Phylogenetics in the genomic era: Reconstructing the evolutionary tree of rails (family Rallidae)

A phylogenomic study reports some interesting new relationships.

The life of a “phylogeneticist” used to be so simple. You sequence a couple of genes, align them with your favorite software (mostly Clustal), and run some phylogenetic analyses (maximum likelihood, maximum parsimony and perhaps something Bayesian). Then genomic data arrived. Suddenly, there were thousands of genes and non-coding elements to take into account. What was worse, different genes often resulted in different gene trees! The life of the phylogeneticist – or should I say phylogenomicist – just became a whole lot more complicated and more exciting.

Obviously, I exaggerated here. Phylogenetics was never that simple. But the advent of genomic data did open up many avenues for further research. These new opportunities came with an expansive toolkit of software and analysis methods. You can check out the details in this recent paper in Nature Reviews Genetics: Phylogenetic tree building in the genomic age.  In this blog post, however, I would like to focus on two general methods to construct phylogenetic trees from genomic data, namely concatenation and coalescent-based consensus approaches.

 

Supermatrix or Supertree?

To explain both methods, I will borrow some text from a paper I published some years ago in Molecular Phylogenetics and Evolution.

In concatenation (or supermatrix) methods all sampled genes are concatenated and analysed as a single ‘‘supergene”. Supertree methods, on the other hand, involve separate analyses of the sampled genes and subsequent integration of the resulting trees into a species tree. Certain supertree methods incorporate the multispecies coalescent model to estimate the species tree from a set of heterogeneous gene trees.

In short, during a concatenation analysis you paste all the genes together and analyse them as if they are one big gene. In supertree methods, you generate a gene tree for each gene and then combine them into a species tree. Simple.

supermatrix_tree

The difference between supermatrix and supertree methods. From: Delsuc et al. (2003) Nature Reviews Genetics

 

A tree of rails

A recent study in the journal Diversity applied both methods to reconstruct the evolutionary history of the rail family. The researchers analyzed 393 loci from 63 species. In the abstract, they report that “Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support.” That is good news and suggests that the phylogeny has been resolved reliably. There are several intriguing findings, so let’s have a look at a few unexpected results.

First, a bombshell: the family Rallidae (as we know it) is not monophyletic. The Forbes’ Forest rail (Rallicula forbesi) does not cluster with the other rails, but is more closely related to the flufftail (Sarothrura rufa). Together, these species are best classified in a distinct family: the Sarothruridae. Another new insight concerns the African Nkulengu rail (Himantornis haematopus). This species now occupies its own separate branch (which is in agreement with morphological data)

rail_tree

The phylogenetic relationships between different rail species. Notice the location of Rallicula forbesi outside the core family. Colors correspond to different genera. From: Garcia-R et al. (2020) Diversity

 

Unstable genera

The analyses revealed some other interesting relationships that rendered several genera non-monophyletic.

  • The African crake (Crex egregia) is more closely related to Rouget’s rail (Rougetius rougetii) than to its congeneric, the corn crake (C. crex).
  • The positions of the New Guinea flightless rail (Megacrex inepta) and the watercock (Gallicrex cinerea) break the monophyly of the genus Amaurornis.
  • The Inaccessible rail (Atlantisia rogersi) falls within the genus Laterallus.

Clearly, there is some taxonomic work ahead of us.

crex_egregia

Two African crakes © Derek Keats | Flickr

 

Stems and crown groups

Finally, the researchers also attempted to date the resulting phylogenetic tree. When did all these species arise? The answer to that question strongly depends on the placement of the Belgirallus fossil. This taxon represents the oldest known fossil of the Rallidae, but the exact relationship with extant species is unknown: it can be considered as a representative of the stem or the crown group. What is the difference, you ask? Well, a crown group is the smallest clade that includes all living members of a group and any fossils nested within it. A stem group is a set of extinct taxa that are not in the crown group but are more closely related to the crown group than to any other.

If you consider Belgirallus as part of the stem group, the Rallidae originated around 26 million years ago. But if you place it within the crown group, the origin of Rallidae shifts to about 33 million years ago. More fossils are needed to resolve this issue.

Fig.3.8

The difference between crown and stem groups. From: Noriyuki Satoh (2016) Chordate Origins and Evolution

 

References

Garcia-R, J. C., Lemmon, E. M., Lemmon, A. R., & French, N. (2020). Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution. Diversity12(2), 70.

Kapli, P., Yang, Z., & Telford, M. J. (2020). Phylogenetic tree building in the genomic age. Nature Reviews Genetics, 1-17.

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