Ancient gene flow complicates phylogenetic analyses of leaf warblers

Understanding underlying processes helps to select the “correct” genomic loci.

Different genes tell different stories. This simple statement captures the essence of phylogenomic analyses. The evolutionary history of a particular gene (or genomic region) can be shaped by several processes, such as interspecific gene flow and natural selection. This insight raises the question which genomic regions we should use to estimate the “true” species tree. Some authors have argued that regions of low recombination are most suitable for phylogenetic analyses. Genetic variants flowing in from another species that end up in these rarely recombining regions might become linked to deleterious alleles and will be quickly removed from the population. Hence, regions of low recombination are expected to be immune to introgression, potentially retaining the “true” evolutionary history of the species. However, phylogenomic analyses of Ficedula flycatchers revealed that low recombination regions can produce misleading results due to strong selection. Clearly, the debate on the most suitable genomic regions for phylogenetic analyses has not been settled. A recent study in the journal Systematic Biology provided another perspective on this issue by exploring the evolutionary history of several leaf warblers.

Three Hypotheses

Dezhi Zhang and his colleagues sequenced the whole genomes of 78 leaf warblers, representing 8 species. Previous analyses – using a limited number of genetic markers – could not confidently resolve the phylogenetic relationships among these species. Specifically, the position of Martens’s Warbler (Phylloscopus omeiensis) turned out to be problematic. The researchers proposed three hypotheses to explain the phylogenetic issues with this species:

  • Hypothesis 1: Martens’s Warbler is the sister species of Whistler’s Warbler (P. whistleri) and Bianchi’s Warbler (P. valentini), but gene flow from another species – Alström’s Warbler (P. soror) – results in Martens’s Warbler clustering with Alström’s Warbler.
  • Hypothesis 2: Martens’s Warbler is the sister species of Alström’s Warbler, but ancient gene flow from the ancestor of Whistler’s Warbler and Bianchi’s Warbler results in Martens’s Warbler clustering with these species.
  • Hypothesis 3: Martens’s Warbler is a hybrid species originating from hybridization between Alström’s Warbler and the ancestor of Whistler’s Warbler and Bianchi’s Warbler.

I can imagine that these three scenarios are difficult to follow. Luckily, the authors provided a clear overview of their hypotheses in the figure below.

An overview of the three hypotheses on the phylogenetic position of the Martens’s warbler (Phylloscopus omeiensis). From: Zhang et al. (2021).

Demographic Analyses

Using a suite of phylogenetic analyses, the researchers tried to figure out which hypothesis depicts the most likely scenario. I will not go into the technical details of all these analyses, but I will summarize the main results:

  • Comparing several demographic models with the coalescent simulator fastsimcoal2 revealed that scenarios with ancient gene flow between Martens’s Warbler and the ancestor of Whistler’s Warbler and Bianchi’s Warbler received the highest support.
  • D-statistic analyses suggested high levels of gene flow between Martens’s Warbler and Whistler’s Warbler and between Martens’s Warbler and Bianchi’s Warbler. These patterns were corroborated with demographic analyses using the software DADI.
  • Phylogenetic network analyses pointed to Martens’s Warbler and Alström’s Warbler as sister species, but with ancient gene flow between Martens’s Warbler and the ancestor of Whistler’s Warbler and Bianchi’s Warbler.

If you compare these findings with the three hypotheses outline above, you will quickly see that hypothesis two comes out on top. It seems that Martens’s Warbler is the sister species of Alström’s Warbler, but ancient gene flow from the ancestor of Whistler’s Warbler and Bianchi’s Warbler has thrown a wrench in previous phylogenetic analyses.

Phylogenetic network analyses consistently cluster Martens’s Warbler (P. omeiensis) and Alström’s Warbler (P. soror), but also indicate gene flow between Martens’s Warbler and the ancestor of Whistler’s Warbler (P. whistleri) and Bianchi’s Warbler (P. valentini). The three graphs show results for (a) one, (b) two, and (c) three reticulations. From: Zhang et al. (2021).

Gene Flow and Selection

So, we have managed to resolve the phylogenetic mystery of the leaf warblers. But what about the question posed at the beginning of this blog post: which genomic regions are most suitable for phylogenetic analyses? Taking a closer look at the genome of Martens’s Warbler, the researchers discovered that regions of low recombination were mostly affected by ancient gene flow. They suspect that the introgressed variants from other species ended up in these low recombination regions and were retained in the population by strong positive selection. This observation suggests that “low recombination […] may not be a good indicator of genomic regions suitable for inferring the true phylogeny in the context of ancient gene flow.”

Does this mean that we can safely discard regions of low recombination in phylogenomic analyses and continue working with the rest of the genome? Not necessarily. Which genomic regions are most suitable for phylogenetic analyses will depend on the evolutionary history of the study system. Because the evolution of these leaf warblers has been shaped by high levels of ancient gene flow and strong positive selection on the introgressed regions, it turns out that low recombination regions are not reliable for phylogenetics. In other study systems, ancient gene flow might be less pervasive or introgressed variants were quickly removed from the population. In those scenarios, low recombination regions might be good candidates to reconstruct the true species phylogeny. In other words, which genomic regions should be used in phylogenetic analyses will depend on the evolutionary history of the study system. Due to the contingent nature of evolution, there will probably be no silver bullet to reconstruct the “true” species tree.

And there is also the question whether the “true” species tree actually exists. Perhaps evolution is just one big reticulated network that cannot be captured in a simple bifurcating tree. But that is a discussion for another blog post.

References

Zhang, D., Rheindt, F. E., She, H., Cheng, Y., Song, G., Jia, C., Qu, Y., Alström, P. & Lei, F. (2021). Most genomic loci misrepresent the phylogeny of an avian radiation because of ancient gene flow. Systematic Biology70(5), 961-975.

Featured image: Whistler’s Warbler (Phylloscopus whistleri) © Raju Kasambe | Wikimedia Commons

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