Admixture in Amazonia: Reconstructing the evolutionary history of the Pectoral Sparrow

Genomic data tell the story of how this passerine spread across South America.

Apart from managing the Avian Hybrids Project, I regularly contribute to the blog of the British Ornithologists’ Union (the BOUblog, you can find an overview of my blog posts here). A few weeks ago, I published my 50th story for the BOUblog, which focused on the phylogenetics of the Pectoral Sparrow (Arremon taciturnus). A recent study used mitochondrial DNA to unravel the evolutionary history of this neotropical species. The researchers uncovered six distinct lineages and speculated about the factors responsible for their origins. Here is my summary:

Could it be that the origin of these rivers drove the diversification of the Pectoral Sparrow? Not exactly, because these rivers started crisscrossing the South American landscape between 9 and 2.5 million years ago. The rivers certainly prevent neighboring populations from mixing extensively, but they are not the main cause for the origin of these lineages. Rather, the researchers suspect that ‘past ecological barriers must have played a role in accounting for the observed phylogeographical structure.’ During the glacial cycles of the Pleistocene, forests contracted and expanded. The Pectoral Sparrows became isolated in forest fragments during contraction phases and followed the spreading forests during the expansions. At rivers, however, the birds could not disperse further, giving rise to the geographical boundaries between the six lineages. Amazing what you can deduce from a string of A, T, G and Cs.

Although this scenario seems plausible, it remains largely speculative. Indeed, the authors indicated the uncertainties in their proposed model and wrote that “alternative scenarios could be tested with more powerful genomic datasets.” Luckily, another recent paper did just that. Using genomic data, Nelson Buainain and his colleagues provided a more fine-grained picture of the evolution of the Pectoral Sparrow.

Analyses of mitochondrial DNA indicated six distinct lineages within the Pectoral Sparrow. From: Carneiro de Melo Moura et al. (2020) Ibis.

Genotypes and Phenotypes

In contrast to the six mitochondrial lineages, the genomic data suggested four main genetic clusters. The genetic make-up of these four groups reveals an interesting pattern. Individuals from the Guyana Shield (region A in the figure above), southwestern Amazonia (region F) and the Atlantic Forest (region D) generally have “pure” genotypes. In other words, they do not share genetic variation with other regions. In central Amazonia (regions B, C and E), however, individuals have admixed genotypes.

The genetic patterns are mirrored in the plumage of the birds. In the genetically “pure” populations, pectoral band patterns are mostly homogenous, whereas the admixed populations show a variety of shapes and sizes in the pectoral bands. The most likely scenario is that populations became isolated in different forest patches across central Amazonia and established secondary contact, giving rise to the genetic and morphological variety we see today. This interpretation was further supported by ecological niche modelling.

Genetic and morphological variation across the range of the Pectoral Sparrow. Notice the admixed nature of the populations in central Amazonia. From: Buainain et al. (2020) Molecular Ecology.

North to South

The genetic analyses indicated that the populations north and south of the Amazon separated about 160,000 to 380,000 years ago. The higher genetic diversity in the northern populations of the Guyana Shield suggest that the Pectoral Sparrow started its journey across South America here. As birds spread to the south, they separated into distinct populations, settling in the patches of suitable habitat. These populations were probably separated in at least three regions south of the Amazon River, namely southwestern Amazonia and south‐central Amazonia and the Atlantic Forest. These regions functioned as refugia during harsh climatic periods when forest fragments were isolated. Occasionally, climatic changes would cause these forests to expand, resulting in the secondary contact that I described above. This scenario nicely builds upon the patterns that arose from the mitochondrial study. Step by step, we are unraveling the complex evolutionary history of South American birds.


Buainain, N., Canton, R., Zuquim, G., Tuomisto, H., Hrbek, T., Sato, H., & Ribas, C. C. (2020). Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus. Molecular Ecology29(15), 2922-2939.

Featured image: Pectoral Sparrow (Arremon taciturnus) © Caio Brito | eBird