BIOL 471
Computational Methods in Systematics
General Information
This class is for either biology majors or computer science majors. Biology majors should have excellent familiarity with the use of PC computers for Microsoft Excel, the use of text editors for manipulating text files, and Web navigation. Computer Science majors should have a strong interest in the application of computer science to biodiversity research and conservation, evolution, or bioinformatics.
Meeting 3 hrs per week, 1/3 is used for lecture, 2/3 for lab exercises on the computer. Exams and quizzes are often performed by executing tasks on the computer.
Although taught by Dr. Hardy, this course is not a plant course. The methods and theory taught are broadly applicable.
Prerequisites are Concepts of Botany (BIOL 221) and Concepts of Zoology (BIOL 211), or permission of Dr. Hardy (the latter particularly for computer science majors who may not have taken both of those biology courses).
Syllabus
Exercises and Projects Information
Module 01: Biodiversity Informatics
Exercise 01 - Sources of Biodiversity Data and Simple Biodiversity Mashups (10 pts; due Jan 26 at begining of lab)
Exercise 02 Preparation for Interactive Key Construction (no points)
demo-sliks-key to selected hardwood trees
demo-data-set to conifer genera
Exercise to Conifer Key constructionProject 01 SLIKS Key Construction for PA Trees (25 pts; due Mar 9 at beginning of class)
Module 02: Biogeographic Mapping, Analysis, and Modeling
Literature & Learning Goals for this Module
DIVA-GIS Tutorial (in class 16 Feb, no points):
procedure pdf, Bolivian tutorial data in zip folder,
DIVA-GIS Users ManualDIVA-GIS Assignment (10 pts; due Wed 25 Feb by 5 pm):
procedure pdf, Wild potato data in zip folderGEOLOCATE of Herbarium Specimens Assignment (10 pts; due Mon Mar 9 at beginning of class)
procedure pdf, GEOLOCATE Users ManualBIOCLIM Modeling Exercise (no pts; performed 9 Mar 2009):
procedure pdfMAXENT Tutorial (no pts; performed 9 Mar 2009):
procedure pdfProject 02 - Climatic Envelope Modeling (35 pts; due Fri Apr 3 by 5 pm)
Module 03: Phylogenetic Inference
Learn theory and practice of reconstructing the evolutionary history of species.
Learn how to construct cladograms manually and with computer programs.
Learn how to reconstruct ancestral states.
Learn how to find DNA sequence data on the Web and to analyze the data to infer phylogenetic relationships.
Module 04: Species Delimitiation, Diagnostics, and Conservation Forensics
Learn algorithms for delimiting species.
Learn how to use DNA sequence data to identify unknown organisms to species.
Past Semesters
Visit Spring 2007 Course Website or Manual
Herbarium Web Productions
Herbarium Poster Productions
Herbarium Research Articles
Hardy CR, NW Hardy (2008) Simple biodiversity mashups for non-tech-savvy biologists: a demonstration using the liana flora of Pennsylvania, USA. Journal of the Torrey Botanical Society 135: 585-594.
Hardy CR, P Moline, HP Linder (2008)
A Phylogeny for the African Restionaceae, and New Perspectives on Morphology's Role in Generating Complete Species Phylogenies for Large Clades. International Journal of Plant Sciences 169: 377-390.
(Please contact Keeper for pdf of article; click here for supporting electronic appendices, matrices, and cladograms)
2007
Hardy CR, HP Linder (2007)
Phylogeny and historical ecology of Rhodocoma (Restionaceae) from the Cape Floristic Region. Aliso 23: 213-226.
(pdf
available)
2006
Hardy CR (2006)
Reconstructing ancestral ecologies: challenges and
possible solutions. Diversity & Distributions 12: 7-19.
(pdf
available)
Davis JI, G Petersen, O Seberg, DW Stevenson, CR Hardy, MP Simmons, FA Michelangeli, DH Goldman, LM Campbell, CD Specht, JI Cohen (2006) Are mitochondrial genes useful for the analysis of monocot relationships? Taxon 55: 857-870.
Petersen G, O Seberg, JI
Davis, D Goldman, DW Stevenson, LM Campbell, FA
Michelangeli, CD Specht, MW Chase, MF Fay, JC Pires, JV
Freudenstein, CR Hardy, MP Simmons (2006)
Mitochondrial data in monocot phylogenetics. Aliso 22: 52-62.
(pdf
available)
Hardy CR, HP Linder (2005)
Intraspecific variability and timing in ancestral
ecology reconstruction: A test case from the Cape flora. Systematic Biology 54 (2): 299-316.
(pdf
available)
Linder HP, CR Hardy (2005)
Speciation in the
Bakker, L. W. Chatrou, B. Gravendeel and P. B. Pelser, eds. Plant species-level systematics: new perspectives on
pattern & process. Koeltz, Königstein
(pdf
available)
Linder HP, CR Hardy, F
Rutschmann (2005) Taxon sampling effects in molecular
clock dating: An example from the African Restionaceae. Molecular Phylogenetics & Evolution 35: 569-582.
(pdf
available)
Hardy CR, RB Faden (2004). Commelinaceae. Pp 425-427 in Smith N, S
Mori, A Henderson, DW Stevenson, SV Heald (eds.) Flowering Plants of the Neotropics.
Hardy CR, RB Faden (2004) Plowmanianthus, a new genus of Commelinaceae
with five new species from tropical America. Systematic Botany 29 (2): 316-333.
(pdf
available)
Hardy
CR, JI Davis, DW Stevenson (2004) Floral
organogenesis in Plowmanianthus (Commelinaceae).
International Journal of Plant Sciences 165 (4):
511-519.
(pdf
available)
Davis JI, DW Stevenson, G Petersen,
O Seberg, LM Campbell, JV Freudenstein, DH Goldman, CR Hardy, FA Michelangeli, MP Simmons, CD Specht, F Vergara-Silva, MA 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 (3): 467-510.
(pdf
available)
Linder HP, CR Hardy (2004)
Evolution of the species-rich
(pdf
available)
2003
Hardy
CR (2003)
Hardy
CR, DL
Lipscomb, KC Nixon, H Ochoterena (2003) WinClada ver. 1.0, a basic users manual.
Available upon request from Kevin C. Nixon, Bailey Hortorium, 462 Mann Library, Cornell
University, Ithaca, NY 14853.
2001
Hardy CR (2001) Systematics of Cochliostema, Geogenanthus, and an undescribed genus in the spiderwort
family Commelinaceae. Ph.D. Dissertation,
2000
Dyer AF, JC Parks, S Lindsay (2000) Historical review of the uncertain taxonomic status of Cystopteris dickieana R.Sim (Dickie's bladder fern). Edinburgh Journal of Botany 57 (1): 71-81.
(Millersville Library Bibliography)
Hardy CR,
DW Stevenson (2000) Floral organogenesis in some species
of Tradescantia and Callisia (Commelinaceae). International Journal of Plant
Sciences 161 (4): 551-562.
(pdf
available)
Hardy
CR, DW Stevenson (2000) Development of the
flower, gametophytes, and floral vasculature in Cochliostema odoratissimum (Commelinaceae). Botanical Journal of the Linnean Society 134
(1): 131-157.
(pdf
available)
Hardy CR, DW Stevenson, HG Kiss
(2000) Development of the flower, gametophytes, and floral
vasculature in Dichorisandra thyrsiflora (Commelinaceae). American Journal of Botany 87 (9): 1228-1239.
(pdf
available)
Parks JC, AF Dyter, S Lindsay (2000) Allozyme, spore and frond variation in some Scottish populations of the ferns Cystopteris dickieana and Cystopteris fragilis. Edinburgh Journal of Botany 57 (1): 83-105.
(Millersville Library Bibliography)
Parks JC (2000). Lycopodiaceae. Pp 64-70 in Rhoads AF, TA Block (eds.) The plants of Pennsylvania: an illustrated manual.
(Millersville Library Bibliography)
Parks JC, JD Montgomery (2000). Ferns. Pp 71-106 in Rhoads AF, TA Block (eds.) The plants of Pennsylvania: an illustrated manual.
(Millersville Library Bibliography)
Stevenson DW, JI Davis, JV Freudenstein, CR Hardy, MP
Simmons, CD Specht (2000)
A phylogenetic analysis of the
monocotyledons based on morphological and molecular
character sets, with comments on the placement of Acorus and Hydatellaceae. Pp 17-24 in Wilson KL and DA Morrison (eds.) Monocots: systematics and
evolution. CSIRO Publishing:
1998
Parks JC, KA Mosser (1998) A morphological and allozymal study of a Cystoperis tennesseensis (Dryopteridaceae) population: first report of the species in Lancaster County, PA. Journal of the Pennsylvania Academy of Sciences 71 (2): 78-83.
(Millersville Library Bibliography)
1989
Parks JC (1989) Distribution of gametophytic populations of Vittaria and Trichomanes in Pennsylvania. Rhodora 91: 201-206.
(Millersville Library Bibliography)
1985
Parks JC (1985) Erigenia bulbosa in Lancaster County, Pennsylvania. Bartonia 51.
(Millersville Library Bibliography)
Stober SS, JC Parks (1985) Chromosomal studies of Physalis virginiana var. subglabrata and Physalis heterophylla. Bartonia 51: 65-68.
(Millersville Library Bibliography)
1984
Parks JC (1984) A first report of the fern genus Vittaria in New York. Rhodora 86 (848): 421-423.
(Millersville Library Bibliography)
Parks JC (1984) New Pennsylvania locality of Cryptogramma stelleri. Bartonia 50: 63.
(Millersville Library Bibliography)
1983
Parks JC (1983) The fern genera Vittaria and Trichomanes in the Northeastern United States. Rhodora 85 (841): 83-92.
(Millersville Library Bibliography)
1973
Parks JC (1973) A revision of North American and Caribbean Melanthera (Compositae). Rhodora 75: 169-210.
(Millersville Library Bibliography)
1969
Parks JC (1969) Simple technique for demonstrating chromosomal coils using Tradescantia pollen mother cells. Proceedings of the Pennsylvania Academy of Science 43: 61-63.
(Millersville Library Bibliography)
1968
Parks JC (1968) A revision of the genus Melanthera Rohr (Compositae): in North America and the Caribbean. Ph.D. Dissertation,
Vanderbilt
(Millersville Library Bibliography)