ORCID Profile
0000-0001-8238-5052
Current Organisation
Uppsala University
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Publisher: Springer Science and Business Media LLC
Date: 13-10-2022
DOI: 10.1038/S41467-022-33723-W
Abstract: Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a s ling of retroviral ersity across time. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all s les indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches.
Publisher: Elsevier BV
Date: 07-2010
DOI: 10.1016/J.JNEUMETH.2010.05.003
Abstract: This study proposes a method for estimating force loss during fatiguing maximal isokinetic knee extension contractions using a set of features from surface EMG signals recorded from multiple locations over the quadriceps muscle. Nine healthy participants performed fatiguing tests which consisted of 50 and 75 isokinetic leg extensions at a speed of 30 degrees /s and 80 degrees /s in two experimental sessions on different days. The set of data recorded from one of the experimental sessions (at both velocities) was used to train a multi-layer perceptron neural network to associate force loss (direct measure of fatigue) to EMG features. The data from the other session (obtained from the tests at both velocities) were used for testing the neural network performance. The proposed method was compared with a previous approach for the assessment of fatigue (Mapping Index, MI) using a signal to noise metrics computed on the estimated trend of fatigue. The signal to noise ratio obtained with the proposed approach was greater (8.83+/-1.07) than that obtained with the MI (5.67+/-1.17) (P<0.05) when the subjects were analyzed in idually and when the network was trained over the entire subject group (8.07 vs. 4.42). In conclusion, the proposed approach allows estimation of force loss during maximal dynamic knee extensions from surface EMG signals with greater accuracy than previous methods.
Publisher: Public Library of Science (PLoS)
Date: 12-06-2009
Publisher: Springer Science and Business Media LLC
Date: 03-2010
DOI: 10.1038/NATURE08832
Abstract: Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic ersity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.
Publisher: Springer Science and Business Media LLC
Date: 21-12-2015
DOI: 10.1038/NG.3475
Publisher: Cold Spring Harbor Laboratory
Date: 26-03-2022
DOI: 10.1101/2022.03.25.485756
Abstract: Endogenous retroviruses (ERVs) are inherited remnants of past retroviruses that colonized host germline over millions of years, providing a s ling of retroviral ersity across time. The utility of ERVs as markers of host genome evolution is augmented by their ability to reveal historic retrovirus-host interactions, given that ERVs are ex les of active retroviruses at the time of germline invasion. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system as a natural model for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We found shared ERVs among all s les indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggest historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, as well as across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches.
Publisher: Springer Science and Business Media LLC
Date: 19-09-2018
No related grants have been discovered for Carl-Johan Rubin.