Applying the Biological Species Concept to Bacteria

Introgression is not limited to Eukaryotes.

Over the years, I have written several blog posts about species concepts (see for example here and here). I argued that most biologists currently follow the General Lineage Concept or the Evolutionary Species Concept, which both regard species as independently evolving lineages. Laypeople are probably most familiar with the Biological Species Concept (or BSC), defining species as “a group of organisms that can successfully interbreed and produce fertile offspring.” However, this concept can be difficult to apply in certain situations, such when populations are geographically isolated and will never meet. Another common criticism is that the BSC cannot be applied to Bacteria because they do not reproduce sexually. You can imagine my surprise when I came across a recent paper in the journal Genome Biology where researchers applied the BSC to Bacteria:

Some bacteria can engage in gene flow via homologous recombination and this observation has led a growing number of researchers to suggest that bacterial species and speciation might be best defined using the same evolutionary theory developed for sexual organisms; the biological species concept (BSC).

Introgression and Recombination

Awa Diop and her colleagues studied more than 30,000 bacterial genomes. First, they classified these genomes into species by using a cut-off value of 94% genetic similarity in a set of core genes. This arbitrary threshold is commonly applied to delineate bacterial “species”. In this study, however, it mainly allowed the researchers to create a set of “species” for further analyses. To determine whether there has been introgression between these different bacterial “species”, the researchers calculated the ratio between homoplasmic (h) and non-homoplasic (m) alleles. A homoplasmic allele is a genetic variant that is not the result of inheritance from parent to offspring (i.e. vertical inheritance). Instead, such an allele can be the outcome of introgression between bacterial species (i.e. horizontal transfer) or convergent evolution (i.e. bacteria that independently acquire the same mutation). Clonal species – that reproduce asexually – are expected to have few homoplasmic alleles and thus a low h/m ratio. Introgression will result in an increased h/m ratio due to the accumulation of homoplasmic alleles.

In addition, introgression will be accompanied by recombination, the exchange of homologous sections of chromosomes. This process leads to the breakdown of linkage between certain alleles – also known as linkage disequilibrium (LD) – across chromosomes. Clonal species don’t engage in recombination and will thus show no reduction in linkage disequilibrium.

The researchers simulated bacterial genomes without gene flow and compared these patterns – in terms of h/m ratio and LD – with the actual data. These analyses revealed that most bacterial “species” showed signs of introgression and only 2.6% were truly clonal. Some kind of sexual reproduction among Bacteria seems to be more common than we expected.

Genomic analyses pointed to high levels of gene flow (or introgression) between bacterial species. From: Diop et al. (2022).

MEPS

Although the level of introgression among bacterial “species” varied extensively (see figure above), it correlated nicely with sequence similarity. The more similar two species are on a genetic level, the higher the level of introgression uncovered in this study. This pattern can be explained by the observation that homologous recombination requires nearly identical stretches of DNA (also known as MEPS, Minimal Efficient Processing Segments). As genomes diverge, the density of these MEPS decreases and recombination becomes less likely. The relationship reported in this study shows a rapid reduction in introgression between 2% and 10% of sequence divergence. This result explains why an arbitrary threshold to define species of about 95% has been so useful in the past. However, introgression occurred between species that were 90% to 98% divergent. The exact threshold for bacterial species boundaries will thus depend on the study system. There is no silver bullet.

The relationship between sequence identify and level of introgression shows a sharp turn at ca. 90% sequence divergence. From: Diop et al. (2022).

From Bacteria to Birds

You might be wondering why I am covering a paper about bacterial species on a blog dedicated to birds. There are two main reasons: (1) I have a broad interest and don’t want to limit myself to literature on avian hybridization, and (2) you can learn a lot from other study systems. In this case, I noticed an interesting parallel between the arbitrary species threshold in birds (ca. 2% divergence in mitochondrial genes) and in Bacteria (ca. 95% divergence in core genes). These thresholds can be useful as a starting point, but are not always reliable (see for example this blog post). Moreover, this study confirmed a growing consensus among biologists studying speciation: introgression is more common than we previously thought. It doesn’t matter whether we are talking about Bacteria or birds.

References

Diop, A., Torrance, E. L., Stott, C. M., & Bobay, L. M. (2022). Gene flow and introgression are pervasive forces shaping the evolution of bacterial species. Genome Biology23(1), 1-19.

Featured image: Neisseria gonorrhoeae © Dr. Norman Jacobs | Wikimedia Commons

What determines range shifts up and down tropical mountains?

Exploring the impact of different ecological traits.

Some bird species might be on an “escalator to extinction.” As the climate changes and the suitable habitat shifts upslope, the birds have no choice but to move along. At some point, however, the mountain stops and the species might go extinct. This scenario makes intuitive sense, but is obviously too simple. Several other factors play a role in elevational range shifts and not all species will move up the mountain. Indeed, several studies reported that between a third and a fifth of species actually shift downslope.

In a recent Frontiers in Ecology and Evolution paper, Montague Neate-Clegg and his colleagues compiled a dataset of elevational range shifts for 421 bird species. They found that the species tend to move upslope with an average speed of 1.6 meter per year. However, this speed is only an average which does not capture the variation in underlying range shifts. These shifts are influenced by several ecological traits. Let’s head up this mountain of data and explore.

Species Traits

The dataset contained information from eight study sites across the tropics, from Peru to New Guinea. Detailed statistical analyses revealed that “elevational shift rates are associated with species’ traits, particularly body size, dispersal ability and territoriality.” The finding that dispersal ability plays a role in range shifts is not that surprising. Birds that disperse farther are more likely to explore new locations outside of their current distribution. Similarly, the influence of territoriality is also logical. Birds that do not hold territories are more free to move around and colonize new areas. Finally, the relationship between body size and elevational shifts can be explained within the context of life history theory. Small-bodies species shifted their ranges faster. Smaller species tend to have faster life histories, allowing them to rapidly respond to changing environments. Hence, we have three factors – dispersal ability, territoriality, and body size – that make ecological sense.

The analyses showed that body mass and territoriality have an effect on elevational shifts in tropical birds. These graphs illustrate the relationships with mean elevation (A and B), lower limit (C) and upper limit (D) of the distribution. From: Neate-Clegg et al. (2021).

Downhill

As mentioned above, not all bird species move upslope. And indeed, this study also found that a third of the shifts were downslope. What could explain this reversed movement? The authors offer two main ideas: (1) competitor release and (2) tracking of ecological requirements. The first explanation entails the scenario that a competitor goes extinct downhill, allowing another species to extend its distribution into the freely available niche and extend its range downslope. The second explanation is quite intuitive: species move where there is food. If your favorite food source happens to be down the mountain, that is where you will go there.

In the end, this study provides several ecological features to understand the movement of tropical bird species up and down mountains. However, they did not explicitly consider large-scale factors, such as the topography of the landscape and the configuration of the vegetation. A nice opportunity for further research into elevational range shifts. Much remains to be discovered, so I guess it is not all downhill from here.

The percentage of species that shifted downslope. The different shared of grey correspond to mean elevation, upper limit and lower limit. From: Neate-Clegg et al. (2021).

References

Neate-Clegg, M. H., Jones, S. E., Tobias, J. A., Newmark, W. D., & Şekercioǧlu, Ç. H. (2021). Ecological correlates of elevational range shifts in tropical birds. Frontiers in Ecology and Evolution9, 621749.

Featured image: Andean Motmot (Momotus aequatorialis) © Alejandro Bayer Tamayo | Wikimedia Commons

What is a species anyway?

Seeing “species as individuals” helps to understand taxonomic disagreements.

More than ten million years. It has been more than ten million years since the Rose-breasted Grosbeak (Pheucticus ludovicianus) and the Scarlet Tanager (Piranga olivacea) diverged. Despite this significant evolutionary gap, these species still managed to produce a hybrid (see this paper for the complete description). This unusual hybrid attracted some media attention – including this piece in National Geographic – prompting some Twitter-accounts to ask the age-old question: what is a species?

Most people still think about the Biological Species Concept, defining species as “a group of organisms that can successfully interbreed and produce fertile offspring.” A very strict application of this species concept will merge any two species that produce the occasional fertile hybrid. If the cross between the Rose-breasted Grosbeak and the Scarlet Tanager turns out to be fertile, should we consider these drastically different birds as members of the same species? No, because the reality is more nuanced and complicated than blindly following the Biological Species Concept.

As I have explained in a previous blog post, most biologists adhere to the General Lineage Concept or the Evolutionary Species Concept. Both of these concepts emphasize the independent evolutionary trajectory of a species. The General Lineage Concept talks about “separately evolving metapopulation lineages”, whereas the Evolutionary Species Concept mentions “the independent evolutionary fate and historical tendencies” of a species. An occasional hybrid – such as the one described above – will not impact the evolutionary trajectory of both species and we should thus not worry about the species status of the Rose-breasted Grosbeak or the Scarlet Tanager. But what about species that regularly hybridize?

Photographs of the hybrid from (a-c) and the putative parental species: Rose-breasted Grosbeak (d) and Scarlet Tanager (e). From: Toews et al. (2022).

Species as Individuals

The situation becomes more complicated when we consider species that regularly interbreed. Think of the Golden-winged Warbler (Vermivora chrysoptera) and the Blue-winged Warbler (V. cyanoptera) in North America, or the Hooded Crow (Corvus [c.] cornix) and the Carion Crow (C. [c.] corone) in Europe. Does the production of hybrids influence the evolutionary trajectories of these lineages? Here, it is important to consider that the origin of species (or speciation) is a gradual process. Before the development of “separately evolving metapopulation lineages”, these lineages might engaged in a complicated and intricate dance of merging and diverging. Due to the continuous nature of the speciation process, it can thus be difficult to establish clear species boundaries.

To understand this issue, I have always found it useful to consider species as individuals (a philosophical perspective introduced by David Hull). An evolutionary lineage can be regarded as an individual that is born (i.e. start of the speciation process) and will die (i.e. extinction). Some individuals will reach adulthood (i.e. become species) while others will not. However, at what point does an individual become an adult? When I look at the children of my nieces, I am confident that they are not adults yet. And when I meet my uncle or aunt at a family gathering, they are clearly adults. But somewhere between the transition from child to adult, there is a gray zone. Just ask any cashier that needs to check the age of her costumers when they buy alcohol.

Seeing species as individuals. But where do you draw the line between child and adult?

Species Criteria

What characteristics would you use to define an adult? You could focus on particular morphological features, such as secondary sexual traits (e.g., the development of a beard in men or breasts in women). Or you could pay attention to particular behaviors that you consider typical for adults. You could even devise a genetic test to measure the length of telomeres. But when you apply these criteria to a group of people – aged 16 to 25, for example – you will probably come to drastically different conclusions depending on the features you focus on. Different traits – whether morphological, behavioral or genetic – will develop at different rates in different people.

The same reasoning applies to species: during the speciation process, different criteria will evolve at different times in the speciation process. The order in which these criteria evolve will be contingent upon the speciation process. In some cases, morphological differences might emerge before genetic differentiation (see for example Redpolls). In other cases, lineages might be genetically distinct despite little morphological change (i.e. cryptic species, such as in the Warbling Vireo). The result is a taxonomic grey zone where different species criteria lead to different conclusions.

This simplified diagram represents a single lineage splitting into two independently evolving lineages (or species). The horizontal lines represent the times at which the lineages acquire different species criteria. This results in a taxonomic grey zone where alternative species criteria come into conflict. Adapted from De Queiroz (2007) Systematic Biology.

Labeling Life

From the perspective of “species as individuals”, it becomes clear where most taxonomic disputes come from. Lineages that are still in the process of speciation – or even subject to reverse speciation, such as American crows and bean geese – end up in a taxonomic grey zone where species criteria come into conflict. Classifying the inhabitants of this grey zone can be extremely difficult because personal preferences of certain taxonomists and political issues (e.g., protection of endangered species) come into play. This will inevitably lead to some man-made “species” that are not strongly supported by biological data. And the ensuing debate can become heated and unfriendly.

Personally, I prefer to acknowledge the fact that some lineages cannot be easily divided into distinct species. It might be better to just refer to them as taxa – not trying to label them as “species” or “subspecies” – and focus on understanding their ecology and evolution. These resulting insights will be more interesting and fulfilling compared to putting an arbitrary label on an individual.

References

Hull, D. L. (1976). Are species really individuals?. Systematic zoology, 25(2), 174-191.

Ottenburghs, J. (2019). Avian species concepts in the light of genomics. In Avian Genomics in Ecology and Evolution (pp. 211-235). Springer, Cham.

Toews, D. P., Rhinehart, T. A., Mulvihill, R., Galen, S., Gosser, S. M., Johnson, T., … & Latta, S. C. (2022). Genetic confirmation of a hybrid between two highly divergent cardinalid species: A rose‐breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). Ecology and Evolution, 12(8), e9152.

Featured image: Birds of North America infographic © Pop Chart | Trendhunter

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

What is the difference between hard and soft selection?

An interesting perspective on the nature of natural selection.

You might be surprised to read that my employer – Wageningen University – houses several creationists. Their scientific work generally focuses on non-evolutionary topics, such as nitrogen deposition, but that does not prevent some colleagues from commenting on evolutionary biology. One professor, for example, said the following in an interview: “Humans not only share 96 percent of their DNA with monkeys, but also 88 percent with mice, while according to the theory of evolution humans are not descended from mice.” This statement clearly shows that he has no clue how evolution works. Humans are not directly descended from monkeys or mice, but share a common ancestor with both. And because the common ancestor of humans and monkeys is more recent than the one of humans and mice, we share more genetic material with monkeys. This “critique” on evolution actually contains supporting evidence for the fact that all life on our planet evolved. Unfortunately, this professor is blinded by religious dogma and cannot approach evolutionary questions unbiased. Any discussion is thus useless (see for example this blog post).

Another common creationist argument is that “random mutations and natural selection” are insufficient to explain the diversity of life. However, evolution is so much more than “random mutations and natural selection” (otherwise, evolutionary textbooks would be quite short). There are several other evolutionary processes, such as genetic drift and sexual selection, to consider. In addition, the term natural selection covers a whole range of possible selective mechanisms, such as directional selection or balancing selection. In fact, I recently came across an Ecology Letters paper on the concepts of hard and soft selection. An interesting framework that I had not thought about yet. So, in this blog post, I will try to explain the difference between these two types of selection.

Population Genetic Paradox

The concepts of hard and soft selection were introduced by Bruce Wallace to resolve an apparent paradox in population genetics. In the 1960s, evolutionary biologists assumed that any given environment has one optimal genotype. Any other genotypes in the population would thus have a lower fitness compared to this optimal genetic combination. This reasoning implies that populations with high levels of genetic variation will have a low mean fitness. When researchers were able to quantify genetic diversity in wild populations, they were surprised to find high levels of variation (see for example Hubby and Lewontin 1966). These observations were at odds with the proposed relationship between genetic variation and mean fitness. To resolve this paradox, Wallace introduced the concept of soft selection where the fitness of an individual is not quantified relative to an optimal genotype, but against the fitness of its conspecifics.

Bears and Hares

The theoretical explanation might make your head spin, so let’s use an example to clarify these concepts. Imagine a population of bears that are competing for a certain number of caves for hibernation. The bears are either aggressive or submissive. And obviously, aggressive bears will outcompete the submissive ones. When there are enough caves for all bears, there will be no selection. However, once there are more bears than caves, selection will occur. Now, the selection dynamics will depend on the behavioral composition of the population. In a situation with few aggressive bears, some submissive bears will be able to secure a cave and will have a higher relative fitness. But when there are more aggressive bears, the submissive bears will be outcompeted and will have a lower relative fitness. The fitness of the submissive bears thus depends on the amount of aggressive bears in the population. This is soft selection.

To understand how hard selection is different, consider another example: predation on snowshoe hares. The risk of predation depends on the coat color of the individual. Better camouflaged hares will survive better. The relative fitness of the different coat colors does not depend on the composition of the population. Badly camouflaged individuals – such as a white hare in a brownish landscape – will have a lower chance of survival regardless of the number of well-camouflaged conspecifics. This situation would result in hard selection.

Two examples to illustrate soft and hard selection. In the bear example, the fitness of the submissive individuals depends on the behavioral composition of the population. In the hare example, however, the fitness of badly camouflages (white) snowshoe hares is independent of the number of well-camouflaged individuals. From: Bell et al. (2021) Ecology Letters.

Slushy Selection

These two examples only scratch the surface when it comes to hard and soft selection. Bruce Wallace developed a population genetic model to explore the strength of selection in different scenarios. And numerous authors have expanded on these ideas. Some have argued that hard and soft selection are just two extremes on a continuum, while others have suggested that both types of selection might operate on the same traits (i.e. slushy selection). Diving into these details and exploring the ecological and evolutionary impacts of hard versus soft selection would takes us too far down the rabbit (or hare?) hole.

My goal was to introduce these concepts and show that evolution is more complex than “random mutations and natural selection”. If creationists would take to the time to really understand the intricacies of the evolutionary process, they would quickly realize how silly some of their arguments are. More importantly, they might discover how interesting and exciting evolutionary biology is.

References

Bell, D. A., Kovach, R. P., Robinson, Z. L., Whiteley, A. R., & Reed, T. E. (2021). The ecological causes and consequences of hard and soft selection. Ecology Letters24(7), 1505-1521.

Wallace, B. (1975). Hard and soft selection revisited. Evolution, 465-473.

Featured image: Grizzly Bear (Ursus arctos) © Gregory “Slobirdr” Smith | Wikimedia Commons

Genomic evidence for sexual traits as honest indicators of immune function in birds?

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.

Purifying Selection

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.

An overview of the genomic resources used in this study (Figure A) and an example of variation in sexual dichromatism scores (Figure B). From: Jaiswal et al. (2021) Frontiers in Ecology and Evolution.

Correlated Evolution

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.

A network representation of gene pairs showing patterns of correlated evolution (Figure A). And a section of this network where only the immune-related, feather-related, and pigmentation-related are shown (Figure B). From: Jaiswal et al. (2021).

References

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.

Featured image: Indian Peafowl (Pavo cristatus) © Gabriel Castaldini | Wikimedia Commons

Social bonds and migratory behavior determine the likelihood of hybridization in birds

What behavioral mechanisms underlie these associations?

Sometimes the title of a paper says it all: “Sociality and migration predict hybridization across birds.” In a recent study in the Proceedings of the Royal Society B, Gavin Leighton and his colleagues correlated the incidence of hybridization across birds with several life history traits. These analyses revealed that bird species with long-lasting social bonds are less likely to hybridize. In addition, a migratory lifestyle increases the likelihood of hybridization. Some interesting findings that require more exploration. What behavioral mechanisms could be driving these associations between sociality, migration and hybridization?

Pair Bonds and Migration

Species with no pair bonds will look for a new partner every year, increasing the opportunities for making the “wrong” choice and hybridize. Species with long-lasting social bonds, on the other hand, will often pair for several mating seasons. This reproductive strategy can lead to substantial fitness costs if an individual mates with the “wrong” species. The resulting hybrids might be sterile or unviable, culminating in a significant waste of reproductive effort. Such maladaptive hybridization can lead to increased selection for proper species recognition. An interesting exception to this result – which might prove the rule – concerns my own study system: geese. Most goose species tend to form long-lasting pair bonds, but still engage in regular hybridization. The production of hybrids has been attributed to several behavioral mechanisms, such as forced extra-pair copulations, interspecific brood parasitism and vagrant individuals (see this paper for an overview).

The last mechanism related to goose hybridization – vagrant individuals – leads into the next main finding of the study: migratory species are more likely to hybridize. To again focus geese, migratory goose species might have a higher chance of reaching new habitats where they interbreed with local species. For example, North American Snow Geese (Anser caerulescens) are occasionally observed in Europe during migration and hybrids between Snow Goose and several European species have indeed been reported. An additional explanation relates to mate choice in sedentary species: these birds might have extended periods of mate searching and pair formation, lowering the probability of choosing a partner from another species.

Phylogenetic distribution of hybridization (grey, inner circle), social bond length (green, middle circle), and migratory status (blue/yellow, outer circle). From: Leighton et al. (2021).

Future Research

Clearly, there are multiple mechanisms to explain the associations uncovered in this study. The details might differ across the avian phylogeny, but the broad-scale importance of sociality and migration seems justified. This macroevolutionary perspective opens new exciting avenues for further research, disentangling how these life history traits (and probably many other factors) interact to determine the probability of hybridization.

A final note on the dataset. The researchers assembled a dataset of bird hybrids using the Handbook of Avian Hybrids of the World, indicating that they took “a liberal approach and included any reported hybridization where an individual was identified by sight as a putative hybrid.” I completely understand this pragmatic choice as it is nearly impossible to assess the reliability of each hybrid combination mentioned in the Handbook of Avian Hybrids of the World. However, I have become more skeptical about the list of bird hybrids that Eugene McCarthy has produced (see for example this blog post). I do not think that the inclusion of less reliable hybrids has affected the analyses in the present study, but I do encourage ornithologists to be careful in using this book in their future work. Always check the original source before including a dubious hybrid record.

References

Leighton, G. M., Lu, L. J., Holop, E., Dobler, J., & Ligon, R. A. (2021). Sociality and migration predict hybridization across birds. Proceedings of the Royal Society B288(1947), 20201946.

Featured image: Greylag Goose (Anser anser) x Canada Goose (Branta canadensis) © Dirk Ottenburghs

The benefits and drawbacks of living on an island

If you were a bird, would you want to live on an island?

Island populations have played a key role in the development of evolutionary theory. I guess everyone is familiar with the scientific work on Darwin’s Finches – including groundbreaking work by Charles Darwin himself, David Lack, and more recently Peter and Rosemary Grant. Other examples include convergent evolution of anole lizards on tropical islands and the adaptive radiation of honeycreepers on Hawaii. Evolution on islands can take surprising turns. Just think of the extinct giant swan (Cygnus falconeri) on Sicily and Malta or the flightless Kakapo (Strigops habroptilus) of New Zealand. Studying evolution on islands is certainly worthwhile, but what about actually living on island? Do organisms that colonize island environments do better or worse than their mainland counterparts? The answer to that question depends on the aspect you focus on, as nicely illustrated by some recent studies in Biology Letters and Current Biology.

Adult Survival

Let’s start by looking at the individual level. Using a dataset of no less than 697 bird species, Guy Beauchamp investigated whether adult birds survive better on islands. He first needed to correct for certain confounding factors. Birds with a larger body size tend to have higher survival rates. And due to the well-known trade-off between reproduction and survival, a lower clutch size is often associated with better survival. Finally, species with a cooperative breeding system survive better as adults. After controlling for these factors, Beauchamp still found that “birds living on islands showed higher apparent survival than their mainland counterparts.” The exact mechanisms behind the higher survival rate on islands remain to be determined but might be related to the absence of predators and parasites on islands. So, from an individual perspective, it would be a good idea to settle on an island.

Apparent survival of adult birds is higher on islands (blue lines) compared to the mainland (red line). This pattern holds across latitudes and on both hemispheres. From: Beauchamp (2021).

Slightly Deleterious Mutations

Adult survival is thus higher on islands. But the situation is quite different on a population level. Thibault Leroy and his colleagues compared the effective population size (Ne) – a measure of genetic diversity – between songbirds on islands and on the mainland. Based on whole-genome sequences of almost 300 individuals, representing 25 species, they found that “island species exhibit significantly lower mean Ne than continental species over the last one million years.” This reduction in effective population size has serious consequences for evolutionary dynamics on islands. According to the nearly neutral theory of molecular evolution, small populations will accumulate slightly deleterious mutations due to the stronger effect of genetic drift. And indeed, the researchers found more slightly deleterious mutations in island species compared to mainland species. Hence, on a population level, island birds are genetically less healthy than their mainland relatives.

Island species (filled circles) have smaller effective population sizes and more slightly deleterious alleles (estimated by the πNS ratio) compared to their mainland counterparts. From: Leroy et al. (2021).

Paradox

These two studies appear to contradict each other. How can island birds live longer when the populations accumulate slightly deleterious mutations? The answer to this paradox is probably related to the interaction between the deleterious mutations and the island environment. As you might have guessed from the term, these mutations are only slightly deleterious. Individuals might experience some inconvenience from these mutations, but they are not deadly and they often do not impact individual survival rates that much. In addition, the absence of certain predators and parasites on islands leads to weaker selective pressures, potentially allowing island birds to live longer.

However, a sudden change in the environment or the introduction of a predator can quickly increase selective pressures on the island population. The lower level of genetic diversity and the higher mutational load of island populations might then prevent rapid adaptation, potentially resulting in extinction. Indeed, numerous island species have perished in recent times. You could say that life on an island is great until the environment changes. And unfortunately, the environment is currently changing rapidly due to human activities.

References

Beauchamp, G. (2021). Do avian species survive better on islands?. Biology Letters17(1), 20200643.

Leroy, T., Rousselle, M., Tilak, M. K., Caizergues, A. E., Scornavacca, C., Recuerda, M., … & Nabholz, B. (2021). Island songbirds as windows into evolution in small populations. Current Biology31(6), 1303-1310.

Featured image: Blue Chaffinch (Fringilla teydea) © Bartkauz | Wikimedia Commons

Body size and phylogenetic history constrain the evolution of bird song

Although there seems to be a minor role for sexual selection as well.

Different bird species produce sounds across a wide range of frequencies. From the low-frequency booming calls of the Eurasian Bittern (Botaurus stellaris) to the high-pitched sounds of the Common Firecrest (Regulus ignicapilla). Ornithologists have formulated several hypotheses to explain the evolution of these frequency differences. The Acoustic Adaptation Hypothesis, for instance, suggests that acoustic signals are adapted to maximize the effectiveness of their transmission in a particular environment. Because low-frequency sounds travel better in dense vegetation than high-frequency sounds, bird species in forests are expected to produce calls at lower frequencies because of physical constraints. The Morphological and Phylogenetic Constraint Hypothesis, however, states that body size and/or evolutionary history limit the range of frequencies that a species can reach. Larger species tend to produce lower-frequency sounds. Finally, the Sexual Selection Hypothesis posits that frequency might act as an indicator of an individual’s size, dominance or fighting ability. Low-frequency sounds give the impression of a larger individual and might thus be selected for in the context of male-male competition.

Explaining Variation

To discriminate between these possible explanations, a recent study in the journal Ecology Letters took a closer look at the songs of more than 5000 songbirds. The researchers used the public database xeno-canto to collect information on the highest frequencies in different bird songs. Next, they correlated these peak frequencies with several evolutionary and ecological variables. The analyses revealed that evolutionary history (43-56%) and body mass (10-15%) explained the largest proportion of variation in peak song frequency. Heavier birds sang at lower frequencies. After accounting for these two factors, there was also a significant association with sexual size dimorphism (although the explained variation was very low: 1-3%). Peak frequencies were lower in species where males are larger than females, suggesting strong sexual selection. Song frequency might thus be a proxy for the competitive ability of males.

These patterns indicate that phylogenetic history and body size constrain the range of frequencies that a species can produce. Within the consequently limited range of frequencies, sexual selection appears to influence the peak frequency in particular species.

Most of the variation in song peak frequency was explained by body mass. Sexual size dimorphism accounted for a small fraction of the remaining variation, while there was no clear effect of tree cover. From: Mikula et al. (2021) Ecology Letters.

No Acoustic Adaptation?

Interestingly, there was no support for the Acoustic Adaptation Hypothesis. Although this hypothesis makes intuitive sense, there was no clear effect of tree cover (a proxy for habitat density) in the large dataset. The researchers propose several explanations for this negative result:

  • The analyses lacked information about bird behavior or habitat at the recording location. These factors could influence the produced frequency.
  • The estimates of habitat density were quite crude. Better measurements might pick up subtle signals.
  • Other biotic and abiotic factors that might influence background noise were not included in the analyses.

More research is thus needed to explore how important acoustic adaptation is in the evolution of bird song. Nonetheless, phylogenetic constraints seem to restrict the available evolutionary pathways (similar to genomic constraints in hybrid species). Evolution is a powerful process, but that doesn’t mean that anything is possible.

References

Mikula, P., Valcu, M., Brumm, H., Bulla, M., Forstmeier, W., Petrusková, T., Kempenaers, B. & Albrecht, T. (2021). A global analysis of song frequency in passerines provides no support for the acoustic adaptation hypothesis but suggests a role for sexual selection. Ecology letters24(3), 477-486.

Featured image: European Robin (Erithacus rubecula) © Charles J. Sharpe | Wikimedia Commons

Rampant introgression across the evolutionary tree of suboscine birds

An extensive genomic study detects numerous cases of interspecific gene flow.

Introgression – the exchange of genetic material through hybridization and backcrossing – seems to be an integral part of avian evolution. In 2017, I published a review paper on this phenomenon, trying to provide an overview of the known cases and the methods to detect introgression. At the time, my search uncovered 165 genetic studies that were published between 1987 and 2017. Most of these papers focused on members of the Passeriformes (songbirds), Galliformes (gamefowl), Anseriformes (waterfowl) and Charadriiformes (gulls, waders and auks), bird orders that display high levels of hybridization. However, I did not attempt to quantify the incidence of introgression, because this would probably be a gross underestimate. Numerous bird species have not been studied with genetic tools yet. Such as quantification would involve a large genomic data set, comprising many species. And that is exactly the approach of a study that recently appeared in the journal Evolution Letters.

D-statistics

Sonal Singhal and her colleagues focused on the suboscines, a clade of passerine birds that comprises more than 1000 species, most of which can be found in South America. Using a genomic dataset of 2389 loci (consisting of ultraconserved elements and exons) for 1306 species, the researchers looked for signatures of introgression. They relied on one of my favorite methods: the D-statistic (also known as the ABBA-BABA test). I have explained this approach so many times that I regularly dream about it (and no, the dream does not involve ABBA-songs). Here is the short explanation from my review:

The D-statistic considers ancestral (‘A’) and derived (‘B’) alleles across the genomes of four taxa. Under the scenario of incomplete lineage sorting without gene flow, two particular allelic patterns ‘ABBA’ and ‘BABA’ should occur equally frequent. An excess of either ABBA or BABA, resulting in a D-statistic that is significantly different from zero, is indicative of gene flow between two taxa.

The researchers calculated this statistic for numerous trios of species. They found that 49 out of 130 trios (38%) had a significant D-statistic. The highest five D-statistics were detected in Dendrocolaptes woodcreepers, Smithornis broadbills, Neopelma manakins, Grallaria antpittas, and Phlegopsis antbirds. I have described hybridization in some of these taxa on their family pages at Avian Hybrids Project (you can click the links if you want to learn more).

An example of the ABBA-BABA test for a trio of species (plus an outgroup). From: Singhal et al. (2021) Evolution Letters.

An Underestimate?

To understand the mechanisms underlying the introgression patterns, the researchers correlated the D-statistics with several environmental variables. These analyses revealed some expected relationships. For example, introgression was most common between species that were geographically close and that experienced higher rates of climate change (which moves species around and might lead to secondary contact). In addition, introgression occurred more between species at lower latitudes. It could be that tropical regions provide more opportunities for introgressive hybridization due to the higher species richness in these areas. It would be interesting to repeat these analyses with more species-specific traits to better understand the drivers of introgression in suboscine birds.

Although an introgression incidence of 38% seems quite high, I think it is probably even an underestimate. The analyses only included trios of closely related species and might thus have missed introgression between more distantly related species. Moreover, the D-statistic does detect gene flow between sister species. It only reports only gene flow between the third species and one of the first two in the phylogenetic tree. The researchers did also not take ghost introgression into account: the exchange of genetic material with unsampled or extinct lineages (see my recent review on this topic for more details). And finally, the analyses involved only a subset of the genome. Who knows how many introgressed regions are hiding in the rest of the genome?

An overview of significant D-statistics (highlighted in orange) across the phylogeny of the suboscines. From: Singhal et al. (2021) Evolution Letters.

References

Singhal, S., Derryberry, G. E., Bravo, G. A., Derryberry, E. P., Brumfield, R. T., & Harvey, M. G. (2021). The dynamics of introgression across an avian radiation. Evolution letters5(6), 568-581.

Featured image: Green-and-black Fruiteater (Pipreola riefferii) © Francesco Veronesi | Wikimedia Commons