Genomics of Secondary Contact in Panamanian Birds

Secondary Contact

In birds, essentially all speciation events begin in allopatry (Price 2008, Speciation in Birds). Historically, the study of speciation in Neotropical birds has focused on how geographically isolated bird populations form. But, as any tropical ecologist knows, what makes the Neotropics special is the extreme local species richness, which can only occur when multiple species (that descended from a common ancestor) co-occur in the same geographic locale. Therefore, to truly understand avian diversification in the Neotropics, we need to understand what happens when formerly isolated geographic species co-occur in space: secondary contact.

In fact, the outcome of secondary contact is anything but certain. And in fact, it can be best described as a continuum of genomic outcomes. On the one extreme, the descendant species freely interbreed ultimately fuse together. Thus, from a certain point of view -- diversity is destroyed. On the other extreme, the two species co-occur in space without sharing genes, and from the ecologist's point of view, alpha diversity has just increased. In the middle, the two species hybridize, neither completely fusing together nor increasing local species richness.


Previous research in our group has demonstrated a surprisingly high level of secondary contact in the lowlands birds of Panama. This secondary contact is largely cryptic, because it involves eastern and western populations that are not recognized as separate species (or many times as separate subspecies!). But the results from broad surveys of mitochondrial DNA sequence variation across Panama, show that secondary contact is widespread. This situation gives us a unique opportunity to study the phenomenon of secondary contact. We have begun sequencing the same set of 5000 genomic loci from 10 birds species across Panama, and are hoping to recruit a Phd student to explore the following questions in this group:

The goals of this project are to:

1. Identify the degree of genome-wide introgression across abrupt mitocondrial breaks in these species;

2. Identify if there is common pattern of degree of introgression among loci, or among chromosomes (based on mapping loci to chromosomes);

3. Identify whether key ecological traits in birds (such as diet; see Miller et al. in review) predict the outcome of secondary contact;

4. Test whether mitonuclear incompatibilities are responsible for limited introgression of certain loci.

5. Develop a framework for correctly establishing species limits of Panamanian birds, and evaluate the consequences of revised species limits on conservation plannig in the region.