| 1. |
- Chase, Madeline A., et al.
(författare)
-
Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs
- 2021
-
Ingår i: Evolution. - : John Wiley & Sons. - 0014-3820 .- 1558-5646. ; 75:9, s. 2179-2196
-
Tidskriftsartikel (refereegranskat)abstract
- A current debate within population genomics surrounds the relevance of patterns of genomic differentiation between closely related species for our understanding of adaptation and speciation. Mounting evidence across many taxa suggests that the same genomic regions repeatedly develop elevated differentiation in independent species pairs. These regions often coincide with high gene density and/or low recombination, leading to the hypothesis that the genomic differentiation landscape mostly reflects a history of background selection, and reveals little about adaptation or speciation. A comparative genomics approach with multiple independent species pairs at a timescale where gene flow and ILS are negligible permits investigating whether different evolutionary processes are responsible for generating lineage-specific versus shared patterns of species differentiation. We use whole-genome resequencing data of 195 individuals from four Ficedula flycatcher species comprising two independent species pairs: collared and pied flycatchers, and red-breasted and taiga flycatchers. We found that both shared and lineage-specific FST peaks could partially be explained by selective sweeps, with recurrent selection likely to underlie shared signatures of selection, whereas indirect evidence supports a role of recombination landscape evolution in driving lineage-specific signatures of selection. This work therefore provides evidence for an interplay of positive selection and recombination to genomic landscape evolution.
|
|
| 2. |
- Ellegren, Hans
(författare)
-
En akademi finner sin väg
- 2020
-
Bok (övrigt vetenskapligt/konstnärligt)abstract
- Året är 1744. Anders Celsius har i nära 20 år drivit verksamheten inom Sveriges första lärda sällskap när han plötsligt går bort. Kungl. Vetenskaps-Societeten i Uppsala står utan sekreterare och inom den lilla grupperingen finns inte många kandidater att ta över efter Celsius. Den som till slut tar på sig uppgiften är ingen mindre än Carl von Linné. Men är han rätt person för uppdraget?Det blir en svacka i Societetens verksamhet under Linnés sekretariat kring mitten av 1700-talet. Man tvingas göra uppehåll i utgivningen av sin tidskrift Acta Societatis Regiæ Scientiarum Upsaliensis och i perioder är mötesfrekvensen låg. Men när Hertig Karl 1765 träder in som Preses Illustris fås en nytändning och Societeten börjar på nytt finna sin väg. Man gör ett omtag med tidskriften – den blir till Nova Acta – och fyller den med uppsatser av tidens främsta vetenskapsmän, bl.a. Torbern Bergman, Daniel Melanderhjelm, Carl Peter Thunberg och Pehr Wargentin.Det allra viktigaste för den fortsatta verksamheten blir donationen 1789 från Johan Abraham Gyllenhaal och Fredric Ziervogel. Societeten får det hus på S:t Larsgatan i Uppsala där man än idag träffas och samtidigt ansvar för landets kanske största naturaliesamling. I donationen ingår också det unika Museum Schefferianum, byggt redan 1660.En akademi finner sin väg är en fortsättning på boken Hvad nytt och nyttigt – Tillkomsten av Sveriges första lärda sällskap: Kungl. Vetenskaps-Societeten i Uppsala. Tillsammans beskriver de Societetens utveckling fram till sekelskiftet 1800. Hans Ellegren, nuvarande sekreterare för Societeten, har åter grävt i arkiven och tecknar bilden av en akademi som är en del av det lärda Uppsalas historia och också en del av den svenska vetenskapshistorien.
|
|
| 3. |
|
|
| 4. |
- Mugal, Carina, et al.
(författare)
-
Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids
- 2020
-
Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 30:12, s. 1727-1739
-
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.
|
|
| 5. |
- Nadachowska-Brzyska, Krystyna, et al.
(författare)
-
Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis)
- 2021
-
Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 30:16, s. 3965-3973
-
Tidskriftsartikel (refereegranskat)abstract
- Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (N-e) has been estimated for numerous species and populations. However, estimating contemporary N-e is difficult and in practice this parameter is often unknown. In principle, contemporary N-e can be estimated using either analyses of temporal changes in allele frequencies, or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches to estimate contemporary N-e of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and applied several temporal methods to estimate N-e at a few thousand (4000-7000). The approach based on LD provided higher estimates of N-e (20,000-32,000) and was associated with high variance, often resulting in infinite N-e. We conclude that whole-genome sequencing data offers new possibilities to estimate high (>1000) contemporary N-e, but also note that such estimates remain challenging, in particular for LD-based methods for contemporary N-e estimation.
|
|
| 6. |
- Ottenburghs, Jente, et al.
(författare)
-
Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation
- 2020
-
Ingår i: Heredity. - : NATURE PUBLISHING GROUP. - 0018-067X .- 1365-2540. ; 125:1-2, s. 73-84
-
Tidskriftsartikel (refereegranskat)abstract
- Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes of closely related species. Specifically, genetic differentiation is often concentrated in particular genomic regions ("islands of differentiation") that might contain barrier loci contributing to reproductive isolation, whereas the rest of the genome is homogenized by introgression. Alternatively, linked selection can produce differentiation islands in allopatry without introgression. We explored the influence of introgression on the landscape of genetic differentiation in two hybridizing goose taxa: the Taiga Bean Goose (Anser fabalis) and the Tundra Bean Goose (A. serrirostris). We re-sequenced the whole genomes of 18 individuals (9 of each taxon) and, using a combination of population genomic summary statistics and demographic modeling, we reconstructed the evolutionary history of these birds. Next, we quantified the impact of introgression on the build-up and maintenance of genetic differentiation. We found evidence for a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Subsequent introgression events led to high levels of gene flow, mainly from the Tundra Bean Goose into the Taiga Bean Goose. This scenario resulted in a largely undifferentiated genomic landscape (genome-wide F-ST = 0.033) with a few notable differentiation peaks that were scattered across chromosomes. The summary statistics indicated that some peaks might contain barrier loci while others arose in allopatry through linked selection. Finally, based on the low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argue that the Taiga and the Tundra Bean Goose should be treated as subspecies.
|
|
| 7. |
- Smeds, Linnea, et al.
(författare)
-
Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations
- 2021
-
Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 14:3, s. 721-734
-
Tidskriftsartikel (refereegranskat)abstract
- Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human-mediated hybridization between a domesticated species and its wild relative. We analysed whole-genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and Admixture showed that wolves and dogs were well-separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had <1% mixed ancestry, levels comparable to the degree of mixed ancestry in many dogs, and likely not resulting from recent wolf-dog hybridization. We also show that the founders of the Scandinavian wolf population were genetically inseparable from Finnish and Russian Karelian wolves, pointing at the geographical origin of contemporary Scandinavian wolves. Moreover, we found Scandinavian-born animals among wolves sampled in Finland, demonstrating bidirectional gene flow between the Scandinavian Peninsula and eastern countries. The low incidence of admixture between wolves and dogs in Fennoscandia may be explained by the fact that feral dogs are rare in this part of Europe and that careful monitoring and management act to remove hybrids before they backcross into wolf populations.
|
|
| 8. |
- Warmuth, Vera, et al.
(författare)
-
Major population splits coincide with episodes of rapid climate change in a forest-dependent bird
- 2021
-
Ingår i: Proceedings of the Royal Society B: Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 288:1962
-
Tidskriftsartikel (refereegranskat)abstract
- Climate change influences population demography by altering patterns of gene flow and reproductive isolation. Direct mutation rates offer the possibility for accurate dating on the within-species level but are currently only available for a handful of vertebrate species. Here, we use the first directly estimated mutation rate in birds to study the evolutionary history of pied flycatchers (Ficedula hypoleuca). Using a combination of demographic inference and species distribution modelling, we show that all major population splits in this forest-dependent system occurred during periods of increased climate instability and rapid global temperature change. We show that the divergent Spanish subspecies originated during the Eemian-Weichselian transition 115-104 thousand years ago (kya), and not during the last glacial maximum (26.5-19 kya), as previously suggested. The magnitude and rates of climate change during the glacial-interglacial transitions that preceded population splits in pied flycatchers were similar to, or exceeded, those predicted to occur in the course of the current, human-induced climate crisis. As such, our results provide a timely reminder of the strong impact that episodes of climate instability and rapid temperature changes can have on species' evolutionary trajectories, with important implications for the natural world in the Anthropocene.
|
|
