The hybrid genome of the Italian Sparrow: endless genetic variation?

The Italian Sparrow shows that hybrid genomes are variable, but with some important constraints.

Hybridization can create new species. Although this process is rare, there have been several well documented cases in birds (see a recent post). One of the best studied examples is the Italian Sparrow (Passer italiae), a cross between House Sparrow (P. domesticus) and Spanish Sparrow (P. hispaniolensis). You can read more about this hybrid species here and here.

An Italian Sparrow (from http://www.gobirding.eu)

 

Genomic Mixture

A closer look at the genome of the Italian Sparrow showed that it is indeed a mixture of both parental species. But how much is inherited from each parent? And how many hybrid combinations are possible? Do some genes come from only one parent or are the possibilities endless? These are exactly the questions that Anna Runemark and her colleagues tried to tackle in a recent Nature Ecology & Evolution paper.

Compare it with dealing a deck of cards. Each card is a specific genomic region. Black cards represent the House Sparrow and red cards the Spanish Sparrow.  The players receive cards from both colors. Some players end up with a winning hand, while some combinations of cards ensure a painful defeat.

 

Islands Populations

To compare such differently dealt hands, the researchers needed independent populations of Italian Sparrows. They also needed to be sure that there has been no sneaky exchange of cards. Or to put it in genetic terms: no gene flow. Luckily there are four such populations on the islands of Crete, Corsica, Malta and Sicily. The researchers sequenced birds from these islands and compared the genomes with their parental species.

The results showed that Italian Sparrows from Crete and Corsica received most of their DNA from the House Sparrow, while birds from Malta and Sicily resembled the Spanish Sparrow more. There is plenty of variation in the genomes of these hybrids, allowing them to adapt quickly to new environments. The authors state that “these results illustrate how selection in concert with the parental mosaic is able to form unique features in the genomes of hybrid populations.”

 

Constraints

Some genes, however, came exclusively from one parent. In my card analogy, this would correspond to a situation where you always receive a black queen, never a red one. There are thus some constraints on the formation of hybrid genomes: not all combinations are possible.

The genes that came from Spanish Sparrow affect external phenotypes, whereas the House Sparrow genes are involved in DNA-repair and functions related to the mitochondria (so-called mitonuclear genes). These genes might contribute to reproductive isolation between the Italian Sparrow and its parents.

A Spanish Sparrow (from http://www.hbw.com)

 

Z-chromosome

Interestingly, the genes that came exclusively from House Sparrow were mostly situated on the Z-chromosome (see here for more information on ZW sex determination in birds). This chromosome might be an important driver in the speciation process of the Italian Sparrow. However, the Z-chromosome is quite peculiar and we should be careful with drawing conclusions (see this excellent review by Darren Irwin).

As I have written before: the Italian Sparrow is a goldmine for geneticists!

 

References

Runemark, A., Trier, C.N., Eroukhmanoff, F., Hermansen, J.S., Matschiner, M., Ravinet, M., Elgvin, T.O. & Saetre, G.-P. (2018) Variation and constraints in hybrid genome formation. Nature Ecology & Evolution, 2:549-556.

 

The paper has been added to the Passeridae page.

Reader’s Hybrids: A Canada Goose x Greylag Goose in the UK

A hybrid goose in North Yorkshire (UK)

The posts on the Avian Hybrids Project have mostly featured summaries of scientific publications. But we should not forget that these publications would not be possible if people in the field are not reporting hybrids. Therefore, I decided to start a new series “Reader’s Hybrids” in which I post pictures of recent hybrid sightings. The first one to kick of the series is Gareth Jones, a conservation volunteer from the UK. Here are his pictures and accompanying text.

I am a conservation volunteer at the Nosterfield local nature reserve part of the Lower Ure Conservation Trust in North Yorkshire. I regularly visit the reserve as a birder and the morning on 9th April I saw an unusually marked goose. It was nearly a Canada Goose but the head markings were different. Rather the clear white bar it had a white circle on the cheek that faded at the edges into the dark coloured head. I asked around and it appears to be a Canada Goose x Greylag hybrid.

This observation reminds me of a report by Simon Delany from 1992 where they surveyed introduced geese in the UK: “No fewer than 18 types of hybrid between these species were found, mostly in very small numbers, but there were 261 Canada x Greylag Geese.”

Want to know more about goose (and other waterfowl) hybrids? Check out the Anseriformes page.

 

Feel free to send your hybrid observations to jente.ottenburghs[at]hotmail.com.

 

Don’t forget the hybrids! Antbird study shows that not taking into account hybridization leads to the wrong species tree

A study on Ash-breasted Antbird indicates that we should consider hybridization when estimating species trees.

Before the advent of genomic data, phylogenetics (i.e. the construction of evolutionary trees) was relatively simple: sequence your favorite gene, align the sequences and estimate the gene tree using the available algorithms. Then genomics came along. The explosive increase in the amount of genetic data revealed something terrifying: different genes result in different gene trees! This phenomenon – called gene tree discordance – can be caused by several biological processes, such as incomplete lineage sorting (ILS), hybridization and gene duplication. New methods needed to be developed to take this processes into account.

 

ILS for Dummies

Most methods focused on ILS, which occurs when lineages fail to coalesce in the ancestral population. Let me explain this process with an analogy. Imagine that three friends from Spain, Italy and Greece decide to go on holiday in Sweden. They each drive from their respective countries and agree to meet in Sweden. However, the friends from Spain and Italy will meet in France and then continue together to Sweden. This scenario (figure A) is comparable to the species tree, the expected pattern. Unfortunately, the friend from Italy gets lost and runs into his Greek friend in Germany. They decide to go to Sweden together. This scenario (figure B) can be seen as a gene tree that deviates from the species tree because two lineages (Spain and Italy) failed to coalesce in France.

An example of incomplete lineage sorting (ILS) based on a road trip. Scenario B (the gene tree) deviates from the expected pattern in Scenario A (the species tree).

Several methods have been developed to estimate the species tree from a collection of gene trees, taking some discordance into account (keeping in mind the lost Italians from my analogy). Hybridization, however, is not always considered. But this process can also complicate the estimation of a species tree. A recent study in Systematic Biology on the Ash-breasted Antbird (Myrmoborus lugubris) nicely illustrates this issue.

 

Hybridization

The Ash-breasted Antbird is passerine species that inhabits the floodplain forests along the Amazonian rivers. It is divided into four subspecies: lugubris, berlepschi, femininus and stictopterus. Gregory Thom and his colleagues collected morphological and genetic data on these birds. They uncovered a wide hybrid zone between femininus and lugubris.

Several species tree methods (that only consider ILS) clustered femininus and lugubris together as sister subspecies. However, other models (that take hybridization into account) revealed that these subspecies are not each others closed relatives. It turned out that femininus is sister to stictopterus. If the researchers had not considered gene flow in their models, they would have drawn the wrong conclusions.

An Ash-breasted Antbird (Myrmoborus lugubris) – from http://www.hwb.com/

 

Networks and Models

Based on these analyses, the authors recommend the use of phylogenetic networks and model-based approaches (such as fastsimcoal2 or Approximate Bayesian Computation). I provided the same advice in two review papers in The Auk and Avian Research. I hope other ornithologists will follow this line of reasoning: keep hybridization in mind when you are estimating species trees!

 

References

Thom, G., Raposo do Amaral, F., Hickerson, M.J., Aleixo, A., Araujo-Silva, L.E., Ribas, C.C., Choueri, E. & Miyaki, C.Y. (2018) Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Systematic Biology

Ottenburghs, J., Kraus, R.H.S, van Hooft, P., van Wieren, S.E., Ydenberg, R.C. & Prins, H.H.T. (2017). Avian Introgression in the Genomic Era. Avian Research. 8:30

Ottenburghs, J., van Hooft, P., van Wieren, S.E., Ydenberg, R.C. & Prins, H.H.T. (2016). Birds in a Bush: Towards an Avian Phylogenetic Network. The Auk. 133:577-582

 

This paper has been added to the Thamnophilidae page.

 

Are Wagtail subspecies supported by genetic data?

A phylogenetic perspective on the relationships between Wagtail species and subspecies.

Ornithologists love to delineate subspecies. One differently colored feather can already trigger a response in the most extreme splitters. But are subspecific divisions always supported by genetic data? Rebecca Harris and her colleagues test this idea for a bird group that has its fair share of subspecies: the Wagtails (genus Motacilla). The paper was published in Molecular Phylogenetics and Evolution.

 

Some Subspecies

There are 12 species of Wagtails, distributed across the Old World. Two species complexes have fallen prey to subspecific splitters: the Western Yellow Wagtail (M. flava) consists of 13 subspecies, while the White Wagtail (M. alba) “only” comprises 9 subspecies. Some time ago I wrote about hybridization between two White Wagtail subspecies (alba and personata, read all about it here).

An overview of the subspecies in White Wagtail (left) and Yellow Wagtail (right) – from http://www.rebzharris.com/research/wagtails/

 

An African Assembly

The researchers managed to collect samples from all 12 species and constructed the first time-calibrated species tree for this genus. Impressive work.

Let’s have a look at the phylogeny. In line with previous studies, they find an African and a Eurasian group. In the African group, we encounter Cape Wagtail (M. capensis), Mountain Wagtail (M. clara), Madagascan Wagtail (M. flaviventris) and Sao Tome Shorttail (M. bocagii). The latter species was previously thought to belong to the superfamily Sylvioidea, but turned out to be a Wagtail (members of the superfamily Passeroidea). This misclassification can be forgiven: who would have thought a short-tailed bird would be a wagtail?!

The Sao Tome Shorttail (M. bocagii) – from http://www.wikipedia.com/

 

Color-coded Clades

Now for the Eurasian group, which is subdivided according to plumage color: a black-and-white and a yellow clade. Alongside the White Wagtail, the black-and-white group contains African Wagtail (M. aguimp), Japanese Wagtail (M. grandis) and Mekong Wagtail (M. samveasnae). We can probably add Large Pied Wagtail (M. maderaspatensis) to this group, but the researchers did not manage to obtain SNP data for this species. The yellow clade houses three species: Western Yellow Wagtail , Grey Wagtail (M. cinerea) and Citrine Wagtail (M. citreola).

The phylogenetic tree I described above is based nuclear DNA. They also constructed a tree based solely on mitochondrial DNA, which is strongly incongruent and probably does not reflect the actual species tree. For example, Western Yellow Wagtail and Citrine Wagtail form a mixed group. This could be due to rapid speciation or hybridization. More research is needed to clarify this.

A Citrine Wagtail (M. citreola) – from http://www.hbw.com/

 

Genetic Subspecies?

Let’s return to the question I posed in the beginning: are the subspecific divisions of White Wagtail and Western Yellow Wagtail supported by genetic data? The short answer: no. The authors write that “the pronounced plumage differences among the many subspecies are not at all reflected in any of our genetic datasets. Instead, the only indications of genetic divergence are between geographical regions, each of which is home to two or more different-looking subspecies.”

So, we might be dealing with parallel evolution: different populations that develop similar plumage patterns independently. However, recent studies have shown that plumage differences can evolve rapidly in a few genomic regions without corresponding divergence in the rest of the genome (see here for a recent Avian Hybrids story on warbler coloration). Perhaps the same has happened in Wagtails.

A White Wagtail (M. alba) on a barbed wire – from http://www.hbw.com/)

 

References

Harris, R. B., Alström, P., Ödeen, A., & Leaché, A. D. (2018). Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla). Molecular phylogenetics and evolution, 120: 183-195.

Sorry I’m late. Less hybrid Flycatchers due to climate-driven changes in timing of breeding?

Pied and Collared Flycatchers adjust their breeding time differently to advancing springs, possibly leading to temporal isolation.

When you study speciation, there is no escaping from reproductive isolation. In order to understand how new species arise, you need to know what prevents them from interbreeding. There are several reproductive isolation mechanisms (see here for an overview), but in this post I will focus on temporal isolation. The rationale behind this particular mechanism is straightforward: members of different species cannot interbreed, because they reproduce at different times.

Classic cases of temporal isolation are plant species that flower at different times. A nice example in birds concerns the Madeiran Storm Petrel (Oceanodroma castro) which breeds on the Azores, Portugal. On some islands there are distinct populations that breed four to five months apart. These populations are diverging morphologically, they are probably on their way to become different species.

 

Flycatchers

A similar process might be unfolding on the Swedish Island of Öland where Collared Flycatcher (Ficedula albicollis) and Pied Flycatcher (F. hypoleuca) coexist. Päivi Sirkiä and her colleagues found that both species have advanced their timing of breeding in response to increasing spring temperatures. However, Pied Flycatchers showed a slower response compared to Collared Flycatchers. So, both species are now breeding at slightly different times. Is this the build-up of temporal isolation?

A Pied Flycatcher (Ficedula hypoleuca)

 

Caterpillars

The change in breeding times is driven by increasing spring temperatures that cause earlier development of leaves on deciduous trees and a consequent peak in caterpillar larvae. Intriguingly, the difference in breeding times between the two Flycatcher species is only apparent in low quality habitats. The researchers explain this result by fact that Pied Flycatchers have a broader diet than Collared Flycatchers, “making them less obliged to match their onset of breeding with the climate-driven seasonal advancement of the peak of larval abundance.”

 

Reinforcement

Even if temporal isolation only arises in low quality habitat, it might contribute to selection against hybridization (a process known as reinforcement). Because Flycatcher hybrids suffer from fertility problems, it makes sense to avoid hybridizing. In the end, climate-driven temporal isolation might lead to less hybrids.

 

A Collared Flycatcher (Ficedula albicollis)

 

References

Monteiro, L.R. & Furness, R.W. (1998) Speciation through temporal segregation of Madeiran storm petrel (Oceanodroma castro) populations in the Azores? Philosophical Transactions of the Royal Society B, 353(1371): 945-953.

Sirkiä, P.M., McFarlane, S.E., Jones, W., Wheatcroft, D., Ålund, M., Rybinski, J. & Qvarnström, A. (2018) Climate‐driven build‐up of temporal isolation within a recently formed avian hybrid zone. Evolution, 72(2): 363-374.

 

This paper has been added to the Muscicapidae page.

It’s not a tree, but a network! New insights into the evolution of baleen whales

The evolution of baleen whales was influenced by introgressive hybridization.

For some time I have been advocating the use of phylogenetic networks (see here). Due to processes such as hybridization and rapid speciation, it can be impossible to capture the evolutionary history of a certain clade in a strictly bifurcating tree. A recent study in Science Advances shows that this also holds for the largest mammals on this planet: whales. Ulfur Arnason (Lund University) and his colleagues write that “the evolution of rorquals can only be accurately understood by phylogenetic networks.” I couldn’t agree more!

Putting things into perspective: a diver and a blue whale (from https://ourplnt.com/)

 

Six Genomes

The study focuses on the rorqual family (Balaenopteridae) which includes the iconic blue whale (B. musculus). It just occurred to me that one of the smallest mammals, the house mouse (Mus musculus), has the same species name (musculus) as one of the biggest mammals on this planet. Is this some kind of taxonomic inside-joke? Anyhow…the researchers sequenced the genomes of six species, namely:

• Fin whale (Balaenoptera physalus)
• Blue whale (Balaenoptera musculus)
• Sei whale (Balaenoptera borealis)
• Mink whale (Balaenoptera acutorostrata)
• Gray whale (Eschrichtius robustus)
• Humpback whale (Megaptera novaeangliae)

As you might have noticed, the last two species belong to different genera. This classification is based on morphological characteristics, but is not supported by recent genetic studies. Indeed, also the current study finds that gray whale and humpback whale are embedded within the genus Balaenoptera. This indicates that – despite their divergent morphology – they should be reclassified into that genus.

The phylogeny of rorquals (from Arnason et al. 2018). Notice the position of gray whale and humpback whale within the genus Balaenoptera.

 

A Network

Apart from a tentative taxonomic turnover, the results showed a high degree of gene tree discordance (i.e. different genes showing different gene trees). Further analyses revealed that this incongruence is probably due to several hybridization events. For instance, there has been gene flow between the ancestors of blue/sei whale and fin/humpback whale. Hence, the evolution of whales is better represented by a phylogenetic network.

The evolution of whales is best depicted as a phylogenetic network (from Arnason et al. 2018)

 

Hybrid Whales

It might come as a surprise that whales hybridize. But it actually makes sense. First, the marine environment has no physical barriers, so whales are essentially sympatric. Second, rorquals have a very conserved karyotype with 22 pairs of chromosomes, which facilitates the production of fertile offspring. And finally, hybrid whales have been observed. In 1991, for example, scientists reported a hybrid between blue whale and fin whale.

But how can whales diversify in a homogeneous marine habitat while hybridizing? Killer whales (Orcinus orca) might provide a clue. These familiar animals are diversifying into specific ecotypes: a “transient” ecotype preying on mammals and a “resident” ecotype preying on fish. This ecological specialization drives sympatric speciation in killer whales. Something similar might have happened in rorquals.

Killer whales might provides clues on how whales diversify in a homogeneous marine environment (from: http://us.whales.org/)

 

References

Arnason et al. (2018) Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Science Advances, 4:eaap9873.

Foote et al. (2016) Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nature Communications, 7:11693.

Ottenburghs et al. (2016) Birds in a Bush: Towards an Avian Phylogenetic Network. The Auk, 133:577-582.

Spilliaert et al. (1991) Species Hybridization between a Female Blue Whale (Balaenoptera musculus) and a Male Fin Whale (B. physalus): Molecular and Morphological Documentation. Journal of Heredity,  82(4):269–274.

 

 

Two new hybrids for the checklist: an Australian Ibis and a South-American Brush Finch

Two recent studies describe new hybrid combinations.

Most scientific papers on avian hybridization try to answer particular questions. How often do these two species interbreed? Are the hybrids able to reproduce? Has there been introgression? But before you can start answering such questions, you need to know which species are hybridizing. So, it is important to describe newly discovered hybrids. And two recent studies do just that.

 

A Hybrid Ibis?

Let’s start by travelling to Australia. In the state of New South Wales, Corey Callaghan and his colleagues observed a possible hybrid between Australian White Ibis (Threskiornis moluccus) and Straw-necked Ibis (T. spinicollis). The plumage of this bird showed characteristics of both putative parental species. It is not the first time that this particular hybrid has been reported. In 1983, Disher described a similar bird, although he also considered the possibility that it was a bird with aberrant plumage. So, to be absolutely sure about the identity of this peculiar bird DNA analysis is probably necessary.

On the left, a possible hybrid between Australian White Ibis (Threskiornis moluccus) and Straw-necked Ibis (T. spinicollis). The bird on the right is a Straw-necked Ibis. – from Callaghan et al. (2017)

 

A Bizarre Brush finch

Now we cross the Pacific Ocean to pay a visit to South America, Colombia to be precise. Here, in the foothills of the Andes, Diego Carantón‑Ayala and his colleagues found a strange specimen of Brush-finch (genus Atlapetes). Was it a hybrid or an aberrant individual from a local species? To figure this out, the researchers applied several morphological and genetic analyses.

The genetic data suggested that it is a hybrid between White-naped Brush finch (Atlapetes albinucha) and Dusky-headed Brush finch (Atlapetes fuscoolivaceus). The mitochondrial DNA of the hybrid, which is only transmitted through the female lineage, clustered with Dusky-headed Brush finch, indicating that this was the female parent. The nuclear DNA, on the other hand, pointed to White-naped Brush finch as the father. The morphological characteristics of the hybrid were in line with this conclusion.

(A) White-naped Brush finch (Atlapetes albinucha), (B) the hybrid, and (C) Dusky-headed Brush finch (Atlapetes fuscoolivaceus). – from Diego Carantón‑Ayala et al. (2018).

 

References

Callaghan C., Ryall S. & Kingsford R. (2017) A probable Australian White Ibis Threskiornis moluccus × Straw-necked Ibis T. spinicollis hybrid. Australian Field Ornithology 34, 47-48.

Carantón‑Ayala D., Avendaño J.E., Cadena, C.D. (2018) Hybridization in brushfinches (Atlapetes , Emberizidae) from the southeast Andes of Colombia: a consequence of habitat disturbance? Journal of Ornithology

Disher, P. (1983). An unusual ibis. Bird Observer 620, 77.

 

The papers have been added to the Pelecaniformes and Emberizidae pages.