Department of Biology

Renn Lab

Fish 'N Chips: Comparative Functional Genomics in African Cichlid Fishes. The evolution of behavior.

 

Current Lab Members

 

 

Heather Machado M.S. - Research Associate

Genome Architecture of Adaptive Radiation - Gene duplications are prevalent in genomes of organisms belonging to all three domains of life and it is now a well established force for evolutionary novelty. Gene duplication can result in phenotypic change by making multiple copies of genes available for dosage effects, partitioning of gene expression pattern and/or gene function or through the evolution of novel gene function. We aim to test whether this important evolutionary force has contributed to the remarkable evolutionary radiation of East African cichlid fishes (link to poster).  To quantify and identify gene duplications among radiating and non-radiating lineages, we employ competitive genomic DNA hybridization to a custom spotted microarray. In support of this technique we have conducted proof-of-concept experiments using 4 species of Drosophila (link to Renn et al submitted; link to Machado et al. submitted). (SEE HEATHER'S RESEARCH PAGES FOR PAST AND FUTURE WORK (currently under construction)).

Julia Carleton B.S. - Research Assistant

Thirty years of research have contributed to our understanding of the molecular, hormonal, and physiological mechanisms of the socially regulated switch between dominant and subordinate phenotypes among males of the African cichlid species Astatotilapia burtoni. Meanwhile, the female phenotypes have been largely ignored by all but a few studies regarding the reproductive cycle and affiliative behavior. Females of a recently collected A. burtoni wild stock from Zambia display a "good mother" phenotype that includes defensive aggression to protect free-swimming fry for up to 15 days post-release, whereas labstock females show similar aggression but eat their fry within 2-3 days post-release. Our current research employs a systems biology approach to investigate the neuroendocrine and genomic contribution to the novel phenotype of maternal aggression in A. burtoni. We use a cDNA microarray to identify incredible differences in gene expression between stocks. A module of gene expression, specific to the wild stock in the post-release, maternal stage contains some genes previously identified as important in male territorial behavior and also a novel set of genes related to maternal aggression.

Kelsey Wood Senior Thesis Student

For many animals, the expression of sex-typical behavior can be plastic depending on the social environment. We use the African Julidochromis transcriptus cichlid fish as a model to determine the underlying physiological and molecular mechanisms that account for differences and plasticity in expression of sex-typical behaviors. Among these fish the reversal in sex-role behavior is size dependent. In size-reversed pairs the larger mate is dominant and more aggressive towards intruders regardless of sex or species. To examine the molecular changes that accompany this plastic phenotype, we compare gene expression and hormone levels between sexes in size-conventional and size-reversed pairs. We compare the plasticity of gene expression to that of a sister species that is naturally sex-role reversed.

 

Kavita Krishnakant Senior Thesis Student

Behavioral studies show that the cichlid species J. transcriptus follows sex-role conventional behavioral phenotypes. However, the sister species, J. marlieri, exhibits a reversal of sex-roles in that  J. marlieri females are dominant to their mates and are clearly the aggressive sex. Previous work has identified a handful of genes that appear to be upregulated in the dominant individuals, the J. trancriptus males and the J. marlieri females. Our current goal involve the identification of important neural structures and thus we aim to validate these past microarray results through qPCR and in situ hybridization. 

 

Dan Bernstein Senior Thesis Student

Recently, the RNA-seq has been proposed as a method to measure the “transcriptome". While still in its infancy we see this tool as a potentiall powerful approach to address the evolution of gene expression patterns among African Cichlid fishes. It is our goal to perform a pilot experiment tp compare the gene expression patterns among several species of fish from Lake Tanganyika which show different mating styles. We will use 454 sequencing of normalized cDNA libraries from a single species in order to build a reference transcriptome. This reference will be used for RNA-seq expression profiling in 5 heterologous species. This effort will require extensive collaboration with Dr. Hofmann (U.T.Austin) Walter Salzburger (Univ. Basil) and other members of the Renn lab (Kevin Lynagh see below).

 

Noah Oppenheim Senior Thesis Student

Shifting demographics in the gulf of maine ecosystem yields altered top down predation dynamics for the American lobster (Homarus americanus). We will address three hypotheses through behavioral analysis of juvenile lobster predation.
1) There is a concurrent decline in apex predator population inshore and an unprecidented rise in lobster population density.
2) This high density lobster population is the cause of novel population density feedback mechanism among them, for example, cannibalism.
3) Lobster cannibalism, although the major factor in top down regulation of juvenile lobsters is a less efficient predation process than the more historically established ones such as crabs and fish.

 

Kevin Lynagh Independent Research Student

Recently, the RNA-seq has been proposed as a method to measure the “transcriptome". This new high throughput technology will likely replace modern microarray techniques however it is currently somewhat limited by the need for a complete reference genome sequence. As it is our goal to compare the gene expression patterns among many cichlid fish species we will face special challenges in the need to use a heterologous reference genome. Such cross-species studies may be best served by altenate assembly and counting algorithms. We will first replicate our anitcipated situation by using available RNA-seq data from model organisms and the genome from a closely related organism in order to compare available pipleines and algorithms.

 

Anny 2009/2010 Prospective Thesis students should look at past thesis projects, scan the "Student Projects Page" and then enquire about the possiblity of specific projects by emailing Prof. Suzy Renn renns@reed.edu

 

 

Past Thesis Projects

 Past Summer Research

 Past Lab Members

Past Independent Research

 

PAST THESIS PROJECTS

click on the name for a short summary.
click on "thesis" for abstract and representative data.

2009 Alumni with Thesis

Julia Carleton               thesis               (2 in prep)
Helen Magee                 thesis                publication
My Linh Nguyen            thesis                publication
Clare Parker                  thesis
Molly Schumer              thesis                in prep
Katie Tanner                  thesis                publication

 

2008 Alumni with Thesis

Alex Winters                  thesis
 Seyram Butame             thesis
Evan Bremer                  thesis
Cate Mingoya                 thesis

2007 Alumni with Thesis

Monika Wieland                thesis                publication
Cadence True                    thesis
Jessica Thompson            thesis
Victoria Zero                     thesis                in prep

 

 

PAST SUMMER RESEARCH

click on the name for a short summary.
click on "thesis" for abstract and representative data.

2009 Summer

Quinn Langdon --Reed College Science Research Fellowship --  poster
    Molecular mechanisms of environmentally induced sex-role reversal.
Homer Strong -- NSF-REU Summer Research Fellowship --  poster
    Mathematical clustering and visualization of microarray data.
Gavin Brown -- NSF Summer Research Fellowship --  poster
   Optimal normalization of microarray data.
Matt Hagen -- NIH Summer Research Fellowship --  
    Neuroanatomical localizaiton of socially regulated gene expression.

2008 Summer

Clare Parker -- NIH Summer Research Fellowship --  poster
    Neuroendocrine regulation of maternal behavior in A. burtoni.
Kelsey Wood -- NIH Summer Research Fellowship -- poster
    Is there a Hormonal Basis for the Observed Gender Biased Behaviors in African Cichlid Species of the Genus Julidochromis?

My Linh Nguyen -- Reed College Science Research Fellowship -- poster
   Do All Males Perceive "Social Opportunity" or Only the 2nd Most Dominant Male?
Dan Bernstein -- Murdock Life Sciences Research Fellowship -- poster
   DNA Sequence Comparison Based on EST Data from 4 Cichlid Species.
Natalie Morgenstern -- Murdock Life Sciences Research Fellowship -- poster
   Is "Good Maternal Care" theRresult of "Good Moms" or "Good Fry"?
(a Cross-Fostering Study in the African Cichlid Fish Species Astatotilapia burtoni.)
Julia Carleton -- Murdock Life Sciences Research Fellowship
 The expression profile of maternal behavior in A. burtoni.
Helen Magee -- Summer Student Volunteer
   Variation in male dominance behavior between wild and laboratory stocks of A. burtoni cichlid fish.
Jenny Leonard -- Arch and Fran Diack Student Field Research Award
    Peoples' impact on plants in Ha’Makuya, N.E. Limpopo Province, South Africa
Melati Kaye -- Milton L. Fischer Summer Field Research Fellowship --  website
    The Effects of Coastal “Dead Zones” on Oregon’s Salmon Fisheries
Victoria (Vicky) Zero-- Mellon Postbac Research Assistant
   Genomic Mechanisms for Environmental and Genetic Plasticity of Gender Biased Behavior.

2007 Summer

Christian Reilly - postdoc
Victoria Zero - research assistant                                                poster
Robby Kunkle - Murdock Life Sciences postbac                            poster
   Microsatellite index for Cichlid Species.                                   manuscript
Molly Schumer - Miller Foundation Summer Student Fellowship poster
   Gene Duplication and Gene Divergence among the Genus Julidochromis.
Julia Carleton - Reed College Summer Research Fellowship        poster
   Hormonal Mechanisms of Maternal Aggression in A. burtoni.
Peter Jantzen - Murdock Life Sciences Summer Student              poster
   Alingment and Bioinformatic Analysis of Cichlid ESTs.
Doug Borst - Postbac Volunteer                                                   poster
   Gene Expression Profiling from Field Samples.


Past Independent Research

Kelsey Wood

481 Indpendpent Research
Is there a Hormonal Basis for the Observed Gender Biased Behaviors in African Cichlid Species of the Genus Julidochromis?                                    proposal



Past Lab Members

Christian Reilly - M.S. Research Associate

Research Associate
I'm broadly interested in sensory ecology in general, and in the visual
ecology of fishes in particular. Sensory ecology is the study of the
mechanisms through which fitness of organisms is optimized though
adaptations to environmental constraints on information transfer.
Implicit in this study is the notion that an organism's natural
behaviors require some information about environmental states, and
that evolution shapes both behavior and sensory structures to match
local conditions. I've come to the Renn lab to learn modern,
quantitative techniques for studying behavior in fishes and measuring
the footprints of the underlying evolutionary changes. Here I'm
focusing on using heterologous Comparative Genomic Hybridizations
(hCGH) to examine rapid evolutionary change in closely related cichlid
fishes and correlating these differences with interspecies differences
in parental care strategies.

Evan Bremer

2008 Senior Thesis Research
Assessing the Presence, Stability, and Linearity of Dominance Hierarchies Among Female Cichlids of the Species Astatotilapia burtoni
Since Astatotilapia burtoni females school in the wild and in laboratory settings, the potential for the development of a social structure is significant.  I chose to study female A. burtoni with respect to their dominance structures and establish the groundwork for future studies of female dominance to complement the wealth of research conducted with males of this same species. (more detail)

Seyram Butame

2008 Senior Thesis Research
The Dominant Female: A Look at the Possible Sex-Role Reversal in Julidochromis marlieri, from a Behavioral and Hormonal Perspective.
The fish family Cichlidae is characterized as monogamous and biparental. Typically, the males are larger and more aggressive and hence are able to dominate their mates. The genus Julidochromis or “Julies” as they are affectionately called, is part of this family of fish localized to Lake Tanganyika in Eastern Africa. Julidochromis marlieri, is one of five species belonging to the genus. They are unique, in that they differ from other species by having the females larger than their male counterparts and hence, females develop the potential to dominate the males.(more detail)
This research project was supported in part by a grant from the James F. &Marion L. Miller Foundation made to Reed College.

Julia Carleton

The expression profile of maternal behavior in A. burtoni

 

This research project was supported in part by a grant from the James F. &Marion L. Miller Foundation made to Reed College.

 
Helen Magee

Variation in male dominance behavior between wild and laboratory stocks of A. burtoni cichlid fish.

 

This research project was supported in part by a grant from the James F. &Marion L. Miller Foundation made to Reed College.

Cate Mingoya

2008 Senior Thesis Research
Intraspecies Recognition in A. burtoni Cichlids
The African Cichlid species, Astatotilapia burtoni, is a maternal mouth brooding species. The fry spend approximately 2 weeks within the buccal cavity of the mother. This sustained close physical contatct could provide stimulus necessary for filial imprinting. Since such detailed care and high expenditures of energy are required to raise the young to maturity, evolutionary theory stipulates that in the case of the cichlid, in order to maximize efficiency in benefiting it’s own reproductive success, it would be important for it to expend the least amount of energy in deriving the greatest benefit in caring for its biological offspring. Imprinting might allow fry and mother to recognize each other. (more detail)

My Linh Nguyen

A. burtoni maternal mouth-brooding cichlids as a new model for appetite regulation.

 

This research project was supported in part by a grant from the James F. &Marion L. Miller Foundation made to Reed College.

Clare Parker

Regulation of Sexual Differentiation in Astatotilapia burtoni.

Molly Schumer

2009 Senior Thesis Research

The Expression profile of Gender Biased Behaviors in African Cichlid Species of the Genus Julidochromis.

 

 

Katie Tanner

2009 Senior Thesis Research

The Challenge Hypothesis, originally put forth by Wingfield and colleagues in 1990, has since become central to understanding male aggressive behavior through the lens of endocrinology. 

Jessica Thompson

2007 Senior Thesis Research
Currently I am working on an experiment to test the strength of mate choice as a gene flow barrier among allopatric populations of the species Astatotilapia burtoni from Lake Tanganyika using microsatelites coupled with behavioral experiments.
.....
When I'm not in the lab, I fill my days with cooking, rock climbing, mountaineering, playing guitar and running the student bike shop.
more about Jessica

Cadence True

2007 Senior Thesis Research
Previous microarray analysis of gene expression differences in territorial and non-territorial male phenotypes present a candidate list of genes including many neurotransmitters and neuropeptides.  This thesis presents the first evidence for colocalization of GnRH and AVT neuropeptides in the POA of this teleost fish.
more about Cadence


Monika Wieland

2007 Senior Thesis Research
Academic passions include animal behavior and social communication. Other passions include writing, wildlife photography, bird-watching, and hockey watching.
more about Monika

Alex Winters

2008 Senior Thesis Research
Maternal Care and Aggression in the African Cichlid Astatotilapia burtoni
Despite a wealth of research regarding the hormonal and molecular basis of aggression in male A. burtoni, little work has been done with the females of this species. While the females of the inbred lab strain show little maternal care and aggression, a recently collected wild stock exhibit a rich repertoire of maternal care. My thesis describes the behavioral differences between these two stocks and evaluates the relative levels of steroid hormones. (more detail)
This research project was supported in part by a grant from the James F. &Marion L. Miller Foundation made to Reed College.

Victoria Zero

2007 Senior Thesis Research
more about Vicky