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Andersson, Leif
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Publications (10 of 197) Show all publications
Rafati, N., Blanco-Aguiar, J. A., Rubin, C.-J., Sayyab, S., Sabatino, S., Afonso, S., . . . Carneiro, M. (2018). A genomic map of clinal variation across the European rabbit hybrid zone. Molecular Ecology, 27(6), 1457-1478
Open this publication in new window or tab >>A genomic map of clinal variation across the European rabbit hybrid zone
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2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 6, p. 1457-1478Article in journal (Refereed) Published
Abstract [en]

Speciation is a process proceeding from weak to complete reproductive isolation. In this continuum, naturally hybridizing taxa provide a promising avenue for revealing the genetic changes associated with the incipient stages of speciation. To identify such changes between two subspecies of rabbits that display partial reproductive isolation, we studied patterns of allele frequency change across their hybrid zone using whole-genome sequencing. To connect levels and patterns of genetic differentiation with phenotypic manifestations of subfertility in hybrid rabbits, we further investigated patterns of gene expression in testis. Geographic cline analysis revealed 253 regions characterized by steep changes in allele frequency across their natural region of contact. This catalog of regions is likely to be enriched for loci implicated in reproductive barriers and yielded several insights into the evolution of hybrid dysfunction in rabbits: (i) incomplete reproductive isolation is likely governed by the effects of many loci, (ii) protein-protein interaction analysis suggest that genes within these loci interact more than expected by chance, (iii) regulatory variation is likely the primary driver of incompatibilities, and (iv) large chromosomal rearrangements appear not to be a major mechanism underlying incompatibilities or promoting isolation in the face of gene flow. We detected extensive misregulation of gene expression in testis of hybrid males, but not a statistical overrepresentation of differentially expressed genes in candidate regions. Our results also did not support an X chromosome-wide disruption of expression as observed in mice and cats, suggesting variation in the mechanistic basis of hybrid male reduced fertility among mammals.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
Speciation, reproductive isolation, expression, hybrid
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-314393 (URN)10.1111/mec.14494 (DOI)000430183100010 ()29359877 (PubMedID)
Funder
EU, European Research Council, SFRH/BPD/65464/2009EU, FP7, Seventh Framework Programme, 286431
Note

Title in thesis list of papers: The early stages of species formation revealed by a genomic map of clinal variation across the European rabbit hybrid zone

Available from: 2017-02-02 Created: 2017-02-02 Last updated: 2018-06-19Bibliographically approved
Sutherland, D. A., Honaker, C. F., Dorshorst, B., Andersson, L. & Siegel, P. B. (2018). Asymmetries, heterosis, and phenotypic profiles of red junglefowl, White Plymouth Rocks, and F-1 and F-2 reciprocal crosses. Journal of Applied Genetics, 59(2), 193-201
Open this publication in new window or tab >>Asymmetries, heterosis, and phenotypic profiles of red junglefowl, White Plymouth Rocks, and F-1 and F-2 reciprocal crosses
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2018 (English)In: Journal of Applied Genetics, ISSN 1234-1983, E-ISSN 2190-3883, Vol. 59, no 2, p. 193-201Article in journal (Refereed) Published
Abstract [en]

During the domestication of farm animals, humans have manipulated genetic variation for growth and reproduction through artificial selection. Here, data are presented for growth, reproductive, and behavior traits for the red junglefowl, a line of White Plymouth Rock chickens, and their F-1 and F-2 reciprocal crosses. Intra- and intergenerational comparisons for growth related traits reflected considerable additive genetic variation. In contrast, those traits associated with reproduction exhibited heterosis. The role of sexual selection was seen in the evolution of prominent secondary sexual ornaments that lend to female choice and male-male competition. The large differences between parental lines in fearfulness to humans were only mitigated slightly in the intercross generations. Whereas, overall F-1 generation heterosis was not transferred to the F-2, there was developmental stability in the F-2, as measured by relative asymmetry of bilateral traits. Through multigenerational analyses between the red junglefowl and the domestic White Plymouth Rocks, we observed plasticity and considerable residual genetic variation. These factors likely facilitated the adaptability of the chicken to a broad range of husbandry practices throughout the world.

Place, publisher, year, edition, pages
SPRINGER HEIDELBERG, 2018
Keywords
Chickens, Body weight, Breast weight, Fat, Symmetries
National Category
Genetics and Breeding in Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-352568 (URN)10.1007/s13353-018-0435-8 (DOI)000429835700009 ()29500604 (PubMedID)
Available from: 2018-08-07 Created: 2018-08-07 Last updated: 2018-08-07Bibliographically approved
Bornelöv, S., Seroussi, E., Yosefi, S., Benjamini, S., Miyara, S., Ruzal, M., . . . Friedman-Einat, M. (2018). Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction. BMC Genomics, 19, Article ID 295.
Open this publication in new window or tab >>Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
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2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 295Article in journal (Refereed) Published
Abstract [en]

Background: The mammalian adipose tissue plays a central role in energy-balance control, whereas the avian visceral fat hardly expresses leptin, the key adipokine in mammals. Therefore, to assess the endocrine role of adipose tissue in birds, we compared the transcriptome and proteome between two metabolically different types of chickens, broilers and layers, bred towards efficient meat and egg production, respectively.

Results: Broilers and layer hens, grown up to sexual maturation under free-feeding conditions, differed 4.0-fold in weight and 1.6-fold in ovarian-follicle counts, yet the relative accumulation of visceral fat was comparable. RNA-seq and mass-spectrometry (MS) analyses of visceral fat revealed differentially expressed genes between broilers and layers, 1106 at the mRNA level (FDR ≤ 0.05), and 203 at the protein level (P ≤ 0.05). In broilers, Ingenuity Pathway Analysis revealed activation of the PTEN-pathway, and in layers increased response to external signals. The expression pattern of genes encoding fat-secreted proteins in broilers and layers was characterized in the RNA-seq and MS data, as well as by qPCR on visceral fat under free feeding and 24 h-feed deprivation. This characterization was expanded using available RNA-seq data of tissues from red junglefowl, and of visceral fat from broilers of different types. These comparisons revealed expression of new adipokines and secreted proteins (LCAT, LECT2, SERPINE2, SFTP1, ZP1, ZP3, APOV1, VTG1 and VTG2) at the mRNA and/or protein levels, with dynamic gene expression patterns in the selected chicken lines (except for ZP1; FDR/P ≤ 0.05) and feed deprivation (NAMPT, SFTPA1 and ZP3) (P ≤ 0.05). In contrast, some of the most prominent adipokines in mammals, leptin, TNF, IFNG, and IL6 were expressed at a low level (FPKM/RPKM< 1) and did not show differential mRNA expression neither between broiler and layer lines nor between fed vs. feed-deprived chickens.

Conclusions: Our study revealed that RNA and protein expression in visceral fat changes with selective breeding, suggesting endocrine roles of visceral fat in the selected phenotypes. In comparison to gene expression in visceral fat of mammals, our findings points to a more direct cross talk of the chicken visceral fat with the reproductive system and lower involvement in the regulation of appetite, inflammation and insulin resistance.

Keywords
Chickens, Adipose tissue, Adipokines, PTEN-pathway, Adipolin, SFTPA1, TNF, PLIN1, Yolk proteins, RNA-seq, Mass spectrometry
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-356095 (URN)10.1186/s12864-018-4675-0 (DOI)000431263300001 ()29695257 (PubMedID)
Available from: 2018-07-19 Created: 2018-07-19 Last updated: 2018-07-19Bibliographically approved
Makino, T., Rubin, C.-J., Carneiro, M., Axelsson, E., Andersson, L. & Webster, M. T. (2018). Elevated proportions of deleterious genetic variation in domestic animals and plants. Genome Biology and Evolution, 10(1), 276-290
Open this publication in new window or tab >>Elevated proportions of deleterious genetic variation in domestic animals and plants
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2018 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, no 1, p. 276-290Article in journal (Refereed) Published
Abstract [en]

A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken and silkworm) and two domestic plant species (rice and soybean) compared to their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more SNPs in highly conserved elements in domestic species and a tendency for domestic species to harbour a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species.

Place, publisher, year, edition, pages
Oxford University Press, 2018
Keywords
artificial selection, domestication, effective population size, mutational load, natural selection, population bottleneck
National Category
Evolutionary Biology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-339437 (URN)10.1093/gbe/evy004 (DOI)000424893500020 ()29325102 (PubMedID)
Available from: 2018-01-18 Created: 2018-01-18 Last updated: 2018-04-10Bibliographically approved
Berg, F., Almeland, O. W., Skadal, J., Slotte, A., Andersson, L. & Folkvord, A. (2018). Genetic factors have a major effect on growth, number of vertebrae and otolith shape in Atlantic herring (Clupea harengus). PLoS ONE, 13(1), Article ID e0190995.
Open this publication in new window or tab >>Genetic factors have a major effect on growth, number of vertebrae and otolith shape in Atlantic herring (Clupea harengus)
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2018 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 1, article id e0190995Article in journal (Refereed) Published
Abstract [en]

Atlantic herring, Clupea harengus, have complex population structures. Mixing of populations is known, but the extent of connectivity is still unclear. Phenotypic plasticity results in divergent phenotypes in response to environmental factors. A marked salinity gradient occurs from Atlantic Ocean (salinity 35) into the Baltic Sea (salinity range 2–12). Herring from both habitats display phenotypic and genetic variability. To explore how genetic factors and salinity influence phenotypic traits like growth, number of vertebrae and otolith shape an experimental population consisting of Atlantic purebreds and Atlantic/Baltic F1 hybrids were incubated and co-reared at two different salinities, 16 and 35, for three years. The F1-generation was repeatedly sampled to evaluate temporal variation. A von Bertalanffy growth model indicated that reared Atlantic purebreds had a higher maximum length (26.2 cm) than Atlantic/Baltic hybrids (24.8 cm) at salinity 35, but not at salinity 16 (25.0 and 24.8 cm, respectively). In contrast, Atlantic/Baltic hybrids achieved larger size-at-age than the wild caught Baltic parental group. Mean vertebral counts and otolith aspect ratios were higher for reared Atlantic purebreds than Atlantic/Baltic hybrids, consistent with the differences between parental groups. There were no significant differences in vertebral counts and otolith aspect ratios between herring with the same genotype but raised in different salinities. A Canonical Analysis of Principal Coordinates was applied to analyze the variation in wavelet coefficients that described otolith shape. The first discriminating axis identified the differences between Atlantic purebreds and Atlantic/Baltic hybrids, while the second axis represented salinity differences. Assigning otoliths based on genetic groups (Atlantic purebreds vs. Atlantic/Baltic hybrids) yielded higher classification success (~90%) than based on salinities (16 vs. 35; ~60%). Our results demonstrate that otolith shape and vertebral counts have a significant genetic component and are therefore useful for studies on population dynamics and connectivity.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-343378 (URN)10.1371/journal.pone.0190995 (DOI)000419952400090 ()29324892 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationKnut and Alice Wallenberg Foundation
Available from: 2018-02-28 Created: 2018-02-28 Last updated: 2018-03-02Bibliographically approved
Younis, S., Kamel, W., Falkeborn, T., Wang, H., Yu, D., Daniels, R., . . . Andersson, L. (2018). Multiple nuclear-replicating viruses require the stress-induced protein ZC3H11A for efficient growth. Proceedings of the National Academy of Sciences of the United States of America, 115(16), E3808-E3816
Open this publication in new window or tab >>Multiple nuclear-replicating viruses require the stress-induced protein ZC3H11A for efficient growth
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 16, p. E3808-E3816Article in journal (Refereed) Published
Abstract [en]

The zinc finger CCCH-type containing 11A (ZC3H11A) gene encodes a well-conserved zinc finger protein that may function in mRNA export as it has been shown to associate with the transcription export (TREX) complex in proteomic screens. Here, we report that ZC3H11A is a stress-induced nuclear protein with RNA-binding capacity that localizes to nuclear splicing speckles. During an adenovirus infection, the ZC3H11A protein and splicing factor SRSF2 relocalize to nuclear regions where viral DNA replication and transcription take place. Knockout (KO) of ZC3H11A in HeLa cells demonstrated that several nuclear-replicating viruses are dependent on ZC3H11A for efficient growth (HIV, influenza virus, herpes simplex virus, and adenovirus), whereas cytoplasmic replicating viruses are not (vaccinia virus and Semliki Forest virus). High-throughput sequencing of ZC3H11A-cross-linked RNA showed that ZC3H11A binds to short purine-rich ribonucleotide stretches in cellular and adenoviral transcripts. We show that the RNA-binding property of ZC3H11A is crucial for its function and localization. In ZC3H11A KO cells, the adenovirus fiber mRNA accumulates in the cell nucleus. Our results suggest that ZC3H11A is important for maintaining nuclear export of mRNAs during stress and that several nuclear-replicating viruses take advantage of this mechanism to facilitate their replication.

Keywords
ZC3H11A, mRNA export, stress response, virus infection
National Category
Microbiology in the medical area Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-354118 (URN)10.1073/pnas.1722333115 (DOI)000430191900026 ()29610341 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2018-06-19 Created: 2018-06-19 Last updated: 2018-06-19Bibliographically approved
Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R. & Grant, P. R. (2018). Rapid hybrid speciation in Darwin's finches.. Science, 359(6372), 224-228
Open this publication in new window or tab >>Rapid hybrid speciation in Darwin's finches.
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2018 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 359, no 6372, p. 224-228Article in journal (Refereed) Published
Abstract [en]

Homoploid hybrid speciation in animals has been inferred frequently from patterns of variation, but few examples have withstood critical scrutiny. Here we report a directly documented example, from its origin to reproductive isolation. An immigrant Darwin's finch to Daphne Major in the Galápagos archipelago initiated a new genetic lineage by breeding with a resident finch (Geospiza fortis). Genome sequencing of the immigrant identified it as a G. conirostris male that originated on Española >100 kilometers from Daphne Major. From the second generation onward, the lineage bred endogamously and, despite intense inbreeding, was ecologically successful and showed transgressive segregation of bill morphology. This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-340986 (URN)10.1126/science.aao4593 (DOI)000419816600048 ()29170277 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2018-02-14Bibliographically approved
Younis, S., Schönke, M., Massart, J., Hjortebjerg, R., Sundström, E., Gustafson, U., . . . Andersson, L. (2018). The ZBED6-IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals. Proceedings of the National Academy of Sciences of the United States of America, 115(9), E2048-E2057
Open this publication in new window or tab >>The ZBED6-IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 9, p. E2048-E2057Article in journal (Refereed) Published
Abstract [en]

A single nucleotide substitution in the third intron of insulin-like growth factor 2 (IGF2) is associated with increased muscle mass and reduced subcutaneous fat in domestic pigs. This mutation disrupts the binding of the ZBED6 transcription factor and leads to a threefold up-regulation of IGF2 expression in pig skeletal muscle. Here, we investigated the biological significance of ZBED6-IGF2 interaction in the growth of placental mammals using two mouse models, ZBED6 knock-out (Zbed6(-/-)) and Igf2 knock-in mice that carry the pig IGF2 mutation. These transgenic mice exhibit markedly higher serum IGF2 concentrations, higher growth rate, increased lean mass, and larger heart, kidney, and liver; no significant changes were observed for white adipose tissues. The changes in body and lean mass were most pronounced in female mice. The phenotypic changes were concomitant with a remarkable up-regulation of Igf2 expression in adult tissues. Transcriptome analysis of skeletal muscle identified differential expression of genes belonging to the extracellular region category. Expression analysis using fetal muscles indicated a minor role of ZBED6 in regulating Igf2 expression prenatally. Furthermore, transcriptome analysis of the adult skeletal muscle revealed that this elevated expression of Igf2 was derived from the P1 and P2 promoters. The results revealed very similar phenotypic effects in the Zbed6 knock-out mouse and in the Igf2 knock-in mouse, showing that the effect of ZBED6 on growth of muscle and internal organs is mediated through the binding site in the Igf2 gene. The results explain why this ZBED6 binding site is extremely well conserved among placental mammals.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-329188 (URN)10.1073/pnas.1719278115 (DOI)000426152500018 ()
Funder
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish Research Council, 2012-1760Swedish Research Council, 2015-00165Swedish Research Council, 80576801Swedish Research Council, 70374401
Available from: 2017-09-10 Created: 2017-09-10 Last updated: 2018-04-26Bibliographically approved
Negro, S., Imsland, F., Valera, M., Molina, A., Sole, M. & Andersson, L. (2017). Association analysis of KIT, MITF, and PAX3 variants with white markings in Spanish horses. Animal Genetics, 48(3), 349-352
Open this publication in new window or tab >>Association analysis of KIT, MITF, and PAX3 variants with white markings in Spanish horses
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2017 (English)In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 48, no 3, p. 349-352Article in journal (Refereed) Published
Abstract [en]

Several variants in the KIT, PAX3 and MITF genes have previously been associated with white markings in horses. In this study, we examined eight variants of these genes in 70 Menorca Purebred horses (PRMe, only black solid-coloured horses) and 70 Spanish Purebred horses (PRE, different coat colour patterns) that were scored for the extent of white markings. A maximum-likelihood chi-square test, logistic regression model and ridge regression analyses showed that a missense mutation (p.Arg682His) in KIT was associated with white facial markings (P<0.05) and with total white markings (P<0.05) in PRMe horses. The relative contribution of this variant to white markings in PRMe horses was estimated at 47.6% (head) and 43.4% (total score). In PRE horses, this variant was also associated with hindlimb scores (P<0.05) with a relative contribution of 41.2%. The g.20147039C>T intronic variant located 29.9kb downstream from the transcription start site of the MITF gene was associated with less white markings on forelimbs (P<0.05) in PRMe horses, with a relative contribution of 63.9%, whereas in PRE horses this variant was associated with white facial markings (P<0.05), with a relative contribution of 63.9%. No significant associations were found for PAX3 variants in these breeds. These results show that KIT and MITF variants are involved in the white marking patterns of both PRMe and PRE horses, providing breeders with an opportunity to use genetic testing to aid in breeding for their desired level of white markings.

Keywords
Menorca Purebred, phenotypic variance, Purebred, SNP, white spotting
National Category
Genetics Medical Biotechnology
Identifiers
urn:nbn:se:uu:diva-322506 (URN)10.1111/age.12528 (DOI)000399953100010 ()28084638 (PubMedID)
Available from: 2017-05-30 Created: 2017-05-30 Last updated: 2017-05-30Bibliographically approved
Seroussi, E., Pitel, F., Leroux, S., Morisson, M., Bornelöv, S., Miyara, S., . . . Friedman-Einat, M. (2017). Correction to: Mapping of leptin and its syntenic genes to chicken chromosome 1p. BMC Genetics, 18(113)
Open this publication in new window or tab >>Correction to: Mapping of leptin and its syntenic genes to chicken chromosome 1p
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2017 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 18, no 113Article in journal (Other academic) Published
National Category
Genetics Public Health, Global Health, Social Medicine and Epidemiology
Identifiers
urn:nbn:se:uu:diva-347716 (URN)10.1186/s12863-017-0587-2 (DOI)000418073200001 ()
Note

Correction in: BMC Genetics, vol. 18, issue 77.

DOI: 10.1186/s12863-017-0587-2

Available from: 2018-04-06 Created: 2018-04-06 Last updated: 2018-04-06Bibliographically approved
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