A recent paper by CEB graduate student Daniel Hooper and CEB faculty Trevor Price investigates chromosome inversions in Estrildid finch species. The paper, “Rates of karyotypic evolution in Estrildid finches differ between island and continental clades” (Evolution 69(4):890-903 (2015)), can be found here. Daniel also wrote a piece for the Ecology and Evolution Graduate News website. An excerpt from this article is included below. The full article can be viewed here.
Chromosome inversions in finches
Genomic divergence occurs not only from changes in DNA sequence, but also from changes of genome architecture. Chromosome inversions, structural rearrangements that affect the order of genes upon a chromosome, are of particular interest in evolutionary biology because they are often found as polymorphisms segregating within species and as fixed differences between species. Inversions can play a role in speciation by one of two mechanisms: either directly by inducing sterility or inviability in hybrid offspring heterozygous for an inversion or indirectly by suppressing recombination between genes within an inversion that are responsible for nascent reproductive isolation. Empirical evidence across a broad range of taxa largely favors the indirect contribution via the suppression of recombination, as genes for species-specific differences and reproductive isolation are often located within inversions fixed between closely related species. While the contribution of chromosome inversions to speciation is increasingly appreciated, we still know relatively little about the evolutionary processes by which inversions originate and spread to fixation between populations in the first place.
In a new paper now out in the journal Evolution, we use cytological descriptions of genomic architecture from finches in the family Estrildidae in order to address the drivers of inversion fixation and the relative contributions of genetic drift versus selection. To this end, we wanted to know 1) what is the genomic, 2) phylogenetic, and 3) geographic distribution of inversions that have fixed between Estrildid finch species.
The Estrildid finches are an ideal group for this task. Distributed across the Old World tropics and southern hemisphere temperate zone, the family comprises 7 geographically discrete clades that can be classified either as ‘continental’ or ‘island’. Continental clades are made up of species with large ranges that often overlap with closely related species while island clades are made up of species with small ranges that often do not overlap. We utilize this geographic distribution of Estrildid finches, and previously published cytological records for a quarter of all Estrildid species, along with a new time-dated phylogeny for the family in order to assess the degree to which the rate of inversion fixation is affected by differences in population size (i.e. range size) and degree of sympatry (i.e. range overlap) between continental and island clades.
Our results suggest that inversions in Estrildid finches are likely to be evolving because they are adaptive. Between clades, we observe that inversion fixation rate is more than 3x higher within 3 continental compared to 2 island chain clades. The rate of inversion fixation on all chromosomes was strongly influenced by average range size, suggesting inversions spread by selection rather than genetic drift (in drift models, fixation should be independent of population size). Moreover, fixation rate is strongly associated with the proportion of sympatric species pairs within clades independent of the effects of range size. We also find that inversions have fixed twice as often on the sex chromosomes as they have on the autosomes and their genomic distribution cannot be explained by mutagenic differences between chromosomes alone. The greater repeat density of the sex chromosomes, however, may play a role. The elevated number of inversions on the sex chromosomes relative to the autosomes, the positive association between inversion fixation rate with range size, and the positive association with sympatry are all together consistent with theoretical models that predict inversions are selected for when gene flow occurs during speciation. Indeed, these results suggest that under certain demographic conditions, inversions may have regularly contributed to speciation within the Estrildid finches.
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