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

Direct link
BETA
Weissensteiner, Matthias
Alternative names
Publications (9 of 9) Show all publications
Knief, U., Bossu, C. M., Saino, N., Hansson, B., Poelstra, J., Vijay, N., . . . Wolf, J. B. W. (2019). Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nature Ecology & Evolution, 3(4), 570-576
Open this publication in new window or tab >>Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone
Show others...
2019 (English)In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, no 4, p. 570-576Article in journal (Refereed) Published
Abstract [en]

The evolution of genetic barriers opposing interspecific gene flow is key to the origin of new species. Drawing from information on over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a similar to 2.8-megabase region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.

National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-382256 (URN)10.1038/s41559-019-0847-9 (DOI)000462542100018 ()30911146 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationEU, European Research Council, ERCStG-336536 FuncSpecGen
Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-04-23Bibliographically approved
Peona, V., Weissensteiner, M. & Suh, A. (2018). How complete are "complete" genome assemblies?: An avian perspective. Molecular Ecology Resources, 18(6), 1188-1195
Open this publication in new window or tab >>How complete are "complete" genome assemblies?: An avian perspective
2018 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, no 6, p. 1188-1195Article in journal (Refereed) Published
Abstract [en]

The genomics revolution has led to the sequencing of a large variety of non-model organisms often referred to as 'whole' or 'complete' genome assemblies. But how complete are these, really? Here we use birds as an example for non-model vertebrates and find that, although suitable in principle for genomic studies, the current standard of short-read assemblies misses a significant proportion of the expected genome size (7 to 42%; mean 20 ± 9%). In particular, regions with strongly deviating nucleotide composition (e.g., guanine-cytosine-[GC]-rich) and regions highly enriched in repetitive DNA (e.g., transposable elements and satellite DNA) are usually underrepresented in assemblies. However, long-read sequencing technologies successfully characterize many of these underrepresented GC-rich or repeat-rich regions in several bird genomes. For instance, only ~2% of the expected total base pairs are missing in the last chicken reference (galGal5). These assemblies still contain thousands of gaps (i.e., fragmented sequences) because some chromosomal structures (e.g., centromeres) likely contain arrays of repetitive DNA that are too long to bridge with currently available technologies. We discuss how to minimize the number of assembly gaps by combining the latest available technologies with complementary strengths. Finally, we emphasize the importance of knowing the location, size, and potential content of assembly gaps when making population genetic inferences about adjacent genomic regions.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
birds, genomics, hybrid assembly, long reads, multiplatform sequencing, repeats
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-358682 (URN)10.1111/1755-0998.12933 (DOI)000449535600002 ()30035372 (PubMedID)
Available from: 2018-08-30 Created: 2018-08-30 Last updated: 2019-06-26Bibliographically approved
Weissensteiner, M. H., Pang, A. W. C., Bunikis, I., Höijer, I., Pettersson, O. V., Suh, A. & Wolf, J. B. W. (2017). Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications. Genome Research, 27(5), 697-708
Open this publication in new window or tab >>Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
Show others...
2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 5, p. 697-708Article in journal (Refereed) Published
Abstract [en]

Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [ OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (rho) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.

Place, publisher, year, edition, pages
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-323040 (URN)10.1101/gr.215095.116 (DOI)000400392400005 ()28360231 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)Swedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536
Available from: 2017-06-01 Created: 2017-06-01 Last updated: 2019-01-07Bibliographically approved
Vijay, N., Weissensteiner, M., Burri, R., Kawakami, T., Ellegren, H. & Wolf, J. B. W. (2017). Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa. Molecular Ecology, 26(16), 4284-4295
Open this publication in new window or tab >>Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa
Show others...
2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 16, p. 4284-4295Article in journal (Refereed) Published
Abstract [en]

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N-e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N-e. Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N-e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (rho), nucleotide diversity (pi) and measures of genetic differentiation between populations (F-ST, PBS, d(xy)) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.

Place, publisher, year, edition, pages
WILEY, 2017
Keywords
background selection, genetic diversity, genetic draft, genetic hitchhiking, linked selection, recombination rate, speciation genetics
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-333716 (URN)10.1111/mec.14195 (DOI)000407255100013 ()28570015 (PubMedID)
Funder
Swedish Research Council, 621-2010-5553, 2014-6325, 2013-08721EU, European Research Council, ERCStG-336536Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)
Available from: 2017-11-16 Created: 2017-11-16 Last updated: 2019-01-07Bibliographically approved
Vijay, N., Bossu, C. M., Poelstra, J. W., Weissensteiner, M. H., Suh, A., Kryukov, A. P. & Wolf, J. B. W. (2016). Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex. Nature Communications, 7, Article ID 13195.
Open this publication in new window or tab >>Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
Show others...
2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 13195Article in journal (Refereed) Published
Abstract [en]

Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.

National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-308915 (URN)10.1038/ncomms13195 (DOI)000386500600001 ()27796282 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2010-5553EU, European Research Council, ERCStG-336536
Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2019-01-07Bibliographically approved
Shafer, A. B. A., Wolf, J. B. W., Alves, P. C., Bergström, L., Colling, G., Dalen, L., . . . Zielinski, P. (2016). Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application Reply [Letter to the editor]. Trends in Ecology & Evolution, 31(2), 83-84
Open this publication in new window or tab >>Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application Reply
Show others...
2016 (English)In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, no 2, p. 83-84Article in journal, Letter (Refereed) Published
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-282988 (URN)10.1016/j.tree.2015.11.010 (DOI)000369462400002 ()26704456 (PubMedID)
Available from: 2016-04-15 Created: 2016-04-08 Last updated: 2017-11-30Bibliographically approved
Shafer, A. B., Wolf, J. B., Alves, P. C., Bergström, L., Colling, G., Dalén, L., . . . Zielińsk, P. (2016). Reply to Garner et al [Letter to the editor]. Trends in Ecology & Evolution, 31(2), 83-84
Open this publication in new window or tab >>Reply to Garner et al
Show others...
2016 (English)In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, no 2, p. 83-84Article in journal, Letter (Refereed) Published
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-286880 (URN)10.1016/j.tree.2015.11.010 (DOI)
Available from: 2016-04-22 Created: 2016-04-22 Last updated: 2017-11-30Bibliographically approved
Shafer, A. B. A., Wolf, J. B. W., Alves, P. C., Bergström, L., Bruford, M. W., Brannstrom, I., . . . Zielinski, P. (2015). Genomics and the challenging translation into conservation practice. Trends in Ecology & Evolution, 30(2), 78-87
Open this publication in new window or tab >>Genomics and the challenging translation into conservation practice
Show others...
2015 (English)In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 30, no 2, p. 78-87Article in journal (Refereed) Published
Abstract [en]

The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-247145 (URN)10.1016/j.tree.2014.11.009 (DOI)000349270700003 ()
Funder
Swedish Research Council, 70720201
Available from: 2015-03-17 Created: 2015-03-13 Last updated: 2017-12-04Bibliographically approved
Weissensteiner, M. H., Poelstra, J. W. & Wolf, J. B. W. (2015). Low-budget ready-to-fly unmanned aerial vehicles: an effective tool for evaluating the nesting status of canopy-breeding bird species. Journal of Avian Biology, 46(4), 425-430
Open this publication in new window or tab >>Low-budget ready-to-fly unmanned aerial vehicles: an effective tool for evaluating the nesting status of canopy-breeding bird species
2015 (English)In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 46, no 4, p. 425-430Article in journal (Refereed) Published
Abstract [en]

Remotely controlled, unmanned aerial vehicles (UAVs) promise to be of high potential for a variety of applications in ecological and behavioural research. Off-the-shelf solutions have recently become available for civil use at steeply decreasing costs. In this study, we explored the utility of an UAV equipped with an on-board camera (14 megapixel photo and 1920 x 1080 pixel video resolution) in assessing the breeding status, offspring number and age of a canopy-breeding bird species, the hooded crow Corvus [corone] cornix. We further quantified performance and potential time savings using the UAV versus inspection with alternative approaches (optical instruments, camera on a telescopic rod, tree climbing). Nesting status, number and approximate age of nestlings could be assessed with good success in all 24 attempts using the UAV. Eighty-five percent of the time required for inspection by climbing could be saved. Disturbance was moderate and lower than caused by climbing or using a camera on a telescopic rod. Additionally, UAV usage avoided tree damage and circumvented health risks associated with tree-climbing.

National Category
Zoology
Identifiers
urn:nbn:se:uu:diva-260310 (URN)10.1111/jav.00619 (DOI)000357949300014 ()
Funder
EU, European Research Council, ERC StG 336536 FuncSpecGenSwedish Research Council, 621-2013-4510
Available from: 2015-08-20 Created: 2015-08-18 Last updated: 2017-12-04Bibliographically approved
Organisations

Search in DiVA

Show all publications