A Mitochondrial Mystery: Why are there two deeply divergent lineages in the Savannah Sparrow?

Genetic study searches for the most likely scenario to explain this peculiar pattern.

Does the name John Avise ring a bell? The work of this American biologist laid the foundation for phylogeography, the study of historical processes responsible for the present-day geographic distributions of populations. In the early days, phylogeographic research relied heavily on mitochondrial DNA (mtDNA), the circular genome of mitochondria (the powerhouses of the cell). The study of this molecular marker revealed many peculiar patterns, such as deeply divergent lineages within a single species. A recent study in the journal Molecular Ecology tries to explain such a pattern in the Savannah Sparrow (Passerculus sandwichensis).

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A Savannah Sparrow in Ontario, Canada © Mdf | Wikimedia Commons

 

Five Possible Scenarios

Previous work on the Savannah Sparrow uncovered two divergent mtDNA lineages (A and B) within a largely panmictic population. Lineage B clusters with a third clade (C) which contains several subspecies (beldingi, rostratus and sanctorum) from northwestern Mexico. However, the focus of this study is on lineages A and B which occur in the nominate subspecies sandwichensis. What could explain this pattern? Here are five possible explanations:

  1. Selection for both mtDNA haplotypes
  2. Sex-biased dispersal (mtDNA is only transmitted through the female line)
  3. Introgression of mtDNA is much quicker than nuclear introgression
  4. Independent sorting of mtDNA haplotypes in a large population
  5. Complete admixture of two previously isolated populations

The first two explanations can already be discarded. There was no evidence for selection based on statistical tests (specifically the McDonald-Kreitman test) in previous work. And it is unlikely that Savannah Sparrows have sex-specific differences in dispersal. That leaves three possibilities. Enter Phred Benham and Zachary Cheviron, who used genomic data to resolve this mitochondrial mystery.

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The deeply divergent mtDNA lineages (A and B) in the Savannah Sparrow. The distribution on the map already shows a lack of geographical structure. What is going on here? (from: Benham & Cheviron 2019 Molecular Ecology).

 

No Population Structure

First, the researchers looked at population structure. If the divergent mtDNA lineages are the outcome of past population division, this should be clear in the nuclear genome. This was, however, not the case. The Savannah Sparrow showed a lack of population structure despite the fact that their breeding distribution runs from Alaska to California, New Mexico, and Virginia. This finding indicates that scenario 3 (differential introgression of mtDNA and nuclear DNA) can be ruled out. Lower levels of nuclear introgression would have resulted in some population structure.

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No population structure in the Savannah Sparrow (the cluster of blue dots). Other colors represent Mexican subspecies. Picture by © Cephas | Wikimedia Commons

 

Large Population Size

To discriminate between the last two scenarios, the researchers performed some demographic modelling (using the software δaδi). They simulated numerous scenarios and compared the resulting patterns with the actual data. These analyses supported the idea that the divergent mtDNA lineages arose in a large, panmictic population.

The researchers couldn’t get enough of simulations and explored the demographic conditions under which divergent lineages can develop. This exercise revealed that really large populations – effective population size (Ne) > 350,000 – are needed. This conclusion fits with other avian examples, such as the Passenger Pigeon (Ectopistes migratorius). This extinct species is known for its enormous flocks (Ne has been estimated at 13 million) and also showed deeply divergent mtDNA lineages.

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The large effective population size of the Passenger Pigeon can explain the existence of divergent mtDNA lineages in this extinct species. Left: stuffed specimen at James St. John at the Field Museum of Natural History, Chicago, Illinois, USA © James St. John | Wikimedia Commons. Right: Passenger pigeon flock being hunted in Louisiana. The Illustrated Shooting and Dramatic News. © Smith Bennett | Wikimedia Commons

 

Pleistocene

This study suggests that the Savannah Sparrow maintained a constant population size throughout the Pleistocene ice ages. This situation is different from other bird species that show population subdivision during this period. How the Savannah Sparrow managed to resist population contraction and fragmentation remains to be investigated. But it seems likely that this generalist thrived in the continuous band of grasslands, tundra and steppe that ran across the southern edge of advancing glaciers.

 

References

Benham P.M. & Cheviron Z.A. (2019) Divergent mitochondrial lineages arose within a large, panmictic population of the Savannah sparrow (Passerculus sandwichensis). Molecular Ecology.

 

This paper has been added to the Passerellidae page.

 

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Are Chinese indigenous chicken breeds genetically “polluted” by commercial broilers?

Genomic study finds high levels of gene flow between Chinese indigenous chicken breeds and commercial broilers.

In total, 1714 out of 10 446 bird species (16.4%) have been documented to have hybridized with at least one other bird species in nature. When hybridization in captivity is included, this figure increases to 2204 species (21.1%).” These numbers are from my Ibis-paper where I quantified the incidence of hybridization in birds. Although this blog mainly focuses on avian hybrids in the wild, hybridization in captivity is quite common. In fact, interbreeding different species or varieties has been an important tool for animal breeders. The domestic chicken, for example, is probably the outcome of hybridization between several wild species.

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The domestic chicken is probably the outcome of hybridization between several wild species. ©Didactohedron | Wikimedia Commons

 

Double-edges Sword

Hybridization is a double-edged sword. On the one hand, it can introduce new genetic variation and drive adaptation. On the other hand, it can threaten the “genetic purity” of endangered species (see for example the case of the Milky Stork). Similar processes occur in captivity. For instance, interbreeding Large White pigs with Chinese pigs probably resulted in the exchange of the AHR haplotype which contributes to increased litter size, a desired trait in animal breeding practices. In Vietnam, however, mixing different pig breeds culminated in loss of genetic diversity of the Vietnamese Black H’mong pig breed. These examples show the complexities of hybridization in the context of animal breeding.

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Large White pigs have a larger litter size due to hybridization with Asian breeds (from: https://www.indiamart.com/)

 

Indigenous Chickens

A recent study in the journal Evolutionary Applications assessed the situation for Chinese indigenous chicken breeds. In China, these chickens constitute important genetic resources and are valued for several traits, such as early puberty, meat quality and resistance to certain diseases. However, they have a slower growth rate compared to commercial broilers. To increase the growth rate of these indigenous chickens, breeders have created several hybrid breeds, including Shiqi Za chicken, Three-Yellow chicken and Kuaida Silkie. These breeds are known to be admixed, but what about the original indigenous ones? Chunyuan Zhang (China Agricultural University) and her colleagues compared the genomes of several breeds to figure this out.

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A Silkie chicken breed (from: https://countrysidenetwork.com/).

 

High Levels of Introgression

The genetic analyses revealed high levels of introgression between indigenous chickens and commercial broilers. On average, about 15% of the genomes was of commercial origin. The highest percentage (21.5%) was found in the Huiyang Bearded chicken. These high percentages are probably due to the naive practices of local farmers that cross indigenous breeds with commercial ones. Although the impact of this widespread genetic exchange remains to be determined, the authors fear that it could “threaten current genetic resources and result in genetic pollution.”

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The Huiyang Bearded chicken breed (from: https://www.newscientist.com/)

 

References

Zhang, C., Lin, D., Wang, Y., Peng,. D., Li, H., Fei, J., Chen. K., Yang, N., Hu, X., Zhao, Y. & Li. N. (2019) Widespread introgression in Chinese indigenous chicken breeds from commercial broiler. Evolutionary Applications, 12(3): 610-621.

 

This paper has been added to the Galliformes page.

Barking up the wrong species tree: How gene flow shaped canine evolution

Complex patterns of gene flow in the family Canidae.

Hybridization between wolves and dogs is relatively common. A recent study in Spain, for example, reported a wolf with about one‐third dog-DNA. But what about other members of the canine family? A large team of international scientists sequenced the genomes of all members of the genus Canis. Comparing the genetic code of these animals revealed a complex evolutionary history shaped by gene flow. The results appeared in the journal Current Biology.

 

From Trees to Networks

The analyses revealed gene flow among numerous species. The figure below summarizes the findings. Solid arrows indicate known admixture events, dashed arrows refer to newly discovered patterns of gene flow. This widespread exchange of genetic material indicates that capturing canine evolution in a bifurcating tree is difficult (if not impossible). A network approach might be a better here. This is in line with recent studies on other animals, such as bats, baboons, whales, mammoths and – of course – birds. Scientists that try to force such evolutionary histories into a single species tree are probably barking up the wrong tree.

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The complex evolutionary history of Canidae. Solid arrows indicate known admixture events, dashed arrows refer to newly discovered patterns of gene flow (from Gopalakrishnan et al. 2018 Current Biology).

 

Dogs and Dholes

Let’s have a look at some admixture events. The analyses provided strong evidence for gene flow between African hunting dog (Lycaon pictus) and dhole (Cuon alpinus). This finding is a bit surprising, because these species currently do not overlap. African hunting dogs roam the plains of – you guessed it- Africa while dholes live in Asia. Perhaps dholes used to occur in the Middle East and interbred with African hunting dog from North Africa. Clearly, more research is needed to determine the timing and location of admixture.

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African hunting dogs (© Derek Keats | Wikimedia Commons) and dholes (© Raju Venkatesha Murthy | Wikimedia Commons) exchanged genes.

 

A Hybrid Species?

Apart from the expected dog introgression into gray wolves (Canis lupus), gene flow was also uncovered between gray wolves, golden jackals (Canis aureus) and African golden wolves (Canis anthus). In addition, the African golden wolf also received genetic material from the Ethiopian wolf (Canis simensis). This complex web of interactions prompted the researchers to have a closer look at the African golden wolf. Detailed analyses indicated that this wolf is probably a hybrid species between Ethiopian wolf and gray wolf, which contributed 28% and 72% of the genetic material, respectively.

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The African golden wolf (© xorge | Wikimedia Commons) is probably a hybrid species.

 

Spooky Introgression

Finally, the genomes of gray wolf and coyote (Canis latrans) contain a fraction of DNA that cannot be attributed to any extant species. The researchers suggest that this is the outcome of hybridization with an as-yet-unidentified species, a so-called ghost lineage. A similar scenario has recently been proposed in human evolution, based on deep learning analyses. I wouldn’t be surprised if more “spooky introgression in the distant past” will be uncovered in other systems. Stay tuned!

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Coyote probably received genetic material from a now extinct lineage (© matt knoth | Wikimedia Commons).

 

References

Gopalakrishnan, S., Sinding, M.S., Ramos-Madrigal, J., Niemann, J., Samaniego Castruita, J.A., Vieira, F.G.,Carøe, C., Montero, M., Kuderna, L., Serres, A., González-Basallote, V.M., Liu, Y., Wang, G., Marques-Bonet, T., Mirarab, S., Fernandes, C., Gaubert, P., Koepfli, K., Budd, J., Rueness, E.K., Heide-Jørgensen, M.P., Petersen, B., Sicheritz-Ponten, T., Bachmann, L., Wiig, Ø., Hansen, A.J. & Gilbert, M.T.P. (2018) Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Current Biology, 28(21):3441-3449.

Tracing the origins of the giant raptors on New Zealand

Genetic study reconstructes the evolutionary history of Haast’s Eagle and Eyles’ Harrier. 

Weird things happen on islands. I am not talking about the series Lost, I am referring to the way some organisms change when they colonize an island. The fossil record has several striking examples of animals that shrink in size, such as the dwarf hippopotamus on Malta. The opposite of this insular dwarfism has also been observed: small animals become giants on the island. Examples of island gigantism include giant shrews on Corsica and giant dormice on Mallorca. A recent study in the journal Molecular Phylogenetics and Evolution investigated two avian examples: the huge birds of prey of New Zealand: Haast’s Eagle (Hieraaetus moorei) and Eyles’ Harrier (Circus teauteensis).

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Haast’s Eagle hunting on moa (from: http://www.wikpedia.com/)

Big Birds

The largest extant eagle, the Harpy (Harpia harpyja) weights about 9 kilograms. The huge Haast’s Eagle was even heavier, estimated at up to 15 kilograms. Its wingspan measured 2.5 to 3 meters. This eagle probably preyed on various species of moa.

Eyles’ Harrier was a bit smaller than Haast’s Eagle. With a wingspan of about 2 meters and a weight of around 3 kilograms it is still the largest known harrier in the world. Its preys were probably smaller species of moa as well as kea (Nestor notabilis), kaka (Nestor meridionalis) and pigeons.

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Eyles Harrier with a prey (from: http://nzbirdsonline.org.nz/)

Living Relatives

Both species went extinct within the last 700 years, probably due to human-driven habitat change. But where did these giant birds come from? To answer this question, Michael Knapp (University of Otago) and his colleagues sequenced the mitochondrial DNA from fossil material and compared it to extant species.

It turned out that the Haast’s Eagle is most closely related to the much smaller Little Eagle (Hieraaetus morphnoides) from Australia. Similarly, the Eyles’ Harrier is related to a small Australian species, the Spotted Harrier (Circus assimilis).

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Closest iving relatives of the giant birds of prey from New Zealand. The Little Eagle (left, picture by David Kleinert) and the Spotted Harrier (right, picture by Ian Colley).

Apex Predators

Molecular dating indicated that the ancestors of Haast’s Eagle and Eyles’ Harrier arrived on New Zealand about 2 million years ago. At this time, the changing climate resulted in deforestation culminating in open grasslands that provided ideal hunting grounds. Because there were no mammalian predators on the island, the raptors could quickly increase in size and establish their position as apex predator.

As mentioned in the beginning, organisms tend to become smaller or bigger on islands. This phenomenon is known as Foster’s Rule. If you are interested in this evolutionary process, I can highly recommend the videos by PBS Eons below. Enjoy!

References

Knapp, M., Thomas, J.E., Haile, J., Prost, S., Ho, S.Y.W., Dussex, N., Cameron-Christie, S., Kardailsky, O., Barnett, R., Bunce, M., Gilbert, M.T.P. & Scofield, R.P. (2019) Mitogenomic evidence of close relationships between New Zealand’s extinct giant raptors and small-sized Australian sister-taxa. Molecular Phylogenetics and Evolution, 134:122-128.

Chaffinches on the Canary Islands: A new subspecies on Gran Canaria

Ornithologists describe a new taxon of Common Chaffinch based on morphology, genetics and song.

Recording the song of a Great Tit (Parus major) is nearly impossible when a Chaffinch (Fringilla coelebs) is singing nearby. During my Master in Antwerp, I ventured into the forest to record Great Tit songs. Several recordings were useless because a neighboring Chaffinch overpowered the Great Tits symphony. Male Chaffinches typically sing two or three different song types, and there are regional dialects too.

Apart from differences in song, Chaffinches can also differ in plumage color. The Eurasian subspecies (coelebs), for example, has a bright orange breast and a blue cap. On Madeira, birds of the subspecies maderensis are less orange but they have a beautiful yellow back. Currently, there are 15 to 18 subspecies (depending on who you ask). A recent study in the Journal of Avian Biology focused on the Macaronesian subspecies (Azores, Madeira and Canary Islands).

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The brightly colored Eurasian Chaffinch (from: http://www.wikipedia.com/)

 

Three Archipelagos, Five subspecies

Macaronesia consists of three archipelagos: Azores, Madeira and the Canary Islands. You can find one subspecies on the Azores (moreletti) and on Madeira (maderensis). The Canary Islands, however, house three subspecies on different islands: palmae on La Palma, ombriosa on El Hierro, and canariensis on Gran Canaria, Tenerife and La Gomera.

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The Canary Islands, home to three Chaffinch subspecies.

 

Colonization History

Juan Carlos Illera (Oviedo University) and his colleagues collected specimens from all five subspecies and studied them morphologically and genetically. The analyses support the different subspecies. The researchers found that individuals from each archipelago grouped together. They were also able to reconstruct the colonization history of the Macaronesian islands. The finches probably started off on the European mainland and consequently discovered the Azores, Madeira and the Canary Islands. Essentially, they followed a stepping stone route from north to south. The birds reached the Canary Islands about 600,000 years ago.

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A La Palma Chaffinch (from http://www.wikipedia.com/)

 

A New Taxon

Within the Canary Islands, birds from Gran Canaria were clearly differentiated from the other islands. The researchers conclude that it differs to much that it should be considered a new taxon: bakeri. This conclusion is supported by previous studies on song and sperm morphology. Morphologically, the new taxon can be distinguished from its relatives by the color pattern on one of the tail feathers (R4). Males of bakeri show a tiny white edge or small white spot, while canariensis males have an conspicuous white spot. A small, but possibly significant difference.

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A Chaffinch on Gran Canaria, the member of a brand-new taxon © Juan Emilio (from: https://commons.wikimedia.org/)

 

References

Illera J Rando J Rodriguez‐Exposito E Hernández M Claramunt S Martín A. (2019) Acoustic, genetic, and morphological analyses of the Canarian common chaffinch complex Fringilla coelebs ssp. reveals cryptic diversification. Journal of Avian Biology, 49(12): jav.01885.

 

More than one way: How the open vegetation corridor influences the evolution of South American birds

Genetic study of two neotropical bird species reveals different evolutionary responses to a common barrier.

South America is known for its diversity in bird species. But how did this multitude of species evolve? The classical explanation is geographic isolation. Several landscape features, such as Amazonian rivers and Andean mountains, break up species in different populations which consequently diverge into separate species. In reality, however, things are more complex. This is illustrated by a recent study in Molecular Ecology.

 

Corridor

Open and dry environments can form open vegetation corridors between rainforests. In South America, for example, Amazonia and the Andean forests are isolated from the Atlantic Forest by such an open vegetation corridor. Several populations of birds are distributed east and west of this corridor. Pablo Lavinia and his colleagues investigated the influence of this corridor on the evolution of two bird species: the Large-headed Flatbill (Ramphotrigon megacephalum) and the Fawn-breasted Tanager (Pipraeidea melanonota).

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The Open Vegetation Corridor (OVC) separates the Andes and Amazonia from the Atlantic Forest (map adapted from https://kids.britannica.com/)

 

The Specialist

The Large-headed Flatbill is a lowland, forest specialist in the bamboo understory where it forages on insects. It comprises four subspecies: one in the Atlantic Forest (megacephalum) and three in Amazonia and at the base of Andes (bolivianiumpectorale and venezuelense).

Genetic analyses of two subspecies (megacephalum and bolivianium) revealed a deep split, indicating that these populations diverged about 3.4 million years ago. How this divergence happened is not clear. Perhaps the Atlantic Forest was colonized when it was connected with the Amazonian region. A likely colonization route would have been the Chapare Buttress in present-day Bolivia which connected the Andes to the Brazilian shields. Alternatively, the continuous distribution of the Large-headed Flatbill was disrupted by the formation of the open vegetation corridor during the Plio-Pleistocene (beginning about 5 million years ago).

In any case, there is clear genetic divergence between the subspecies, which is accompanied by differences in song. The researchers found that “the disyllabic whistle of R. m. megacephalum sounds more high-pitched and slowly paced than that of R. m. bolivianum.” Moreover, a second type of vocalization – the dawn song – is only sung by bolivianum.

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The Large-headed Flatbill © Sergio Gregorio da Silva from https://neotropical.birds.cornell.edu/

 

The Generalist

In contrast to the Large-headed Flatbill, the Fawn-breasted Tanager is a generalist that occurs in a variety of closed and semi-open environments where it feeds on fruits and insects. Although its movement patterns are poorly documented, it is considered a seasonal migrant. One population (subspecies melanonota) is restricted to the Atlantic Forest while another population (subspecies venezuelensis) is found in the Andes region.

Genetically, these subspecies are very similar. Demographic modelling of these populations suggest a complex history of divergence and secondary contact. Indeed, the analyses pointed to gene flow from the Andes region into the Atlantic Forest. The subspecies also differ in plumage: the brightness of the chest and rump is higher in venezuelensis than in melanonota. This difference could have been driven by divergent sexual selection.

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The Fawn-breasted Tanager © José Carlos Motta-Junior (from: https://www.hbw.com/)

 

Ecology Matters

Reconstructing the evolutionary histories of Large-headed Flatbill and Fawn-breasted Tanager indicated that these species have been affected differently by the open vegetation corridor. The researchers nicely summarize their findings:

The shallow genetic divergence and signs of gene flow between its subspecies as a result of secondary contacts, together with differentiation in plumage coloration but not in vocalizations, might be reflecting the early stages of the speciation process in P. melanonota . On the contrary, the deep genetic divergence and the consistent song differentiation between R. m. megacephalum and R. m. bolivianum suggest that these geographically isolated subspecies could actually constitute two different species.

This study illustrates that the diversification of birds in South America is more complicated than simple geographic isolation. The ecology of the species should also be taken into account (similar to this study on islands colonization).

 

References

Lavinia, P.D., Barreira, A.S., Campagna, L., Tubaro, P.L. & Lijtmaer D.A. (2019) Contrasting evolutionary histories in Neotropical birds: divergence across an environmental barrier in South America. Molecular Ecology.

 

This paper has been added to the Thraupidae page.

Scrutinizing a Superspecies: Patterns of Gene Flow among Common, Long-legged and Upland Buzzard

Genetic study explores population structure of Palearctic Buzzards.

“That is clearly a honey buzzard (Pernis apivorus),” says the raptor expert while I squint my eyes to find a little black dot barely visible against a white cloud. I am always amazed at how some birdwatchers can recognize raptor species by their silhouette. Of course there are some obvious ones, such as the red kite (Milvus milvus) with its forked tail. But can you tell the difference between a common buzzard (Buteo buteo) and a long-legged buzzard (Buteo rufinus) when they soar up high? A recent paper in the journal Molecular Phylogenetics and Evolution shows that they are also genetically difficult to tell apart.

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Silhouettes of common buzzard and long-legged buzzard. Can you tell which is which?

 

Superspecies

The taxonomy of Palearctic buzzards (genus Buteo) is – to put it mildly – challenging. Several ornithologists have tried to create order in the subspecific chaos of this species complex. The failure to achieve this has been attributed to extensive gene flow between the different (sub)species. Therefore, common buzzard is often treated as a superspecies, comprised of several allospecies. Here is a recent classification proposed by Luise Kruckenhauser et al. (2004)

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A classification for the genus Buteo (from: Kruckenhauser et al. (2004) Zoologica Scripta)

 

Three species and three markers types

Michael Jowers (University of Porto) and his colleagues decided to focus on three members of this superspecies: the common buzzard, the long-legged buzzard and the Upland buzzard (B. hemilasius). They collected samples across the range of these species and sequenced three types of markers: mitochondrial DNA, nuclear markers and microsatellites. Together these genetic markers provide a window on the recent history of the three buzzard species.  Let’s look at the results one marker type at a time.

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Common Buzzard in Belgium © Jente Ottenburghs

 

Mitochondrial Clusters and a Nuclear Mess

The mitochondrial markers differentiated between the species and agreed with the taxonomic classification. The Upland buzzard is clearly distinct from the other buzzards. The situation of common buzzard and long-legged buzzard is a bit more complicated. One subspecies of the long-legged buzzard (rufinus) forms a separate cluster whereas another subspecies (cirtensis, also known as Atlas long-legged buzzard) groups with two subspecies of the common buzzards (buteo and vulpinus). The clustering of cirtensis with common buzzard might be due to hybridization. In recent years, hybrids have been reported in Tunisia and the Strait of Gibraltar.

I can be short about the nuclear markers: everything is mixed. There is no clear clustering of particular subspecies or even species. This pattern is probably due to a combination of gene flow and the recent origin of the buzzard taxa.

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Mitochondrial haplotype network for three buzzard species. The Upland buzzard (dark blue) is clearly distinct from the others. One subspecies of long-legged buzzard (rufinus, light blue) is separate while another subspecies (cirensis, green) clusters with two subspecies of the common buzzard: buteo (red) and vulpinus (orange). From: Jowers et al. 2019 MPE.

 

More Gene Flow?

The microsatellites, finally, uncovered three clusters that correspond to the three species in this study. There were, however, signs of gene flow between the different clusters. Individuals from contact zones between particular species showed admixed genomes. In accordance with the mitochondrial network, there is probably gene flow between Atlas long-legged buzzard and common buzzard. Moreover, long-legged buzzard has also been exchanging genetic material with Upland buzzard. Indeed, hybrids between these species have been documented in central Asia.

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Long-legged buzzard (from: http://www.ebird.com/)

 

Speciation in Progress

These analyses reveal the taxonomic difficulties of Palearctic buzzards and indicate that the speciation process is still ongoing (and might never be complete). Speciation is a continuous process that prevents taxonomists from pigeonholing populations. Buzzards are a clear example of this.

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Upland buzzard (from: http://www.hbw.com/)

 

References

Jowers, M.J., Sánchez-Ramírez, S., Lopes, S., Karyakin, I., Dombrovski, V., Qninba, A., Valkenburg, T., Onofre, N., Ferrand, N., Beja, P., Palma, L. & Godinho, R. (2019) Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards. Molecular Phylogenetics and Evolution, 134:269-281.

 

This paper has been added to the Accipitriformes page.

The genetic recipe for a bird-of-paradise radiation

Genome assemblies of several birds-of-paradise reveal the genes that have driven the evolution in this bird group.

WTF, Evolution?! is a website that gathers the crazy outcomes of the evolutionary process. No purposeful design, just evolution tinkering with the available material and producing what is needed to survive and reproduce, no matter how wacky the end result. When we turn to the avian diversity, there are many species with unusual features or behaviors. Think of the knob-billed duck or the “moon-walking” manakins. Another great candidate is the bird family Paradisaeidae, better known as the birds-of-paradise. This diverse assemblage of passerines – 41 species in 16 genera – displays a bewildering array of extravagant plumage and courtship displays. A recent GigaScience paper explored the genomes of a few birds-of-paradise to pinpoint the genetic basis of this diversity.

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The amazing diversity of birds-of-paradise. © Tim Laman | National Geographic

 

Five Lineages

Stefan Prost and his colleagues studied the genomes of five birds-of-paradise, representing the five major lineages in this family: the paradise-crow (Lycocorax pyrrhopterus), the paradise riflebird (Ptiloris paradiseus), the Huon astrapia (Astrapia rothschildi), the King of Saxony bird-of-paradise (Pteridophora alberti) and the red bird-of-paradise (Paradisaea rubra).

Next, they scanned these genomes for genes under positive selection and rapidly evolving gene families. The result is a list of candidate genes that could explain the diversity of birds-of-paradise. As I have written before, we should be careful with making up just-so-stories based on a handful of candidate genes. But we are of course free to speculate a bit.

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The King of Saxony bird-of-paradise (from: https://charismaticplanet.com/)

 

Plumage Color and Vision

Because of the diversity in plumage, the researchers expected genes related to coloration and feather structure to be under positive selection. Indeed, they found a few of these genes under positive selection (although they turned out non-significant after correcting for multiple testing). These genes include ADAMTS20 and ATP7B, which are both involved in the production of melanin, an important pigment.

Colors have to be perceived, so you might also expect the find genes with roles in eye function and eye development to be under selection. Three genes (GNB1, ATP6AP2 and MYOC) popped up as significant when testing for positive selection. There might thus be some co-evolution between coloration and vision. For example Lawes’s parotia (Parotia lawesii) modifies the color of its plumage by altering the angle of light reflection. Birds need a visual system that is able to process these color changes. However, vision is used for a wide range of other activities, such as foraging and detecting predators. Finding evidence for co-evolution of coloration and vision is thus tricky.

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The plumage color of the Lawes’s parotia changes based on the angle of light reflection (from: https://alchetron.com/)

 

Smelling and Startling

Let’s look at the gene families that expanded in the birds-of-paradise. A first family that increased in size holds the olfactory receptors, which are important in smelling. The branch leading to the core bird-of-paradise (i.e. excluding the paradise-crow) showed an increase of 5 genes, with another addition of 6 genes in the Huon astrapia. These genes could serve several functions, ranging from species recognition to foraging. Clearly, more research is needed here.

A second gene family that expanded is involved in the startle response, a behavioral trait that allows birds to react quickly to a stimulus. This behavior could be important in the context of leks where several males gather to woo the females. During this mating display, the males are exposed and have to react quickly to incoming predators.

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Several males of the greater bird-of-paradise displaying to a female. © Tim Laman | National Geographic

 

Transposable Elements

The researchers also explored the amount of transposable elements (TEs) in the bird-of-paradise genomes. TEs are short stretches of DNA that jump around the genome using copy/paste or cut/paste mechanisms. This search revealed the activity a particular class of TEs, namely retroviral LTRs. Interestingly, this activity coincides with the radiation of birds-of-paradise about 24 million years ago. Could it be that the evolution of this bird family was partly driven by transposable elements? Possibly, but let’s not jump to conclusions yet.

So, what is the recipe for a radiation of birds-of-paradise? Just select your favorite genes involved in coloration, vision, smell and startling response. Mix them in a big pot and add a dash of transposable elements. And let it boil for a few million years.

 

References

Prost, S., Armstrong, E,.E., Nylander, J., Thomas, G.W.C., Suh, A., Petersen, B., Dalen, L., Benz, B.W., Blom, M.P.K., Palkopoulou, E., Ericson, P.G.P. & Irestedt. M. (2019) Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise. GigaScience

A Puzzle of Primates: Disentangling the complex evolutionary history of Baboons

The evolution of Papio baboons cannot be captured in a simple bifurcating tree.

Hybridization shaped human evolution. Our evolutionary history has been punctuated by introgression events with Neanderthals, Denisovans and probably a third unknown lineage. But what about other primates? Reports of hybrids are known from several primate groups, such as chimpanzees, macaques and baboons (see this blog post for more details). A recent study in the journal Science Advances focused on baboons of the genus Papio. How much gene flow has there been between the six extant species?

Olive_baboon_Ngorongoro.jpg

Olive baboon (from: http://www.wikipedia.com/)

 

Wild and Captive Hybrids

There are currently six recognized species of baboon. These species are morphologically and behaviorally distinct and occupy different parts of the African continent.

  • Olive baboon (P. anubis)
  • Yellow baboon (P. cynocephalus)
  • Kinda baboon (P. kindae)
  • Hamadryas baboon (P. hamadryas)
  • Chacma baboon (P. ursinus)
  • Guinea baboon (P. papio)

Hybrids between several species are known from captivity and the wild. For example, hamadryas baboons and anubis baboons interbreed along a hybrid zone in eastern Africa.

hamadryas baboon.JPG

Hamadryas baboon © LadyofHats | Wikimedia Commons

 

Discrepancies

But recent hybridization does not necessarily mean that there was ancient gene flow. To figure out whether the evolution of baboons has been shaped by hybridization, a large team of researchers sequenced and analyzed the genomes of all six species.

When they attempted to reconstruct the evolutionary tree (or phylogeny) of the baboons, the researchers noted several discrepancies. Different parts of the genome resulted in different relationships. For example, sometimes hamadryas baboon clustered with olive baboon while on other occasions hamadryas baboon grouped with Guinea baboon. These discrepancies suggest that there has been gene flow between several baboon species.

yellow baboon

Yellow baboon © Alexander Landfair | Wikimedia Commons

 

Network

Further analyses (based on f-statistics) supported the notion that hybridization was a frequent phenomenon in baboon evolution. The authors write that “no one simple dichotomously branching tree accurately reflects all aspects of genomic differentiation among extant baboon species.” Therefore, they reconstructed the evolutionary history of these primates taking into account gene flow between several species. The result is a complicated network with multiple interconnections and different amounts of exchanged DNA. These reticulated scenarios seem to be a common aspect of mammalian evolution (see for instance whales, cows and bats).

baboon network.jpg

The reticulated evolutionary history of baboons (genus Papio) inferred from whole genome data (from: Rogers et al. 2019 Science Advances)

 

Jumping Genes

Finally, the researchers also used transposable elements (TEs) in their phylogenetic analyses. TEs are short stretches of DNA that jump around the genome using copy/paste or cut/paste mechanisms. In this study, the researchers focused in Alu-elements, a particular group of TEs that is also common in humans genomes. They observed a marked increase in Alu insertions in baboons relative to other primates. Some studies have suggested that hybridization can result in activation of silenced TEs. Whether this happened in baboon evolution remains to be investigated.

 

References

Rogers et al. (2019) The comparative genomics and complex population history of Papio baboons. Science Advances, 5(1):eaau6947.

Hybrids all the way down: Interbreeding musk turtles in Alabama

Habitat alteration might have triggered formation of a hybrid zone between two species of musk turtle.

“Hybrid swarms can only survive in hybridized habitats.” Edgard Anderson wrote this in his 1948 Evolution paper entitled “Hybridization of the Habitat”. Based on experiments in the plant genus Tradescantia, he argued that human-modified habitats were conducive for hybridization. A recent study in the journal Molecular Ecology provides an example of this scenario in animals.

 

Ecological Transition

The distribution of two musk turtle (Sternotherus) species in southeastern USA is a but peculiar. The flattened musk turtle (S. depressus) is endemic to the Black Warrior River system in Alabama. The range of this species is completely encompassed by its sister species, the stripe-necked musk turtle (S. peltifer). The distribution map of these two species is reminiscent of a Russian doll.

The Black Warrior River flows across the Fall Line, an ecological transition from rocky underground to sandy soils. Early studies on the musk turtles uncovered a morphological hybrid zone at this transition. More recent work showed introgression of mitochondrial DNA from stripe-necked into flattened musk turtle. But the exact extent of gene flow between these species remains elusive. Therefore, Peter Scott (University of Alabama) and his colleagues undertook an extensive genetic study of this hybrid zone.

flattened-musk-turtle.jpg

Flattened musk turtle (from: https://www.petguide.com/)

 

Altered River System

The analyses revealed that all individuals from the hybrid zone were admixed, while the remainder of the samples turned out to be pure. Gene flow was unidirectional from stripe-necked into flattened musk turtle, confirming the mitochondrial pattern. Moreover, hybridization seems to be a recent phenomenon. Most individuals were second-generation hybrids or backcrosses to flattened musk turtle.

Recent hybridization suggests that human intervention triggered the formation of the hybrid zone. In the 1940s-1960s, installation of big dams restructured the river system in Alabama. This change probably led to the breakdown of natural ecological barriers between the two turtle species, resulting in hybridization. A nice example of “hybridization of the habitat”.

stripe-necked-musk-turtle.jpg

Stripe-necked musk turtle (from: https://www.petguide.com/)

 

References

Scott, P.A., Glenn, T.C. & Rissler, L.J. (2019) Formation of a recent hybrid zone offers insight into the geographic puzzle and maintenance of species boundaries in musk turtles. Molecular Ecology, 28:761-771.