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).


Spring 2009 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 construction

Project 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 Manual

DIVA-GIS Assignment (10 pts; due Wed 25 Feb by 5 pm):
procedure pdf, Wild potato data in zip folder

GEOLOCATE of Herbarium Specimens Assignment (10 pts; due Mon Mar 9 at beginning of class)
procedure pdf, GEOLOCATE Users Manual

BIOCLIM Modeling Exercise (no pts; performed 9 Mar 2009):
procedure pdf

MAXENT Tutorial (no pts; performed 9 Mar 2009):
procedure pdf

Project 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

invasives web lancaster web md web

A Website containing information and photos of some non-native plants in and around Pennsylvanian woodlands.

An interactive checklist of Lancaster County plants with links to illustrations. Searchable by habit plus federal and state conservation, wetland, and nativity designations.

An authoritative informatics website providing just about everything one could ever want to know about the 31 species of woody vines in Pennsylvania.

f woody plants pa manuel's plants

An interactive checklist of MD plants with links to illustrations. Searchable by habit plus federal and state conservation, wetland, and nativity designations.

An interactive checklist of woody PA plants with links to illustrations. Searchable by habit, conservation status, and taxonomic class.

For Manuel.

Herbarium Poster Productions

invasives poster invasives poster

A 22x28" poster-version of an illustrated glossary of botanical terminology.

A 22x28" poster-version of a photographic guide to plants invasive to Mid-Atlantic woodlands

A 24x36" poster-version of a photographic guide to lawn weeds

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)


Hardy CR, HP Linder (2007) Phylogeny and historical ecology of Rhodocoma (Restionaceae) from the Cape Floristic Region. Aliso 23: 213-226.
(pdf available)


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 Cape flora: A macroevolutionary and macroecological perspective. Pp. 46-73 in F. T.
r, 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. Princeton University Press.

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 Cape flora. Philosophical Transactions of the Royal Society of London B 359 (1450): 1623-1632.
(pdf available)


Hardy CR (2003) Malawi . Natural History 112 (travel issue, supplement 4A): 75.

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.  


Hardy CR (2001) Systematics of Cochliostema, Geogenanthus, and an undescribed genus in the spiderwort family Commelinaceae. Ph.D. Dissertation, Cornell University , Ithaca , NY .  


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. University of Pennsylvania Press.
(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. University of Pennsylvania Press.
(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: Australia.


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)


Parks JC (1989) Distribution of gametophytic populations of Vittaria and Trichomanes in Pennsylvania. Rhodora 91: 201-206.
(Millersville Library Bibliography)


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)


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)


Parks JC (1983) The fern genera Vittaria and Trichomanes in the Northeastern United States. Rhodora 85 (841): 83-92.
(Millersville Library Bibliography)


Parks JC (1973) A revision of North American and Caribbean Melanthera (Compositae). Rhodora 75: 169-210.
(Millersville Library Bibliography)


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)


Parks JC (1968) A revision of the genus Melanthera Rohr (Compositae): in North America and the Caribbean. Ph.D. Dissertation, Vanderbilt University.  
(Millersville Library Bibliography)