Two American sparrows with similar mtDNA: Rapid speciation or hybridization?

Analyses of the nuclear genome provide the answer to this question.

An important aspect of the scientific process is considering and testing several explanations. Imagine, for example, that you sequence the mitochondrial DNA of two bird species. When you compare the genetic sequences, you notice that the two species hardly differ. What could explain this pattern? In scientific papers, you will generally come across two possible solutions: (1) the two species have only recently diverged and still share some genetic variation, or (2) the two species have hybridized and mitochondrial DNA flowed from one species into the other. In technical terms, these explanations are known as incomplete lineage sorting (see this blog post for more details on this concept) and introgressive hybridization.

The mitochondrial situation that I just described applies to the Golden-crowned Sparrow (Zonotrichia atricapilla) and White-crowned Sparrow (Z. leucophrys). In 2001, Jason Weckstein and his colleagues reported “extraordinarily low levels of sequence divergence between Z. leucophrys and Z. atricapilla, despite distinct plumage, song, and allozymes.” Moreover, several mitochondrial haplotypes were shared between these species. Although they could not rule out rapid speciation (and thus incomplete lineage sorting), they hypothesized that introgression was the most likely explanation. Recently, a study in the journal Molecular Phylogenetics and Evolution put this hypothesis to the test by exploring the nuclear DNA of these sparrows. Undifferentiated nuclear genomes would suggest rapid speciation, while distinct nuclear genomes in combination with shared mtDNA would point to introgression.

Phylogenetic Trees

Based on 73 specimens of the two species, Rebecca Taylor and her colleagues estimated phylogenetic trees for two mitochondrial genes (COI and the control region) and several thousands of nuclear genetic variants. In line with previous work, the species shared mitochondrial haplotypes and could not be separated into distinct clusters. The nuclear analyses, however, uncovered clear differences between the Golden-crowned Sparrow and White-crowned Sparrow. These contrasting patterns suggest introgression of mitochondrial DNA.

This explanation was supported by additional analyses that revealed ancient gene flow between these species. Using the software TreeMix, for instance, the researchers detected introgression from Golden-crowned into White-crowned Sparrow. And the commonly used D-statistic further corroborated this introgression event (see this blog post for an explanation how this test works). Clearly, introgressive hybridization seems to be the most likely explanation.

Phylogenetic analyses of the mitochondrial genes (left figure) could not separate the two species into distinct groups, whereas the nuclear variants uncovered clear clusters (right figure). The Golden-crowned Sparrow is depicted in red, the other colors represent subspecies of the White-crowned Sparrow. From: Taylor et al. (2021).

Adaptive or Neutral Introgression?

Answering one question mostly leads to a bunch of other mysteries. Now that we know about introgression of mitochondrial DNA, we can move on to the next aspect: was the introgression driven by neutral or selective processes? Currently, we don’t have enough information to answer this question. However, the researchers do speculate about a possible scenario:

While it is only informed speculation, populations of Z. atricapilla and Z. leucophrys could have been forced into common refugia by ice sheets and shifting vegetation during the Pleistocene, leading some individuals to seek out heterospecific mates. Several rounds of bottlenecking due to climate change might have occurred during this period and similarly caused the fixation of one haplotype in both species during periods when population sizes were small. Selection may have acted in combination with periods of small population sizes and augmented this process, if one mitochondrial haplotype conferred a fitness advantage.

This certainly sounds like a plausible scenario, but it remains to be tested with more detailed analyses. The mitochondrial mystery of the Golden-crowned Sparrow and the White-crowned Sparrow continues…


Taylor, R. S., Bramwell, A. C., Clemente-Carvalho, R., Cairns, N. A., Bonier, F., Dares, K., & Lougheed, S. C. (2021). Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrysMolecular Phylogenetics and Evolution162.

Featured image: Golden-crowned Sparrow (Zonotrichia atricapilla) © V. J. Anderson | Wikimedia Commons

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