| 1. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 2. |
- Lansink, G. M. J., et al.
(författare)
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Potential for increased connectivity between differentiated wolverine populations
- 2022
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Ingår i: Biological Conservation. - : Elsevier. - 0006-3207 .- 1873-2917. ; 272
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Tidskriftsartikel (refereegranskat)abstract
- Information on genetic population structure provides important knowledge for species conservation. Yet, few studies combine extensive genetic data to evaluate the structure and population dynamics of transboundary populations. Here we used single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial haplotypes to analyze the genetic population structure of wolverines (Gulo gulo) across Fennoscandia using a long-term monitoring dataset of 1708 individuals. Clear population subdivision was detected between the Scandinavian and the eastern Finnish population with a steep cline in the contact zone. While the Scandinavian population showed isolation by distance, large swaths of this population were characterized by high connectivity. Areas with high resistance to gene flow are likely explained by a combination of factors, such as historical isolation and founder effects. From a conservation perspective, promoting gene flow from the population in eastern Finland to the northwest of Scandinavia could augment the less variable Scandinavian population, and increase the demographic resilience of all subpopulations. Overall, the large areas of low resistance to gene flow suggest that transboundary cooperation with aligned actions of harvest and conflict mitigation could improve genetic connectivity across Finland, Sweden, and Norway.
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| 3. |
- Mugal, Carina, et al.
(författare)
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Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids
- 2020
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 30:12, s. 1727-1739
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Tidskriftsartikel (refereegranskat)abstract
- Changes in interacting cis- and trans-regulatory elements are important candidates for Dobzhansky-Muller hybrid incompatibilities and may contribute to hybrid dysfunction by giving rise to misexpression in hybrids. To gain insight into the molecular mechanisms and determinants of gene expression evolution in natural populations, we analyzed the transcriptome from multiple tissues of two recently diverged Ficedula flycatcher species and their naturally occurring F1 hybrids. Differential gene expression analysis revealed that the extent of differentiation between species and the set of differentially expressed genes varied across tissues. Common to all tissues, a higher proportion of Z-linked genes than autosomal genes showed differential expression, providing evidence for a fast-Z effect. We further found clear signatures of hybrid misexpression in brain, heart, kidney, and liver. However, while testis showed the highest divergence of gene expression among tissues, it showed no clear signature of misexpression in F1 hybrids, even though these hybrids were found to be sterile. It is therefore unlikely that incompatibilities between cis-trans regulatory changes explain the observed sterility. Instead, we found evidence that cis-regulatory changes play a significant role in the evolution of gene expression in testis, which illustrates the tissue-specific nature of cis-regulatory evolution bypassing constraints associated with pleiotropic effects of genes.
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| 4. |
- Nam, Kiwoong, 1979-
(författare)
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Molecular Evolution of the Vertebrate Genome
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, I studied molecular evolution of the vertebrate genome, focusing on sex chromosomes, protein coding genes, and genome size variation. The evolutionary history of avian sex chromosomes was analyzed by comparing substitution rate among 12 gametologous gene pairs on the Z and W chromosomes. Divergence estimates were distributed into three discrete clusters, evolutionary strata, implying stepwise cessations of recombination. Stratum 3 and stratum 2 are located the intervals 1-11Mb and 16-53Mb on the chicken Z chromosome, respectively. Stratum 1 was located in the middle of stratum 2, suggesting a chromosomal inversion. Using a molecular clock, the estimated times for cessation of recombination between Z and W are 132–150 (stratum 1), 71–99 (stratum 2), and 47–57 (stratum 3) million years ago.Higher divergence rate in the Z chromosome than in autosomes (faster-Z) can be explained by positive selections on recessive alleles in hemizygous females, or by stronger genetic drift due to the smaller effective population size of the Z chromosomes. I found there was no difference in the intensity of the faster-Z effect among male-biased, female-biased, and unbiased genes, as might have been expected under a selection model. This result therefore supports the hypothesis that faster-Z is predominantly due to genetic drift.Next, I analyzed molecular evolution of protein-coding genes in birds. In the comparison of zebra finch, chicken and non-avian outgroups, I found that neutral substitution rate was highest in zebra finch, intermediate in chicken, and lowest in ancestral birds. This difference seems attributable to differences in generation time, ancestral birds being most long-lived. Several functional categories were overrepresented among positively selected genes in avian lineages, such as transporter activity and calcium ion binding. I also found that many genes involved with cognitive processes including vocal learning were positively selected in zebra finch. I also found evidence for Hill-Robertson interference acting against the removal of slightly deleterious mutations at linked loci.Finally, I studied the impact of recombination on genome size variation. I found that highly recombining regions have a more condensed genome structure, including shorter lengths of intron, intergenic spacer, transposable elements and higher gene density. In chicken and zebra finch I found that recombination rate was positively correlated with deletion bias, estimated by sequence comparisons between individual transposable elements (LINEs) and the corresponding master sequences. These observations indicate that the more compact genome structure in highly recombining region is due to a higher rate of sequence loss. Higher deletion bias in autosomes than in sex chromosomes supports this idea. I also found that sequence loss due to the deletion bias can explain nearly 20% of genome size reduction after the split of birds from other reptiles. In human, the recombination rate was positively correlated with the deletion bias estimated from polymorphic indels. These results support the hypothesis that the recombination drives genome contraction via the mutation process.
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| 5. |
- Uebbing, Severin
(författare)
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On the Evolution of the Avian Transcriptome
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Change in gene expression is a powerful tool for evolution, because seemingly small expression changes can contribute important steps towards adaptation without necessarily affecting the whole organism. There is still much to learn about how gene expression evolves on genome- and population-wide levels, especially in non-model organisms. This thesis addresses some important questions in gene expression evolution via the quantitative measurement of RNA and protein levels in birds.First, I confirmed the state of incomplete dosage compensation in birds by sequencing the transcriptome of collared flycatchers (Ficedula albicollis). I showed that pleiotropy governs the evolution of expression male-bias from the Z chromosome. Sex-linked genes in females were more highly expressed than half the male expression level, indicative of a partial up-regulation. A comparison with data from ostrich (Struthio camelus), a bird with non-degenerated sex chromosomes, showed that sex-linked expression male-bias evolved following sex chromosome degradation.Second, using a combination of RNA sequencing and proteome mass spectrometry in chicken (Gallus gallus), I asked whether complete dosage compensation was achieved through regulation at translation. I showed that this was not the case and that incomplete dosage compensation extends to the protein level in birds. In addition, sex-linked genes showed more often an increased amount of regulation at translational level than autosomal genes.Third, I investigated gene expression divergence between collared and pied flycatchers (Ficedula hypoleuca) using RNA sequencing in multiple tissues and individuals. Tissues differed in the degree of expression variance and in the number of divergent genes, which I identified using expression QST. Variance within species was negatively correlated with expression breadth and protein interactivity, indicating that evolutionary constraints act predominantly within interbreeding populations. Among genes unique to one of the species, I identified one gene, DPP7, falling into a large genomic deletion fixed in pied flycatchers.Fourth, I investigated allele-specific expression (ASE) in the two flycatcher populations. ASE was identified from genetic variants within transcripts using RNA sequencing reads. We developed a Bayesian negative binomial approach that gained statistical power by estimating expression variance from combined SNPs within a transcript and overdispersion from the whole dataset.
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| 6. |
- Silva, C. N. S., et al.
(författare)
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Insights into the genetic architecture of morphological traits in two passerine bird species
- 2017
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 119:3, s. 197-205
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (V-P), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of V-P). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.
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| 7. |
- Husby, Arild, et al.
(författare)
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Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait
- 2015
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 282:1806
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.
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| 8. |
- Kawakami, Takeshi, et al.
(författare)
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A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
- 2014
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 23:16, s. 4035-4058
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Forskningsöversikt (refereegranskat)abstract
- Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50K SNP array to develop a high-density linkage map with 37262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132cM and a mean genetic distance between markers of 0.12cM. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2Mb and with 1.042Gb (of 1.116Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5-2.0 event (6.6-7.5Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1cM/Mb and correlated closely with chromosome size, from 2cM/Mb for chromosomes >100Mb to >10cM/Mb for chromosomes <10Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50cM was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.
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| 9. |
- Hagenblad, Jenny, et al.
(författare)
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Population genomics of the inbred Scandinavian wolf
- 2009
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 18:7, s. 1341-1351
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Tidskriftsartikel (refereegranskat)abstract
- The Scandinavian wolf population represents one of the genetically most well-characterized examples of a severely bottlenecked natural population (with only two founders), and of how the addition of new genetic material (one immigrant) can at least temporarily provide a 'genetic rescue'. However, inbreeding depression has been observed in this population and in the absence of additional immigrants, its long-term viability is questioned. To study the effects of inbreeding and selection on genomic diversity, we performed a genomic scan with approximately 250 microsatellite markers distributed across all autosomes and the X chromosome. We found linkage disequilibrium (LD) that extended up to distances of 50 Mb, exceeding that of most outbreeding species studied thus far. LD was particularly pronounced on the X chromosome. Overall levels of observed genomic heterozygosity did not deviate significantly from simulations based on known population history, giving no support for a general selection for heterozygotes. However, we found evidence supporting balancing selection at a number of loci and also evidence suggesting directional selection at other loci. For markers on chromosome 23, the signal of selection was particularly strong, indicating that purifying selection against deleterious alleles may have occurred even in this very small population. These data suggest that population genomics allows the exploration of the effects of neutral and non-neutral evolution on a finer scale than what has previously been possible.
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| 10. |
- Knief, Ulrich, et al.
(författare)
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A prezygotic transmission distorter acting equally in female and male zebra finches Taeniopygia guttata
- 2015
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 24:15, s. 3846-3859
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Tidskriftsartikel (refereegranskat)abstract
- The two parental alleles at a specific locus are usually inherited with equal probability to the offspring. However, at least three processes can lead to an apparent departure from fair segregation: early viability selection, biased gene conversion and various kinds of segregation distortion. Here, we conduct a genome-wide scan for transmission distortion in a captive population of zebra finches (Taeniopygia guttata) using 1302 single-nucleotide polymorphisms (SNPs) followed by confirmatory analyses on independent samples from the same population. In the initial genome-wide scan, we found significant distortion at three linked loci on chromosome Tgu2 and we were able to replicate this finding in each of two follow-up data sets [overall transmission ratio=0.567 (95% CI=0.536-0.600), based on 1101 informative meioses]. Although the driving allele was preferentially transmitted by both heterozygous females [ratio=0.560 (95% CI=0.519-0.603)] and heterozygous males [ratio=0.575 (95% CI=0.531-0.623)], we could rule out postzygotic viability selection and biased gene conversion as possible mechanisms. Early postzygotic viability selection is unlikely, because it would result in eggs with no visible embryo and hence no opportunity for genotyping, and we confirmed that both females and males heterozygous for the driving allele did not produce a larger proportion of such eggs than homozygous birds. Biased gene conversion is expected to be rather localized, while we could trace transmission distortion in haplotypes of several megabases in a recombination desert. Thus, we here report the rare case of a prezygotically active transmission distorter operating equally effectively in female and male meioses.
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