Similar plumage, but different songs: How many subspecies of Willow Flycatcher are there?

Acoustic analyses support the recognition of a distinct southwestern subspecies.

Classifying birds into species and subspecies can be a tricky exercise. Different criteria – such as morphology, genetics or behavior – can result in drastically different taxonomic arrangements. The incongruence between these criteria is expected when you understand that speciation is a gradual process. As two populations follow their own evolutionary trajectories, different traits will evolve at different rates. For example, populations might become genetically distinct while they do not develop morphological differences (or vice versa). When it comes to tyrannid flycatchers (genus Empidonax), song and plumage are evolving at contrasting speeds. These small songbirds show very little differentiation in plumage patterns, but tend to sing distinct songs. But how to classify these birds? A recent study in the Journal of Avian Biology took a closer look at one species: the Willow Flycatcher (Empidonax traillii).

Unsupervised Clustering

Despite the lack of clear plumage differences, the Willow Flycatcher has been divided into four subspecies that can be found in different parts of the USA: trailii in the east, brewsteri in the northwest, adastus in the interior west and extimus in the southwest. The studies underlying this subdivision have been criticized because they lacked rigorous statistical analyses, had small sample sizes and used wild birds that were released and could thus not be re-analyzed (see this paper for an overview of the critique). In a recent study, Sean Mahoney and his colleagues addressed these shortcomings by measuring museum specimens and analyzing publicly available song recordings. Moreover, they used unsupervised clustering algorithms that do not take into account the current taxonomic arrangement and are thus more objective.

Distribution of the four Willow Flycatcher subspecies across the USA. From: Mahoney et al. (2020) Journal of Avian Biology.

Song Groups

The clustering based on plumage coloration suggested two main groups that did not follow the subspecies classification. This result highlights the lack of plumage differentiation in these flycatchers. The song analyses, however, did align with the taxonomy of the Willow Flycatcher. The algorithm pointed to two clusters that correspond to the subspecies extimus and the remaining three subspecies (trailii, brewsteri, and adastus). Hence, the authors conclude that “our song data support the recognition of the southwestern population as a distinct subspecies.” This finding is relevant for the conservation of the Willow Flycatchers, because this subspecies is currently listed as endangered by the US Fish and Wildlife Service. Uncertainty around its taxonomic status would have complicated its protection.

Unsupervised clustering of song characteristics suggested two main groups, corresponding to the subspecies extimus (in black) and the other three subspecies (in grey). From: Mahoney et al. (2020) Journal of Avian Biology.


Mahoney, S. M., Reudink, M. W., Pasch, B., & Theimer, T. C. (2020). Song but not plumage varies geographically among willow flycatcher Empidonax traillii subspecies. Journal of Avian Biology51(12).

Featured image: Willow Flycatcher (Empidonax traillii) © VJ Anderson | Wikimedia Commons

The phylogeographic story of a Manakin and a Bamboo Tyrant

Ecology explains the genetic differences in two Atlantic Forest species.

One of my favorite science stories is the discovery of the neutrino by the Austrian physicist Wolfgang Pauli. During an experiment, he found that energy appeared not to have been conserved. Reluctant to give up the universal idea of conservation of energy, Pauli developed an explanation. He speculated that the missing energy was carried off by a new particle. Next, he developed a mathematical model to predict certain properties of this new particle, so that its existence could be verified. Twenty-five years later this new particle was found and is now a well-established member of particle physics, even if still hard to detect. This story illustrates the power of formulating explanations and hypotheses which can consequently be tested with new experiments and observations.

A recent study in the journal Molecular Phylogenetics and Evolution took a similar approach when examining the genetic population structure of of two species in the Montane Atlantic Forest: the blue manakin (Chiroxiphia caudata) and the drab-breasted bamboo tyrant (Hemitriccus diops). What explanations could account for the similarities and differences in population structure between these species?

Last Glacial Maximum

Reconstructing the past distributions of these species revealed that they responded similarly to the climatic conditions during the Last Glacial Maximum (about 20,000 years ago). At this time, the Montane Atlantic Forest covered a larger area of South America, allowing both species to expand their range. This finding was also supported by the genetic analyses where several statistics (Fu’s Fs and R2) indicated population expansion in both species.

Despite these similarities, additional genetic analyses of the mitochondrial ND2 gene revealed some striking differences. The blue manakin did not display a clear phylogeographic structure, whereas the drab-breasted bamboo tyrant showed a phylogeographic break near the Doce River. What could explain these differences?

The blue manakin did not show any phylogeographic study, while the drab-breasted bamboo tyrant showed a clear phylogeographic break. From: da Silva Ribeiro et al. (2020) Molecular Phylogenetics and Evolution.

Ecological Differences

The researchers discuss several explanations for this phylogeographic incongruence. A first possibility is that there has been more gene flow between several blue manakin populations, preventing the build-up of genetic differences. This higher exchange of individuals (and genes) between populations could relate to the diet and mating system of this species. The blue manakin is a frugivore. Given that fruit is a more ephemeral resource in time and space, frugivorous species are expected to travel large distances to find food. In addition, the blue manakin exhibits lekking behavior in which females visit several locations where multiple males display (see video below). Again, lekking species are expected to disperse over larger distances during their visits. The drab-breasted bamboo tyrant, on the other hand, is a insectivore (plenty of those around) and has a territorial mating system (no need to travel far). These characteristics might lead to less gene flow between populations and the accumulation of genetic differentiation.

A second explanation concerns the different generation times of both species. Female manakins start breeding when they are 2–3 years old and have a generation time of 4.9 years. This is roughly three times larger than the average generation time of non-lekking passerine birds (ca. 1.7 years). Hence, the authors suggest that “the shorter generation time of H. diops could have favored the accumulation of differences between geographically isolated populations.”

The complex courtship ritual at a manakin lekking spot.

More Research

Similar to Pauli postulating the existence of a new particle, the formulation of all these explanations is just the first step in this scientific endeavor. Now, the researchers will need to dig deeper and test these explanations with other analytical tools and new datasets. Indeed, they mention that “the incongruent population structure pattern shown in our comparative study indicates that life history and ecological traits can be important in diversification processes. Further investigations of these traits are needed to clarify their micro-evolutionary role.” Whether you are a physicist or a biologist, further investigations are the way forward.


da Silva Ribeiro, T., Batalha-Filho, H., Silveira, L. F., Miyaki, C. Y., & Maldonado-Coelho, M. (2020). Life history and ecology might explain incongruent population structure in two co-distributed montane bird species of the Atlantic Forest. Molecular Phylogenetics and Evolution153, 106925.

Featured image: Blue Manakin (Chiroxiphia caudata) © Dave Curtis | Flickr

Three bird species show how to travel between the Andes and the Atlantic Forest

Would they recommend the dry Chaco and the open-vegetation Cerrado?

“A wealth of phylogeographic data is available for many terrestrial and aquatic organisms of the Northern Hemisphere. In fact, a disproportionately 77% of all empirical surveys of the field (or 1874 papers) have focused exclusively on Northern Hemisphere study systems.” This statement comes from a 2008 review by ‪Luciano Beheregaray on the state of phylogeography. His analysis clearly showed a bias towards studies in the Northern Hemisphere, indicating that more studies in the Southern Hemisphere are needed. I do not know whether this bias is still so pronounced, but there seems to be a clear increase in the number of phylogeographic papers on South American birds.

I have covered some of these studies on this blog, telling the evolutionary story of several species, such as the Buff-browed Foliage Gleaner (Syndactyla rufosuperciliata) and the Variable Antshrike (Thamnophilus caerulescens). Both species occur in the Atlantic Forest on the east coast of South America and the Andean region in the west. Interestingly, these regions are separated by the dry Chaco and the open vegetation of the Cerrado. Could it be that bird populations in the Atlantic Forest and the Andean region were connected in the past? And which route did the birds take from one region to the other? These questions provided the starting point for a recent study in the journal Molecular Phylogenetics and Evolution.

An overview of the different regions in South America. The Andes and the Atlantic Forest could have been connected through the Cerrado (path 1) in the north or the Chaco (path 2) in the South. From: Trujillo-Arias et al. (2020) Molecular Phylogenetics and Evolution.


Cerrado or Chaco?

Natalia Trujillo-Arias and her colleagues decided to focus on three species that occur in the Atlantic Forest and the Andes: the Ochre-faced Tody-flycatcher (Poecilotriccus plumbeiceps), the  Mottle-cheeked Tyrannulet (Phylloscartes ventralis) and the Golden-winged Cacique (Cacicus chrysopterus). Genetic analyses clearly differentiated between populations in the Atlantic Forest and the Andes, supporting the idea that both regions have been isolated for some time and probably acted as refugia during the Pleistocene.

To test whether these regions have been connected by gene flow, the researchers ran several demographic models (using Approximate Bayesian Computation, for the interested readers). The models with the highest statistical support pointed to a connection through the Cerrado. There was no evidence for gene flow through the Chaco, suggesting that this area forms a formidable barrier for small passerines due to its dry forests, savannahs and wide rivers (e.g., the Paraná-Paraguay river).

The three species in this study can be found in the Andes and in the Atlantic Forest. From: Trujillo-Arias et al. (2020) Molecular Phylogenetics and Evolution.


Morphology Lagging Behind

The clear genetic differences between the populations on both sides of the South American continents were not reflected in their morphology. The researchers noted that “A morphologic-genetic disagreement suggests that the phenotype of these species has been impacted by factors other than the demographic history of populations.” What other factors could have prevented the morphological traits from catching up with the genetic differentiation. In other words, why do birds from Andean and Atlantic Forest populations still look alike?

One possibility is neutral evolution: the phenotypes might have been changing by chance, which results in slower evolutionary change compared to strong natural or sexual selection. Alternatively, there might have been balancing selection that maintained certain morphological traits in both environments (also known as phenotypic conservatism). At the moment, the researchers could not discriminate between these possible explanations, opening the door for future research (check out this PNAS paper for more information on phenotypes in phylogeography). This is a common theme in science: answer one question (finding a Cerrado connection) and you are faced with a collection of new challenges (explaining morphological evolution).

A Golden-winged Cacique in Brazil © Dario Sanches | Wikimedia Commons



Trujillo-Arias, N., Rodríguez-Cajarville, M. J., Sari, E., Miyaki, C. Y., Santos, F. R., Witt, C. C., … & Cabanne, G. S. (2020). Evolution between forest macrorefugia is linked to discordance between genetic and morphological variation in Neotropical passerines. Molecular phylogenetics and evolution149, 106849.

Featured image: An Ochre-faced Tody-flycatcher in Brazil. © Dario Sanches | Wikimedia Commons