Genetic mismatches in the Long-tailed Finch

Exploring the interactions between mitochondria, sex chromosomes and beak color.

Hybrids are often sterile or unviable. These developmental issues can mostly be traced back to genetic incompatibilities: mismatches between certain genetic variants. During the 1930 and 1940s, Theodosius Dobzhansky and Herman Muller developed a theoretical model to explain the evolution of these incompatibilities. Here is the short version:

Consider two allopatric populations diverging independently, with the same ancestral genotype AABB in both populations. In one population, a mutation (A -> a) appears and goes to fixation, resulting in aaBB, which is fertile and viable. In the other population, another mutation (B -> b) appears and goes to fixation, resulting in AAbb, which is also fertile and viable. When these populations meet and interbreed, this will result in the genotype AaBb. Alleles a and b have never “met” each other and it is possible that allele a has a deleterious effect that becomes apparent when allele b is present, or vice versa. Over evolutionary time, numerous of these incompatibilities may arise, each possibly contributing to hybrid sterility or unviability.

These genetic incompatibilities can arise between countless interacting genes, but one specific situation concerns mitonuclear genes. The mitochondria – also known as the powerhouses of the cell – only contain 13 protein-coding genes. However, this small collection of genes interacts with thousands of genes in the nuclear genome. The rapid evolution of mitochondrial DNA requires compensatory changes in the nuclear genes to ensure proper functioning. The resulting high rate of molecular evolution in mitonuclear genes increases the likelihood of genetic incompatibilities as closely related species adapt to different environments. Moreover, a mismatch in the mitonuclear machinery can have devastating consequences for the energy balance – and thus livelihood – of hybrid individuals.

A graphical representation of the Dobzhansky-Muller model of genetic incompatibilities. From: Wikipedia.

Sex Chromosomes and Colors

Another place to look for genetic incompatibilities are sex chromosomes, which often play an important role in speciation (see for example this study in Barn Swallows). Numerous studies have reported how sex-linked genes contribute to hybrid dysfunction. And the situation becomes even more complicated – and interesting – when we consider the interaction between sex-linked and mitonuclear genes. A genomic survey of the Zebra Finch found that about 5% of the mitonuclear genes can be found on the Z-chromosome. Plenty of opportunities for the evolution of genetic incompatibilities there.

A final twist to this incompatibility story concerns coloration. Experiments with House Finches (Haemorhous mexicanus) uncovered a relationship between mitochondrial function and the synthesis of carotenoids (i.e. the pigments producing yellow, orange and red colors). Hybrids with mitonuclear issues will have less efficient mitochondria, which could impact the production of these pigments. The lack of red colors in male hybrids could make them less attractive to females, resulting in selection against hybrids.

Cline Analyses

In summary, it seems likely to find genetic incompatibilities in mitochondrial and sex-linked genes, possibly related to the production of reddish colors. In a recent Evolution paper, Kelsie Lopez and her colleagues tested this idea in the Long-tailed Finch (Poephila acuticauda). This Australian passerine is comprised of two subspecies with different beak colors – yellow in acuticauda and red in hecki – that interbreed along a hybrid zone. By following the distribution of genetic variants across this hybrid zone, the researchers hoped to gain more insights into potential genetic incompatibilities. Here, they relied on cline theory. I recently covered this mathematical framework in a short paper, so let me provide you with the basics:

Imagine a white and a black bird species that produce gray offspring in a hybrid zone. Tracking their plumage color along a geographical transect will reveal a clinal transition from white, to gray, to black birds. The shape of the cline provides information on the strength of selection against hybrids. If the gray hybrids interbreed with each other and the parental species, there will be a variety of differently colored backcrosses. This will result in a smooth transition from white through different shades of gray to black: a wide cline. However, if the hybrids do not reproduce, there will be similarly colored gray birds in the narrow contact zone, resulting in a rapid transition from white to black plumage: a steep cline.

In the context of the Long-tailed Finch, we would expect steep clines for genetic variants that contribute to hybrid dysfunction. Moreover, interacting genetic incompatibilities will show congruent clines.

The shape of different clines within a hypothetical hybrid zone between a black and a white bird species. The steep red cline suggests strong selection against hybrids. From: Ottenburghs (2022).

Good and Bad news

So, what did the researchers find? Let me start with the bad news: there was no relationship between mitochondrial variants and the color of the beak. The cline centers of mtDNA and bill color were almost 400 kilometers apart. It thus seems that mitochondrial function does not influence the synthesis of carotenoids in the beaks of these birds. Most sex-linked genes also showed different clines compared to the mtDNA, except for three variants. Hence, the researchers suggested that these variants might represent sex-linked mitonuclear incompatibilities. However, more research is needed to confirm this association and provide a mechanistic basis. As we all know, correlation is not causation.

It took me a long time to build up to these results, from the basic Dobzhansky-Muller model over mitonuclear interactions to cline analyses. But I hope this step-by-step explanation will help you to understand the situation in Long-tailed Finches. This study nicely illustrates how messy nature is compared to the clean theoretical models that scientists develop. It is always more complicated, especially when it comes to genetic incompatibilities.

Geographic clines of the mitochondrial DNA (in red) and several sex-linked genes showed congruent patterns with three sex-linked variants (in blue). These patterns suggests possible genetic incompatibilities. From: Lopez et al. (2021).

References

Hill, G. E., Hood, W. R., Ge, Z., Grinter, R., Greening, C., Johnson, J. D., … & Zhang, Y. (2019). Plumage redness signals mitochondrial function in the house finch. Proceedings of the Royal Society B, 286(1911), 20191354.

Lopez, K. A., McDiarmid, C. S., Griffith, S. C., Lovette, I. J., & Hooper, D. M. (2021). Evaluating evidence of mitonuclear incompatibilities with the sex chromosomes in an avian hybrid zone. Evolution, 75(6), 1395-1414.

Ottenburghs, J. (2022). Digest: Following clines along an Amazonian hybrid zone. Evolution. 76(3): 677-678.

Featured image: Long-tailed Finch (Poephila acuticauda) © Lip Kee Yap | Wikimedia Commons

Stuck in a Ruff: Having a supergene is not always super

Female Ruffs with a large inversion have lower reproductive success.

Occasionally, a section of DNA might be flipped around. Such inversions can be quite large and hold a collection of genes, giving rise to so-called supergenes. In the Ruff (Calidris pugnax), for example, a genomic chuck of roughly 4.5 million DNA-letters – containing 125 genes – was inverted about 3.8 million years ago. This chromosomal rearrangement resulted in two distinct morphs: the large and territorial Independent morph (with the “normal” section of DNA) and the smaller Faeder morph (with the inversion). The latter morph developed a new mating strategy in which males sneakily try to copulate in the territories of Independents by pretending to be a female. Later on, a third morph arose through the recombination between the ancestral DNA-section and the inversion. The resulting Satellite morphs are semi-cooperative, they display on the territories of Independent males to attract more females, even though they don’t always manage to mate.

This complicated mating system has been extensively studied from the male perspective. However, these three morphs also occur in females. A recent study in the journal Nature Communications provided a female perspective: what are the fitness consequences of this supergene for females?

Following Females

Lina Giraldo-Deck and her colleagues monitored the reproductive success of 186 female Ruffs, covering the three morphs: 118 Independents, 48 Satellites and 20 Faeders. These experiments revealed that “Faeder females laid fewer and smaller eggs with reduced offspring survival compared to Independent and Satellite females.” The exact mechanisms underlying the lower reproductive success of Faeder females remain to be determined. It could be related to the accumulation of deleterious alleles in the supergene due to the lack of recombination (see this study for more details on mutational accumulation in inversions). A detailed genomic analysis is needed to this test idea.

Faeder females have lower reproductive success in terms of hatching probability (left graph). The resulting offspring also showed a lot of variation in the probability of leaving the nest (right graph). From: Giraldo-Dec et al. (2022).

Sexual Conflict

But if female Faeders have such low reproductive success, why doesn’t the supergene disappear from the population? The researchers argue that this female disadvantage is compensated for by the higher reproductive success of male Faeders. This hypothesis was supported by an analytical model, showing that male Faeders need to fertilize 2.4% of the females to keep the supergene at a stable frequency in the population. This mathematical model remains to be confirmed with field observations, but it does seem like a reasonable explanation.

The resulting situation – female disadvantage and male advantage from the supergene – is a beautiful example of intralocus sexual conflict. At a particular genetic locus (the supergene, in this case), males and females have different evolutionary interests. We would not have discovered this extra layer of complexity if we only focused on the role of males in this mating system. A female perspective can be refreshing.

A graphical representation of the conflict between the sexes in Ruffs. The lower reproductive success of Faeder females leads to less offspring of this morph. However, male Faeders have a higher reproductive success, maintaining this morph in the population. From: Giraldo-Deck et al. (2022).

References

Giraldo-Deck, L. M., Loveland, J. L., Goymann, W., Tschirren, B., Burke, T., Kempenaers, B., … & Küpper, C. (2022). Intralocus conflicts associated with a supergene. Nature Communications, 13(1), 1-8.

Featured image: Ruff (Calidris pugnax) © Åsa Berndtsson | Wikimedia Commons

Should we save the Kākāpō?

A philosophical perspective on nature conservation.

At the moment, there are only 252 adult Kākāpōs (Strigops habroptilus) left on this planet. This species almost went extinct after the introduction of non-native predators, such as cats and rats, to New Zealand during the British colonization. Without the extensive efforts of the Kakapo Recovery Program, we would have probably lost this iconic owl parrot forever. The extinction of a species sounds disastrous, but is that really the case? Recently, I read the book “Plastic Panda’s” by the Dutch philosopher Bas Haring in which he argues that the disappearing of species is not always a problem. We can survive with less species, less biodiversity. A provocative statement that requires more thought than Haring gave it in his book. The book – already published in 2011 – was terribly bad, mainly a collection of irrelevant anecdotes and a cherry-picking of scientific studies, written in a childish way that disrespects the intellect of the reader. However, it did force me to think about the rationale behind nature conservation. Do we need to save all species, such as the Kākāpō?

Ecosystem Services

Currently, the world is driven by economics. It is thus no surprise that scientists have tried to quantify the “economic value” of species in terms of the services that they provide. Some species might be important because they can be used as food sources and other species might play an important role in nutrient cycles. Although I am not a big fan of the concept of ecosystem services, it could be that this perspective contributes convincing evidence for protecting certain species. So, which ecosystem services does the Kākāpō provide? A quick search on Google Scholar revealed no clear studies that addressed this question. At first glance, it seems that the Kākāpō has little to offer in terms of ecosystem services.

There was, however, one PNAS-paper that mentioned how an endemic plant in New Zealand (the Wood Rose, Dactylanthus taylorii) probably relied on the Kākāpō for seed dispersal. Hence, even though the Kākāpō might not be useful for humans (within the context of ecosystem services), other organisms might rely on it. This observation brings me to another argument for nature conservation: ecosystem stability. The extinction of one species might trigger a cascade of negative effects, resulting in the collapse of entire ecosystems. This effect will be most severe when keystone species disappear. Such species tend to have little functional redundancy, meaning that no other species would be able to fill its ecological niche and stabilize the ecosystem. However, not all species are keystone species and the extinction of some species might have little to no effect on the entire ecosystem. It seems reasonable to assume that the Kākāpō does not play a central role in the New Zealand ecosystem. Its extinction would probably have few consequences for ecosystem stability.

Wood roses from the Whanganui Regional Museum. These plants probably relied on the Kākāpō for seed dispersal. Source: Wikimedia Commons.

Intrinsic Value

So far, we have not found any good arguments for preventing the Kākāpō from going extinct. However, the previous paragraphs mainly explored direct advantages of species in terms of ecosystem services. Perhaps the Kākāpō is just valuable in itself. Indeed, a common argument for conserving a species is that each species has intrinsic value: “the value that an entity has in itself, for what it is, or as an end”. In his book, however, Haring argues that species do not have intrinsic value. He states that nothing is valuable in itself, including species. Is that it? The Kākāpō has no value and its extinction is no big problem.

Not so fast. Here, Bas Haring show some philosophical shortcomings. He fails to discriminate between objective and subjective intrinsic value (see here for more information about these concepts). His argument relies on the objective intrinsic value, which is not conferred by humans. And indeed, if humans were to disappear from this planet, the Kākāpō will most likely not have any intrinsic value. But we should not forget about subjective intrinsic value, which is “created by valuers through their evaluative attitudes or judgments.” You only need one person to care about the Kākāpō to give it value. And luckily many people care about this beautiful species.

The Importance of Science

In this blog post, I have tried to follow the rational arguments for saving certain species. And although I am a strong advocate for the power of rationality, it should not blind us. Emotion is an important aspect of nature conservation. Some species might not provide clear ecosystem services or might play a minor role in stabilizing an ecosystem, but that does not mean they have no value. As long as biologists care about a species, it is valuable. And this appreciation for certain species often arises from studying them. Discovering the beauty of species through understanding its ecology and evolution. That is why science is so crucial for nature conservation, and why I will continue to write about the amazing diversity of the natural world.

References

Haring, B. (2011) Plastic Panda’s. Nijgh & Van Ditmar, Amsterdam.

Featured image: Kākāpō (Strigops habroptilus) © Dianne Mason | Wikimedia Commons

Does founder-effect speciation occur in the Silvereye?

Testing this controversial speciation model with genomic data.

Speciation typically takes thousands to millions of years as geographically isolated populations slowly accumulate genetic differences. However, theoretical work suggests that speciation can occur more rapidly. In combinatorial speciation models, for example, the rearrangement of existing genetic variation might give rise to new species in the evolutionary blink of an eye. Another possibility for rapid speciation concerns founder effects, an idea first articulated by Ernst Mayr in 1954. He envisioned how a small number of individuals became geographically isolated from the mainland population. Building on the theoretical work of Sewall Wright (1942), he described a scenario in which the reduced genetic variation and the effects of random genetic drift contribute to the genetic differentiation between the island and mainland population. In addition, extensive inbreeding between the few founders might result in more homozygous loci which are exposed to natural selection. The synergy between genetic drift and stronger selection could speed up the speciation process. Or as Mayr put it in his paper: “It may have the character of a veritable ‘genetic revolution’.” Theoretically, this reasoning makes sense, but what does the actual data say? A recent study in the journal Molecular Ecology tested this founder-effect speciation model for the Silvereye (Zosterops lateralis), a species that has colonized numerous islands in the Pacific Ocean.

Countless Colonization Events

Over the last 200 years, Silvereyes have spread across several islands from their source population on Tasmania. They sequentially reached South Island (New Zealand), Chatham Island, North Island (New Zealand), Norfolk Island and Tahiti. In addition, there have been much older colonization events from the Australian mainland to Heron Island and Lord Howe Island that occurred thousands of years ago. This study system allowed researchers to compare the genetic consequences of founder effects between recent and ancient colonization events. If Mayr’s proposal of “genetic revolutions” is correct, recently founded populations would quickly approach the level of genetic divergence observed in the older island populations. To test this idea, Ashley Sendell-Price and his colleagues sequenced the genomes (using RADseq) of Silvereyes from nine different island populations in the Pacific Ocean.

An overview of the colonization events from Tasmania (in black) to several Pacific Islands, and from Australia (pink) to Heron Island (blue) and Lord Howe Island (purple). The graph on the right shows differences in morphology between the island populations. From: Sendell-Price et al. (2021).

Accumulating Divergence

The genomic analyses showed that genetic divergence accumulates with the sequential colonization events. A more detailed look at these genetic differences revealed that distinct genomic regions diverged in each of the island populations, reflecting the stochastic nature of the founder effect. Although genetic divergence increases with each founder event, the recent island populations do not reach the level of genetic divergence observed in the older populations. This finding indicates that founder-effect speciation is not as rapid as Mayr envisioned it to be. Over time, the recently founded populations might reach the divergence level of the older populations, but it is not a “genetic revolution.” Hence, the authors conclude that “founder-event speciation may be rare in nature.”

The level of genetic divergence (measured as Fst) increases across sequential colonization events, but does not reach the level of genetic divergence at the older populations. From: Sendell-Price et al. (2021).

References

Sendell‐Price, A. T., Ruegg, K. C., Robertson, B. C., & Clegg, S. M. (2021). An island‐hopping bird reveals how founder events shape genome‐wide divergence. Molecular Ecology, 30(11), 2495-2510.

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

How did snowfinches adapt to high-altitude environments?

Were the adaptations already present in the ancestor or not?

In the Origin of Species, Charles Darwin succinctly defined natural selection as the “preservation of favorable variations and the rejection of injurious variations.” This seemingly simple mechanism has given rise to a mind-boggling array of adaptations. However, the exact series of events leading up to an adaptation is often difficult to reconstruct. This issue is especially apparent in groups of closely related species that show the same adaptations. Were these traits already present in a common ancestor or did the species independently evolve these similarities? A recent study in the journal PNAS addressed this question for snowfinches, an assemblage of closely related passerines that have successfully adapted to life at high altitude on the Qinghai-Tibet Plateau. Several adaptations (such as a more efficient metabolism) have been described in great detail, but the underlying evolutionary history remains to be unraveled.

Positive Selection

A large team of Chinese scientists sequenced the whole genomes of three species: the White-rumped Snowfinch (Onychostruthus taczanowskii), the Rufous-necked Snowfinch (Pyrgilauda ruficollis), and the Black-winged Snowfinch (Montifringilla adamsi). Comparing these genetic sequences with several lowland species, such as the Eurasian Tree Sparrow (Passer montanus), allowed the researchers to identify genes under positive selection in the three snowfinch species and their common ancestor. These analyses revealed that about 95% of the positively selected genes (PSGs) differed between the ancestor and descendant species. Moreover, these genes tend to perform drastically different functions. For example, PSGs in the Black-winged Snowfinch are mainly involved in developmental processes, whereas PSGs in the Rufous-necked Snowfinch largely play a role in cellular processes.

Despite these species-specific patterns, some high-altitude adaptations were probably already present in the ancestor. Specifically, the analyses indicated signs of positive selection in genes related to certain developmental processes, cellular signaling and DNA repair systems. Taken together, the researchers concluded that “After initial adaptation in the ancestor, the descendant species have adapted divergently in response to local selective pressures and microhabitats unique to each species, leading to a deviation of adaptations between the ancestor and each of its descendants.”

An overview of positively selected genes (PSG) in three snowfinches and their common ancestor. Analyses of the gene functions revealed significant differences between the ancestor and its descendants. From: Qu et al. (2021).

DNA Repair

To identify genes under positive selection, the researchers partly relied on the ratio between synonymous and nonsynonymous substitutions. Synonymous substitutions do not change the amino acid in the protein sequence due to the redundancy in the genetic code (see this blog post for more details on the genetic code). Hence, these substitutions are generally assumed to be neutral. Nonsynonymous substitutions, however, do lead to a change in the protein sequence which can affect the function of the protein and subject it to natural selection. A gene with more nonsynonymous than synonymous substitutions might thus be under positive selection.

However, a recent study in the journal Nature questioned the neutral nature of synonymous substitutions. Experiments with yeasts revealed that three-quarters of synonymous mutations resulted in a significant fitness reduction. Whether these results can be extended to other organisms remains to be investigated. Indeed, evolutionary dynamics on the molecular level can be drastically different between single-celled yeast and vertebrates, such as birds. Nonetheless, one should always be careful with interpreting the ratio between synonymous and nonsynonymous substitutions. It is only one indication for positive selection. The best strategy is to perform multiple tests to figure out if a gene has been positively selected.

And that is exactly what the researchers in this study did. They focused on DTL, a gene that is possibly under strong positive selection in the snowfinches. This gene plays a role in the repair of UV-induced DNA damage, an important feature when living at high altitude where UV-radiation can be intense. The researchers chemically synthesized the genetic sequences for the DTL-gene in all three snowfinches species, their ancestor and a lowland species (the Eurasian Tree Sparrow). Experiments with the synthetic genes revealed that the DNA-repair capacity of the snowfinch-genes was significantly better than the lowland-version. These results are thus in line with the assumption that DTL has been under strong positive selection in the snowfinches. A great example of how use different lines of evidence to support a conclusion.

Experiments with synthetic DTL-genes indicated that the snowfinch-versions (in different colors) are more efficient compared to a lowland-version (in black). The two graphs represent different ways of quantifying DNA-damage repair based on their molecular products (6-4PP and CPD). From: Qu et al. (2021).

References

Qu, Y., Chen, C., Chen, X., Hao, Y., She, H., Wang, M., … & Lei, F. (2021). The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai–Tibet Plateau. Proceedings of the National Academy of Sciences, 118(13), e2012398118.

Shen, X., Song, S., Li, C., & Zhang, J. (2022). Synonymous mutations in representative yeast genes are mostly strongly non-neutral. Nature, 1-7.

Featured image: Rufous-necked Snowfinch (Pyrgilauda ruficollis) © Dibyendu Ash | Wikimedia Commons