The taxonomic story of the Stipplethroats

A recent phylogenetic study proposes nine distinct species.

Worldwide, there might be about 50 billion individual wild birds (according to this recent PNAS paper). Taxonomists classified all this diversity in about 10,000 species. Each species has been given a binomial name, consisting of genus and a species name. For example, the house sparrow is also known as Passer domesticus, ever since Linneaus named in 1758. The taxonomic position of the house sparrow has been stable for centuries, but other bird groups have been prone to more changes. Some have been promoted from subspecies to species rank (or the other way around), while others have received different genus names.

A nice example of this taxonomic instability concerns the stipplethroats of South America (currently in the genus Epinecrophylla). These small passerines were considered close relatives of the Myrmotherula antwrens and were classified in the same genus. Genetic studies revealed that the stipplethroats were actually more closely related to the bushbirds of the genera Neoctances and Clytotanctes. This finding resulted in the naming of a new genus for the group: Epinecrophylla. Since taxonomists have pinned down the genus name for the stipplethroats (at least for now), they turned to the species level. A recent study in the journal Molecular Phylogenetics and Evolution proposed to recognize nine distinct species. Let’s meet the stipplethroats!

Genetic Splits

The genus Epinecrophylla contains 21 recognized taxa, but their classification into species and subspecies is still a matter of debate. Using thousands of ultraconserved elements (UCEs), Oscar Johnson and his colleagues reconstructed the phylogenetic relationships between these taxa. At the base of the phylogeny, we find the checker-throated stipplethroat (E. fulviventris), followed by the ornate stipplethroat (E. ornata). The latter one showed deep genetic splits and clear population structure between three subspecies (meridionalis, hoffmannsi and atrogularis), suggesting that there might be multiple species hiding in this section of the phylogeny. However, the situation could be complicated by a potential hybrid zone between atrogularis and meridionalis in southern Peru. More research on the ornate stipplethroat is definitely warranted.

Next, the researchers reported a clear split between the rufous-tailed stipplethroat (E. erythrura) and the white-eyed stipplethroat (Epinecrophylla leucophthalma). These taxa are clearly distinct species, but the classification of subspecies within the white-eyed stipplethroat needs more work (currently containing leucophthalma, phaeonota, sordida and dissita).

Dated phylogenies for the genus Epinecrophylla based on (A) ultraconserved elements and (B) mitogenomes. From: Johnson et al. (2021) Molecular Phylogenetics and Evolution.

Short Branches

The classification of the first four species was rather straightforward, but now we arrive at the “Epinecrophylla haematonota group” which holds eight taxa that have undergone many taxonomic rearrangements. Apart from the position of the brown-bellied stipplethroat (E. gutturalis), the researchers found considerable disagreement between the phylogenetic methods regarding the relationships among the three other main clades in this group (see figure below). The rapid evolution of these birds probably resulted in very short branches between the clades, making it extremely difficult to uncover the exact branching order. More detailed analyses – perhaps using genomic data – might be necessary to solve this phylogenetic knot.

Despite this methodological issue, the researchers could identify four species that diverged at roughly the same time (about 2 to 3 million years ago): the rufous-backed stipplethroat (E. haematonota), the Rio Madeira stipplethroat (E. amazonica), the foothill stipplethroat (E. spodionota) and the Negro stipplethroat (E. pyrrhonota). The classification into genera and species seems to be quite stable, so now taxonomists can dive into the subspecies level.

Different phylogenetic methods lead to different outcomes. From: Johnson et al. (2021) Molecular Phylogenetics and Evolution.


Johnson, O., Howard, J. T., & Brumfield, R. T. (2021). Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla). Molecular Phylogenetics and Evolution154, 106962.

Featured image: brown-bellied stipplethroat (E. gutturalis) © Hector Bottai | Wikimedia Commons

This paper has been added to the Thraupidae page.

Inferring introgression: Genomic study on hybridizing Darwin’s Finches highlights the importance of field observations

Explaining patterns of introgression required a thorough knowledge of the study system.

Yesterday I assisted in a field course on habitat analysis for ecologists. The students would visit an field site and explore different aspects of the ecosystem. In my section, we would walk through forest plot and try to identify common Dutch tree species. Due to the Corona-measures, most students had learned about these species in an online course, without hands-on experience in the field. And it showed. Some students struggled to identify the species at first. But once they knew which traits to focus on, they managed to identify most species correctly. This experience highlights the importance of fieldwork.

During my postdoc in Sweden, most of my colleagues worked on the genetics of the black-and-white flycatcher system: pied flycatcher (Ficedula hypoleuca) and collared flycatcher (F. albicollis). To my surprise, some colleagues had not seen these species in the wild and seemed uninterested in the natural history of these beautiful birds. They preferred to focus on abstract genetic concepts (which is also interesting). But how can you interpret the genetic data when you don’t know the ecology of the species? A recent paper in the journal Nature Ecology & Evolution illustrates the importance of knowing the ins and outs of your study system.

The pointed beak of the cactus finch (Geospiza scandens) © Mike’s Birds | Wikimedia Commons


Geospiza Finches

When I say “Peter and Rosemary Grant”, you will probably say “Darwin’s Finches”. Indeed, the Grants are known for their long-term study of these small passerines on the Galapagos Islands. On the island of Daphne Major, they documented hybridization between medium ground finch (Geospiza fortis) and cactus finch (G. scandens). Their meticulous study revealed that these species are converging morphologically: the long beaks of G. scandens became blunter and the robust beaks of G. fortis became more pointed. The change of beak morphology was greater in G. scandens, suggesting that genes are primarily flowing from G. fortis into G. scandens.

A recent genomic study confirmed this suggestion and went one step further. Sangeet Lamichhaney and his colleagues – including the Grants – compared the patterns of genetic exchange (i.e. introgression) for different parts of the genome. The genetic analyses pointed to extensive introgression of the autosomes (i.e. any chromosome that is not a sex chromosome) and the mitochondrial DNA, but not of the Z-chromosome.

The genetic analyses indicated introgression of the autosomes and of mtDNA, as shown by the position of SLB (G. scandens with blunt beak). On the Z-chromosome, this group of birds clusters with the other G. scandens samples. (Red = G. scandens, Blue = G. fortis). From Lamichhaney et al. (2020) Nature Ecology and Evolution


If you would show this result to my genetics-focused colleague in Sweden, she might attribute it to genetic incompatibilities on the sex chromosomes. And indeed, numerous other studies have found strong selection on sex-linked genes, contributing in reproductive isolation (check out this review on sex chromosomes and speciation). In this case, however, the ecology of the species is important. The field observations provided some crucial insights.

All female finches, including hybrid daughters, preferentially mate with males that sing the same song as their fathers’ song: mate choice is based on the imprinting of offspring on the parental morphology and song. The net result of this pattern of mating is the introgression of mtDNA and autosomal genes but few Z chromosomes from G. fortis to G. scandens. Hybrid females from these matings carry a G. scandens Z chromosome and cannot introgress any G. fortis Z chromosome. Hybrid sons, being relatively small, are at a disadvantage in competition with G. scandens males for high-quality territories and mates.

So, the reduced introgression on the Z-chromosome is not due to genetic incompatibilities, but can be explained by the behavior of the birds. The moral of this story: go into the field before you get into the lab.



Lamichhaney, S., Han, F., Webster, M. T., Grant, B. R., Grant, P. R., & Andersson, L. (2020). Female-biased gene flow between two species of Darwin’s finches. Nature Ecology & Evolution, 1-8.


This paper has been added to the Thraupidae page.