How the Fasciated Antshrike met the Bamboo Antshrike

An evolutionary journey across South America, culminating in secondary contact.

The Chinese philosopher Lao Tzu wrote that “the journey of a thousand miles begins with a single step.” This perspective can also be applied to the evolution of life on our planet. Countless species have spread across the globe – or particular parts of it – one step or one wingbeat at a time. Occasionally, these evolutionary journeys would culminate in the meeting of closely related populations that diverged thousands or millions of years ago. If reproductive isolation between these populations is still incomplete, hybridization and consequent introgression might occur. On this blog, I have mostly focused on the final part of this process: introgression and its consequences (see for example here and here). But it is definitely worthwhile to change perspectives and explore the evolutionary trajectories that different species followed before they established secondary contact. A recent study in the Biological Journal of the Linnean Society provides the ideal opportunity to do just that. Time to delve into the evolutionary story of two Antshrike species (genus Cymbilaimus)!

Spreading across South America

Let me start by introducing the main characters in our story: the Bamboo Antshrike (C. sanctaemariae) and the Fasciated Antshrike (C. lineatus). These two cryptic species have recently been split based on subtle morphological, vocal and ecological differences. For our ensuing journey across South America, however, it is not that relevant whether taxonomists classify them as species or subspecies.

Using molecular analyses and species distribution models, Leonardo Miranda and his colleagues reconstructed the evolutionary history of these two species. A good place to start the story of the Cymbilaimus Antshrikes is at the beginning. Between 1.85 and 0.6 million years ago, the Bamboo Antshrike and the Fasciated Antshrike went their separate ways. The ancestors of the Bamboo Antshrike probably followed their preferred habitat, which is – you guessed it – bamboo-dominated forests. This type of vegetation could be found in the lowlands of Amazonia during the Pleistocene, allowing the Bamboo Antshrikes to move into southern part of the Amazon region (blue and yellow regions in the figure below). The ancestors of the Fasciated Antshrike, on the other hand, resided in the northeastern part of South America and spread across the Guiana Shield (pink region) between 0.86 and 0.42 million years ago.

The evolutionary history of the Bamboo Antshrike and the Fasciated Antshrike. The colors on the phylogenetic tree indicate the inferred locations of the ancestral populations. The arrows on the right point to gene flow between several populations of both species. From: Miranda et al. (2021).

Secondary Contact

The story of the Fasciated Antshrike does not stop there. The researchers indicate that “our data also support a pattern of sequential dispersal episodes, almost simultaneous between 0.6 and 0.2 mya.” Similar to the Bamboo Antshrike following bamboo-dominated forests, the different populations of the Fasciated Antshrike probably tracked their favorite habitat across South America. These dispersal events established new populations in Central America and the southern section of the Amazon. In the latter region, the Fasciated Antshrike came into secondary contact with the Bamboo Antshrike which it had left behind more than one million years ago. Both species hybridized, resulting in the exchange of genetic material. The consequence of these introgression events remain to be elucidated. So, that is where our story ends (for now).

Classifying Cymbilaimus

Although the taxonomy of these Antshrikes has little impact on our evolutionary story, it is interesting to briefly explore the relevance of the genetic patterns for classifying these birds. Currently, there are two species of Cymbilaimus with three subspecies within the Fasciated Antshrike. Based on the molecular analyses in this study, the authors noted that “current subspecific limits with C. lineatus are inconsistent with its evolutionary history.” Indeed, the genetic results point to three main groups that correspond to:

1. The Bamboo Antshrike (C. sanctaemariae)
2. The Guinana group of the Fasciated Antshrike (C. lineatus, subspecies lineatus)
3. The remaining populations of the Fasciated Antshrike (C. lineatus, subspecies, intermedius and fasciatus)

The taxonomy of these birds might thus have to be updated. But that is a different story.

References

Miranda, L. S., Prestes, B. O., & Aleixo, A. (2021). Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary. Biological Journal of the Linnean Society, 132(2), 431-450.

Featured image: Fasciated Antshrike (Cymbilaimus lineatus) © Brian Gratwicke | Wikimedia Commons

Postzygotic isolation drives speciation in Warbling-antbirds

Several lines of evidence indicate strong selection against hybrids.

An interesting debate in avian speciation concerns the relative importance of prezygotic versus postzygotic isolation mechanisms. Prezygotic isolation mechanisms operate before the fertilization of the egg. They can be behavioral, for example when members from different species don’t see each other as potential mates because they look or sound too different. When such behavioral isolation is imperfect and copulation does occur, fertilization might still fail if sperm and egg are incompatible (see this review paper for more on these so-called postcopulatory prezygotic barriers). Postzygotic isolation mechanisms act after fertilization and can be either intrinsic or extrinsic. Intrinsic mechanisms lead to sterility or unviability of the offspring, while extrinsic mechanisms encompass lower fitness of the hybrid offspring due to ecological or behavioral issues. For example, some hybrid hummingbirds display aberrant courtship behavior and cannot attract a mate (see this blog post). But which of these mechanisms contributes most to reproductive isolation during the formation of new bird species?

In some cases, the prezygotic isolation mechanisms are crystal-clear (although they can still be incomplete). Think of the distinct plumage patterns of the Golden-winged (Vermivora chrysoptera) and Blue-winged Warbler (V. cyanoptera, you can read more on these species in this blog post). Or just listen to the drastically different songs of the Common Chiffchaff (Phylloscopus collybita) and the Willow Warbler (Phylloscopus trochilus). However, the situation becomes more complicated when you venture into the Amazonian rainforest. Here, some bird species show minor differences in morphology or song despite millions of years of evolution. The Rondonia Warbling-antbird (Hypocnemis ochrogyna) and the Spix’s Warbling-antbird (H. striata), for example, look and sound almost similar, but have been on separate evolutionary trajectories for more than one million years. What keeps these species distinct? Could it be postzygotic isolation mechanisms? A recent study in the journal Evolution tried to find out.

An overview of different prezygotic isolation mechanisms (from my PhD thesis)

Hybrid Triangles and Clines

Áurea Cronemberger and her colleagues took a genetic approach to study a hybrid zone between the two warbling-antbird species. They applied several methods to quantify the strength of selection against hybrids. First, they constructed “hybrid triangles” to determine the frequency of first-generation hybrids and backcrosses in the hybrid zone. These triangles combine information from a hybrid index (i.e. genetic ancestry of an individual) and heterozygosity to discriminate between different hybrid classes. In general, “pure” individuals are located in the lower corners, while first generation hybrids are at the top. The sides of the triangles indicate backcrosses. This analysis revealed six first-generation hybrids and a series of backcrossed individuals. One individual (in the center of the plot) looks like a second-generation hybrid (i.e. the offspring of two hybrids).

The presence of several backcrosses seems to suggest that there is no strong selection against hybrids. However, the production of backcrosses does not mean that the species are exchanging genetic material (i.e. introgression). It is possible that these backcrosses do not reproduce themselves due to genetic incompatibilities in their genomes. To check whether the production of backcrosses leads to introgression, the researchers turned to cline analyses. I have covered this approach in a previous blog post, but I will quickly recap the most important lessons here: “a steep cline suggests strong reproductive isolation between hybridizing species, while a wide cline points to weak isolation. And a displaced cline suggests gene flow from one species into the other.”

The researchers calculated the expected cline width under neutral conditions (no selection against hybrids), which amounted to 211 kilometers. The genetic analyses revealed that only one locus out of 5387 exceeded this threshold and 95% of the loci even showed cline widths less than 45 kilometers. In other words, a lot of steep clines. In addition, the researchers reported little variability in the geographic positions of the clines. The lack of displaced clines suggests that there is no introgression between the hybridizing species. In summary, the shape and position of the clines point to strong selection against hybrids and backcrosses.

The triangle plot shows several first-generation hybrids (on top) and backcrosses (on the diagonals). Cline analyses reveal steep clines that are not displaced from the center, suggesting strong selection against hybrids and no introgression. From: Cronemberger et al. (2020) Evolution.

More Species?

This study provides strong evidence for postzygotic isolation between the Rondonia Warbling-antbird and the Spix’s Warbling-antbird. Despite minor differences in morphology and vocalization, these birds can thus be considered distinct species. Similar results have been reported for other Amazonian birds, such as antbirds and woodcreepers (see this blog post), suggesting that postzygotic isolation mechanisms are the main driver of avian speciation in Amazonia. This finding might have important consequences for the species richness in this area. If postzygotic isolation evolves between morphologically cryptic species, how many species are still waiting to be discovered with genetic analyses. Indeed, the researchers conclude that “Our results thus suggest the strong possibility that species richness could be dramatically underestimated in Amazonia, especially for antbirds and other understory specialists.” Time for the next expedition!

References

Cronemberger, Á. A., Aleixo, A., Mikkelsen, E. K., & Weir, J. T. (2020). Postzygotic isolation drives genomic speciation between highly cryptic Hypocnemis antbirds from Amazonia. Evolution, 74(11), 2512-2525.

Featured image: Spix’s Warbling-antbird (Hypocnemis striata) © Hector Bottai | Wikimedia Commons

This paper has been added to the Thamnophilidae page.

Following the Forests: How the Variable Antshrike spread around the Amazon

Genetic analyses help to explain the peculiar circum-Amazonian distribution of this species.

In February 2020, I started a new position as lecturer at Wageningen University (the Netherlands). I was looking forward to interacting with students during a variety of ecology courses. Then the Corona-virus spread across Europe and I was forced to start teaching online. Although the switch to an online format was challenging, I tend to focus the bright side and reflect on all the new skills I learned during the past months. For example, I recently recorded two knowledge clips about the evolution of birds that you can watch on YouTube (on the origins of feathered flight and the diversity in beak morphology).

Today, I came across a TEDxtalk by Aaron Barth about the importance of story-telling in online education. He criticized the one-way style of teaching where an instructor gives a bullet-point-rich lecture and provides some reading material. Teaching (and by extension, science communication in general) should be interactive and can benefit from storytelling. That is also something I try to do on this blog – for instance, I announce new blog posts as “Avian Hybrids stories”. In this post, I will share the evolutionary story of the Variable Antshrike (Thamnophilus caerulescens), based on a recent study in the journal Molecular Phylogenetics and Evolution.

The Variable Antshrike © Dario Sanches | Wikimedia Commons

 

Around the Amazon

As the name suggests, the Variable Antshrike shows extensive plumage variation. Another interesting feature about this species is its peculiar distribution. Populations are namely wrapped around the Amazon – spanning the Atlantic Forest, Cerrado, Chaco, and the foothills of the Andes – culminating in a so-called circum-Amazonian distribution (see map below). This geographic arrangement does not fit neatly into the classical South American domains, such as Amazonia, the Atlantic Forest or the Llanos.

What processes led to this circum-Amazonian distribution? The evolutionary history of South American birds is thought to be shaped by two main processes: geological and climatic events that affected the spread of tropical forests and the birds living in them (the Forest Refugia Hypothesis) or the isolating effects of rivers (the Riverine Barrier Hypothesis). Do these hypotheses also apply to the Variable Antshrike?

The circum-Amazonian distribution of the Variable Antshrike. From: Bolívar-Leguizamón et al. (2020) Molecular Phylogenetics and Evolution

 

Three Groups

Sergio Bolívar-Leguizamón and his colleagues extracted DNA from 53 museum specimens, representing all known subspecies of the Variable Antshrike. Genetic analyses of one mitochondrial gene and the flanking regions of several ultraconserved elements (UCEs) uncovered three main geographical groups. If you are not familiar with the different South American regions, you can compare the colors on the phylogenetic tree below with the distribution map of the Variable Antshrike. But I will walk you through this circum-Amazonian trip.

The caerensis group contains individuals from the Atlantic Forest north of the river Rio São Francisco (in darkblue). The caerulescens group is composed of samples from southeastern Cerrado and central Atlantic Forest (in orange, green, and purple). Finally, the aspersiventer group spans the transition from the drier environments in the Chaco and southern Yungas in Argentina, Bolivia, and Paraguay (in red and grey) to the more humid forests in the northern Yungas and Central Andes in northern Bolivia and Peru (in pink and lightblue).

The phylogenetic tree of the Variable Antshrike, based on mtDNA. The colors correspond to different subspecies. From: Bolívar-Leguizamón et al. (2020) Molecular Phylogenetics and Evolution

 

Pleistocene Climate

To reconstruct the evolutionary history of these three main genetic clusters, the researchers ran several demographic models. The results from these analyses provided them with divergence times, patterns of gene flow and past population dynamics. It seems that the evolution of this passerine was mainly driven by the expansion and contraction of forest habitat, supporting the Forest Refugia Hypothesis. Putting all this information together, we can tell the story of the Variable Antshrike.

The results of our analyses suggest that the history of T. caerulescens began in the Late Miocene-Pliocene, with an initial widespread population distributed across the Cerrado, Atlantic Forests, the Chaco and the central Andes. During the Early – Middle Pleistocene (0.81–0.59 Ma), climatic fluctuations promoted expansions and contractions of forested habitats separating populations in the northern Atlantic Forest from those farther south. During the Middle Pleistocene (0.50–0.36 Ma), the continued effects of wet-dry cycles caused the contraction of populations in the southern Atlantic Forest and in the Chaco-Andes, but at the same time allowed sufficient opportunities to maintain gene flow via the onset of dry-forest corridors that connected these two regions.

Sounds like a wonderful, ornithological bedtime story.

 

References

Bolívar-Leguizamón, S. D., Silveira, L. F., Derryberry, E. P., Brumfield, R. T., & Bravo, G. A. (2020). Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients. Molecular Phylogenetics and Evolution, 148, 106810.

Feature image © Francesco Veronesi | Wikimedia Commons

 

This paper has been added to the Thamnophilidae page.

Figuring out the origin of two Fire-eye Antbird species in the Atlantic Forest

Genetic study uncovers a complicated series of events.

A common mistake in discussions is the “False Dilemma”, which states that if X is wrong than Y must be true. Creationists often apply this style of reasoning when attacking evolutionary theory. They claim that if evolution is wrong, then creationism must be true (which explains why they put so much effort in discrediting evolution). This statement is obviously not true: an inconsistency in the current evolutionary theory does not automatically support creationism.

But let’s not get caught up in this useless and silly debate, because there is a much more interesting discussion about the origin of bird species in the Atlantic Forest of South America. Two main hypotheses have been put forward to explain how new species arise in this region. The refuge hypothesis states that during the Pleistocene vast stretches humid forests were replaced with dry vegetation, creating isolated forest patches in which species diversified. The river-barrier hypothesis, however, focuses on the role of rivers as isolating barriers between populations. It seems that there are only two possibilities: refuges versus rivers. But a recent study in the journal Molecular Phylogenetics and Evolution revealed that this is a false dilemma. There is another option to consider.

A White-shouldered Fire-eye in Brazil © Dario Sanches | Wikimedia Commons

 

Refuges and Rivers

Using genetic data, Manuelita Sotelo-Muñoz and her colleagues reconstructed the evolutionary history of two Atlantic Forest species: the white-shouldered fire-eye (Pyriglena leucoptera) and the fringe-backed fire-eye (P. atra). The analyses revealed that these species diverged about 260,000 years ago, probably driven by habitat fragmentation. The species recently established secondary contact, resulting in the exchange of genetic material. Clearly, these fire-eyes were not isolated long enough for reproductive isolation to evolve. All in all, this scenario seems to support the refuge hypothesis. But wait, there is more…

Within the white-shouldered fire-eye, the researchers uncovered more fine-grained population structure. This species can be divided into three genetically distinct populations: a northern, central and southern lineage. Some of these populations come into contact around the major rivers in the Atlantic Forest. The northern and central population meet at the interfluvium of the de Contas and Pardo rivers, while the southern and the central population mix at the Doce and Grande rivers. These results support the river hypothesis, right? Well, not quite…

The distribution and genetic structure of the white-shouldered and the fringe-backed fire-eye in the Atlantic Forest. Notice the hybrid zones between the different populations (locations 25-27 and 37-44). From Sotelo-Muñoz et al. (2020) Molecular Phylogenetics and Evolution

 

Extinction and Dispersal

A detailed look at the genetic patterns points to a complicated scenario. After divergence from the fringe-backed fire-eye, individuals from the white-shouldered fire-eye spread southwards and diversified into several populations. At some point, the population north of the Pardo river went extinct. This gap was later filled when birds from the central population dispersed northwards. Similarly, the southern populations originated when birds from the central population dispersed southwards. Later on, these populations re-established contact at the rivers. These rivers probably limited dispersal, accentuating the genetic differences between the populations.

Based on this information, the authors argue that “our results support neither the river-barrier nor the refuge hypothesis as originally conceived. Here, dispersal as opposed to vicariance, seems to be the main cause of intraspecific differentiation.” As I mentioned in the beginning of this blog post, there is more to evolution in the Atlantic Forest than refuges and rivers. Don’t ignore dispersal.

 

References

Sotelo-Muñoz, M., Maldonado-Coelho, M., Svensson-Coelho, M., dos Santos, S. S., & Miyaki, C. Y. (2020). Vicariance, dispersal, extinction and hybridization underlie the evolutionary history of Atlantic forest fire-eye antbirds (Aves: Thamnophilidae). Molecular Phylogenetics and Evolution, 106820.

 

This paper has been added to the Thamnophilidae page.