Publications
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Rekdal, Silje Larsen; Anmarkrud, Jarl Andreas; Johnsen, Arild & Lifjeld, Jan Terje (2018). Genotyping strategy matters when analyzing hypervariable major histocompatibility complex-Experience from a passerine bird. Ecology and Evolution.
ISSN 2045-7758.
8(3), s 1680- 1692 . doi:
10.1002/ece3.3757
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Sinding, Mikkel Holger Strander; Tervo, Outi; Grønnow, Bjarne; Gulløv, Hans Christian; Toft, Peter Andreas; Bachmann, Lutz; Fietz, Katharina; Rekdal, Silje Larsen; Christoffersen, Mads; Heide Jørgensen, Mads Peter; Olsen, Morten T. & Foote, Andrew D. (2016). Sex determination of baleen whale artefacts: Implications for ancient DNA use in zooarchaeology. Journal of Archaeological Science: Reports.
ISSN 2352-409X.
10, s 345- 349 . doi:
10.1016/j.jasrep.2016.11.001
Show summary
Methods to determine the sex from tissue samples of mammals include the amplification of Y chromosome specific regions, which should only amplify from males, or amplification of homologous regions of the X and Y chromosome containing XY specific SNPs. A disadvantage of the first approach is that PCR failure can be misinterpreted as the identification of a female. The latter approach is proposed to identify PCR failure through non-amplification of the X homologue, which should be present in both sexes. This method is therefore potentially more suitable for molecular sexing of degraded DNA with a high probability of PCR failure, such as for example, ancient DNA samples. Here, we investigate the validity of this assumption regarding the use of XY homologue PCR assays for molecular sexing of ancient DNA. We tested a primer set targeting the ZFX/ZFY alleles using ancient DNA extracts from 100 to 4500 years old bowhead whale samples, and for comparison on dilution series from modern bowhead whales of known sex. DNA sequencing of PCR products obtained from the ancient material confirmed a higher proportion of successful PCR amplifications of the X homologue over the Y homologue. This potentially biased sex determination was further assessed by testing highly diluted DNA extracts of modern samples, for which a consistently higher success rate of PCR amplification and lower PCR cycle threshold was found for the X homologue from females than either homologue from males. This is most likely due to the higher copy number of the X homologue in females, although other yet unknown attributes of the protocol may also cause the observed bias. The current case study provides a valuable example of a potential pitfall in molecular sex determination of ancient mammal DNA in zooarchaeology. High-throughput sequencing methods, in which sufficiently large numbers of reads can be unambiguously mapped to X and Y regions, should overcome such biases and be the most robust approach for molecular sex determination using degraded DNA.
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Støstad, Hanna Nyborg; Rekdal, Silje Larsen; Kleven, Oddmund; Laskemoen, Terje; Marthinsen, Gunnhild; Johnsen, Arild & Lifjeld, Jan Terje (2016). Weak geographical structure in sperm morphology across the range of two willow warbler Phylloscopus trochilus subspecies in Scandinavia. Journal of Avian Biology.
ISSN 0908-8857.
47(5), s 731- 741 . doi:
10.1111/jav.00981
Full text in Research Archive.
Show summary
Sperm morphology is highly diversified among species and at higher taxonomic levels. In birds, there is also increasing evidence of geographical differentiation in sperm traits within species, especially in those with strong sperm competition. Geographical divergences in sperm traits might imply the formation of a reproductive barrier in a speciation process. Here we study sperm morphology variation of willow warblers Phylloscopus trochilus in a geographical context in Scandinavia, across the range of two subspecies that are differentiated in certain genetic markers, morphology and migratory routes. We describe geographical patterns in genotypes (two previously described single-nucleotide polymorphism (SNP) markers and four polymorphic microsatellites); in wing length, tarsus length and body mass; and in sperm traits of 330 male willow warblers sampled at 33 localities across Norway (58°N–69°N). Birds were on average larger and longer-winged in the north (spp. acredula) than in the south (spp. trochilus), and showed a sigmoid change in the SNP allele frequencies and body morphology around 65°N. We found no evidence of genetic structuring in the microsatellites. There was no geographical variation in sperm traits across Norway, except that sperm heads were on average longer in the south. Sperm head length was also associated with the two SNP markers, with longer sperm heads for the southern alleles, and midpiece length was weakly associated with one of the SNP markers. Similar among-male variances in total sperm length among the 33 sampling sites indicate uniform levels of sperm competition across Norway. We conclude that sperm morphology remains a rather undifferentiated trait between the two willow warbler subspecies in Scandinavia, which is consistent with a pattern of a shallow genetic divergence. This indicates that sperm morphology is not a reproductive barrier maintaining the narrow hybrid zone.
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Rekdal, Silje Larsen; Guldborg Hansen, Rikke; Borchers, David L.; Bachmann, Lutz; Laidre, Kristin L.; Wiig, Øystein; Hjort Nielsen, Nynne; Fossette, Sabrina; Tervo, Outi & Heide Jørgensen, Mads Peter (2015). Trends in bowhead whales in West Greenland: aerial surveys versus genetic capture-recapture analyses. Marine mammal science.
ISSN 0824-0469.
31, s 133- 154 . doi:
10.1111/mms.12150
Show summary
We contrast two methods for estimating the trends of bowhead whales (Balaena mysticetus) in West Greenland: (1) double platform visual aerial survey, corrected for missed sightings and the time the whales are available at the surface; and (2) a genetic capture-recapture approach based on a 14-yr-long biopsy sampling program in Disko Bay. The aerial survey covered 39,000 km2 and resulted in 58 sightings, yielding an abundance estimate of 744 whales (CV = 0.34, 95% CI: 357–1,461). The genetic method relied on determining sex, mitochondrial haplotypes and genotypes of nine microsatellite markers. Based on samples from a total of 427 individuals, with 11 recaptures from previous years in 2013, this resulted in an estimate of 1,538 whales (CV = 0.24, 95% CI: 827–2,249). While the aerial survey is considered a snapshot of the local spring aggregation in Disko Bay, the genetic approach estimates the abundance of the source of this aggregation. As the whales in Disko Bay primarily are adult females that do not visit the bay annually, the genetic method would presumably yield higher estimates. The studies indicate that an increase in abundance observed between 1998 and 2006 has leveled off.
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Published Oct. 13, 2014 6:55 PM
- Last modified Jan. 13, 2016 11:55 AM
