Ecological speciation in the saltmarshes

Scientists search the genomes of Saltmarsh and Nelson’s Sparrow (A. nelsoni) for candidate genes under divergent ecological selection.

There are numerous speciation models, but recently ecological speciation has caught the attention of several evolutionary biologists. In this model, populations diverge as they adapt to different ecological conditions, eventually resulting in reproductive isolation. Ideally, the traits under divergent ecological selection are correlated with mating traits (e.g., beak morphology). Although this model makes intuitive sense, it is difficult to disentangle ecological factors from non-ecological ones, such as genetic drift. One way around this challenge is to study species along an environmental gradient where divergent selection is very pronounced. A recent study in the journal Ecology and Evolution used this approach to understand the evolutionary history of Saltmarsh (Ammospiza caudacutus) and Nelson’s Sparrow (A. nelsoni).


A Saltmarsh Sparrow © Dominic Sherony | Wikimedia Commons


Divergent Regions

Jennifer Walsh and her colleagues scanned the genomes of 20 individuals (10 of each species), looking for particular regions that showed markedly higher divergence compared to the rest of the genome. Based two methods – using either Fst or the number of fixed SNPs – the researchers uncovered 33 highly divergent regions that were examined in greater detail. This approach culminated in a list of candidate genes under divergent selection. Let’s have a look at the most interesting genes…


Regions of elevated divergence (indicated with stars) in the genomes of Saltmarsh Sparrow and Nelson’s Sparrow. The different tracks correspond to relative divergence Fst (blue), absolute divergence Dxy (green) and number of fixed SNPs (pink). From: Walsh et al. (2019) Ecology and Evolution


Candidate Genes

The first candidate gene is SLC41A2, a transporter that moves magnesium-ions across the cell membrane. Hence, this gene plays an important role in osmoregulation, a crucial mechanism when you live in a salty environment. Moreover, SLC41A2 popped up in another study on these sparrows, showing signs of reduced introgression and increased selection. 

Candidate gene number two listens to the name CRY1 and is associated with the circadian clock. How does circadian rhythm relate to saltmarshes? Well, the marshes are affected by flooding during spring when the birds are breeding. To avoid nest failure, it is important to synchronize the nesting cycle (which takes between 23 and 26 days) with the 28-day tidal cycle.

Finally, there is TYRP1. This gene is part of the melanin biosynthesis pathway which determines plumage color. Saltmarsh Sparrow and Nelson’s Sparrow differ in plumage patterns: Saltmarsh Sparrow have darker breast and flank streaking compared to Nelson’s Sparrow. The darker coloration is saltmarshes might be beneficial because it helps the birds avoid predators by blending in with the muddy background. Or the darker feathers might be more resistant to degradation (more melanin slows down degradation by salt-tolerant bacteria).


A Nelson’s Sparrow © Andy Reago & Chrissy McClarren | Wikimedia Commons


Genetic Drift

These divergent regions (and their candidate genes) indicate that divergent ecological selection has shaped the genomes of these sparrows. Importantly, one of the candidate genes (TYRP1) affects plumage coloration which could be used in mate choice, thus providing a link between ecological selection and reproductive isolation.

However, the researchers found that genetic drift has also influenced the evolutionary history of Saltmarsh Sparrow and Nelson’s Sparrow. Demographic analyses pointed to reductions in population size, possibly related to glacial cycles. Smaller populations are more prone to genetic drift, which can also lead to divergence in particular genomic regions. Hence, the evolution of these species is best explained by a combination of genetic drift and strong ecological selection. The most likely scenario was nicely outlined in the introduction of the paper:

The prevailing evolutionary hypothesis suggests a history of vicariance for the saltmarsh and Nelson’s sparrow, whereby an ancestral population spanning a coastal to interior range was split by Pleistocene glaciation, resulting in an isolated interior population. Following differentiation, this interior population then spread eastward back toward the Atlantic coast after recession of the Wisconsin ice mass, making secondary contact with ancestral coastal populations and establishing the current ranges and ecotypes within this species complex.


The demographic history of Saltmarsh Sparrow (orange) and Nelson’s Sparrow (purple) shows reductions in effective population size, resulting in higher levels of genetic drift. From: Walsh et al. (2019) Ecology and Evolution



Walsh, J., Shriver, W. G., Olsen, B. J., & Kovach, A. I. (2016). Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone. BMC Evolutionary Biology16(1):65.

Walsh, J., Clucas, G. V., MacManes, M. D., Thomas, W. K., & Kovach, A. I. (2019). Divergent selection and drift shape the genomes of two avian sister species spanning a saline–freshwater ecotone. Ecology and Evolution9(23):13477-13494.


This paper has been added to the Passerellidae page.

One thought on “Ecological speciation in the saltmarshes

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s