Where did all these penguins come from?

Genomic analyses unravel the evolutionary history of these flightless diving birds.

The evolution of penguins (order Sphenisciformes) remains a mystery. Different genetic studies disagree about the evolutionary relationships between particular species, the timing of speciation events and the original distribution of these iconic seabirds. The divergence time of the crown group (all living representatives of the penguins) ranges from 9.9 million years ago (during the Miocene) to 47.6 million years ago (during the Eocene). And the exact area of origin is also a matter of debate: some ornithologists suggest Antarctica with a subsequent expansion into warmer waters, while others point to Australia or New Zealand followed by colonization of the colder Antarctica. One way to settle these debates is to bring out the big guns: genomic data. A recent study in the journal PNAS applied this strategy and analyzed 22 genomes, representing 18 penguin species. Time to find out what they discovered about the evolution of penguins – a word that Benedict Cumberbatch has some difficulty pronouncing (see video below).

From Australia to Antarctica?

Let’s start with the most likely area of origin for penguins. The authors reconstructed the ancestral distributions of the sampled species and identified the coastlines of Australia, New Zealand, and nearby islands as the original range of the ancestor of extant penguins. From there, these birds colonized Antarctica and South America where they diversified into several species. The genomic analyses provide estimates for the timing of these events.

The first branching event led to the establishment of the genus Aptenodytes in the Antarctic, and reconstructions of the ancestral Pygoscelis species indicate that they colonized the Antarctic Peninsula soon after Aptenodytes, pointing to a long history of Antarctic occupation. In the mid-Miocene, the lineage leading to the Spheniscus/Eudyptula ancestor colonized the South American coast, with members of the genera Eudyptes, Eudyptula, Megadyptes, and Spheniscus progressively diversifying and colonizing warmer at-sea environments.

During the cooling event at the transition of the Pliocene and Pleistocene (about 2.5 million years ago), ice shelves expanded across the Southern Ocean, probably reducing connectivity between several penguin populations. This culminated in more speciation events within the genera Pygoscelis, Spheniscus, Eudyptes and Aptenodytes. The figure below provides a nice overview of all these events.

The evolutionary history of penguins based on genomic data. Reconstruction of ancestral distributions (the colored letters on the nodes in the tree) suggest that the ancestor of modern penguins lived in Australia and New Zealand. From: Vianna et al. (2020) PNAS.

Genes Going with the Flow

The phylogenetic tree from the genomic analyses largely agreed with another recent study based on complete mitochondrial genomes (which I also covered on this blog). A few differences between these studies can be explained by hybridization between several penguin species. The researchers write that “some of the main episodes of genomic introgression were detected among erect-crested and the ancestral rockhopper penguin species (17 to 23%), erect-crested and macaroni/royal penguins (25%), and the Galápagos/Humboldt ancestor and Magellanic penguins (11%).” Interestingly, the direction of introgression in some of these species followed the clockwise flow of the Antarctic Circumpolar Current, the ocean current that circles around Antarctica. Individual penguins might have drifted off during foraging trips and were transported to nearby populations where they interbred with another resident species. Quite literally, gene flow.

This study nicely illustrates the power of genomic analyses. There is an enormous treasure of information hidden in the seemingly meaningless strings of A, T, G and C. With clever methods and careful analyses we are now able to find meaning in these DNA sequences and reconstruct the wonderful evolutionary history of life on our planet.

Patterns of introgression between different penguins species and their ancestors. From: Vianna et al. (2020) PNAS.

References

Vianna, J. et al. (2020). Genome-wide analyses reveal drivers of penguin diversification. Proceedings of the National Academy of Sciences, 117(36), 22303-22310.

Featured image: King Penguins (Aptenodytes patagonicus) © Ben Tubby | Wikimedia Commons

This paper has been added to the Sphenisciformes page.

The role of neutral mutations in adaptive evolution

Although these mutations have no direct effects on fitness, they can have far-reaching consequences.

Genetic mutations are often classified into three main categories: deleterious, advantageous and neutral. Highly deleterious mutations are swiftly eliminated from the gene pool by natural selection, while advantageous ones can quickly spread through the population. And the neutral mutations? They just fluctuate in frequency due to chance processes, such as genetic drift. This simplistic view of molecular evolution suggests that neutral mutations do not play a major role in the adaptive evolution of organisms. A recent paper in the journal Current Biology challenged this perspective: neutral mutations do contribute to adaptive evolution.

The Adaptive Landscape

Evolution can be depicted as the exploration of an adaptive landscape. Hills and mountains represent genetic combinations of high fitness (so-called adaptive peaks), while valleys correspond to regions of low fitness. Advantageous genetic variants – either from standing genetic variation or from de novo mutations – can push populations up new adaptive peaks. At first sight, neutral mutations seem unimportant. They only allow populations to wander around a fitness-plateau without any adaptive benefits. However, aimlessly strolling through a landscape can lead to unexpected discoveries. Indeed, an important contribution of neutral mutations is that they allow populations to explore the adaptive landscape. Some mutations might bring populations to base of new adaptive peaks, where advantageous mutations can take over.

A visualization of the adaptive landscape. The blue color indicates a low fitness value, while the red regions correspond to adaptive peaks. © Rhiever&action | Wikimedia Commons

Volatile Codon

This process is nicely illustrated by the effect of neutral mutations on protein evolution. As you probably remember from high school biology, proteins are strings of amino acids. Each amino acid is coded for by particular three-letter-combinations in the DNA (i.e. codons). For example, the codon GGC corresponds to glycine, while AGC represents arginine. This genetic code is redundant and some amino acids have multiple codons. Glycine, for instance, is not only linked with GGC, but also with GGT, GGA and GGG. Neutral mutations in these codons do not change the amino acid in the protein. To stick with the examples above: a mutation from GGC to GGT will still result in the addition of a glycine during protein synthesis. Such neutral mutations – also known as synonymous mutations – do not directly contribute to adaptive evolution. But they do allow proteins to explore the adaptive landscape.

The codons CGG and AGG correspond to the amino acid arginine. The first codon (CGG) is one mutational step away from five other amino acids (glycine, tryptophan, glutamine, leucine, and proline) while a mutation in the second codon (AGG) gives access to another set of amino acids (glycine, tryptophan, lysine, threonine, methionine, and serine). So, a neutral mutation from CGG to AGG opens up a new section of the adaptive landscape to explore.

Neutral mutations in codons (i.e. synonymous mutations) can give access to new sets of amino acids for consequent mutations. Here, a change from CGG to AGG (both coding for glycine) leads to a change in amino acids that are one mutational step away. From: Tenaillon & Matic (2020) Current Biology.

Mutation and Recombination

Apart from exploring unchartered territory on the adaptive landscape, neutral mutations can also affect genomic processes, such as mutation and recombination rates. Experimental evolution with bacterial strains showed that the probability of a mutation occurring is partly determined by the surrounding DNA-letters. For example, mutations affecting a G in a CGT sequence were found to be about 10 times more likely than mutations affecting G in an AGT sequence. Neutral mutations that change the genomic context can thus result in higher mutation rates, potentially speeding up adaptive evolution.

Finally, neutral mutations might also influence local recombination rates. Homologous recombination produces new combinations of DNA sequences during meiosis by swapping genomic sections between chromosome pairs. Certain enzymes, such as DNA recombinases, initiate this process at particular combination of DNA-letters (i.e. motifs). Neutral mutations can slightly change such motifs across the genome, which might result in recombination between non-identical DNA sequences. This situation leads to issues for the recombination machinery and can give rise to changes in genome structure, such as inversions or duplications.

Local reductions in recombination rate can also contribute to speciation. The authors write that “the accumulation of neutral diversity may be enough to create long-lasting barriers to genetic exchange and the further accumulation of genetic diversity.” Do not underestimate the power of neutral mutations!

References

Tenaillon, O., & Matic, I. (2020). The Impact of Neutral Mutations on Genome Evolvability. Current Biology, 30(10), R527-R534.

Featured image: A point mutation © Jing.fm

Did sexual selection drive the evolution of Gallopheasants?

The variety of extravagant plumage patterns certainly suggests a pivotal role for sexual selection.

“The sight of a feather in a peacock’s tail, whenever I gaze at it, makes me sick,” Charles Darwin wrote. He was trying to figure out why natural selection would produce such an elaborate and seemingly useless extravagance. Surely, the colorful tail of a peacock would lower its chances of survival. Pondering this conundrum led Darwin to develop his theory of sexual selection, in which males compete for access to females. Male peacocks use their beautiful plumage patterns to attract potential mates and show off their “good genes”. A bird that can produce such extravagant feathers while fending off parasites and predators should definitely become the father of your offspring.

Peacock is actually a common name that refers to several species in the genera Pavo and Afropavo, which have been classified in the family Phasianidae (the gallopheasants). A quick glance at other members of this bird family reveals an additional wealth of colorful feathers in species such as Bulwer’s Pheasant (Lophura bulweri) or Golden Pheasant (Chrysolophus pictus). It is not surprising that several ornithologists have argued that sexual selection has been the driving force behind the diversification of this bird group. A recent study in the journal Zoologica Scripta put this idea to the test.

Problematic Phylogeny

Before we can infer the evolutionary importance of sexual selection, we need a proper phylogeny. However, previous molecular studies of the gallopheasants could not confidently resolve the evolutionary relationships between and within genera. This rampant phylogenetic conflict was attributed to the rapid succession of several speciation events. In this study, Peter Hosner and his colleagues used ultraconserved elements, nuclear introns and mitochondrial DNA sequences to unravel this phylogenetic knot. Their analyses resulted in a well-resolved evolutionary tree with few conflicting branches (see figure below). The issues in previous analyses were probably due to a limited number of genetic loci. Sometimes just adding more data can work.

Next, the researchers determined the strength of sexual selection by quantifying the degree of sexual dimorphism in different species. Sexual dimorphism refers the differences in appearance between males and females of the same species. Larger differences, such as more colorful males, suggest stronger sexual selection. If the evolution of gallopheasants was driven by sexual selection, then the gain of sexual dimorphism on certain branches should have resulted in accelerated diversification.

Evolutionary tree of gallopheasants based on ultraconserved elements, nuclear introns and mitochondrial DNA sequences. From Hosner et al. (2020) Zoologica Scripta.

Other Factors

In contrast to the expectations, there was no clear phylogenetic signal that the strength of sexual selection accelerated the speed of evolution. Moreover, other factors, such as female morphology and ecological differences, also contributed to the diversification patterns across the phylogeny. For example, divergence in environmental niche can explain the evolution of Golden Pheasant (Chrysolophus pictus) and Lady Amherst’s Pheasant (C. amherstiae). The authors concluded that their findings add “to the growing body of literature suggesting that multiple factors work in concert and that focusing on sexual selection alone as a driver of diversification may lead to erroneously narrow conclusions.”

Indeed, although sexual selection has played an important role in certain gallopheasant species (as exemplified by their extravagant plumage), we should not automatically discard other processes. Evolution involves the complex interplay of numerous selective pressures, spiced up with some chance events.

References

Hosner, P. A., Owens, H. L., Braun, E. L., & Kimball, R. T. (2020). Phylogeny and diversification of the gallopheasants (Aves: Galliformes): Testing roles of sexual selection and environmental niche divergence. Zoologica Scripta, 49(5), 549-562.

Featured image: Golden Pheasant (Chrysolophus pictus) © Eric Kilby | Wikimedia Commons

With or without gene flow? Studying speciation in the Grey-headed Bullfinch species complex

Has there been past gene flow between populations on the Asian mainland and Taiwan?

In 2008, Albert Phillimore and his colleagues concluded that “allopatric speciation is the dominant geographic mode of speciation in birds.” Allopatric speciation refers to the situation where two populations become geographically isolated and genetically diverge, ultimately giving rise to new species. In recent years, however, the focus of speciation research has shifted from a purely geographical perspective (e.g., allopatry, parapatry and sympatry) to the consideration of gene flow. Geographical isolation is still an important component of speciation, but diverging populations often continue to exchange genes during the process. The high incidence of divergence-with-gene-flow examples has led to the idea that this might be the dominant mode of speciation in birds.

Land Bridges

The presence of some gene flow during speciation appears to have become the null hypothesis that many ornithologists start from. For instance, a recent study in the journal Molecular Phylogenetics and Evolution reconstructed the evolutionary history of Grey-headed Bullfinch (Pyrrhula erythaca) species complex. Different populations can be found on the Asian mainland (subspecies erythaca and erythrocephala) and on the island Taiwan (subspecies owstoni). During the Pleistocene ice ages, land bridges connected Taiwan with the mainland, potentially allowing gene flow between these populations. We can thus expect to find some signatures of past gene flow between the Grey-headed Bullfinch populations.

However, genetic analyses clearly separated the mainland and island populations. This separation does not completely rule out past gene flow, so the researchers performed coalescent modelling to test different speciation scenarios. This exercise pointed to a strictly allopatric speciation model. It seems that there has been no gene flow between the Asian mainland and Taiwan.

Sampling locations of the different populations in the Grey-headed Bullfinch species complex. Genetic analyses revealed a clear separation between island and mainland populations. From: Dong et al. (2020) Molecular Phylogenetics and Evolution.

Sky Islands

Why did these populations not exchange DNA despite the land bridges between Taiwan and the Asian mainland? The answer lies in their habitat preferences. Reconstructing the past distributions of these populations revealed that they never overlapped. The mainland populations resided in the mountainous areas and could not expand their ranges to the lowlands. Birds in these “sky islands” were thus isolated from lowland populations, such as the birds expanding from Taiwan. The researchers conclude that “unlike lowland species, incipient sky island species might have had
limited opportunities for intermittent secondary contact and gene flow during late Pleistocene sea-level fluctuations.” Indeed, other highland species, such as the Vinaceous Rosefinch (Carpodacus vinaceus) and the Taiwan Rosefinch (C. formosanus) also diverged without gene flow. The allopatric speciation model is alive and kicking!

References

Dong, F., Li, S. H., Chiu, C. C., Dong, L., Yao, C. T., & Yang, X. J. (2020). Strict allopatric speciation of sky island Pyrrhula erythaca species complex. Molecular Phylogenetics and Evolution, 153, 106941.

Featured image: Grey-headed Bullfinch (Pyrrhula erythaca) © Robert tdc | Wikimedia Commons

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.

References

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 Research, 59(1), 277-293.

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

The evolution of the genomic landscape in Silvereyes does not follow theoretical predictions

The accumulation of genetic differences is unrelated to the development of genomic islands.

Imagine going for a walk through a mountainous region. You work your way up steep slopes, venture into valleys and stroll across expansive plateaus. You don’t even have to go outdoors to explore such heterogenous landscapes, just sequence a few genomes and compare the level of genetic differentiation of two species along these seemingly endless stretches of A, T, C and Gs. Indeed, numerous studies have described a heterogenous genomic landscape with highly divergent mountains and undifferentiated valleys. I have made my modest contribution to this field of research by exploring the genomic landscape of two goose taxa (you can read the whole story here).

The mechanisms responsible for these heterogenous genomic landscapes are still a matter of debate. The most often invoked verbal model goes as follows. At the onset of speciation, genetic differentiation is restricted to a few genomic regions that are under strong selection, resulting in peaks of divergence (the so-called “genomic islands”). As the speciation process continues and the diverging populations go their separate evolutionary ways, these genomic islands are predicted to expand through the linkage with neutral and weakly selected loci. This process – known as genetic hitchhiking – can be influenced by gene flow. The exchange of DNA between the diverging populations can homogenize certain genomic regions and slow down the expansion of genomic islands.

Testing Predictions

These theoretical predictions make intuitive sense but remains to be tested in different study systems. One possible approach is to compare diverging populations at different stages of the speciation process. A recent study in the journal G3: Genes|Genomes|Genetics applied this approach to the Silvereye (Zosterops lateralis), comparing population pairs that varied in their divergence timeframes (early stage:,150 years, mid stage: 3,000-4,000 years, and late stage: 100,000s years) and their mode of divergence (with gene flow or without gene flow).

In contrast to the predictions outlines above, the researchers did not find support for the genetic hitchhiking model. They write that “Genomic islands were rarely associated with SNPs putatively under selection and genomic islands did not widen as expected under the divergence hitchhiking model of speciation.” It seemed that the build-up of genetic divergence mostly occurred outside genomic islands. In addition, simulations suggested that the transition from localized divergence to genome-wide divergence can proceed without selection. All in all, these results question the theoretical model of genetic hitchhiking.

In contrast to the predictions of the genetic hitchhiking model, the genomic islands of differentiation did not expand with increasing divergence times. From: Sendell-Price et al. (2020) G3: Genes|Genomes|Genetics.

Theory and Practice

The authors concluded that “Genome-wide divergence in silvereyes does not hinge on the formation and growth of genomic islands.” Does this mean that we should discard the genetic hitchhiking model of speciation? Not necessarily, because the current study focused on recently diverged populations (with a late stage of ca. 100,000 years). Perhaps genetic hitchhiking becomes more apparent at larger times scales, such as millions of years. Comparisons between more diverged Zosterops species are needed to confirm this.

This study nicely illustrates the interplay between theory and practice. The genetic hitchhiking model is based on solid, theoretical thinking and provides several testable predictions (as a good model should). Results that are not in line with these predictions will help to improve the theoretical model (or discard it if too many incongruent observations start piling up). Hence, with rigorous analyses and the fine-tuning of our thinking, we slowly expand our knowledge on the genomic mechanisms underlying the origin of new species. This quote from Yogi Berra seems like fitting end to this blog post: “In theory there is no difference between theory and practice. In practice there is.”

References

Sendell-Price, A. T., Ruegg, K. C., Anderson, E. C., Quilodrán, C. S., Van Doren, B. M., Underwood, V. L., Coulson, T. & Clegg, S. M. (2020). The genomic landscape of divergence across the speciation continuum in island-colonising silvereyes (Zosterops lateralis). G3: Genes|Genomes|Genetics, 10(9), 3147-3163.

Featured image: Silvereye (Zosterops lateralis) © Bernard Spragg | Wikimedia Commons

Black-and-white birds: The influence of climatic conditions on gull plumage

Thermoregulation and protection against solar radiation determine black plumage patterns in gulls.

When you pay close attention to the distribution of animals across the globe, some interesting patterns emerge. For example, some animals tend to be darker in warm and humid areas. This pattern – known as Gloger’s Rule – has been described for several animal groups, but the underlying mechanisms are still a matter of debate. Proposed explanations include camouflage, protection against parasites and dealing with solar radiation (recently reviewed by Delhey 2019). A related pattern is Bogert’s Rule which states that darker animals occur in colder regions because dark coloration absorbs more solar radiation and thus ensures proper thermoregulation. In both cases, we have clear predictions that can be tested with climatic data on solar radiation, temperature and precipitation. All we need is a group of animals that shows variation in dark plumage patterns…

A recent study in the journal Global Ecology and Biogeography found the ideal study system for this challenge: gulls. In these black-and-white birds, the researchers decided to focus on the mantle color and the proportion of black on the wing tips. These traits are sexually monochromatic (i.e. males and females look alike), suggesting that there is little sexual selection for certain plumage patterns that could complicate the analyses. They quantified these plumage colors for 80 subspecies (representing 52 species) and correlated them with several climatic variables. Did the results follow Gloger’s Rule of Bogert’s Rule?

An overview of the dataset on gull plumage patterns. The researchers focused on mantle color (KGS) and proportion of black on the wingtips (PB). From: Dufour et al. (2020) Global Ecology and Biogeography

Thermoregulation and Solar Radiation

Statistical analyses revealed that climatic conditions experienced during the non-breeding season had a stronger effect than those of the breeding season. Let’s start with the mantle color. It turned out that darker mantle coloration was negatively correlated with air temperature, and positively with solar radiation (see figures below). These findings can be explained by the fact that darker-mantle species winter in colder regions and experience more solar radiation compared to lighter species. Their black plumage allows the gulls in these regions to retain heat in freezing conditions (i.e. black objects trap heat better). And the dark plumage protects against solar radiation because melanin pigments increase the resistance of feathers against harmful UV radiation.

Similarly, the proportion of black color on the wingtips was mostly influenced by the positive interaction between solar radiation and migration distance. In other words, gulls migrating over long distances and overwintering in areas with high level of solar radiation have more black on wing tips, whereas sedentary species in areas of low solar radiation have less black feathers on their wingtips. The researchers explain these results are follows: “Species with a high proportion of black are thus more likely to tolerate long migration distances, which may cause mechanical damage, and more likely to spend the winter in highly insolated conditions where UV radiation can also damage their plumage.”

The statistical analyses revealed a positive relationship between darker mantle color and solar radiatin (figure a) and a negative relationship with temperature (figure b). The black lines between the dots represent phylogenetic relationships. From: Dufour et al. (2020) Global Ecology and Biogeography

Immature Birds

In summary, the black coloration of gull plumage plays a crucial role in both thermoregulation and protection against solar radiation. The reported patterns are in line with Bogert’s Rule which predicted darker animals in colder regions. In contrast, there was little support for Gloger’s Rule (darker animals in warm and humid areas) because there was no clear relationship with precipitation. The present study focused on plumage patterns of adult birds. Hence, these results remain to be confirmed with immature plumage patterns. But as any birdwatcher knows, immature gull plumage is more complex (just open any field guide to experience the mindboggling variation) and will be more daunting to analyze. I wish the researchers that will pick up this challenge the best of luck.

References

Dufour, P., Guerra Carande, J., Renaud, J., Renoult, J. P., Lavergne, S., & Crochet, P. A. (2020). Plumage colouration in gulls responds to their non‐breeding climatic niche. Global Ecology and Biogeography, 29(10), 1704-1715.

Featured image: Great Black-backed Gull (Larus marinus) © Ken Billington | Wikimedia Commons

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 Auk, 137(4), ukaa044.

Featured image from Sutton (1938).

This paper has been added to the Icteridae page.