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 Sciences118(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

How can Snowfinches and Tree Sparrows survive at high altitudes?

Experimental work points to a more efficient metabolism in highland birds.

Life in the mountains is not easy. At very high altitudes, the concentration of oxygen drops, potentially leading to severe health risks. Nonetheless, several animal species – including humans – manage to thrive in these extreme conditions, despite facing many physiological challenges. Apart from the low oxygen concentrations in mountainous areas, temperature can also significantly drop. One important hurdle for high altitude animals thus concerns keeping a stable body temperature in these cold environments. Moreover, you will also need to move around to gather food and find a mate. An efficient energy metabolism is thus crucial.

There are several ways to amp up your metabolism, such as bigger muscles to do the work, more capillaries to transport the little oxygen that is available, and having more mitochondria (the powerhouse of the cell) in your muscle fibers. A recent study in the journal PLoS Genetics took a closer look at three high altitude bird species: the White-rumped Snowfinch (Onychostruthus taczanowskii), the Rufous-necked Snowfinch (Pyrgilauda ruficollis), and the Tree Sparrow (Passer montanus). It turned out that these species do indeed have bigger pectoral muscles and more mitochondria in their muscle fibers. But these phenotypic features were just the tip of the iceberg.


Glucose

Experimental work on these species revealed that they showed more efficient use of glucose (i.e. blood sugar). After a meal, the level of glucose in the blood increases. This rise in blood sugar triggers the production of the hormone insulin which converts some glucose into glycogen for later use and makes body cells take up the circulating glucose. These processes bring the blood sugar level down to stable levels. The researchers compared the processing of glucose in highland and lowland birds. The experiments indicated that “highlanders exhibited a more rapid normalization of blood glucose.” The difference between highland and lowland birds was even more pronounced when they were injected with insulin (an extra trigger to convert the glucose), suggesting that highland birds are more sensitive to this hormone. The extra insulin sensitivity can be regarded as an adaptation to life at high altitudes.

The left figure showed that Highland species (indicated in red and blue) exhibited more efficient glucose processing compared to lowland species (in green). In addition, the highland species were more sensitive to insulin than the lowland species (right figure). From: Xiong et al. (2020) PLoS Biology.

Candidate Genes

Next, the researchers focused on the genetic basis of these adaptations. They correlated the muscle phenotypes with genetic data in search of candidate genes, and they looked at gene expression data to see which genes were active in the muscle tissue. These analyses uncovered two interesting genes: EPAS1 and MEF2C. Readers familiar with the literature on hybridization might recognized the first gene. EPAS1 has been found in several human populations that adapted to high altitudes. Moreover, one variant of this gene probably introgressed from the extinct Denisovans into Tibetans. EPAS1 becomes active in low oxygen conditions. The other gene – MEF2C – ensures the maintenance of muscle mass and healthy glucose levels, important features when living in the mountains.

Finally, more detailed genomic analyses on highland and lowland populations of the Tree Sparrow revealed additional candidate genes. Several of these genes have also been identified in other high altitude species, such as the Andean House Wren (Troglodytes aedon) and the Band-winged Nightjar (Hydropsalis longirostris), pointing to convergent evolution. The most important ones were:

  • HBB (involved in oxygen affinity)
  • BNIP3L (breakdown of mitochondria when oxygen levels are low)
  • METTL8 (associated with metabolic diseases in humans)

The last gene in this list (METTL8) is especially interesting, because certain variants of this gene were significantly associated with the expression of MEF2C (the gene found in the previous analyses). Additional experiments showed that birds with an particular mutations at sites 326 and 395 in this gene developed larger muscles and expressed more MEF2C. A few genes might thus make life at high altitudes a little bit easier.

Two mutations in the METTL8-gene (highlighted with red arrows) result in higher muscle mass (left figure H) and more production of the gene MEFC2 (right figure H). From: Xiong et al. (2020) PLoS Genetics.

References

Xiong, Y., Fan, L., Hao, Y., Cheng, Y., Chang, Y., Wang, J., Lin, H., Song, G., Qu, Y. & Lei, F. (2020). Physiological and genetic convergence supports hypoxia resistance in high-altitude songbirds. PLoS Genetics16(12), e1009270.

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

The constrained evolution of a hybrid species, the Italian Sparrow

Unraveling the complex interplay between standing genetic variation and genetic incompatibilities.

The genome of a hybrid species is a mosaic of its parental species. In the case of the Italian Sparrow (Passer italiae), it is a mixture of the genetic material from the Spanish Sparrow (P. hispaniolensis) and the House Sparrow (P. domesticus). Combining the gene pools of two species might provide hybrid species with an unprecedented level of evolvability, allowing them to quickly adapt to new environments. There is, however, an important catch: genetic incompatibilities. The parental species have diverged over time and some genetic combinations might not work in a hybrid. Such incompatible variants can result in significant evolutionary constraints. In a previous blog post, I illustrated this situation with dealing cards. Each card can be seen as a specific genomic region. Black cards represent the House Sparrow and red cards the Spanish Sparrow. Some genomic regions might come exclusively from one parent. For example, you will always receive a black queen, but never a red one. There are thus some constraints on the formation of hybrid genomes: not all combinations are possible. A recent study in the journal Molecular Ecology explored whether such constraints have influenced the evolution of the Italian Sparrow.

Genetic Variation

Angélica Cuevas and her colleagues took a closer look at the genomes of 131 Italian Sparrows and uncovered moderate genetic differentiation between eight populations. Interestingly, the genetic differences between these Italian Sparrow populations were mainly found in genomic regions that are not divergent between the House Sparrow and Spanish Sparrow. This observation suggests that not all parental variation is available for the Italian Sparrow. Some (divergent) genetic variants might be incompatible and will be purged from the hybrid population.

Do these incompatibilities hamper the evolution of the Italian Sparrow? Although they might prevent certain variants from reaching this hybrid species, there is still plenty of genetic variation available for adaptation. In fact, the analyses provided no evidence for novel variation (i.e. recent mutations in the Italian Sparrow) being important in local adaptation. Instead, the researchers write that “Standing genetic variation inherited from the parental species is a likely explanation for much of the genomic variation in the hybrid species, and some of the variation may be involved in subsequent local adaptation.” Indeed, detailed genomic analyses revealed several genomic regions under selection, containing some interesting candidate genes involved in the development of beak morphology.

Genomic analyses uncovered moderate population structure in the Italian Sparrow. The genetic variants underlying this differentiation were not divergent between the parental species, suggesting some evolutionary constraints. From: Cuevas et al. (2021) Molecular Ecology.

Delicate Balance

This study nicely illustrates the benefits and downsides of hybrid genomes. On the one hand, genetic variation from both parental species provides the opportunity for rapid adaptation. On the other hand, genetic incompatibilities prevent the formation of certain genomic combinations and can thus constrain evolutionary changes. In the end, some hybrid species will manage to find a viable balance between these opposing forces, allowing them to thrive in novel environments that are unavailable to their parental species. As Anna Runemark, Mario Vallejo-Marin, and Joana Meier wrote in a recent review: “Hybrid genomes are important components of biodiversity and hybrid origin may spur adaptation. Future investigations into the properties of hybrid genomes will improve our understanding of the potential of hybridization to produce novel adaptive variation.” The Italian Sparrow will certainly continue to contribute to our quest to understand the evolution of hybrid genomes.

References

Cuevas, A., Ravinet, M., Sætre, G. P., & Eroukhmanoff, F. (2021). Intraspecific genomic variation and local adaptation in a young hybrid species. Molecular Ecology30(3), 791-809.

Featured image: Italian Sparrow (Passer italiae) © Omar Bariffi | Flickr