The genomic landscape of species divergence in Ficedula flycatchers

By H. Ellegren, Linnéa Smeds, R. Burri, Pall I. Olason, N. Backström, T. Kawakami, Axel Künstner, H. Mäkinen, K. Nadachowska-Brzyska, A. Qvarnström and 2 more. Nature, 2012

654 citations recorded by the source corpus.

Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map 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 genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions 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 background 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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/959af499f4989d8a0647a9616ac39119c7c02815

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Citations in the corpus

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow (2014, methodology): “Divergence between the collared flycatcher ( F. albicollis ) and the pied flycatcher ( F. hypoleuca ) was previously assessed by sequencing the genomes of 10 males from each species (Ellegren et al. 2012).”
Genome-wide evidence for speciation with gene flow in Heliconius butterflies (2013, background): “2010, 2012) and Ficedula flycatchers (Ellegren et al. 2012) revealed patterns of divergence consistent with a model of ‘‘islands’’ of divergence amidst a sea of gene flow.”
What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species (2018, methodology): “With the advantage of genomic characterization via high-throughput sequencing combined with recent developments in statistical methods, investigators can now, for nearly any species of interest, estimate parameters to describe the demographic aspects of speciation history with unprecedented resoluti”
A framework for incorporating evolutionary genomics into biodiversity conservation and management (2015, background): “The genetic basis for many of these is likely to be concentrated in islands of adaptive divergence, such as seen in Eurasian Ficedula flycatchers [151] and Heliconius”
The Genome 10K Project: A Way Forward (2015, neutral): “Passerine birds (5756, 127) Parrots (367, 5) Falcons (64, 2) Seriemas (2, 1) Kingfisher and allies (152, 9) Woodpeckers (406, 8) Hornbills (62, 2) Trogons (44, 1) Cuckoo roller (1, 1) Mousebirds (5, 1) Owls (213, 2) Hawks, eagles, vultures (249, 4) Pelicans, frigatebirds, cormorants (174, 4) Petrels”
Applications of next-generation sequencing to the study of biological invasions (2015, background): “, 2014), the detection of multi-locus selective sweeps (Messer and Petrov, 2013) still requires a reference genome for homology-based mapping (Ellegren et al., 2012; Poelstra et al., 2014).”