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Title Population genetic analyses in Atlantic cod (Gadus morhua) using historical DNA
Author Therkildsen, Nina Overgaard (Section for Population Genetics, National Institute of Aquatic Resources, Technical University of Denmark, DTU, DK-2800 Kgs. Lyngby, Denmark)
Institution Technical University of Denmark, DTU, DK-2800 Kgs. Lyngby, Denmark
Thesis level Master's thesis
Year 2009
Abstract In recent years, many commercial fish stocks have declined dramatically and some have completely collapsed due to overexploitation. The enormous fisheries-induced reductions in abundance down to 0.1% of known historical levels could potentially lead to erosion of genetic diversity in the affected populations. However, it has traditionally been assumed that marine fish generally are immune towards adverse genetic effects associated with population reductions because they exist in very large populations that number millions of individuals even after a collapse. Nevertheless, it is the effective and not the census population size that determines the rate of change in genetic diversity, and recent research has suggested that the ratio between these two parameters may be extremely small for marine fish. Consistent with this, apparent loss of genetic diversity due to fishing has indeed been reported for several harvested populations. Archived otoliths—that originally were collected by fisheries research institutes for age determination—are a valuable source of historical DNA that can be utilized to directly study the genetic impacts of fisheries. Such samples were used in the present thesis (Chapter 3) to study temporal variation in the genetic diversity of an overexploited population of Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence in the eastern Canada. This population collapsed in the early 1990s and still has not recovered to its historical abundance. Based on nine microsatellite loci, I compared the genetic variation of the population between 1928 before the fishery intensified, and 2008 when the population was at the lowest abundance ever recorded. There was no significant reduction in genetic diversity over this period. I also used the samples to estimate the effective size of this population, and the results from several different methods suggested that it is at least 500 and probably much higher. Based on these findings, the studied cod population does not appear to have lost genetic diversity because of the fisheries-induced population collapse. As demonstrated in the study of cod, analysis of historical DNA samples provides unique insights into the past, but it also poses technical challenges because the DNA is degraded and only available in small quantities. Therefore it is necessary to take special precautions and optimize laboratory procedures. To this end, I compared three DNA extraction protocols and both evaluated the extract quality and assessed whether the procedures caused damage to the physical and chemical composition of the otoliths that DNA was extracted from (Chapter 2). The protocols did not differ significantly in terms of the DNA quality gained and none of them caused 6 physical damage to the otoliths. The concentrations of most of the measured trace elements were also unaffected. In a second methodological study (Chapter 4), I examined the pattern and frequency of errors generated while genotyping the historical sample. The error rates in single reactions was nonnegligible, but with the applied replication scheme, the error rate in the final data set should be reduced to <1%. Hence, it is possible to produce reliable data sets from archived samples despite the degraded nature and low quantity of the DNA.
Note Supervisors: Jes Søe Pedersen (Department of Biology, University of Copenhagen) and Einar Eg Nielsen (National Institute of Aquatic Resources, Technical University of Denmark)
Pages 144
Original PDF M_Sc_Nina_Therkildsen.pdf (6.14 MB)
Admin Creation date: 2009-08-14    Update date: 2009-08-14    Source: dtu    ID: 248119    Original MXD