Population Genomics of Mangrove Warblers: Looking for candidate genes in Costa Rica

Study on the mangrove warbler shows ecological speciation in action.

The American Yellow Warbler (Setophaga petechia) is extremely variable. This passerine, which breeds in the whole of North America and the northern part of South America, has been divided into 35 subspecies. Based on the breeding plumage of the males, ornithologists recognize three main groups: the golden warbler (petechia group, 17 subspecies), the mangrove warbler (erithachorides group, 12 subspecies), and the American yellow warbler (aestiva group, 6 subspecies). Hence, if you want to study this species, there is plenty of choice. A recent study in the journal Ecology and Evolution focused on a subspecies in the mangrove warbler group, namely xanthotera.


Ecological Speciation

This subspecies of mangrove warbler is distributed along an ecological gradient on the Pacific Coast of Costa Rica (not a bad place for fieldwork…). Loyal readers of this blog will probably know that such gradients are ideal locations to study ecological speciation. This process concerns the evolution of reproductive isolation between populations due to divergent natural selection along ecological gradients. As populations adapt to the changing conditions along these gradients, they diverge in certain characters which might result in the origin of new species.


A mangrove warbler in Costa Rica © Åsa Berndtsson | Wikimedia Commons


Some Predictions

At the start of an ecological speciation event, populations might already show some phenotypic differences. Despite these differences, there will be no clear genetic population structure, because the populations are connected by occasional gene flow (i.e. birds from neighboring populations can interbreed). However, this lack of genetic population structure is based on the whole genome. If you zoom in on particular genomic regions, you might find some genes that are slowly diverging. Which genes depends on the ecological gradient.

Tania Chavarria-Pizarro and her colleagues expected that differences in salinity and water availabilty might result in divergent selection on osmoregulation genes (i.e. regulation of salt concentrations in the body). Moreover, the size of prey also changes along the Pacific Coast, which could influence the evolution of bill morphology. Based on this background information, we can formulate some general predictions:

  1. There will be differentiation in some phenotypic traits, but no genetic differentiation.
  2. Genes involved in osmoregulation will be divergent
  3. Genes involved in beak morphology will be divergent



Genetic analyses confirmed the first prediction. The researchers did not detect any genetic population structure along the ecological gradient, suggesting that there are still high levels of gene flow between the populations. But is there differentiation in some phenotypic triats? This can be tested by comparing two statistics: Pst and Fst. Pst measures the differentiation in certain phenotypes, whereas Fst captures genetic differentiation. The first prediction is supported when Pst is significantly higher than Fst. And that was indeed the case for two traits: bill height and bill length!


Pst (grey line) is signficantly higher than Fst (red line) for bill height and bill lenght but not for wing length. From: Chavarria-Pizarro et al. (2019) Ecology and Evolution


Candidate Genes

The Pst-Fst patterns already indicated that there is divergent selection on beak morphology. But is this also reflected in the genome? To explore this issue, the researchers performed a genome scan, looking for divergent genes. This search uncovered 19 genes, of which several were involved in beak morphology and osmoregulation. This confirms predictions 2 and 3.

Let’s have a closer look at these candidate genes. In terms of osmoregulation, two aquaporins (AQP1 and APQ4) popped up. These genes code for proteins that regulate body water balance in various tissues. Very useful in a salty environment. Another gene involved in osmoregulation is NPNT, which is related to kidney development. The candidate genes for beak morphology were BMP1 and BMP5. These genes have also been linked to the evolution of beak morphology in Darwin’s Finches.


The genome scan revealed several genes under selection (red dots). Some genes are involved in osmoregulation (APQ1) and beak morphology (BMP5). From: Chavarria-Pizarro et al. (2019) Ecology and Evolution


Tip of the Iceberg?

This study nicely shows the environmental conditions are driving genetic and phenotypic differentiation in this mangrove warbler subspecies. This leaves still 34 other subspecies to be studied in greater detail, which will lead to new insights into the evolution of these songbirds. Indeed, the researchers conclude: “Further studies in other groups within S. petechia can lead to a better understanding the early stages of the formation of biological diversity in a group in which numerous populations could potentially constitute incipient or full biological species.” To be continued…



Chavarria‐Pizarro, T., Gomez, J. P., Ungvari‐Martin, J., Bay, R., Miyamoto, M. M., & Kimball, R. (2019). Strong phenotypic divergence in spite of low genetic structure in the endemic Mangrove Warbler subspecies (Setophaga petechia xanthotera) of Costa Rica. Ecology and Evolution, 9(24): 13902-13918.

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