Extensive analyses point to selection on ADCY8, a gene involved in long-term memory.
Many bird species undertake impressive migrations. Think of the Bar-tailed Godwit (Limosa lapponica), a small wader that can cover more than 29,000 kilometers in one year – travelling from Alaska to New Zealand and back. These achievements become even more mindboggling when you consider that several bird species are able to return to their exact breeding grounds. These birds must have a solid long-term memory. And indeed, a recent study in the journal Nature provided convincing evidence for selection on memory-related genes in long-distance migrants of the Peregrine Falcon (Falco peregrinus). Let’s have a look at the details of this exciting finding.
First, the researchers used GPS-transmitters to track the migration of 41 Peregrine Falcons from several Russian locations. The resulting patterns pointed to five distinct migration routes which could be divided into short-distance (Kola and Kolguev) and long-distance (Yamal, Popigai, Lena and Kolyma) migration strategies. Attentive readers might have counted six locations even though I mention only five migration routes. That is because the short-distance migrants from Kola and Kolguev followed the same migration route and were thus clustered together.
Time for some genomic analyses. The researchers sequenced the genomes of 35 Peregrine Falcons and compared the genetic make-up of short-distance and long-distance migrants. This comparison uncovered signatures of 149 selective sweeps – targeting 37 genes – between the two groups. The most significant outlier in this analysis was the gene ADCY8. A closer look at this candidate gene revealed an interesting genetic locus with two alleles: C or T. All long-distance migrants possessed the T-variant, suggesting that there has been strong selection for this particular variant.
When the researchers inspected the DNA-letters surrounding this genetic variant, they recognized the sequence CGTCA, which is a binding motif for the transcription factor CREB. Transcription factors are proteins that control the expression of particular genes by binding with specific DNA sequences. The presence of this motif suggests that the expression of ADCY8 might be tightly regulated. And indeed, when the researchers quantified the expression levels of the different ADCY8-variants in brain tissue, they found that the T-variant was expressed at higher levels than the C-variant. Previous research has shown that this gene is involved in long-term memory by regulating the activity of other memory-related genes. The precise molecular details remain to be unraveled, but the researchers can already conclude:
The higher activity of ADCY8 that we identified in long-distance peregrine migrants may increase their long-term memory. Our analysis reveals a unique mutation that facilitates the binding of the transcription factor CREB1 to ADCY8, and fixation of this variation happened after the divergence of long-distance and short-distance populations. Our work thus not only reveals a causative gene that may explain migratory differences, but also provides a mechanistic basis for these differences.
Genomic data and plumage patterns do not agree with mtDNA in the Western Whistler.
Imagine being able to identify any species by quickly scanning a section of their DNA. That is the rationale behind DNA barcoding where each species is linked to a specific DNA sequence (mostly the mitochondrial gene COI). This approach – introduced by Paul Hebert and his colleagues – sounds promising but has several shortcomings and pitfalls. An opinion paper on insect taxonomy succinctly summarized the situation: “While we do believe that barcode clusters are indeed useful as grouping statements, there is no compelling reason why they should be described as species.” I could not agree more: DNA barcodes can generate taxonomic hypotheses, but these remain to be confirmed with additional data, such as genomics, morphology or behavior. Taxonomy is a pluralistic practice that requires expert knowledge, and cannot be condensed into an automated procedure of scanning DNA barcodes. The possible problems with only relying in DNA barcodes were nicely illustrated by a recent Emu paper on the taxonomy of Australian Whistlers (genus Pachycephala).
Genomicsand Plumage Patterns
In 2014, Leo Joseph and his colleagues argued to split the Golden Whistler (P. pectoralis) into two, adding the Western Whistler (P. occidentalis) to the checklist of Australian birds. This decision was largely based on analyses of the mitochondrial DNA which separated the western populations of the Western Whistler (then classified as the subspecies P. pectoralis fuliginosa) from all other populations of the Golden Whistler. Interestingly, the mtDNA of eastern populations of P. pectoralis fuliginosa was different from the western populations, leading the researchers to include them in the Golden Whistler. The nuclear markers (eight loci) in these analyses did not provide any additional insights. Hence, the researchers decided to recognize only the western populations as a separate species: the Western Whistler.
This taxonomic arrangement is now called into question by a recent genomic study (again by Leo Joseph and his colleagues). Using almost 20,000 genetic markers, the researchers identified three main clusters:
Eastern mainland and Tasmanian subspecies of the Golden Whistler (pectoralis, youngi and glaucura)
Western subspecies of the Golden Whistler (fuliginosa)
Western Whistler (P. occidentalis)
More importantly, the latter two clusters – the western subspecies and the Western Whistler – are closely related to each other. This genetic connection is further strengthened by morphological data. In the eastern subspecies, adult females and immatures have grey chests and bellies accompanied by yellow or white under-tail coverts. The plumage patterns are quite different in the western subspecies and the Western Whistler where adult females and immatures are cinnamon from the chest to the under-tail coverts (see drawings on the figure below).
These patterns present a taxonomic conundrum: based on genomic data and plumage patterns, the fuliginosa subspecies clusters with the Western Whistler, while mtDNA places it with the eastern populations. The most parsimonious explanation for these findings entails that what had been retained in the 2014 paper as the fuliginosa subspecies of the Golden Whistler P. pectoralis is most closely related to what the same paper called the Western Whistler P. occidentalis. This population was isolated in southwestern Australia, but has received mtDNA from the mainland eastern populations of Golden Whistler through introgressive hybridization. Based on this scenario, the researchers propose that the Western Whistler should be expanded to include what was the fuliginosa subspecies of P. pectoralis. Because the name P. fuliginosa Vigors & Horsfield, 1827 has priority over P. occidentalis Ramsay, 1878, the scientific name of the Western Whistler will be changed to P. fuliginosa. Possibly, introgression is still in progress and has not yet reached the western populations of the Western Whistler that now become known as P. fuliginosa occidentalis. However, it is more likely that 200 kilometers of unsuitable habitat between the two subspecies of P. fuliginosa poses a significant barrier.
Apart from this taxonomic bookkeeping, this finding carries an important warning on the use of DNA barcodes. Solely relying on mtDNA and a few incompletely sorted nuclear loci for delineating species led to the wrong classification among these whistlers. The analyses of genomic data and plumage patterns provided the complete picture. To reiterate the message from the start of this blog post: DNA barcodes can generate taxonomic hypotheses, but these remain to be confirmed with additional data.
Joseph, L., Campbell, C. D., Drew, A., Brady, S. S., Nyári, Á., & Andersen, M. J. (2021). How far east can a Western Whistler go? Genomic data reveal large eastward range extension, taxonomic and nomenclatural change, and reassessment of conservation needs. Emu-Austral Ornithology, 121(1-2), 90-101.
This evolutionary process shaped the morphological patterns among these animals.
On the Avian Hybrids blog, I often write about introgression, the exchange of genetic material through hybridization and backcrossing. This phenomenon can be detected with numerous methods (which I covered in this review), including the observation that some gene trees deviate from the species tree. When a gene is transferred from one species to another, it is logical that its trajectory might deviate from the main evolutionary history. However, a discordant gene tree does not automatically imply introgression. Other evolutionary processes can produce similar patterns. A recent study in the journal Celltook a closer look at one of these processes: incomplete lineage sorting.
ILS and M&Ms
I have always found incomplete lineage sorting (or ILS) a difficult concept to grasp. In essence, it refers to the sorting of genetic variation from an ancestral population into several descendant lineages. An analogy might be helpful. Consider a big jar of differently colored M&Ms (i.e. the ancestral population with genetic variants). If you would randomly divide these colorful candies into four small jars (i.e. the descendant lineages), you can expect that these jars will share some colors. You will likely not end up with one color per jar. The bigger the ancestral jar, the less likely that the candies will be completely sorted per color in the small jars. Over time, the contents of the small jars might become homogenized through the removal of certain colors (either randomly or by a selected eater that might prefer certain colors). At some point, you might end up with nicely color-sorted M&M-jars. Obviously, this analogy is not perfect but I hope you get the general idea. ILS is the random distribution of ancestral variation into descendant lineages.
Now that we have a good understanding of ILS, we can dive into the paper which focused on the evolution of marsupials. I am aware that marsupials are not birds, but the methods and findings of this study were so cool that I could not let it slide. There is more to life than avian hybrids. In the study, the researchers focused on the phylogenetic position of the Monito del Monte (Dromiciops gliroides). It is unclear whether this South American species is most closely related to the Diprotodontia (e.g., the Koala, Phascolarctos cinereus) or the Dasyuromorphia (e.g., the Tasmanian Devil, Sarcophilus harrissii). Some studies have found that the Monito del Monte is the sister species to these two clades, while other studies placed it within one of the two groups. Using whole genome sequences, Shaohong Feng and colleagues provided some clarity in this evolutionary mystery and presented convincing evidence that the Monito del Monte is indeed the sister species to the two Australian groups.
Next, the researchers quantified the level of gene tree discordance (i.e. the number of gene trees deviating from the species tree). They found that more than 50% of the investigated genes did not follow the evolutionary pattern of the species tree. In about 30% of the cases, the Monito del Monte clustered with the Diprotodontia. And roughly 28% of the gene trees combined the Monito del Monte with the Dasyuromorphia. To determine whether these patterns are due to ILS or hybridization, the researchers performed a suite of additional analyses. I will focus on one particularly interesting approach: comparing divergence times of gene trees. Hybridization occurs when speciation has already started whereas ILS can be traced back to the ancestral population. Hence, deviating gene trees with older divergence times point to ILS. And indeed, the researchers noted:
Our analyses confirmed that the ILS regions had an older divergence time between monito del monte and the Dasyuromorphia (52.3 mya) or the Diprotodontia (54.0 mya) than the genomic regions that corresponded with the actual species differentiation (45.8 mya). Moreover, the biogeographic data show that the final separation of Australia and Antarctica along the South Tasman Rise occurred at ca. 45 mya, i.e., at the time that early diversification of the Australian marsupials began according to our estimation.
This results was corroborated by several other analyses, such as D-statistics, quantifying introgression via branch lengths (QuIBL) and coalescent hidden Markov models (CoalHMM). I will not dive into the details of these methods. The main message is that ILS has been a dominant force in the evolution of marsupials.
The finding that ILS has played such a big role during the radiation of marsupials is definitely interesting, but the best part of the study is yet to come. Numerous studies have documented ILS, but few have explored the consequences of this process. In the Cell-paper, the researchers did go one step further. They identified several genes that have been impacted by ILS and determined the morphological effects of these genes. Using experiments with transgenic mice.
The gene WFIKKN1, for example, is involved in the development of vertebrae. The Monito del Monte and the Koala carry one version of this gene (with a glutamine at position 76), whereas the Tasmanian Devil has another version (with am arginine). These species also differ the structure of the spinous process, which is a bony projection off the back of each vertebra. In the Monito del Monte and the Koala, the first spinous process on the vertebra is quite long. In the Tasmanian Devil, however, the first spinous process is significantly shorter. When the researchers introduced the Tasmanian Devil-variant in transgenic mice, they observed a decrease in the spinous process. Direct evidence of the morphological effect of this gene!
What does this all mean? The observation that ILS can create similar morphologies in distantly related species forces us to partly rethink how evolution works. These morphological similarities are generally explained as the result of convergent evolution. Distantly related species have independently evolved the same phenotype, probably driven by different genetic changes. When ILS is involved, this picture changes. The morphological similarities can be traced back to the same genetic changes that were present in the distant ancestors of these species. These traits did not arise multiple times independently, but originated once and were then distributed across distinct descendant lineages. A subtle but crucial difference. The observation that not all morphological similarities between distantly related species are the outcome of convergent evolution has important implications for (macro)evolutionary analyses. Moreover, considering that introgression can also transfer traits across the evolutionary tree (e.g., the white coat of snowshoe hares), it is clear that reconstructing the evolutionary history of a trait is no easy feat.
Feng, S., Bai, M., Rivas-González, I., Li, C., Liu, S., Tong, Y., … & Zhang, G. (2022). Incomplete lineage sorting and phenotypic evolution in marsupials. Cell.
The number of sympatric species can constrain the evolutionary process.
When closely related species occur in the same area, they might occasionally interbreed. If the resulting hybrids are unfit – for example, sterile or unviable – there will be a strong selection against hybridization. This selective pressure would then promote increased divergence between the species. In other words, the species will look or sound more different over time. This reasoning makes intuitive sense, but that doesn’t mean we should not test it. We might have missed a crucial aspect in our reasoning. Armchair theorizing can be valuable, but needs to be validated with direct observations or experiments. That is exactly what a recent study in the Proceedings of the Royal Society B did, using wood-warblers (family Parulidae) as a study system.
First, Richard Simpson and his colleagues tested the prediction that sympatric species are more divergent in sexual signals, such as plumage and song, compared to allopatric species. In addition, they went one step further and assessed the influence of the number of co-occurring species on the evolution of these sexual signals. When multiple species co-exist, the options for divergence become more constrained. The evolution of different plumage patterns or songs might push a species into the signal space of another related species. You can compare this situation with a busy party where you are trying to avoid some obnoxious guests. As you move away from one annoying person, you might accidently bump into another one. Again, this idea makes sense, but is it supported by the data?
The researchers amassed an impressive dataset on the morphological and acoustic features of numerous wood-warblers. For 818 museum specimens (representing 93 species), the plumage reflectance of 15 body regions was measured. The resulting patterns did not support the first prediction: allopatric wood-warbler species showed more divergent plumage patterns compared to sympatric ones. The researchers attributed this finding to the effect of habitat: “Species that occur in allopatry likely do not share similar habitats, while those in sympatry likely do (i.e. light environment, visual background, predatory species.” This explanation sounds reasonable, but requires further investigation.
When limiting the analyses to sympatric species, the prediction was borne out though. The more species overlapped in distribution, the more divergent their plumage patterns. Moreover, the number of sympatric species had a clear effect on the evolution of sexual signals. As more wood-warbler species were found in the same area, the occupied space of colors tended to reach a plateau. This pattern suggests that further divergence becomes constrained by the available signal space. To return to our analogy: the more annoying people at the party, the less room you will have to more around safely.
The predictions formulated at the beginning of this blog post seem to hold for plumage patterns. But what about song features: do sympatric birds sing more divergent songs? Based on the analyses of 494 song recordings – representing 102 species – the answer is a resounding no. In fact, the exact opposite pattern was observed. Species with more overlapping distributions produced similar songs. The researchers called upon the “acoustic adaptation hypothesis” to explain this finding: “Species that exhibit higher degrees of sympatric overlap likely occur in more similar habitats, and these habitats are driving song evolution so that songs are optimally transmitted within the local environment.” A reasonable explanation that needs to be tested in future studies.
These findings nicely show that we should take into account alternative explanations and test our ideas with observations and experiments. Reasoning from a comfortable armchair only gets you so far. Don’t forget to test your ideas. I cannot help but think of these words by physicist Richard Feynman:
If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is … If it disagrees with experiment, it’s wrong. That’s all there is to it.
Simpson, R. K., Wilson, D. R., Mistakidis, A. F., Mennill, D. J., & Doucet, S. M. (2021). Sympatry drives colour and song evolution in wood-warblers (Parulidae). Proceedings of the Royal Society B, 288(1942), 20202804.
What genes determine the migratory strategies of birds? Several studies have tried to answer this question in a variety of study systems, such as Vermivora warblers, European Blackcaps (Sylvia atricapilla) and Willow Warblers (Pylloscopus trochilus). Interestingly, different candidate genes have popped up in different studies, suggesting that the genetic basis for migration varies between species. In the Willow Warbler, for example, researchers took advantage of the divergent migratory strategies of two subspecies: trochilus migrates to the southwest, whereas acredula follows a southeastern route. These migratory differences were associated with three genomic regions, located on chromosomes 1, 3 and 5. However, a previously identified genetic variant – using the older AFLP-technique – could not be assigned to a particular genomic region. Given that most avian genome assemblies are far from complete, it could be that this variant – known as WW2 – resides in a difficult-to-assemble section of the genome, such as a region with repetitive sequences. That is why Violeta Caballero-López and her colleagues used an updated version of the Willow Warbler genome to determine the location and identity of the WW2-variant. Their findings recently appeared in the journal Molecular Ecology.
The newest Willow Warbler genome was sequenced using a long-read technique which allows scientists to reconstruct highly repetitive sections of the genome. Within one of these section, the researchers found the WW2-variant. Additional analyses indicated that it concerns a transposable element, which is a selfish genetic element that “jumps” around the genome using either a copy-and-paste or a cut-and-paste mechanism. This particular transposable element turned out to be an endogenous retrovirus (ERV) that inserted itself into the genome of an ancestral songbird a long time ago. A similar variant is also present in the genome of the Zebra Finch (Taeniopygia guttata), which diverged from the Willow Warbler at least 20 million years ago.
A detailed look at the WW2-variant revealed additional evolutionary changes. Apart from the ancestral version shared with the Zebra Finch, the researchers also uncovered a derived version. The latter version probably originated after a duplication and an inversion event. The resulting sequence then accumulated mutations, leading to divergence from the ancestral state. Interestingly, the derived version was much more abundant in the acredula-subspecies (7 to 45 copies) compared to the trochilus-subspecies (0 to 6 copies).
The different number of copies of the derived version in the two subspecies suggests that the transposable element might be involved in their migratory behavior. The genomic region surrounding the WW2-variant contains several olfactory receptors. It is tempting to speculate that olfaction might help Willow Warblers during their migration (as shown in homing pigeons), but the researchers warn that more analyses are needed to test this hypothesis. Alternatively, the WW2-variants might interact with other genomic regions – perhaps the ones on chromosomes 1, 3 and 5 – to influence migratory behavior. A similar mechanism has been described in Carrion Crow (Cornix c. corone) and Hooded Crow (C. c. cornix) where a transposable element might be involved in the regulation of plumage coloration. Clearly, there are many new exciting questions to investigate in the Willow Warbler. Just as transposable elements “jump” around the genome and explore new territories, scientists keep delving into knowledge gaps to uncover surprising new insights. You never know where the next analysis will take you…
Caballero‐López, V., Lundberg, M., Sokolovskis, K., & Bensch, S. (2022). Transposable elements mark a repeat‐rich region associated with migratory phenotypes of willow warblers (Phylloscopus trochilus). Molecular Ecology, 31(4), 1128-1141.
Recent study reports correlated evolution of immune and pigmentation genes.
Charles Darwin famously wrote: “The sight of a feather in a peacock’s tail, whenever I gaze at it, makes me sick!” He was referring to the fact that the elaborate tail of this colorful bird could not be explained by his recently published theory of natural selection. How could such a clumsy feature improve the survival chances of a male peacock? Later on, Darwin proposed a solution to this conundrum in another book The Descent of Man, and Selection in Relation to Sex: sexual selection. According to this mechanism, males compete for access to females, either directly through male-male competition (think of the antlers of male deer) or indirectly by advertising themselves with beautiful songs and extravagant feathers.
But how do females make a choice? Some authors have argued that females pick a partner based on aesthetic preferences; females just select what they “like”. Richard Prum has defended this neutral model of sexual selection in his book The Evolution of Beauty. Alternatively, the elaborate traits of males are honest signals that females use to discriminate between males with “good” and “bad” genes. One particular hypothesis – proposed by William Hamilton and Marlene Zuk – suggests that sexual traits indicate the immune function of a bird. Males that can easily fend off parasites will have plenty of energy left to develop extravagant feathers, while males infected with parasites will look drab and sickly. A recent study in the journal Frontiers in Ecology and Evolution tested this Hamilton-Zuk hypothesis with genomic data.
Shubham Jaiswal and his colleagues used a set of eleven high-quality bird genomes to gain more insights into the genomic basis of sexual selection. First, they estimated the strength of sexual selection for each species, making a distinction between pre-copulatory selection (i.e. females picking a partner) and post-copulatory selection (i.e. sperm competition). Pre-copulatory selection was estimated by scoring the degree of sexual dimorphism: the more different males and females look, the stronger sexual selection. For example, the Indian Peafowl (Pavo cristatus) scored high for this index, while the Budgerigar (Melopsittacus undulatus) had the lowest score. Post-copulatory selection could be assessed through the ratio of testis to body weight. Species with fierce sperm competition need to produce more sperm cells and will probably have bigger testes.
These two measures of sexual selection – sexual dimorphism and testis weight – were consequently correlated with several parameters of gene evolution, such as substitution rates and estimates of selection. The analyses resulted in a set of 60 candidate genes that are potentially targets of sexual selection. Interestingly, most of these genes are involved in the regulation of gene expression and some are known to coordinate the development of sexual dimorphism. Additional tests of selection indicated that the majority of these genes are subject to purifying selection, the removal of (slightly) deleterious genetic variants. This evolutionary model is in line with the Hamilton-Zuk hypothesis where males with inferior immune systems are selected against.
The observation of purifying selection on the candidate genes might make sense within the framework of the Hamilton-Zuk hypothesis. However, it is not direct evidence for this controversial idea. The most convincing piece of evidence came from a second set of analyses, namely patterns of correlated evolution between different genes. The researchers identified 228 genes that showed significant signs of correlated evolution and had well-defined functional annotations. Within this network of correlated evolution, many gene pairs were involved in immunity and feather development or pigmentation. Based on these findings, the researchers noted that:
[This] provides a “mechanistic link” or a connection between genome and phenotypic coevolution which in such cases would include plumage color and other secondary sexual characters responsible for sexual selection and honest signaling. Therefore, the Hamilton-Zuk explanation for the persistence of variation in the phenotypes of sexual selection as a consequence of the arms-race between parasite and immune genes is substantiated by this study.
However, it is important to keep in mind that these are correlations. Remember the age-old warning: correlation is not causation. These candidate genes are a promising starting point for future research, but we should not jump to conclusions. There is still much to learn about the genetic basis of sexual selection, whether it involves the immune system or not.
Jaiswal, S. K., Gupta, A., Shafer, A., PK, V. P., Vijay, N., & Sharma, V. K. (2021). Genomic Insights Into the Molecular Basis of Sexual Selection in Birds. Frontiers in Ecology and Evolution, 2.
A few genomic regions might contribute to strong pre-mating isolation.
The French biologist François Jacob described the evolutionary process as tinkering. Evolution does not create new organs or functions out of thin air, but instead works with what is available. On the molecular level, the constant influx of (nearly) neutral mutations expands the pool of genetic variation. When the environment suddenly changes, populations might benefit from certain genetic variants that were already present and quickly adapt. For example, this process probably allowed some populations of the Vinous-throated Parrotbill (Sinosuthora webbiana) to rapidly adapt to high altitude conditions on Taiwan. Apart from speedy adaptation, the reshuffling of genetic variants can also fuel the origin of new species. A recent study in the journal Science documents a beautiful example of so-called combinatorial speciation in Sporophila Seedeaters.
Three Genomic Regions
In October 2001, the Ibera Seedeater (S. iberaensis) was first observed within the breeding range of the closely related Tawny-bellied Seedeater (S. hypoxantha). Both species belong to a radiation of southern capuchino seedeaters that originated within the last million years. The perfect study system to understand the genetic underpinnings of rapid speciation. When the researchers compared the genomes of the Ibera Seedeater and the Tawny-bellied Seedeater they noticed that the differences between these species are concentrated in three genomic regions (located on the Z-chromosome and chromosomes 1 and 11). The regions contain several genes involved in plumage coloration, such as TYRP1, OCA2 and HERC1. These patterns suggest that differences in plumage patterns might contribute to reproductive isolation between these species (more on that later).
Interestingly, the genetic variants in these three genomic regions were also found in other seedeater species. The combination in the Ibera Seedeater, however, was unique for this species. The researchers noted that “this result implies that the S. iberaensis phenotype likely arose through the reshuffling of standing genetic variation that already existed within the other southern capuchinos, providing a mechanism for rapid speciation without the long period required for relevant mutations to arise de novo.” An intriguing conclusion that nicely aligns with previous work on this radiation (see for example this blog post).
In the previous section, I already hinted at a possible role of plumage in reproductive isolation. The researchers provided convincing evidence that this is indeed the case. First, they tested for assortative mating by genotyping several nests of both species. These analyses revealed that all partners belonged to the same species, no hybrids were found (even after accounting for the high rate of extra-pair copulations). Next, the researchers performed playback experiments in which territorial males were presented with different combinations of conspecific and heterospecific song and plumage. These experiments corroborated the patterns of assortative mating: “Each species responded most aggressively to the combination of conspecific song and plumage, exhibited intermediate responses to the treatments with mismatched traits, and largely ignored the heterospecific capuchino traits and those of the control species.”
Together, these analyses point to strong pre-mating isolation between Ibera Seedeater and Tawny-bellied Seedeater. And as explained above, the traits underlying this reproductive isolation probably originated through the reshuffling of already existing genetic variants. Isn’t evolution a wonderful tinkerer?
Turbek, S. P., Browne, M., Di Giacomo, A. S., Kopuchian, C., Hochachka, W. M., Estalles, C., … & Campagna, L. (2021). Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater. Science, 371(6536), eabc0256.
Comparing four species of Ficedula flycatchers to unravel their genomic landscape of differentiation.
One of the most interesting debates in speciation research revolves around the genomic landscape of differentiation. Scan across the genomes of two closely related species and calculate the level of genetic differentiation as you go along. This exercise will probably reveal a heterogenous picture with some genomic regions that show little genetic differences, and other regions that are highly divergent. With some imagination, you can recognize a hilly landscape with valleys and peaks. Most research efforts have focused on the origin of the peaks in this landscape, so-called “genomic islands of differentiation”. What evolutionary processes underlie the formation of these differentiated regions?
Reproductive Isolation and Selection
The earliest studies interpreted these patterns in the context of speciation-with-gene-flow, suggesting that these genomic islands contain loci that contribute to reproductive isolation. When two species interbreed, these barrier loci are expected to be immune to introgression. Hence, they will diverge while the remainder of the genome is homogenized by introgression. This explanation might apply to some study systems, such as bean geese.
Alternatively, selection events might be responsible for origin of genomic islands. This can either be negative selection against recurring deleterious alleles (also known as background selection) or positive selection for beneficial alleles. Because peaks in genetic differentiation are often shared between species, some authors have argued that positive selection is not a reasonable explanation. The rationale is that positive selection is unlikely to occur in the same genomic regions over long evolutionary periods. Instead, background selection is presented as the dominant force shaping genomic landscapes. Because the genomes of birds are relatively stable – in terms of recombination rate and gene density – the targets of background selection will remain the same over millions of years.
To discriminate between background selection and positive selection, it would make sense to choose on a study system where introgression plays a minor role. That is why Madeline Chase and her colleagues focused on two independent species pairs of Ficedula flycatchers: the Pied Flycatcher (F. hypoleuca) and the Collared Flycatcher (F. albicollis), and the Red-breasted Flycatcher (F. parva) and the Taiga Flycatcher (F. albicilla). First, they constructed the genomic landscapes of these species pairs and identified the location of numerous genomic islands of differentiation (based on the summary statistic FST). Next, the researchers performed several tests for positive selection, namely Fay and Wu’s H and the composite likelihood test (CLR). The analyses revealed that most selective sweeps coincided with the previously identified peaks in FST. These findings suggest that positive selection plays an important role in shaping the genomic landscape of these flycatchers (similar to patterns uncovered in Sporophila Seedeaters using a different method).
Now that we know that positive selection is involved, we can go one step further: when did these selective sweeps happen? Are these genetic signatures the result of repeated selection in these species and their ancestral population (i.e. recurrent selection model) or do they represent species-specific selection after speciation occurred (i.e. selection in allopatry model). Some researchers proposed that you can discriminate between these models by looking at three different summary statistics: FST, DXY and π (see this blog post for a detailed explanation). The rationale behind this approach was nicely described in the paper:
Because DXY is unaffected by current levels of diversity, under the selection in allopatry scenario, DXY is expected to be similar both within and outside of FST peaks. However, when selection has recurrently impacted a region from the common ancestor of two species, ancestral diversity will have also been reduced, leading to a reduction in DXY in FST peaks.
Calculating DXY across the species pairs indicated that this summary statistic was consistently lower in the FST peaks for Pied and Collared Flycatcher. A pattern that is consistent with recurrent selection. In the Red-breasted and Taiga Flycatcher comparison, however, this was not the case: DXY was higher in the FST peaks. What is going on here? The researchers think that as species differentiation proceeds, substitutions become fixed in certain genomic regions – perhaps due to positive selection – resulting in a higher DXY value. Because Red-breasted and Taiga Flycatcher diverged before Pied and Collared Flycatcher, they have had more time to accumulate substitutions and inflate their DXY. The shared FST peaks might thus still be the outcome of recurrent selection. Hence, the timescale of species divergence is important to keep in mind when interpreting these summary statistics.
Finally, the researchers also uncovered several lineage-specific signatures of selection that seemed to coincide with changes in local recombination rates. All in all, the patterns uncovered in this study highlight the interplay of positive selection and recombination in the evolution of genomic landscapes of differentiation.
Chase, M. A., Ellegren, H., & Mugal, C. F. (2021). Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs. Evolution, 75(9), 2179-2196.