| 11. |
- Backström, Niclas, et al.
(författare)
-
Inferring the demographic history of European Ficedula flycatcher populations
- 2013
-
Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13, s. 2-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results: We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations. Conclusions: Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.
|
|
| 12. |
- Backström, Niclas, et al.
(författare)
-
Levels of linkage disequilibrium in a wild bird population
- 2006
-
Ingår i: Biology Letters. - : The Royal Society. - 1744-9561 .- 1744-957X. ; 2:3, s. 435-438
-
Tidskriftsartikel (refereegranskat)abstract
- Population-based mapping approaches are attractive for tracing the genetic background to phenotypic traits in wild species, given that it is often difficult to gather extensive and well-defined pedigrees needed for quantitative trait locus analysis. However, the feasibility of association or hitch-hiking mapping is dependent on the degree of linkage disequilibrium. (LD) in the population, on which there is yet limited information for wild species. Here we use single nucleotide polymorphism (SNP) markers from 23 genes in a recently established linkage map of the Z chromosome of the collared flycatcher, to study the extent of LD in a natural bird population. In most but not all cases we find SNPs within the same intron (less than 500 bp) to be in perfect LD. However, LD then decays to background level at a distance 1 cM or 400-500 kb. Although LD seems more extensive than in other species, if the observed pattern is representative for other regions of the genome and turns out to be a general feature of natural bird populations, dense marker maps might be needed for genome scans aimed at identifying association between marker and trait loci.
|
|
| 13. |
- Backström, Niclas, et al.
(författare)
-
No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps
- 2010
-
Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:16, s. 3394-3405
-
Tidskriftsartikel (refereegranskat)abstract
- Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridization, these two species demonstrate a high degree of intrinsic post-zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-chromosome. Could rearrangements of the Z-chromosome between the species explain their reproductive isolation? We developed high coverage Z-chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57-62 gene markers with an estimated average density of one every 1-1.5 Mb. We estimated the recombination rates in flycatcher Z-chromosomes to 1.1-1.3 cM/Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex chromosome rearrangements have caused the relatively strong post-zygotic reproductive isolation between these two Ficedula species.
|
|
| 14. |
- Backström, Niclas, et al.
(författare)
-
Sex- and species-biased gene flow in a spotted eagle hybrid zone.
- 2011
-
Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Recent theoretical and empirical work points toward a significant role for sex-chromosome linked genes in the evolution of traits that induce reproductive isolation and for traits that evolve under influence of sexual selection. Empirical studies including recently diverged (Pleistocene), short-lived avian species pairs with short generation times have found that introgression occurs on the autosomes but not on the Z-chromosome. Here we study genetic differentiation and gene flow in the long-lived greater spotted eagle (Aquila clanga) and lesser spotted eagle (A. pomarina), two species with comparatively long generation times.RESULTS: Our data suggest that there is a directional bias in migration rates between hybridizing spotted eagles in eastern Europe. We find that a model including post divergence gene flow fits our data best for both autosomal and Z-chromosome linked loci but, for the Z-chromosome, the rate is reduced in the direction from A. pomarina to A. clanga.CONCLUSIONS: The fact that some introgression still occurs on the Z-chromosome between these species suggests that the differentiation process is in a more premature phase in our study system than in previously studied avian species pairs and that could be explained by a shorter divergence time and/or a longer average generation time in the spotted eagles. The results are in agreement with field observations and provide further insight into the role of sex-linked loci for the build-up of barriers to gene flow among diverging populations and species.
|
|
| 15. |
- Backström, Niclas, et al.
(författare)
-
The recombination landscape of the zebra finch Taeniopygia guttata genome
- 2010
-
Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 20:4, s. 485-495
-
Tidskriftsartikel (refereegranskat)abstract
- Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.
|
|
| 16. |
|
|
| 17. |
|
|
| 18. |
- Boman, Jesper, et al.
(författare)
-
Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui)
- 2023
-
Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:13, s. 3513-3523
-
Tidskriftsartikel (refereegranskat)abstract
- Seasonal environmental fluctuations provide formidable challenges for living organisms, especially small ectotherms such as butterflies. A common strategy to cope with harsh environments is to enter diapause, but some species avoid unsuitable conditions by migrating. Despite a growing understanding of migration in the life cycles of some butterfly species, it remains unknown how individuals register and store environmental cues to determine whether and where to migrate. Here, we explored how competition and host plant availability during larval development affect patterns of DNA methylation in the migratory painted lady (Vanessa cardui) butterfly. We identify a set of potentially functional methylome shifts associated with differences in the environment, indicating that DNA methylation is involved in the response to different conditions during larval development. By analysing the transcriptome for the same samples used for methylation profiling, we also uncovered a non-monotonic relationship between gene body methylation and gene expression. Our results provide a starting point for understanding the interplay between DNA methylation and gene expression in butterflies in general and how differences in environmental conditions during development can trigger unique epigenetic marks that might be important for behavioural decisions in the adult stage.
|
|
| 19. |
- Boman, Jesper, et al.
(författare)
-
Evolution of hybrid inviability associated with chromosome fusions
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. However, less is known about how other rearrangements, such as chromosome fissions and fusions, can affect the evolution of reproductive isolation. Here, we used crosses between populations of the wood white butterfly (Leptidea sinapis) with different karyotypes to identify genomic regions associated with hybrid inviability. We mapped candidate loci for hybrid inviability by contrasting allele frequencies between F2 hybrids that survived until the adult stage with individuals of the same cohort that succumbed to hybrid incompatibilities. Hybrid inviability factors were predominantly found in fast-evolving regions with reduced recombination rates, especially in regions where chromosome fusions have occurred. By analyzing sequencing coverage, we excluded aneuploidies as a direct link between hybrid inviability and chromosome fusions. Instead, our results point to an indirect relationship between hybrid inviability and chromosome fusions, possibly related to reductions in recombination rate caused by fusions. These results highlight that the extensive variation in chromosome numbers observed across the tree of life does not only distinguish species but can also be involved in speciation by being hotspots for the early evolution of postzygotic reproductive isolation.
|
|
| 20. |
- Boman, Jesper
(författare)
-
Genetic architecture of speciation
- 2024
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- New species are formed either by the splitting of a lineage in two or through hybridization of divergent lineages. Using genetics to understand the origin and persistence of species is a central theme in evolutionary biology. The genetic architecture of speciation refers to the number, types and effect sizes of different genetic loci underlying the process of speciation. Insightful models and painstaking laboratory and field work have provided the first sketches of the genetic architecture of speciation in a handful of model organisms. In this thesis, I explore different aspects of speciation genetics in several less studied model systems: from birds to butterflies. In Paper I, I investigate the genetic architecture of hybrid inviability between chromosomal races of the wood white butterfly (Leptidea sinapis) and find an association between chromosome fusions and the evolution of hybrid inviability. In Paper II, I study whether the many chromosomal differences separating the L. sinapis races show evidence of non-Mendelian inheritance. We observe the preferential inheritance of the ancestral state at chromosome fusions in line with the meiotic drive model. Thus, meiotic drive acts against karyotype change and thus potentially opposes the evolution of reproductive isolation. Recent work has highlighted that epigenetic mechanisms, such as DNA methylation, could be important for the dysfunction of hybrids. In Paper III, we test this prediction in naturally occurring hybrids between the collared flycatcher (F. albicollis) and the pied flycatcher (F. hypoleuca). I show that DNA methylation differences in promoter regions are often correlated with signatures of differential gene expression between species, but does not predict misexpression in hybrids. Hybridization between species is expected to reduce the genetic differentiation and erode species differences. However, hybridization can also be the trigger of speciation if the combination of alleles and traits allow the hybrid species to persist. In Paper IV, I discover a hybrid Aricia butterfly species on the island of Öland in the Baltic Sea. Using whole-genome resequencing data and species models I infer that the main hybridization event occurred approximately 54,000 years ago, long before Öland arose from the sea after the last ice age. To conclude, this thesis highlights different aspects of speciation genetics: from the genetic underpinnings of viability of hybrids (Paper I and III) to causes of speciation (Paper II and IV). Hopefully this work will provide a few more lines to the blueprint that is our understanding of the genetic architecture of speciation
|
|
