Fascinating Finches: Patterns of Gene Flow in South American Siskins

Multiple hybridization events in South American siskins.

Although hybridization is a widespread phenomenon in birds, detecting gene flow between species (i.e. introgression) is still challenging. In my Avian Research review – “Avian Introgression in the Genomic Era” – I provided an overview of several methods that can be used to infer genetic exchange between species. Most of these methods assume that you know the evolutionary relationships between the species under investigation. In other words, these methods are dependent on a resolved phylogeny. Unfortunately, this information is not always readily available, especially in recent radiations. A recent study in Molecular Ecology tries to circumvent this phylogenetic uncertainty and shows that you can infer introgression without a proper phylogeny.

hooded siskin

Hooded siskin (Spinus magellanicus) – from: http://www.wikipedia.com/



South American siskins (genus Spinus) are a group of 11 species that diversified about 550,000 years ago. Previous work indicated that species in the same area share identical mitochondrial haplotypes. This sharing might be due to rapid speciation or hybridization. To figure this out, Elizabeth Beckman and her colleagues focused on four species: hooded siskin (Spinus magellanicus), black siskin (S. atratus), thick-billed siskin (S. crassirostris), and yellow-rumped siskin (S. uropygialis).

black siskin.jpg

Black siskin (Spinus atratus) – from: http://www.hbw.com/


Testing for Introgression 

The evolutionary relationships between the siskin species are uncertain. To deal with this uncertainty, the researchers did the following. First, they assessed the population structure of the siskins and delineated particular groups based on their geographical distribution. Next, they generated a phylogenetic tree based on 45,000 SNPs. Finally, they conducted several tests for introgression on a collection of smaller trees that were compatible with the main phylogenetic tree. Using this approach, they were able to pinpoint introgression between the following species:

  • Hooded siskin (from Peru) and thick-billed siskin
  • Hooded siskin (from Peru) and yellow-rumped siskin
  • Hooded siskin (from southern Peru) and black siskin
  • Hooded siskin (from Bolivia) and black siskin

Most of these introgression events probably occurred in the past, around the time these species diversified. However, there might also be recent introgression in Bolivia between hooded siskin and black siskin.

yellow-rumped siskin.jpg

Yellow-rumped siskin (Spinus uropygialis) – from: http://www.hbw.com/


Network Analysis

One caveat of this study – as the authors discuss themselves – is that they did not assess these introgression events in a single analysis. Here, a promising approach could be the implementation of phylogenetic networks, which deviate from the classical bifurcating trees by allowing for reticulations. I have actually argued for these networks before, here are the final sentences from my 2016 paper in The Auk:

[I]n birds, phylogenetic networks will provide a powerful tool to display and analyze the evolutionary history of many bird groups. The genomic era might thus result in a paradigm shift in avian phylogenetics from trees to bushes.

tick-billed siskin

Thick-billed siskin (Spinus crassirostris) – from: http://www.flickr.com/ – picture by Pablo Caceres Contreras



Beckman, E.J., Benham, P.M., Cheviron, Z.A. & Witt, C.C. (2018) Detecting introgression despite phylogenetic uncertainty: the case of the South American siskins. Molecular Ecology.


This paper has been added to the Fringillidae page.


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