Genomic analyses point to speciation with gene flow in the Northern Saw-whet Owl

“Good advice is always certain to be ignored, but that’s no reason not to give it.”

– Agatha Christie

More than one year ago (in January 2018 to be precise), I wrote a blog post about the evolutionary history of the Northern Saw-whet Owl (Aegolius acadicus). A genetic study revealed that two subspecies – brooksi and acadicus – are genetically differentiated with extremely low levels of gene flow. In fact, there might not be any gene flow. I then provided the following advice: “a genomic approach is necessary to be sure.” The authors followed my suggestion (or they were already working on it) and revisited this system using genomic data. Has there been gene flow or not?

1280px-Aegolius_acadicus_-Fossil,_Oregon,_USA_-juvenile-8.jpg

Three juvenile Northern Saw-whet Owls in Fossil, Oregon, USA. © Kathy & Sam | Wikimedia Commons

 

Heteropatric

The situation of the Saw-whet Owl is peculiar. The acadius subspecies, which breeds from Alaska to California, is mostly migratory. The brooksi subspecies, on the other hand, is sedentary and only occurs in the Haida Gwaii island. For most of the year, these subspecies are geographically isolated. But during migration and in winter, some acadius individuals reside on Haida Gwaii where they mingle with their brooksi relatives. This distribution has been described as heteropatric.

distribution owls

The distribution of the Northern Saw-whet Owl. The year-round
range of brooksi is shown in black (Haida Gwaii), the breeding
range of acadicus is shown in gray, and light gray indicates
areas where acadicus occurs only during migration. From: Winker et al. (2019) The Auk

 

Gene Flow?

The temporary co-occurrence of acadius and brooksi provides the opportunity for hybridization. Previous work, based on a subset of molecular markers, found some evidence for low levels of gene flow. But a genomic approach was needed to be completely sure. Kevin Winker and his colleagues used more than 2500 ultraconserved elements to provide a more detailed picture of Saw-whet Owl’s evolution.

Their analyses confirmed low levels of gene flow between the subspecies. Gene flow is stronger from brooksi into acadicus (about 4 individuals per generation) than the other way (about 1 individual per generation). The absence of hybrid specimens and the clear differences between the subspecies suggest that the detected gene flow is probably historical. The authors conclude that “this is a case of speciation with gene flow, and the Haida Gwaii owl (A. a. brooksi) might be considered a young biological species.”

Northern_Saw-whet_Owl,_Reifel_BC_1

Northern Saw-whet Owl at Reifel Migratory Bird Sanctuary, Delta, BC, Canada. © Brendan Lally | Wikimedia Commons

 

References

Winker, K. (2010). On the origin of species through heteropatric differentiation: a review and a model of speciation in migratory animals (No. 69). Ornitological Monographs, 69.

Winker, K., Glenn, T.C., Withrow, J., Sealy, S.G., & Faircloth, B.C. (2019). Speciation despite gene flow in two owls (Aegolius ssp.): Evidence from 2,517 ultraconserved element loci. The Auk, 136(2):ukz012.

Withrow, J.J., Sealy, S.G., & Winker, K. (2014). Genetics of divergence in the Northern Saw-whet Owl (Aegolius acadicus). The Auk, 131(1):73-85.

 

This paper has been added to the Strigiformes page.

Advertisements

What drives plumage evolution in woodpeckers?

Habitat and climate profoundly influence woodpecker plumage, but many species show remarkable convergence that cannot be explained by these factors alone.

There are a couple of rules in biology, generalized principles that describe patterns observed in living organisms. Gloger’s Rule, for example, states that “more heavily pigmented forms tend to be found in more humid environments.” A recent review paper in Biological Reviews indicated that there are actually two versions of Gloger’s Rule. A simple version that predicts that animals are darker in warm and humid areas due to more deposition of eumelanin (i.e. the pigment responsible for dark colors). The complex version, however, makes a distinction between temperature and humidity which have different effects on the deposition of pheomelanin, the pigment that leads to red coloration. It is deposited more in warm climates, but less in humid ones. The figure below gives a good overview of the simple and complex versions of Gloger’s Rule.

gloger.jpg

The simple and complex versions of Gloger’s Rule. From: Delhey (2019) Biological Reviews

 

Woodpeckers

Both versions of Gloger’s Rule are used in the scientific literature and it is important to know which version is being tested. A recent paper in Nature Communications, for example, tested the simple version in woodpeckers. Eliot Miller and his colleagues used the online database eBird to gather information on 230 woodpecker species.

The analyses revealed a clear correlation between plumage color and humidity. Darker species tend to occur in regions with higher annual precipitation, supporting Gloger’s Rule. The exact mechanism behind this pattern, however, remains unknown. There are several hypotheses, such as improved background matching because of higher predation pressure in humid areas or defense against feather-degrading parasites.

Black_Woodpecker_(Dryocopus_martius),_Parc_de_Woluwé,_Brussels_1.jpg

A Black Woodpecker (Dryocopus martius) in Parc de Woluwé (Brussels, Belgium) © Frank Vassen | Wikimedia Commons

 

Plumage Mimicry

Another interesting pattern emerged from the analyses: woodpeckers from the same area looked more alike than predicted by climate and habitat alone. The authors argue that this plumage convergence is due to another process, namely mimicry. This phenomenon occurs when multiple species evolve similarly in response to a shared signal receiver (e.g., a predator). A classic example concerns butterflies. Some butterfly species don’t taste good and they advertise this with bright warning colors. Predators learn quickly and tend to avoid these species. Other edible butterfly species adopt the same colors and fool predators into thinking that they are distasteful. Over time the edible and distasteful species converge on similar color patterns.

ID_Monarch_Viceroy.jpg

An example of mimicry. The edible Viceroy Butterfly closely resembles the distasteful Monarch Butterfly. From: http://www.learner.org/

What drives plumage mimicry in woodpeckers remains to be investigated. Perhaps smaller species use particular plumage patterns to fool other species into thinking that they are a bigger, more dominant species. This has been proposed as an explanation for resemblance between the small Downy Woodpecker (Picoides pubescens) and the more dominant Hairy Woodpecker (Leuconotopicus villosus).

 

A Role for Hybridization?

An intriguing question that arises from these plumage patterns is how convergence is achieved genetically. Are multiple mutations needed? Does selection choose between a subset of genetic modules (similar to head patterns in wagtails)? Are genes related to plumage patterning occasionally exchanged when species hybridize? The latter mechanism seems plausible given the relatively high incidence of hybridization in woodpeckers

1024px-Downy_Woodpecker01.jpg

Does this Downy Woodpecker resemble the Hairy Woodpecker to fool other species? © Wolfgang Wander | Wikimedia Commons

 

References

Burtt, E.H. & Ichida, J.M. (2004) Gloger’s Rule, Feather-Degrading Bacteria, and Color Variation Among Song Sparrows. The Condor, 71:223-239.

Delhey, K. (2018) Darker where cold and wet: Australian birds follow their own version of Gloger’s rule. Ecography, 41:673-683.

Delhey, K. (2019) A review of Gloger’s rule, an ecogeographical rule of colour: definitions, interpretations and evidence. Biological Reviews, Early View.

Leighton, G.M., Lees, A.C. & Miller, E.T. (2018) The hairy–downy game revisited: an empirical test of the interspecific social dominance mimicry hypothesis. Animal Behaviour, 137:141-148.

Miller, E.T., Leighton, G.M., Freeman, B.G., Lees, A.C., & Ligon, R.A. (2019). Ecological and geographical overlap drive plumage evolution and mimicry in woodpeckers. Nature communications, 10(1), 1602.

Hybridization and Tinkering: High levels of gene flow between Yellow-fronted and Red-fronted Tinkerbird

Genetic study uncovers rampant introgression between distantly related bird species.

How long does it take before two species cannot hybridize any longer? In 1975, Ellen Prager and Allan Wilson estimated that ” the average hybridizable species pair diverged
from a common ancestor about 22 million years ago.” That is a long time! In comparison, mammals lose the ability to hybridize after about 3 million years. It is thus not so surprising that hybrids between distantly related bird species have been documented. A recent study in the Biological Journal of the Linnean Society reports gene flow between two species of African Barbets that diverged more than four million years ago.

Yellow-fronted_tinkerbird.jpg

Yellow-fronted tinkerbird at Walter Sisulu National Botanical Garden, South Africa. © Derek Keats | Wikimedia Commons

 

Orange-fronted Tinkerbirds

Yellow-fronted Tinkerbird (Pogoniulus chrysoconus extoni) and Red-fronted Tinkerbird (P. pusillus pusillus) meet along a contact zone in Southern Africa. Ornithologists didn’t know whether these species hybridized, although Graham Ross documented orange-colored birds in this area. He wrote that this observation “strongly suggested that intergrading between the two species had occurred.”

 

No Sisters

Emmanuel Nwankwo and his colleagues collected birds within and outside the contact zone. Genetic analyses of these birds led to two striking findings. First, the Yellow-fronted Tinkerbird and Red-fronted Tinkerbird were not even sister species. In fact, the Red-fronted Tinkerbird is more closely related to another Yellow-fronted Tinkerbird: Pogoniulus chrysoconus chrysoconus. Hybridization between non-sister species occurs, but it less common than hybridization between sister species (see this review).

tinkerbirds phylogeny.jpg

The two species of Tinkerbird (marked with red circles) turned out to be distantly related. They are not even sister species and diverged more than 4 million years ago. From: Nwankwo et al. (2019) Biological Journal of the Linnean Society 

 

Rampant Introgression

Second, the contact zone housed a lot of hybrids. The researchers write that “almost all individuals in the contact zone [showed] some evidence of introgression, as do some individuals in near allopatry.” It is no surprise that they mention “rampant introgression” in the title of their paper. The genetic analyses also showed that backcrossing mostly occurred in the Yellow-fronted Tinkerbird. This indicates that females of both species might have a preference for red-fronted males.

tinkerbirds structure.jpg

The genetic analysis of these birds revealed high levels of introgression, as shown in this STRUCTURE plot. Individuals, represented as bars, with two colors (red and yellow) are not ‘pure’. This genetic sharing extends outside of the contact zone. From: Nwankwo et al. (2019) Biological Journal of the Linnean Society 

 

References

Gholamhosseini, A., Vardakis, M., Aliabadian, M., Nijman, V., & Vonk, R. (2013). Hybridization between sister taxa versus non-sister taxa: a case study in birds. Bird Study, 60(2):195-201.

Nwankwo, E.C., Mortega, K.G., Karageorgos, A., Ogolowa, B.O., Papagregoriou, G., Grether, G.F., Monadjem, A. & Kirschel, A.N.G. (2019). Rampant introgressive hybridization in Pogoniulus tinkerbirds (Piciformes: Lybiidae) despite millions of years of divergence. Biological Journal of the Linnean Society, 127(1):125-142.

Prager, E.M., & Wilson, A.C. (1975). Slow evolutionary loss of the potential for interspecific hybridization in birds: a manifestation of slow regulatory evolution. Proceedings of the National Academy of Sciences, 72(1):200-204.

Ross, G.J.B. (1970). The specific status and distribution of Pogoniulus pusillus (Dumont) and Pogoniulus chrysoconus (Temminck) in southern Africa. Ostrich, 41(3):200-204.

 

This paper has been added to the Piciformes page.

 

East or West? Different populations of Red-necked Phalaropes use distinct migration routes

A study using geolocators uncovered a migratory divide in this wader species.

Choosing a holiday destination can be a difficult choice: a lazy beach holiday on the Canary Islands or an adventurous trip to east Asia? Birds face a similar dilemma when they embark for their wintering grounds. Should they fly east or west? In some species, different individuals use different migration routes. A classical example is the Blackcap (Sylvia atricapilla) in Central Europe: one part of the population migrates to the southeast, while the other part prefers the southwest. This phenomenon is known as a migratory divide. A recent study in the journal Frontiers in Ecology and Evolution uncovered a similar pattern in the Red-necked Phalarope (Phalaropus lobatus).

 

Two Migration Routes

An international team of scientists equipped several Red-necked Phalaropes from different populations with geolocators. The results showed two distinct migrations routes. Birds breeding in Scotland, Iceland and Greenland migrated to the west and wintered in the Pacific. Birds from Scandinavia, Finland and Russia, on the other hand, flew to the Arabian Sea in the east.

The birds that migrated west covered more distance (~10,000 km) compared to the birds that followed an eastern route (~6,000 km). This difference in migration distance is also reflected in their morphology. West-migrating birds had longer wings that were probably more pointed. This wing type is aerodynamically more efficient for longer migration.

phalarope migration.jpg

Geolocators uncovered different migration routes for different Red-necked Phalarope populations. From: van Bemmelen et al. (2019) Frontiers in Ecology and Evolution

 

More Differences

Once at the wintering grounds, the birds also behaved differently. Red-necked Phalaropes wintering in the Arabian Sea moved between several areas, while birds wintering at the Pacific Ocean remained roughly in the same area. What causes this difference remains to be investigated, but the distribution of food sources seems a plausible explanation.

 

Hybrids?

One aspect that the study did not address concerns possible interbreeding between the different migratory populations. In the Eurasian Blackcap, hybrids between populations with different migration routes head in an intermediate direction: straight to the south. This suggests a strong genetic component for migratory behavior. Whether the same is true for Red-necked Phalaropes is unknown, but I would love to find out…

Red-necked_phalarope_(6203370883).jpg

A Red-necked Phalarope at Blackwater National Wildlife Refuge (Maryland, USA) © U.S. Fish and Wildlife Service Headquarters | Wikimedia Commons

 

References

Helbig, A. J. (1991). SE‐and SW‐migrating Blackcap (Sylvia atricapilla) populations in Central Europe: Orientation of birds in the contact zone. Journal of Evolutionary Biology, 4(4):657-670.

Minias, P., Meissner, W., Włodarczyk, R., Ożarowska, A., Piasecka, A., Kaczmarek, K., & Janiszewski, T. (2015). Wing shape and migration in shorebirds: a comparative study. Ibis, 157(3):528-535.

van Bemmelen, R.S.A., Kolbeinsson, Y., Ramos, R., Gilg, O., Alves, J.A., Smith, M., Schekkerman, H., Lehikoinen, A., Petersen, I.K., Þórisson, B., Sokolov, A.A., Välimäki, K., van der Meer, T., Okill, J.D., Bolton, M., Moe, B., Hanssen, S.A., Bollache, L. Petersen, A., Thorstensen, S., González-Solís, J., Klaassen, R.H.G & Tulp, I. (2019). A migratory divide among red-necked phalaropes in the Western Palearctic reveals contrasting migration and wintering movement strategies. Frontiers in Ecology and Evolution, 7:86.

Island formation drove penguin evolution

Most penguin species orginated within the last 2 million years.

Penguins did not just waddle into existence. This iconic group of birds has a fossil record that extends back to as far as 60 million years, suggesting a rich evolutionary history. But when did the majority of living pengiun species – the so-called crown group – originate? A study from 2006 suggested that global cooling drove penguins out of Antarctica during the Eocene (56 to 34 million years ago). As Antarctica became covered with ice, the penguins expanded outwards and colonized several oceanic islands. A recent study in the journal Molecular Biology and Evolution questions this timeframe, living penguin species might be considerably younger.

 

Mitogenomes

Theresa Cole and her colleagues sequenced the entire mitochondrial genome of all extant penguin species and several recently extinct groups. Molecular clock analyses revealed that the penguin crown group originated during the Miocene (23 to 5 million years ago), which is earlier than previous estimated. Moreover, most penguin species arose during the past 2 million years.

Penguin phylogeny

The evolutionary history of penguins. The crown group originated during the Miocene while most extant species came to the scene within the last 2 million years. From: Cole et al. (2019) Molecular Biology and Evolution

 

Rockhoppers

An interesting observation is that penguin species on islands are consistently younger than the islands they inhabit. This led the researchers to propose that penguin speciation is tightly linked with island formation. For example, the divergence between Moseley’s Rockhopper Penguin (Eudyptes moseleyi) and two other Rockhopper species – E. chrysocome and E. filholi – dates back to between 2.7 and 1.2 million years ago. The island on which this species lives, Gough Island, emerged around 2.5 million years ago.

This scenario of island colonization is in line with the 2006 study in which the authors stated that “as Antarctica became ice-encrusted, modern penguins expanded via the circumpolar current to oceanic islands within the Antarctic Convergence, and later to the southern continents.” The timeframe, however, is a bit different.

Northern_Rockhopper_Penguin_on_Inaccessible_Island_(portrait)

Northern Rockhopper Penguin on Inaccessible Island © Brian Gratwicke | Flickr

References

Baker, A.J., Pereira, S.L., Haddrath, O.P., & Edge, K.A. (2005). Multiple gene evidence for expansion of extant penguins out of Antarctica due to global cooling. Proceedings of the Royal Society B: Biological Sciences, 273(1582):11-17.

Cole, T.L., Ksepka, D.T., Mitchell, K.J., Tennyson, A.J.D., Thomas, D.B., Pan, H., Zhang, G., Rawlence, N.J., Wood, J.R., Bover, P., Bouzat, J.L., Cooper, A., Fiddaman, S.R., Hart, T., Miller, G., Ryan, P.G., Shepherd, L.D., Wilmshurst, J.M. & Waters, J.M. (2019) Mitogenomes uncover extinct penguin taxa and reveal island formation as a key driver of speciation. Molecular Biology and Evolution, 36(4):784–797.

Oh My Gosh! The complicated taxonomy of the Northern Goshawk superspecies

How many allospecies are there within the Accipiter gentilis superspecies?

Birds of prey are often classified as “superspecies”. You might think that taxonomists do this because they consider these birds so cool. However, “superspecies” is a taxonomic term that refers to “monophyletic groups of allo- or semispecies that are less differentiated from one another than closely related species usually are. Allospecies are allopatric, while semispecies are connected by a stable hybrid zone.” I have written about the Common Buzzard (Buteo buteo) superspecies. A recent study in the Journal of  Zoological Systematics and Evolutionary Research focuses on another raptorial superspecies: the Northern Goshawk (Accipiter gentilis).

Accipiter_gentilis_by_Iosto_Doneddu.jpg

A Northern Goshawk with its prey. © Iosto Doneddu | CC BY-SA 2.0 | Flickr

 

Four Allospecies

The Northern Goshawk forms a superspecies with three other allospecies: the Black Sparrowhawk (A. melanoleucus), the Meyer’s Goshawk (A. meyerianus) and the Henst’s Goshawk (A. henstii). As you can deduce from the terminology, these four allospecies occur in different parts of the world. The Northern Goshawk is widely distributed across the Holarctic (i.e. Eurasia, North Africa and North America). You can find the Black Sparrowhawk in sub-Saharan Africa. The Henst’s Goshawk is confined to Madagascar and the Meyer’s Goshawk to New Guinea including its surrounding islands. The map below gives a nice overview of this superspecies’ distribution.

goshawk distribution.jpg

The distribution of the Accipiter gentilis superspecies. The Northern Goshawk (blue, orange, pink and yellow) occupies most of the Holarctic. The other three allospecies occur in sub-Saharan Africa (Black Sparrowhawk, light green), Madagascar (Henst’s Goshawk, dark green) and New Guinea (Meyer’s Goshawk, purple). From: Kunz et al. 2019 Journal of  Zoological Systematics and Evolutionary Research.

 

Holartic = Nearctic + Palearctic

Florian Kunz and his colleagues collected samples from these four allospecies, including all 10 recognized subspecies of the Northern Goshawk. Based on two mitochondrial genes – the control region and cytochrome b – they determined the relationships between these birds of prey.

The analyses revealed that the Northern Goshawk is not monophyletic. The different populations in this allospecies cannot be traced back to one common ancestor. Instead, the Northern Goshawk is comprised of two unrelated groups: one in the Nearctic (i.e. North America) and one in the Palearctic (i.e. Eurasia and North Africa). The Palearctic group is nested within Meyer’s Goshawk, while the Nearctic group represents a separate lineage.

goshawk phylogeny

The relationships between the different allospecies. Notice that Northern Goshawk is comprised of two unrelated groups: a Nearctic (dark blue) and a Palearctic lineage (orange). From: Kunz et al. 2019 Journal of  Zoological Systematics and Evolutionary Research.

 

Five Allospecies?

This result indicates that the taxonomy of this superspecies needs revision. The most plausible solution would be to split the Northern Goshawk into two allospecies. However, more research – based on nuclear DNA and morphology –  is needed to gain more insights into this superspecies. One thing is certain though, it will be super-interesting!

Black_Sparrowhawk_in_flight_x.jpg

Black Sparrowhawk in flight. © Oggmus | CC BY-SA 4.0 | Wikimedia Commons

 

References

Kunz, F., Gamauf, A., Zachos, F.E. & Haring, E. (2019) Mitochondrial phylogenetics of the goshawk Accipiter [gentilis] superspecies. Journal of  Zoological Systematics and Evolutionary Research, Early View.

The head of the finch: A small genetic region controls colour morphs in the Gouldian Finch

Two studies figured it out independently.

A rainbow painted on a bird. That seems a fitting description of the Gouldian Finch (Erythrura gouldiae). This small passerine is very popular among bird breeders and comes in a variety of colour morphs. In the wild, the two most common ones are the red and black head-colour morphs. A third orange morph occurs in very low frequency (less than 0.1%). What is the genetic basis of this diversity in head plumage?

color morphs gouldian

The three head morphs (orange, red and black) of Gouldian finches. © Sarah R. Pryke

 

An Inversion?

The observation that colour morphs also show distinct behaviours suggests that an inversion might be involved. An inversion is a region in the DNA that has been flipped around, linking several genes together (you can check out this blog post for more avian inversions). Perhaps this happened in the Gouldian Finch, capturing genes involved in plumage colour and behaviour in one chunk of DNA.

This seems like a reasonable hypothesis, but two recent studies independently show it is not the case. The two studies, which appeared in Nature Communications and Proceedings of the Royal Society B, both honed in on a small non-coding region on the Z-chromosome.

GWAS-finch.jpg

The difference between the colour morphs can be traced back to a small region on the Z-chromosome (in the circle). From: Kim et al. (2019) Nature Communications

 

Control Switch

This genomic region is about 72,000 base pairs long and lies within two genes: MOSC2 and FST. This intergenic location suggests that the region plays a regulatory role, controlling the expression levels of particular proteins. Matthew Toomey and his colleagues investigated the expression levels of the two neighbouring genes. But MOSC2 nor FST showed any differences between the colour morphs. The exact role of the candidate region remains to be determined.

expression-finch

The genes surrounding the candidate (FST and MOCS2) are not differentially expressed.  The green dots represent other genes that do show differential expression between the colour morphs. From: Toomey et al. (2018) Proceedings of the Royal Society B

 

Balancing Selection

Further analyses revealed that the genomes of the black and red colour morphs are very similar, except for the candidate region on the Z-chromosome. Kang-Wook Kim and his colleagues showed that this region is even more divergent between the colour morphs than it is between distinct species. This high level of divergence suggests that the colour morphs are being maintained by balancing selection.

Balancing selection refers “to a number of selective processes by which multiple alleles (different versions of a gene) are actively maintained in the gene pool of a population at frequencies larger than expected from genetic drift alone.” It is still unclear which processes are maintaining the different alleles. Here are some possible mechanisms.

Frequency-dependent selection. This mechanisms entails the situation in which selection depends on the frequency of a trait. Let’s say females prefer red-headed males (a reasonable assumption since Liverpool just made it to the Champions League final). When there are a lot of red-headed males, competition between them is fierce. This results in considerable stress and low reproductive output. Rare black-headed males benefit from this and increase in frequency. Until they are in the majority and the tables turn.

Sexual anatagonism. A genetic battle of the sexes can also explain the occurrence of different head morphs. Perhaps the genetic variant for a red head is beneficial in males but detrimental in females. This will prevent one colour morph from taking over the population, resulting in a balanced collection of head plumages.

800px-Erythrura_gouldiae_1849

A painting of two Gouldian Finches. © Marc Athanase Parfait Œillet Des Murs (1804-1878) | Wikimedia Commons

 

A Final Note on the Orange Morph

You might be wondering what happened to the orange morph in these studies. At the candidate region, these birds are identical to the red-headed birds, but they use a different pigment in their head plumage. This differential expression is controlled by a genetic region on another chromosome. If your Italian is good enough (mine isn’t), you can check this study: Pigmenti e sistematica degli uccelli.

 

References

Kim, K.W., Jackson, B.C., Zhang, H., Toews, D.P.L., Taylor, S.A., Greig, E.I., Lovette, I.J., Liu, M.M., Davison, A., Griffith, S.C., Zeng, K. & Burke, T. (2019). Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird. Nature Communications10:1852.

Toomey, M.B., Marques, C.I., Andrade, P., Araújo, P.M., Sabatino, S., Gazda, M.A., Afonso, S., Lopes, R.J., Corbo, J.C. & Carneiro, M. (2018). A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch. Proceedings of the Royal Society B, 285(1888):20181788.

 

 

Cartilaginous crosses: A short overview of hybridization in sharks and rays

duunnn dunnn… duuuunnnn duun… duuunnnnnnnn dun dun dun dun dun dun dun dun dun dun dunnnnnnnnnnn dunnnn

– Jaws theme song

Hybridization in birds is quite common. The latest estimate states that about 16 percent of all bird species has hybridized with at least one other species. In other animal groups, the incidence of hybridization is less clear. In cartilaginous fish (sharks and rays), for example, this process remains largely unstudied. There are several reasons for this gap in our knowledge: difficult sampling, morphological similarities and few molecular markers. However, more and more studies are documenting hybridization between species of cartilaginous fish. Let’s have a look at some recent studies.

 

From Dusky till …

The Galapagos Shark (Carcharhinus galapagensis) and Dusky Shark (C. obscurus) are morphologically very similar. The main features to tell them apart are the dorsal fin heights and the number of precaudal vertebrae. The Galapagos Shark has between 103 and 109 of these vertebrae, while the Dusky Shark has only 86 to 97. Genetically, however, they are more difficult to separate. A study based on mtDNA failed to distinguish them and even questioned their status as distinct species.

More recent work, using genome-wide data, contradicted this mitochondrial study and showed that Galapagos Shark and Dusky Shark are clearly separate species. In a first genomic study, Shannon Corrigan and her colleagues found evidence for historic hybridization, including the exchange of mtDNA (which can explain why the mitochondrial study could not differentiate between the species). A second genomic analysis by Diana Pazmiño and her colleagues indicated that hybridization is still ongoing. Gene flow is going in both directions, from Dusky till Dawn Galapagos and the other way around.

Carcharhinus_galapagensis_revillagigedo.jpg

A Galapagos Shark at the Revillagigedo Islands (Mexico). © Tam Warner Minton | Wikimedia Commons

 

Hammerheads and Blacktips

Similarly, using a genomic approach, Amanda Barker and her co-workers uncovered ongoing hybridization between Carolina Hammerhead (Sphyrna lewini) and Scalloped Hammerhead (S. gilberti). In a sample of more than 550 sharks, they found 10 first-generation hybrids and about 15 putative backcrosses. The presence of backcrosses indicates that hybrids are fertile. Interestingly, all hybrids possessed mtDNA from Carolina Hammerhead, indicating that introgression is sex-biased.

You can find another pair of shark species that are currently hybridizing in Australia. Here, Australian Blacktip Shark (Carcharhinus tilstoni) and Common Blacktip Shark (C. limbatus) are interbreeding. A study by Jess Morgan and others ran into a mismatch between mtDNA and species identification using morphological characters. This prompted them to sequence a species-specific nuclear gene. Analyses of this gene uncovered extensive hybridization.

Scalloped_hammerhead_cocos.jpg

A Scalloped Hammerhead off Cocos Island, Costa Rica. © Barry Peters | Wikimedia Commons

 

Everybody Loves Rays

Hybrids between rays have also been reported recently. An interesting case occurred in Paraguay where the construction of a hydroelectric dam in Itaipu in 1982 facilitated the invasion of Upper Paraná River by two species of freshwater stingray: Potamotrygon motoro and Potamotrygon falkneri. A first genetic study, using mtDNA and a set of microsatellites, found evidence for hybridization. These results were later confirmed with genomic data.

Finally, Stephen Donnellan and his co-workers discovered hybrids between Eastern Fiddler Ray (Trygonorrhina fasciata) and Southern Fiddler Ray (T. dumerilii) while they were investigating the taxonomic status of extremely rare Magpie Fiddler Ray (T. melaleuca). For those interested, the Magpie Fiddler Ray turned out to be a rare color variant of the Southern Fiddler Ray.

Trygonorrhina_fasciata_jervis_bay2.jpg

Eastern Fiddler Ray in Jervis Bay, New South Wales. © Rick Stuart-Smith / Reef life Survey | Wikimedia Commons

 

More to Come?

This short overview of hybridization in rays and sharks could just be the tip of the iceberg. As more genomic data floods in, fish biologists might discover more and more hybrids in the shallow waters, deep seas, and murky rivers.

 

References

Barker, A.M., Adams, D.H., Driggers, W.B., Frazier, B.S. & Portnoy, D.S. (2019) Hybridization between sympatric hammerhead sharks in the western North Atlantic Ocean. Biology Letters, 15(4):20190004.

Corrigan, S., Delser, P.M., Eddy, C., Duffy, C., Yang, L., Li, C., Chenhong, L., Bazinet, A.L., Mona, S. & Naylor, G.J.P. (2017). Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks. Molecular Phylogenetics and Evolution, 110:122-126.

Cruz, V.P., Vera, M., Mendonça, F.F., Pardo, B.G., Martinez, P., Oliveira, C., & Foresti, F. (2015). First identification of interspecies hybridization in the freshwater stingrays Potamotrygon motoro and P. falkneri (Myliobatiformes, Potamotrygonidae). Conservation Genetics, 16(1):241-245.

Cruz, V.P., Vera, M., Pardo, B.G., Taggart, J., Martinez, P., Oliveira, C., & Foresti, F. (2017). Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays. Molecular Ecology Resources, 17(3):550-556.

Donnellan, S.C., Foster, R., Junge, C., Huveneers, C., Rogers, P., Kilian, A., & Bertozzi, T. (2015). Fiddling with the proof: the Magpie Fiddler Ray is a colour pattern variant of the common Southern Fiddler Ray (Rhinobatidae: Trygonorrhina). Zootaxa, 3981(3):367-384.

Morgan, J.A., Harry, A.V., Welch, D.J., Street, R., White, J., Geraghty, P.T., Macbeth, W.G., Tobin, A., Simpfendorfer, C.A. & Ovenden, J.R. (2012). Detection of interspecies hybridisation in Chondrichthyes: hybrids and hybrid offspring between Australian (Carcharhinus tilstoni) and common (C. limbatus) blacktip shark found in an Australian fishery. Conservation Genetics, 13(2):455-463.

Naylor, G.J.P., Caira, J.N., Jensen, K., Rosana, K.A.M., White, W.T. & Last, P.R. (2012) A DNA sequence-based approach to the identification of shark and ray species and its implications for global elasmobranch diversity and parasitology. Bulletin of the American Museum of Natural History, 367:1-262.

Pazmiño, D.A., van Herwerden, L., Simpfendorfer, C.A., Junge, C., Donnellan, S.C., Mauricio Hoyos-Padilla, E., Duffy, C.A.J., Huveneers, C., Gillanders, B.M., Butcher, P.A. & Maes G.E. (2019) Introgressive hybridisation between two widespread sharks in the east Pacific region. Molecular Phylogenetics and Evolution, 136:119-217.

 

 

The evolution of bird coloration: Exploring the complex interplay between natural and sexual selection

Which evolutionary force is more important: natural or sexual selection?

Charles Darwin and Alfred Russel Wallace independently hit upon the idea of evolution through natural selection. They did, however, disagree on some aspects of the theory. For instance, Wallace stated that human evolution is vastly different from the way animals evolve. He even ventured into spiritualism to explain the human mind. Darwin, on the other hand, saw humans as just another branch on the primate tree. Another main disagreement concerns the evolution of animal coloration. Darwin considered dull colors as the default and called upon sexual selection to explain conspicuous colors, while Wallace viewed showy colors as the default and argued that natural selection favors dull colors to improve camouflage. Two recent studies indicate that both men had a valid point (at least when it comes to the evolution of animal coloration).

 

Fifty Shades of Brown

The Furnariida, a group of more than 600 species of Neotropical birds, can best be described as dull. The title of an Evolution paper by Rafael Marcondes and Robb Brumfield captures the plumage diversity in this bird group nicely: “Fifty shades of brown”. But what is driving the evolution of these different shades of brown? To answer this question, Marcondes and Brumfield compared color data from 3096 museum specimens and reconstructed the evolutionary history of the Furnariida.

The macro-evolutionary analyses revealed that birds tend to be darker in darker habitats. This findings indicates that natural selection for camouflage is the main evolutionary force driving plumage coloration in this bird group. There was no difference in the speed of plumage evolution between males and females, suggesting that sexual selection (which usually speeds up the evolution of male traits) is not involved here.

Dendroplex_picus_-_Straight-billed_Woodcreeper.JPG

A dull member of the Furnariida, the Straight-billed Woodcreeper (Dendroplex picus). © Hector Bottai | Wikimedia Commons

 

Red-shifted Evolution

The evolutionary pattern in the Furnariida could not be more different from that in the colorful Tyrannida. Christopher Cooney and his colleagues explored the evolution of plumage coloration in this large radiation of songbirds. Their study, published in the journal Nature Communications, shows faster evolution of plumage coloration in males compared to females. This pattern points to sexual selection as the main driver.

In addition, evolution tended to be fastest when red and yellow plumage was involved. These colors are based on carotenoids, the yellow, orange, and red organic pigments that are produced by plants. Birds acquire these pigments through their diet. Previous work has shown that carotenoid-based colors are good signals of individual quality. So, females can use these colors to select the best male.

Purple-throated_Fruitcrow_RWD.jpg

The bright red throat patch of a Purple-throated Fruitcrow (Querula purpurata) has probably been under strong selection. © Dick Daniels | Wikimedia Commons

 

Plumage Patches

Although both studies found different evolutionary forces driving plumage coloration, they did converge on a common theme, namely variation in evolutionary rates of different plumage patches. In the Furnariida, evolution was more rapid in ventral plumage coloration compared to dorsal feathers. This differences could be due to social selection in which the birds use these patches in sexual signalling. Similarly, in the Tyrannida, plumage patches involved in signalling (e.g., crown, throat, breast) showed faster rates of evolution.

A logical next step will thus be to study the evolution of distinct plumage patches. It seems that both Darwin and Wallace had a point. The evolution of animal coloration is probably the outcome of sexual and natural selection on particular plumage patches.

 

References

Cooney, C.R., Varley, Z.K., Nouri, L.O., Moody, C.J.A., Jardine, M.D. & Thomas, G.H. (2019) Sexual selection predicts the rate and direction of colour divergence in a large avian radiation. Nature Communications, 10:1773.

Marcondes, R.S. & Brumfield, R.T. (2019) Fifty shades of brown: Macroevolution of plumage brightness in the furnariida, a large clade of drab neotropical passerines. Evolution, 73(4):704-719.

Weaver, R.J., Santos, E.S.A., Tucker, A.M., Wilson, A.E. & Hill, G.E. (2018) Carotenoid metabolism strengthens the link between feather coloration and individual quality. Nature Communications, 9:73.

How to turn a Carrion Crow into a Hooded Crow (and vice versa)?

It might be as simple as flipping a genetic switch.

One of the most famous and well-studied avian hybrid zones runs across central Europe. Here, Carrion Crow (Cornix corone) and Hooded Crow (C. cornix) come into contact and interbreed. Hybridization is limited due to differences in plumage. The all-black Carrion Crows and the grey-coated Hooded Crows prefer to mate with birds of the same plumage type (i.e. they mate assortatively). Despite the clear differences in plumage, these species are genetically almost identical. Previous work uncovered just a few genomic regions that are differentiated, representing less than 1 percent of the genome. This begs the question: what do these genomic regions actually do? Two recent studies provide the first clues into this mystery.

Carrion_Crow_(Corvus_corone)_(4).JPG

The all-black Carrion Crow © Ken Billington | Wikimedia Commons

 

Three Regions

To pinpoint the genes underlying a particular trait, biologists often resort to an approach called genome-wide association (GWA) mapping. This method indicates which genetic variants are most strongly associated with a certain trait, in this case plumage color. Based on a dataset of more than 400 individuals, Ulrich Knief, Christen Bossu and their colleagues found three genomic regions. A big region – spanning 2,800,000 base pairs – on chromosome 18 and two smaller regions on chromosomes 1 and 1A. Interestingly, these regions also popped up in previous work looking for differentiation.

Crow_GWAS.jpg

The genetic variants (red dots) associated with plumage color in crows fall into three main regions: two small regions on chromosome 1 and 1A, and a big region on chromosome 18. From: Knief et al. 2019 Nature Ecology & Evolution.

The genetic variant on chromosome 1A lies within the gene LRP6, whereas the region on chromosome 1 holds two interesting genes: NDP and EFHC2. These names probably do not ring a bell. Although you might have heard of NDP, because I have written about it before. This gene is responsible for the plumage patterns in pigeons. And it might also explain the difference between a Carrion and a Hooded Crow. The big region on chromosome 18 contains 88 genes. It is thus difficult to pinpoint the exact genes responsible for the plumage differences.

 

Genetic Switch

And then there is the transcription factor MITF. For readers not familiar with molecular biology, a transcription factor is a protein that controls the activity patterns of other genes. A kind of genetic control switch. If MITF is important in the regulation of plumage color, you would expect it to show increased activity during the formation of feathers.

Previous work failed to find support for the idea that MITF is a crucial genetic switch. The reason for this could be that MITF has multiple roles during development and is active in multiple cell types. The solution to this issue is to quantify the activity of MITF on a single cell level. And that is exactly what Chi-Chih Wu and his colleagues did. They managed to quantify gene expression in melanocytes – the cells producing the pigment – and show that MITF is indeed activated in these cells.

So, MITF seems to be key regulator in the development of plumage color. A few weeks ago, I met Jochen Wolf in Uppsala. He has been the driving force behind unraveling the mechanisms at work in the crow hybrid zone. At one point during our chat, he said: “Turning a Carrion Crow into a Hooded Crow? It could be as simple as flipping a switch!”

Bonte_Kraai_(24671438290).jpg

The grey-coated Hooded Crow © Kees Torn | Wikimedia Commons

 

References

Knief, U., Bossu, C.M., Saino, N., Hansson, B., Poelstra, J., Vijay, N., Weissensteiner, M. & Wolf, J.B.W. (2019) Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone. Nature Ecology & Evolution, 3:570-576.

Wu, C., Klaesson, A., Buskas, J., Ranefall, P., Mirzazadeh, R., Söderberg, O. & Wolf, J.B.W. (2019) In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation. The Journal of Experimental Biology, 222: jeb194431.

 

These papers have been added to the Corvidae page.