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Nadachowska-Brzyska, Krystyna
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Publications (10 of 13) Show all publications
Dutoit, L., Mugal, C., Bolivar, P., Wang, M., Nadachowska-Brzyska, K., Smeds, L., . . . Ellegren, H. (2018). Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome. Molecular Ecology, 27(18), 3572-3581
Open this publication in new window or tab >>Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome
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2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 18, p. 3572-3581Article in journal (Other academic) Published
Abstract [en]

Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on sexually antagonistic mutations in males and females. This prediction, so far not been empirically tested on a genome-wide scale, could potentially contribute towards genomic heterogeneity in levels of genetic diversity. We used large-scale population genomic and transcriptomic data from the collared flycatcher (Ficedula albicollis) to analyse how sex-biased gene expression – one outcome of sexual conflict – relates to genetic variability. Here, we demonstrate that the extent of sex-biased gene expression of both male-biased and female-biased genes is significantly correlated with levels of nucleotide diversity in gene sequences and that this correlation extends to the overall levels of genomic diversity. We find evidence for balancing selection in sex-biased genes, suggesting that sex-biased gene expression could be seen as a component counteracting the diversity-reducing effects of linked positive and purifying selection. The observation of significant genetic differentiation between males and females for male-biased genes indicates ongoing sexual conflict and sex-specific viability selection, potentially driven by sexual selection. Our results thus provide a new perspective on the long-standing question in evolutionary biology of how genomes can remain so genetically variable in face of strong natural and sexual selection.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-331832 (URN)10.1111/mec.14789 (DOI)000444577100002 ()30055065 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2017-10-18 Created: 2017-10-18 Last updated: 2018-11-15Bibliographically approved
Figuet, E., Nabholz, B., Bonneau, M., Carrio, E. M., Nadachowska-Brzyska, K., Ellegren, H. & Galtier, N. (2016). Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes. Molecular biology and evolution, 33(6), 1517-1527
Open this publication in new window or tab >>Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes
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2016 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 6, p. 1517-1527Article in journal (Refereed) Published
Abstract [en]

The nearly neutral theory of molecular evolution predicts that small populations should accumulate deleterious mutations at a faster rate than large populations. The analysis of nonsynonymous (dN) versus synonymous (dS) substitution rates in birds versus mammals, however, has provided contradictory results, questioning the generality of the nearly neutral theory. Here we analyzed the impact of life history traits, taken as proxies of the effective population size, on molecular evolutionary and population genetic processes in amniotes, including the so far neglected reptiles. We report a strong effect of species body mass, longevity, and age of sexual maturity on genome-wide patterns of polymorphism and divergence across the major groups of amniotes, in agreement with the nearly neutral theory. Our results indicate that the rate of protein evolution in amniotes is determined in the first place by the efficiency of purifying selection against deleterious mutations-and this is true of both radical and conservative amino acid changes. Interestingly, the among-species distribution of dN/dS in birds did not follow this general trend: dN/dS was not higher in large, long-lived than in small, short-lived species of birds. We show that this unexpected pattern is not due to a more narrow range of life history traits, a lack of correlation between traits and Ne, or a peculiar distribution of fitness effects of mutations in birds. Our analysis therefore highlights the bird dN/dS ratio as a molecular evolutionary paradox and a challenge for future research.

Keywords
substitution rate, synonymous, birds, mammals, reptiles, effective population size, longevity, body mass
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-298075 (URN)10.1093/molbev/msw033 (DOI)000376170300010 ()26944704 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2016-06-30 Created: 2016-06-29 Last updated: 2018-02-22Bibliographically approved
Nadachowska-Brzyska, K., Burri, R., Smeds, L. & Ellegren, H. (2016). PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers. Molecular Ecology, 25(5), 1058-1072
Open this publication in new window or tab >>PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers
2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, p. 1058-1072Article, review/survey (Refereed) Published
Abstract [en]

Climatic fluctuations during the Quaternary period governed the demography of species and contributed to population differentiation and ultimately speciation. Studies of these past processes have previously been hindered by a lack of means and genetic data to model changes in effective population size (N-e) through time. However, based on diploid genome sequences of high quality, the recently developed pairwise sequentially Markovian coalescent (PSMC) can estimate trajectories of changes in N-e over considerable time periods. We applied this approach to resequencing data from nearly 200 genomes of four species and several populations of the Ficedula species complex of black-and-white flycatchers. N-e curves of Atlas, collared, pied and semicollared flycatcher converged 1-2million years ago (Ma) at an N-e of approximate to 200000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate N-e trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100-200thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in N-e differed among species, and for pied flycatcher, the temporal dynamics of N-e differed between Spanish birds and central/northern European populations. This cautions against extrapolation of demographic inference between lineages and calls for adequate sampling to provide representative pictures of the coalescence process in different species or populations. We also empirically evaluate criteria for proper inference of demographic histories using PSMC and arrive at recommendations of using sequencing data with a mean genome coverage of 18X, a per-site filter of 10 reads and no more than 25% of missing data.

Keywords
Atlas flycatcher, collared flycatcher, coverage, effective population size, pied flycatcher, PSMC, semicollared flycatcher, whole-genome sequencing
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-294812 (URN)10.1111/mec.13540 (DOI)000371433400004 ()26797914 (PubMedID)
Funder
Swedish Research Council, 2007-8731 2010-5650 2013-8271Knut and Alice Wallenberg FoundationEU, European Research Council, AdG 249976
Available from: 2016-08-19 Created: 2016-05-27 Last updated: 2018-02-22Bibliographically approved
Nadachowska-Brzyska, K., Li, C., Smeds, L., Zhang, G. & Ellegren, H. (2015). Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences. Current Biology, 25(10), 1375-1380
Open this publication in new window or tab >>Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences
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2015 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, no 10, p. 1375-1380Article in journal (Refereed) Published
Abstract [en]

Global climate fluctuations have significantly influenced the distribution and abundance of biodiversity [1]. During unfavorable glacial periods, many species experienced range contraction and fragmentation, expanding again during interglacials [2- 4]. An understanding of the evolutionary consequences of both historical and ongoing climate changes requires knowledge of the temporal dynamics of population numbers during such climate cycles. Variation in abundance should have left clear signatures in the patterns of intraspecific genetic variation in extant species, from which historical effective population sizes (Ne) can be estimated [3]. We analyzed whole-genome sequences of 38 avian species in a pairwise sequentially Markovian coalescent (PSMC, [5]) framework to quantitatively reveal changes in Ne from approximately 10 million to 10 thousand years ago. Significant fluctuations in Ne over time were evident for most species. The most pronounced pattern observed in many species was a severe reduction in Ne coinciding with the beginning of the last glacial period (LGP). Among species, Ne varied by at least three orders of magnitude, exceeding 1 million in the most abundant species. Several species on the IUCN Red List of Threatened Species showed long-term reduction in population size, predating recent declines. We conclude that cycles of population expansions and contractions have been a common feature of many bird species during the Quaternary period, likely coinciding with climate cycles. Population size reduction should have increased the risk of extinction but may also have promoted speciation. Species that have experienced long-term declines may be especially vulnerable to recent anthropogenic threats.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-256842 (URN)10.1016/j.cub.2015.03.047 (DOI)000354785900032 ()25891404 (PubMedID)
Available from: 2015-06-26 Created: 2015-06-26 Last updated: 2018-02-22Bibliographically approved
Nadachowska-Brzyska, K., Burri, R., Olason, P., Kawakami, T., Smeds, L. & Ellegren, H. (2013). Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data. PLOS Genetics, 9(11), e1003942
Open this publication in new window or tab >>Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data
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2013 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 9, no 11, p. e1003942-Article in journal (Refereed) Published
Abstract [en]

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000–80,000) and census sizes (5–50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-214186 (URN)10.1371/journal.pgen.1003942 (DOI)000330369000029 ()
Available from: 2014-01-08 Created: 2014-01-08 Last updated: 2018-02-22Bibliographically approved
Herdegen, M., Nadachowska-Brzyska, K., Konowalik, A., Babik, W. & Radwan, J. (2013). Heterozygosity, sexual ornament and body size in the crested newt. Journal of Zoology, 291(2), 146-153
Open this publication in new window or tab >>Heterozygosity, sexual ornament and body size in the crested newt
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2013 (English)In: Journal of Zoology, ISSN 0952-8369, E-ISSN 1469-7998, Vol. 291, no 2, p. 146-153Article in journal (Refereed) Published
Abstract [en]

Both genome-wide heterozygosity and heterozygosity at major histocompatibility complex (MHC) genes are often associated with higher fitness. Recent theoretical work indicates that sexual ornaments may reveal information about individual heterozygosity, and that preference for such ornaments may benefit females via the increased heterozygosity of their progeny. Here, we used path analysis to investigate the direct and indirect (via body size used as an index of condition) effects of heterozygosity at six microsatellite loci and the MHC class II DAB gene on the size of a sexual ornament, the crest, in the crested newt Triturus cristatus. We found that microsatellite heterozygosity, but not MHC heterozygosity, significantly predicted male body size, and that male body size significantly predicted crest height. However, there was no direct effect of MHC or microsatellite heterozygosity on crest height. Furthermore, microsatellite heterozygosity significantly increased with age, indicating that it had a positive effect on survival. Overall, our results are consistent with the hypothesis that heterozygosity determines condition, and that variation in condition is expressed as variation in sexual ornamentation.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-214191 (URN)10.1111/jzo.12056 (DOI)000325007900007 ()
Note

Nadachowska-Brzyska, Krystyna - Current address: Evolutionary Biology Center, Department of Evolutionary Biology, Uppsala, Sweden.

Available from: 2014-01-08 Created: 2014-01-08 Last updated: 2017-12-06Bibliographically approved
Zielinski, P., Nadachowska-Brzyska, K., Wielstra, B., Szkotak, R., Covaciu-Marcov, S. D., Cogalniceanu, D. & Babik, W. (2013). No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni). Molecular Ecology, 22(7), 1884-1903
Open this publication in new window or tab >>No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni)
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2013 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 7, p. 1884-1903Article in journal (Refereed) Published
Abstract [en]

Patterns of interspecific introgression may vary geographically, and the distribution of introgressed variants can yield insight into the historical dynamics of genetic interactions between hybridizing species. Urodele amphibians, often characterized by limited mobility, deep intraspecific genetic structuring and vulnerability to climatic changes, constitute suitable models for such historical inferences. Here, we combine an extensive survey of the mitochondrial (mtDNA) and nuclear (15 microsatellites) genomes in the Carpathian newt, Lissotriton montandoni (Lm) with species distribution modelling (SDM). Populations of the smooth newt, L.vulgaris (Lv) from the areas surrounding the Lm range were also sampled to test whether gene flow between these hybridizing species extends beyond the area of strict syntopy. The extent of introgression differs dramatically between the mitochondrial genome and the nuclear genome. While multiple, spatially and temporally distinct introgression events from Lv resulted in complete mtDNA replacement in Lm, there was little evidence of recent interspecific nuclear gene flow in the assayed markers. Microsatellite differentiation within Lm defines three units, probably derived from separate glacial refugia, located in the northern, eastern and southern part of the Carpathians. In situ survival and range fragmentation of Lm are supported by SDM, corroborating the role of the Carpathians as a major refugial area. Our results, in combination with previous reports of extensive introgression of the major histocompatibility complex (MHC) genes, emphasize the complexity of historical gene exchange between Lm and Lv.

Keywords
genetic structure, introgression, Lissotriton, mtDNA replacement, natural hybridization, newt
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-198909 (URN)10.1111/mec.12225 (DOI)000316575800010 ()
Available from: 2013-05-02 Created: 2013-04-29 Last updated: 2017-12-06Bibliographically approved
Kajtoch, L., Nadachowska-Brzyska, K. & Babik, W. (2012). Development and characterization of microsatellite loci in the Centricnemus leucogrammus weevil. Molecular Biology Reports, 39(12), 11131-11136
Open this publication in new window or tab >>Development and characterization of microsatellite loci in the Centricnemus leucogrammus weevil
2012 (English)In: Molecular Biology Reports, ISSN 0301-4851, E-ISSN 1573-4978, Vol. 39, no 12, p. 11131-11136Article in journal (Refereed) Published
Abstract [en]

Centricnemus leucogrammus is a weevil characteristic of European xerothermic habitats and steppes. The species was probably more widespread during the Pleistocene glaciations, while its current distribution is limited to "warm-stage refugia." It may be regarded as a typical representative of flightless xerothermophilous beetles. Previous studies concentrated on its genetic variation using mitochondrial genes. Here, we identified, tested and characterized 24 polymorphic microsatellite loci with the use of 454 sequencing of microsatellite enriched genomic libraries. The new set of loci will be used in studies on the population structure of this weevil and may provide valuable information for its conservation.

Keywords
Coleoptera, Curculionidae, Conservation, Population genetics, Short tandem repeats, 454 Sequencing
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-187623 (URN)10.1007/s11033-012-2021-1 (DOI)000310586700134 ()
Available from: 2012-12-10 Created: 2012-12-10 Last updated: 2017-12-07Bibliographically approved
Nadachowska-Brzyska, K., Zielinski, P., Radwan, J. & Babik, W. (2012). Interspecific hybridization increases MHC class II diversity in two sister species of newts. Molecular Ecology, 21(4), 887-906
Open this publication in new window or tab >>Interspecific hybridization increases MHC class II diversity in two sister species of newts
2012 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 4, p. 887-906Article in journal (Refereed) Published
Abstract [en]

Our understanding of the evolutionary mechanisms generating variation within the highly polymorphic major histocompatibility complex (MHC) genes remains incomplete. Assessing MHC variation across multiple populations, of recent and ancient divergence, may facilitate understanding of geographical and temporal aspects of variation. Here, we applied 454 sequencing to perform a large-scale, comprehensive analysis of MHC class II in the closely related, hybridizing newts, Lissotriton vulgaris (Lv) and Lissotriton montandoni (Lm). Our study revealed an extensive (299 alleles) geographically structured polymorphism. Populations at the southern margin of the Lvdistribution, inhabited by old and distinct lineages (southern Lv), exhibited moderate MHC variation and strong population structure, indicating little gene flow or extensive local adaptation. Lissotriton vulgaris in central Europe and the northern Balkans (northern Lv) and almost all Lm populations had a high MHC variation. A much higher proportion of MHC alleles was shared between Lm and northern Lvthan between Lm and southern Lv. Strikingly, the average pairwise FST between northern Lv and Lm was significantly lower than between northern and southern Lv for MHC, but not for microsatellites. Thus, high MHC variation in Lm and northern Lv may result from gene flow between species. We hypothesize that the interspecific exchange of MHC genes may be facilitated by frequency-dependent selection. A marginally significant correlation between the MHC and microsatellite allelic richness indicates that demographic factors may have contributed to the present-day pattern of MHC variation, but unequivocal signatures of adaptive evolution in MHC class II sequences emphasize the role of selection on a longer timescale.

Keywords
introgression, Lissotriton montandoni, Lissotriton vulgaris, MHC variation, positive selection, 454 genotyping
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-236850 (URN)10.1111/j.1365-294X.2011.05347.x (DOI)000299416900009 ()22066802 (PubMedID)
Available from: 2014-11-24 Created: 2014-11-24 Last updated: 2017-12-05Bibliographically approved
Ellegren, H., Smeds, L., Burri, R., Ólason, P. I., Backström, N., Kawakami, T., . . . Wolf, J. B. W. (2012). The genomic landscape of species divergence in Ficedula flycatchers. Nature, 491(7426), 756-760
Open this publication in new window or tab >>The genomic landscape of species divergence in Ficedula flycatchers
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2012 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 491, no 7426, p. 756-760Article in journal (Refereed) Published
Abstract [en]

Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre-as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-188120 (URN)10.1038/nature11584 (DOI)000311606000045 ()
Available from: 2012-12-13 Created: 2012-12-12 Last updated: 2018-02-22Bibliographically approved
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