of the Celastreae (Celastraceae) and the
relationships of Catha edulis (qat) inferred from morphological
characters and nuclear and plastid genes. Molecular Phylogenetics and Evolution
48: 745-757.
50. Simmons,
M.P. In press. Celastraceae. In: Nuevo Catálogo de la Flora de Venezuela (O. Hokche, ed.). Fundación
Instituto Botánico de Venezuela, Caracas.
51. Simmons, M.P.,
K.F. Müller and C.T. Webb. In press. The relative sensitivity of different
alignment methods and character codings in sensitivity analysis. Cladistics.
1.
Simmons, M.P., W.J. Hayden, and D.M.E. Ware. 1993. The vascular flora of the
Potomac River watershed of King George County, Virginia. Virginia Academy of
Science Annual Meeting, Norfolk, Virginia.
2.
Simmons, M.P. and W.J. Hayden. 1994. Revision of the cerrado hemicryptophytic Chamaesyce of Boissier's Pleiadeniae (Euphorbiaceae). Virginia
Academy of Science Annual Meeting, Harrisonburg, Virginia.
3. Simmons, M.P. and J.P. Hedin. 1998.
Relationships and morphological character change among genera of the
Celastraceae sensu lato (including Hippocrateaceae). American Institute of
Biological Sciences Annual Meeting, Baltimore, Maryland.
4.
Simmons, M.P., H. Ochoterena, and T. Carr. 2000. Incorporation, relative
homoplasy, and effect of gap characters in sequence-based phylogenetic
analyses. Botany 2000, Portland, Oregon.
5.
Simmons, M.P., V. Savolainen, C.C. Clevinger, R.H. Archer, and J.I. Davis.
2000. Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA,
phytochrome B, rbcL, atpB, and
morphology. Botany 2000, Portland, Oregon.
6. Simmons, M.P., H. Ochoterena and J.V. Freudenstein. 2001. Amino acid vs.
nucleotide characters: challenging preconceived notions. Botany 2001,
Albuquerque, New Mexico.
7. Simmons,
M.P. and J.V. Freudenstein. 2001. The effects of increasing genetic distance on
alignment of, and tree construction from, rDNA internal transcribed spacer
sequences. Botany 2001, Albuquerque, New Mexico.
9. Simmons, M.P. and J.V. Freudenstein. 2002.
Uninode coding vs. gene-tree parsimony for phylogenetic reconstruction using
duplicate genes. Evolution 2002, Urbana, Illinois.
10. Simmons, M.P., J.V. Freudenstein, K.M. Pickett,
and J.W. Wenzel. 2002. From basepairs to birdsongs: phylogenetic data in the
age of genomics. Evolution 2002, Urbana, Illinois.
11. Simmons, M.P. and J.V. Freudenstein. 2002.
Independence of alignment and tree search. Evolution 2002, Urbana, Illinois.
12. Simmons, M.P. and J.V. Freudenstein. 2002. Phylogenetic
reconstruction from duplicate genes via uninode coding or gene-tree parsimony.
Botany 2002, Madison, Wisconsin.
13. Simmons, M.P.,
J.V. Freudenstein, K.M. Pickett, and J.W. Wenzel. 2002. Whither phenotypic characters in the age of
genomics? Botany 2002, Madison, Wisconsin.
14. Simmons, M.P., T.G. Carr, and K. O’Neill.
2003. Nucleotide vs. amino acid characters: relative character-state space,
amount of potential phylogenetic information, and heterogeneity. Willi Hennig
Society Annual Meeting, New York City.
15. Simmons,
M.P. and M. Miya. 2003. Efficiently resolving the basal clades of a
phylogenetic tree using Bayesian and parsimony approaches. Botany 2003, Mobile,
Alabama.
16. Simmons,
M.P., T.G. Carr, and K. O’Neill. 2003. Relative character-state space, amount
of potential phylogenetic information, and heterogeneity of nucleotide and
amino acid characters. Botany 2003, Mobile, Alabama.
17. Simmons,
M.P., A. Reeves, and J.I. Davis. 2004. The relationship between character-state
space and rate of evolution for phylogenetic inference. Evolution 2004, Fort
Collins, Colorado.
18. Simmons,
M.P., L.-B. Zhang, C.T. Webb, A. Reeves, and J.A. Miller. 2004. Parsimony vs.
Bayesian likelihood for phylogenetic inference from heterogeneous datasets.
Botany 2004, Salt Lake City, Utah.
19. Simmons,
M.P., A. Reeves, and J.I. Davis. 2004. Character-state space versus rate of
evolution in phylogenetic inference. Botany 2004, Salt Lake City, Utah.
20. Simmons,
M.P. and K. Müller. 2006. The relative performance of indel-coding methods in
simulations. Botany 2006, Chico, California.
21. Simmons,
M.P. and K. Müller. 2006. Can the correct alignment be improved upon for
phylogenetic inference? Botany 2006, Chico, California.
22. Simmons,
M.P. and K. Müller. 2006. The relative performance of indel-coding methods in
simulations. Willi Hennig Society Annual Meeting, Oaxaca, Mexico.
23. Simmons,
M.P. and K. Müller. 2006. Can the correct alignment be improved upon for
phylogenetic inference? Willi Hennig Society Annual Meeting, Oaxaca, Mexico.
24. Simmons,
M.P., K. Müller, and C.T. Webb. 2007. The deterministic effects of alignment
methods to phylogenetic inference. Willi Hennig Society Annual Meeting, New Orleans.
25. Simmons,
M.P., K. Müller, and C.T. Webb. 2007. The deterministic effects of alignment
methods to phylogenetic inference. Botany & Plant Biology 2007 Joint
Congress, Chicago.
26.
Simmons, M.P., J.J. Cappa, R.H. Archer, A.J. Ford, D. Eichstedt and C.C.
Clevinger. 2008. Phylogeny of the Celastreae (Celastraceae) and the
relationships of Catha edulis (qat) inferred from morphological
characters and nuclear and plastid genes. Botany 2008, Vancouver, Canada.
27.
Simmons, M.P., K.F. Müller and C.T. Webb. 2008. The relative sensitivity of
different alignment methods and character codings in sensitivity analysis.
Botany 2008, Vancouver, Canada.
1. Simmons, M.P., H. Ochoterena and J.V. Freudenstein. 2001. Conflict between
amino acid and nucleotide characters. Congruence Symposium, Willi Hennig
Society Annual Meeting, Corvallis, Oregon.
2. Simmons,
M.P. and M. Miya. 2003. Efficiently resolving the basal clades of phylogenies
and gene trees. Seventh Rocky Mountain Plant Biotechnology and Molecular
Biology Symposium, Fort Collins, Colorado.
3. Simmons, M.P. and M. Miya. 2003.
Efficiently resolving the basal clades of a phylogenetic tree using Bayesian
and parsimony approaches: a case study using mitogenomic data from 100 higher
teleost fishes. Competing Methods for Phylogenetic Analysis Symposium, Willi
Hennig Society Annual Meeting, New York City.
4. Symposium
organizer, “Competing Methods for Sequence Alignment,” Willi Hennig Society
2003 Annual Meeting, New York City.
5. Colloquium
co-organizer, “Methods and Theory of Phylogenetic Inference,” Botany 2004, Salt
Lake City, Utah.
6. Simmons,
M.P., L.-B. Zhang, T.G. Carr, and K. Müller. 2005. A penalty of using anonymous
dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference. The
Character Concept in the Phylogeny and Evolution of Plants Symposium,
International Botanical Congress 2005, Vienna.
7. Symposium
co-organizer, “Character Coding in Phylogenetic Inference,” International
Botanical Congress 2005, Vienna.
8. Symposium
organizer, “Character-Sampling Strategies for Phylogenetic Inference,” Willi
Hennig Society 2006 Annual Meeting, Oaxaca.
9. Symposium
organizer, “Alignment for Phylogenetic Inference,” Willi Hennig Society 2007
Annual Meeting, New Orleans.
2000: Carnegie Museum of Natural History
Ohio State University Herbarium
2001: Dept. of Biology, Colorado State University
Dept. of Biology, Idaho State
University
Sigma Xi, Colorado State University
2002: Dept. of Botany, University of Wyoming
Colorado Native Plant Society, Fort
Collins Chapter
2003: Colorado Native Plant Society, Denver Chapter
Dept. of EPOB, University of
Colorado, Boulder
Dept. of Biological Sciences,
University of Northern Colorado
2004: Dept. of Biology, New Mexico State University
Deep Time Meeting and Workshop,
George Washington University
2006: Dept. of Biology, Colorado State University
2007: Dept. of Biology, University of Colorado,
Denver
Missouri Botanical Garden
Dept. of Biochemistry, Colorado
State University
2008: Denver Botanic Gardens
American
Journal of Botany associate editor (28 manuscripts), 2007 – present
Systematic
Botany
associate editor (15 manuscripts), 2006 – present
|
American Journal of Botany Annals of Botany Belgian Journal of Botany Biochemical Systematics and Ecology Bioinformatics BMC Bioinformatics BMC Evolutionary Biology BMC Genomics Botanical Journal of the Linnean Society Bothalia Brittonia Cat. of the vasc. plants of the southern cone Cladistics Electronic Journal of Biotechnology Evolution Flora of China |
Genetics International Journal of Plant Sciences Journal of Molecular Evolution Molecular Biology and Evolution Molecular Phylogenetics and Evolution Novon Parsimony, phylogeny, and genomics Plant Systematics and Evolution Proc. of the Entomological Society of Washington South African Journal of Botany Systematic Biology Systematic Botany Systematics and Biodiversity Taxon Telopea Weed Science |
National
Science Foundation, Systematic Biology panel member, 2007
Austrian Science Fund
Colorado Native Plant Society
National Geographic Society
National Science Foundation, Assembling
the Tree of Life
National Science Foundation, Biological
Research Collections
National Science Foundation, Systematic
Biology
U.S. Civilian Research and Development
Foundation
Scholarship Committee, College of Natural
Sciences, Colorado State Univ., 2004 – present
Awards Committee, Dept. of Biology,
Colorado State Univ., 2005 – present
Executive Committee, Dept. of Biology,
Colorado State Univ., 2005 – 2007
Local co-organizer, “Evolution 2004”
annual meeting
Board of Directors, Colorado Native Plant
Society, 2002 – 2004
Co-chair, Seminar Committee, Dept. of
Biology, Colorado State Univ., 2002 – 2004