uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Andersson, Leif
Alternative names
Publications (10 of 193) Show all publications
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
Show others...
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
Keyword
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)
Show others...
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
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.
Show others...
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
Show others...
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
Show others...
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.

Keyword
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
Show others...
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
Bornelöv, S., Seroussi, E., Yosefi, S., Pendavis, K., Burgess, S. C., Grabherr, M., . . . Andersson, L. (2017). Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost. Genome Biology, 18, Article ID 112.
Open this publication in new window or tab >>Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost
Show others...
2017 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 18, article id 112Article in journal (Refereed) Published
Abstract [en]

Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases. Hence, the occurrence of syntenic groups of vertebrate genes that have not been observed in Aves does not prove the evolutionary loss of such genes.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-327369 (URN)10.1186/s13059-017-1231-1 (DOI)000403239100007 ()28615067 (PubMedID)
Funder
EU, European Research Council
Available from: 2017-08-10 Created: 2017-08-10 Last updated: 2017-08-10Bibliographically approved
Carneiro, M., Hu, D., Archer, J., Feng, C., Afonso, S., Chen, C., . . . Andersson, L. (2017). Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus. Genetics, 205(2), 955-965
Open this publication in new window or tab >>Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus
Show others...
2017 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 205, no 2, p. 955-965Article in journal (Refereed) Published
Abstract [en]

The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is recessive lethal and dwarf homozygotes die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal, although smaller when compared to other breeds. Here, we show that the dwarf allele constitutes a similar to 12.1 kb deletion overlapping the promoter region and first three exons of the HMGA2 gene leading to inactivation of this gene. HMGA2 has been frequently associated with variation in body size across species. Homozygotes for null alleles are viable in mice but not in rabbits and probably not in humans. RNA-sequencing analysis of rabbit embryos showed that very few genes (4-29 genes) were differentially expressed among the three HMGA2/dwarf genotypes, suggesting that dwarfism and inviability in rabbits are caused by modest changes in gene expression. Our results show that HMGA2 is critical for normal expression of IGF2BP2, which encodes an RNA-binding protein. Finally, we report a catalog of regions of elevated genetic differentiation between dwarf and normal-size rabbits, including LCORL-NCAPG, STC2, HOXD cluster, and IGF2BP2. Levels and patterns of genetic diversity at the LCORL-NCAPG locus further suggest that small size in dwarf breeds was enhanced by crosses with wild rabbits. Overall, our results imply that small size in dwarf rabbits results from a large effect, loss-of-function (LOF) mutation in HMGA2 combined with polygenic selection.

Place, publisher, year, edition, pages
GENETICS SOCIETY AMERICA, 2017
Keyword
whole-genome sequencing, RNA-seq, body size, IGF2BP2, mtDNA
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-320763 (URN)10.1534/genetics.116.196667 (DOI)000394144900034 ()27986804 (PubMedID)
Funder
EU, European Research Council, 286431
Available from: 2017-04-25 Created: 2017-04-25 Last updated: 2017-04-25Bibliographically approved
Han, F., Lamichhaney, S., Grant, B. R., Grant, P. R., Andersson, L. & Webster, M. T. (2017). Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches.. Genome Research, 27(6), 1004-1015
Open this publication in new window or tab >>Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches.
Show others...
2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 6, p. 1004-1015Article in journal (Refereed) Published
Abstract [en]

Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-340985 (URN)10.1101/gr.212522.116 (DOI)28442558 (PubMedID)
Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2018-02-05
Hill, G. E., Lopes, R. J., Johnson, J. D., Toomey, M. B., Ferreira, M., Melo-Ferreira, J., . . . Hill, G. (2017). Genetic Basis for Red Coloration in Birds. Paper presented at Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), JAN 04-08, 2017, New Orleans, LA. Integrative and Comparative Biology, 57, E292-E292
Open this publication in new window or tab >>Genetic Basis for Red Coloration in Birds
Show others...
2017 (English)In: Integrative and Comparative Biology, ISSN 1540-7063, E-ISSN 1557-7023, Vol. 57, p. E292-E292Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
OXFORD UNIV PRESS INC, 2017
National Category
Zoology
Identifiers
urn:nbn:se:uu:diva-328837 (URN)000398668701418 ()
Conference
Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), JAN 04-08, 2017, New Orleans, LA
Available from: 2017-10-30 Created: 2017-10-30 Last updated: 2017-10-30Bibliographically approved
Organisations

Search in DiVA

Show all publications