The Pleistocene Arc Hypothesis explains the evolution of the Rufous-fronted Thornbird

Genetic patterns in this species follow the distribution of dry forests around Amazonia.

The evolution of South American birds is a complicated story, to put it mildly. Different species have been affected by different environmental barriers, such as the open vegetation corridor between the Andes and Amazonia or the myriad of rivers that crisscross the Amazon rainforest. And don’t forget about the climatic fluctuations during the Pleistocene (between 2.5 million and 11,000 years ago) which impacted vegetation patterns across South America, and consequently shaped the distribution patterns of the avifauna inhabiting certain vegetation types. For example, the evolutionary history of the Variable Antshrike (Thamnophilus caerulescens) was mainly driven by the expansion and contraction of forest habitat (see this blog post for the details). The evolution of this species follows the so-called “Rainforest Refugia Hypothesis”, which proposes that the fragmentation of the rainforests during cold and dry periods resulted in allopatric speciation by separating birds into distinct rainforest “refugia” surrounded by open habitat.

The “Rainforest Refugia Hypothesis” mainly focuses on birds in the wet rainforest, but what about species that inhabit dry forests? Their evolution might adhere to a related scenario: the “Pleistocene Arc Hypothesis” which states that dry periods might have promoted the expansion of dry forests, culminating in a continuous arc around the southern half of Amazonia from Peru to Brazil. A recent study in the journal Molecular Ecology tested this hypothesis for the Rufous-fronted Thornbird (Phacellodomus rufifrons), a common dry forest bird species.

Past Connections

Eamon Corbett and his colleagues collected samples across the range of the Rufous-fronted Thornbird, which has been divided into several subspecies that follow the distribution of dry forests around Amazonia (see figure below). Genetic analyses of the different populations uncovered patterns that are in line with the “Pleistocene Arc Hypothesis”. Specifically, the researchers found evidence that certain populations in currently distinct patches of dry forest were connected in the recent past.

For example, even though the subspecies peruvianus and sincipitalis are separated by more than 1000 kilometers of lush rainforest, they share genetic variants and show signatures of recent divergence. The authors write that “the most likely scenario is that peruvianus and sincipitalis were connected through formerly suitable habitat in central and southern Peru in the recent past, and that the large modern-day disjunction between them is a recent phenomenon.” Similarly, the subspecies sincipitalis and rufifrons are currently isolated by 500 kilometers of unsuitable Cerrado habitat, but they nonetheless show low genetic differentiation. Interestingly, the genetic splits between the different subspecies did not occur in the same time period, suggesting that particular patches of dry forest along the Pleistocene Arc became isolated at different times.

Range and sampling localities of the Rufous-fronted Thornbird, showing a highly disjunct distribution that corresponds to the extent of the dry forest biome. From: Corbett et al. (2020) Molecular Ecology.

Putative Hybrid Zone

Apart from the recent divergence between geographically isolated subspecies, the authors uncovered the opposite pattern between two neighboring subspecies (rufifrons and specularis). Although these subspecies have overlapping distributions in eastern Brazil, the genetic analyses pointed to a relatively deep divergence compared to the other subspecies. The exact geographic barriers responsible for this genetic divergence remain to be determined. The São Francisco River seems like an unlikely candidate because several rufifrons individuals were found on the other side of the river (where specularis resides) when following it inland. Perhaps the ecological transition between the dry Caatinga and wet Cerrado habitats can explain this genetic pattern?

Moreover, despite the deep genetic divergence between rufifrons and specularis, the researchers reported evidence for recent gene flow. There might thus be a hybrid zone between these subspecies in Brazil. The authors nicely set the stage for future research: “Detailed vocal, morphological, and genetic data at a fine geographic scale will be needed to illuminate the evolutionary dynamics at work in this putative contact zone.” As I wrote at the beginning of this blog post: the evolution of South American birds is a complicated story, to put it mildly.


Corbett, E. C., Bravo, G. A., Schunck, F., Naka, L. N., Silveira, L. F., & Edwards, S. V. (2020). Evidence for the Pleistocene Arc Hypothesis from genome‐wide SNPs in a Neotropical dry forest specialist, the Rufous‐fronted Thornbird (Furnariidae: Phacellodomus rufifrons). Molecular Ecology29(22), 4457-4472.

Featured image: Rufous-fronted Thornbird (Phacellodomus rufifrons) © Hector Bottai | Wikimedia Commons

This paper has been added to the Furnariidae page.

More than meets the eye: How many species does the bird genus Dendrocolaptes contain?

Genetic analyses point to fifteen distinct lineages, but are they all separate species?

Morphology is not always helpful to resolve evolutionary relationships, especially when different lineages independently develop similar traits (i.e. convergent evolution). Take, for example, the Neotropical bird genus Dendrocolaptes: a morphological analysis of these brownish birds resulted in mixed clusters containing representatives from other genera, such as Xiphocolaptes and Hylexetastes. The most likely explanation is that species in these distinct genera convergently evolved similar plumage patterns (in this case, a “streaked” phenotype). One solution to clean up this morphological mess is to turn to genetic analyses. A recent study in the Journal of Zoological Systematics and Evolutionary Research did just that.

Genetic Analyses

Using 43 specimens from all five recognized species in the genus, Antonita Santana and her colleagues reconstructed the phylogeny of these birds and performed a species delimitation analysis (using the software BP&P). These analyses revealed two main phylogenetic groups that correspond to the certhia and picumnus species complexes. Interestingly, these genetic groups mirror the morphological split into “barred” and “streaked” phenotypes. Past studies could not confidently place Hoffmanns woodcreeper (D. hoffmannsi) in one of these groups because of its intermediate plumage patterns. The genetic analyses show that it belongs to the “streaked” picumnus group.

The species delimitation exercise pointed to 15 lineages. However, this does not mean that there are 15 distinct species. These analyses are based on the multispecies coalescent model which captures genetic population structure. Whether these 15 lineages represent actual species remains to be determined with other data sources, such as morphology, song and ecology. As Jeet Sukumaran and Lacey Knowles warn in their PNAS paper: “Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.”

Based on their current knowledge, the authors suggest four species in the picnumnus group (D. hoffmannsi, D. picumnus, D. platyrostris, and D. transfasciatus) and seven species in the certhia group (D. certhia, D. concolor, D. juruanus, D. medius, D. radiolatus, D. retentus, and D. ridgwayi). The remaining lineages require further investigation.

A map with sampling locations and a resolved phylogeny with 15 lineages. Are they also distinct species? From: Santana et al. (2020) Journal of Zoological Systematics and Evolutionary Research.

Integrative Taxonomy

This study nicely illustrates the importance of combining data from multiple sources to solve taxonomic issues. There is no “silver bullet” for decisions on species boundaries. Genetic analyses can reveal independently evolving lineages and indicate whether these lineages are still exchanging DNA. But other analyses are needed to quantify the level of reproductive isolation and determine if the proposed species can be diagnosed based on morphology or behavior. In some cases, however, taxonomists will uncover conflicts between different data sources, which can be explained by the gradual process of speciation (you cannot easily pigeonhole a continuum), convergent evolution or other processes. Here, a thorough understanding of the evolutionary history of the study species is crucial. This perspective was recently highlighted by Carlos Daniel Cadena and Felipe Zapata who argued that “studies using phenotypic data and methods properly grounded on evolutionary theory offer unique insight to delimit species because they shed light on the role of selection in generating and maintaining biodiversity.” I definitely agree.


Santana, A., Silva, S. M., Batista, R., Sampaio, I., & Aleixo, A. (2021). Molecular systematics, species limits, and diversification of the genus Dendrocolaptes (Aves: Furnariidae): Insights on biotic exchanges between dry and humid forest types in the Neotropics. Journal of Zoological Systematics and Evolutionary Research59(1), 277-293.

Featured image: Amazonian Barred Woodcreeper (Dendrocolaptes certhia) © Kent Nickell | Wikimedia Commons