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Speciation genomics: A perspective from vertebrate systems
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
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. , 52 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1326
Keyword [en]
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: urn:nbn:se:uu:diva-265342ISBN: 978-91-554-9425-4 (print)OAI: oai:DiVA.org:uu-265342DiVA: diva2:872426
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
List of papers
1. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
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, 1410-1414 p.Article 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
2. Idiosyncratic patterns and processes of genomic differentiation in replicate contact zones in crows
Open this publication in new window or tab >>Idiosyncratic patterns and processes of genomic differentiation in replicate contact zones in crows
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(English)Manuscript (preprint) (Other academic)
Keyword
speciation, hybrid zone, linked selection, crow, diversity
National Category
Natural Sciences
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-266263 (URN)
Available from: 2015-11-10 Created: 2015-11-05 Last updated: 2016-01-13
3. Genome-culture coevolution promotes rapid divergence in the killer whale
Open this publication in new window or tab >>Genome-culture coevolution promotes rapid divergence in the killer whale
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(English)Manuscript (preprint) (Other academic)
National Category
Natural Sciences
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-265341 (URN)
Available from: 2015-11-05 Created: 2015-10-27 Last updated: 2016-01-13
4. Genomic signatures of species diversification – a comparative perspective
Open this publication in new window or tab >>Genomic signatures of species diversification – a comparative perspective
(English)Manuscript (preprint) (Other academic)
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-267095 (URN)
Available from: 2015-11-17 Created: 2015-11-17 Last updated: 2016-01-13

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