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

Direct link
BETA
Poelstra, Jelmer W.
Alternative names
Publications (8 of 8) 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
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
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
Poelstra, J. W., Vijay, N., Hoeppner, M. P. & Wolf, J. B. W. (2015). Transcriptomics of colour patterning and coloration shifts in crows. Molecular Ecology, 24(18), 4617-4628
Open this publication in new window or tab >>Transcriptomics of colour patterning and coloration shifts in crows
2015 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 18, p. 4617-4628Article in journal (Refereed) Published
Abstract [en]

Animal coloration is one of the most conspicuous phenotypic traits in natural populations and has important implications for adaptation and speciation. Changes in coloration can occur over surprisingly short evolutionary timescales, while recurrence of similar colour patterns across large phylogenetic distances is also common. Even though the genetic basis of pigment production is well understood, little is known about the mechanisms regulating colour patterning. In this study, we shed light on the molecular elements regulating regional pigment production in two genetically near-identical crow taxa with striking differences in a eumelanin-based phenotype: black carrion and grey-coated hooded crows. We produced a high-quality genome annotation and analysed transcriptome data from a 2 3 2 design of active melanogenic feather follicles from head (black in both taxa) and torso (black in carrion and grey in hooded crow). Extensive, parallel expression differences between body regions in both taxa, enriched for melanogenesis genes (e.g. ASIP, CORIN, and ALDH6), indicated the presence of cryptic prepatterning also in all-black carrion crows. Meanwhile, colour-specific expression (grey vs. black) was limited to a small number of melanogenesis genes in close association with the central transcription factor MITF (most notably HPGDS, NDP and RASGRF1). We conclude that colour pattern differences between the taxa likely result from an interaction between divergence in upstream elements of the melanogenesis pathway and genes that provide an underlying prepattern across the body through positional information. A model of evolutionary stable prepatterns that can be exposed and masked through simple regulatory changes may explain the phylogenetically independent recurrence of colour patterns that is observed across corvids and many other vertebrate groups.

Keywords
birds, coloration, colour patterning, pigmentation, speciation, transcriptomics
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-264665 (URN)10.1111/mec.13353 (DOI)000361555900004 ()26302355 (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: 2015-10-16 Created: 2015-10-15 Last updated: 2017-12-01Bibliographically approved
Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Mueller, I., . . . Wolf, J. B. W. (2014). The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414
Open this publication in new window or tab >>The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
Show others...
2014 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, no 6190, p. 1410-1414Article in journal (Refereed) Published
Abstract [en]

The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-228535 (URN)10.1126/science.1253226 (DOI)000337531700043 ()
Available from: 2014-07-17 Created: 2014-07-16 Last updated: 2017-12-05Bibliographically approved
Poelstra, J. W., Ellegren, H. & Wolf, J. (2013). An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone. Heredity, 111(6), 467-473
Open this publication in new window or tab >>An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone
2013 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 111, no 6, p. 467-473Article in journal (Refereed) Published
Abstract [en]

Colouration patterns have an important role in adaptation and speciation. The European crow system, in which all-black carrion crows and grey-coated hooded crows meet in a narrow hybrid zone, is a prominent example. The marked phenotypic difference is maintained by assortative mating in the absence of neutral genetic divergence, suggesting the presence of few pigmentation genes of major effect. We made use of the rich phenotypic and genetic resources in mammals and identified a comprehensive panel of 95 candidate pigmentation genes for birds. Based on functional annotation, we chose a subset of the most promising 37 candidates, for which we developed a marker system that demonstrably works across the avian phylogeny. In total, we sequenced 107 amplicons (~3 loci per gene, totalling 60 kb) in population samples of crows (n=23 for each taxon). Tajima’s D, Fu’s FS, DHEW and HKA (Hudson–Kreitman–Aguade) statistics revealed several amplicons that deviated from neutrality; however, none of these showed significantly elevated differentiation between the two taxa. Hence, colour divergence in this system may be mediated by uncharacterized pigmentation genes or regulatory regions outside genes. Alternatively, the observed high population recombination rate (4Ner~0.03), with overall linkage disequilibrium dropping rapidly within the order of few 100 bp, may compromise the power to detect causal loci with nearby markers. Our results add to the debate as to the utility of candidate gene approaches in relation to genomic features and the genetic architecture of the phenotypic trait in question.

Keywords
speciation, population genetics, bird colouration, pigmentation genes, recombination rate, linkage disequilibrium
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-209238 (URN)10.1038/hdy.2013.68 (DOI)000327178100003 ()
Available from: 2013-10-15 Created: 2013-10-15 Last updated: 2018-02-22Bibliographically approved
Vijay, N., Poelstra, J. W., Kuenstner, A. & Wolf, J. B. W. (2013). Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Molecular Ecology, 22(3), 620-634
Open this publication in new window or tab >>Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments
2013 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 3, p. 620-634Article in journal (Refereed) Published
Abstract [en]

Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism p, alternative splicing), technological processing (sequencing error e, library normalization) and bioinformatic workflow (de novo vs. mapping assembly, reference genome quality) impact transcriptome quality and inference of differential gene expression (DE). We find that transcriptome assembly and gene expression profiling (EdgeR vs. BaySeq software) works well even in the absence of a reference genome and is robust across a broad range of parameters. We advise against library normalization and in most situations advocate mapping assemblies to an annotated genome of a divergent sister clade, which generally outperformed de novo assembly (Trans-Abyss, Trinity, Soapdenovo-Trans). Transcriptome complexity (size, paralogs, alternative splicing isoforms) negatively affected the assembly and DE profiling, whereas the effects of sequencing error and polymorphism were almost negligible. Finally, we highlight the challenge of gene name assignment for de novo assemblies, the importance of mapping strategies and raise awareness of challenges associated with the quality of reference genomes. Overall, our results have significant practical and methodological implications and can provide guidance in the design and analysis of RNA-seq experiments, particularly for organisms where genomic background information is lacking.

Keywords
bioinformatics, comparative genomics, differential gene expression, RNA-seq, simulation, systems biology, transcriptome assembly
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-194741 (URN)10.1111/mec.12014 (DOI)000313726300007 ()
Available from: 2013-02-19 Created: 2013-02-19 Last updated: 2017-12-06Bibliographically approved
Poelstra, J. (2013). The Genetics of Speciation and Colouration in Carrion and Hooded Crows. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>The Genetics of Speciation and Colouration in Carrion and Hooded Crows
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

A fundamental goal in biological research is to gain an understanding of the evolutionary processes and genetic elements that drive speciation. Genes responsible for reproductive isolation in young divergent lineages are particularly poorly known. In this thesis, the speciation genetics of carrion (Corvus (corone) corone) and hooded (C. (corone) cornix) crows were studied. These taxa differ strikingly in colouration and meet in a narrow hybrid zone in Europe, yet appear to be very similar genetically. A major component of reproductive isolation is social selection on colour differences.

First, we investigated the genetic basis of plumage divergence between carrion and hooded crows using a candidate gene approach. Nucleotide divergence was confirmed to be low, while there was no evidence for any of the sequenced genes to be associated with colour differences.

Second, we performed a simulation study to assess the performance of RNA-seq, a relatively novel approach that we later employed ourselves. We asked how variation in transcriptome complexity and bioinformatic workflow affected the accuracy of gene expression profiling. We generally found reassuring robustness and made a number of specific recommendations.

Third, we compared the corticosterone stress response of carrion and hooded crows. In accordance with the hypothesis that the degree of melanization and physiological traits are correlated due to pleiotropy, we found a higher stress response in hooded crows, and detected possibly associated gene expression in pituitary.

Fourth, we investigated genomic divergence by assembling a hooded crow reference genome followed by whole-genome resequencing of four European population samples. Northern European carrion crows were more similar to hooded crows than to Spanish carrion crows, pointing towards rampant introgression far beyond the hybrid zone. Nevertheless, several narrow genomic regions harboured high between-taxon divergence and were potentially associated with phenotypic traits.

Fifth, we compared whole-transcriptome gene expression profiles between crows, focusing on skin with developing feathers. We used a design that allowed to differentiate between taxon-specific, colour-specific and body patterning effects. Widespread underexpression of genes in the melanogenesis pathway was associated with grey colour, and we detected several genes that may contribute to colour divergence in this system.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2013. p. 48
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1088
Keywords
evolutionary genetics, genomics, birds, next-generation sequencing, pigmentation, pigmentation genetics, eumelanin, social selection, gene expression, population genomics
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-209243 (URN)978-91-554-8777-5 (ISBN)
Public defence
2013-11-29, Lindahlssalen, Evolutionary Biology Centre, Norbyvägen 18D, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2013-11-08 Created: 2013-10-15 Last updated: 2014-01-23
Organisations

Search in DiVA

Show all publications