A genomic perspective on the classic hybrid zone between Baltimore and Bullock’s Oriole

How much has this hybrid zone changed over the past decades?

In the introductory chapter of my PhD thesis, I used a quote by John Michael Crichton (who wrote Jurassic Park): “If you don’t know history, you don’t know anything. You are a leaf that doesn’t know it is part of a tree.” This quote can be interpreted in two ways. On the one hand, it refers to the importance of reconstructing the evolutionary history of a species to understand present-day patterns. This idea was nicely captured by Theodosius Dobzhansky (Dobby for the friends): “Nothing in biology makes sense, except in the light of evolution.” On the other hand, the quote by John Michael Crichton can also refer to the importance of the history of science. Ideas do not pop into existence in a vacuum. They are the outcome of countless hours of observations, experiments and thinking by numerous scientists. Diving into the scientific literature and reading “old” papers can lead to new insights and can help you to understand complex concepts.

With regard to hybridization in birds, for example, there is a long history of hybrid zone studies. During my PhD, I read classic papers on avian hybrid zones by Jürgen Haffer (in South America), Julian Ford (in Australia) and Charles Sibley (in North America). Several of these hybrid zones have been revisited with modern genomic techniques. Recently, Jennifer Walsh, Shawn Billerman and their colleagues provided a genomic perspective on the hybrid zone between Baltimore oriole (Icterus galbula) and Bullock’s oriole (I. bullockii) in North America.

Oddly Plumaged Orioles

The Baltimore and Bullock’s orioles hybridize along the riparian corridors that cut through the Great Plains of North America. The scientific history of this hybrid zone goes back to Sutton (1938) who described hybrid specimens as “oddly plumaged” orioles. In the 1960s and 1970s, Charles Sibley and James Rising (among others) published several studies on the interactions between these orioles, providing a detailed overview of the hybrid zone structure.

The application of genomic data can refute hypotheses based on morphological inferences (see for example this blog post about Brewster’s and Lawrence’s Warbler). In the oriole case, however, the researchers found that “classically scored plumage traits are an accurate predictor of pure vs. hybrid genotypes.” This allowed them to compare past and present hybrid zone dynamics. What has changed since the first description of this hybrid zone?

The distribution of Baltimore Orioles (orange) and Bullock’s Orioles (yellow) across North America. From: Walsh et al. (2020) The Auk.

To the West

The new analyses supported previous studies suggesting that the center of the hybrid zone has moved to the west. The exact mechanism behind this westward shift remains unclear, but could be related to the expansion of suitable woodland habitat. Alternatively, climatic changes might allow Baltimore orioles to expand their range westwards. Regardless of the underlying mechanism, the westward spread is also apparent in the genomic patterns. When hybrid zones move, selectively neutral genes are expected to flow from the receding species (Bullock’s oriole) into the advancing species (Baltimore oriole). This theoretical mechanism can result in a “tail of introgression” that lags behind the moving hybrid zone. And that is exactly what we observe in the oriole case.

In addition to the westward movement, the hybrid zone has also become narrower over time. The width of a hybrid zone is an indication for the strength of selection against hybrids. If there is weak selection, hybrids will frequently backcross with parental species, resulting in a geographically widespread sharing of genetic material. However, if there is strong selection against hybrids, they will not be able to backcross with parental species and the genetic admixture will be concentrated in the center of the hybrid zone. Hence, the narrowing of the oriole hybrid zone suggests that reproductive isolation between Baltimore and Bullock’s oriole has strengthened.

Geographic cline analyses revealed that the hybrid zone has moved westwards and became narrower. From: Walsh et al. (2020) The Auk.

Species Concepts

The study of Baltimore and Bullock’s oriole hybrids was also relevant for their species status. In the 1960s, Charles Sibley argued that hybridization was extensive and that there was little evidence for selection against hybrids. Based on this information, the American Ornithologists’ Union decided to lump both taxa in the “Northern Oriole”. The refinement of Biological Species Concept (taking into account hybrid fitness) and additional information from genetic studies has provided a new perspective on the species status of these orioles. The authors concluded that “Our interpretation of these patterns is that Baltimore and Bullock’s orioles are best considered distinct species, with strong selection likely acting to restrict the expansion of the hybrid zone, which is in turn evidence of substantial post-zygotic reproductive isolation despite widespread admixture within the hybrid zone.”

References

Walsh, J., Billerman, S. M., Rohwer, V. G., Butcher, B. G., & Lovette, I. J. (2020). Genomic and plumage variation across the controversial Baltimore and Bullock’s oriole hybrid zone. The Auk137(4), ukaa044.

Featured image from Sutton (1938).

This paper has been added to the Icteridae page.

Isolated Icterids: Unraveling the evolutionary history of the Altamira Oriole

What processes explain the genetic and morphological variation in this neotropical species?

Speciation involves the build-up of genetic differences between populations in isolation. But this “isolation” can take many forms. Populations might be separated over large distances, preventing the exchange of genetic material (isolation by distance). Or populations might become isolated by historical processes that affect topographic features, such as rivers and mountain ranges (isolation by history). Or populations might adapt to different environmental conditions in a heterogenous landscape, lowering the chances of interbreeding (isolation by environment). These types of isolation are not mutually exclusive and can interact. Not an easy knot to disentangle. A recent study in the journal Molecular Ecology, however, rose up to the challenge and attempted to figure out what isolating factors can explain the evolution of the Altamira oriole (Icterus gularis).

 

Genetic Patterns

The Altamira oriole is a brightly colored songbird from Central America. Taxonomists recognize three subspecies based on body size: the large gularis, the small mentalis, and the intermediate flavescens. Lucas Moreira and his colleagues studied populations from all subspecies, using molecular and morphological methods.

The genetic analyses revealed two distinct clusters, divided by the Chivela Pass, a narrow mountain gap separating three mountain chains in southern Mexico. The split between these populations occurred about 150,000 years ago, but the populations remained connected by occasional gene flow. It seems that the Chivela Pass functioned as a kind of funnel that limited dispersal between the northern and southern populations. Within both populations, the researchers detected signatures of isolation by distance, but no effect of environmental factors. Hence, the genetic data point to isolation by history and isolation by distance.

The genetic data suggested two main cluster (one in blue and one in red/green) separated by the Chivela Pass. From: Moreira et al. (2020) Molecular Ecology.

 

Morphological Measurements

The morphological data tell a completely different story. Measurements of wing, bill and tarsus length indicated two main groups, representing small and large individuals. These differences in body size were best explained by climatic variables, such as precipitation and temperature. In general, Altamira orioles are larger in hotter and drier areas. Whether these morphological differences have a genetic basis or are due to phenotypic plasticity remains to be determined. Nonetheless, morphological variation can best be explained by isolation by environment.

Morphological variation (here: wing length) correlates with environmental factors, such as (a) temperature and (b) precipitation. From: Moreira et al. (2020) Molecular Ecology.

 

Discrepancy Explained

The fact that genetic and morphological patterns are driven by different isolation mechanisms makes sense from a genomic point of view. Isolation by history and isolation by distance tend to affect the entire genome, and it is thus easier to pick up these patterns with molecular markers that cover the whole genome (RADseq in this study). The morphological differences are often the outcome of natural selection, which tends to target small genomic regions and is thus more difficult to detect without whole genome data. A genomic study of the Altamira oriole might thus uncover some contribution of isolation by history to the morphological differences.

In addition, the different processes underlying genetic and morphological variation also explain the disagreement in taxonomic studies where genetically focused ornithologists clash with morphologically minded ones. This study again highlights that it is more insightful to understand the evolutionary and ecological processes behind speciation instead of having endless discussions about species status based on every small genetic difference or morphological detail.

 

References

Moreira, L. R., Hernandez_Ba_os, B. E., & Smith, B. T. (2020). Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis). Molecular Ecology, 29(16), 3084-3101.

Featured image: Altamira Oriole (Icterus gularis) © Kati Fleming | Wikimedia Commons

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 evolution149, 106849.

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