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Vijay, Nagarjun
Publications (10 of 11) 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
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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
Dutoit, L., Vijay, N., Mugal, C. F., Bossu, C. M., Burri, R., Wolf, J. & Ellegren, H. (2017). Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting. Proceedings of the Royal Society of London. Biological Sciences, 284(1849), Article ID 20162756.
Open this publication in new window or tab >>Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
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2017 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1849, article id 20162756Article in journal (Refereed) Published
Abstract [en]

Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird speciescollared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's rho = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.

Place, publisher, year, edition, pages
ROYAL SOC, 2017
Keywords
nucleotide diversity, linked selection, recombination rate, birds
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-320453 (URN)10.1098/rspb.2016.2756 (DOI)000395893200017 ()
Available from: 2017-04-26 Created: 2017-04-26 Last updated: 2018-02-22Bibliographically 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
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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
Foote, A. D., Vijay, N., Avila-Arcos, M. C., Baird, R. W., Durban, J. W., Fumagalli, M., . . . Wolf, J. B. W. (2016). Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nature Communications, 7, Article ID 11693.
Open this publication in new window or tab >>Genome-culture coevolution promotes rapid divergence of killer whale ecotypes
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2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11693Article in journal (Refereed) Published
Abstract [en]

Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.

National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-298690 (URN)10.1038/ncomms11693 (DOI)000376823800001 ()27243207 (PubMedID)
Funder
EU, European Research Council, ERCStG-336536European Science Foundation (ESF)Knut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC)
Available from: 2016-08-10 Created: 2016-07-06 Last updated: 2017-11-28Bibliographically approved
Vijay, N. (2016). Speciation genomics: A perspective from vertebrate systems. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Speciation genomics: A perspective from vertebrate systems
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Species are vital entities in biology. Species are generally considered to be discrete entities, consisting of a group of (usually interbreeding) individuals that are similar in phenotype and genetic composition, yet differ in significant ways from other species. The study of speciation has focussed on understanding general evolutionary mechanisms involved in the accumulation of differences both at the genetic and phenotypic level. In this thesis, I investigate incipient speciation, an early stage of divergence towards evolutionary independence in closely related natural populations. I make ample use of recent advances in sequencing technology that allow 1) characterizing phenotypic divergence at the level of the transcriptome and 2) delineate patterns of genetic variation at genome-scale from which processes are inferred by using principles of population genetic theory.

In the first paper, we assembled a draft genome of the hooded crow and investigated population differentiation across a famous European hybrid zone. Comparing sequence differentiation peaks between and within the colour morphs, we could identify regions of the genome that show differentiation only between colour morphs and that could be related to gene expression profiles of the melanogenesis pathway coding for colour differences.

The second paper expands on the first paper in that it includes crow population samples from across the entire Palaearctic distribution spanning two additional zones of contact between colour morphs. The results suggest that regions associated with selection against gene flow between colour morphs were largely idiosyncratic to each contact zone and emerged against a background of conserved 'islands of differentiation' due to shared linked selection.

The third paper focusses on five killer whale ecotypes with distinct feeding and habitat specific adaptations. Differing levels of sequence differentiation between these ecotypes places them along a speciation continuum and provides a unique temporal cross-section of the speciation process. Using genome scans we identified regions of the genome that show ecotype specific differentiation patterns which might contain candidate genes involved in adaptation.

In the fourth and final paper, I assumed a comparative genomic perspective to the problem of heterogeneous genomic differentiation during population divergence. The relatively high correlations in the diversity landscapes as well as differentiation patterns between crow, flycatcher and Darwin's Finch populations is best explained by conservation in broad-scale recombination rate and/or  association with telomeres and centromeres conducive to shared, linked selection.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. p. 52
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1326
Keywords
evolution, speciation, genomics, vertebrate, adaptation, selection, linked selection, crow, killer whale, hybrid zone, transcriptomics, population genetics, behaviour, colouration
National Category
Natural Sciences
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-265342 (URN)978-91-554-9425-4 (ISBN)
Public defence
2016-01-22, Lindahlsalen, Evolutionary Biology Centre, EBC, Norbyvägen 14-18, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2015-12-21 Created: 2015-10-27 Last updated: 2016-01-13
Foote, A. D., Liu, Y., Thomas, G. W. C., Vinar, T., Alfoeldi, J., Deng, J., . . . Gibbs, R. A. (2015). Convergent evolution of the genomes of marine mammals. Nature Genetics, 47(3), 272-275
Open this publication in new window or tab >>Convergent evolution of the genomes of marine mammals
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2015 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 47, no 3, p. 272-275Article in journal (Refereed) Published
Abstract [en]

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-248826 (URN)10.1038/ng.3198 (DOI)000350327900020 ()25621460 (PubMedID)
Available from: 2015-04-08 Created: 2015-04-08 Last updated: 2017-12-04Bibliographically 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
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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
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
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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
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
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