Don’t forget the hybrids! Antbird study shows that not taking into account hybridization leads to the wrong species tree

A study on Ash-breasted Antbird indicates that we should consider hybridization when estimating species trees.

Before the advent of genomic data, phylogenetics (i.e. the construction of evolutionary trees) was relatively simple: sequence your favorite gene, align the sequences and estimate the gene tree using the available algorithms. Then genomics came along. The explosive increase in the amount of genetic data revealed something terrifying: different genes result in different gene trees! This phenomenon – called gene tree discordance – can be caused by several biological processes, such as incomplete lineage sorting (ILS), hybridization and gene duplication. New methods needed to be developed to take this processes into account.

 

ILS for Dummies

Most methods focused on ILS, which occurs when lineages fail to coalesce in the ancestral population. Let me explain this process with an analogy. Imagine that three friends from Spain, Italy and Greece decide to go on holiday in Sweden. They each drive from their respective countries and agree to meet in Sweden. However, the friends from Spain and Italy will meet in France and then continue together to Sweden. This scenario (figure A) is comparable to the species tree, the expected pattern. Unfortunately, the friend from Italy gets lost and runs into his Greek friend in Germany. They decide to go to Sweden together. This scenario (figure B) can be seen as a gene tree that deviates from the species tree because two lineages (Spain and Italy) failed to coalesce in France.

An example of incomplete lineage sorting (ILS) based on a road trip. Scenario B (the gene tree) deviates from the expected pattern in Scenario A (the species tree).

Several methods have been developed to estimate the species tree from a collection of gene trees, taking some discordance into account (keeping in mind the lost Italians from my analogy). Hybridization, however, is not always considered. But this process can also complicate the estimation of a species tree. A recent study in Systematic Biology on the Ash-breasted Antbird (Myrmoborus lugubris) nicely illustrates this issue.

 

Hybridization

The Ash-breasted Antbird is passerine species that inhabits the floodplain forests along the Amazonian rivers. It is divided into four subspecies: lugubris, berlepschi, femininus and stictopterus. Gregory Thom and his colleagues collected morphological and genetic data on these birds. They uncovered a wide hybrid zone between femininus and lugubris.

Several species tree methods (that only consider ILS) clustered femininus and lugubris together as sister subspecies. However, other models (that take hybridization into account) revealed that these subspecies are not each others closed relatives. It turned out that femininus is sister to stictopterus. If the researchers had not considered gene flow in their models, they would have drawn the wrong conclusions.

An Ash-breasted Antbird (Myrmoborus lugubris) – from http://www.hwb.com/

 

Networks and Models

Based on these analyses, the authors recommend the use of phylogenetic networks and model-based approaches (such as fastsimcoal2 or Approximate Bayesian Computation). I provided the same advice in two review papers in The Auk and Avian Research. I hope other ornithologists will follow this line of reasoning: keep hybridization in mind when you are estimating species trees!

 

References

Thom, G., Raposo do Amaral, F., Hickerson, M.J., Aleixo, A., Araujo-Silva, L.E., Ribas, C.C., Choueri, E. & Miyaki, C.Y. (2018) Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Systematic Biology

Ottenburghs, J., Kraus, R.H.S, van Hooft, P., van Wieren, S.E., Ydenberg, R.C. & Prins, H.H.T. (2017). Avian Introgression in the Genomic Era. Avian Research. 8:30

Ottenburghs, J., van Hooft, P., van Wieren, S.E., Ydenberg, R.C. & Prins, H.H.T. (2016). Birds in a Bush: Towards an Avian Phylogenetic Network. The Auk. 133:577-582

 

This paper has been added to the Thamnophilidae page.