Genetic evidence for hybrids between Copper Seedeater and Pearly-bellied Seedeater

Or could the genetic patterns be explained by incomplete lineage sorting?

Last year, I published a short paper on tinamou hybrids in which I introduced a scoring scheme to assess the reliability of hybrid records (see this blog post for a summary). In short, I assigned points for different criteria, namely:

  • Observation of a putative hybrid with photographic evidence or a detailed description (1 point)
  • Thorough morphological analyses in which the putative hybrid is compared with potential parental species (2 points)
  • Genetic analyses of the putative hybrid with reference material from potential parental species (3 points)

I decided to put most weight on genetic evidence, because it can be difficult to confidently identify hybrids based on morphology. A specimen with aberrant plumage might be a hybrid, but could also be a color morph. Genetic analyses can often resolve such morphological mysteries. This is nicely illustrated by a recent study in the journal PLoS ONE in which researchers provide some genetic evidence for hybridization between two Sporophila species.

Scoring Plumage Patterns

An extensive survey of Copper Seedeater (Sporophila bouvreuil) and Pearly-bellied Seedeater (Sporophila pileata) across Brazil uncovered a large variation in plumage patterns. The researchers noted that across several Brazilian states “more than one plumage color occurred”, which they explained by age-related changes in coloration. However, the presence of some intermediate plumage patterns points to the possibility of hybrid individuals. To test this hypothesis, Cesar Medolago and his colleagues turned to genetic data by sequencing the mitochondrial gene COI and several microsatellites across a putative contact zone.

First, the researchers scored the plumage coloration of individuals birds from 1 to 4. Individuals were considered as parental species with a score of 1 or 4, and intermediates when scoring 2 or 3. Next, they constructed an evolutionary tree with the mitochondrial data and checked the positions of the intermediate birds in this phylogeny. In general, intermediate birds with score 2 were closer to Pearly-bellied Seedeater, whereas intermediate birds with score 3 were found in a cluster with Copper Seedeater. However, the combination of plumage pattern and mtDNA was not perfect, suggesting that some individuals might represent backcrosses.

Pictures showing the four classes, from pure Pearly-bellied Seedeater (1) through intermediates (2 and 3) to pure Copper Seedeater (4). From: Medolago et al. (2020) PLoS ONE.

Incomplete Lineage Sorting

Based on the microsatellites, the researchers determined the parents at several nests. The analyses revealed all possible parental combinations, including Pearly-bellied Seedeater couples (3 nests), Copper Seedeater couples (3 nests), and mixed couples (6 nests). In four nests, the male was a Pearly-bellied Seedeater and the female a Copper Seedeater. And in two nests, it was the other way around. These findings suggest ongoing hybridization between these two species.

There is, however, an important issue to discuss here. The genetic patterns seem to suggest hybridization, but there is another possibility: incomplete lineage sorting. Imagine a bowl filled with red and blue marbles (representing an ancestral population). As you pour this bowl into two smaller ones (representing the two Seedeater species), you will not get a perfect division between red and blue marbles. A similar process occurred during the speciation process of these birds, some genetic variation present in the ancestral population was incompletely sorted into the two lineages. The sharing of mitochondrial or nuclear variants can thus be explained by incomplete lineage sorting. And indeed, a genomic study on the genus Sporophila suggested that a recent radiation resulted in high levels of incomplete lineage sorting.

The distribution of mitochondrial haplotypes of Pearly-bellied Seedeater (green) and Copper Seedeater (blue) across Brazil. From: Medolago et al. (2020) PLoS ONE.


Nonetheless, the authors from the present study make a convincing case for the possibility of hybridization. They nicely summarized the supporting evidence at the beginning of the discussion:

The main evidence include: i) the widely disjunct distribution of the two species with records of individuals with intermediate plumage patter concentrated near the contact zone; ii) the similar proportion of haplotypes belonging to pileata and bouvreuil clades only in the area embedded within the contact zone, the only of our three areas in which we found the two typical parental plumage patterns together; iii) the presence of males with intermediate plumage in both of the well-supported clades; iv) the decreasing frequencies of males with intermediate plumage and of mtDNA haplotypes that are exclusive of the bouvreuil clade in the direction of the core area of pileata, and v) the fact that intermediate plumage patterns occur frequently in nature only in this pair of southern capuchinos, differently from the other congeners that do reproduce in sympatry.


Medolago, C. A., Costa, M. C., Silveira, L. F., & Francisco, M. R. (2020). Hybridization between two recently diverged neotropical passerines: The Pearly-bellied Seedeater Sporophila pileata, and the Copper Seedeater S. bouvreuil (Aves, Passeriformes, Thraupidae). PloS one15(3), e0229714.

Featured image: Copper Seedeater (Sporophila bouvreuil) © Dario Sanches | Wikimedia Commons

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