The genomics of being a raptor

Comparing the genomes of different birds of prey reveals the genetic basis of their predatory lifestyles.

This week, I managed to see a Great Grey Owl (Strix nebulosa). For several weeks, bird watchers reported this species in the Swedish nature reserve Hågadalen. On Monday, I took the bus from my office – the Evolutionary Biology Center in Uppsala – to this forest area. After a brisk walk, I arrived at the location and patiently waited. And sure enough, a few minutes later a Great Grey Owl flew over a meadow and landed on a wooden pole. While enjoying this bird, a second individual suddenly appeared around the corner. It soared past – just a few meters in front of me – holding a freshly killed rodent in its beak. This wonderful experience made me think about the evolutionary history of these magnificent birds. How has natural selection sculpted these deadly raptors? Luckily, several recent studies provided a genomic perspective to this question.

The Great Grey Owl © Olaf Oliviero Riemer | Wikimedia Commons

 

Birds of Prey

Before we dive into the genomics of raptor-hood, we need to understand that raptors are a mixed bunch. They are divided over three bird orders that are not closely related: Accipitriformes (hawks and eagles), Falconiformes (falcons) and Strigiformes (owls). In technical terms: raptors are polyphyletic (see this blog post for more information on these phyletic terms).

The polyphyletic nature of raptors is important to keep in mind when studying their evolution. Because they arose from different ancestors, some adaptations are probably the result of convergent evolution. However, by comparing the genomes of members from the three raptor orders, we can gain more insights into the large-scale genetic changes that accompany a predatory lifestyle. A recent study in the journal Genome Biology did just that. They compared the genomes of 20 birds of prey to understand the genomics of being a raptor.

Birds of prey are distributed over three orders: Strigiformes (purple), Accipitriformes (green) and Falconiformes (blue). A recent study compared the genomes of 20 species to understand the genetic underpinnings of being a raptor. From: Cho et al. (2019) Genome Biology

 

Gene Families

There are several ways to investigate the genomic background of certain traits. One way is to study the expansion and contraction of gene families. An expansion suggests that the genes are important for a particular trait, while a contraction indicates that the genes are not necessary. Yun Sung Cho and colleagues compared the sizes of gene families of birds of prey with other non-raptorial species. This comparison revealed that all three bird orders experienced an expansion in gene families associated with “sensory perception of sound, regulation of anatomical structure morphogenesis, postsynaptic density and specialization, and learning functions.” How these gene families relate to specific phenotypes remains to be investigated.

Next, the researchers turned to nocturnal species. They contrasted two night-active bird groups (owls and kiwis) with diurnal birds. This analysis showed that several vision-associated gene families contracted. Interestingly, all nocturnal birds seem to have lost the gene SWS1, a violet/ultraviolet sensitive protein. These birds have thus lost part of their color vision. These findings point to vision-related adaptations to a nocturnal lifestyle. But again, more research is needed to sort out the details.

An overview of the expanding and contracting gene families in the different bird orders. From: Cho et al. (2019) Genome Biology

 

Positive Selection

A second approach to identify the genetic basis of particular lifestyles is to search for genes under positive selection. Here, the widely used dN/dS-statistic comes into play. This statistic is based on the genetic code underlying the translation of genes into proteins. As you might remember from high school, a gene can be divided into codons: three-letter combinations that code for a particular amino acid. For instance, TCC codes for Serine while ACC gives you Threonine.

The genetic code has some redundancy, different codons result in the same amino acid. For example, TCT, TCC, TCA and TCG all correspond to Serine. This means that some mutations will not affect the amino acid sequence (e.g., if TCT mutates into TCC, you still have a Serine in the protein). These mutations are called synonymous mutations (dS). However, other mutations do change the amino acid sequence: When TCC turns into ACC, a Serine is replaced by a Threonine. These are non-synonymous mutations (dN).

Now that we know the difference between synonymous (dS) and non-synonymous mutations (dN), we can combine them. A synonymous mutation will not affect the functioning of a protein and can be considered neutral. A non-synonymous mutation, on the other hand, might change the way a protein works. If the protein improves the new mutation will be selected for and increase in frequency. A gene with more non-synonymous mutations (dN) than synonymous (dS) might thus be under positive selection. By calculating this ratio – dN/dS – for numerous genes, researchers can pinpoint putative positively selected genes.

The genetic code has some redundancy (i.e. several codons result in the same amino acid). We can use this information to find gene under positive selection.

 

Nocturnal Life

The analyses of the dN/dS-statistic resulted in a long list of positively selected genes. Let’s look at a few interesting owl-cases. In nocturnal birds, the researchers found several hearing-and vision-related under positive selection. For example, the gene ROH is positively selected in night-active birds. This gene encodes a rhodopsin that enables vision in low-light conditions. Another recent study in the journal Scientific Reports performed a similar analysis on the genome of the Oriental Scops Owl (Otus sunia) and discovered that the gene ALCAM is under positive selection. This gene is associated with retina development in owls. Detailed analyses revealed that ALCAM has two owl-specific mutations that possibly possibly enhances low-light sensitivity. It seems that natural selection has improved the nocturnal vision and other sensory systems in owls to compensate for the loss of color vision (i.e. loss of gene SWS1 mentioned above).

The Oriental Scops Owl © Rejaul karim.rk | Wikimedia Commons

 

Convergent Evolution

The identify of positively selected genes varied between the different bird orders. Only two genes are under positive selection in all three bird orders (RHCE and CENPQ), while other genes are restricted to only two orders (e.g., SFTPA1 in Strigiformes and Falconiformes; TFF2 and PARL in Strigiformes and Accipitriformes). This low number of shared genes suggests that the different raptor groups followed distinct genetic routes to their predatory lifestyles. Clearly, there are numerous genetic ways to be a raptor.

 

References

Cho, Y.S. et al. (2019) Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles. Genome Biology 20:181.

Zhou, C. et al. (2019). Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. Scientific reports, 9:2249.

A taxonomic riddle: Where does the extinct Canary Islands Oystercatcher fit in?

Which living species is the closest relative of this extinct species?

The Canary Islands used to have their very own Oystercatchers. Members of this species (Haematopus meadewaldoi) has glossy black plumage with the exception of white patches on the wings. It closely resembled the African Oystercatcher (H. moquini), but the exact taxonomic position of the Canary Islands Oystercatcher remained a mystery. Recently, Tereza Senfeld and her colleagues sequenced the DNA of several Canary Islands Oystercatchers and compared it with the extant species. Their findings appeared in the journal Ibis.

The Canary Islands Oystercatcher. Artwork by Henrik Gronvold (1858–1940) | Wikimedia Commons

 

Eight Specimens

Canary Islands Oystercatcher probably went extinct around 1940 (although it was officially declared extinct in 1994). The drivers of this extinction event are difficult to infer, but it was probably a combination of habitat disturbances and human activities (e.g., hunting by humans and predation by introduced rats and cats). Currently, there are eight specimens left: three at the Natural History Museum in Tring (UK), two at the Zoological Research Museum Alexander Koenig in Bonn (Germany), one at the Liverpool World Museum (UK) and two at the Manchester Museum (UK). The researchers managed to extract DNA from the specimens in Tring, Liverpool and Manchester.

 

Could the Canary Islands Oystercatcher be related to the Eurasian Oystercatcher? © Richard Bartz | Wikimedia Commons

 

Subspecies?

Analyses of several mitochondrial genes revealed that the Canary Islands Oystercatcher clustered with the Eurasian Oystercatcher (H. ostralegus). Despite its similarity to the African Oystercatcher, it is thus more closely related to the Eurasian Oystercatcher. The authors suggest that it might represent a local melanistic subspecies of the Eurasian Oystercatcher.

Another possibility is that the mitochondrial similarity between the Canary Islands and Eurasian Oystercatcher is due to hybridization. Perhaps the birds on the Canary Islands were an offshoot of the African Oystercatcher but obtained mitochondrial DNA after interbreeding with some visitors from Europe? Genomic analyses are needed to explore this scenario.

Based on mtDNA, the Canary Island Oystercatcher (H. meadewaldoi) clusters with the Eurasian Oystercatcher (H. ostralegus). From: Senfeld et al. (2019) Ibis

 

Mystery Bird

After figuring out the taxonomic position of the Canary Islands Oystercatcher, the researchers turned their attention to a mystery bird in the Tring collection. Specimen NMHUK.1938.11.15.1 was captured in Gambia in 1938. It was transported to the UK where it lived in captivity for several years. Due to artificial feeding, it developed an abnormally long beak. Beak morphology is an important trait to identify Oystercatcher species, so it became impossible to determine the species identity of this specimen. The black plumage of this bird suggests that it might be the last known Canary Islands Oystercatcher. However, DNA analyses showed that it concerns a vagrant African Oystercatcher, about 4500 kilometers outside of its range. Still a significant finding, but not as exciting as finding the last Canary Islands Oystercatcher. Perhaps it is still out there?

The mystery bird turned out to be a vagrant African Oystercatcher. © Dick Daniels | Wikimedia Commons

 

References

Senfeld, T., Shannon, T. J., van Grouw, H., Paijmans, D. M., Tavares, E. S., Baker, A. J., Lees, A. C. & Collinson, J. M. (2019). Taxonomic status of the extinct Canary Islands Oystercatcher Haematopus meadewaldoi. Ibis. Early View.

A lesson in cladistics with the Plain-brown Woodcreeper

Genetic study indicates that the Plain-brown Woodcreeper is paraphyletic.

Every taxonomist enjoys a nice monophyletic group. Paraphyletic or polyphyletic groupings are best avoided. But what do these terms actually mean? We owe this wonderful terminology to the German entomologist Willi Hennig who published the book Phylogenetic Systematics. This book introduced cladistics, a new method to classify organisms based on their morphological differences and similarities. Cladistics came with a whole suite of new tong-twisting term, such as symplesiomorphy and autapomorphy. But let’s focus on the phyletic terms for now.

 

Cladistics for Dummies

The evolutionary relationships between different organisms can be depicted in a cladogram. The endpoints of a cladogram – the twigs if you will – correspond to living species, whereas the nodes represent extinct ancestors. A group of organisms (several twigs) is called a clade. A monophyletic clade comprises an ancestor and all of its descendants. For instance, in figure a, species D, E, G and H can be traced back to a common ancestor B.

We could decided to cluster species E and G (see figure b), but then we would create a so-called polyphyletic group. These species originate from different ancestors (C and F) that are not included in the group. We could also cluster species J and K (see figure c), but now we ignore the many descendants of their common ancestor (A). The result is a paraphyletic group.

Examples of the different types of groupings in cladistics.

 

Fish do not exist

A famous example of a non-monophyletic group concerns fish. They share a common ancestor with all other vertebrates. By excluding these vertebrates from the fish-group, we are creating a group that does not include all descendants of this common ancestor. In other words, fish are paraphyletic. Technically, fish do not exist.

An example of a polyphyletic group can be found in the bible where birds and bats were grouped together: “These are the birds you are to regard as unclean and not eat because they are unclean: the eagle, the vulture, the black vulture, the red kite, any kind of black kite, any kind of raven, the horned owl, the screech owl, the gull, any kind of hawk, the little owl, the cormorant, the great owl, the white owl, the desert owl, the osprey, the stork, any kind of heron, the hoopoe and the bat (Leviticus 11:13-19).” A clear sign that the bible is not a science book…

Fish as paraphyletic and do technically not exist…

 

Woodcreepers

But let’s focus on birds (this is after all a blog about our feathered friends). A recent study in the journal Molecular Phylogenetics and Evolution reconstructed the evolutionary history of the Plain-brown Woodcreeper (Dendrocincla fuliginosa), which has been divided into 12 subspecies. Eduardo Schultz and his colleagues assessed the relationships between these subspecies using genetic data from over 200 individuals.

The Plain-brown Woodcreeper (Dendrocincla fuliginosa) © Gail Hampshire | Flickr

 

Non-monophyletic

The genetic analyses revealed that two other species are embedded with the Plain-brown Woodcreeper, namely the Tawny-winged Woodcreeper (D. anabatina) and the Plain-winged Woodcreeper (D. turdina). This phylogenetic result renders the Plain-brown Woodcreeper paraphyletic because it does not include all descendants of the common ancestor. A possible solution is to elevate some subspecies to the species level, creating several monophyletic groups.

The Plain-brown Woodcreeper is paraphyletic due to the position of the Tawny-winged Woodcreeper (D. anabatina, top) and the Plain-winged Woodcreeper (D. turdina, bottom). From: Schultz et al. (2019) Molecular Phylogenetics and Evolution

 

Hybrids

The study also mentioned some possible hybridization events. The observation of a individual of the subspecies rufoolivacea within the range of the subspecies fuliginosa suggests ongoing gene flow. But this will need to be confirmed with denser sampling in that region.

Interestingly, rufoolivacea is known to interbreed with another subspecies (atrirostris). The paper describing this situation speculated that the hybrid zone originated because Amazonian rivers (Tapajos and Teles-Pires) split an ancestral population in two (a so-called vicariant event). However, the current study indicates that rufoolivacea and atrirostris are not each others closest relatives, suggesting that they established secondary contact due to changes in their distribution. No need for a vicariant event.

 

References

Schultz, E. D., Pérez-Emán, J., Aleixo, A., Miyaki, C. Y., Brumfield, R. T., Cracraft, J., & Ribas, C. C. (2019). Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): Insights from broad geographic sampling. Molecular Phylogenetics and Evolution 140,106581.

Weir, J. T., Faccio, M. S., Pulido-Santacruz, P., Barrera-Guzman, A. O. & Aleixo, A. (2015). Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds. Evolution 69, 1823-1834.

Unraveling the origin of the Visorbearers

Did they originate by vicariant events or due to extinction of related lineages?

Hybrid hummingbirds are relatively common. Gary Graves has described numerous hybrid species combinations (see here for an overview). The widespread occurrence of hybridization – and possibly gene flow – complicates the taxonomic work on hummingbirds. In some cases, such as the Visorbearers (genus Augastes), the taxonomy is even complicated without hybridization. This genus houses two species: the Hyacinth Visorbearer (A. scutatus) and the Hooded Visorbearer (A. lumachella). They are probably closely related to the genus Schistes, but this remains to be confirmed. A recent study in the journal Ibis reconstructed the evolutionary history of the Visorbearers to settle this taxonomic issue.

The Hooded Visorbearer (Augastes lumachella) © Joao Quental | Flickr

 

Two Hypotheses

In addition to the mystery of the closest relative of the Visorbearers, their evolutionary history is still unclear. Two hypotheses have been put forward to explain the origin of these hummingbirds. Silva (1995) proposed that genus used to be widespread across South America, but that extinction of several ancestral lineages during the Pleistocene (less than 2 million years ago) resulted in the current two species. An alternative scenario was put forward by Vasconcelos and colleagues (2012): they envisioned that a barrier arose in Brazil, separating the two Augastes species.

The Hyacinth Visorbearer (Augastes scutatus) © Norton Defeis | Wikimedia Commons

 

Divergence Times

To figure out which scenario is more likely, Anderson Chaves and his colleagues sequenced several mitochondrial and nuclear genes to reconstruct the evolutionary history of the Visorbearers. The analyses confirmed the idea that these hummingbirds are closely related to the genus Schistes. Moreover, the researchers managed to date the divergence events: the genera Schistes and Augastes split about 7.34 million years ago, and the two Visorbearer species went their separate ways around 3.2 million years ago.

The latter divergence time is more consistent with the vicariance-hypothesis of Vasconcelos and colleagues. The timing corresponds to the uplift of the Brazilian plateau which may have resulted in distinct climatic conditions. The ancestral lineages probably adapted to the different climates and diverged into different species.

The phylogenetic relationships between Visorbearers (genus Augastes) and other hummingbirds. From: Chaves et al. (2019) Ibis

 

References

Chaves, A. V., Vasconcelos, M. F., Freitas, G. H., & Santos, F. R. (2019). Vicariant events in the montane hummingbird genera Augastes and Schistes in South America. Ibis. Early View.

Silva, J.M.C. 1995. Biogeographic analysis of the South American Cerrado avifauna. Steenstrupia 21: 49– 67.

Vasconcelos, M.F., Chaves, A.V. & Santos, F.R. 2012. First record of Augastes scutatus for Bahia refines the location of a purported barrier promoting speciation in the Espinhaço Range. Brazil. Rev. Bras. Ornitol. 20: 443– 446.

White-throated Sparrows influence gene expression in their offspring

Less parental care leads to an increased stress response in the nestlings.

Parents have a profound impact on the development of their offspring. In birds, the mother directly influences the condition of the offspring by adding particular hormones to the egg. Also, the location of the nest and the incubation schedules of the parents impact consequent egg development. Once the chicks crawl out of the egg, the feeding behavior of the parents determines the amount of stress the young birds experience. Not only will they have to compete with their siblings, they might also experience anxiety when left alone for too long. All in all, the parents cause a certain amount of stress on their offspring which affects their future development. A recent study in the journal Molecular Ecology investigated the effect of parental behavior on the stress experienced by young White-throated Sparrows (Zonotrichia albicollis).

An super-gene in the White-throated Sparrow genome results in two morphs: white-striped and tan-striped (from: https://www.northcountrypublicradio.org/).

 

Super-gene

The researchers choose White-throated Sparrows for a reason: these passerines show peculiar behavioral differences due to a genetic phenomenon. White-throated Sparrows come in two morphs: tan and white. These morphs are determined by a large super-gene (an inversion to be more specific, you can read more about it in this blog post). Tan morphs have the same version of the super-gene (i.e. they are homozygous) whereas white morphs have two different versions (i.e. they are heterozygous).

This super-gene contains more than 1000 genes that influence the morphology and behavior of the birds. White-morph males are promiscuous and provide little parental care. Tan-morph males, however, are great partners: they defend their nest and take care of their offspring. Compared to the male morphs, females typically provide intermediate care.

Interestingly, birds tend to prefer the opposite morph. This results in two pair types in terms of parental care. A white-morph male and a tan-morph female (W x T) will provide female-biased care. A tan-morph male and a white-morph female (T x W) will provide biparental care. Are you still with me?

The different morphs of the White-throated Sparrow (A and B) prefer to mate with the opposite morph (see percentages in C). The differences between the morphs can be traced back to a super-gene (D). From: Campagna (2016) Current Biology

 

Stress

Daniel Newhouse and his colleagues took advantage of this situation to explore the effects of differential parental care on the offspring. They focused on patterns of gene expression in 32 nestlings. The analyses revealed 881 genes that were differentially expressed between the pair types. Detailed analyses of these genes revealed that nestlings raised by W x T pairs (female-biased care) expressed more stress-related genes than nestlings raised by T x W pairs (biparental care).

This finding raises another question: which mechanism is responsible for the differences in genes expression? Do females of different morphs deposit different amounts of hormones in the eggs? Or does the parental care influence gene expression? The authors argue that “the difference in parental provisioning is the most plausible explanation.” But – as always – more research is needed to confirm this idea.

 

References

Campagna, L. (2016). Supergenes: the genomic architecture of a bird with four sexes. Current Biology, 26(3): R105-R107.

Newhouse, D. J., Barcelo-Serra, M., Tuttle, E. M., Gonser, R. A., & Balakrishnan, C. N. (2019). Parent and offspring genotypes influence gene expression in early life. Molecular Ecology, 28: 4166-4180.

Taking advantage of hybridization to find a migration gene in warblers

A genetic study of Golden-winged and Blue-winged Warbler reveals the gene underlying their migration direction.

Every evolutionary biologist dreams of finding that one gene underlying a particular trait under selection. For example, extensive work on the Threespine Stickleback (Gasterosteus aculeatus) uncovered the genetic basis of armor-plating: marine forms of this fish are heavily armored while lake populations are not (probably because of the absence of predators). Stickleback in lakes have repeatedly lost pelvic hindfins, which is due to recurrent deletions of a pelvic enhancer of the Pitx1 gene. Mostly, however, things are not that straightforward. Human height, for instance, is determined by numerous genes of small effect instead one single candidate gene. A recent study in the journal PNAS attempted to find the genetic basis of another complex trait: the direction of bird migration.

Looking for the genes underlying migration in the Golden-winged Warbler © Bettina Arrigoni | Wikimedia Commons

 

Genomic Regions

Several studies have tried to pinpoint the genes underlying migratory behavior in birds. In the Swainson’s Thrush (Catharus ustulatus), researchers found a region on chromosome 4 that is strongly associated with the direction of migration. And a study on the Willow Warbler (Phylloscopus trochilus) uncovered three genomic regions – on chromosomes 1, 3 and 5 – that corresponded to different migratory strategies (see also this blog post). In both cases, large genomic regions, containing hundreds of genes, were identified. Certainly a step in the right direction, but there is still a long way to go.

David Toews and his colleagues focused on another study system: the Golden-winged (Vermivora chrysoptera) and the Blue-winged Warbler (V. cyanoptera). These species were chosen for a reason: due to extensive hybridization, their genomes are largely undifferentiated (mainly “plumage genes” seem to be different). This lack of genetic differentiation makes it easier to find genes related to migration. Compare it to finding a needle in a very small haystack.

 

Z-chromosome

Both species breed in North America and winter in two particular regions: South America (mainly Venezuela) and Central America (Panama to Guatemala). By linking these migration strategies to genomic sequences, the researchers attempted to find the genetic basis of migration. And they did: the analyses converged on a small region (120,000 base pairs) on the Z-chromosome. This region showed reduced genetic diversity in warblers migrating to South America and Tajima’s D (a statistic to identify selective processes) was also much lower in these birds.

This region contained only one gene: VPS13A. The function of this gene in birds is not known, but recent work showed that it is associated with mitochondria. The researchers speculate that “selection on VPS13A may enhance the capacity in SA wintering birds to more efficiently remove reactive oxygen species resulting from a prolonged migration.”

The genomic region underlying migration direction in Golden-winged and Blue-winged Warbler. (A) The highly differentiated region on the Z-chromosome is highlighted with the arrow. (B) This region (marked in grey) has a low Tajima’s D (suggesting selection) and (C) contain one gene: VPS13A. From: Toews et al. (2019) PNAS.

 

Go Hybrids!

This study shows the importance of choosing the right study system to answer your research question. The undifferentiated genomes of these warblers provided the perfect background to find genes related to migration. And it also highlights the importance of hybrids: if Golden-winged and Blue-winged Warbler did not hybridize, their genomes might have been too diverged to easily find migration genes. Do not underestimate the power of hybridization!

 

References

Delmore, K. E., Toews, D. P., Germain, R. R., Owens, G. L., & Irwin, D. E. (2016). The genetics of seasonal migration and plumage color. Current Biology, 26(16), 2167-2173.

Lello, L., Avery, S. G., Tellier, L., Vazquez, A. I., de los Campos, G., & Hsu, S. D. (2018). Accurate genomic prediction of human height. Genetics, 210(2), 477-497.

Lundberg M, Liedvogel M, Larson K, Sigeman H, Grahn M, Wright A, Åkesson S, Bensch S 2017. Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks. Evolution Letters 1: 155-168.

Toews, D. P., Taylor, S. A., Streby, H. M., Kramer, G. R., & Lovette, I. J. (2019). Selection on VPS13A linked to migration in a songbird. Proceedings of the National Academy of Sciences, 116(37), 18272-18274.

Xie, K. T. et al. (2019). DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science, 363(6422), 81-84.