Splitting the Black-throated Trogon into five species

An integrative approach to taxonomy leads to the description of a new species.

When people hear that I work on speciation and hybridization in birds, I often get the question: are you a lumper or a splitter? For readers unfamiliar with these terms: “lumpers” prefer to reduce the number of taxonomic groups by merging them, while “splitters” tend to break up larger groups into smaller ones based on small differences. My own position – to answer the question posed at the start – is difficult to determine. I prefer to take an integrative approach where multiple lines of evidence are combined into a taxonomic decision (see this blog post for the details). Based on the strength of the evidence, I will be a lumper or a splitter. Hence, it depends on the situation (a popular phrase among biologists). Just as it can be difficult to pigeonhole variation in nature, it is challenging to classify biologists into lumpers and splitters. A recent study in the Zoological Journal of the Linnean Society provides a nice example of my own approach to taxonomy. The researchers present convincing evidence for splitting one species into five.

Six subspecies

The taxonomy of the Black-throated Trogon (Trogon rufus) has been relatively stable since 1943 when W.E. Clyde Todd proposed six subspecies:

• T. r. rufus in the Guiana Shield
• T. r. sulphureus in upper Amazonia
• T. r. chrysochlorosin the Atlantic forest
• T. r. tenellus throughout Central America
• T. r. cupreicauda in the Chocó-Magdalena region
• T. r. amazonicus in lower Amazonia

Over the years, several authors have proposed a species status for some of these subspecies. To provide some clarity in this taxonomic turmoil, Jeremy Kenneth Dickens and his colleagues amassed an impressive set of data. They examined the morphology and plumage of 906 museum specimens of the Black-throated Trogon, carefully analyzed 273 song recording and sequenced the mitochondrial DNA of 29 birds.

Barred Patterns

Morphologically, almost all male specimens were assigned to the correct taxon. Only one individual from the subspecies amazonicus was confused with rufus (but more on these taxa later). The different barring patterns on the undertail were one of the most defining features. This finding is not that surprising because this trait is known to play a role in species recognition (see for example this study). Interestingly, the iridescent colors on the head and body were not informative to classify these birds. In fact, an experimental study showed that feather coloration can change rapidly depending on the local humidity level. Not the most reliable feature to use in taxonomy. The morphological patterns were corroborated by the song analyses where 88% of the recordings could be assigned to the correct taxon. We already have two convincing lines of evidence for splitting the Black-throated Trogon into several species. What about genetics?

Linear discriminant analyses of several morphological and plumage traits revealed clear clusters corresponding to the currently recognized subspecies. The patterns were most obvious for males (left figure). From: Dickens et al. (2021).

Genetics

Phylogenetic analyses of two mitochondrial genes (ND2 and cytb) recovered several well-supported clades that correspond to the taxa tenellus, cupreicauda and chrysochloros. Moreover, one population from Alagoas was genetically distinct from the other samples. The three taxa that encircle the Amazon (rufus, sulphureus and amazonicus) clustered together but could not be separated into monophyletic clades. The genetic overlap between these taxa was also reflected in the morphological patterns. Across their distribution, there are zones of intergradation between rufus and amazonicus, and between amazonicus and sulphureus. It is likely that some hybridization is occurring in these regions, but more sampling is needed to confirm this suspicion.

Genetic analyses of 29 specimens were in line with the morphological analyses, leading to the decision to elevate several subspecies to the species level. From: Dickens et al. (2021).

A New Classification

Based on the congruent patterns across the different data sets, the authors propose to elevate four subspecies to species rank, namely T. rufus, T. tenellus, T. cupreicauda and T. chrysochloros. The population in Alagoas is recognized as a new species: T. muriciensis. You can check the original paper for detailed descriptions of these species, but I will leave you with these beautiful drawings by Eduardo Brettas. Whether you agree with the splitting of the Black-throated Trogon or not, I am sure that you will admit that these are stunning birds.

Illustrations of the Trogon species described in the blog post. From: Dickens et al. (2021).

References

Dickens, J. K., Bitton, P. P., Bravo, G. A., & Silveira, L. F. (2021). Species limits, patterns of secondary contact and a new species in the Trogon rufus complex (Aves: Trogonidae). Zoological Journal of the Linnean Society, 193(2), 499-540.

Featured image: Black-throated Trogon (Trogon rufus) © Charlie Jackson | Wikimedia Commons

The extinct cave-rails were not rails

Ancient DNA analyses also uncover an interesting biogeographic connection.

For my MSc thesis at Antwerp University, I studied the phylogenetic relationships between several snail species (genus Plutonia) on the Azores (the island group that belongs to Portugal). Using a few genes, I hoped to determine the evolutionary position of Plutonia atlantica, a carnivorous species within a group of herbivores. One of my supervisors, however, was not very supportive of this approach. António Frias Martins told me that he does “not trust the molecules” and preferred to focus on morphological characters, such as detailed differences in genitalia. We agreed to disagree and I finished my molecular analyses. More than 10 years later, I still have to disagree with António. I would even argue that I don’t trust the morphology. Convergent evolution – unrelated species evolving similar features – complicates phylogenetic analyses and often leads to wrong conclusions. Molecular data can usually shine some light on the morphological smokescreen of convergent evolution and pinpoint the actual phylogenetic relationships. A recent study in the journal Biology Letters nicely illustrates the power of genetic data.

Ancient DNA

The Greater Antilles used to house three peculiar species of flightless cave-rails. Bones of the Antillean Cave-rail (Nesotrochis debooyi) were found in archeological sites on the Virgin Islands and in caves on Puerto Rico. The other two species were known from fossil remains on Cuba (the Cuban cave-rail, N. picipicensis) and Hispaniola (the Haitian cave-rail, N. steganinos). Originally, scientists classified the three species as rails in the family Rallidae. However, more recent work indicated that these birds also share some features with flufftails (family Sarothruridae). Given the morphological and ecological convergence between rails and flufftails, it is extremely difficult to determine the evolutionary history of Nesotrochis using only morphological data.

That is why Jessica Oswald and her colleagues turned to ancient DNA. They managed to obtain a nearly complete mitochondrial DNA sequence from the Haitian cave-rail. Comparing this sequence with the DNA of several other species revealed that the cave-rails are not closely related to rails, but cluster with the flufftails and the extinct adzebills (family Aptornithidae) from New Zealand. The exact relationships between these three groups – cave-rails, flufftails, and adzebills – could not be resolved, but we can already conclude that the cave-rails were not rails. The scientists that described these species were misled by convergent evolution.

Phylogenetic analyses of mitochondrial DNA indicates that the cave-rails (Nesotrochis) are closely related to flufftails (Sarothruridae) and adzebills (Aptornithidae). From: Oswald et al. (2021).

Long-distance Dispersal?

Apart from pinpointing the phylogenetic position of the cave-rails, this study also uncovered an interesting biogeographical pattern. As explained above, the cave-rails were restricted to the Greater Antilles, a group of islands in the Caribbean Sea. Their closest relatives, however, occurred on different continents: the flufftails can be found in Africa and New Guinea, while the adzebills lived on New Zealand. How did the cave-rails end up in the Caribbean region? The authors offer two main hypotheses:

Nesotrochis could be a relictual taxon that survived in the Caribbean after extinction on the adjacent mainland, or an example of long-distance dispersal from the Old World to the Caribbean.

Based on the high incidence of convergent evolution on this branch of the evolutionary tree, I would argue that morphological data will not be very helpful to solve this biogeographical mystery. My money is on more detailed analyses of ancient and modern DNA. But I would be happy to be proven wrong. Who knows what morphological insights remain to be discovered?

Geographical distribution of cave-rails (green), flufftails (blue) and adzebills (red). From: Oswald et al. (2021).

References

Oswald, J. A., Terrill, R. S., Stucky, B. J., LeFebvre, M. J., Steadman, D. W., Guralnick, R. P., & Allen, J. M. (2021). Ancient DNA from the extinct Haitian cave-rail (Nesotrochis steganinos) suggests a biogeographic connection between the Caribbean and Old World. Biology Letters, 17(3), 20200760.

Featured image: Bones of the Antillean Cave-rail (Nesotrochis debooyi) © Wetmore | Wikimedia Commons

The evolution of mechanical sounds in Doraditos

Tracing the evolutionary history of modified feathers and aerial displays.

The evolution of bird song has received a lot of attention (see for example this blog post), but some birds produce sounds in drastically different ways. Some Doradito species of genus Pseudocolopteryx, for example, generate mechanical wing sounds due to structural modifications on their feathers. Modified primary feathers have been described in three species: the Crested Doradito (P. sclateri), the Subtropical Doradito (P. acutipennis), and the Dinelli’s Doradito (P. dinelliana). The remaining two species in this genus – the Warbling Doradito (P. flaviventris) and the Ticking Doradito (P. citreola) – lack this feature. In addition, males in all species with modified feathers also perform aerial displays, indicating that these traits probably coevolved. As an evolutionary biologist, I cannot help but ponder how these feather modifications and aerial displays originated. Did they arise once or did each species independently alter its feathers? To answer this question, we need a solid phylogenetic framework. Once we know how these five species are related to each other, we can explore the evolutionary history of particular traits. A recent study in the journal Zoological Scripta provided the first steps in our quest to understand the evolution of mechanical sounds in these songbirds.

Phylogenetic Analyses

Emilio Jordan and his colleagues obtained genetic data for 37 individuals, representing all five species. Analyses of two mitochondrial (COI and ND2) and two nuclear (MYO and OCD) markers recovered a clear phylogeny in which the “non-mechanical species” are embedded within the three species that produce mechanical sounds with their modified feathers. This phylogenetic arrangement suggests that modified primary feathers (and the aerial displays) evolved in the common ancestor of all Doraditos and were consequently lost in the Warbling Doradito and the Ticking Doradito.

A phylogenetic tree showing the relationships between the five Doradito species and the putative evolutionary history of the modified feathers and aerial displays. From: Jordan et al. (2021).

It’s Complicated

When we take a closer look at the modified feathers, however, the situation becomes less clear. Although three species produce mechanical sounds with their feathers, the structural modifications to their plumage are quite different. In the Crested Doradito and the Dinelli’s Doradito, the sixth and seventh primary feather are miniaturized, whereas the Subtropical Doradito has modifications on the third to seventh primary feathers. It is thus possible that these modified feathers have distinct evolutionary origins. In addition, the evolutionary history of the four molecular markers might not correspond to the evolutionary trajectory of the trait. Certain traits do not follow the species tree due to incomplete lineage sorting (as shown in marsupials) or introgressive hybridization. It might thus be necessary to unravel the genetic basis of the modified feathers and estimate phylogenetic trees for the underlying genes. Will they follow the species tree or not? In the end, the evolution of this trait might be more complicated than we expected.

References

Jordan, E. A., Tello, J. G., Benitez Saldivar, M. J., & Areta, J. I. (2021). Molecular phylogenetics of Doraditos (Aves, Pseudocolopteryx): Evolution of cryptic species, vocal and mechanical sounds. Zoologica Scripta, 50(2), 173-192.

Featured image: Warbling Doradito (Pseudocolopteryx flaviventris) © Dominic Sherony | 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 Letters, 24(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

Do gut microbiota contribute to reproductive isolation between Nightingale species?

A recent study explores this intriguing hypothesis.

The expression “gut feeling” has received an entirely different meaning. Recent studies have documented how the microorganisms in an individual’s intestines can influence its behavior (see for example this paper). These findings suggest that gut microbiota might play an underappreciated role in several biological processes. They could even contribute to speciation. Experiments with fruit flies (Drosophila), for instance, indicated that lineage-specific microbiota influenced assortative mating among the flies, potentially giving rise to a premating barrier. Alternatively, microbiota could act after mating if hybrids suffer from incompatible microbiotic combinations. Regardless of the exact mechanism, it seems feasible that gut microbiota could play a role in the origin of new species. A recent study in the journal BMC Ecology and Evolution tested this idea in two closely related bird species: the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia).

Individual Variation

Camille Sottas and her colleagues studied the gut microbiota of 18 Common Nightingales and 18 Thrush Nightingales. For both species, half of the individuals were collected in sympatric regions, while the other half originated from allopatric locations. This sampling design allowed the researchers to disentangle the different factors contributing to the diversity in gut microbiota. They nicely explain the reasoning behind potential patterns in the introduction: “A higher divergence [in gut microbiota] in sympatry would imply a stronger effect of habitat use or diet, while a higher divergence in allopatry would indicate a stronger effect of geographical region on the gut microbiota divergence.”

Sequencing the microorganism community at three sections of the intestine (duodenum, jejenum and ileum) uncovered twelve bacterial phyla and 126 genera. Analyses of the consequent diversity patterns revealed no significant differences between the species and their geographic origins. In fact, 79% of the variation in microbiota could be explained by individual differences. These results suggest that the gut microbiota composition is unlikely to contribute to reproductive isolation between these nightingale species.

Statistical analyses of different diversity measures in allopatry and sympatry revealed no significant differences in the gut microbiota of Thrush Nightingale (TN, in blue) and Common Nightingale (CN, in red). From Sottas et al. (2021).

Negative Results

The answer to the title of this blog post is thus a resounding no. Gut microbiota do not play a role in speciation (at least when it comes to these nightingales). You might be wondering why I decided to dedicate a blog post to a negative result. This decision aligns with the goal of this blog – and my personal mission – to generate attention for less “sexy” topics. Most newspapers and popular science websites tend to focus on scientific research that captures the imagination of the general public and generates clicks. A negative result is thus not that interesting for these attention mongers. From a scientific perspective, however, negative results are a crucial piece of the puzzle in our quest to advance human knowledge. Finding out that something does not work is also a relevant discovery (even though it will generate less publicity).

Most scientists are working extremely hard behind the scenes, and only a few will get the attention that they deserve. Indeed, most media attention and awards for the happy few are often the result of favoritism and knowing the right people. That is why I try to direct the spotlight to lesser-known scientists and the fruits of their unseen labor. Even if – or perhaps especially if – their results are negative.

References

Sottas, C., Schmiedová, L., Kreisinger, J., Albrecht, T., Reif, J., Osiejuk, T. S., & Reifová, R. (2021). Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distance. BMC Ecology and Evolution, 21(1), 1-14.

Featured image: Common Nightingale (Luscinia megarhynchos) © Marcel Burkhardt | Wikimedia Commons

A supergene determines morphological variation in redpolls

But are these redpolls different species or not?

“Thus, redpolls appear to function as a single species harboring ecotypic variation, rather than three distinct species.” This statement caught my attention while I was reading a recent Nature Communications paper by Erik Funk and his colleagues. Using genomic data from 73 individuals, they managed to pinpoint the genetic basis of three redpoll taxa that are currently described as separate species: the Hoary Redpoll (Acanthis hornemanni), the Common Redpoll (A. flammea), and the Lesser Redpoll (A. cabaret). The morphological variation between these three taxa could be traced back to a big inversion – about 55 million DNA-letters long – on chromosome one (see this blog post for more information on inversions). This genomic region contains almost 500 genes, several of which are involved in plumage pigmentation and beak morphology. As all these genes are tightly linked and inherited together, the researchers describe it as a “supergene”.

The taxonomically-orientated reader might now be confused by the first sentence of this blog post. These redpolls are morphologically distinct and we now know the genetic basis of these differences. Why refer to them as ecotypes, and not species? Let’s find out.

Morphological differences between the three redpolls species – or ecotypes – in the study. From: Funk et al. (2021).

Three Genotypes

Detailed analyses of the inversion revealed three clusters that do not completely correspond to the three redpoll taxa. Two clusters contain multiple species, namely Lesser Redpolls with Common Redpolls, and Hoary Redpolls with Common Redpolls. The third cluster consists almost entirely of Hoary Redpolls. The researchers assigned these clusters to three inversion genotypes: AA, AB and BB. Interestingly, these genotypes seem to align with plumage patterns:

Transitioning from the AA, to AB, to BB genotype also broadly mirrors a transition in phenotype from dark to light plumage coloration, where the AA genotype is associated with dark plumage, BB is associated with light plumage, and AB is intermediate.

Moreover, the geographical distribution of the three genotypes follows a latitudinal gradient with AA-birds at low latitudes and BB-birds at high latitudes. The heterozygotes (AB) occupy an intermediate position. These patterns suggest that the inversion might play a role in local adaptation. Indeed, bird species with white plumage and small beaks, such as the BB-redpolls, tend to occur in high-altitude regions.

The three inversion genotypes do not correspond to the three redpolls species (left figure), but do show a relationship with latitude (right figure). From: Funk et al. (2021).

Reproductive Isolation

The observation of heterozygotes (AB-birds) indicates that no combination of the supergene is lethal. This situation is different from other cases where certain combinations are often sterile or unviable due to genetic incompatibility. In Ruffs (Philomachus pugnax), for example, homozygotes with an inverted region are unviable and heterozygotes show low survival rates. The lack of lethal combinations in redpolls suggests that the inversion does not play an important role in reproductive isolation between the taxa. In fact, intermediate individuals and mixed pairs have been observed in the wild. Moreover, the genetic analyses in the current study indicated significant levels of gene flow between the redpoll taxa.

With this additional information about local adaptation and reproductive isolation, we can return to the statement about ecotypes versus species that kicked off this blog post. Here is the complete quote from the paper.

In light of the link between the redpoll supergene and phenotype and differences in breeding distribution between ecotypes, the supergene may impart local adaptation to the environment. However, given the detection of inversion heterozygotes and the presence of gene flow, the inversion likely does not influence reproductive isolation. Thus, redpolls appear to function as a single species harboring ecotypic variation, rather than as three distinct species.

It is clear that the authors are referring to “biological species” where a certain level of reproductive isolation is required. However, some ornithologists might focus on the morphological and genetic differences between the taxa, and downplay the relevance of reproductive isolation. I will not get involved in this debate and will leave the final decision with taxonomists. Honestly, I do not care whether these redpolls are classified as species, subspecies or ecotypes. I prefer to focus on the ecological and evolutionary impact of their supergene, which is obviously super-interesting.

References

Funk, E. R., Mason, N. A., Pálsson, S., Albrecht, T., Johnson, J. A., & Taylor, S. A. (2021). A supergene underlies linked variation in color and morphology in a Holarctic songbird. Nature communications, 12(1), 1-11.

Featured image: Common Redpoll (Acanthis flammea) © Jyrki Salmi | Wikimedia Commons

Why do some female hummingbirds look like males?

Testing different adaptive and non-adaptive explanations for this phenomenon.

In almost one fourth of hummingbird species, some females sport the same colorful feathers as males. This estimate is based on a recent study in the Proceedings of the Royal Society B in which the researchers inspected no less than 16,542 museum specimens. They suggested that this phenomenon – known as female-limited polymorphism – occurs in every major group of hummingbirds, suggesting that it arose independently at least 28 times (but see this paper for another perspective). These patterns raise the question why some females resemble males in so many hummingbird species. We have the reflex to immediately look for adaptive explanations. A trait that is so widespread should be beneficial, right? However, we should not forget about the possibility of non-adaptive origins. As evolutionary biologist Stephen Jay Gould nicely put it: “The primary flexibility of evolution may arise from non-adaptive by-products that occasionally permit organisms to strike out in new and unpredictable directions.” In the present study, Eleanor Diamant and her colleagues followed the advice of Gould and tested two non-adaptive explanations for the evolution of female-limited polymorphism in hummingbirds.

Genetic Conflict

The first non-adaptive explanation entails a shared genetic architecture for certain traits between the sexes. Strong selection on plumage patterns in males (and the underlying genes) might also affect the genetic make-up of females. Because males and females tend to have opposite evolutionary interests – males need to be colorful to attract mates while females need to be inconspicuous to avoid nest predation – a genetic conflict arises. Theoretically, this situation can be resolved if the genetic basis for particular plumage traits becomes sex-linked, resulting in clear sexual dichromatism (i.e. males and females always look different).

This scenario suggests that female-limited polymorphism is an intermediate stage between sexual monochromatism and sexual dichromatism. Following this reasoning, we can expect that the transitions from sexual monochromatism to female-limited polymorphism to sexual dichromatism are more likely than the other way around. When the researchers calculated transition rates between these different stages, they found that they were all similar. Hence, they concluded that “these results do not support the non-adaptive hypothesis that FLP [i.e. female-limited polymorphism] is an intermediate state.”

Ancestral state reconstruction of sexual monochromatism (black), female-limited polymorphism (red) and sexual dichromatism (grey) across the hummingbird phylogeny. From: Diamant et al. (2021).

Bill Sizes

Moving on to the second non-adaptive explanation: perhaps the male-like traits in females are the outcome of selection on other traits with a shared genetic basis (i.e. pleiotropy). The researchers focused on bill length which often differs between the sexes. Possibly, selection for certain bill sizes indirectly causes male-like plumage to develop in females. An intriguing hypothesis, but the analyses did not support it. Overall, there were no clear relationships between relative bill length and the plumage-type of females across the tested species (see figure below). This result led the researchers to dismiss the pleiotropy hypothesis, although they mention that “correlations with other unmeasured morphological traits could exist.” Indeed, we should not throw out the baby with the bathwater and test other traits for pleiotropic effects. Bill length was an obvious first candidate, but more morphological features remain to be tested.

Correlations between relative bill length and male-like plumage in females (summarized in the variable LD) did not support the pleiotropy explanation. From: Diamant et al. (2021).

Social Selection

Given the limited support for non-adaptive explanations, the researchers turned to adaptive reasons for the evolution of female-limited polymorphism. Towards the end of the discussion, they noted that:

We found significant associations with migratory status, lower mean precipitation, and marginal association of FLP with social dominance, all of which are linked to interspecific interactions and competition over resources.

Although these patterns are certainly interesting, I am not convinced yet. It is tricky to draw general conclusions from such statistical associations. And indeed, the researchers remain careful and present these results as “preliminary support” for social selection. A promising starting point, but more analyses are warranted. Because female-limited polymorphism has evolved independently so many times, it is possible that different evolutionary mechanisms are operating in different species. For example, the Anna’s hummingbird (Calypte anna) did show a positive correlation between bill length and female plumage, suggesting that a pleiotropic effect might be present in this species.

It would worthwhile to explore each hummingbird species with female-limited polymorphism separately to determine which adaptive or non-adaptive explanation is most likely. A recent study in the journal Current Biology provides a nice example, showing how female White-necked Jacobins (Florisuga mellivora) have evolved male-like plumage to avoid social harassment. Combining such behavioral studies with genomic analyses to pinpoint the genetic basis of female-limited polymorphism across different hummingbird species will provide exciting insights into the evolution of this phenomenon.

References

Diamant, E. S., Falk, J. J., & Rubenstein, D. R. (2021). Male-like female morphs in hummingbirds: the evolution of a widespread sex-limited plumage polymorphism. Proceedings of the Royal Society B, 288(1945), 20203004.

Featured image: White-necked Jacobins (Florisuga mellivora, female, male-like female and male) © Jillian Ditner | Falk et al. (2021) Current Biology

How low can you go? Exploring sex-linked genetic diversity in Barn Swallows

What evolutionary processes determine levels of genetic diversity on the Z-chromosome?

“Theory and empirical patterns suggest a disproportionate role for sex chromosomes in evolution and speciation.” This opening sentence from Darren Irwin’s excellent review on sex chromosomes perfectly illustrates why evolutionary biologists are so interested in these chromosomes. They often show peculiar patterns of genetic change, allowing researchers to formulate precise theoretical predictions which can consequently be tested with actual data. Take, for example, genetic diversity on the Z-chromosome. In birds, males have two Z-chromosomes, whereas females have one Z-chromosome and one W-chromosome. Hence, the Z-chromosome will be present in a population at a frequency of 3/4 compared to “normal” chromosomes (or autosomes). Similarly, the W-chromosome will be found at a frequency of 1/4 relative to autosomes. These lower frequencies mean that sex chromosomes will harbor less genetic diversity than autosomes.

If no other ecological or evolutionary processes are at play, we can expect the level of genetic diversity on the Z-chromosome to be 3/4 of the autosomes. But Z-linked genetic diversity can be reduced even more when the mating success of males is highly skewed. If a few males account for the majority of the offspring, there will be a significant reduction in genetic diversity on the Z-chromosome. To visualize this process, imagine a population of colorful candies (red, blue, green, yellow, orange, purple). If only red candies are allowed to “reproduce” and make it to the next generation, you will end up with a very low level of diversity. Brian Charlesworth calculated that this mating effect can push the level of genetic diversity to a minimum of 0.56 (compared to 0.75 under standard conditions). A recent study in the journal Molecular Ecology explored patterns of genetic diversity on the Z-chromosomes of Barn Swallows (Hirundo rustica). Do these birds conform to theoretical expectations?

Bottlenecks and Linked Selection

Drew Schield and his colleagues analyzed the levels of genetic diversity for 160 individuals, representing six subspecies of the Barn Swallow. For each subspecies (and several hybrid zones), they calculated the ratio between genetic diversity on the Z-chromosome and the autosomes. As explained above, theoretical work suggests that this ratio should be 0.75 under neutral conditions and can drop to 0.56 in cases of extreme skews in mating success. In Barn Swallows, the average ratio was even lower: 0.48. In fact, most subspecies were well below the theoretical minimum of 0.56. These patterns suggest that other evolutionary forces are at play here. The researchers point to “recent demographic history, linked selection and divergence hitchhiking” as possible explanations (see this paper for a short explanation of linked selection).

Previous work indicated that Barn Swallows have experienced recent population bottlenecks. These demographic changes are expected to affect the Z-chromosome more relative to autosomes, contributing to further reductions in genetic diversity on this sex chromosome. In addition, the Z-chromosome exhibits lower recombination rates compared to autosomes. Because less genetic reshuffling occurs on the Z-chromosome, larger genomic sections will be impacted by selection. If one genetic variant is under strong selection, all neighboring variants that are linked to it will hitchhike along. Large regions might thus lose genetic diversity.

Comparisons of genetic diversity on autosomes and Z-chromosomes for six subspecies and several hybrid zones (figure a) revealed that the ratio between these chromosomes is will below the theoretical minimum of 0.56 (orange region in figures b and c). From: Schield et al. (2021).

Genomic Islands

In addition to the low genetic diversity on the Z-chromosome, the researchers also noted increased genetic differentiation between the subspecies on this sex chromosome. Indeed, the Z-chromosome clearly stands out in the genomic landscape of differentiation (see this blog post for more details on this concept). The exact mechanism underlying these peaks in genetic differentiation remain to be determined. The main contenders are linked selection (as explained above) or reduced introgression on the Z-chromosome. The latter explanation entails that the Z-chromosome harbors genomic regions that contribute to reproductive isolation. If these regions are immune to introgression, they will diverge over time. Disentangling the relative contribution of these processes will require a more detailed exploration of the genes on the Z-chromosome. Clearly, sex chromosomes still hold many secrets.

Exploring the genomic landscape of differentiation (using the Population Branch Statistic) in the six subspecies revealed highly differentiated regions on the Z-chromosome (in green). From: Schield et al. (2021).

References

Schield, D. R., Scordato, E. S., Smith, C. C., Carter, J. K., Cherkaoui, S. I., Gombobaatar, S., … & Safran, R. J. (2021). Sex‐linked genetic diversity and differentiation in a globally distributed avian species complex. Molecular Ecology, 30(10), 2313-2332.

Featured image: Barn Swallow (Hirundo rustica) © Stefan Berndtsson | Wikimedia Commons

How the Fasciated Antshrike met the Bamboo Antshrike

An evolutionary journey across South America, culminating in secondary contact.

The Chinese philosopher Lao Tzu wrote that “the journey of a thousand miles begins with a single step.” This perspective can also be applied to the evolution of life on our planet. Countless species have spread across the globe – or particular parts of it – one step or one wingbeat at a time. Occasionally, these evolutionary journeys would culminate in the meeting of closely related populations that diverged thousands or millions of years ago. If reproductive isolation between these populations is still incomplete, hybridization and consequent introgression might occur. On this blog, I have mostly focused on the final part of this process: introgression and its consequences (see for example here and here). But it is definitely worthwhile to change perspectives and explore the evolutionary trajectories that different species followed before they established secondary contact. A recent study in the Biological Journal of the Linnean Society provides the ideal opportunity to do just that. Time to delve into the evolutionary story of two Antshrike species (genus Cymbilaimus)!

Spreading across South America

Let me start by introducing the main characters in our story: the Bamboo Antshrike (C. sanctaemariae) and the Fasciated Antshrike (C. lineatus). These two cryptic species have recently been split based on subtle morphological, vocal and ecological differences. For our ensuing journey across South America, however, it is not that relevant whether taxonomists classify them as species or subspecies.

Using molecular analyses and species distribution models, Leonardo Miranda and his colleagues reconstructed the evolutionary history of these two species. A good place to start the story of the Cymbilaimus Antshrikes is at the beginning. Between 1.85 and 0.6 million years ago, the Bamboo Antshrike and the Fasciated Antshrike went their separate ways. The ancestors of the Bamboo Antshrike probably followed their preferred habitat, which is – you guessed it – bamboo-dominated forests. This type of vegetation could be found in the lowlands of Amazonia during the Pleistocene, allowing the Bamboo Antshrikes to move into southern part of the Amazon region (blue and yellow regions in the figure below). The ancestors of the Fasciated Antshrike, on the other hand, resided in the northeastern part of South America and spread across the Guiana Shield (pink region) between 0.86 and 0.42 million years ago.

The evolutionary history of the Bamboo Antshrike and the Fasciated Antshrike. The colors on the phylogenetic tree indicate the inferred locations of the ancestral populations. The arrows on the right point to gene flow between several populations of both species. From: Miranda et al. (2021).

Secondary Contact

The story of the Fasciated Antshrike does not stop there. The researchers indicate that “our data also support a pattern of sequential dispersal episodes, almost simultaneous between 0.6 and 0.2 mya.” Similar to the Bamboo Antshrike following bamboo-dominated forests, the different populations of the Fasciated Antshrike probably tracked their favorite habitat across South America. These dispersal events established new populations in Central America and the southern section of the Amazon. In the latter region, the Fasciated Antshrike came into secondary contact with the Bamboo Antshrike which it had left behind more than one million years ago. Both species hybridized, resulting in the exchange of genetic material. The consequence of these introgression events remain to be elucidated. So, that is where our story ends (for now).

Classifying Cymbilaimus

Although the taxonomy of these Antshrikes has little impact on our evolutionary story, it is interesting to briefly explore the relevance of the genetic patterns for classifying these birds. Currently, there are two species of Cymbilaimus with three subspecies within the Fasciated Antshrike. Based on the molecular analyses in this study, the authors noted that “current subspecific limits with C. lineatus are inconsistent with its evolutionary history.” Indeed, the genetic results point to three main groups that correspond to:

1. The Bamboo Antshrike (C. sanctaemariae)
2. The Guinana group of the Fasciated Antshrike (C. lineatus, subspecies lineatus)
3. The remaining populations of the Fasciated Antshrike (C. lineatus, subspecies, intermedius and fasciatus)

The taxonomy of these birds might thus have to be updated. But that is a different story.

References

Miranda, L. S., Prestes, B. O., & Aleixo, A. (2021). Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary. Biological Journal of the Linnean Society, 132(2), 431-450.

Featured image: Fasciated Antshrike (Cymbilaimus lineatus) © Brian Gratwicke | Wikimedia Commons