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Mitonuclear co-introgression opposes genetic differentiation between
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phenotypically divergent songbirds
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Ellen Nikelski
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, Alexander S. Rubtsov
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, and Darren Irwin
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Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia,
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Vancouver, BC, Canada
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State Darwin Museum, Moscow, Russia
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*
Present address: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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Running Title:
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Co-introgression opposes differentiation
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Corresponding Author:
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Ellen Nikelski, Department of Ecology and Evolutionary Biology, University of Toronto,
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Toronto, ON, Canada. Email: ellen.nikelski@mail.utoronto.ca
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Keywords:
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mitonuclear co-introgression, mtDNA, mitonuclear gene, genetic differentiation, chromosome Z,
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Aves
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Abstract
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Comparisons of genomic variation among closely related species often show more differentiation
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in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected
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due to the relative effective population sizes of these genomic components. Differential
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introgression can cause some species pairs to deviate dramatically from this pattern. The
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yellowhammer (Emberiza citrinella) and the pine bunting (E. leucocephalos) are hybridizing
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avian sister species that differ greatly in appearance but show no mtDNA differentiation. This
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discordance might be explained by mtDNA introgression—a process that can select for co-
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introgression at nuclear genes with mitochondrial functions (mitonuclear genes). We investigated
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genome-wide nuclear differentiation between yellowhammers and pine buntings and compared it
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to what was seen previously in the mitochondrial genome. We found clear nuclear differentiation
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that was highly heterogeneous across the genome, with a particularly wide differentiation peak
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on the sex chromosome Z. We further tested for preferential introgression of mitonuclear genes
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and detected evidence for such biased introgression in yellowhammers. Mitonuclear co-
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introgression can remove post-zygotic incompatibilities between species and may contribute to
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the continued hybridization between yellowhammers and pine buntings despite their clear
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morphological and genetic differences. As such, our results highlight the potential ramifications
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of co-introgression in species evolution.
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Introduction
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Evolution in eukaryotes is shaped by changes in multiple genomic components that differ
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in their modes of inheritance: mitochondrial DNA (mtDNA) is usually inherited through the
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matrilineal line, autosomes are inherited through both parental lines and sex chromosomes are
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inherited differentially depending on the sex of both parent and offspring (Avise, 2000). There is
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often much variation among these genomic components in the degree of genetic differentiation
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between related populations or species (reviewed in Coyne & Orr, 2004; reviewed in Price,
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2008), suggesting that their dynamics differ during the process of speciation of a single species
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into two or more. This variation can arise through differences in both the rate at which specific
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DNA sequences evolve and the degree to which different components contribute towards genetic
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incompatibilities that reduce gene flow between populations. A common pattern observed
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between speciating taxa is clear differentiation in mtDNA (eg. Hebert et al. 2004; Kerr et al.
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2007), moderate differentiation in sex chromosomes (eg. Thornton & Long, 2002; Borge et al.
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2005; Lu & Wu, 2005; Harr, 2006; Ruegg et al. 2014; Sackton et al. 2014), and comparatively
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modest differentiation across autosomes (Harr, 2006; Nadeau et al. 2012; Irwin et al. 2018).
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Measures of mtDNA differentiation are often used to identify and classify genetically
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distinct populations (eg. Hebert et al. 2004; Kerr et al. 2007) and to infer their histories (Moore,
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1995; Zink & Barrowclough, 2008). Due to its uniparental inheritance, mtDNA has one quarter
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the effective population size and coalescence time of autosomal nuclear DNA (Moore, 1995).
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This characteristic combined with mtDNA’s relatively high mutation rate (Lynch et al. 2006)
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mean that genetic differences arise and fix relatively quickly, creating patterns of clear mtDNA
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differentiation between recently diverged populations.
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Sex chromosomes are another genomic region that often shows higher between-
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population genetic differentiation compared to autosomes between speciating taxa, in both Z/W
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(Borge et al. 2005; Ruegg et al. 2014; Sackton et al. 2014) and X/Y systems (Thorton & Long,
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2002; Lu & Wu, 2005; Harr, 2006). To explain this “faster Z/X effect,” researchers have noted
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(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
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that, because beneficial recessive mutations on the Z or X chromosome are immediately exposed
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to selective forces in the heterogametic sex, fixation of these mutations should proceed faster
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than if the mutations appeared on autosomes (reviewed in Meisel & Connallon, 2013; Irwin,
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2018). Also contributing to genetic differentiation on the Z and X chromosomes are the lower
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effective population sizes of these chromosomes compared to autosomes (Mank et al. 2010;
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reviewed in Irwin, 2018). A lower effective population size allows for the fixation of a greater
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number of slightly deleterious mutations due to less effective purifying selection and a larger role
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of genetic drift. It is likely that both forces—the faster Z/X effect and less effective purifying
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selection—contribute to the moderate amount of genetic differentiation seen between the sex
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chromosomes of diverging taxa (Thorton & Long, 2002; Borge et al. 2005; Lu & Wu, 2005;
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Harr, 2006; Ruegg et al. 2014; Sackton et al. 2014).
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Differentiation across autosomes, which tends to be lower than on mtDNA and sex
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chromosomes, can be highly heterogeneous. In fact, many researchers report “islands of
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differentiation” on autosomes where peaks of high relative differentiation are found against a
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background of low relative differentiation (e.g., Harr, 2006; Nadeau et al. 2012; Hejase et al.
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2020). Explanations for these “islands” usually invoke reduced gene flow (reviewed in Wu,
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2001) and/or repeated bouts of selection (Cruickshank and Hahn, 2014; Irwin et al. 2018). In the
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former scenario, differentiation peaks are hypothesized to house the loci responsible for
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reproductive barriers between interacting taxa and, as a result, they are resistant to the gene flow
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that homogenizes the rest of the nuclear genome. In contrast, explanations invoking repeated
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selection hypothesize that differentiation islands are areas of the genome that experienced
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repeated reductions in genetic diversity as a result of selection or selective sweeps in both
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ancestral and daughter populations.
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Despite the general patterns of differentiation discussed above, an increasing number of
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studies report remarkably low differentiation between populations at what are normally highly
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divergent genetic components when compared to other genetic regions or observable phenotypes
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(e.g., Irwin et al. 2009; Yannic et al. 2010; Bryson et al. 2012). In a number of cases, mtDNA
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shows dramatically low differentiation when compared to differentiation of the nuclear genome,
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a pattern referred to as “mitonuclear discordance” (reviewed in Toews & Brelsford, 2012).
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Discordance between marker types may be explained by hybridization and introgression between
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populations, perhaps due to a selective advantage of the introgressing genetic region. For
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example, Hulsey et al. (2016) documented low mtDNA differentiation—likely due to
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introgression—and clear differentiation in nuclear DNA (nucDNA) between two hybridizing
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cichlid species (Hulsey & García de León, 2013). The researchers further reported high mtDNA
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differentiation between isolated populations of cichlids at genetic sites associated with thermal
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tolerance and a significant correlation between mtDNA divergence and water temperature
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(Hulsey et al. 2016). Altogether, these results suggest that mtDNA introgression produced the
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discordance seen between marker types and that this outcome was potentially driven by adaptive
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selection for tolerance of extreme water temperatures.
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The hypothesis of adaptive introgression increases in complexity if we consider the
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potential for coevolution between genomic components. Research investigating coevolution
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between mitochondrial and nuclear genomes is relatively novel as mtDNA was often treated as a
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neutral marker in past evolutionary research (Avise, 2000). Nevertheless, recent empirical and
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theoretical work has provided greater context regarding how mitonuclear coevolution may
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influence the progression of differentiation and speciation between taxa (Hill, 2019).
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(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted August 8, 2021. ; https://doi.org/10.1101/2021.08.08.455564doi: bioRxiv preprint
