Unravelling the genomic landscape of divergence between lineages
is key to understanding speciation1. The naturally hybridizing col-
lared flycatcher and pied flycatcher are important avian speciation
models2–7 that show pre- as well as postzygotic isolation8,9. We
sequenced and assembled the 1.1-Gb flycatcher genome, physically
mapped the assembly to chromosomes using a low-density linkage
map10 and re-sequenced population samples of each species. Here
we show that the genomic landscape of species differentiation is
highly heterogeneous with approximately 50 ‘divergence islands’
showing up to 50-fold higher sequence divergence than the geno-
mic background. These non-randomly distributed islands, with
between one and three regions of elevated divergence per chro-
mosome irrespective of chromosome size, are characterized by
reduced levels of nucleotide diversity, skewed allele-frequency
spectra, elevated levels of linkage disequilibrium and reduced pro-
portions of shared polymorphisms in both species, indicative of
parallel episodes of selection. Proximity of divergence peaks
to genomic regions resistant to sequence assembly, potentially
including centromeres and telomeres, indicate that complex repeat
structures may drive species divergence. A much higher back-
ground level of species divergence of the Z chromosome, and
a lower proportion of shared polymorphisms, indicate that sex
chromosomes and autosomes are at different stages of speciation.
This study provides a roadmap to the emerging field of speciation
genomics.
%0 Journal Article
%1 ellegren2012genomic
%A Ellegren, Hans
%A Smeds, Linnea
%A Burri, Reto
%A Olason, Pall I.
%A Backstrom, Niclas
%A Kawakami, Takeshi
%A Kunstner, Axel
%A Makinen, Hannu
%A Nadachowska-Brzyska, Krystyna
%A Qvarnstrom, Anna
%A Uebbing, Severin
%A Wolf, Jochen B. W.
%D 2012
%I Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
%J Nature
%K flycatchers islands_of_speciation population_genomics speciation
%N 7426
%P 756--760
%R 10.1038/nature11584
%T The genomic landscape of species divergence in Ficedula flycatchers
%U http://dx.doi.org/10.1038/nature11584
%V 491
%X Unravelling the genomic landscape of divergence between lineages
is key to understanding speciation1. The naturally hybridizing col-
lared flycatcher and pied flycatcher are important avian speciation
models2–7 that show pre- as well as postzygotic isolation8,9. We
sequenced and assembled the 1.1-Gb flycatcher genome, physically
mapped the assembly to chromosomes using a low-density linkage
map10 and re-sequenced population samples of each species. Here
we show that the genomic landscape of species differentiation is
highly heterogeneous with approximately 50 ‘divergence islands’
showing up to 50-fold higher sequence divergence than the geno-
mic background. These non-randomly distributed islands, with
between one and three regions of elevated divergence per chro-
mosome irrespective of chromosome size, are characterized by
reduced levels of nucleotide diversity, skewed allele-frequency
spectra, elevated levels of linkage disequilibrium and reduced pro-
portions of shared polymorphisms in both species, indicative of
parallel episodes of selection. Proximity of divergence peaks
to genomic regions resistant to sequence assembly, potentially
including centromeres and telomeres, indicate that complex repeat
structures may drive species divergence. A much higher back-
ground level of species divergence of the Z chromosome, and
a lower proportion of shared polymorphisms, indicate that sex
chromosomes and autosomes are at different stages of speciation.
This study provides a roadmap to the emerging field of speciation
genomics.
@article{ellegren2012genomic,
abstract = {Unravelling the genomic landscape of divergence between lineages
is key to understanding speciation1. The naturally hybridizing col-
lared flycatcher and pied flycatcher are important avian speciation
models2–7 that show pre- as well as postzygotic isolation8,9. We
sequenced and assembled the 1.1-Gb flycatcher genome, physically
mapped the assembly to chromosomes using a low-density linkage
map10 and re-sequenced population samples of each species. Here
we show that the genomic landscape of species differentiation is
highly heterogeneous with approximately 50 ‘divergence islands’
showing up to 50-fold higher sequence divergence than the geno-
mic background. These non-randomly distributed islands, with
between one and three regions of elevated divergence per chro-
mosome irrespective of chromosome size, are characterized by
reduced levels of nucleotide diversity, skewed allele-frequency
spectra, elevated levels of linkage disequilibrium and reduced pro-
portions of shared polymorphisms in both species, indicative of
parallel episodes of selection. Proximity of divergence peaks
to genomic regions resistant to sequence assembly, potentially
including centromeres and telomeres, indicate that complex repeat
structures may drive species divergence. A much higher back-
ground level of species divergence of the Z chromosome, and
a lower proportion of shared polymorphisms, indicate that sex
chromosomes and autosomes are at different stages of speciation.
This study provides a roadmap to the emerging field of speciation
genomics.
},
added-at = {2014-06-08T22:04:29.000+0200},
author = {Ellegren, Hans and Smeds, Linnea and Burri, Reto and Olason, Pall I. and Backstrom, Niclas and Kawakami, Takeshi and Kunstner, Axel and Makinen, Hannu and Nadachowska-Brzyska, Krystyna and Qvarnstrom, Anna and Uebbing, Severin and Wolf, Jochen B. W.},
biburl = {https://www.bibsonomy.org/bibtex/27dc5f5ea15af256596fcbcfbbefdf20f/peter.ralph},
doi = {10.1038/nature11584},
interhash = {7d8ebd003c10a206d25440e5ea5b2c9b},
intrahash = {7dc5f5ea15af256596fcbcfbbefdf20f},
issn = {00280836},
journal = {Nature},
keywords = {flycatchers islands_of_speciation population_genomics speciation},
month = nov,
number = 7426,
pages = {756--760},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
timestamp = {2014-06-08T22:15:34.000+0200},
title = {The genomic landscape of species divergence in {Ficedula} flycatchers},
url = {http://dx.doi.org/10.1038/nature11584},
volume = 491,
year = 2012
}