EUGENE D. GALLAGHER 
Associate Professor
Environmental, Earth and Ocean Sciences
Highest Degree
Ph.D. (1983) University of Washington School of Oceanography
Office Phone (617) 287-7453 FAX (617) 287-7474
EMail Eugene.Gallagher@umb.edu
Main Specialties: Benthic Ecology, Biological Oceanography
Page last revised: 5/22/07 (check out new features marked
with 
)
Guide to the page
Research Interests
- Benthic Community Structure
- Multivariate Statistical Analysis
- Succession
- Mathematical Modeling
- Polychaete Biology
Research in my laboratory focuses on processes controlling
soft-bottom
benthic community structure in space and time. This research ranges
from
studies of process, like competition (Gallagher
et al., 1990), to that of pure pattern (e.g. , Trueblood
et al., 1994), to the covariation of environmental variables and
species
composition (Gallagher &
Grassle
1997, Legendre &
Gallagher
2001). My students and I work on methods to analyze patterns in
community
structure and developed PCA-H, short for Principal
Components
Analysis
of Hypergeometric probabilities. A major emphasis of our work
is
to assess the relative effects of pollution and natural factors on
benthic
community structure. I am co-PI of an MIT SeaGrant project to assess
the
effects of capping of dredged material. Most recently, I've been
analyzing
patterns affecting Boston Harbor and Massachusetts Bay community
structure
as part of the ongoing MWRA monitoring program to assess the effects of
the new Massachusetts Bay sewage outfall. Gallagher
& Keay (1998) review processes controlling Boston Harbor
community
structure. An expanded version of this paper is available for
viewing
in
html format or
as an Adobe 
.
Boston Harbor provides ideal field sites for studies of pollution
on community structure. My students may elect to study processes that
are
affected by the activities of benthic organisms, such as bioturbation,
and those processes that directly affect the growth of benthic
populations,
such as microphytobenthos (Gould and Gallagher 1990),
multivariate spatial and successional patterns in intertidal community
structure (Trueblood et al. 1994), and
patterns
of PAH metabolism in polychaetes (Kane-Driscoll & McElroy, 1996).
David
Shull complete his Ph.D. in 2000, testing new bioturbation models in
the
field. He is now on the faculty at Gordon College.
Masters
students have worked on factors controlling sediment fabric, models and
statistical analysis of the spring bloom, models of bioturbation, and
multivariate
statistical analyses of benthic community structure.
Representative Publications
Gallagher, E. D., G. B. Gardner, and P. A.
Jumars. 1990. Competition among the pioneers in a seasonal soft-bottom
benthic succession: field experiments and analysis of the Gilpin-Ayala
model. Oecologia 83: 427-442.
Gould, D. M. and E. D. Gallagher. 1990. Field
measurement of specific growth rate, biomass and primary production of
benthic diatoms of Savin Hill Cove, Boston. Limnol. Oceanogr. 35:
1757-1770.
Trueblood, D. D, E. D. Gallagher, and D.
M. Gould. 1994. The three stages of seasonal succession on the Savin
Hill
Cove mudflat, Boston Harbor. Limnol. Oceanogr. 39: 1440-1454. [The
Matlab m.files for performing the analyses in this paper are provided
below
as self-extracting zip files.]
Gallagher, E. D. and K. E.
Keay.
1998. Organism-sediment-contaminant interactions in Boston Harbor. Pp.
89-132 in K. D. Stolzenbach and E. E. Adams, eds., Contaminated
sediments
in Boston harbor. MIT Sea Grant Publication 98-1. [An earlier version
of
this document is available as an html
file or an
Adobe ]
Legendre, P. and E.
Gallagher.
2001. Ecologically meaningful transformations for ordination of
species
data. Oecologia: 129: 271-280.
A
zip file containing Matlab 6 files to perform the transformations,
correspondence
analysis and PCA
A zip file containing
Matlab 4.2 m.files to perform transformations, correspondence analysis
and PCA
The documentation for Gallagher's Matlab m.files is available here
Download
a draft of the paper
Tecnical documents
Gallagher, E. D. and J.
F. Grassle. 1997. Virginian Province Macroinfaunal
Community
Structure: PCA-H Analyses and an Assessment of Pollution Degradation
Indices.
126 page technical report submitted to the EPA on 2/12/1997 [This
4.7 mb document can be downloaded as an Adobe]
Gallagher, E. D. 1999.
Statistical
Analyses of MA Bay Benthos 1992-1999. A 154-page technical report
submitted to Battelle New England on 8/17/99 as part of the MWRA-funded
Harbor Outfall Monitoring. [This 3.7 mb document can be
downloaded
as an Adobe as an Adobe ]
Gallagher, E. D. and D. Shull. 1999.
Statistical Analyses of Boston Harbor Benthos 1991-1999. A
39-page
technical report submitted to Battelle New England on 8/22/99 as part
of
the MWRA-funded Harbor Outfall Monitoring. [This 1.2 mb document
can be downloaded as an Adobe as an Adobe ]
The recovery of Boston Harbor
The recovery of Boston Harbor from the woeful state described in
Gallagher
& Keay (1998)
has continued. The following image, modified from the latest MWRA
annual report (URL: http://world.std.com~enquad)<
/a> shows the increasing extent of dense amphipod mats, dominated by
Ampelisca
abdita. As described in Gallagher
&
Keay (1998), these mats were rare in the harbor during the 1980s.
These
mats indicate an early stage in the recovery of the harbor's benthos.
They
have increased dramatically as sewage input to the harbor has declined.
The image in the lower right is a 1997 sediment-profile image of a
dense
ampeliscid amphipod mat from Hull Bay (Only the upper 12 cm of the
sediment
is shown, images courtesy of B. Howes, R. Diaz, Izzy Williams, and
ENSR).
The recovery of Boston Harbor is discussed on the PBS Scienti
fic American Frontiers web page.
Courses Offered at UMASS/Boston
All courses listed here and most other graduate courses at
UMASS/Boston
are available to non-matriculated students (with instructor's
permission).
Send an Email to
receive
a printed copy of a course syllabus.
EEOS 601:Introduction to
Applied Statistics
The Summer 2007 syllabus is available
in html
and
as a pdf file.
EEOS 611:Applied Statistics (Every
Spring, including Spring
2007)
Spring 2007 (MW 10-11:15, S-2-066).
The syllabus for the Spring
2007 EEOS611 is now available in html
and as.
(revised 2/7/07)
Course flyer
The textbook is Ramsey & Schafer's (2002) Statistical
Sleuth
(ordering information below)
Log on to WebCT, the
UMASS Online server
EEOS 612:Multivariate Statistics
(Spring
2002, and about every 3 years)
I offered this course in Spring 2002 and as a small tutorial in Fall
2004. The
syllabus
is available as a pdf
or as html. The primary text is
Legendre & Legendre's Numerical Ecology,
2nd
Edition (ordering
information below).
We will cover diversity analyses, cluster analysis, ordination, Factor
Analysis and structural equation modeling, and spatial analysis. We
will
use Matlab throughout (ordering information), supplemented with SPSS
and
SAS where appropriate (all available on the UMB computer system).
EEOS 630:Biological Oceanographic
Processes
(Every Fall)
I designed this course to provide a rigorous introduction to the
major
processes in biological oceanography using many classic papers from the
primary literature. The course covers:1) phytoplankton ecology, 2)
zooplankton
ecology, 3) ecosystem modeling, and 4) benthic processes, including the
effects of pollution on marine ecosystems. In the ecosystem modeling
portion,
we analyze John Steele's North Sea Ecosystem model.
The syllabus
for the Fall 2006 course is available as a pdf
and html file. All
handouts
posted on WebCT:
Log on to WebCT, the
UMASS Online server
EEOS 720:Benthic Boundary Layer Processes
I designed Benthic Boundaries to focus on the interdisciplinary
aspects
of benthic environments. We discuss processes important for
understanding
the environment faced by benthic organisms and the effects of benthic
organisms
on geochemical processes. This course should aid chemists,
microbiologists,
and geologists understand how benthic organisms affect the chemistry,
geology,
and physics of the benthic boundary layer.
The syllabus a as a pdf
and html file.in html or pdf
(revised 10/24/00)
BIO640: Discrete
Mathematical
Modeling
The goals are to introduce, discuss, and implement (on computer)
discrete
mathematical models having applications for ecology, genetics,
geochemistry,
geology, and policy. Major emphasis is is devoted to 4 areas of
modeling:
1) Interval graph theory (with food-web and phylogenetic applications),
2) Markov chain theory, 3) ordination and classification analysis of
environmental
data, and 4) Factor analysis. This disparate group of models share 2
features:
the data are usually portrayed graphically, and their structure can be
analyzed using matrices. We use MATLABtm
throughout the course and COMPAH96 for cluster
analysis
and creating data files for MATLABtm
analysis.
The
syllabus
for the Spring 1999 course is available.
Short Courses & Talks
USING A WEIGHT OF EVIDENCE APPROACH TO SEDIMENT
ASSESSMENT
June 16, 1998 - Boston University Sponsored by: The North Atlantic
Chapter
of the Society of Environmental Toxicology and Chemistry View
the slides used in the talk (graphic intensive, 15 minutes to view with
a 28.8 modem)
Free Software
COMPAH96
I distribute free of charge the program COMPAH, which stands for
Combinatorial
Polythetic Agglomerative Hierarchical clustering. The figure above was
generated with COMPAH, with final editing in Corel's Presentations 8.
The
program was originally written by Don Boesch, now at the University of
Maryland. I've rewritten the FORTRAN program to run under DOS, as a DOS
application under Windows 3.1, and as a rudimentary Windows application
(Win31, WIN95 - haven't tried Win98). The latest version is called
COMPAH96
and is available as an 1589kb self-extracting zip file (COMPAH.EXE).
This
file should be placed in a directory and extracted by simply running
the
COMPAH.EXE file from Program or File Manager. I've included full
documentation
as a text file, as a WordPerfect 5.1 (DOS), WP6.1, an Adobe pdf file
and
as a MSWord 6.0 document. An example of COMPAH trees can be seen in
Trueblood
et. al. (1994). There is also a list of about 40 test data files
and
outputs in a variety of input formats available in the self-executing
zip-file
TESTDATA.EXE.
COMPAH program last revised: 7/29/98. Documentation revised
1/6/99
(Download documentation
as an Adobe)
Download COMPAH.EXE
now (1589 kb, includes documentation)
Download TESTDATA.EXE
now (65kb)
Steele's North Sea Ecosystem Model
Dr. Bernie Gardner and Kathy Hall adapted John Steele's North Sea
Ecosystem
model for PC's. The FORTRAN code was originally written by Mike Laundry
(now at U. HI). The self-extracting zip file STEELE.EXE contains the
FORTRAN
code, and executable files for the Landry single-cohort and
multi-cohort
versions of the Steele model. The FORTRAN program is compiled to run
under
DOS and will run as a DOS application under Windows. I use these
programs
in my Biological Oceanography course. Documentation is included as a
WordPerfect
5.1 (DOS) file, Windows Word, and a text file. Download
Steele.exe now
A screen capture from Landry's single-cohort version of
the
Steele North Sea Ecosystem model.
PCA-H MATLAB FILES
The following figure shows an example of a PCA-H analysis of benthic
data from Trueblood et al. (1994):
A Gabriel Euclidean distance biplot showing the change
in benthic
community structure through time as a solid purple line and those
species,
shown as arrows, that contribute most to the seasonal succession
pattern
(Hp: Harpacticoid copepods, Cp: Capitella spp., Py:
Pygospio elegans, Ol: Oligochaetes, Sb: Streblospio
benedicti, Pl:Polydora
cornuta, and Os: Ostracods). From Trueblood
et
al. (1994). Faunal distances calculated using CNESS and all
analyses
done with Matlab 4.2c.
The figures in Trueblood et al. (1994)
were
generated with Matlab 3.5 (for DOS). All of the PCA-H Matlab m.files
have
been upgraded for Matlab 4.2c (for Windows). Copies of the m.files to
generate
the figures from Trueblood et al. (1994) are available as
self-executing
zip files.
Download ddtmat35.exe
(for Matlab 3.5)
Download ddtmat42.exe
(for Matlab 4.2)
Matlab 6 programs for
Correspondence Analysis, PCA, PCA-H, rarefaction & CNESS
Correspondence analysis, with column chi-square distances
preserved
as described in Legendre
& Gallagher
(2001). This image produced by Matlab 4.2.
Matlab programs, updated 1/4/03, to perform the analyses in
Legendre
& Gallagher (2001) are included in a zip file for Matlab 6 LegGal6.zip.
and Matlab 4.2 LegGal4.zip&
nbsp; The documentation is available here
My MCAS Analyses
My 9/29/01
compilation of errors in the 2001 and 2000 10th grade math tests
Slides from
10/22/01 talk to EEOS graduate students & faculty on MCAS Science
errors,
html
Handout
of slides from MCAS science talk
Odds ratios
for failure among African-American, Latino and Whites on MCAS (9/1/02)
One Effect
of Retention on Projected High School Dropout Rates (11/20/01)
Handout of
slides used in my April 8, 2002 talk at MIT on flaws in the MCAS
science
test
The Mismeasure
of MA (an unpublished op-ed to the Globe, submitted 4/28/02)
An analysis
of standard errors on the 2001 MCAS ELA and Math exams (6/4/03)
On Boxes, Hinges,
Leaves, Quartiles, Stems & Whiskers in the May 2003 High-Stakes
MCAS
Math Exam (7/9/03)
Other MCAS links
Robert
Gaudet's annual report on socioeconomic factors & MCAS
Chen
& Ferguson's spatially explicit regression of socioeconomic factors
& MCAS
Be
acon Hill Institue Regression
LINKS TO OTHER WEB PAGES
- EEOS601/611/612 Statistics Links
- Statistical packages
- Statistics Textbooks that I use (click on the book image
for
catalog
descriptions)
Other Interesting Statistics Material on the web
EEOS630: Biological Oceanography
- Systematics
- Plankton
- Phytoplankton
- Zooplankton
- Benthos
- Upwelling, ENSO & PDO
- Boston Harbor/Gulf of Maine
- Gyres
- Satellite Remote Sensing
- Mnemiopsis leidyi invasion
- Global Carbon cycle
- Benthic Pollution
EEOS720: Benthic Boundaries
- Benthic Pollution
- Plate Tectonics
- Continental Margins
- Gulf of Maine - MA Bay
Ordination & Cluster analysis
Email:
Eugene.Gallagher@umb.edu | Tel: 617 287-7453 |
Fax: 617
287-7474
Environmental, Earth and Ocean Sciences,
UMASS/Boston,
Boston MA 02125-3393
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