Exploring the speciation continuum of hummingbirds

The comparison of three species pairs leads to some surprising findings.

In 2005, Thomas Turner and his colleagues reported on “genomic speciation islands” in the African malaria mosquito (Anopheles gambiae). In their PLoS Biology paper, the authors described how some genomic regions remain differentiated despite considerable gene flow, and they speculated that these regions might contain the genes responsible for reproductive isolation. However, further studies on other organisms, such as Heliconius butterflies and Ficedula flycatchers, indicated that the term “speciation islands” was a bit premature. Other evolutionary processes can give rise to differentiated genomic islands. To understand how these genomic islands can arise, we must first take a closer look at the popular summary statistic Fst.

The fixation index (Fst) is a measure of population differentiation due to genetic structure. It is important to realize that Fst is a relative measure because it compares the genetic diversity between populations while taking into account the genetic diversity within each population (you can nicely see this in the formula below, where π is genetic diversity). Hence, you can get a peak in Fst at a certain genomic region when one population has low genetic diversity at this location. This reduction in genetic diversity can be the outcome of genetic drift or a selective sweep, and might thus be unrelated to reproductive isolation. This issue with Fst can be resolved by calculating another summary statistic (Dxy) which is not influenced by genetic diversity within populations. The relationship between Fst and Dxy can be very insightful: Fst peaks that result from locally reduced gene flow are predicted to have elevated Dxy, while Fst peaks resulting from lower genetic diversity in a population are not.

One way to calculate Fst which nicely shows the effect of genetic diversity within a population.

Hummingbirds and Chromosomes

With this knowledge in mind, evolutionary biologists try to understand how genetic differentiation accumulates in the genome during speciation. Are peaks in Fst related to reproductive isolation or are they the outcome of reduced genetic diversity? Because it is mostly not feasible to document the entire speciation process (which takes at least thousands of years), researchers compare closely related species pairs at different stages of divergence. A recent study in the journal BMC Evolutionary Biology focused on three pairs of hummingbirds that diverged at different times, namely:

• Anna’s (Calypte anna) and Costa’s hummingbird (C. costae) – 2.5 million years
• Black-chinned (Archilochus alexandri) and Ruby-throated hummingbird (A. colubris) – 1.5 million years
• Allen’s (Selasphorus sasin) and Rufous hummingbirds (S. rufus) – 0.93 million years

The researchers – Elisa Henderson and Alan Brelsford – were mainly interested in the role of recombination in the build-up of genetic differentiation. Low recombination rates are predicted to lead to reduced genetic diversity because selection on one genetic variant will affect large genomic regions that are linked to this variant. If recombination rate is high, however, the genetic variant under selection will be confined to a smaller genomic region and the reduction in genetic diversity will be more localized. Given that large chromosomes have lower recombination rates, we can expect bigger reductions in genetic diversity and consequently more peaks in Fst. In other words, larger chromosomes will diverge faster compared to smaller chromosomes. In addition, sex chromosomes (Z and W for birds) also show reduced recombination and can thus accumulate genetic differentiation faster than autosomes.

The genomic landscape of differentiation for three pairs of hummingbird species. From: Henderson & Brelsford (2020) BMC Evolutionary Biology.

Fast Microchromosomes

The genomic analyses resulted in some interesting results. The authors found that “speciation seems to progress at different rates based on chromosome type, with the sex chromosome diverging first, the microchromosomes diverging next, and divergence only appearing on the macrochromosomes in late stages of reproductive isolation.” The finding that sex chromosomes diverge first is logical. These chromosomes show reduced rates of recombination and are known to accumulate incompatible alleles that can contribute to reproductive isolation (see for example this blog post on the Reunion grey white-eye, Zosterops borbonicus).

Given the predictions outlined above, the result that microchromosomes diverge before macrochromosomes is quite surprising. Given the lower recombination rate on larger chromosomes, we would have expected the opposite pattern. The authors suspect that the early accumulation of Fst peaks on microchromosomes may be due to certain characteristics of these small chromosomes. For example, microchromosomes have a high gene density which might provide more targets for selection, leading to lower genetic diversity and consequently peaks in Fst. Or perhaps these small chromosomes might harbor specific genes that contribute to reproductive isolation? More research is needed to pinpoint the exact mechanisms.

Genomic analyses showed that genetic differentiation (measured as Fst) accumulated faster on sex chromosomes (red), followed by microchromosomes (blue) and macrochromosomes (purple). From: Henderson & Brelsford (2020) BMC Evolutionary Biology.

Barrier Loci?

Apart from Fst, the researchers also calculated Dxy. As explained above, Fst peaks that result from locally reduced gene flow are predicted to have elevated Dxy, while Fst peaks resulting from lower genetic diversity in a population are not. In this case, there was a negative correlation between Fst and Dxy, suggesting that most differentiated regions are the outcome of lower genetic diversity in one population (due to genetic drift or selection). There might be some genomic regions that are involved in reproductive isolation, but more detailed analyses are needed to find these.

This study shows how we can gain insights into the process of speciation by comparing species pairs at different stages of divergence. There is, however, an important issue to take into account when performing these kinds of analyses. Namely, species-specific differences in natural history and morphology can lead to different genetic signatures during the speciation process. The authors nicely formulated this caveat at the end of their paper.

These differences across the species used in this study highlight that each species pair is subject to its own evolutionary trajectory leading to a unique speciation event. While this is a general caveat of using independent species pairs as a proxy for the speciation continuum, we believe that the differences we observe among chromosome types can inform the ongoing debate about the roles of selection and recombination in the genetics of speciation.

References

Henderson, E. C., & Brelsford, A. (2020). Genomic differentiation across the speciation continuum in three hummingbird species pairs. BMC Evolutionary Biology, 20(1), 1-11.

Featured image: Ruby-throated hummingbird (A. colubris) © JeffreyW | Wikimedia Commons

The paper has been added to the Apodiformes page.

You only need one genome to unravel the demographic history of the Chinese Grouse

Genomic analyses reveal population fluctuations during the Pleistocene.

A few weeks ago, scientists announced that they almost completed a sequence of the human genome. This might come as a surprise: did we not sequence the human genome in 2003 when the results from the Human Genome Project were published? That genome sequence was actually incomplete, about 15% was missing (especially stretches of repetitive DNA are difficult to assemble). Similarly, many avian genome assemblies contain significant gaps (see this blog post for more details). However, scientists can still extract a lot of information from incomplete genome assemblies. For instance, you can reconstruct the demographic history of a species from one genome using a pairwise sequentially Markovian coalescent (PSMC) analysis. This technique – developed by Heng Li and Richard Durbin – is nicely explained by David Reich in his book Who We Are and How We Got Here:

A 2011 paper by Heng Li and Richard Durbin showed that the idea that a single person’s genome contains information about a multitude of ancestors was not just a theoretical possibility, but a reality. To decipher the deep history of a population from a single person’s DNA, Li and Durbin leveraged the fact that any single person actually carries not one but two genomes: one from his or her father and one from his or her mother. Thus it is possible to count the number of mutations separating the genome a person receives from his or her mother and the genome the person receives from his or her father to determine when they shared a common ancestor at each location. By examining the range of dates when these ancestors lived—plotting the ages of one hundred thousand Adams and Eves—Li and Durbin established the size of the ancestral population at different times. In a small population, there is a substantial chance that two randomly chosen genome sequences derive from the same parent genome sequence, because the individuals who carry them share a parent. However, in a large population the chance is far lower. Thus, the times in the past when the population size was low can be identified based on the periods in the past when a disproportionate fraction of lineages have evidence of sharing common ancestors.

Population Fluctuations

A recent study in the journal BMC Genomics applied this PSMC analysis to the genome of a Chinese Grouse (Tetrastes sewerzowi). This forest-dwelling species can be found in the mountains east of the Qinghai-Tibet Plateau. It is currently considered “Near Threatened” because of population declines due to ongoing deforestation and fragmentation of its habitat.

The genomic analyses revealed that the population size of the Chinese Grouse has fluctuated over time. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene (between 30,000 and 40,000 years ago), followed by a sharp decline during the last glacial maximum (about 20,000 years ago). Similar patterns have been found in other bird species, highlighting the influence of the climatic cycles during the Pleistocene (see for example this study by Krystyna Nadachowska-Brzyska and her colleagues).

The PSMC analysis showed population fluctuations of the Chinese Grouse during the Pleistocene. From: Song et al. (2020) BMC Biology.

Coniferous Forests

Next, the researchers focused on the underlying mechanisms of these population fluctuations. Why did the number of Chinese Grouse wax and wane during the Pleistocene? To answer this question, the researchers turned to Ecological Niche Modelling and reconstructed the distribution of the Chinese Grouse throughout the Pleistocene. This exercise showed that the population expansion during the late Pleistocene (30,000–40,000 years ago, also known as the Greatest Lake Period) can be explained by the warmer weather which allowed conifer forests, the primary habitat for Chinese Grouse, to reach their greatest extent. Later on, during colder periods, the coniferous habitat shrunk and the Chinese Grouse populations moved westwards into higher altitudes.

These findings indicate that the distribution of the Chinese Grouse is strongly dependent on the coniferous forest cover. It is thus essential to protect these fragmented forests and safeguard the future of this beautiful bird.

Ecological Niche Modelling showed how the suitable habitat for Chinese Grouse increased during the late Pleistocene (figure a), followed by extensive loss of habitat later on (figure b). The current distribution is depicted in figure c. From: Song et al. (2020) BMC Genomics.

References

Song, K., Gao, B., Halvarsson, P., Fang, Y., Jiang, Y. X., Sun, Y. H., & Höglund, J. (2020). Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowi. BMC genomics, 21(1), 1-9.

Featured image: A drawing of Chinese Grouse (Tetrastes sewerzowi) © Ornithological Miscellany. Volume 2 | Wikimedia Commons

Gene flow is an integral part of speciation in Beringian birds

Eight bird lineages with a trans-Beringian distribution show clear signatures of past gene flow.

Most people know Beringia as the land bridge that allowed humans to travel from Siberia to North America during the Ice Ages. Indeed, throughout the Pleistocene (between 2.5 million to 11,000 years ago) cold snaps resulted in low sea levels, which led to the formation of land bridges between the two continents. When the climate warmed again, these land bridges disappeared under the rising sea levels. This cycle of exposure and inundation of central Beringia occurred at least nine times (and perhaps up to twenty times or more). Not only did this facilitate the spread of humans across the globe, it also affected the numerous bird species that can be found on both sides of the Bering Strait.

These climatic cycles have probably shaped the genetic make-up of several Beringian bird species. During periods of high sea levels, bird populations were geographically isolated and diverged genetically. When sea levels dropped and land bridges formed, some of these populations might have come into secondary contact and exchanged some genetic material. This raises the question how much gene flow (if any) occurred during these periods of contact. A recent study in the journal Molecular Ecology took a closer look at eight population pairs to answer this question.

A view of Beringia throughout time. During glacial maxima in the Pleistocene, a land bridge existed between the continents. This land bridge disappeared during warmer interglacials. From: Laughlin et al. (2020) Molecular Ecology.

Eight Pairs

Jessica McLaughlin and her colleagues focused on eight bird lineages that cover the taxonomic range from populations over subspecies to distinct species. They used ultraconserved elements (UCEs) to determine the level of genetic divergence and the amount of gene flow between the following pairs:

• Long-tailed duck (Clangula hyemalis – populations)
• Bluethroat (Luscinia svecica – populations)
• Green-winged teal (Anas crecca crecca and A. c. carolinensis – subspecies)
• Whimbrel (Numenius phaeopus variegatus and N. p. hudsonicus – subspecies)
• Pine grosbeak (Pinicola enucleator kamschatkensis and P. e. flammula – subspecies)
• Eurasian and American wigeon (Mareca penelope and M. americana – species)
• Grey-tailed and wandering tattler (Tringa brevipes and T. incana – species)
• Eurasian and black-billed magpie (Pica pica and P. hudsonia – species)

The researchers tested several demographic models to reconstruct the evolutionary history of these species. In each case, gene flow was an integral part of the divergence process. Three pairs (whimbrel, pine grosbeak and magpies) followed a scenario of divergence-with-gene flow, while the evolution of two other pairs (long-tailed duck and wigeons) was best captured by gene flow at secondary contact. For the remaining three pairs (bluethroat, green-winged teal and tattlers), the analyses could not discriminate between divergence-with-gene-flow or secondary contact.

An overview of the different models that were tested. All species pairs followed a scenario with gene flow, either divergence-with-gene-flow (c and d) or gene flow during secondary contact (e and f).

Divergence Continuum

Given that these eight pairs span the taxonomic range from populations to species, you might expect to see this reflected as a continuum of genetic divergence and gene flow. This was, however, not the case. First, the genetic divergence (measured as Fst) did not follow the taxonomic classification. Some distinct species – such as Eurasian and American wigeon – were genetically quite similar (Fst = 0.04), while some subspecies – such as whimbrel (Fst = 0.27) or pine grosbeak (Fst = 0.44) – were more genetically distinct. Taxonomy is thus not a good predictor of genetic divergence.

Second, there is no clear continuum when plotting the relationship between genetic divergence and gene flow. Instead, two distinct groups are visible (see figure below). This result follows recent theoretical work that considers speciation as a two-state system with most populations pairs clustering near the two ends of the continuum (either showing genetic small differences or full reproductive isolation). Diverging populations are moving towards the right end of this continuum, but can be pulled back to the left end when gene flow occurs. Once a certain threshold of reproductive isolation has been achieved, populations will remain on the right end of the spectrum. The Beringian birds nicely represent both sides of this continuum.

Out of curiosity, I returned to my recent paper on the evolution of taiga and tundra bean goose (which I covered in this blog post). Using whole genome re-sequencing data, we found low genetic divergence (Fst = 0.033) and high levels of gene flow (M = 13). These numbers clearly put the bean geese on the left side of the spectrum. How general these patterns are remains to be determined, but Beringia seems like the perfect place to start.

The relationship between genetic divergence (Fst) and gene flow (M) reveals two distinct groups that correspond to predictions from theoretical work. From: McLaughlin et al. (2020) Molecular Ecology.

References

McLaughlin, J. F., Faircloth, B. C., Glenn, T. C., & Winker, K. (2020). Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds. Molecular Ecology, 29(18), 3526-3542.

Featured image: Whimbrel (Numenius phaeopus) © Andreas Trepte | Avi-Fauna

How did the Ground Tit get its long beak?

Genomic analyses lead to a list of candidate genes, including one with a major effect.

The Ground Tit (Pseudopodoces humilis) is a peculiar species. Based on its morphology – specifically its long, curved beak –  ornithologists thought this small songbird belonged to the family Corvidae (crows, ravens, jays and their relatives). Hence, they referred to it as Hume’s Ground Jay or Tibetan Ground jay. Molecular analyses, however, showed that the Ground Tit is the largest member of a completely different bird family: the Paridae (tits, chickadees, and titmice). A good reminder that morphology is not always a reliable guide in taxonomy. Correctly classifying this species raised an intriguing question: Where did this long, curved beak come from? The shape of the beak seems to be an adaptation to foraging on the open grasslands of the Qinghai-Tibet Plateau. As its name suggests, the Ground Tit collects its food on the ground, eating a wide range of arthropods. Although it also searches rock crevices and holes for a tasty grub. A recent study in the journal Molecular Biology and Evolution tried to unravel the genetic underpinnings of this long beak.

 

Beak Morphology

In a previous blog post and a YouTube-video, I discussed the genetic basis of beak morphology. Analyses of 72 bird genomes indicated that coding and non-coding regions work together to create the spectacular diversity of avian beaks. And although there are some common underlying developmental pathways (such as Wnt signalling pathway and the ESC pluripotency pathways), it seems that different protein-coding genes are under selection in different species. For example, in Darwin’s Finches several genes are associated with beak morphology (e.g., BMP4, CALM1, ALX1 and HGMA), while a different gene (COL4A5) determines the beak morphology of Great Tits (Parus major). So, what about its relative, the Ground Tit?

To answer this question, Yalin Cheng and his colleagues compared the genome of the Ground Tit with 13 short-beaked parid species. The researchers applied two methods to identify genomic regions that differed between these species. First, they calculated Z-transformed FST-values for different genomic regions. FST is a measure for genetic differentiation and can be standardized with a Z-transformation, which allows for easier comparison between species. Next, they compared genetic outliers with beak lengths using a partial Mantel test. These analyses resulted in 25 genomic regions, containing 23 candidate genes.

Genome-wide FST analysis between long-beaked Ground Tit and short-beaked parids (upper panel) and partial Mantel tests (lower panel) pointed to several candidate genes. The ones identified by both analyses are indicated in red. From: Cheng et al. (2020) Molecular Biology and Evolution.

 

Natural Selection

Among these 23 candidate genes were two genes (FZD3 and ROR1) involved in the Wnt signalling pathway, highlighting the importance of common developmental pathways in the evolution of beak morphology. To narrow down the list of candidates, the researchers performed several tests to detect signatures of selection (such as Tajiima’s D and Fu & Li’s D). These tests showed the strongest positive selection in the gene COL27A1. Interestingly, this gene is homologous to COL4A5, which is associated with the elongated beak of Great Tits as a response to supplementary feeding at bird feeders. A closer look at the genetic code of COL27A1 indicated several mutations under positive selection, including two in a particular domain of the protein that probably changed its biological function. This finding suggests that COL27A1 has a major effect on the extreme beak evolution in the Ground Tit.

Two mutations in the COL27A1 gene of the Ground Tit (Q and L on the top row) probably changed the function of the protein, resulting in the long beak of this species. From: Cheng et al. (2020) Molecular Biology and Evolution.

 

References

Cheng, Y., Miller, M. J., Zhang, D., Song, G., Jia, C., Qu, Y., & Lei, F. (2020). Comparative genomics reveals evolution of a beak morphology locus in a high-altitude songbird. Molecular biology and evolution, 37(10), 2983-2988.

Featured image: Ground Tit (Pseudopodoces humilis) © Dibyendu Ash | Wikimedia Commons

The speciation cycle of Taiga and Tundra Bean Goose

Are these bean geese merging into one species or not?

“I’ve been following your progress into the world of bird speciation and I wondered whether you’d be interested in a proposal.” This was the first sentence of an e-mail from Joe Tobias that I received in December 2019. He had been invited to write a review on bird diversification for the journal Annual Reviews in Ecology, Evolution, and Systematics and was looking for co-authors to write some sections. The only catch: the deadline was approaching fast (19th of January 2020). I did not have to think long about my decision, this was a great opportunity to work with one of the leading scientists in avian research and publish in one of my favorite journals. Moreover, I enjoy writing and I am always up for a challenge. A few days later, Alex Pigot joined the writing team and together we produced an extensive review that recently appeared online: “Avian Diversity: Speciation, Macroevolution, and Ecological Function“.

 

Road Trip along the Speciation Cycle

The resulting review paper centered around the concept of the speciation cycle (see figure below) which involves a series of evolutionary and ecological events. First, populations become geographically isolated and diverge in allopatry. When these populations establish secondary contact, several scenarios are possible. They might be reproductively isolated and transition into sympatry (and the cycle can start again). Or they might still be able to hybridize and establish a hybrid zone. The dynamics in these hybrid zones consequently determine the next phase in the speciation cycle. If hybrids are unfit – for instance, sterile or unable to find a mate – selection against hybrids can lead to character displacement, leading to further differentiation between the hybridizing species that eventually transition to sympatry. Alternatively, hybridization levels are so high that the populations collapse into one species. Regardless of the outcome (sympatry or collapse), the cycle can start again.

The different phases of the speciation cycles. The colored circles surrounding the diagram indicate different fields of research that are relevant to specific phases. From: Tobias et al. (2020) Annual Review in Ecology, Evolution, and Systematics.

 

Crossroads

The review paper elaborates on numerous interesting aspects of the speciation cycle. In this blog post, however, I want to focus on one particular point in this cycle: the crossroads at the hybrid zone phase. Will the populations transition into sympatry or will they merge into one species? One of my recent papers, published in the journal Heredity, provides a nice case study of this situation. During my postdoc at Uppsala University (Sweden), I studied the evolutionary history of the taiga bean goose (Anser fabalis fabalis) and the tundra bean goose (Anser fabalis serrirostris). Using whole genome resequencing data, I reconstructed their evolution history and tried to understand the genetic make-up of these birds.

It turned out that these geese diverged about 2.5 million years ago in allopatry and came into secondary contact ca. 60,000 years ago. Their genomes are largely undifferentiated but a few genomic regions – so-called ‘islands of differentiation’ – stand out. These islands might contain genes that contribute to reproductive isolation. For example, we found the gene KCNU1 which is involved in spermatogenesis. However, other evolutionary forces, such as background selection, can also give rise to these islands of differentiation. These results raise an important question: Are taiga and tundra bean goose now merging into one species?

A strolling taiga bean goose © Marton Berntsen | Wikimedia Commons

 

Merging or Diverging?

Which path of the speciation cycle the bean geese will follow, is difficult to predict. I suspect that these two populations have been stuck in a cycle of merging and diverging for thousands of years. With the genomic analyses, we managed to capture the latest merging event about 60,000 years ago. More powerful techniques might be able to find evidence for older hybridization events. In the future, taiga and tundra bean goose might start diverging again, possibly driven by the differences in the genetic islands of differentiation that we uncovered. However, if levels of hybridization increase, they might collapse into one species. Clearly, they are at an important crossroads in their evolution and future studies will reveal which turn they eventually took.

The current situation complicates the taxonomy of the bean geese. Should they be considered separate species or are they better classified as subspecies? Personally, I find this discussion nonsensical and uninteresting. Taiga and tundra bean goose are obviously in the grey zone of the speciation continuum where subjective taste determines their taxonomic status. Although I was a bit reluctant to enter this discussion, my co-authors and the reviewers advised me to discuss the taxonomy of the bean geese in the paper. So, based on low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argued that taiga and tundra bean goose should be treated as subspecies.

A tundra bean goose flying over Sweden. © Stefan Berndtsson | Wikimedia Commons

 

Trivial Taxonomy

This conclusion struck a chord with some birdwatchers, who reacted furiously to the taxonomic recommendations (even though they were only a minor part of the study) on Twitter. One random birder – who would not recognize a DNA-sequence if it hit him in the face – even had the audacity to question how the paper made it through peer review. Just because you disagree with a certain conclusion, doesn’t mean that you should trash the entire study. To use a common saying: Don’t throw the baby out with the bathwater! Instead of reacting in the same manner as the birdwatchers, I did not lower myself to their level and politely explained the reasoning behind my conclusions (which you can also find in the paper).

Unfortunately, the unnuanced and emotional responses of these birdwatchers reflect the current level of discourse in our society, especially on social media. When someone doesn’t agree with the statement of a particular person, they immediately vilify everything about that person. I hope this style of discussion does not find its way into science and we can continue to carefully consider each others arguments, culminating in a strong consensus or at least politely agree to disagree.

But to end on a positive note: there was also a nice discussion on the website Dutch Birding about the taxonomy of the Bean Geese. In contrast to the blunt messages on Twitter, several birders provided constructive feedback. It is possible!

An online posting guide that the birdwatchers should have followed…

 

References

Ottenburghs, J., Honka, J., Muskens, G. & Ellegren, H. (2020) Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation. Heredity. 125: 73–84.

Tobias, J.A., Ottenburghs, J. & Pigot, A. (2020) Avian Diversity: Speciation, Macroevolution, and Ecological Function. Annual Review of Ecology, Evolution and Systematics. Early View.

Are we missing something? Exploring the diversity of white-eye species on the African mainland

Most white-eye species have been found on islands, but what about the diversity on the mainland?

When I say white-eyes, you say islands (if you are an ornithologist). About 90 percent of described white-eye species – the bird family Zosteropidae – occurs on islands. This bias is also apparent on the Avian Hybrids blog: all the papers about white-eyes that I covered took place on islands, such as the interactions between Solomons white-eye (Zosterops kulambangrae) and Kolombangara white-eye (Z. murphyi) on Kolombangara Island (see here) and the evolution of the Reunion grey white-eye (Z. borbonicus) on the small island of Reunion (see here). Could this focus on islands distort our perspective on these small passerines? What about the species diversity on the mainland? A recent study in the journal Molecular Phylogenetics and Evolution explored the diversity of white-eye species on the African mainland.

Cape white-eye (Zosterops virens) © Alandmanson | Wikimedia Commons

 

A Single Colonization Event

Frederico Martins and his colleagues collected genetic material from the 14 white-eye species and 18 subspecies that are currently recognized on the African mainland. Comparing these specimens with species from Asia revealed that the African mainland was colonized about 1.3 million years ago. After this single colonization event, the white-eyes spread to different African oceanic islands (for example, in the Gulf of Guinea) and several ecological sky-islands in the mountains. There, they diversified into a range of new species and subspecies. This begs the question: how many species are there on the African mainland?

The distribution of white-eyes on the African continent. The colors indicate the main species groups. From: Martins et al. (2020) Molecular Phylogenetics and Evolution

 

Species Boundaries

A species delimitation analysis based on mitochondrial DNA indicated that several taxa should be elevated to species level, resulting in 27 African white-eye species (remember, we started with 14). However, the researchers realize that this analysis relies on just one molecular marker. Clearly, there is more to a species than mitochondrial DNA (see this blog post on species concepts), indicating that more detailed studies are needed to describe all the white-eye species on the African continent. Nonetheless, this study shows that we are probably underestimating the diversity of white-eye species on the mainland.

 

References

Martins, F. C., Cox, S. C., Irestedt, M., Prŷs-Jones, R. P., & Day, J. J. (2020). A comprehensive molecular phylogeny of Afrotropical white-eyes (Aves: Zosteropidae) highlights prior underestimation of mainland diversity and complex colonisation history. Molecular Phylogenetics and Evolution, 149, 106843.

Blackcaps help to unravel the genetic basis of bird migration

An extensive study on Eurasian blackcaps indicates that there are multiple genetic ways for birds to become migratory.

Bird migration has a genetic basis. Ornithologists reached this conclusion by studying European blackcaps (Sylvia atricapilla) with some clever experiments. Blackcaps orient their migration either southwest or southeast, depending on their migration routes. Hybrids between birds that use different migratory strategies direct their migration intermediate, namely south. This simple set-up suggests a genetic basis for bird migration. But which genes underlie this complex trait that integrates morphology, physiology and behavior? Several researchers have searched the genomes of various bird species for these “migration genes”. Different studies found different genomic regions related to migration (among others in thrushes, willow warblers and Vermivora warblers). The discrepancies between these species indicates that there are multiple genetic ways to a migratory lifestyle. A recent study in the journal eLife returned to the bird species that started it all – the Eurasian blackcap – and continued the search for migration genes.

A Eurasian blackcap in Germany © Kathy Büscher | Wikimedia Commons

 

Whole Genomes

Kira Delmore and her colleagues assembled the whole genome for this iconic species. This genome provided the backbone for genomic sequences that were generated for 110 individual birds. This huge dataset covered the entire spectrum of migratory behavior, from exclusively migratory populations in the north to short distance and partially migratory populations in the Mediterranean, and including non-migratory, or resident, populations from the European continent (Iberian Peninsula) and the Atlantic islands.

Comparing the genomes of all the populations revealed that migratory and resident populations went their separate ways about 30,000 years ago. This divergence led to some genetic differentiation between the distinct migration strategies. The perfect set-up to find migration genes. Indeed, the researchers did not hide their enthusiasm in the paper: “Evidence for limited population differentiation combined with dramatic differences in the migratory behaviour of blackcaps is ideal for identifying genomic regions that are associated with this focal trait.”

The genomic analyses revealed significant differences between the resident and the migratory populations. From: Delmore et al. (2020) eLife

 

Candidate Genes

The researchers ran several analyses to pinpoint putative migration genes under selection. The search resulted in a short list of candidate genes, including SDC1. This gene codes for a transmembrane protein in the Wnt-pathway which is involved embryonic development. Perhaps a change in this pathway affects morphological traits important in migration, such as the shape of the wings? At the moment, we can only speculate about the possible roles of candidate genes. More research is obviously needed here.

Interestingly, none of the genes under selection in blackcaps overlapped with genomic regions in other migratory species, such as a region on chromosome 4 in Swainson’s thrushes (Catharus ustulatus) and regions on chromosomes 1 and 5 in willow warblers (Phylloscopus trochilus). As I mentioned in the beginning, there seem to be multiple genetic ways to a migratory lifestyle.

A scan of the genome revealed several genes under selection in migratory populations, including SDC1. From: Delmore et al. (2020) eLife

 

Regulating Residents

Apart from scanning the genomes for migration genes, the researchers also investigated the transition from migratory to resident. These analyses uncovered strong selection on a few genomic regions. A closer look at these regions showed that the genetic variants under selection were located in non-coding sections of the DNA. This suggests that changes in gene regulation underlie the transition to a resident lifestyle. Whether this finding can be extrapolated to other species remains to be determined, but it might indicate that a shift in migratory behavior can occur relatively quickly. In fact, a recent study on tyrannid flycatchers showed that a migratory strategy was lost multiple times during the evolution of this bird family. Could it all be regulatory changes?

 

References

Delmore, K., Illera, J. C., Pérez-Tris, J., Segelbacher, G., Ramos, J. S. L., Durieux, G., Ishigohoka, J. & Liedvogel, M. (2020). The evolutionary history and genomics of European blackcap migration. Elife, 9, e54462.

How many members of the Lesser Whitethroat complex breed in Iran?

And is the taxon zagrossiensis valid?

Just because you see a bird in a certain country doesn’t mean that it breeds there. It could be passing through. Or perhaps it is a lost migrant, blown off course by strong winds. In Iran, you can observe several species of the lesser whitethroat complex (Sylvia curruca). Ornithologists are quite certain that the nominal species (S. curruca) and Hume’s whitethroat (S. althaea) breed in this Middle-Eastern country. But the jury is still out on some other members of this widespread species complex. For example, some researchers argue that the desert whitethroat (S. minula) breeds in northeastern Iran, while others think it just visits the area in winter. A recent study in the Journal of Ornithology sampled more than 30 individuals across Iran to solve this mystery.

A lesser white-throat © Imran Shah | Wikimedia Commons

 

Mitochondrial DNA

The latest molecular studies divide the lesser whitethroat complex into six geographical groups (based on mitochondrial DNA): althaea, blythi, halimodendri, margelanica, curruca and minula. Raziyeh Abdilzadeh and his colleagues compared the genetic make-up of the Iranian birds with these six groups. This analysis revealed that all samples could assigned to three groups: curruca, althaea and halimodendri. The samples of halimodendri – which is considered a subspecies of Hume’s whitethroat – were collected in February and represent wintering or migrating birds. Moreover, none of the samples were members of the minula group. There is thus no evidence that the desert whitethroat breeds in Iran.

The genetic analyses pointed to three groups in Iran, of which halimodrendi is migratory. From: Abdilzadeh et al. (2020) Journal of Ornithology

 

Another taxon?

This study also sheds some light on another mystery: the taxon zagrossiensis. In 1911, Sarudny considered the birds in the Zagros mountains to be a distinct taxon, classified as S. althaea zagrossiensis. Birds from this area are slightly darker compared to the nominal lesser white-throat. The current analyses do not support this classification. Indeed, the researchers note that “Our data suggest that birds inhabiting the mountains of western Iran and the central Zagros mountains, at least as far east as Shiraz, sometimes recognized as caucasica and zagrossiensis, respectively, belong to the curruca clade sensu Olsson et al. (2013), based on mitochondrial haplotypes.” The origin of the darker plumage of these birds remains to be investigated. Did they acquire it through hybridization with another member of this species complex?

 

References

Abdilzadeh, R., Aliabadian, M., & Olsson, U. (2020). Molecular assessment of the distribution and taxonomy of the Lesser Whitethroat Sylvia curruca complex in Iran, with particular emphasis on the identity of the contentious taxon, zagrossiensis Sarudny, 1911. Journal of Ornithology, 161:665–676.

What drives avian speciation in the Amazonian floodplains?

Genomic analyses suggest an important role for past climate changes.

The Amazonian floodplains are among the most diverse places on our planet. This collection of habitats covers over 300,000 square kilometres and houses about 10% of endemic tree species and 15% non-aquatic bird species. But where did all this diversity come from? What factors drive the origin of new species on these flooded plains? Numerous studies have attempted to answer these questions. Some researchers pointed to the role of rivers (as you can read in this blog post), while others suggested that climatic events are more important (such as in this blog post). Clearly, the jury is still out on the drivers of avian speciation on the Amazonian floodplains. A recent study in the journal Science Advances revisited this age-old conundrum.

The leaden antwren (Myrmotherula assimilis) © Hector Bottai | Wikimedia Commons

Three Species Complexes

The researchers focused on three species complexes:

• Ash-breasted antbird (Myrmoborus lugubris)
• Blackish-grey antshrike (Thamnophilus nigrocinereus) and Castelnau’s antshrike (T. cryptoleucus)
• Leaden antwren (Myrmotherula assimilis)

They obtained genetic material from all known subspecies in these species complexes and meticulously mapped the genetic patterns across the Amazonian floodplains. These analyses revealed that the three species showed similar genetic population structure across different sections of the floodplains. For example, all species exhibited higher genetic diversity in central portion of the Amazon River, suggesting the existence of hybrid zones. This finding already indicates that these populations have been geographically isolated in the past. Let’s have a closer look at the results.

The three species complexes showed similar genetic population structure. Top: M. lugubris. Middle: T. nigrocinereus/T. cryptoleucus. Bottom: M. assimilis. From: Thom et al. (2020) Science Advances

Patterns and Processes

The uncovered genetic population structure could be explained by three non-mutually exclusive effects: (1) isolation-by-distance in which populations become more genetically divergent the farther they are apart, (2) ecological gradients where different populations adapt to different environmental conditions, and (3) long-term geographic changes to the Amazon River basin.

Although the first two processes – isolation-by-distance and ecological gradients – explain some part of the genetic patterns, the main driver appears to be previous geographic changes to the Amazon Basin. Indeed, the diversification of the three species complexes coincides with the Mid- and Late Pleistocene when major reorganization of Amazonian tributaries occurred and when the current transcontinental Amazon River arose. Specifically, climatic changes affected the sediment dynamics and floodplain structure, isolating bird species adapted to life on the river edges. During the Holocene (less than 11,000 years ago), the floodplains expanded, resulting in the establishment of secondary contact zones in the central part of the distribution.

A female ash-breasted antbird © Hector Bottai | Wikimedia Commons

 

Refugia

This scenario is reminiscent of the “forest refugia hypothesis” that explains the origin of numerous forest species. But instead of forest habitat contracting and expanding, it is now “the contraction or interruption of river edge forest resulting in isolated blocks restricted to the main Amazonian rivers.” This parallel between forest and river habitats suggests that a South American synthesis on the role of climate changes in avian speciation is getting closer.

 

References

Thom, G., Xue, A. T., Sawakuchi, A. O., Ribas, C. C., Hickerson, M. J., Aleixo, A., & Miyaki, C. (2020). Quaternary climate changes as speciation drivers in the Amazon floodplains. Science Advances, 6(11), eaax4718.

Selection on metabolism and memory in a moving Chickadee hybrid zone

Genetic study confirms experimental work on black-capped and Carolina chickadee.

Hybrid zones are rarely static. In a recent review, Ben Wielstra stated that “the commonality of contemporary hybrid zone movement—with shifts in hybrid zones tracked over years to decennia—cannot be disputed, given the many examples available.” An excellent example of a moving hybrid zone can be found in North America where populations of black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee interbreed. Genetic studies indicated that this hybrid zone is moving northward in response to climate change. As the minimum daily winter temperature increased, Carolina chickadees can expand their range to the north where they meet the closely related black-capped chickadees. This hybrid zone is quite narrow (less than 60 kilometres), which suggests strong selection against hybrids.

But what kind of selection is acting on the hybrids? A quick look at several experimental studies provides some possible answers. Physiological experiments indicated that hybrids have higher basal metabolic rates, which may be due to metabolic inefficiency. And other experiments revealed that hybrids also exhibit deficiencies in learning and memory (you can read the entire story in this blog post). If you were to scan the genomes of these species for genes under selection, you can expect to find genes related to metabolism and brain function to pop up.

A Carolina chickadee © Dan Pancamo | Wikimedia Commons

 

Metabolism and Memory

We now have some straightforward hypotheses to test. This is a refreshing approach to speciation genomics. A lot of studies just data-mine a genomic data set for genetic outliers and build a story around these. Although this approach can be fruitful, you run the risk of telling just-so stories. In the chickadee case, however, there have clear predictions: the genetic outliers should be involved in metabolism or brain function. Dominique Wagner and his colleagues analyzed genomic data for 154 individual birds to put these predictions to the test. They published their findings in the journal Evolution.

And lo and behold: the researchers found what they were looking for! They write that “our results suggest that genes underlying metabolic and neural signaling pathways may experience consistent selection across the chickadee hybrid zone.” The analyses pointed to a significant over-representation of genes involved in “regulation of metabolic process” and “catabolic process”. This suggests that hybrids might encounter deficiencies in metabolic processes due to genetic incompatibilities. In addition, several genetic outliers play a role in learning and memory function. For example, one set of genes is classified as “glutamatergic synaptic transmission”. Interestingly, glutamate is known to affect learning capacity in rats and mice. This is clearly a good candidate for further research to elucidate the exact mechanism behind this hybrid breakdown.

The genomic analyses in this study confirmed the findings from earlier genetic work, showing that the hybrid zone move northwards. From: Wagner et al. (2020) Evolution

 

Selection

The findings of this study make intuitive sense if you know the biology of these small songbirds. Chickadees are able to overwinter in cold environments, partly by caching food for winter. To survive the cold winters, they have to efficiently regulate their metabolism and remember where they hid their food. Hybrids experience metabolic issues and have bad memory, which probably compromises their chances of survival.

Interestingly, the selective pressures on hybrids seem to vary over time. Although the main biological processes were consistently under selection, the genetic outliers varied between years. This suggests that different metabolic and cognitive pathways are selected depending on the environmental conditions of the season. Perhaps a year with heavy snowfall favors birds that can locate their food stash despite a homogeneous white landscape, while an extremely cold year puts more strain on a particular metabolic pathway. As always more research is needed to figure this out. The ornithologists will keep working and the hybrid zone will keep moving.

 

References

Wagner, D. N., Curry, R. L., Chen, N., Lovette, I. J., & Taylor, S. A. (2020). Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent in a moving avian hybrid zone. Evolution.

 

This paper has been added to the Paridae page.