Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

Nordic Journal of English Studies : Irish Studies in the Nordic Countries

This special issue of Nordic Journal of English Studies is devoted to the research in Irish Studies being carried out in Scandinavia by a group of scholars based in Denmark, Norway and Sweden, as well as scholars associated—in one way or another—with Scandinavia. Denmark is represented by the University of Aalborg; Norway, by scholars affiliated to the Universities of Agder, the Artic University of Norway, Bergen, and Stavanger; and Sweden is represented by scholars from the universities of Dalarna, Göteborg, Stockholm, Södertörn and Umeå. Included also in this special issue is the work of two former students, who completed their Masters’ degree in Irish literature at DUCIS (Dalarna University Centre for Irish Studies), Sweden—from Norway and China respectively. The collection also contains an article by Dara Waldron, Limerick Institute of Technology, Ireland, whof recently presented his research at the Higher Seminar in Dalarna. Contributions by the Irish poet, Mary O’Donnell, who participated in the Nordic Irish Studies Network (NISN) conference, hosted by DUCIS in December 2012, are also included.

The priority of temporal aspects in L2-Swedish prosody : Studies in perception and production

Foreign accent can be everything from hardly detectable to rendering the second language speech unintelligible. It is assumed that certain aspects of a specific target language contribute more to making the foreign accented speech intelligible and listener friendly, than others. The present thesis examines a teaching strategy for Swedish pronunciation in second language education. The teaching strategy “Basic prosody” or BP, gives priority to temporal aspects of Swedish prosody, which means the temporal phonological contrasts word stress and quantity, as well as the durational realizations of these contrasts. BP does not prescribe any specific tonal realizations. This standpoint is based on the great regional variety in realization and distribution of Swedish word accents. The teaching strategy consists virtually of three directives: · Stress the proper word in the sentence. · Stress proper syllables in stressed words and make them longer. · Lengthen the proper segment – vowel or subsequent consonant – in the stressed syllable. These directives reflect the view that all phonological length is stress-induced, and that vowel length and consonant length are equally important as learning goals. BP is examined in the light of existing findings in the field of second language pronunciation and with respect to the phonetic correlates of Swedish stress and quantity. Five studies examine the relation between segment durations and the categorization made by native Swedish listeners. The results indicate that the postvocalic consonant duration contributes to quantity categorization as well as giving the proper duration to stressed syllables. Furthermore, native Swedish speakers are shown to apply the complementary /V: C/ - /VC:/ pattern also when speaking English and German, by lengthening postvocalic consonants. The correctness of the priority is not directly addressed but important aspects of BP are supported by earlier findings as well as the results from the present studies.