Taxonomy in flux: The story of three flatbills and a flammulated flycatcher

Genetic study clarified the phylogenetic relationships between the genera Ramphotrigon and Deltarhynchus.

Here is a fun ornithological quiz question: What is the largest family of birds? The answer is … the tyrant flycatchers (Tyrannidae). This family of songbirds contains over 400 different species. Within this species-rich assembly, you can find the genus Ramphotrigon which holds just three species: the large-headed flatbill (R. megacephalum), the dusky-tailed flatbill (R. fuscicauda) and the rufous-tailed flatbill (R. ruficauda). The exact phylogenetic position of this genus within the Tyrannidae family is still a matter of debate.

The closest living relative of the flatbills is probably the flammulated flycatcher (Deltarhynchus flammulatus), at least according to morphological and behavioral data. A recent study in the Journal of Avian Biology provided a genetic perspective on this evolutionary issue.

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Geographic distributions of the three Ramphotrigon species and their relative Deltarhynchus flammulatus represented by different colors. From: Lavinia et al. (2020) Journal of Avian Biology

 

Taxonomic Shifts

The genetic analyses – based on three mitochondrial and one nuclear marker – uncovered some surprising relationships. The flammulated flycatcher falls right in the middle of the genus Ramphotrigon, clustering with dusky-tailed flatbill and rufous-tailed flatbill. In technical terms: the genus Ramphotrigon is paraphyletic (you can check this blog post for an overview of these phyletic terms).

The third Ramphotrigon species – the large-headed flatbill – is not only genetically quite distinct from the other species. Morphological measurements indicated that it is significantly smaller than the other three species: “it has a lower body weight and a beak that is narrower and shorter in length and height, as well as shorter wings and tail.”

These results call for a taxonomic revision of this small section with the Tyrannidae. There are two options: (1) moving flammulated flycatcher to the genus Ramphotrigon or (2) placing the large-headed flatbill to its own genus.

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The phylogenetic analyses revealed that the genus Ramphotrigon is not monophyletic: the flammulated flycatcher (D. flammulatus) clusters with the dusky-tailed flatbill (R. fuscicauda) and the rufous-tailed flatbill (R. ruficauda). From: Lavinia et al. (2020) Journal of Avian Biology

 

Biogeographic Patterns

The findings in this study also pointed to an interesting biogeographic history. The three Ramphotrigon species are restricted to South America, while the flammulated flycatcher is endemic to the Pacific Coast of Mexico. What happened?

Our story begins about 11 million years ago when the large-headed flatbill split from the common ancestor of the other three species. This event could be associated with the uplift of the Andean mountains and the development of large lakes in western Amazonia. About 5 million years later, the ancestors of the flammulated flycatcher went their separate way. A population of birds might have become isolated in the northern Andes and subsequently migrated along the Isthmus of Panama to Mexico. The populations on the other side of the Andes would eventually give rise to the dusky-tailed flatbill and the rufous-tailed flatbill. Many details of this biogeographic scenario remain to be clarified, but the main story is already there.

 

References

Lavinia, P. D., Escalante, P., Tubaro, P. L., & Lijtmaer, D. A. (2020). Molecular phylogenetics and phenotypic reassessment of the Ramphotrigon flycatchers: deep paraphyly in the context of an intriguing biogeographic scenario. Journal of Avian Biology, 51(4).

Saving the Snowy Plover: How many conservation units should we protect?

Genomic data reveals more fine-scale population structure in this plover species.

When I started my PhD in 2012, I was an enthusiastic birder (I still am, by the way). I traveled to several countries, trying to tick off as many species as possible. But as I developed a scientific mindset, I transitioned from collecting species to thinking about how species originate and evolve (in other words, the speciation process). The clash between my now process-based perspective and the stamp-collecting attitude of some “species-hunters” became apparent a few weeks ago when I published a paper on taiga bean goose (Anser fabalis) and tundra bean goose (Anser serrirostris). In this study, I argued – based on extensive genomic analyses – that these geese should be considered subspecies. This conclusion infuriated some birdwatchers (they might lose a species on their life list…) that reacted based on emotions instead of looking at the facts. These taxonomic discussions can be interesting and entertaining, but honestly I don’t give a hoot (or should I say a honk) whether you call these bean geese species or subspecies. What interests me most is their evolutionary history.

A similar issue appears in conservation. Should we allocate more resources to conserve species than to protect subspecies? In this context, it is more productive to think in terms of conservation units (i.e. populations to protect regardless of whether they are considered distinct species or subspecies). A recent study in the journal Conservation Genetics nicely illustrates this approach with the Snowy Plover (Charadrius nivosus).

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Snowy Plover © Albert Herring | Wikimedia Commons

 

Three subspecies

From a taxonomic point of view, there are three subspecies of Snowy Plover: nivosus, tenuirostris and occidentalis. Does this mean there are three conservation units to protect? Not necessarily, there might be more fine-scale populations structure that is not captured in this subspecies classification. Josephine D’Urban Jackson and her colleagues used several genetic markers – microsatellites, mtDNA and single nucleotide polymorphisms (SNPs) – to assess the genetic population structure of this small plover.

The analyses revealed some interesting patterns and highlighted the added value of genomic data. The SNP dataset and the microsatellites (with prior locations) pointed to three distinct clusters that correspond to the subspecies classification above. The detection power of microsatellites only reached to these three clusters, whereas the SNP data could take it one step further. These genomic loci allowed the researchers to discriminate between eastern and western populations of the nivosus subspecies.

This result confirms a statement in a book chapter that I recently wrote with several colleagues: “In general, genomic data has increased the potential for fine-scale resolution of population structure and determination of population boundaries and population membership.”

admixture

The cluster analyses of Snow Plover populations illustrate the power of genomic data. Both microsatellites and SNP data can discriminate between three clusters (top row), but the genomic data are also able to find even more fine-scale population structure (bottom row). From: D’Urban Jackson et al. (2020) Conservation Genetics

 

Bottlenecks

The delineation of separate lineages allowed the researchers to retrace the demographic history of these four conservation units. They reported “strong population bottlenecks in all genetic lineages/demes that have occurred within the last 1000 years. As a result of these bottlenecks, the effective population sizes of the genetic lineages/demes have been reduced by at least 98%.” These findings underline the importance of conservation efforts to preserve these four lineages.

I hope you can forgive my rant at the beginning of this blog post (sometimes you just need to let it all out). But I also hope that I have convinced about the importance of conservation units. Protecting biodiversity is not about labeling populations as species or subspecies, but about understanding the biology and evolution of these populations and delineating meaningful conservation units. And then implementing appropriate actions.

And if you are curious: I consider taiga and tundra bean goose separate conservation units. But their taxonomic rank is less interesting compared to their evolutionary history (but this is a story for another time).

plover_stretch

A stretching Snowy Plover © ADJ82 | Wikimedia Commons

 

References

Jackson, J. D. U. et al. (2020). Population differentiation and historical demography of the threatened snowy plover Charadrius nivosus (Cassin, 1858). Conservation Genetics, 1-18.

Can you deduce the activity patterns of owl species from their eye color?

Do day-active species have bright eyes, while night-active ones have dark eyes?

This week, I was watching the Belgian television show Iedereen Beroemd (which translates to Everyone Famous). This show is a collection of small clips about everyday life in Belgium, including the adventures of biologist and movie-maker Pim Niesten. Every week, he shares great footage of local wildlife and provides some background information. This time, he focused on the little owl (Athene noctua). While showing some videos of the nestlings in a cavity and the adults gathering food, he starts explaining an interesting fact about owls. Pim states that you can deduce the hunting behavior of an owl species from its eye color:

  • Yellow eyes point to day-active species, such as little owl.
  • Orange eyes indicate that the species is active at dusk and dawn, such as long-eared owl (Asio otus).
  • Black eyes are for night-active species, such as tawny owl (Strix aluco).

Whenever I hear such bold statements in the media, I get suspicious. Can you make this claim based on only a handful of examples? To test this statement, I dove into the scientific literature and found a 2018 study in the Journal of Avian Biology.

little owl

The bright yellow eyes of a little owl in Israel © Artemy Voikhansky | Wikimedia Commons

 

Exceptions

In this paper, a team of Spanish ornithologists gathered data on eye color and activity rhythm for over 200 owl species. The analyses revealed that dark irises were more frequent among strictly nocturnal owls (41 out of 70 nocturnal species) compared to owls that are active during or at the end of the day (37 out of 131 diurnal or crepuscular species). These numbers indicate that the statement from the television show was too general. There are plenty of exceptions to the rule. To name just two: the barn owl (Tyto alba) is diurnal and crepuscular but has pitch-black eyes. And the Sokoke scops owl (Otus ireneae) has bright eyes despite being active at night.

Sokoke_Scops_Owl

The Sokoke scops owl has bright eyes but is active during the night. © Steve Garvie | Flickr

 

Ancestors

The paper also delved into the evolutionary history of owl eye color and uncovered a peculiar pattern: the ancestors of the two extant owl families (Tytonidae and Strigidae) probably had different eye colors. The ancestor of the family Strigidae was more likely bright‐eyed whereas the ancestor of Tytonidae was more likely dark‐eyed. This finding might relate to the different evolutionary paths these owls followed early on. The exact evolutionary changes remain to be unraveled.

In conclusion: there is certainly a correlation between eye color and activity rhythm in owls, but the pattern is not universal. And more importantly, don’t take everything you hear or read in the media at face value, question everything!

 

References

Passarotto, A., Parejo, D., Cruz‐Miralles, A., & Avilés, J. M. (2018). The evolution of iris colour in relation to nocturnality in owls. Journal of Avian Biology49(12).

Black hoods or bright eyes: The evolution of plumage patterns in gulls

A macroevolutionary study of the Laridae revealed some peculiar patterns.

You can easily recognize the black-headed gull (Chroicocephalus ridibundus) by its – you guessed it – black head. There are, however, several other gull species that develop a black hood during the breeding season. Think of the Andean Gull (C. serranus) or the Sabine’s gull (Xema sabini). A recent study in the Journal of Evolutionary Biology explored the evolutionary history of this trait and uncovered some surprising patterns.

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A black-headed gull (Chroicocephalus ridibundus) in Finland © Estormiz | Wikimedia Commons

 

Correlated Selection

Piotr Minias and Tomasz Janiszewski took a closer look at 52 gull species. They correlated the presence or absence of a black hood with several morphological and ecological traits. The analyses revealed that species with a black hood tend to have red or dark colored bare parts (e.g., bill and legs). This association could be the result of a shared genetic basis, so-called pleiotropic effects (where one gene has an effect on multiple traits). Alternatively, the correlation between the black hood and the dark bare parts could be due to strong correlated selection.

The researchers think that correlated selection best explains their results. However, the selection pressures on the black hood and the bare parts are slightly different. Because gulls only develop a black head during the breeding season, this trait is likely under sexual selection. The color of the bare parts, in contrast, is present year-round and might thus be more important in social interactions.

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The analyses revealed significant associations between the black hood and the bare parts. From: Minias & Janiszewski (2020) Journal of Evolutionary Biology

 

Look into my eyes

Another peculiar pattern emerged from this analysis. Gulls without a black head tend to have a yellow or white iris. Why would evolution avoid the origin of black-hooded gulls with yellow irises? One possibility concerns the different mechanisms underlying these traits. The dark hood is the outcome of melanin-based processes, whereas the yellow iris coloration depends on the production of other compounds (namely pterins and purines). A dark iris, on the other hand, is pigmented with melanin. There might thus be a shared underlying mechanism between dark irises and dark hoods.

In addition to yellow or white eyes, gulls without a black hood occurred more often at high latitudes. The most striking example is the ivory gull (Pagophila eburnea) which can be found in the high arctic and is covered in completely white plumage. The main reason for the absence of a black hood in polar regions is probably better camouflage in the snowy surroundings. Moreover, white plumage has better thermal properties: white feathers have small air spaces that may lead to better isolation and speed up the transfer of solar radiation to the skin.

ivory_gull

The completely white ivory gull © Josh M. London | Flickr

 

Ancestor

Finally, did the ancestor of present-day gulls have a black hood? The researchers attempted to answer this question by plotting the presence/absence of a black hood on the evolutionary tree of gulls. Unfortunately, this approach did no lead to a conclusive answer. The analyses suggested a 45% chance for a black-hooded ancestor and a 55% chance for an ancestral gull without a black head.

Luckily, they found a neat trick. Apart from the two basic states (black hood present or black hood absent), they considered a third option: a remnant hood in immature or winter plumage. Some gull species, such as the slender-billed gull (Chroicocephalus genei), develop the faint traces of a black hood during certain parts of the year. This approach did point to the ancestral state: a 76% chance of a black hood. In fact, this result is not that surprising, given that the sister group of gulls – the terns (family Sternidae) – typically have a black head.

Chroicocephalus_genei_first-winter_1

A first winter slender-billed gull (Chroicocephalus genei) with a faint black spot.

 

References

Minias, P., & Janiszewski, T. (2020). Evolution of a conspicuous melanin‐based ornament in gulls Laridae. Journal of Evolutionary Biology, 33(5), 682-693.

A Caribbean connection: How thrushes conquered the world

A phylogenomic study reconstructs the evolution of the genus Turdus.

The genus Turdus contains some of the most familiar birds in the world. European readers will certainly know the Blackbird (T. merula), while most readers from North America have seen an American Robin (T. migratorius). In total, there are about 86 different Turdus species worldwide that show a variety of plumage patterns and ecological peculiarities. Despite their commonness, the evolutionary relationships between these species remain controversial. As a consequence of this phylogenetic instability, ornithologists are still not sure how these thrushes managed to spread across the globe. A recent study in the journal Proceedings of the Royal Society B resorted to genomic data in order to solve this biogeographic riddle.

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A black-breasted thrush (Turdus dissimilis) in Thailand © J.J. Harrison | Wikimedia Commons

 

Enter Genomics

Previous genetic studies attempted to unravel the evolutionary history of this genus. Johan Nylander and his colleagues, for example, found one Eurasian, three American, and three African groups. They suggested that several dispersal events occurred between Africa and South America. However, the evolutionary tree in this study contained several relationships with low statistical support, making some biogeographic inferences uncertain.

What can you do when phylogenies have low statistical support? Add more data. That is exactly what Romina Batista and her colleagues did. Based on a large genomic dataset (about 2 million base pairs), they managed to reconstruct the evolutionary history of the genus Turdus with more confidence than previous studies.

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A tree of thrushes. The colors indicate different biogeographic regions and can be used to infer the evolutionary history of these birds. From: Batista et al. (2020) Proceedings of the Royal Society B

 

Arriving on the Antilles

The phylogenomic analyses suggest that the genus Turdus originated in Eurasia. The most basal species are two Western Palearctic species: the song thrush (T. philomelos) and mistle thrush (T. viscivorus). From Europe, ancestral thrush species colonized Africa and spread eastwards into Asia.

In contrast to previous studies, this phylogeny points to a single colonization event from Eurasia (and thus not Africa) into the New World. A closer look at the species in the evolutionary tree shows that the Antilles were colonized first. Indeed, two Caribbean species – the white-chinned thrush (T. aurantius) and the forest thrush (T. lherminieri) – are located at the base of the New World group.

From the Caribbean Islands, these thrushes consequently colonized Panama (perhaps over a land bridge) and South America. Interestingly, the genus Turdus is not the only bird group that reached South America via the Caribbean: New World orioles (genus Icterus) and screech-owls (genus Megascops) probably took the same route. And who could blame them. I wouldn’t mind a stop-over on a tropical island…

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A white-necked thrush  (Turdus albicollis) in Brazil © Dario Sanches | Wikimedia Commons

 

References

Batista, R., Olsson, U., Andermann, T., Aleixo, A., Ribas, C. C., & Antonelli, A. (2020). Phylogenomics and biogeography of the world’s thrushes (Aves, Turdus): new evidence for a more parsimonious evolutionary history. Proceedings of the Royal Society B287(1919), 20192400.

African adventures: Human-mediated hybridization between Common and Black-faced Impala

Translocation of subspecies resulted in the production of hybrids.

At the moment, I am teaching the course Animal Ecology with several colleagues. One part of this course is a modelling practical where students have to recreate a savanna model from a study in the journal Ecology. Once they get this model running, the students have to change it. They can introduce predators, simulate climate change or study the effects of diseases. Some students decided to focus on particular herbivore species, such as the impala (Aepyceros melampus). Recently, I came across a paper on hybridization between two impala subspecies in the journal Conservation Genetics. Let’s see what they found.

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Red-billed Buffalo Starling on the head of an impala female in Chobe National Park, Botswana © Charles J. Sharpe | Wikimedia Commons

 

Genetic studies

Taxonomists recognize two subspecies of impala: the black-faced impala (A. m. petersi) and the common impala (A. m. melampus). These subspecies have been geographically separated until humans started translocating them across southern Africa. This anthropogenically induced contact might lead to hybridization. However, previous studies – based on mitochondrial DNA and microsatellites – found no evidence for hybrid impalas. In a more recent paper, Susan Miller and her colleagues sampled in two Namibian locations: Etosha National Park and Southern Cross Private Game Reserve.

 

Hybrids

Using a set of 13 microsatellites, the researchers confirmed the genetic distinctness of the black-faced impala and the common impala. More importantly, the genetic markers could also be used to identify hybrid individuals: four in Southern Cross Private Game Reserve and two in Etosha National Park. However, the analyses were restricted to early generation hybrids. Backcrosses could not be detected with confidence. A genomic approach might uncover even more admixture between these subspecies.

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(a) Black-faced male (b) possible hybrid male and (c) common impala male. From: Miller et al. (2020) Conservation Genetics

 

Translocations

These findings highlight the potential dangers of translocating animals across the globe. Although hybridization can be beneficial (e.g., transfer of adaptive alleles), it can result in the loss of local genetic variation. The impala situation is no isolated case, numerous other African herbivores have been moved across the continent, occasionally resulting in hybridization. Notable examples include blesbok (Damaliscus pygargus phillipsi) x bontebok (D. p. pygargus) and blue wildebeest (Connochaetes taurinus) x black wildebeest (C. gnou). Human-mediated hybridization is clearly an issue in Africa. Surprisingly, my students have not implemented this in their savanna models yet…

 

References

Miller, S. M., Moeller, C. H., Harper, C. K., & Bloomer, P. (2020). Anthropogenic movement results in hybridisation in impala in southern Africa. Conservation Genetics.

Ancient DNA helps to place two extinct duck species on the Tree of Life

Mitochondrial DNA from Chendytes lawi and the Labrador Duck reveals some interesting evolutionary patterns.

The fossil record of birds is not great (to start with an understatement), but occasionally some wonderful fossils pop up. Some even contain traces of ancient DNA which can be used to pinpoint the phylogenetic position of these extinct species. On this blog, I have written about studies on ancient DNA from the Creighton’s Caracara (Caracara creightoni) and the Poūwa (an extinct Black Swan from New Zealand). Another recent paper in the journal Molecular Phylogenetics and Evolution took a closer look at two extinct waterfowl species: Chendytes lawi and the Labrador Duck (Camptorhynchus labradorius).

labrador duck

The extinct Labrador Duck © James St. John | Wikimedia Commons

 

Sea ducks or not?

The genus Chendytes was erected in 1925 to classify Holocene fossils from the California coast and nearby Channel Islands and holds two species. One species (C. lawi) is the size of a goose and shows degeneration of the wings. The second species (C. milleri) is smaller with larger wings. It might represent an intermediate form between a flying ancestor and the flightless C. lawi (similar to Tachyeres ducks, see this blog post). Based on several morphological traits, these extinct species were considered sea ducks (tribe Mergini).

In 2018, Janet Buckner and her colleagues managed to extract mitochondrial DNA from a C. lawi fossil. Comparing these DNA sequences with extant species revealed that Chendytes ducks are not sea ducks, but basal dabbling ducks (tribe Anatini). Hence, this lineage represents an independent evolution towards a diving lifestyle. The traits shared with sea ducks are thus the outcome of convergent evolution.

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The phylogenetic positions of two extinct species inferred from mtDNA. From: Buckner et al. (2018) Molecular Phylogenetics and Evolution

 

What about the Labrador Duck? In contrast to the Chendytes ducks, this species does belong to the sea ducks. Indeed, the Labrador Duck is closely related to the Steller’s Eider (Polysticta stelleri). This finding refutes the morphological work by Bradley Livezey, who considered the Labrador Duck a scoter in the genus Melanitta.

However, one should always be careful with mitochondrial phylogenies and ducks because of hybridization. Waterfowl are known for their high levels of hybridization and mtDNA can easily be transferred between species (i.e. mitochondrial capture, see for example Jacamars). The Labrador Duck might be closely related to the Steller’s Eider, but you never know whether hybridization mixed things up a bit.

 

References

Buckner, J. C., Ellingson, R., Gold, D. A., Jones, T. L., & Jacobs, D. K. (2018). Mitogenomics supports an unexpected taxonomic relationship for the extinct diving duck Chendytes lawi and definitively places the extinct Labrador Duck. Molecular phylogenetics and evolution122, 102-109.

This blog post was written to celebrate #BlackBirdersWeek. Check out the wonderful work of Janet Buckner on her website.

Cryptic Crows: Genetic study uncovers a wide hybrid zone between American and Northwestern Crow

These crow species represent distinct lineages but interbreed along the western coast of North America.

What is the difference between an American Crow (Corvus brachyrhynchos) and a Northwestern Crow (C. caurinus)? Some ornithologists argued that Northwestern Crows are clearly smaller, but that turned out to be a false impression. Perhaps they produce different sounds? That is also a tricky trait because these birds learn vocalizations from their social group. Morphology and sound are thus not sufficient to discriminate between these species. This raises the question whether they are even distinct species. A genetic approach might provide some crucial insights. A recent study in the journal Molecular Ecology explored the genomes of American and Northwestern Crows to shed some light on this ornithological mystery.

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A Northwestern Crow in Canada © Gordon Leggett | Wikimedia Commons

 

Two Lineages

David Slager and his colleagues took a closer look at the mitochondrial and nuclear genomes of these crows. The mitochondrial analyses (based on the gene ND2) revealed two distinct lineages that diverged about 443,000 years ago. Similarly, the nuclear perspective pointed to two clusters that correspond to American and Northwestern Crows. These genetic results indicate that we are dealing with two separate lineages.

However, a closer look at the nuclear data showed that 34 individuals were actually hybrids: not first-generation hybrids (so-called F1s) but backcrosses and late-generation hybrids. These hybrid individuals could be traced back to a 900 kilometre-wide hybrid zone along the west coast of North America.

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Genetic analyses uncovered a cryptic hybrid zone between American Crow and Northwestern Crow. From: Slager et al. (2020) Molecular Ecology

 

Cryptic Hybrid Zone

This study not only confirmed that there are two cryptic crow species, but also revealed the existence of a cryptic hybrid zone. Most hybrid zones have been discovered and described using morphological data. The absence of clear diagnostic traits in American and Northwestern Crows prevented ornithologists from detecting this hybrid zone earlier. This highlights the importance of genomic data in understanding speciation and hybridization. Who knows how many cryptic hybrid zones are still out there!

This finding raises a new question: what mechanisms prevent these crow species from merging into one species? The analyses did not uncover any genomic regions that were highly differentiated between the crows (so-called islands of differentiation). However, the researchers only covered a small percentage of the entire genome (they used a ddRAD approach). Whole genome analyses might be able to detect subtle differences, similar to European crows – Carrion Crow and Hooded Crow – where a large genomic region likely explains the plumage differences between these species. However, given that American and Northwestern Crow are morphologically indistinguishable other genomic regions might pop up. To be continued…

american_crow

An American Crow © Mr.TinDC | Flickr

 

References

Slager, D. L., Epperly, K. L., Ha, R. R., Rohwer, S., Wood, C., Van Hemert, C., & Klicka, J. (2020). Cryptic and extensive hybridization between ancient lineages of American crows. Molecular Ecology, 29(5): 956-969.

This paper has been added to the Corvidae page.