Complicated Cotingas: Can we resolve any phylogeny by just adding more data?

A recent genetic study tried to resolve the phylogeny of two bird genera by generating more data.

Time for a trip down memory lane. In 2012, I started my PhD at the Wageningen University in the Netherlands. The topic of my research project: unraveling the evolutionary history of the True Geese (genera Anser and Branta). To my surprise, there was no resolved phylogeny at the time. Several researchers had tried to determine the phylogenetic relationships between the different goose species, but they all ran into polytomies and branches with low bootstrap support. How could we ever solve this conundrum? My solution was quite straightforward: just use more data! So, I sequenced the whole genomes of all goose species and released several phylogenomic tools on the terabytes data. A few years later, I proudly published a resolved phylogenetic tree for the True Geese (you can find the paper here). A recent study in the journal Molecular Phylogenetics and Evolution applied a similar approach to determine the phylogeny of two tropical bird genera.

Tijuca_condita_Gray-winged_Cotinga

Gray-winged cotinga (Tijuca condita) © Joao Quental | Flickr

 

Cotingidae

Deep within the bird family Cotingidae, you can find the genera Lipaugus (7 species) and Tijuca (2 species). Most of these species are restricted to montane habitats, where they occur along narrow elevational ranges, whereas two species reside in the lowlands. Previous genetic work on the Cotingidae family revealed that these genera are closely related. Interestingly, one Tijuca species – the black-and-gold cotinga (T. atra) – was embedded with the other genus. The reliability of this finding was uncertain, because the relationship had low statistical support. The study only used six genetic markers, so perhaps more data could provide some clarity.

Amie Settlecowski and her colleagues revisited this situation with more data. First, they repeated the previous analysis with the six markers (but including more species). This exercise confirmed the relationships uncovered before, but again with low statistical support. In addition, three nodes in the tree could not be resolved. Next, the researchers generated a large dataset of more than 1,000 ultraconserved elements (UCEs). These conserved sequences are shared among divergent animal genomes and are probably involved in controlling gene expression. Analyses of these elements resulted in a completely resolved phylogeny with high statistical support for all nodes. It turned out that the two Tujica species are indeed embedded with the genus Lipaugus. Moreover, they are not even sister species!

tree_cotingidae

A few genetic markers generated with Sanger sequencing could not resolve the phylogeny. Adding more data with ultraconserved elements revealed that the Tujica species are embedded within the genus Lipaugus. From: Settlecowski et al. (2020) Molecular Phylogenetics and Evolution

 

Problem solved?

What can we learn from my goose story and this study: If you cannot solve a phylogenetic tree, just add more data? Not necessarily. More data can help to resolve some contentious relationships, but it is not a guarantee for success. Take the attempts to reconstruct the complete avian phylogeny, for example. Erich Jarvis and his colleagues used whole genome sequences from 48 species and could not confidently determine the branching order at the base of the tree. Clearly, more data is not always the answer.

If we cannot fix a phylogenetic problem with more data, we run into a heated debate. Some scientists will argue that we will be able to resolve the issue in the future (with even more data or with better methods), while others will say that the problem cannot be fixed (the uncertainty reflects reality). In the latter case, the situation cannot be captured in a simple bifurcating tree. A network approach might then be more suitable to depict complex dynamics, such as high levels of hybridization. It is important to keep in mind that each phylogenetic solution – whether it is a tree or a network – is just a provisional hypothesis. And hypotheses can be rejected with new data…

Lipaugus vociferans

Screaming piha (Lipaugus vociferans) © Hector Bottai | Wikimedia Commons

 

References

Settlecowski, A. E., Cuervo, A. M., Tello, J. G., Harvey, M. G., Brumfield, R. T., & Derryberry, E. P. (2020). Investigating the utility of traditional and genomic multi-locus datasets to resolve relationships in Lipaugus and Tijuca (Cotingidae). Molecular Phylogenetics and Evolution, 106779.

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