Does founder-effect speciation occur in the Silvereye?

Testing this controversial speciation model with genomic data.

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

Countless Colonization Events

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

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

Accumulating Divergence

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

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

References

Sendell‐Price, A. T., Ruegg, K. C., Robertson, B. C., & Clegg, S. M. (2021). An island‐hopping bird reveals how founder events shape genome‐wide divergence. Molecular Ecology30(11), 2495-2510.

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

How did snowfinches adapt to high-altitude environments?

Were the adaptations already present in the ancestor or not?

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

Positive Selection

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

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

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

DNA Repair

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

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

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

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

References

Qu, Y., Chen, C., Chen, X., Hao, Y., She, H., Wang, M., … & Lei, F. (2021). The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai–Tibet Plateau. Proceedings of the National Academy of Sciences118(13), e2012398118.

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

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

Convergent evolution of color morphs in Skuas

How far do the similarities reach on the genetic level?

Convergent evolution refers to different species that independently evolved similar traits. An obvious example concerns the streamlined shapes of sharks and dolphins. The common ancestor of these aquatic creatures lived about 300 million years ago and dolphins descended from land mammals. Hence, it is easy to see that sharks and dolphins have independently evolved their similar shapes.

However, when it comes to closely related species, detecting convergent evolution is more tricky. The more closely related two species are, the more likely that their similarities were inherited from a common ancestor (and are thus not the result of convergent evolution). But looks can be deceiving. Perhaps the similarities are only skin deep. When you start exploring deeper levels – compare it to peeling away the layers of an onion – you might discover genetic differences. The shared traits might be encoded by different genes, or they might be the outcome of different mutations in the same genes. There is only one way to find: start peeling that genetic onion.

Three Skuas

A nice example of possible convergent evolution among closely related species can be found in skuas (genus Stercorarius). All three species in this group of seabirds show several color morphs, based on their ventral plumage. In the Arctic Skua (S. parasiticus) and the Pomarine Skua (S. pomarinus), this plumage polymorphism has been linked to the gene MC1R (melanocortin-1 receptor). Interestingly, the two species experienced different mutations in the MC1R-gene, thus showing convergent evolution at a deep genetic level. But what about the third species, the South Polar Skua (S. maccormicki)?

Kirstin Janssen and her colleagues explored the MC1R-gene for 25 individuals, representing the three color morphs (8 pale, 10 dark and 7 intermediate birds). The DNA sequences revealed two variable sites within the gene: one synonymous mutations (no change in amino acid) and one mutation replacing a glutamate with a lysine. However, these genetic variants did not line up with the color morphs. These patterns suggest that the MC1R-gene is not associated with plumage polymorphism in the South Polar Skua.

Plumage variation in the South Polar Skua, a pale female and a dark male bird. From: Janssen et al. (2021).

Sex-linked Variation

Finding out that the MC1R-gene is not involved might be disappointing. But don’t despair yet (or start crying, which can happen while peeling onions). The researchers tested another candidate gene: TYRP1 (tyrosinase-related protein 1). This particular gene can be found on the Z-chromosome, one of the sex chromosomes in birds. Because the plumage variation in the South Polar Skua seems sex-specific, with males being darker than females, it makes sense to focus on a sex-linked gene.

Unfortunately, this approach was also unsuccessful. The researchers did not find any variation in this gene. We can thus conclude that TYRP1 is not involved in the plumage polymorphism of the South Polar Skua. The search will continue and there are still plenty of options to explore. Perhaps the color morphs are due to differences in gene expression. Or because of mutations in different genes. We will just have to keep peeling away at that onion.

References

Janssen, K., Bustnes, J. O., & Mundy, N. I. (2021). Variation in genetic mechanisms for plumage polymorphism in skuas (Stercorarius). Journal of Heredity112(5), 430-435.

Featured image: South Polar Skua (Stercorarius maccormicki) © Denis Luyten | Wikimedia Commons

Two American sparrows with similar mtDNA: Rapid speciation or hybridization?

Analyses of the nuclear genome provide the answer to this question.

An important aspect of the scientific process is considering and testing several explanations. Imagine, for example, that you sequence the mitochondrial DNA of two bird species. When you compare the genetic sequences, you notice that the two species hardly differ. What could explain this pattern? In scientific papers, you will generally come across two possible solutions: (1) the two species have only recently diverged and still share some genetic variation, or (2) the two species have hybridized and mitochondrial DNA flowed from one species into the other. In technical terms, these explanations are known as incomplete lineage sorting (see this blog post for more details on this concept) and introgressive hybridization.

The mitochondrial situation that I just described applies to the Golden-crowned Sparrow (Zonotrichia atricapilla) and White-crowned Sparrow (Z. leucophrys). In 2001, Jason Weckstein and his colleagues reported “extraordinarily low levels of sequence divergence between Z. leucophrys and Z. atricapilla, despite distinct plumage, song, and allozymes.” Moreover, several mitochondrial haplotypes were shared between these species. Although they could not rule out rapid speciation (and thus incomplete lineage sorting), they hypothesized that introgression was the most likely explanation. Recently, a study in the journal Molecular Phylogenetics and Evolution put this hypothesis to the test by exploring the nuclear DNA of these sparrows. Undifferentiated nuclear genomes would suggest rapid speciation, while distinct nuclear genomes in combination with shared mtDNA would point to introgression.

Phylogenetic Trees

Based on 73 specimens of the two species, Rebecca Taylor and her colleagues estimated phylogenetic trees for two mitochondrial genes (COI and the control region) and several thousands of nuclear genetic variants. In line with previous work, the species shared mitochondrial haplotypes and could not be separated into distinct clusters. The nuclear analyses, however, uncovered clear differences between the Golden-crowned Sparrow and White-crowned Sparrow. These contrasting patterns suggest introgression of mitochondrial DNA.

This explanation was supported by additional analyses that revealed ancient gene flow between these species. Using the software TreeMix, for instance, the researchers detected introgression from Golden-crowned into White-crowned Sparrow. And the commonly used D-statistic further corroborated this introgression event (see this blog post for an explanation how this test works). Clearly, introgressive hybridization seems to be the most likely explanation.

Phylogenetic analyses of the mitochondrial genes (left figure) could not separate the two species into distinct groups, whereas the nuclear variants uncovered clear clusters (right figure). The Golden-crowned Sparrow is depicted in red, the other colors represent subspecies of the White-crowned Sparrow. From: Taylor et al. (2021).

Adaptive or Neutral Introgression?

Answering one question mostly leads to a bunch of other mysteries. Now that we know about introgression of mitochondrial DNA, we can move on to the next aspect: was the introgression driven by neutral or selective processes? Currently, we don’t have enough information to answer this question. However, the researchers do speculate about a possible scenario:

While it is only informed speculation, populations of Z. atricapilla and Z. leucophrys could have been forced into common refugia by ice sheets and shifting vegetation during the Pleistocene, leading some individuals to seek out heterospecific mates. Several rounds of bottlenecking due to climate change might have occurred during this period and similarly caused the fixation of one haplotype in both species during periods when population sizes were small. Selection may have acted in combination with periods of small population sizes and augmented this process, if one mitochondrial haplotype conferred a fitness advantage.

This certainly sounds like a plausible scenario, but it remains to be tested with more detailed analyses. The mitochondrial mystery of the Golden-crowned Sparrow and the White-crowned Sparrow continues…

References

Taylor, R. S., Bramwell, A. C., Clemente-Carvalho, R., Cairns, N. A., Bonier, F., Dares, K., & Lougheed, S. C. (2021). Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrysMolecular Phylogenetics and Evolution162.

Featured image: Golden-crowned Sparrow (Zonotrichia atricapilla) © V. J. Anderson | Wikimedia Commons

How Amazon parrots spread across the Greater Antilles

Mitochondrial DNA points to a stepping-stone scenario from Jamaica to Puerto Rico.

Islands have often been described as “natural laboratories” for evolutionary biologists. But before evolution can start tinkering with the available genetic variation of newly founded island populations, organisms first need to reach and spread across these archipelagos. Reconstructing the chain of colonization of an island group is no easy exercise. A nice example of this challenge concerns Amazon Parrots on the Greater Antilles (an archipelago in the Caribbean Sea including Cuba, Hispaniola, Puerto Rico, Jamaica, and the Cayman Islands). This collection of islands houses five species of Amazon Parrot:

  • The Cuban Amazon (Amazona leucocephala) on Cuba
  • The Black-billed Amazon (Amazona agilis) on Jamaica
  • The Yellow-billed Amazon (Amazona collaria) on Jamaica
  • The Hispaniolan Amazon (Amazona ventralis) on Hispaniola
  • The Puerto Rican Amazon (Amazona vittata) on Puerto Rico

Ornithologists have been speculating about the evolutionary history of these parrots. Patricia Ottens-Wainright and her colleagues suggested that there may have been two independent dispersal events to the Greater Antilles. David Lack, however, argued for a single colonization event based on the morphological similarities between the Cuban Amazon, the Hispaniolan Amazon and the Puerto Rican Amazon. A recent study in the journal Genes attempted to resolve this debate by sequencing the complete mitochondrial genomes of all five species.

A Phylogeny of Parrots

First, Sofiia Kolchanova and her colleagues reconstructed the phylogenetic relationships among the parrots on the Greater Antilles and their South and Central American cousins. These analyses revealed that the five species from the Greater Antilles form a distinct cluster that is sister to the White-fronted Amazon (Amazona albifrons), a species from Central America. This finding suggests that the Greater Antilles were colonized only once, arriving on Jamaica. But how did these parrots subsequently spread across the islands? To answer this question, the researchers explored several biogeographic models with the R-package BioGeoBEARS.

Phylogenetic relationships among Amazona parrots based on the whole mitochondrial genome. The five species from the Greater Antilles are most closely related to the White-fronted Amazon (Amazona albifrons) from Central America. From: Kolchanova et al. (2021).

Stepping Stones

All biogeographic models indicated that the ancestor of Amazon Parrots on the Greater Antilles reached Jamaica about 3.5 million years ago. This date coincides with a period of low sea levels when birds could easily reach the islands from the Central American mainland. About 3.1 million years ago, the founding population on Jamaica split into two species: the Black-billed Amazon and the ancestor of the four other species. However, it is unclear what happened next. Some models indicated that the speciation event happened on the same island (i.e. sympatric speciation), giving rise to the Yellow-billed Amazon. Roughly 1.4 million years ago, part of this population colonized Cuba. However, other models pointed to an allopatric speciation event after dispersal to Cuba (or some islands that have now disappeared). Later on, some of these Cuban birds returned to Jamaica and evolved into the Yellow-billed Amazon. More detailed analyses – with nuclear genetic data – are needed to discriminate between these scenarios.

The remainder of the evolutionary story of these parrots is more clear. The researchers write that “most models agree that once the parrots reached Cuba, they have continued to disperse to Hispaniola and then to Puerto Rico in a stepping stone fashion.” The colonization of Hispaniola occurred ca. 760,000 years ago while Puerto Rico was reached about 690,000 years ago. However, it is important to keep in mind that this scenario, and the accompanying dates, is solely based on mitochondrial DNA. Analyses of the whole nuclear genome might tell a slightly different story. Although it seems almost certain that the Greater Antilles were colonized once by these parrots. David Lack was right.

An overview of the eight biogeographical models tested in this study. Each small circle corresponds to a model and the colors indicate the most likely island where the parrots resided. From: Kolchanova et al. (2021).

References

Kolchanova, S., Komissarov, A., Kliver, S., Mazo-Vargas, A., Afanador, Y., Velez-Valentín, J., … & Oleksyk, T. K. (2021). Molecular phylogeny and evolution of Amazon parrots in the Greater Antilles. Genes12(4), 608.

Featured image: Cuban Amazon (Amazona leucocephala) © Laura Gooch | Wikimedia Commons

Scientists “resurrect” ancient proteins to understand how penguins can hold their breath for so long

Unraveling the evolutionary changes to the hemoglobin protein in penguins.

The study of evolution is sometimes described as “just” a historical science, in comparison to the “superior” experimental sciences. This characterization – popular among creationists – is obviously plain poppycock. Although evolutionary biologists study the history of life on Earth, they use a variety of tools, including experiments. One of the most exciting experimental approaches is the resurrection of ancient proteins to understand how they might have functioned in the ancestors of modern species. A recent study in the journal PNAS provides a beautiful example of this strategy. Researchers reconstructed the hemoglobin protein of the common ancestor of penguins and their non-diving relatives to investigate how this protein has changed over millions of years of evolution.

Ancient Proteins

As you probably know from nature documentaries, penguins dive to great depths to find food. These deep dives require an efficient use of oxygen. Here, the protein hemoglobin plays an important role by binding to oxygen and carrying it to certain tissues. Experimental measurements already showed that hemoglobin in several penguin species has a higher oxygen-binding affinity compared to other bird species. This feature could have evolved in a number of ways: (1) penguins might have evolved an increased affinity for oxygen, (2) non-diving birds might have evolved a decreased affinity for oxygen, or (3) the change happened in both direction, namely increased affinity in penguins and decreased affinity in non-diving birds. To discriminate between these three options, the researchers reconstructed the hemoglobin of the common ancestor of penguins (which they called AncSphen) and the hemoglobin of the common ancestor of penguins and their non-diving relatives (AncPro).

Attentative readers might remark that the non-diving relatives in this scheme – the order Procellariiformes – also dive for food. However, these birds do not perform the extremely deep dives that penguins do.

A phylogenetic overview of the ancient proteins that the researchers reconstructed: AncSphen represents the ancestral condition in penguins while AncPro goes even further back in time to the common ancestor of penguins and non-diving birds. From: Signore et al. (2021).

Bohr Effect

Experiments with the two resurrected proteins – AncSphen and AncPro – revealed that AncSphen has a significantly higher affinity for binding oxygen compared to AncPro. This suggests that penguins have evolved an increased oxygen-binding affinity whereas non-diving birds probably experienced little changes (which fits with scenario 1 mentioned above).

Next, the researchers took a closer look at the role of cofactors, which are chemical compounds that can improve the functioning of proteins. Further experiments revealed that, when cofactors were added to the mix, AncSphen responded two times stronger to changes in pH than AncPro. At lower pH, AncSphen showed a decreased affinity for binding oxygen, releasing it more easily. This particular response to pH – known as the Bohr effect – might compensate for the high oxygen-binding affinity of hemoglobin penguins when it has to unload oxygen at certain tissues.

The addition of cofactors (grey bars) at different pH-levels shows a stronger response in AncSphen compared to AncPro. This Bohr effect allows hemoglobin in penguins to release oxygen more efficiently in acidic tissues. Adapted from: Signore et al. (2021).

The Journey of an Oxygen Molecule

To understand how all of this works, imagine being a oxygen molecule in the blood vessel of a penguin. You have just entered the lungs and become tightly bound to hemoglobin. As you are carried around the body, you wonder how this hemoglobin will ever let you go. Its oxygen-binding affinity is so strong that you cannot escape. However, as the pH starts to drop in the muscle tissue, you feel the grip of the hemoglobin loosening. Once the pH is low enough, you are released and can move into a muscle cell. In other words, the Bohr effect allows hemoglobin to unload its oxygen in acid tissues, resulting in a more efficient oxygen transport around the body.

An amazing adaptation that we managed to understand using an experimental approach. Keep that in mind when someone tells you that evolutionary biology is “just” a historical science.

References

Signore, A. V., Tift, M. S., Hoffmann, F. G., Schmitt, T. L., Moriyama, H., & Storz, J. F. (2021). Evolved increases in hemoglobin-oxygen affinity and the Bohr effect coincided with the aquatic specialization of penguins. Proceedings of the National Academy of Sciences118(13), e2023936118.

Featured image: Gentoo Penguin (Pygoscelis papua) © Ken Funakoshi | Wikimedia Commons

Ancient gene flow complicates phylogenetic analyses of leaf warblers

Understanding underlying processes helps to select the “correct” genomic loci.

Different genes tell different stories. This simple statement captures the essence of phylogenomic analyses. The evolutionary history of a particular gene (or genomic region) can be shaped by several processes, such as interspecific gene flow and natural selection. This insight raises the question which genomic regions we should use to estimate the “true” species tree. Some authors have argued that regions of low recombination are most suitable for phylogenetic analyses. Genetic variants flowing in from another species that end up in these rarely recombining regions might become linked to deleterious alleles and will be quickly removed from the population. Hence, regions of low recombination are expected to be immune to introgression, potentially retaining the “true” evolutionary history of the species. However, phylogenomic analyses of Ficedula flycatchers revealed that low recombination regions can produce misleading results due to strong selection. Clearly, the debate on the most suitable genomic regions for phylogenetic analyses has not been settled. A recent study in the journal Systematic Biology provided another perspective on this issue by exploring the evolutionary history of several leaf warblers.

Three Hypotheses

Dezhi Zhang and his colleagues sequenced the whole genomes of 78 leaf warblers, representing 8 species. Previous analyses – using a limited number of genetic markers – could not confidently resolve the phylogenetic relationships among these species. Specifically, the position of Martens’s Warbler (Phylloscopus omeiensis) turned out to be problematic. The researchers proposed three hypotheses to explain the phylogenetic issues with this species:

  • Hypothesis 1: Martens’s Warbler is the sister species of Whistler’s Warbler (P. whistleri) and Bianchi’s Warbler (P. valentini), but gene flow from another species – Alström’s Warbler (P. soror) – results in Martens’s Warbler clustering with Alström’s Warbler.
  • Hypothesis 2: Martens’s Warbler is the sister species of Alström’s Warbler, but ancient gene flow from the ancestor of Whistler’s Warbler and Bianchi’s Warbler results in Martens’s Warbler clustering with these species.
  • Hypothesis 3: Martens’s Warbler is a hybrid species originating from hybridization between Alström’s Warbler and the ancestor of Whistler’s Warbler and Bianchi’s Warbler.

I can imagine that these three scenarios are difficult to follow. Luckily, the authors provided a clear overview of their hypotheses in the figure below.

An overview of the three hypotheses on the phylogenetic position of the Martens’s warbler (Phylloscopus omeiensis). From: Zhang et al. (2021).

Demographic Analyses

Using a suite of phylogenetic analyses, the researchers tried to figure out which hypothesis depicts the most likely scenario. I will not go into the technical details of all these analyses, but I will summarize the main results:

  • Comparing several demographic models with the coalescent simulator fastsimcoal2 revealed that scenarios with ancient gene flow between Martens’s Warbler and the ancestor of Whistler’s Warbler and Bianchi’s Warbler received the highest support.
  • D-statistic analyses suggested high levels of gene flow between Martens’s Warbler and Whistler’s Warbler and between Martens’s Warbler and Bianchi’s Warbler. These patterns were corroborated with demographic analyses using the software DADI.
  • Phylogenetic network analyses pointed to Martens’s Warbler and Alström’s Warbler as sister species, but with ancient gene flow between Martens’s Warbler and the ancestor of Whistler’s Warbler and Bianchi’s Warbler.

If you compare these findings with the three hypotheses outline above, you will quickly see that hypothesis two comes out on top. It seems that Martens’s Warbler is the sister species of Alström’s Warbler, but ancient gene flow from the ancestor of Whistler’s Warbler and Bianchi’s Warbler has thrown a wrench in previous phylogenetic analyses.

Phylogenetic network analyses consistently cluster Martens’s Warbler (P. omeiensis) and Alström’s Warbler (P. soror), but also indicate gene flow between Martens’s Warbler and the ancestor of Whistler’s Warbler (P. whistleri) and Bianchi’s Warbler (P. valentini). The three graphs show results for (a) one, (b) two, and (c) three reticulations. From: Zhang et al. (2021).

Gene Flow and Selection

So, we have managed to resolve the phylogenetic mystery of the leaf warblers. But what about the question posed at the beginning of this blog post: which genomic regions are most suitable for phylogenetic analyses? Taking a closer look at the genome of Martens’s Warbler, the researchers discovered that regions of low recombination were mostly affected by ancient gene flow. They suspect that the introgressed variants from other species ended up in these low recombination regions and were retained in the population by strong positive selection. This observation suggests that “low recombination […] may not be a good indicator of genomic regions suitable for inferring the true phylogeny in the context of ancient gene flow.”

Does this mean that we can safely discard regions of low recombination in phylogenomic analyses and continue working with the rest of the genome? Not necessarily. Which genomic regions are most suitable for phylogenetic analyses will depend on the evolutionary history of the study system. Because the evolution of these leaf warblers has been shaped by high levels of ancient gene flow and strong positive selection on the introgressed regions, it turns out that low recombination regions are not reliable for phylogenetics. In other study systems, ancient gene flow might be less pervasive or introgressed variants were quickly removed from the population. In those scenarios, low recombination regions might be good candidates to reconstruct the true species phylogeny. In other words, which genomic regions should be used in phylogenetic analyses will depend on the evolutionary history of the study system. Due to the contingent nature of evolution, there will probably be no silver bullet to reconstruct the “true” species tree.

And there is also the question whether the “true” species tree actually exists. Perhaps evolution is just one big reticulated network that cannot be captured in a simple bifurcating tree. But that is a discussion for another blog post.

References

Zhang, D., Rheindt, F. E., She, H., Cheng, Y., Song, G., Jia, C., Qu, Y., Alström, P. & Lei, F. (2021). Most genomic loci misrepresent the phylogeny of an avian radiation because of ancient gene flow. Systematic Biology70(5), 961-975.

Featured image: Whistler’s Warbler (Phylloscopus whistleri) © Raju Kasambe | Wikimedia Commons

The danger of few genetic markers: Revisiting introgression between Chukar and Red-legged Partridge

In contrast to previous studies, genomic analyses point to little gene flow between these species.

For decades, people have been releasing the non-native Chukar Partridge (Alectoris chukar) and farm-reared hybrids into the range of the native Red-legged Partridge (A. rufa). Conservationists feared that these practices would impact the genetic integrity of European Red-legged Partridge populations. And indeed, several genetic studies reported extensive introgression from the Chukar into the Red-legged Partridge (see the Galliformes page for an overview). However, the introgression patterns were based on a limited set of genetic markers, such as microsatellites. These markers only capture a fraction of the genetic variation. Genomic data will tell a more complete story that might be very different. The possible discrepancy between microsatellites and genomic data was nicely illustrated by Mallards (Anas platyrhynchos) and American Black Ducks (A. rubripes). Analyses of microsatellites suggested that hybridization between these duck species might lead to the genetic extinction of the latter species. However, genomic studies of this system revealed little gene flow between the species, indicating that hybridization is not threatening the genetic integrity of the American Black Duck. A recent study in the Proceedings of the Royal Society B investigated whether a similar scenario applies to the Chukar and Red-legged Partridge situation.

Limited Introgression

Giovanni Forcina and his colleagues sequenced the genomes of 81 birds (75 Red-legged Partridges and 6 Chukar Partridges) and obtained almost 170,000 molecular markers. Analyses of this large dataset indicated that introgression from the non-native Chukar into the native Red-legged Partridge was quite limited. Specifically, the authors reported the following patterns for several subspecies (rufa, intercedens and hispanica) of the Red-legged Partridge:

While most populations within the ranges of A. r. rufa and A. r. intercedens showed a low yet detectable level of A. chukar introgression, those of A. r. rufa from Corsica and A. r. hispanica turned out to be probably unaffected.

All in all, the genetic impact of restocking practices appears to be relatively minor. Although there are clear signs of introgression from the Chukar Partridge, the genetic integrity of the Red-legged Partridge is not in serious jeopardy. It is possible that lower fitness of hybrids prevents most of them from mating and contributing to the next generation.

A principal component analysis clearly separated the Chukar Partridges (white squares) from the Red-legged Partridges (colored dots). More detailed analyses pointed to limited introgression between these species. From: Forcina et al. (2021).

Genomic Landscape

The observation of limited introgression between these partridges is certainly good news, but why did previous genetic studies point to high levels of gene flow? In a recent review, I warned about the use of a few markers (such as microsatellites) in conservation because of the so-called genomic landscape of differentiation. When comparing the genomes of closely related species, we generally observe that genetic differences are heterogeneously distributed across the genome. Some genomic regions will be drastically different, while others are largely undifferentiated. The random selection of a few genetic markers might result in a marker set that only captures the undifferentiated section of the genome, giving the impression that the studied species are genetically similar. When the species interbreed, researchers can be quick to conclude that this similarity is due to introgressive hybridization. However, a genomic perspective might lead to very different conclusions, as we have seen with the partridges. Do not underestimate the power of genomic data.

References

Forcina, G., Tang, Q., Cros, E., Guerrini, M., Rheindt, F. E., & Barbanera, F. (2021). Genome-wide markers redeem the lost identity of a heavily managed gamebird. Proceedings of the Royal Society B288(1947), 20210285.

Featured image: Red-legged Partridge (Alectoris rufa) © Juan Lacruz | Wikimedia Commons

Singing a different song: Incipient speciation in the Small Tree Finch

Two island populations are diverging genetically and acoustically.

Speciation – the origin of new species – is one of the best pieces of evidence for evolution. If species were created by some whimsical designer, we would expect to see clear boundaries between them. Instead, we observe populations at different stages of the speciation process. Some populations clearly belong to distinct species while others freely interbreed and cause headaches among taxonomists that try to pigeonhole all this diversity. In addition, the rate at which populations diverge often differs between traits. Genetic changes tend to accumulate over long periods of time whereas behavioral differences can quickly arise (see for example crossbills). Bird song is a beautiful example of a behavioral trait that can kickstart the speciation process. Several species of songbird learn their song from a tutor (mostly the father singing near the nest) and might make mistakes during the learning process. These mistakes can give rise to local dialects and potentially isolate neighboring populations because they do not recognize each others songs. A recent study in the Journal of Evolutionary Biology documented this process in the Small Tree Finch (Camarhynchus parvulus) on the Galapagos Islands.

Genes and Syllables

Diane Colombelli-Négrel and Sonia Kleindorfer focused on two populations of the Small Tree Finch on the islands of Santa Cruz and Floreana. Genetic analyses – based on microsatellites – indicated that these island populations are diverging. The researchers wondered whether these birds have also developed different songs. Studying more than 900 recordings from 112 males revealed 10 syllable types, of which only 4 were shared between the islands. Hence, the Small Tree Finches from Santa Cruz and Floreana are becoming genetically and acoustically different. But do these differences also affect their behavior? When a bird from Santa Cruz ends up on Floreana, will it be able to find a partner and mate?

The Small Tree Finches on Santa Cruz and Floreana differ genetically (left graph) and in the songs that they produce (right graph). Notice that each song is composed of one syllable type. From: Colombelli‐Négrel & Kleindorfer (2021).

Playback

To assess the behavioral response of the birds, the researchers turned to playback experiments. They tested the response of 91 males – 40 on Santa Cruz and 51 on Floreana – to songs from the two islands. These experiments showed that “males had a stronger response to the intruder song from their own geographical area.” This finding suggests that male Small Tree Finches are able to discriminate between local and foreign songs. Whether females are also capable of telling the difference between males from their own island and accidental visitors remains to be tested. If so, it would point to some level of reproductive isolation. Given enough time, we might end up with two distinct species of Small Tree Finch.

Playback experiments showed that male Small Tree Finches responded most to songs from their own island (in black) compared to songs from another island (in grey). From: Colombelli‐Négrel & Kleindorfer (2021).

References

Colombelli‐Négrel, D., & Kleindorfer, S. (2021). Behavioural response to songs between genetically diverged allopatric populations of Darwin’s small tree finch in the Galápagos. Journal of Evolutionary Biology, 34(5), 816-829.

Featured image: Small Tree Finch (Camarhynchus parvulus) © Mike Comber | Wikimedia Commons

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 Society193(2), 499-540.

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