Grantee Research Project Results
2000 Progress Report: A Genetic Test for Vulnerability to Inbreeding Depression in Right Whales and Elephant Seals
EPA Grant Number: R827110Title: A Genetic Test for Vulnerability to Inbreeding Depression in Right Whales and Elephant Seals
Investigators: Hare, Matthew P. , Palumbi, Stephen R.
Institution: University of Maryland - College Park , Harvard University
EPA Project Officer: Hahn, Intaek
Project Period: May 5, 1999 through May 4, 2001 (Extended to May 4, 2002)
Project Period Covered by this Report: May 5, 1999 through May 4, 2000
Project Amount: $152,274
RFA: Exploratory Research - Environmental Biology (1998) RFA Text | Recipients Lists
Research Category: Biology/Life Sciences , Human Health , Aquatic Ecosystems
Objective:
The objectives of this research follow from the enigmatic observation that severe population size reductions (bottlenecks) elicit different levels of inbreeding depression in different species. Theory suggests that one factor affecting the propensity for inbreeding depression is a population's history of inbreeding, or history of population size fluctuations. Populations that have a long history of small population size, or repeated bottlenecks will have lost many of their unfavorable recessive alleles during those prior inbreeding episodes and are, therefore, expected to experience less inbreeding depression from a recent bottleneck compared to a population that has been consistently large.Our goal is to develop a test for the vulnerability to inbreeding depression by estimating historical population sizes. We are examining ancestral population size in the northern elephant seal (NES; Mirounga leonina), a species that rapidly recovered from a population of only 10?30 individuals, and North Atlantic right whales (NRW; Eubalaena glacialis) that continue to have a critically low population size and reproductive rate despite six decades of protection. Both the NES and NRW have closely related sister species in the southern hemisphere (SES and SRW, respectively). Our approach is to compare DNA sequences between sister species because these data are informative about population size in the common ancestor. Non-coding intron DNA is being sequenced to determine sister-species divergence and many unlinked nuclear loci are being sampled to generate a distribution of divergence values. Assuming selective neutrality and constant mutation rates, the shape of this distribution is a function of ancestral population size and divergence time.
Progress Summary:
During the time interval summarized by this report, PCR has been attempted from a total of 25 loci. Thirteen loci (52%) were rejected because of small intron size or complicated amplification patterns (a rate similar to last year, 53%). Amplification products from the remaining 12 loci were isolated by cloning or were directly sequenced. More specific primers were designed for each locus using initial sequence results, and additional individuals were sequenced directly from the target taxa and one or more out-groups. Table 1 lists all of the loci (both years) from which intron sequence has been collected or currently is being collected. Thirteen loci are being assayed in both the seals and whales. Data from other loci are from either whales or seals, but not both.Table 1. Intron sequence data collected to date. Data taken from the literature are underlined. Loci in progress have an asterisk.
Elephant Seals | Right Whales | |||
Locus | Length | Locus | Length | |
CD40 | 977 | CD40 | 960 | |
Beta-Globin | 550 | Beta-Globin | 550 | |
CAMK | 430+ | CAMK | 860 | |
G6PD | 530 | G6PD | 480 | |
Lysozyme | 670 | Lysozyme | 351 | |
ESD | 366 | ESD | 733 | |
ACT* | 1600 | ACT* | 1600 | |
HEXB* | 2000 | HEXB* | 2000 | |
CP* | 1600 | CP* | 1200 | |
FGG* | 1020 | FGG* | 1020 | |
PLP* | 1016 | PLP* | 1016 | |
IGF2* | 1400 | IGF2* | 1500 | |
CDH2* | 2000 | CDH2* | 2000 | |
H2AF* | 250 | CTLA3 | 303 | |
EPO | 860 | OAT* | 1300 | |
ETS2 | 740 | EDNRB* | 1800 | |
APOB | 860 | CYP19* | 1300 | |
PTH* | 1016 | |||
PDGFB | 225 | |||
KRAS1P | 294 | |||
FGFR4 | 630 | |||
PRF1 | 173 | |||
H2AF | 264 | |||
Aldolase-A | 360 |
Preliminary analyses were performed on DNA sequences from 11 seal loci and 8 whale loci. Although variation in intron divergence values across loci was greater than expected from binomial expectations in both seals and whales, there was no evidence that the variation could be explained by differences in nucleotide composition or in purifying selection. Further work is needed on methods to detect the causes of rate heterogeneity. If we can estimate the variance in sister-species divergences contributed by locus-specific rates, perhaps by including more distant out-groups in this study, then all sampled loci can contribute to maximum likelihood estimates of historical parameters.
Preliminary estimates of ancestral population size in elephant seals suggest that the contemporary southern species may provide a reasonable view of long-term population demography. As such, the southern elephant seal provides a suitable comparison with the northern elephant seal to judge the extent of genetic diversity loss experienced in the north from human harvests during the 19th century. This result corroborates evidence from ancient DNA that genetic diversity decreased during the northern elephant seal bottleneck (Weber DS, Stewart BS, Garza JC, Lehman N. Current Biology 2000;10:1287-1290). It remains enigmatic to explain the lack of dramatic inbreeding depression in the northern elephant seals after suffering such a severe population bottleneck. Insufficient data are available for a preliminary test of right whale ancestral population size.
Future Activities:
A no-cost 1 year extension was granted April 2001. The primary future goals are to: (1) collect sequence data from more loci, especially in the whale; (2) collect sequence data from additional out-groups to improve tests for among-locus evolutionary rate heterogeneity; (3) improve tests for selection or other artifacts at loci that have unusually high levels of variation; (4) obtain additional samples of southern hemisphere right whales and determine intraspecific levels of genetic diversity; and (5) analyze the data and prepare manuscripts for peer review.Given the low level of sister-species divergence and the difficulty this will create for estimating ancestral populations size from divergence distributions, it will be important to sample intraspecific diversity in the southern species for both whales and seals. Data on nuclear DNA intraspecific diversity have been published for southern elephant seals, so intraspecific data collection will focus on southern right whales.
Journal Articles:
No journal articles submitted with this report: View all 2 publications for this projectSupplemental Keywords:
inbreeding depression, genetic diversity, population size., RFA, Scientific Discipline, Health, Ecosystem Protection/Environmental Exposure & Risk, Aquatic Ecosystems & Estuarine Research, Ecosystem/Assessment/Indicators, Ecosystem Protection, exploratory research environmental biology, Genetics, Aquatic Ecosystem, Susceptibility/Sensitive Population/Genetic Susceptibility, Habitat, Ecology and Ecosystems, genetic susceptability, Biology, Ecological Indicators, demographic bottleneck, ecological effects, sensitive populations, endangered species, environmental sources of mortality, adaption mechanisms, animal responses, marine biology, seals, genetic vulnerability, aquatic ecosystems, conservation biology, environmental stress, biological indicators, inbreeding depression, whales, environmental hazard exposuresRelevant Websites:
http://www.oeb.harvard.edu/palumbi/project%20summaries/EPA.htmlProgress and Final Reports:
Original AbstractThe perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.