Are Snow Bunting and McKay’s Bunting different species?

A genetic study explores the demographic history of these white passerines.

The description of McKay’s Bunting (Plectrophenax hyperboreus) on Wikipedia reads: “This species closely resembles Snow Bunting (P. nivalis) in all plumages, but is whiter overall.” The close resemblance of these passerine species makes you wonder if they are not different morphs of the same species. A recent study in the journal PeerJ explored the species status of these birds using genetic techniques.

 

High Latitude Birds

Kevin Winker (University of Alaska) and his colleagues studied population genomics of Snow Bunting and McKays Bunting, using ultraconserved elements (UCEs). I will discuss these molecular makers below, but let’s first take a closer look at these buntings. McKay’s Buntings breed on remote islands in the Bering Sea, while Snow Buntings are found throughout the rest of the Holarctic at high latitudes. Previous work suggests that they diverged during the last glacial maximum, about 18,000 to 74,000 years ago.

snow bunting

A Snow Bunting (from: http://www.allaboutbirds.com/)

 

Gene Flow

The researchers tested different demographic models and checked which model fits their genetic data. In the end, the best model indicated a scenario of divergence-with-gene-flow. So, over time these birds became different while still exchanging some genes. In fact, possible hybrids have been reported relatively recently (see for example Sealy 1969), so the gene flow might still be ongoing.

But are they different species? Although they are genetically different, they still share a large amount of genetic variation. The genetic markers used in this study revealed no fixed differences. The researchers think that “given phenotypic differences between the taxa, it seems likely that there are fixed allelic differences in portions of the genome not included in our data.” More genomic analyses are needed to sort out the species question.

mckays bunting

A McKay’s Bunting (from: http://www.birdsna.com/)

 

Ultraconserved Elements

As mentioned above, this study used ultraconserved elements or UCEs. These conserved sequences are shared among divergent animal genomes and are probably involved in controlling gene expression. They have mostly been used to uncover evolutionary relationships at deeper levels, but this study shows that they can also be applied to population genomic questions.

The results obtained using UCEs are different from a previous study that relied on mtDNA and AFLPs (Amplification Fragment Length Polymorphism). Specifically, effective population sizes were lower, divergence was deeper (about 241,000 years) and gene flow levels were lower. These discrepancies are probably due to the differences in effective population sizes of mtDNA and UCEs. Moreover, these markers are subject to quite different selection regimes. Good to keep in mind for further analyses.

 

References

Winker, K., Glenn, T.C., Faircloth, B.C. (2018) Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event. PeerJ 6:e5735.

 

The paper has been added to the Calcariidae page.

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How healthy are juvenile eagle hybrids?

Study of feathers reveals nutritional status of hybrid and pure eagles.

“The available evidence contradicts the assumption that hybridization plays a major
evolutionary role [in animal evolution].” These are the words of biologist Ernst Mayr. At the time of writing (1963, in his book Animal Species and Evolution), he had a point.  Animal hybrids were rarely observed and often turned out to be sterile. These observations led to the idea that hybrids are generally less fit compared to “pure” species. But is this really the case? A recent study in the Journal of Raptor Research assessed this claim for two hybridizing eagle species.

greater_spooted_eagle_707copy_copy

A Greater Spotted Eagle (from: http://www.hbw.com/)

 

Eastern Poland

Hybrids between Greater Spotted Eagle (Clanga clanga) and Lesser Spotted Eagle (C. pomarina) have been reported for over 150 years. For the past 30 years, researchers studied the breeding populations of these species in Eastern Poland. They discovered a substantial amount of mixed pairs. In fact, the proportion of broods producing hybrids increased by over 30% between 1996 and 2012. Hybrids seem to be doing quite well, but are they faring better than their “pure” counterparts?

 

Ptilochronology

To quantify the fitness of the birds, Gregorz Maciorowski and his colleagues relied on ptilochronology. This technique is based on the assumption that each growth bar on a feather represents a 24 hour period. The width of the growth bar is determined by amount of energy and nutrients invested during the growth process. So, the width of the growth bar indicates the nutritional status of an individual bird. The researchers also checked the feather for fault bars. These transparent bands are produced in times of stress.

sedge_warbler

The fault bars on the tail of a Sedge Warbler (from: http://www.birdguides.com/)

 

Water Regime

The feathers from nestlings of 54 Lesser Spotted Eagles, 42 Greater Spotted Eagles and 23 hybrids were compared.  There were no significant differences in the number of fault bars or the average width of growth bars. Hence, there seems to be no difference in nutritional status between the hybrid and the “pure” nestlings.

The researchers noticed a large number of fault bars, suggesting that the nestlings experienced stress. This could be due to the extreme environmental fluctuations in the Biebrza River valley. Variability in water levels could negatively affect the eagles because changing water levels may result in lower prey availability or less suitable foraging areas. How these changes will impact on the hybridization dynamics remains to be investigated.

lesser

A Lesser Spotted Eagle (from http://www.wikipedia.com/)

 

References

Maciorowksi, G., Yosef, R., Väli, Ü & Tryjankowski, P. (2018) Nutritional Condition of Hybrid Nestlings Is Similar To That of Pure-Species Offspring of Spotted Eagles (Clanga clanga x C. pomarina).  Journal of Raptor Research 52(4):484-490.

 

This paper has been added to the Accipitriformes page.

Why do different populations of the Greenish Warbler sing other songs?

The dynamics of sexual selection revealed by the songs of the Greenish Warbler.

Males fight and females choose. That is sexual selection in a nutshell. Charles Darwin called upon sexual selection to explain certain phenomena that didn’t make sense in a natural selection context. For example, why did the peacock have such an elaborate tail? This would make it an easy target for predators. Unless something else is going on. What if females prefer males with long tails? Birds that manage to survive with such cumbersome tails should be amazing partners. In addition, sexual selection also clarified other exaggerated male traits, such as the big antlers of red deer. These over-sized hatstands come in handy when fighting off male rivals in the conquest for females. Darwin explored sexual selection in his book The Descent of Man, and Selection in Relation to Sex and the concept is still widely studied by evolutionary biologists.

Sexual selection.jpg

The peacock’s tail and the red deer’s antlers. Textbook examples of sexual selection.

 

Two Sides of the Sexual Selection Coin

Female choice and male competition are two sides of the same coin. But these two processes do not always act in concert. Let’s explore a hypothetical example. Females might prefer males with long, colorful tails. In order to maintain their beautiful tails, males need high quality habitats with plenty of food. To defend their habitats males will have to fight off competitors, for example by chasing away intruders. But flying around your territory is much easier with a shorter tail. So, female choice selects for longer tails and male competition selects for shorter ones. What will be the outcome of this conflict?

A similar conflict is also apparent in bird song. In many species, females choose males with long, complex songs. But males need to produce short, simple songs to defend their territories. Elizabeth Scordato explored this conundrum in the Greenish Warbler (Phylloscopus trochiloides) and recently reported her results in the journal Evolution.

 

Three Populations

The Greenish Warbler consists of a chain populations around the Tibetan plateau. The ends of this chain meet in Siberia where the birds from both sides are reproductively isolated. A nice example of a ring species (but see Alcaide et al., 2014). The ecological conditions along this chain vary: in the southern populations density is high and food is scarce, while the northern populations are less densely populated and have abundant food. Could these ecological conditions have an impact on the songs of these birds? To answer this question, Elizabeth Scordato studied populations in India, Kyrgyzstan and Siberia.

greenish warbler.jpg

A Greenish Warbler (from: http://www.wikipedia.com/)

 

Population Density and Song Length

In all populations, females preferred males with longer, more complex songs and large repertoires. However, males in the south (India) sang shorter songs compared to males in the north (Kyrgyzstan and Siberia). This latitudinal pattern reflects the degree of male competition. In the south, population density is higher, leading to more interactions between the males and consequently strong selection for shorter songs. In the north, competition between males is weaker and there is a stronger selection by females for longer, complex songs.

explanation_scordato

A graphic showing how population density influences the conflict between male competition and female choice, culminating in different songs. (Drawings from Handbook of Birds of the World and sonograms from Scordato, 2018 Evolution)

 

Resolving Conflict

There is clearly a conflict between female choice (long songs) and male competition (short songs) here. So, how do males cope with this situation? First, they adjust their song depending on the time of the year. Early in the season, when birds establish their territories, they sing short songs. When females are fertile, males produce longer songs. Later on, after most females have mated, males switch back to shorter songs. The figure below shows this pattern in the three populations.

scordati.jpg

Males sing longer songs when female are fertile (grey area in the graph). The pattern holds for the three populations. (from: Scordato, 2018 Evolution)

Another strategy that the males used to resolve the conflict between female choice and male competition was to aim particular components of the song at different receivers. Short, simple songs were directed towards competing males, whereas long, complex songs were sang to attract females. The analyses suggested that not only song length, but also repertoire size was subject to female choice. Males with a larger repertoire had a higher pairing success and fostered larger chicks. By contrast, competing males were not really impressed by the repertoire of their rivals.

 

Speciation

All in all, this study shows how the strength of male competition can influence the degree of female choice. In populations with weak competition between males, birds can produce longer songs, displaying their large repertoire. The distinct selective pressures in the different populations result in song divergence and might ultimately contribute to the origin of new species.

 

References

Scordato, E. (2018) Male competition drives song divergence along an ecological gradient in an avian ring species. Evolution 72(11):2360-2377.

 

The paper has been added to the Phylloscopidae page.

Unraveling the history (or histories?) of the Red-bellied Woodpecker

Reconstructing the history of the Red-bellied Woodpecker.

Florida is not only a popular holiday destination, it also houses a famous suture zone. What is a suture zone, you ask? It is a term from phylogeography, the study of the historical processes that culminated in the present distributions of organisms. In 1968, Remington defined a suture zone as “a band of geographic overlap between major biotic assemblages, including some pairs of species or semispecies which hybridize in the zone.” In other words, it is a region that houses numerous contact zones between various organisms.

suture zones

The expansion from Pleistocene refugia (indicated by the letters) let to the formation of numerous secondary contact zones. Regions where multiple contact zones cluster are called suture zones (from: Swenson & Howard 2005 The American Naturalist)

 

Ice Age Legacy

Suture zones are the outcome of post-Pleistocene expansion. During the Pleistocene, most of North America was covered with ice sheets, pushing animals and plants into southern refugia. Once the ice sheets melted, the organisms expanded from their refugia and recolonized North America. In this process, populations from different refugia came into secondary contact (I have written about this before, see here and here). As a consequence, populations on both sides of the contact zone are genetically differentiated.

Avian examples include Carolina Chicadee (Poecile carolinensis) and Barred Owl (Strix varia). Another putative instance of this scenario is the Red-bellied Woodpecker (Melanerpes carolinus). A recent study in The Wilson Journal of Ornithology investigated whether this species conforms to the expected pattern.

red-bellied woodpecker.jpg

A Red-bellied Woodpecker (from: http://www.allaboutbirds.com/)

 

Different Histories

George Barrowclough (American Museum of Natural History) and his colleagues collected samples from across the range of the Red-bellied Woodpecker. Analyses of the mitochondrial gene ND2 revealed striking patterns. Populations outside of Florida housed one common genetic variant (or haplotype) and a few uncommon ones. This genetic distribution indicates an expanding population. Statistical tests, such as Fu’s Fs, supported this conclusion. Populations in Florida, by contrast, showed little genetic variation and tested negative for population expansion.

The authors state that “these alternate haplotype frequencies and associated demographies suggest that the populations have had separate evolutionary histories and are now in secondary contact in a well-known suture zone.”

 

Plumage Patterns

The genetic results are supported by morphological data. The researchers examined 204 adult males. Each individual was scored for the presence or absence of a distinct tan-colored forehead band between the nostrils and the eyes. This plumage pattern is used to diagnose the subspecies perplexus, which occurs in Florida. Mapping the scores for this characteristic on a map revealed a gradual decrease of this band from south to north.

Taken together, the geographic patterns in mtDNA and plumage might lead to the recognition of the Florida populations as a separate species: the Florida Red-bellied Woodpecker. Another reason to book a holiday to Florida if you are an avid bird watcher.

woodpeckers

Specimens of the Florida subspecies perplexus (two on the left) and the nominate subspecies carolinus (two on the right). Notice the tan-colored forehead on the perplexus individuals (from Barrowclough et al. 2018, The Wilson Journal of Ornithology)

 

References

Barrowclough, G.F., Groth, J.G., Bramlett, E.K., Lai, J.E. & Mauck; W.M. (2018) Phylogeography and geographic variation in the Red-bellied Woodpecker (Melanerpes carolinus): characterization of mtDNA and plumage hybrid zones. The Wilson Journal of Ornithology, 130(3): 671-683.

 

This paper has been added to the Piciformes page.

Flipping DNA: The role of inversions in avian evolution

A short overview of chromosomal inversions and their effect on the ecology and evolution of birds.

The mating system of the Ruff (Calidris pugnax) is peculiar. Males come in three types: aggressive independents, submissive satellites and female-mimicing faeders. The independents, recognizable by their black or chestnut ruffs, hold territories where they hope to attract as many females as possible. The white-ruffed satellites don’t have their own territory, but sneak into the independents’ ranges, trying to mate with the visiting females. The faeders, finally, blend in with the females and copulate secretely. This complicated system is determined by a chromosomal inversion.

ruffs.jpg

The three ruff morphs: (left to right) faeder, satellite & territorial (from: https://www.flickr.com/photos/sfupamr/22674449779/in/photostream/)

 

Flipping DNA

What is an inversion? In essence, it is just a region in the DNA that has been flipped around. Compare it to reading part of a sentence from right to left:

SOME TEXT – THIS IS AN INVERSION – SOME MORE TEXT

SOME TEXT – NOISREVNI NA SI SIHT – SOME MORE TEXT

These inversions were discovered by Alfred Sturtevant in the 1920s when he was studying several Drosophila species. It was thought that most inversions are small. But recent genomic studies revealed that inversions can be huge, ranging from 130 kilobases (130 000 DNA letters) to 100 megabases (100 000 000 DNA letters). A recent paper by Maren Wellenreuther and Louis Bernatchez provides a nice overview of the ecological and evolutionary consequences of these big inversions. In this blog post, I will focus on the avian examples in that paper.

 

Mating Systems

In a 2016 Nature Genetics paper, Clemens Küpper and his colleages described the inversion that controls the mating system in the Ruff. It concerns a chunk of about 4.5 Mb, containing 125 genes, on chromosome 11. If a male carries two copies the ancestral (i.e. not inverted) genomic region, he will develop into an independent. One copy of the inversion results in a satellite or faeder male, depending on the genetic variants within the inversion. An individual with two copies of the inversion will die because of issues in cell division (for those interested in the details, one inversion breakpoint disrupts the CENP-N gene which is essential for mitotic centromere assembly).

A similar situation was described for the White-throated Sparrow (Zonotrichia albicollis). Here, a 100 Mb inversion with 1137 genes is associated with two plumage phenotypes, white-striped and tan-striped birds, that differ in territorial and parental behavior.  Interestingly, the white-striped birds almost exclusively mate with tan-striped birds, giving rise to four “sexes”.

white-throated-sparrows

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

 

Sperm speed

The inversions in the Ruff and the White-throated Sparrow result in clear phenotypes. Other avian cases are not so obvious. For example, in the Zebra Finch (Taeniopygia guttata) an inversion on the sex chromosome is related to sperm morphology. Birds with an ancestral and an inverted copy (i.e. heterozygotes) have the fastest sperm. Since it pays off to be heterozygous, selection preserves a balance between the ancestral and the inverted variant in the population. This finding was published in Nature Ecology & Evolution.

zebra finch.jpg

In Zebra Finches, an inversion explains variation in sperm speed (from: http://www.efinch.com/)

 

Migratory Inversions

Some time ago, I wrote about a study into the migratory behavior of the Willow Warbler (Phylloscopus trochilus) in Europe. One subspecies (P. t. trochilus) migrates to the southwest to wintering areas in West Africa, whereas the other subspecies (P. t. acredula) migrates in a southeastern direction to winter in Eastern and Southern Africa. Genomic analyses of these disparate migration strategies suggested that three genomic regions – on chromosomes 1, 3 and 5 – were involved. These regions are probably inversions.

willow warbler

A Willow Warbler (from http://www.naturespot.org.uk)

 

Speciation and Hybridization

The genetic characteristics of inversions suggest that they can play an important role in speciation. The flipping of DNA captures a host of genes that consequently behave as a kind of “supergene”. Divergent selection on such supergenes can result a barrier against hybridization. In hybrids, the ancestral and the inverted region might become incompatible, resulting hybrid sterility or inviability. Based on this scenario, you expect that species that live in the same area harbour more inversions than geographically isolated species, because the inversions “protect” the species against maladaptive hybridization. This prediction was recently confirmed by Daniel Hooper and Trevor Price.  Clearly, inversions are a crucial component in avian evolution. Something to keep an eye on.

 

References

Campagna, L. (2016) Supergenes: The Genomic Architecture of a Bird with Four Sexes. Current Biology, 16(3):R105-R107.

Hooper, D.M. & Price, T.D. (2017) Chromosomal inversion differences correlate with range overlap in passerine birds. Nature Ecology & Evolution, 1:1526–1534.

Kim, K.-W. (2017) A sex-linked supergene controls sperm morphology and swimming speed in a songbird. Nature Ecology & Evolution, 1:1168–1176.

Küpper, C. et al. (2016) A supergene determines highly divergent male reproductive morphs in the ruff. Nature Genetics, 48:79-83.

Lundberg, M. et al. (2017) Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks. Evolution Letters 1: 155-168.

Wellenreuther, M. & Bernatchez, L. (2018) Eco-Evolutionary Genomics of Chromosomal Inversions. Trends in Ecology & Evolution, 33(6):427-440.

φοβερο! Hybrid dolphins in the Greek Seas

Genetic study confirms hybridization between two dolphin species.

Bird hybrids – the main focus of this website –  are relatively easy to identify. Unusual plumage patterns and mixed songs can provide some clues. But what about less visible animals, such as dolphins and whales? Genomic analyses already revealed hybridization between several whale species (read my blog post about it here). A recent study in Molecular Phylogenetics and Evolution shows that hybridization also readily occurs in dolphins.

 

Mixed Groups

When you take a boat ride on the Greek Seas and explore the Gulf of Corinth – which separates the Peloponnese from mainland Greece – you might see some groups of dolphins composed of several species. Indeed, in this part of the Meditarrean three species of dolphins peacefully swim side by side: the striped dolphin (Stenella coeruleoalba), the short-beaked common dolphin (Delphinus delphis), and Risso’s Dolphin (Grampus griseus). These mixed associations provide the ideal circumstances for hybridization. But does it actually occur?

Delphinus_delphis_with_calf.jpg

A short-beaked common dolphin with calf (from: http://www.wikipedia.com/)

 

Intermediate Pigmentation

To answer this question, Aglaia Antoniou and her colleagues focused on two species: the striped dolphin and the short-beaked common dolphin. Individuals with intermediate pigmentation patterns have been reported, suggesting these species might be interbreeding. The researchers collected samples from 45 striped dolphins, 12 short-beaked common dolphin and 3 intermediates. Based on microsatellites and mitochondrial DNA (mtDNA), they went on their quest to find hybrids.

striped-dolphin-02

A striped dolphin jumping out of the water (from: http://fujairahwhales.com/)

 

Hybridization into the Future

The software package NEWHYBRIDS confirmed their suspicions: the intermediate morphs, along with 12 other individuals, were classified as hybrids. Moreover, two samples that were identified as short-beaked common dolphin contained mtDNA of the other species. Clearly, these dolphins are interbreeding.

In the future, hybridization might become more common. The population of short-beaked common dolphins is declining and these animals tend to associate with striped dolphins because of their tendency to stay in large groups. This behavior can affect the incidence of hybridization and pose a threat for the already endangered short-beaked common dolphin.

 

References

Antoniou, A., Frantzis, A., Alexiadou, P., Paschou, N. & Poulakakis, N. (2018) Evidence of introgressive hybridization between Stenella coeruleoalba and Delphinus delphis in the Greek Seas. Molecular Phylogenetics and Evolution, 129:325-337.

Genetic population structure of the Black-billed Gull, with a hint of Red-billed Gull

Genetic exchange between two gull species in New Zealand.

Gulls are practically anywhere, filling the skies with their screeching sounds. Their widespread occurrence suggests a lack of population structure. But is that really the case? A recent study in the journal Genes explored population structure in a gull species that is endemic to New Zealand, the Black-billed Gull (Larus bulleri).

black-billed gull.JPG

A Black-billed Gull (from: http://www.wikipedia.com/)

 

North and South Islands

New Zealand comprises two main landmasses, the North Island (Te Ika-a-Māui) and the South Island (Te Waipounamu), and about 600 smaller islands. Black-billed Gulls mainly occur on South Island, while approximately 1.6% of the population inhabits North Island. The colonies on the northern island are probably the result of a recent expansion. One of the colonies, Rotorua, was established in the 1930s.

Claudia Mischler (University of Otago) and her colleagues collected samples across the range of the Black-billed Gull and genetically characterized them with mitochondrial  (mtDNA) and nuclear markers (using a Genotyping by Sequencing – GBS – approach).

 

Hybridization

Analyses of the mtDNA showed two major groups without a geographical pattern. Individuals in the smaller group closely matched mtDNA of the Red-billed Gull (Chroicocephalus novaehollandiae scopulinus), suggesting that there has been genetic exchange between these two species. Indeed, Black-billed x Red-billed Gull hybrids have been reported before. Moreover, captive hybrids turned out to be fertile (see Gurr 1967).

red-billed gull

The study suggests introgression with red-billed gull (from: http://www.wikipedia.com/)

 

Management

In contrast to mtDNA , the nuclear markers revealed low, but significant, population structure. The authors write that ‘black-billed gulls are not panmictic across New Zealand, with gene flow primarily occurring in a stepwise system across the landscape.’ In addition, there was a clear difference between the populations on North Island and South Island. Possibly, these populations should be managed as separate units.

 

References

Mischler, C., Veale, A., van Stijn, T., Brauning, R., McEwan, J.C., Maloney, R. & Robertson, B.C. (2018) Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-billed Gulls (Larus bulleri). Genes 9, 544.

 

The paper has been added to the Charadriiformes page.

 

A hybrid between Black-browed Tit and Sooty Tit

Hybrid between Black-browed Tit and Sooty Tit caught on camera.

Going through your e-mails after a holiday can be a daunting task, but now and then you come across an exciting message. Tim Melling send me a picture of a hybrid between Black-browed Tit (A. bonvolati) and Sooty Tit (A. fuliginosus). Molecular studies have documented gene flow between these species, but records of actual hybrids are rare.

Aegithalos

Black-browed Tit and Sooty Tit

 

Above you can see the two species. Below is the hybrid: notice the combination of head patterns in the hybrid.

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The hybrid (picture courtesy of Tim Melling) https://www.flickr.com/photos/timmelling/46635694201/in/dateposted/