Investigating Blue Whale (Balaenoptera Musculus) Population Structure Using Introns of Conserved Nuclear Genes

EPA Grant Number: U915578
Title: Investigating Blue Whale (Balaenoptera Musculus) Population Structure Using Introns of Conserved Nuclear Genes
Investigators: Conway, Carole A.
Institution: University of California - Davis
EPA Project Officer: Packard, Benjamin H
Project Period: August 1, 1999 through August 1, 2002
Project Amount: $79,759
RFA: STAR Graduate Fellowships (1999) RFA Text |  Recipients Lists
Research Category: Academic Fellowships , Ecological Indicators/Assessment/Restoration , Fellowship - Ecology and Ecosystems


The objective of this research project is to investigate whether there are separate stocks (populations that are essentially demographically independent) of blue whales (Balaenoptera musculus) to designate meaningful management units for conservation. If separate stocks exist, the phylogenetic relationships among them will be examined to assess the level of diversity within the species. This work will be conducted using molecular genetic markers, introns, of conserved nuclear genes. An ancillary objective is to evaluate the usefulness of nuclear introns in comparison to other markers for answering questions at the population, subspecies, and species levels.


Skin samples or DNA template for genetic analyses will be obtained from the collections of governmental agencies, private organizations, and other academic institutions worldwide. The variation present in at least 10 introns will be examined using the polymerase chain reaction (PCR), single-stranded conformational polymorphisms (SSCP), and direct sequencing. The experimental design consists of two phases. In the first phase, the PCR amplification of approximately 80 different introns will be tested using published primers. Those introns that can be successfully amplified will be screened for variation using SSCP. Five to 10 individuals from distant regional populations (chosen to represent the entire geographic range) will be used for the screening. Those introns that appear to contain the most potentially informative variation will be carried into the next phase. In the second phase, at least 10 introns will be amplified in all samples and the PCR products resolved on an SSCP gel. SSCP also serves to purify alleles of heterozygotes for subsequent sequencing. All allele variants will be excised from the gel, reamplified, and sequenced using an automated system. The data will be analyzed using population genetic statistical methods and a phylogeographic approach. F-statistics will be calculated for each locus and for all loci combined. DNA sequence data will be analyzed phylogenetically using parsimony and maximum likelihood algorithms. The resulting gene trees will be compared to the biogeography of the species to look for any associations that may indicate separate stocks and the evolutionary relationships among them. The usefulness of introns as markers for answering intraspecific and interspecific questions will be evaluated using the results from this study as well as results published by other researchers. Introns will be evaluated based on three criteria: level of variation, level of homoplasy, and accessibility for use on a broad range of taxa.

Expected Results:

The exploration of the usefulness of nuclear introns may significantly contribute to the conservation of other species by providing information on additional nuclear markers for genetic research.

Supplemental Keywords:

blue whale, population structure, intron, genetics., RFA, Scientific Discipline, Ecosystem Protection/Environmental Exposure & Risk, exploratory research environmental biology, Genetics, Ecosystem/Assessment/Indicators, Ecosystem Protection, Ecological Effects - Environmental Exposure & Risk, Environmental Microbiology, Molecular Biology/Genetics, Biology, Ecological Indicators, species conservation, endangered species, classification, polymerase chain reaction, genetic testing, intron splicing, conservation biology, genetic differentiation

Progress and Final Reports:

  • 2000
  • 2001
  • Final