The evolution of mechanical sounds in Doraditos

Tracing the evolutionary history of modified feathers and aerial displays.

The evolution of bird song has received a lot of attention (see for example this blog post), but some birds produce sounds in drastically different ways. Some Doradito species of genus Pseudocolopteryx, for example, generate mechanical wing sounds due to structural modifications on their feathers. Modified primary feathers have been described in three species: the Crested Doradito (P. sclateri), the Subtropical Doradito (P. acutipennis), and the Dinelli’s Doradito (P. dinelliana). The remaining two species in this genus – the Warbling Doradito (P. flaviventris) and the Ticking Doradito (P. citreola) – lack this feature. In addition, males in all species with modified feathers also perform aerial displays, indicating that these traits probably coevolved. As an evolutionary biologist, I cannot help but ponder how these feather modifications and aerial displays originated. Did they arise once or did each species independently alter its feathers? To answer this question, we need a solid phylogenetic framework. Once we know how these five species are related to each other, we can explore the evolutionary history of particular traits. A recent study in the journal Zoological Scripta provided the first steps in our quest to understand the evolution of mechanical sounds in these songbirds.

Phylogenetic Analyses

Emilio Jordan and his colleagues obtained genetic data for 37 individuals, representing all five species. Analyses of two mitochondrial (COI and ND2) and two nuclear (MYO and OCD) markers recovered a clear phylogeny in which the “non-mechanical species” are embedded within the three species that produce mechanical sounds with their modified feathers. This phylogenetic arrangement suggests that modified primary feathers (and the aerial displays) evolved in the common ancestor of all Doraditos and were consequently lost in the Warbling Doradito and the Ticking Doradito.

A phylogenetic tree showing the relationships between the five Doradito species and the putative evolutionary history of the modified feathers and aerial displays. From: Jordan et al. (2021).

It’s Complicated

When we take a closer look at the modified feathers, however, the situation becomes less clear. Although three species produce mechanical sounds with their feathers, the structural modifications to their plumage are quite different. In the Crested Doradito and the Dinelli’s Doradito, the sixth and seventh primary feather are miniaturized, whereas the Subtropical Doradito has modifications on the third to seventh primary feathers. It is thus possible that these modified feathers have distinct evolutionary origins. In addition, the evolutionary history of the four molecular markers might not correspond to the evolutionary trajectory of the trait. Certain traits do not follow the species tree due to incomplete lineage sorting (as shown in marsupials) or introgressive hybridization. It might thus be necessary to unravel the genetic basis of the modified feathers and estimate phylogenetic trees for the underlying genes. Will they follow the species tree or not? In the end, the evolution of this trait might be more complicated than we expected.

References

Jordan, E. A., Tello, J. G., Benitez Saldivar, M. J., & Areta, J. I. (2021). Molecular phylogenetics of Doraditos (Aves, Pseudocolopteryx): Evolution of cryptic species, vocal and mechanical sounds. Zoologica Scripta, 50(2), 173-192.

Featured image: Warbling Doradito (Pseudocolopteryx flaviventris) © Dominic Sherony | Wikimedia Commons

Studying Willow and Alder Flycatcher at different stages in the speciation process

Researchers follow the evolution of reproductive isolation in two contact zones.

When two species start hybridizing after a period of geographic isolation several scenarios are possible. Barriers of reproductive isolation might break down and the species collapse into one panmictic population. Or new interactions between the hybridizing species might push reproductive isolation towards completion. In most cases, we can only guess what happened in the past by studying present-day patterns of genetic variation. In my own work, for example, I reconstructed the evolutionary history of two Bean Goose species that established secondary contact about 60,000 years ago. It seems that these geese are in the merging into one species, but it is tricky to draw conclusions on a process that could take thousands to millions of years. Sometimes, however, we come across a situation where we can directly study different stages of speciation process. In a recent study in the journal Molecular Ecology, researchers could compare different contact zones between two Empidonax flycatchers to understand how reproductive isolation evolves between these species.

Contact Zones

Willow Flycatcher (E. traillii) and Alder Flycatcher (E. alnorum) interbreed across two contact zones in North America: a broad overlapping area in the east (more than 1000 kilometers) and a narrow one (less than 200 kilometers) in the west. Jordan Bemmels, Ashley Bramwell and their colleagues used whole genome data to investigate patterns of introgression at these contact zones. In the western zone, there was clear evidence for introgression (2.4-8.2%), while no admixture was detected in the eastern zone. These patterns indicate that reproductive isolation is strong in the east and still incomplete in the west. Additional analyses revealed that the western contact zone is of recent origin, whereas the formation of the eastern contact zone can be traced back to the last glacial maximum. Birds in the east have thus had more time to build-up reproductive isolation.

Genomic analyses uncovered different levels of introgression in the western and eastern contact zones between Willow Flycatcher and Alder Flycatcher. From: Bemmels et al. (2021) Molecular Ecology.

Testing Traits

The traits underlying reproductive isolation between these flycatchers remain to be determined. These traits can often be identified by looking for signatures of divergent character displacement. For instance, selection for reduced competition could result in differences in habitat use or beak morphology when species adapt to distinct food sources. Selection can also directly contribute to reproductive isolation. If hybridization is maladaptive, traits involved in species recognition will evolve along different trajectories to prevent birds from hybridizing. The researchers tested several traits, such as beak morphology and the colors of crown feathers, but found no clear evidence for character displacement. Moreover, the species did not appear to differ in habitat use or timing of breeding.

However, there are still plenty of other traits that can be tested, such as differences in song or sperm morphology (see this blog post). The researchers also mentioned that “the genomes of the two species are well differentiated, with numerous Fst peaks that occur on almost every chromosome.” These peaks in genetic differentiation could contain some interesting candidate genes that might point to the traits underlying reproductive isolation between Willow Flycatcher and Alder Flycatcher.

Clear genetic differentiation across the genome of the flycatcher species. Some of these peaks might contain candidate genes involved in reproductive isolation. From: Bemmels et al. (2021) Molecular Ecology.

References

Bemmels, J. B., Bramwell, A. C., Anderson, S. A., Luzuriaga‐Aveiga, V. E., Mikkelsen, E. K., & Weir, J. T. (2021). Geographic contact drives increased reproductive isolation in two cryptic Empidonax flycatchers. Molecular Ecology, 30(19), 4833-4844.

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

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.

References

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 Biology, 51(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.

References

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 Evolution, 153, 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

 

References

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 evolution, 149, 106849.

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