| 1. |
- Hall, Laurie A, et al.
(författare)
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Characterizing dispersal patterns in a threatened seabird with limited genetic structure.
- 2009
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Ingår i: Molecular ecology. - 1365-294X.
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Tidskriftsartikel (refereegranskat)abstract
- Abstract Genetic assignment methods provide an appealing approach for characterizing dispersal patterns on ecological time scales, but require sufficient genetic differentiation to accurately identify migrants and a large enough sample size of migrants to, for example, compare dispersal between sexes or age classes. We demonstrate that assignment methods can be rigorously used to characterize dispersal patterns in a marbled murrelet (Brachyramphus marmoratus) population from central California that numbers approximately 600 individuals and is only moderately differentiated (F(ST) approximately 0.03) from larger populations to the north. We used coalescent simulations to select a significance level that resulted in a low and approximately equal expected number of type I and II errors and then used this significance level to identify a population of origin for 589 individuals genotyped at 13 microsatellite loci. The proportion of migrants in central California was greatest during winter when 83% of individuals were classified as migrants compared to lower proportions during the breeding (6%) and post-breeding (8%) seasons. Dispersal was also biased toward young and female individuals, as is typical in birds. Migrants were rarely members of parent-offspring pairs, suggesting that they contributed few young to the central California population. A greater number of migrants than expected under equilibrium conditions, a lack of individuals with mixed ancestry, and a small number of potential source populations (two), likely allowed us to use assignment methods to rigorously characterize dispersal patterns for a population that was larger and less differentiated than typically thought required for the identification of migrants.
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| 2. |
- Olsen, Morten Tange, et al.
(författare)
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A simple route to single-nucleotide polymorphisms in a nonmodel species : identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida)
- 2011
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 11, s. 9-19
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Tidskriftsartikel (refereegranskat)abstract
- Although single-nucleotide polymorphisms (SNPs) have become the marker of choice in the field of human genetics, these markers are only slowly emerging in ecological, evolutionary and conservation genetic analyses of nonmodel species. This is partly because of difficulties associated with the discovery and characterization of SNP markers. Herein, we adopted a simple straightforward approach to identifying SNPs, based on screening of a random genomic library. In total, we identified 768 SNPs in the ringed seal, Pusa hispida hispida, in samples from Greenland and Svalbard. Using three seal samples, SNPs were discovered at a rate of one SNP per 402 bp, whereas re-sequencing of 96 seals increased the density to one SNP per 29 bp. Although applicable to any species of interest, the approach is especially well suited for SNP discovery in nonmodel organisms and is easily implemented in any standard genetics laboratory, circumventing the need for prior genomic data and use of next-generation sequencing facilities.
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| 3. |
- Olsen, Morten Tange, 1978-, et al.
(författare)
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Empirical evaluation of humpback whale telomere length estimates; quality control and factors causing variability in the singleplex and multiplex qpcr methods
- 2012
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 13, s. 77-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Telomeres, the protective cap of chromosomes, have emerged as powerful markers of biological age and life history in model and non-model species. The qPCR method for telomere length estimation is one of the most common methods for telomere length estimation, but has received recent critique for being too error-prone and yielding unreliable results. This critique coincides with an increasing awareness of the potentials and limitations of the qPCR technique in general and the proposal of a general set of guidelines (MIQE) for standardization of experimental, analytical, and reporting steps of qPCR. In order to evaluate the utility of the qPCR method for telomere length estimation in non-model species, we carried out four different qPCR assays directed at humpback whale telomeres, and subsequently performed a rigorous quality control to evaluate the performance of each assay. Results: Performance differed substantially among assays and only one assay was found useful for telomere length estimation in humpback whales. The most notable factors causing these inter-assay differences were primer design and choice of using singleplex or multiplex assays. Inferred amplification efficiencies differed by up to 40% depending on assay and quantification method, however this variation only affected telomere length estimates in the worst performing assays. Conclusion: Our results suggest that seemingly well performing qPCR assays may contain biases that will only be detected by extensive quality control. Moreover, we show that the qPCR method for telomere length estimation can be highly precise and accurate, and thus suitable for telomere measurement in non-model species, if effort is devoted to optimization at all experimental and analytical steps. We conclude by highlighting a set of quality controls which may serve for further standardization of the qPCR method for telomere length estimation, and discuss some of the factors that may cause variation in qPCR experiments.
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| 5. |
- Olsen, Morten Tange, et al.
(författare)
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Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences
- 2014
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:10, s. 1787-1803
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Tidskriftsartikel (refereegranskat)abstract
- The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci.
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| 6. |
- Olsen, Morten Tange, 1978-
(författare)
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Molecular ecology of marine mammals
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Marine mammals comprise a paraphyletic group of species whose current abundance and distribution has been greatly shaped by past environmental changes and anthropogenic impacts. This thesis describes molecular ecological approaches to answer questions regarding habitat requirements, genetic differentiation, and life-history trade-offs in three species of marine mammals. The annual sea-ice dynamics of the Arctic may have large effects on the abundance and distribution of Arctic species such as the pagophilic ringed seal (Pusa hispida). Paper I describes and applies a simple molecular method for isolating and characterizing a relatively large set of single nucleotide polymorphisms (SNPs) in the ringed seal. These SNPs have been genotyped in a yet-to-be-analysed dataset which will form the basis in an assessment of the micro-evolutionary effects of annual sea-ice dynamics on ringed seal. Current management efforts directed towards the North Atlantic fin whale (Balaenoptera physalus) are hampered by an unclear understanding of population structure. Paper II investigates the DNA basis for the high levels of genetic differentiation that have been reported in allozyme studies of the North Atlantic fin whale. We find that additional processes (at the organismal level) may have contributed to shaping the phenotype of the underlying allozyme variation. Telomeres may potentially serve as markers for determining the chronological and biological age of animals where other means of inference is difficult. Paper III describes the application and evaluation of four qPCR assays for telomere length estimation in humpback whales (Megaptera novaeangliae), finding that reliable telomere length estimates require extensive quality control. Paper IV applies the best performing qPCR assay to test whether telomeres may provide a method for genetic determination of chronological age in whales and concludes that the biological and experimental variation in telomere length estimates is too large to determine age with sufficient resolution. Finally, because telomere length and rate of telomere loss also may be affected by other cellular and organismal processes, such as resource allocation among self-maintenance mechanisms, growth and reproduction, Paper V describes the correlations between individual telomere length and rate of telomere loss, and sex, maturity status and female reproductive output. We found that the costs of reproduction in terms of telomere loss are higher in mature humpback whales than in juveniles; that reproductive costs are higher in males than females; and that differences among females tend to correlate with reproductive output.
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| 10. |
- Palsboll, Per J., et al.
(författare)
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Detecting populations in the 'ambiguous' zone : kinship-based estimation of population structure at low genetic divergence
- 2010
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Ingår i: Molecular ecology notes. - : Wiley. - 1755-098X. ; 10:5, s. 797-805
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Tidskriftsartikel (refereegranskat)abstract
- Identifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Issues arise with most current population genetic inference methods when the genetic divergence is low among putative populations. Low levels of genetic divergence may be as a result of either high ongoing migration or historic high migration but no current, ongoing migration. We direct attention to recent developments in the use of the tempo-spatial distribution of closely related individuals to detect population structure or estimate current migration rates. These 'kinship-based' approaches complement more traditional population-based genetic inference methods by providing a means to detect population structure and estimate current migration rates when genetic divergence is low. However, for kinship-based methods to become widely adopted, formal estimation procedures applicable to a range of species life histories are needed.
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