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Sällman Almén, Markus
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Publications (10 of 32) Show all publications
Lamichhaney, S., Han, F., Berglund, J., Wang, C., Sällman Almen, M., T. Webster, M., . . . Andersson, L. (2016). A beak size locus in Darwin’s finches facilitated character displacement during a drought. Science, 352(6284), 470-474
Open this publication in new window or tab >>A beak size locus in Darwin’s finches facilitated character displacement during a drought
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2016 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6284, p. 470-474Article in journal (Refereed) Published
Abstract [en]

Ecological character displacement is a process of morphological divergence that reducescompetition for limited resources. We used genomic analysis to investigate the geneticbasis of a documented character displacement event in Darwin’s finches on Daphne Majorin the Galápagos Islands: The medium ground finch diverged from its competitor, the largeground finch, during a severe drought. We discovered a genomic region containing theHMGA2gene that varies systematically among Darwin’s finch species with different beaksizes. Two haplotypes that diverged early in the radiation were involved in the characterdisplacement event: Genotypes associated with large beak size were at a strong selectivedisadvantage in medium ground finches (selection coefficients= 0.59). Thus, a majorlocus has apparently facilitated a rapid ecological diversification in the adaptive radiationof Darwin’s finches.

National Category
Genetics and Breeding
Identifiers
urn:nbn:se:uu:diva-279968 (URN)10.1126/science.aad8786 (DOI)000374479700050 ()27102486 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 80576801Swedish Research Council, 70374401
Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2019-11-28Bibliographically approved
Almén, M. S., Lamichhaney, S., Berglund, J., Grant, B. R., Grant, P. R., Webster, M. T. & Andersson, L. (2016). Adaptive radiation of Darwin's finches revisited using whole genome sequencing. Bioessays, 38(1), 14-20
Open this publication in new window or tab >>Adaptive radiation of Darwin's finches revisited using whole genome sequencing
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2016 (English)In: Bioessays, ISSN 0265-9247, E-ISSN 1521-1878, Vol. 38, no 1, p. 14-20Article in journal (Refereed) Published
Abstract [en]

We recently used genome sequencing to study the evolutionary history of the Darwin's finches. A prominent feature of our data was that different polymorphic sites in the genome tended to indicate different genetic relationships among these closely related species. Such patterns are expected in recently diverged genomes as a result of incomplete lineage sorting. However, we uncovered conclusive evidence that these patterns have also been influenced by interspecies hybridisation, a process that has likely played an important role in the radiation of Darwin's finches. A major discovery was that segregation of two haplotypes at the ALX1 locus underlies variation in beak shape among the Darwin's finches, and that differences between the two haplotypes in a 240 kb region in blunt and pointed beaked birds involve both coding and regulatory changes. As we review herein, the evolution of such adaptive haplotypes comprising multiple causal changes appears to be an important mechanism contributing to the evolution of biodiversity.

Keywords
adaptation, evolution, gene flow, genome sequencing
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-282647 (URN)10.1002/bies.201500079 (DOI)000371265200004 ()26606649 (PubMedID)
Available from: 2016-04-06 Created: 2016-04-06 Last updated: 2017-11-30Bibliographically approved
Martínez Barrio, Á., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M., Zhang, H., . . . Andersson, L. (2016). The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLIFE, 5, Article ID e12081.
Open this publication in new window or tab >>The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
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2016 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e12081Article in journal (Refereed) Published
Abstract [en]

Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

National Category
Genetics and Breeding Evolutionary Biology Genetics Fish and Aquacultural Science
Identifiers
urn:nbn:se:uu:diva-279967 (URN)10.7554/eLife.12081 (DOI)000387459700001 ()27138043 (PubMedID)
Funder
EU, European Research CouncilSwedish Research Council FormasKnut and Alice Wallenberg Foundation
Note

Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan and Nima Rafati contributed equally to this work.

Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2017-11-29Bibliographically approved
Rask-Andersen, M., Almén, M. S., Lind, L. & Schiöth, H. B. (2015). Association of the LINGO2-related SNP rs10968576 with body mass in a cohort of elderly Swedes. Molecular Genetics and Genomics, 290(4), 1485-1491
Open this publication in new window or tab >>Association of the LINGO2-related SNP rs10968576 with body mass in a cohort of elderly Swedes
2015 (English)In: Molecular Genetics and Genomics, ISSN 1617-4615, E-ISSN 1617-4623, Vol. 290, no 4, p. 1485-1491Article in journal (Refereed) Published
Abstract [en]

Genome-wide association studies (GWAS) have identified common genetic factors influencing body mass as well as body adiposity. The functional implications of these loci are currently under investigation. Intense scrutiny of the body mass-associated FTO locus revealed age-specific effects, or a weakened effect in elderly populations. In this study, we aimed to determine the effects of single nucleotide polymorphisms (SNPs) representing 35 GWAS-identified body mass- and adiposity-associated genetic loci. In our analysis, 949 participants of the Prospective Investigation of the Vasculature in Uppsala Seniors cohort were included. All participants were born between 1920 and 1924. Data were available for 474 male and 475 female participants at age 70 and 380 male and 390 female participants at age 75. Genetic associations with BMI and change in BMI from age 70 to 75 were analyzed. In our analysis, rs10968576, an intronic SNP within the LINGO2 (LERN3, LRRN6C) gene, was associated with body mass in a cross section of elderly Swedes at age 70. This is the first study to replicate the association of a LINGO2-related genetic variant with body mass in an independent cohort of elderly citizens.

Keywords
Body mass, Obesity, LINGO2, rs10968576
National Category
Medical Genetics Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-260615 (URN)10.1007/s00438-015-1009-7 (DOI)000358246000023 ()25711307 (PubMedID)
Funder
Swedish Research Council, 80576801, 70374401Swedish Heart Lung FoundationThe Swedish Brain Foundation
Note

Funding: Uppsala University, Uppsala University Hospital, Science for Life Laboratory, Uppsala 

Available from: 2015-08-24 Created: 2015-08-21 Last updated: 2018-01-11Bibliographically approved
Rask-Andersen, M., Sällman Almén, M., Jacobsson, J. A., Ameur, A., Moschonis, G., Dedoussis, G., . . . Schiöth, H. B. (2015). Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.. Genetical Research, 97, Article ID e16.
Open this publication in new window or tab >>Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.
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2015 (English)In: Genetical Research, ISSN 0016-6723, E-ISSN 1469-5073, Vol. 97, article id e16Article in journal (Refereed) Published
Abstract [en]

Genome-wide association studies (GWAS) have revealed association of a locus approximately 25b downstream of the TMEM18 gene with body mass and obesity. We utilized targeted re-sequencing of the body mass associated locus in proximity of TMEM18 in a case-control population of severely obese children and adolescents from the Stockholm area. We expanded our study to include the TMEM18 gene itself, with the aim of identifying body mass associated genetic variants. Sequencing was performed on the SOLiD platform, on long-range PCR fragments generated through targeted amplification of the regions of interest. Candidate single nucleotide polymorphisms (SNPs) were validated by TaqMan genotyping. We were able to observe 131 SNPs across the re-sequenced regions. Chi squared tests comparing the allele frequencies between cases and controls revealed 57 SNPs as candidates for association with obesity. Validation and replication genotyping revealed robust associations for SNPs within the haplotype block region located downstream from the TMEM18 gene. This study provides a high resolution map of the genetic variation pattern in the TMEM18 gene, as well as the associated haplotype block, and further strengthens the association of variants within the proximal haplotype block with obesity and body mass.

National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-275285 (URN)10.1017/S0016672315000117 (DOI)000367181100015 ()26365393 (PubMedID)
Funder
Swedish Research CouncilThe Swedish Brain FoundationNovo NordiskSwedish Research Council, 80576801Swedish Research Council, 70374401
Available from: 2016-02-02 Created: 2016-02-02 Last updated: 2018-01-10Bibliographically approved
Voisin, S., Almén, M. S., Moschonis, G., Chrousos, G. P., Manios, Y. & Schiöth, H. B. (2015). Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents. European Journal of Human Genetics, 23, 654-662
Open this publication in new window or tab >>Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents
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2015 (English)In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 23, p. 654-662Article in journal (Refereed) Published
Abstract [en]

The type and the amount of dietary fat have a significant influence on the metabolic pathways involved in the development of obesity, metabolic syndrome, diabetes type 2 and cardiovascular diseases. However, it is unknown to what extent this modulation is achieved through DNA methylation. We assessed the effects of cholesterol intake, the proportion of energy intake derived from fat, the ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA), the ratio of monounsaturated fatty acids (MUFA) to SFA, and the ratio of MUFA+PUFA to SFA on genome-wide DNA methylation patterns in normal-weight and obese children. We determined the genome-wide methylation profile in the blood of 69 Greek preadolescents (∼10 years old) as well as their dietary intake for two consecutive weekdays and one weekend day. The methylation levels of one CpG island shore and four sites were significantly correlated with total fat intake. The methylation levels of 2 islands, 11 island shores and 16 sites were significantly correlated with PUFA/SFA; of 9 islands, 26 island shores and 158 sites with MUFA/SFA; and of 10 islands, 40 island shores and 130 sites with (MUFA+PUFA)/SFA. We found significant gene enrichment in 34 pathways for PUFA/SFA, including the leptin pathway, and a significant enrichment in 5 pathways for (MUFA+PUFA)/SFA. Our results suggest that specific changes in DNA methylation may have an important role in the mechanisms involved in the physiological responses to different types of dietary fat.European Journal of Human Genetics advance online publication, 30 July 2014; doi:10.1038/ejhg.2014.139.

National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-238744 (URN)10.1038/ejhg.2014.139 (DOI)000353028200018 ()25074463 (PubMedID)
Note

Sarah Voisin och Markus S Almén delar förstaförfattarskapet.

Available from: 2014-12-16 Created: 2014-12-16 Last updated: 2018-01-11Bibliographically approved
Dorshorst, B., Henegar, C., Liao, X., Almén, M. S., Rubin, C.-J., Ito, S., . . . Andersson, L. (2015). Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene. PLoS ONE, 10(6), Article ID e0128969.
Open this publication in new window or tab >>Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene
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2015 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 6, article id e0128969Article in journal (Refereed) Published
Abstract [en]

Coat color in Holstein dairy cattle is primarily controlled by the melanocortin 1 receptor (MC1R) gene, a central determinant of black (eumelanin) vs. red/brown pheomelanin synthesis across animal species. The major MC1R alleles in Holsteins are Dominant Black (MC1R(D)) and Recessive Red (MC1R(e)). A novel form of dominant red coat color was first observed in an animal born in 1980. The mutation underlying this phenotype was named Dominant Red and is epistatic to the constitutively activated MC1R(D). Here we show that a missense mutation in the coatomer protein complex, subunit alpha (COPA), a gene with previously no known role in pigmentation synthesis, is completely associated with Dominant Red in Holstein dairy cattle. The mutation results in an arginine to cysteine substitution at an amino acid residue completely conserved across eukaryotes. Despite this high level of conservation we show that both heterozygotes and homozygotes are healthy and viable. Analysis of hair pigment composition shows that the Dominant Red phenotype is similar to the MC1R Recessive Red phenotype, although less effective at reducing eumelanin synthesis. RNA-seq data similarly show that Dominant Red animals achieve predominantly pheomelanin synthesis by down regulating genes normally required for eumelanin synthesis. COPA is a component of the coat protein I seven subunit complex that is involved with retrograde and cis-Golgi intracellular coated vesicle transport of both protein and RNA cargo. This suggests that Dominant Red may be caused by aberrant MC1R protein or mRNA trafficking within the highly compartmentalized melanocyte, mimicking the effect of the Recessive Red loss of function MC1R allele.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-257658 (URN)10.1371/journal.pone.0128969 (DOI)000355701600079 ()26042826 (PubMedID)
Available from: 2015-07-07 Created: 2015-07-06 Last updated: 2017-12-04Bibliographically approved
Lamichhaney, S., Berglund, J., Almen, M. S., Maqbool, K., Grabherr, M., Martinez-Barrio, A., . . . Andersson, L. (2015). Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature, 518(7539)
Open this publication in new window or tab >>Evolution of Darwin's finches and their beaks revealed by genome sequencing
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2015 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 518, no 7539Article in journal (Refereed) Published
Abstract [en]

Darwin's finches, inhabiting the Galapagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives' Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial. development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis) a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and thereby, to an expanded utilization of food resources.

National Category
Medical Genetics Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-247384 (URN)10.1038/nature14181 (DOI)000349547400036 ()25686609 (PubMedID)
Available from: 2015-03-20 Created: 2015-03-18 Last updated: 2018-01-11Bibliographically approved
Krishnan, A., Mustafa, A., Almén, M. S., Fredriksson, R., Williams, M. J. & Schiöth, H. B. (2015). Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families. Molecular Phylogenetics and Evolution, 91, 27-40
Open this publication in new window or tab >>Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families
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2015 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 91, p. 27-40Article in journal (Refereed) Published
Abstract [en]

Heterotrimeric G proteins perform a crucial role as molecular switches controlling various cellular responses mediated by G protein-coupled receptor (GPCR) signaling pathway. Recent data have shown that the vertebrate-like G protein families are found across metazoans and their closest unicellular relatives. However, an overall evolutionary hierarchy of vertebrate-like G proteins, including gene family annotations and in particular mapping individual gene gain/loss events across diverse holozoan lineages is still incomplete. Here, with more expanded invertebrate taxon sampling, we have reconstructed phylogenetic trees for each of the G protein classes/families and provide a robust classification and hierarchy of vertebrate-like heterotrimeric G proteins. Our results further extend the evidence that the common ancestor (CA) of holozoans had at least five ancestral Gα genes corresponding to all major vertebrate Gα classes and contain a total of eight genes including two Gβ and one Gγ. Our results also indicate that the GNAI/O-like gene likely duplicated in the last CA of metazoans to give rise to GNAI- and GNAO-like genes, which are conserved across invertebrates. Moreover, homologs of GNB1-4 paralogon- and GNB5 family-like genes are found in most metazoans and that the unicellular holozoans encode two ancestral Gβ genes. Similarly, most bilaterian invertebrates encode two Gγ genes which include a representative of the GNG gene cluster and a putative homolog of GNG13. Interestingly, our results also revealed key evolutionary events such as the Drosophila melanogaster eye specific Gβ subunit that is found conserved in most arthropods and several previously unidentified species specific expansions within Gαi/o, Gαs, Gαq, Gα12/13 classes and the GNB1-4 paralogon. Also, we provide an overall proposed evolutionary scenario on the expansions of all G protein families in vertebrate tetraploidizations. Our robust classification/hierarchy is essential to further understand the differential roles of GPCR/G protein mediated intracellular signaling system across various metazoan lineages.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-258945 (URN)10.1016/j.ympev.2015.05.009 (DOI)000358270900004 ()26002831 (PubMedID)
Funder
Novo NordiskSwedish Research Council
Available from: 2015-07-22 Created: 2015-07-22 Last updated: 2017-12-04Bibliographically approved
Le Duc, D., Renaud, G., Krishnan, A., Almén, M. S., Huynen, L., Prohaska, S. J., . . . Schoeneberg, T. (2015). Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biology, 16, Article ID 147.
Open this publication in new window or tab >>Kiwi genome provides insights into evolution of a nocturnal lifestyle
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2015 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 16, article id 147Article in journal (Refereed) Published
Abstract [en]

Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Medical Genetics
Identifiers
urn:nbn:se:uu:diva-260619 (URN)10.1186/s13059-015-0711-4 (DOI)000358345900001 ()26201466 (PubMedID)
Funder
Swedish Research CouncilAustralian Research Council
Note

Funding: Deutsche Forschungsgemeinschaft, Medical Faculty, University of Leipzig, NSERC, Max Planck Society, Sao Paulo Research Foundation (FAPESP)  2011/12500-2 

Available from: 2015-08-24 Created: 2015-08-21 Last updated: 2018-01-11Bibliographically approved
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