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 Scripta49(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 Evolution153, 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 Research59(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|Genetics10(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 Biogeography29(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 Auk137(4), ukaa044.

Featured image from Sutton (1938).

This paper has been added to the Icteridae page.

Why do Robust Woodpecker, Lineated Woodpecker and Helmeted Woodpecker look alike?

Could the interspecific social dominance hypothesis explain this plumage convergence?

I recently bought “All the Birds of the World” from Lynx Editions. The title of the book nicely captures its contents, this huge tome contains beautiful drawings of literally all the (known) bird species in the world. Apart from looking up specific species, I enjoy browsing through the pages and admiring the amazing diversity of birds. Skimming the section on woodpeckers (family Picidae), I noticed the striking similarities between distantly related species. For example, several species seem to have converged upon a plumage pattern that consists of a black-and-white body with an eye-catching red crest. Many ornithologists have made this observation (technically known as mimicry complexes) and there are countless hypotheses to explain why certain woodpecker species look alike.

One possible explanation for this plumage convergence is the “interspecific social dominance hypothesis” which states that subordinate species will look like a dominant one to avoid attacks by the dominant species. A recent study in the Journal of Ornithology tested this hypothesis for three South American woodpeckers.

Niche Differentiation

Juan Manuel Fernández and his colleagues studied the ecology of Robust Woodpecker (Campephilus robustus), Lineated Woodpecker (Dryocopus lineatus) and Helmeted Woodpecker (Celeus galeatus) in Argentina. Based on the size of these species, the researchers considered the smaller Lineated Woodpecker and Helmeted Woodpecker as subordinate mimics of the dominant Robust Woodpecker. According to the “interspecific social dominance hypothesis”, the three species should be ecological competitors and thus occupy in the same niches.

However, careful observations revealed clear niche differentiation. It turned out that the three species forage on different parts of the tree. Helmeted Woodpecker collected food on smaller trees and was often seen on dead branches in living trees. Lineated Woodpecker foraged on similar trees compared to Helmeted Woodpecker, but mainly used living healthy trees. And Robust Woodpecker was mainly observed on larger trees and frequently visited dead parts of living and decaying trees. In addition, the researchers did not record any direct interactions between the three species.

From left to right: Robust Woodpecker (Campephilus robustus), Lineated Woodpecker (Dryocopus lineatus) and Helmeted Woodpecker (Celeus galeatus). From: Fernández et al. (2020) Journal of Ornithology.

Deception

These results do not support the “interspecific social dominance hypothesis”. It could be that interspecific interactions in the past have driven these woodpecker species into different niches. But there are alternative explanations. The subordinate species might mimic the dominant species to deceive predators. The larger Robust Woodpecker is not an easy prey for small raptors, such as Sparrowhawks (genus Accipiter). These birds of prey might think twice before attacking a woodpecker that looks like a Robust Woodpecker.

It is also possible that the Lineated Woodpecker and the Helmeted Woodpecker are deceiving members of their own species to avoid direct competition. From a distance, birds might think that a dominant Robust Woodpecker is chiseling away at a tree branch and decide to look for another foraging spot. These explanations remain to be tested with more observations. I won’t mind putting my “All the Birds of the World” book aside and venturing into the Argentine forests.

References

Fernández, J. M., Areta, J. I., & Lammertink, M. (2020). Does foraging competition drive plumage convergence in three look-alike Atlantic Forest woodpecker species?. Journal of Ornithology161(4), 1105-1116.

Featured image; Lineated Woodpecker (Dryocopus lineatus) © panza-rayada | Wikimedia Commons

Admixture in Amazonia: Reconstructing the evolutionary history of the Pectoral Sparrow

Genomic data tell the story of how this passerine spread across South America.

Apart from managing the Avian Hybrids Project, I regularly contribute to the blog of the British Ornithologists’ Union (the BOUblog, you can find an overview of my blog posts here). A few weeks ago, I published my 50th story for the BOUblog, which focused on the phylogenetics of the Pectoral Sparrow (Arremon taciturnus). A recent study used mitochondrial DNA to unravel the evolutionary history of this neotropical species. The researchers uncovered six distinct lineages and speculated about the factors responsible for their origins. Here is my summary:

Could it be that the origin of these rivers drove the diversification of the Pectoral Sparrow? Not exactly, because these rivers started crisscrossing the South American landscape between 9 and 2.5 million years ago. The rivers certainly prevent neighboring populations from mixing extensively, but they are not the main cause for the origin of these lineages. Rather, the researchers suspect that ‘past ecological barriers must have played a role in accounting for the observed phylogeographical structure.’ During the glacial cycles of the Pleistocene, forests contracted and expanded. The Pectoral Sparrows became isolated in forest fragments during contraction phases and followed the spreading forests during the expansions. At rivers, however, the birds could not disperse further, giving rise to the geographical boundaries between the six lineages. Amazing what you can deduce from a string of A, T, G and Cs.

Although this scenario seems plausible, it remains largely speculative. Indeed, the authors indicated the uncertainties in their proposed model and wrote that “alternative scenarios could be tested with more powerful genomic datasets.” Luckily, another recent paper did just that. Using genomic data, Nelson Buainain and his colleagues provided a more fine-grained picture of the evolution of the Pectoral Sparrow.

Analyses of mitochondrial DNA indicated six distinct lineages within the Pectoral Sparrow. From: Carneiro de Melo Moura et al. (2020) Ibis.

Genotypes and Phenotypes

In contrast to the six mitochondrial lineages, the genomic data suggested four main genetic clusters. The genetic make-up of these four groups reveals an interesting pattern. Individuals from the Guyana Shield (region A in the figure above), southwestern Amazonia (region F) and the Atlantic Forest (region D) generally have “pure” genotypes. In other words, they do not share genetic variation with other regions. In central Amazonia (regions B, C and E), however, individuals have admixed genotypes.

The genetic patterns are mirrored in the plumage of the birds. In the genetically “pure” populations, pectoral band patterns are mostly homogenous, whereas the admixed populations show a variety of shapes and sizes in the pectoral bands. The most likely scenario is that populations became isolated in different forest patches across central Amazonia and established secondary contact, giving rise to the genetic and morphological variety we see today. This interpretation was further supported by ecological niche modelling.

Genetic and morphological variation across the range of the Pectoral Sparrow. Notice the admixed nature of the populations in central Amazonia. From: Buainain et al. (2020) Molecular Ecology.

North to South

The genetic analyses indicated that the populations north and south of the Amazon separated about 160,000 to 380,000 years ago. The higher genetic diversity in the northern populations of the Guyana Shield suggest that the Pectoral Sparrow started its journey across South America here. As birds spread to the south, they separated into distinct populations, settling in the patches of suitable habitat. These populations were probably separated in at least three regions south of the Amazon River, namely southwestern Amazonia and south‐central Amazonia and the Atlantic Forest. These regions functioned as refugia during harsh climatic periods when forest fragments were isolated. Occasionally, climatic changes would cause these forests to expand, resulting in the secondary contact that I described above. This scenario nicely builds upon the patterns that arose from the mitochondrial study. Step by step, we are unraveling the complex evolutionary history of South American birds.

References

Buainain, N., Canton, R., Zuquim, G., Tuomisto, H., Hrbek, T., Sato, H., & Ribas, C. C. (2020). Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus. Molecular Ecology29(15), 2922-2939.

Featured image: Pectoral Sparrow (Arremon taciturnus) © Caio Brito | eBird

The role of hybridization in the domestication of geese

Gene flow patterns between wild and domestic geese changed during the domestication process.

Geese probably saved the Roman empire. The Gauls were secretly climbing the Capitoline Hill when they woke up a flock of geese. The noise of the honking geese alarmed the Romans that managed to fend off the Gaul attack. This story indicates that geese were already domesticated in Roman times. The earliest reliable reference to domestic geese can be traced back even further, to the 8th century BCE in Homer’s Odyssey. But when did humans domesticate geese?

This question is difficult to answer because different domestic goose breeds are derived from two species: the Greylag Goose (Anser anser) and the Swan Goose (Anser cygnoides). In addition, some breeds are probably the outcome of hybridization between these species, and several breeds are known to hybridize with their wild relatives. Marja Heikkinen and her colleagues tried to solve this complex puzzle of hybridization and domestication with genetic data. Their results recently appeared in the journal G3: Genes | Genomes | Genetics.

Gene Flow

The researchers collected samples from wild and domestic geese across Eurasia. Genomic data revealed a clear separation between wild Greylag Geese, European domestic breeds and Chinese domestic breeds. Demographic analyses suggested that the wild and domestic lineages diverged around 14,000 years BCE (although the authors indicate that this divergence time has wide confidence intervals and will need to be confirmed with more detailed analyses). This divergence was followed by several episodes of hybridization and consequent gene flow.

At the onset of domestication, gene flow was primarily from domestic into wild geese. Probably, geese were not intensively managed at that time, allowing domestic geese to interbreed with their wild relatives. Moreover, goose farmers might occasionally restock their flock by collecting eggs from the wild and raising them in captivity. By Medieval times, goose-keeping was a common phenomenon and the escaped birds would regularly mix with wild flocks. This resulted in gene flow in the opposite direction, from the wild into the domestic population. A patterns that is still visible in present-day goose populations.

A principal component analysis indicates a clear separation between wild Greylag Geese (blue), European domestic breeds (green) and Chinese domestic breeds (red). Some locations, such as Turkey, show admixture from different lineages.

Turkish Hybrids?

Interestingly, the amount of gene flow from wild into domestic goose populations differs between countries. In Finland and Norway – where goose rearing is not so popular – the genetic influence of wild birds is relatively low. In the Netherlands, however, the genetic signs of hybridization is more pronounced. This can be explained by the popularity of waterfowl collections in this country and the fact that many Greylag Geese winter in the Dutch fields (and a large proportion is even present year-round). There is thus ample opportunity for domestic geese to interbreed with wild ones.

Turkish goose populations showed genetic signatures from both European and Chinese domestic breeds. They might thus be a hybrid population between these independently domesticated breeds. Alternatively, the Turkish geese might represent the ancestral genetic variation of Greylag Geese, supplemented with some gene flow from Chinese breeds. More research is needed to solve this mystery and determine whether the domestication of geese started in Turkey.

References

Heikkinen, M. E., et al. (2020). Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history. G3: Genes, Genomes, Genetics, 10(9), 3061-3070.

Featured image: Domestic geese © Hippopx

This paper has been added to the Anseriformes page.

Convergent evolution of immune proteins in tits, chickadees, and titmice

These small passerines use similar molecular tricks to detect pathogens.

Convergent evolution is a fascinating phenomenon. It concerns the evolution of similar traits in distantly related organisms. Think of the streamlined bodies of fish-eating penguins and auks, birds that diverged more than 60 million years ago. But such similarities are not only limited to morphological traits, evolution can also converge on the same solutions at the molecular level. For example, whales and bats use the same genes for echolocation.

Convergent evolution on the molecular level can be especially important for proteins involved in immunity. These molecular machines need to detect and fight a wide range of pathogens. It is easy to imagine that organisms exposed to the same bacterial or viral species will converge upon similar defense mechanisms. A recent study in the journal Molecular Ecology tested this idea with the bird family Paridae (tits, chickadees, and titmice).

Convergent evolution of body shape in the extinct Great Auk (left) and the Emperor Penguin (right). Credits: Great Auk © Mike Pennington | Emperor Penguin © Samuel Blanc.

 

Toll-like Receptors

Martin Těšický and his colleagues focused on toll-like receptors (TLRs), proteins that recognize signals derived from pathogens and trigger a signaling cascade that starts the innate immune response (first line of defense against all pathogens) and regulates the consequent adaptive immune response (learned response, specific to a particular pathogen). Toll-like receptors have specific structures (called ectodomains, ECD) that contain a ligand-binding region (LBR) which interacts with pathogenic molecules. Because these protein regions have to recognize a wide range of bacteria and viruses, you can expect strong positive selection for successful toll-like receptors.

The study focused on two receptors that are specialized to recognize different signals: TLR4 binds with lipopolysaccharides from gram-negative bacteria, while TLR5 is specific to flagellin (a protein in the bacterial flagellum). The researchers scanned the protein sequences from 29 tit species for sites under positive selection. Next, they investigated whether these positively selected sites altered the structure and binding capacity of the receptors. For instance, a different amino acid in a certain location might have different molecular properties that affect the functioning of the protein. This approach resulted in four positive selected sites in TLR4 and fourteen in TLR5.

Positively selected sites and functionally important sites of the extracellular ectodomain on the great tit TLR4 (a) and TLR5 (b). Positively selected sites are highlighted in blue or orange, and sites under convergent evolution are indicated with red arrows. From: Těšický et al. (2020) Molecular Ecology.

 

Comparing Trees

Now that we have a list of positively selected sites, we can investigate whether they experienced convergent evolution. This can be done by comparing the phylogeny of the Paridae with the evolutionary trajectories of the different sites. These analyses revealed that three positions in
TLR4 and six positions in TLR5 showed signals of molecular convergence. Hence, different tit species independently evolved similar protein structures to fend off invading pathogens. This finding indicates that these species might have experienced similar ecological conditions with shared bacteria or viruses. However, the researchers reported that “the observed evolutionary convergence was not explained by the selected ecological traits, suggesting that more direct evidence on the composition of the microbial communities interacting with TLRs is needed.” Another evolutionary puzzle to solve.

Convergent evolution in Toll‐like receptor 4 (TLR4) in the Paridae family. The species tree on the left does not match the evolutionary history of a particular protein location on the right. Different tit species converged on the same solution independently. From: Těšický et al. (2020) Molecular Ecology.

 

References

Těšický, M., Velová, H., Novotný, M., Kreisinger, J., Beneš, V., & Vinkler, M. (2020). Positive selection and convergent evolution shape molecular phenotypic traits of innate immunity receptors in tits (Paridae). Molecular Ecology29(16), 3056-3070.

Featured image: Black-capped Chickadee (Poecile atricapillus) © USFWS | Wikimedia Commons