The genomics of local adaptation in Blue Tits

Understanding the evolutionary history of the populations helps to pinpoint locally adapted genes.

“It is not the strongest of the species that survives, nor the most intelligent that survives. It is the one that is most adaptable to change.” This quote is often attributed to Charles Darwin, but it turns this sentence does not appear in any of his writings. Instead these words can be traced back to a 1963 speech by Louisiana State University business professor Leon C. Megginson who presented his interpretation of Darwin’s work at the convention of the Southwestern Social Science Association (see here for the whole story). Whoever said it, this quote captures an important aspect of the evolutionary process, namely adaptation to local environments. We already have a good idea of how this works on an individual level, but can we also identify signatures of local adaption in the genome? A recent paper in the journal Evolutionary Applications tried to do this by studying several Blue Tit (Cyanistes caeruleus) populations in France.

 

Genome Scans

Before we travel to southern France (not easy in these Covid-times), we first have to understand how we can detect local adaption in the genome. A common method concerns Fst genome scans, where you calculate the population genetic statistic Fst for different genomic regions (usually referred to as windows). Fst is a measure of genetic differentiation and ranges from 0 to 1. Populations with an Fst = 0 are genetically indistinguishable, while an Fst = 1 points to completely differentiated populations. By calculating this statistic for different genomic regions, you can pinpoint sections of the genome that are significantly differentiated and might contain genes involved in adaptation to particular environments.

Finding locally adapted genes thus boils down to finding peaks in Fst across the genome. Sounds simple, but there is a catch. Other evolutionary processes can also give rise to an increase in Fst. Genetic drift, for example, can lead to genetic differentiation between populations through random fluctuations in the frequency of certain gene variants (or alleles). Recombination – the shuffling of chromosomal segments during meiosis – can also affect Fst. In regions of low recombination, several genes will be linked together (i.e. they reside on the same segment) and selection for one deleterious gene variant will thus affect the frequency of all linked genes. If different deleterious alleles unrelated to local conditions are selected against in different populations, the genomic regions in which they reside will diverge genetically, resulting in higher Fst-values. This process – background selection – can complicate the search for locally adapted genes.

A final process to keep in mind is gene flow: the exchange of genetic material between populations. Similar to mixing two paint cans, gene flow results in homogenization of the genome and can erase the genetic signatures of local adaptation. Several studies – both empirical work and simulations – have shown that a few immigrants can strongly decrease the genetic distance between two populations.

The relationship between genetic differentiation (Fst) and recombination rate in Ficedula Flycatchers. Notice the increase in Fst (top) coincides with a decrease in recombination rate. Adapted from Burri et al. (2015) Genome Research

 

Countless Comparisons

After this quick course in population genetics, we can finally turn to the Blue Tits. Charles Perrier and his colleagues focused on two particular pairs of populations. The first comparison concerns birds living in deciduous and evergreen forests. Previous work revealed differences in morphology and behavior between these populations. Specifically, birds breeding in deciduous forest habitats are taller, more aggressive, and lay larger and earlier broods than birds in evergreen forests. The second comparison comprised mainland versus island populations of Blue Tits. The island birds are smaller and more colorful than their mainland relatives and have been classified as a different subspecies (caeruleus on the mainland and ogliastrae on Corsica and Sardinia).

Let’s start with the deciduous vs. evergreen populations. The researchers sampled and compared four population pairs. Genome scans revealed a few Fst-outliers, but these genomic regions were unique for each comparison. This lack of repeatability is probably due to high levels of gene flow between these populations. And indeed, demographic analyses indicated ongoing gene flow between the deciduous and evergreen populations. As explained above, the mixing of a few migrations can erase genetic differences, including signatures of local adaptation. In addition, these results suggest that the traits involved in adaptation might be encoded by many alleles of small effect (i.e. polygenic architecture). These small effects are extremely difficult to pick up with genome scans and require a different approach, such as quantitative genomics.

Several comparisons of deciduous vs. evergreen forest populations revealed several Fst-outliers that were unique to each comparison. From: Perrier et al. (2020) Evolutionary Applications

 

Recombination Rate

The situation for mainland vs. island birds was slightly different. The demographic analyses showed that gene flow between these populations stopped about 10,000 years ago, most likely due to the isolation of Corsica after a rise in sea level. This abrupt termination in gene flow could have set the scene for local adaption to build-up in the genome. And indeed, the researchers found several outlier regions that could be involved in adaptation to the local conditions. But before we open the champagne (we are in France after all) to celebrate the discovery of several locally adapted genes, we should have a look at recombination rate. The researchers report a correlation between genetic differentiation and recombination rate: high levels of Fst coincide with low recombination rates. Hence, they have to admit that “increased differentiation in regions with low recombination is not necessarily due to positive selection, or at least not alone, and [can be] largely influenced by the effect of recombination in interaction with background selection.” More analyses are needed to disentangle these effects. The search continues.

The correlation between genetic differentiation (Fst) and recombination rate shows that regions of high Fst tend to exhibit low recombination rates. From: Perrier et al. (2020) Evolutionary Applications

 

An Extra Oddity

Apart from the search for locally adapted genes, the researchers uncovered an inversion on chromosome 3. Inversions are essentially regions in the DNA that has been flipped around (see this blog post for more on these peculiar segments) and they can link several genes together that consequently evolve as a single “super-gene”. If the linked genes affect the same traits, they can significantly speed up adaptation. The origin and evolutionary dynamics of this inversion – which is unique to the mainland population – remain to be investigated but the researchers can already speculate:

While the putative genomic inversion on chromosome 3 was absent from Corsica and detected in mainland individuals, its level of divergence from the noninverted sequence indicated that it was likely twice older than the beginning of divergence between blue tit populations from mainland and Corsica. This could first suggest that this polymorphism emerged in mainland blue tit populations and then did not introgress the Corsican populations, maybe due to a local disadvantage and/or genetic incompatibilities or simply due to drift coupled to little gene flow. A second hypothesis could be that this inversion was present in Corsican populations but had been purged out due to a local disadvantage.

More exciting questions to explore in these Blue Tit populations.

 

References

Perrier, C., Rougemont, Q., & Charmantier, A. (2020). Demographic history and genomics of local adaptation in blue tit populations. Evolutionary Applications, 13(6), 1145.

Feature image © Pierre Dalous | Wikimedia Commons

Mitochondrial capture in the Chestnut Quail-thrush: Neutral or adaptive introgression?

Genetic study tries to solve this mitochondrial mystery.

Evolution is the change of populations of time. On a molecular level, evolutionary biologists quantify this change in allele frequencies (i.e. different versions of the same gene). Imagine sampling a population and measuring genetic diversity at a particular mitochondrial gene. It turns out that 20 percent of the individuals have variant A, while the remaining 80 percent carry variant B. A few years later, we return to this population and again measure genetic diversity. This time, the majority of the population (about 90 percent) have gene-variant A. This significant change is allele frequency – from 20 to 90 percent – indicates that the population evolved. But what evolutionary processes underlie these changes?

According to the Neutral Theory of Molecular Evolution, “mutations are either sufficiently deleterious in their effects on fitness that they have little chance of becoming fixed in the population, or are under such weak selection that they may become fixed as a result of genetic drift” (see Jensen et al. 2018). In our example, the increase of variant A might thus be the outcome of genetic drift. Alternatively, variant A provided an advantage for the individuals that carried it. They might have survived better and produced more offspring compared to their conspecifics with variant B. Hence, variant A was under strong natural selection and increased in frequency due to its adaptive advantage (see Kern & Hahn 2018). The importance of neutral vs. adaptive processes in molecular evolution is currently a hot topic in population genetics (the two papers mentioned here nicely summarize both sides of the debate). And this discussion can be applied to the main focus of this blog: introgressive hybridization in birds.

A Chestnut Quail-thrush in Australia © Kevin1243 | Wikimedia Commons

 

Disagreeing DNA

In a recent Ecology and Evolution paper, Kerensa McElroy and her colleagues investigated the genetic population structure of the Copperback Quail-thrush (Cinclosoma clarum) and the Chestnut Quail-thrush (C. castanotum). Two species that can be found in the arid and semi‐arid zones of southern Australia. The genetic analyses clearly separated both species and revealed a striking discordance between nuclear and mitochondrial DNA within the Copperback Quail-thrush. This species can be divided into two populations (referred to as East and West in the study). But the nuclear and mitochondrial DNA do not agree on the assignment of individuals to these populations (clearly visible in the figure below). What is going on here?

Discordance between mitochondrial and nuclear DNA is a relatively common phenomenon and can be the result of several processes (reviewed by Toews & Brelsford 2012). The researchers think that the Quail-thrush case can be explained by introgression of mtDNA. Phenotypic data and the nuclear DNA in this study suggests that there is a hybrid zone between the populations where the mitochondrial genome of the western population is being replaced by the eastern (so gene flow from the eastern into the western population).

Genetic analyses show a clear separation between Chestnut Quail‐thrush (purple) and Copperback Quail‐thrush (blue and green). Nuclear and mitochondrial DNA disagree about the population assignment within the Chestnut Quail‐thrush. From McElroy et al. (2020) Ecology and Evolution

 

Mitochondrial Capture

Which brings us to the topic at the start of this blog post: Is this mitochondrial capture neutral or adaptive? This question is currently difficult to answer because the mitochondrial capture is ongoing (not all individuals have the same color in the figure above). However, the researchers argue that the process is probably neutral, based on a demographic model of population invasion. First, the expanding species is outnumbered and is thus more likely to hybridize with members from the local population. As the expansion proceeds, the resident species and previously produced hybrids are engulfed by the expanding species, thereby overturning the numerical imbalance. Consequently, hybrids have a higher chance of backcrossing into members of the expanding species, resulting in gene flow from the resident into the expanding species. In the Quail-thrush case, the western population expanded and genes should thus flow from the resident eastern into the invading western population. And that is exactly what we observe.

Of course, we cannot completely rule out the adaptive explanation. Perhaps the eastern mtDNA does fare better in southern Australia, but this will require more detailed genomic analyses and perhaps some experimental lab work. For example, David Toews and his colleagues measured mitochondrial respiration in flight muscles of Yellow-rumped Warblers (Setophaga coronata) to determine which variant was best suited for long-distance migration. There is still much to learn about the “powerhouses of the cell”.

 

References

McElroy, K., Black, A., Dolman, G., Horton, P., Pedler, L., Campbell, C. D., Drew, A. & Joseph, L. (2020) Robbery in progress: Historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the Copperback Quail‐thrush Cinclosoma clarum. Ecology and Evolution, 10(13): 6785-6793.

Featured image: A Chestnut Quail-thrush © Peter Jacobs | Wikimedia Commons

 

This paper was added to the Cinclosomatidae page.

How many ancestral species gave rise to the domestic chicken breeds?

Genomic data provide an answer to this long-standing debate?

In 1868, Charles Darwin wrote that “we have not such good evidence with fowls as with pigeons, of all breeds having descended from a single primitive stock.” This statement is rather surprising if you read The Origin of Species – published in 1859 – where he argued that all domestic chicken breeds descend from a single ancestor: the Red Junglefowl (Gallus gallus, then named Gallus bankvia). Where did the uncertainty in 1868 about the origin of domestic chickens come from? A recent paper by Hein van Grouw and Wim Dekkers in the Bulletin of the British Ornithologists’ Club reconstructed the historical events leading up to Darwin’s uncertainty.

 

Giant Chickens

Our story begins with French naturalist Georges–Louis Leclerc, Comte de Buffon who believed that different chicken breeds can be traced back to several ancestral wild species (i.e. a polyphyletic origin). For example, he stated that most European breeds descended from the wild Red Junglefowl, while seven giant chicken breeds could be traced back an unknown wild ancestor. Several decades later, Coenraad Jacob Temminck (director of the State Museum of Natural History in Leiden) received a single foot of very large fowl from Indonesia. He assumed it belonged to a large species of wild junglefowl and described it as the Jago Cock (Gallus giganteus). Could this be the ancestor that Buffon predicted?

Edward Blyth, the curator of the Asian Society of Bengal in Calcutta, rejected the polyphyletic origin of chicken breeds. He argued that the varieties of domesticated chickens had evolved by artificial selection from a single wild ancestor: the Red Junglefowl. This monophyletic theory, published in 1851, caught the attention of Charles Darwin because it supported his analogy between artificial selection by humans and natural selection. If humans can create such diverse creatures in a few generations, imagine what nature can do over millions of years! The two naturalists corresponded about the domestication of chickens and in one letter Blyth firmly buried the polyphyletic ideas of Buffon and Temminck, writing: “My very decided opinion, that we may seek in vain for wild types of G. giganteus.”

The foot of Gallus giganteus (© Jonathan Jackson, Natural History Museum, London) and an artistic impression of a giant domestic breed by Benjamin Waterhouse Hawkins in Gray & Hardwicke’s Illustrations of Indian zoology (© Ben Nathan, Natural History Museum, London)

 

Darwin’s Doubt

In The Origin of Species, Darwin credits Blyth for the monophyletic idea: “Mr. Blyth, whose opinion, from his large and varied stores of knowledge, I should value more than that of almost any one, thinks that all the breeds of poultry have proceeded from the common wild Indian fowl.” So, why did Darwin change his mind a few years later? Following the First Opium War between the Qing dynasty and the United Kingdom (1839-1842), several large chicken breeds reached the English naturalists from Asia. After studying these peculiar specimens, Darwin was unsure whether some morphological characters could have been the result of artificial selection from a single ancestor. Perhaps different domestic chicken breeds did originate from different ancestors, such as the Jago Cock?

Darwin continued to investigate the origin of chicken breeds and studied the skeletons and skulls of several breeds. In one breed – the Cochin – he observed certain features that did not occur in Red Junglefowl or any of the other breeds. Despite the aberrant morphology of the Cochin breed, Darwin focused on the similarities between the other breeds and concluded that these chicken breeds probably had a monophyletic origin.

The Cochin, with its deeply furrowed frontal bones, peculiarly shaped occipital
foramen, short wing-feathers, short tail containing more than fourteen feathers, broad nail to the middle toe, fluffy plumage, rough and dark-coloured eggs, and especially from its peculiar voice, is probably the most distinct of all the breeds. If any one of our breeds has descended from some unknown species, distinct from G. bankiva [Gallus gallus], it is probably the Cochin; but the balance of evidence does not favour this view.

The peculiar Cochin breed. © Willem & Martijn Hoekstra

 

The Genomic Picture

The morphological studies of Darwin and other naturalists did not completely settle the debate about the polyphyletic or monophyletic origin of chicken breeds. The uncertainty is obvious in Darwin’s quotes cited above. Nowadays we can turn to genomic data to answer questions about the domestication of certain animals and plants. And that is exactly what Raman Akinyanju Lawal and his colleagues did. They sequenced the genomes of 53 domestic chickens and several individuals of four wild species: the Red Junglefowl, the Grey Junglefowl (G. sonneratii), the Ceylon Junglefowl (G. lafayettii) and the Green Junglefowl (G. varius).

Phylogenomic analyses revealed that the domestic chickens clustered with the Red Junglefowl (see figure below), suggesting that they all originated from a single ancestor. However, D-statistics pointed to gene flow between between domestic chickens and the Grey, Ceylon, and Green Junglefowl species (see this blog post for details on D-statistics). A closer look at particular introgressed regions suggested that they were recently exchanged between the species. For example, some introgressed tracts were relatively long and have thus not been broken down by recombination. Taken together, these patterns show that domestic chicken breeds originated from a single ancestor (the Red Junglefowl) and received genetic material from other species later on. So, while the origin of domestic chickens is monophyletic, their current genetic make-up is polyphyletic.

The evolutionary tree of chicken breeds and species based on genomic data. Notice that all domestic chickens (darkblue) cluster with Red Junglefowl (red). Adapted from: Lawal et al. (2020) BMC Biology

 

References

Lawal, R. A., et al. 2020). The wild species genome ancestry of domestic chickens. BMC Biology, 18(1), 1-18.

van Grouw, H., & Dekkers, W. (2020). Temminck’s Gallus giganteus; a gigantic obstacle to Darwin’s theory of domesticated fowl origin?. Bulletin of the British Ornithologists’ Club, 140(3), 321-334.

Featured picture: Feral rooster on Kauaʻi © Frank Schulenburg | Wikimedia Commons

 

The papers have been added to the Galliformes page.

The Great Speciator strikes again: Discovery of a Mangrove White-eye in Saudi Arabia

A mangrove population of White-eyes is morphologically distinct from other subspecies of the Abyssinian White-eye.

The constant interplay between speciation and extinction gives rise to the phylogenetic tree of life that evolutionary biologists are trying to reconstruct. Some branches on this tree used to be diverse, but have dwindled down to a few lonely twigs. Think of the Coelacanth (Latimeria chalumnae) or the Hoatzin (Opisthocomus hoazin) that each represent an entire order (check out this video by SciShow about these and other “evolutionary loners”). Other branches, however, are in full bloom, sprouting new species at record-breaking speed – evolutionary speaking. One example concerns the bird family Zosteropidae or white-eyes with over 100 species that originated in the last two million years, earning this group of birds the honorary title of “Great Speciator”. In a recent Journal of Ornithology paper, researchers present what could be the newest addition to this species-rich family.

 

Subspecies

The biggest diversity of white-eyes can be found on tropical islands, although an analysis of African taxa revealed numerous undescribed species. Another uncharted territory is the Middle East where you can find the Abyssinian White-eye (Zosterops abyssinicus). This small songbird has been split into four subspecies:

• abyssinicus in eastern Sudan, Eritrea, and northern and central Ethiopia
• omoensis in western Ethiopia and possibly eastern South Sudan
• socotranus on the island of Socotra (Yemen), and in coastal northern Somalia
• arabs in southwest Saudi Arabia, Yemen, and southwest Oman

An expedition in 1994 discovered a population of White-eyes in a mangrove, located in southwest Saudi Arabia between the villages of Shuqaiq and Amaq. This location suggests that they belong to the subspecies arabs, but the researchers were surprised by the small size and brighter plumage of these birds. Could they belong to a new subspecies?

Left: A montane Abyssinian White-eye (Zosterops abyssinicus arabs) from the Asir Province in Saudi Arabia. Right: A “Mangrove White-eye” (Zosterops sp. indet.) from the Jazan Province in Saudi Arabia. From: Babbington et al. (2020) Journal of Ornithology

 

Morphological Differences

During new expeditions (in 2015-2016) four individuals of this newly discovered “Mangrove White-eye” were caught. Morphological analyses revealed that these birds were significantly smaller than the montane subspecies arabs. Moreover, plumage patterns were clearly different, concisely described in the study.

First, the ‘Mangrove White-eye’ was noticeably more brightly coloured, with much more yellow-green in the head and upperparts. Second, the bright yellowish outer webs to all flight feathers of the ‘Mangrove White-eye’ gave it a prominent yellowish wing panel that was not obvious on Abyssinian White-eye Z. a. arabs. Third, the underparts of ‘Mangrove White-eye’ were slightly buffer than Abyssinian White-eye Z. a. arabs, and the former had more obvious yellow undertail-coverts.

From a morphological point of view, the “Mangrove White-eyes” are thus distinct from the other subspecies. What about genetics?

Morphological analyses clearly show that “Mangrove White-eyes” (green) are smaller than Abyssinian White-eyes (blue). From: Babbington et al. (2020) Journal of Ornithology

 

Matching Mitochondria

The researchers sequenced the mitochondrial gene cytochrome b for the “Mangrove White-eyes” and compared it to members of the Abyssinian White-eye subspecies arabs. The four mangrove specimens had identical DNA sequences, exactly the same as that of one Abyssinian White-eye individual. The other Abyssinian DNA sequences differed by just one or two nucleotides. From a genetic perspective, the Mangrove White-eyes are thus indistinguishable from the subspecies arabs. However, this conclusion is based on only one mitochondrial gene, there might be significant differences elsewhere in the genomes of these birds.

Based on the present data, the researchers suspect that the “Mangrove White-eyes” are the result of a recent colonization of mangrove habitats followed by rapid morphological evolution. Over time, this population might diverge genetically and could eventually give rise to a new (sub)species of White-eye. The Great Speciator keeps speciating…

The DNA sequences of ‘Mangrove White-eyes’ (green) are identical to one Abyssinian specimen (red). The others differ by a few nucleotides. From: Babbington et al. (2020) Journal of Ornithology

 

References

Babbington, J., Boland, C. R., Kirwan, G. M., & Schweizer, M. (2020). Morphological differences between ‘Mangrove White-eye’and montane Abyssinian White-eye (Zosterops abyssinicus arabs) in Arabia despite no differentiation in mitochondrial DNA: incipient speciation via niche divergence?. Journal of Ornithology, 1-10.

 

Building bowers and phylogenies: Genomic study reconstructs the complex evolution of bowerbirds

Phylogenomic analyses suggest that the ability to build bowers arose twice.

In many birds species, males go to great lengths when seducing females. Think of the dazzling colors of a peacocks tail or the elaborate songs of nightingales. In one particular bird family – the Ptilonorhynchidae – males even build elaborate structures with colorful objects and plant material to capture the attention of potential female partners. These birds are better known as bowerbirds and you can check out their amazing architectural skills and captivating courtship in the video below. The resulting structures – or bowers –  are generally divided into two types: avenues and maypoles. Avenues consist of two parallel walls made of vertically placed sticks and grass stems, while maypoles are composed of sticks and other vegetation around young trees or twigs.

The exact function of these bowers remains a matter of debate, with two competing – but not mutually exclusive – hypotheses. Some ornithologists argue that these bowers are an extension of the male plumage ornaments to seduce females. Others think that the bowers provide the females with protection and prevents other males from mating with the courted female. The bowers’ function is not the only mystery about these birds. In fact, the evolutionary history of this bird family is still not entirely clear. Reconstructing the phylogeny of the bowerbirds can help scientists to better understand the evolution of bower construction and courtship. And a genomic study in the journal Systematic Biology did just that.

 

Nuclear DNA

In the 1990s, phylogenetic analyses of the mitochondrial gene cytochrome b provided the first molecular perspective on the evolution of bowerbirds. These studies revealed that Catbirds (genus Ailuroedus) were the sistergroup of all other bowerbirds. Catbirds are the odd one out within the family Ptilonorhynchidae: in contrast to the remaining bowerbird genera, these species are monogamous and do not build bowers. This result thus suggested that the ancestor of bowerbirds was monogamous and that the construction of bowers evolved only once.

If there is one thing we learned during the genomic revolution, it is that different genes tell different stories. Indeed, Per Ericson and his colleagues analyzed more than 12,000 nuclear loci and uncovered a different story. Catbirds are not the sistergroup of the other bowerbirds, instead they are most closely related to a group of species that build maypoles (genera Ambyornis, Prionodura) or just a courtship court (genus Scenopoeetes). The remaining bowerbirds form a monophyletic group that constructs avenue bowers.

Phylogenetic analyses of genomic data reveal three main groups: (A) avenue-building species, (B) maypole-building species, and (C) monogamous species. From: Ericson et al. (2020) Systematic Biology

 

Mitochondrial Mistakes

Interestingly, analyzing the complete mitochondrial genome resulted in the same phylogeny as the cytochrome b studies. What could explain the difference between mtDNA and nuclear loci? One possibility – and especially relevant for this blog – is hybridization. Perhaps an ancient hybridization event resulted in the exchange of mtDNA between the ancestors of the avenue- and maypole building birds. The authors suggest another explanation that relates to the fast evolution of mtDNA. Because mtDNA accumulated mutations faster than nuclear DNA, it becomes unreliable at estimating ancient divergences. The bowerbirds originated about 15 million years, which might be too old for stable mitochondrial analyses. This reasoning is supported by extra analyses of the mitochondrial genome. When you exclude the third codon position of mitochondrial genes – which evolves faster compared to the first two codon positions – the analyses uncover the nuclear phylogeny.

Spotted Catbird (Ailuroedus melanotis) do not build bowers. © Greg Schechter | Wikimedia Commons

 

Once or twice?

The new phylogeny allowed the researchers to retrace the evolution of bower-building and courtship display. Ancestral state reconstruction indicated that the ancestor of these birds did not build bowers. This result raises another question: did the ability to build bowers evolve once or twice? If this behavior arose once, it was subsequently lost in Catbirds (genus Ailuroedus) and the Tooth-billed Bowerbird (Scenopoeetes dentirostris). The latter species does not build bowers, but does prepare a courtship court to attract females.

The researchers argue for the alternative scenario: the ability to build bowers evolved twice. Once in the maypole-constructing genera Prionodura, Archboldia and Amblyornis, and another time in the avenue-building genera Ptilonorhynchus, Sericulus and Chlamydera. This scenario seems likely because both groups evolved different ways of building bowers (maypoles vs. avenues). Moreover, they note that “the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) are conditions that have facilitated the evolution of the extensive male displays and bower-building behavior.” Indeed, the region of the bowerbirds – Australia and New Guinea – houses another bird group with crazy courtship displays: the birds-of-paradise.

Another possible scenario that the researchers did not consider involves hybridization. Perhaps bower-building behavior evolved in one group and was consequently transferred to another group by introgressive hybridization (see my BioEssays paper for more details on this idea). Maybe the mitochondrial results do point to an ancient hybridization event and are not due to mutational saturation? This hypothesis can be tested by determining the genetic basis of bower-building, followed by phylogenetic analyses of the “bower-building genes”. If this behavior was transferred between the ancestors of these groups, these genes would cluster the bower-building genera together (similar to the mitochondrial result). To solve this mystery, we can let the birds build their bowers, while we construct some insightful evolutionary trees.

The new phylogeny enabled the researchers to reconstruct the evolution of several traits, such as plumage, social mating system, bower-building and display court. From: Ericson et al. (2020) Systematic Biology

 

References

Ericson, P. G., Irestedt, M., Nylander, J. A., Christidis, L., Joseph, L., & Qu, Y. (2020). Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics. Systematic Biology, 69(5): 820-829.

Featured image: Satin Bowerbird (Ptilonorhynchus violaceus) © Joseph C. Boone | Wikimedia Commons

 

This paper has been added to the Ptilonorhynchidae page.

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

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

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

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

The Variable Antshrike © Dario Sanches | Wikimedia Commons

 

Around the Amazon

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

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

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

 

Three Groups

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

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

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

 

Pleistocene Climate

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

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

Sounds like a wonderful, ornithological bedtime story.

 

References

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

Feature image © Francesco Veronesi | Wikimedia Commons

 

This paper has been added to the Thamnophilidae page.