Monophyletic Manakins? Not according to mtDNA…

Complex patterns of introgression between three Manakin species.

Gene trees are not species trees. When you construct an evolutionary tree for a particular gene, it might deviate from the actual species tree. This might sound like an annoyance (and it is for some scientists), but it also provides the opportunity to explore the evolutionary forces that underlie this incongruence. A recent study in Molecular Phylogenetics and Evolution shows how “wrong” gene trees can provide important insights.


Three Manakins

The relationships in the Manakin genus Lepidothrix remain poorly resolved. Particularly, the exact configuration of the following three species is still a matter of debate: Opal-crowned Manakin (L. iris), Snow-capped Manakin (L. nattereri), and Golden-crowned Manakin (L. vilasboasi). A phylogenetic study in 2013 reported Opal-crowned and Snow-capped Manakin as sister species. However, this analysis did not include specimens of Golden-crowned Manakin.

A recent genomic assessment of these three species revealed that Golden-crowned Manakin probably originated from hybridization between the other two species. In other words, it is a hybrid species (see here for a blog post about this particlar case, and here for hybrid speciation in general).


The three Manakins (drawings from


Not Monophyletic

Cleyssian Dias and colleagues revisited this case and sequenced two mitochondrial and three nuclear genes. Analyses of these five markers revealed some striking patterns. Particularly, the Opal-crowned Manakin was polyphyletic, meaning that the specimens were scattered across the phylogeny. Some specimens (belonging to the subspecies iris) clustered with the some Snow-capped Manakins, while other specimens (belonging to the subspecies eucephala) grouped with Golden-crowned Manakin and the remaining Snow-capped Manakins.


Exchanging mtDNA

What could explain these peculiar patterns? A glance at the haplotype network for mitochondrial DNA might provide some clues.  You can see that the eucephala subspecies (blue) groups with Golden-crowned Manakin (orange), whereas the iris subspecies (pink) is closer to Snow-capped Manakin (green). You can also see some hints of blue in the green circles. So, the eucephala subspecies also shared DNA with the Snow-capped Manakin. These networks suggest pervasive introgression of mtDNA among these three species (similar patterns have been reported in Jacamars).


Haplotype networks for two mitochondrial genes: (A) ND2 and (B) COI. Based on Dias et al. (2018) Molecular Phylogenetics and Evolution.


Sexual Selection?

What could cause this exchange of mtDNA? That question remains unanswered for the moment. It could be sex-biased dispersal (mtDNA is only passed on through the female lineage) or sexual selection at leks. Currently, there is no data on lek behavior of these species. It would be interesting to see what happens when male Manakins meet to battle it out. Here is already a taste of what might go down at these leks; have a look at this Red-capped Manakin (Ceratopipra mentalis).



Dias, C., de Araujo Lima, K., Araripe, J., Aleixo, A., Vallinoto, M., Sampaio, I., Schneider, H. & Senda do Rego, P. (2018) Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae). Molecular Phylogenetic and Evolution, 126:314-320.

This paper had been added to the Pipridae page.

2 thoughts on “Monophyletic Manakins? Not according to mtDNA…

  1. […] There is, however, something peculiar about lineages B and C. The analyses in this study (based on nuclear and mtDNA) suggest that lineage C is the oldest group, whereas lineages A and B cluster together. Other studies (using only mtDNA) reported that lineages B and C are closely related. The disagreement between the nuclear and mitochondrial genes is most likely due to an ancient hybridization event. Birds from lineages B and C hybridized, resulting in the transfer of mtDNA between these lineages. This phenomenon – mitochondrial capture – has been described in numerous other bird species, including another group of manakins (see this blog post) […]

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