Trouble with the Tinkerbirds: Different subspecies sing the same song

Two genetically distinct subspecies of the Yellow-rumped Tinkerbird sing similar songs, suggesting hybridization.

 

Want to make a biologist stutter? Just ask him or her to define a species in one sentence. The species problem remains one of the most hotly debated questions in biology. Numerous species concepts have been proposed (Richard Mayden listed no less than 22 different concepts in 1997). Recently, taxonomy has become more pluralistic. Instead of focusing on one species concept, biologists compare different data sources, such as genetic markers, morphology and song characteristics. If all the data lead to the same conclusion, one can confidently draw lines between species. But what if some datasets disagree? For example, the three Redpoll species (genus Acanthis) are morphologically clearly distinct, but have largely undifferentiated genomes. Do you follow morphology (3 species) or genetics (1 species) here?

 

A Common Redpoll (Acanthis flammea) http://www.allaboutbirds.com/

 

Speciation

This kind of conundrum is to be expected, given the gradual nature of speciation. Kevin de Quieroz argues that different species concepts correspond to different stages of the speciation process. In some cases, populations might first diverge morphologically, later on followed by genetic divergence (such as the Redpolls). In other cases, it might be the other way around: genetically differentiated populations that look exactly the same (so-called cryptic species). The figure below gives an example of where different species concepts might arise during the origin of new species.

 

Different species concepts (SC) correspond to different stages during the speciation process (From: de Quieroz 2007).

 

Tinkerbirds

A recent study, published in Ecology and Evolution, reports a similar situation of disagreement between different species concepts. Emmanuel Nwankwo and his colleagues focused on three subspecies of the Yellow-rumped Tinkerbird (Pogoniulus bilineatus). They showed that the subspecies conciliator (from the Eastern Arc Mountains in Tanzania and Kenya) is genetically distinct from the Tanzanian subspecies bilineatus. However, both subspecies sing similar songs, suggesting that they might interbreed. In addition, a third subspecies (fischeri from Kenya and Zanzibar) is genetically closer to bilineatus, but sings a completely different song. In summary, there is discordance between genetic data and song characteristics.

Although this study presents an interesting case, it misses one crucial piece of evidence: hybridization. The similar songs of bilineatus and fischeri only suggest interbreeding. The authors don’t provide any evidence for actual interbreeding. Perhaps these subspecies sing similar songs to guard their territories, but use other cues in mate choice. Or, if they do interbreed, hybrid offspring might be inviable due to genetic incompatibilities. In either case, song might not contribute to hybridization and becomes irrelevant in species delimitation. But before we jump to premature conclusions, let’s study these fascinating birds some more.

 

Yellow-rumped Tinkerbird (Pogoniulus bilineatus). From: http://www.hbw.com/

 

References

De Queiroz, K. (2007). Species concepts and species delimitation. Systematic biology 56, 879-886.

Mason, N. A. & Taylor, S. A. (2015). Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird. Molecular Ecology 24, 3009-3025.

Mayden, R. L. (1997). A hierarchy of species concepts: the denouement in the saga of the species problem. In Species: The units of diversity (ed. M. F. Claridge, H. A. Dawah and M. R. Wilson), pp. 381-423. Chapman and Hall, London.

Nwankwo, E. C., Pallari, C. T., Hadjioannou, L., Ioannou, A., Mulwa, R. K. & Kirschel, A. N. (2017). Rapid song divergence leads to discordance between genetic distance and phenotypic characters important in reproductive isolation. Ecology and Evolution.

 

This paper has been added to the Piciformes page.

A Reunion of Three Color Morphs on Reunion

Three color morphs of the Reunion Grey White-eye meet in three narrow contact zones.

Reunion is a small French island, situated east of Madagascar. It houses an endemic bird species, the Reunion Grey White-eye (Zosterops borbonicus), of which three plumage morphs interbreed. All the more reason to visit this island!

 

A Grey-headed morph of the Reunion Grey White-eye (from http://www.hbw.com)

 

Three Little Brown Birds

The three color morphs mainly differ in head coloration. Across the island you can find a brown-headed brown morph (BHB), a grey-headed brown form (GHB), and a brown-naped brown form (BNB). These populations meet in three contact zones across the island. Boris Delhaie and his colleagues explored these contact zones using cline theory (if you want to know more about cline analyses, check out my previous post here) based on plumage characteristics and microsatellites.

 

Lava Streams

The analyses revealed very narrow hybrid zones that coincide with several natural physical barriers, such as dry river beds and lava streams. However, the location of the hybrid zones is shifted compared to the steep changes in vegetation and climatic variables. This suggests that the hybrid zones stabilized on these barriers but are not directly associated with them. Probably, the three color morphs diverged in allopatry and later met at the physical barriers.

 

Distribution of the three color morphs on Reunion (from Delhaie et al. 2017)

 

No Genetic Structure

The plumage characters showed very steep transitions across the contact zones, indicating that they might be important in mate choice. The genetic markers, in contrast, showed no structure. This observation can be explained in two ways: (1) recent origin of these color morphs, or (2) genetic differentiation is limited to a few genomic regions. Unfortunately, the resolution of microsatellites is too weak to discriminate between these alternatives. As so often, genomic data is warranted here.

 

References

Delahaie, B., Cornuault, J., Masson, C., Bertrand, J.A., Bourgeois, Y.X., Milá, B., Thébaud, C., (2017) Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex. Journal of Evolutionary Biology. http://onlinelibrary.wiley.com/doi/10.1111/jeb.13177/abstract

 

This paper has been added to the Zosteropidae page.

Cheating in the Czech Republic: Ducks Putting Their Eggs in the Wrong Basket

From evolutionary point of view, the most important goal in life is reproducing. Getting your genes in the next generation. After you did this, you can lay back, relax and die happily (which is what some species, such as salmon, actually do). But reproduction can be hassle, especially when you are a duck. First, you have to find a suitable mate. Then you have to lay the eggs, incubate them and take care of the little chicks that crawl out of them. I already get tired just writing about this whole process.

 

Brood Parasites

Some duck species have found a way to circumvent this laborious procedure. They just lay their eggs in the nest of another female in the hope that she will raise the dubious ducklings. In general, eggs are laid in the nests of conspecifics, but some birds also target the nests of other species. This behavior – known as heterospecific brood parasitism (or HBP) – was the focus of a recent study in Wildfowl. In South Bohemia (Czech Republic), Petr Musil and his colleagues noted down the proportion of HBP in five different duck species:

• Gadwall (Anas strepera)
• Mallard (Anas platyrhynchos)
• Red-crested Pochard (Netta rufina)
• Common Pochard (Aythya ferina)
• Tufted Duck (Aythya fuligula)

Their analysis revealed that the highest proportion of brood parasitism occurred among Red-crested Pochard, while Tufted Duck showed the lowest proportion.

 

 

Hybridization?

The study did not look into hybridization, but it is feasible that HBP can lead to hybrids. When the ducklings crawl out of the egg, they can get imprinted on their mother. If, for example, a Mallard duckling hatches in a Red-crested Pochard nest, that duckling might grow up thinking it is a Red-crested Pochard (talk about an identity crisis!). Later on, this bird might look for a partner of the latter species, resulting in hybridization. I have described this process in my review paper on goose hybrids:

Hybridization between the species studied by Petr Musil and his colleagues is quite common. Indeed, the top five of most common hybrids in Central Europe includes four crosses among these species (Randler 2008). Here is the list (happy to see my beloved geese grabbing the bronze!):

1. Common Pochard x Tufted Duck (838 records)
2. Common Pochard x Ferruginous Duck (332 records)
3. Greylag Goose x Canada Goose (283 records)
4. Ferruginous Duck x Tufted Duck (94 records)
5. Mallard x Red-crested Pochard (73 records)

It would be interesting to compare the number of hybrids with the proportion of HBP in Czech Republic…

 

References

Musil, P, Z Musilová, K Poláková. (2017) Facultative heterospecific brood parasitism among the clutches and broods of duck species breeding in South Bohemia, Czech Republic. Wildfowl 67:113-122.

Ottenburghs, J, P van Hooft, SE van Wieren, RC Ydenberg, HHT Prins. (2016) Hybridization in geese: a review. Frontiers in Zoology 13:1-9.

Randler, C. (2008) Hybrid wildfowl in Central Europe – an overview. Waterbirds 31:143-146.

A Lesson in Cline Theory with Some Hybridizing Barn Swallows

Two hybrid zones between Barn Swallow subspecies reveal the strength of reproductive isolation.

When you read papers on hybrid zones, you will definitely come across “cline analyses”, a powerful technique (largely developed Nick Barton) to disentangle the change of morphological and genetic traits across a hybrid zone transect. I will not bore you with the mathematical details. Instead, I will quickly explain the rational behind clines.

 

Cline Theory for Dummies

Constructing clines is rather straightforward. You collect data on morphological characters across the hybrid zone and you plot it on a graph. Let’s say you have a white species and a black species that produce gray offspring in a contact zone. You observe birds along a transect and note down their plumage color. When you put the data in the graph, you will see a transition from white birds (when you were in the habitat of the white birds) through grayish birds (in the hybrid zone) to black birds (in the black bird habitat). Easy, no?

The interesting part is that the shape of a cline can tell you something about the biology of the birds. For example, if the gray hybrids interbreed with their parental species, there will be a variety of backcrosses of different colors. Some more white and some more black, depending on the species they crossed with. This will result in a smooth transition from white through different (perhaps 50) shades of gray to black. In other words, a wide cline. However, if gray birds cannot find a mate, there will be mostly gray hybrids in the contact zone. This will result in a rapid transition from white to black plumage, a steep cline.

 

An example of a cline plot. There are only white birds to the left of the hybrid zone and black ones on the right side. In the hybrid zone there are different shades of gray birds.

 

Finally, the position of a cline can also provide useful information. If there is no hybridization outside the hybrid zone, all clines should be centered on the midpoint of the hybrid zone. But if there is gene flow from one species into the other, the cline center can be displaced into the distribution of one of the species. The displaced cline often corresponds to a certain phenotypic character (e.g., plumage color), which indicates that this character is spreading from one species into the other because it confers some kind of advantage, such as in finding a suitable partner.

To recap, a steep cline suggests strong reproductive isolation between hybridizing species, while a wide cline points to weak isolation. And a displaced cline suggests gene flow from one species into the other. Now that you have some understanding of cline theory, let’s put the theory into practice with a recent paper by Elizabeth Scordato and her colleagues in Molecular Ecology. They studied two Russian hybrid zones between three subspecies of Barn Swallow (Hirundo rustica).

 

Barn Swallows

There are six Barn Swallow subspecies that breed across the Northern Hemisphere. Previous analyses indicated an African origin (with subspecies savignii and transitiva) with a consequent colonization of Eurasia (rustica and gutturalis). About 25,000 years ago the Asian gutturalis crossed the Bering Strait to North America, giving rise to the subspecies erythrogaster. Later (roughly 10,000 years ago) the North American birds recolonized Siberia, which resulted in the subspecies tytleri. The present study focused on the three Eurasian subspecies (rustica, gutturalis and tytleri) that interbreed in two hybrid zones.

 

A Barn Swallow (from http://www.wikipedia.com/)

 

For both hybrid zones (rustica-tytleri and tytleri-gutturalis), the researchers constructed clines for several morphological characters, such as wing length and breast color, and for genetic data. The clines in the rustica-tytleri hybrid zone were steep and narrow, whereas the clines in the gutturalis-tytleri hybrid zone were much wider. This suggests that there is stronger reproductive isolation between rustica and tytleri than between gutturalis and tytleri. This suggestion is supported by other analyses as they found fewer hybrid and backcrosses between the former two species.

In addition, the cline for breast color was displaced in the gutturalis-tytleri hybrid zone. This might indicate the spread of darker plumage from tytleri into gutturalis. Indeed, previous work in the North American subspecies has shown that females prefer darker males.

 

References

Scordato, ES, MR Wilkins, G Semenov, AS Rubtsov, NC Kane, RJ Safran. (2017) Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry. Molecular Ecology, 26:5676-5691.  http://onlinelibrary.wiley.com/doi/10.1111/mec.14276/full

The paper has been added to the Hirundinidae page.

 

Different, but the same: How Amazonian rivers and African deserts drive bird speciation

How climate change drives bird speciation on different continents.

Climate change is a hot topic these days (no pun intended). Many researchers are interested in the impact of current alterations in climate on bird populations. However, the evolutionary history of several bird species has been shaped by past climate changes, specifically during the Plio-Pleistocene period (between roughly 3 and 1 million years ago). Today, I will discuss two papers that focused on this period.

 

Hummingbirds

First, let’s travel to South America where a small hummingbird flies frantically through the upland forests of Amazonia. This species, the Straight-billed Hermit (Phaethornis bourcieri) is currently divided into two subspecies: boucieri and major. But the validity of this taxonomic treatment is not fully elucidated yet. Therefore, Lucas E. Araujo-Silva and his colleagues set out unravel the evolutionary history of this small bird.

The Straight-billed Hermit (from http://neotropical.bird.cornell.edu/)

 

Amazonian Rivers

The construction of an evolutionary tree for this species revealed several groups. The subspecies major clustered with two other species, the Needle-billed Hermit (P. philippii) and the Koepcke’s Hermit (P. koepckeae), and should thus be regarded as separate species. The other subspecies (boucieri) is divided into several cryptic lineages that originated during the Pleistocene. These lineages might also represent different species as there was no evidence of gene flow between them.

The split between both subspecies occurred at the end of the Pliocene (about 4 million years ago), coinciding with the time when the Amazon river originated. Divergence within the groups happened around the transition from Pliocene to Pleistocene (about 3 to 1 million years ago) when the Tapajos River formed and the landscape between the Negro and the Branco rivers changed. These findings show the importance of Amazonian rivers in the diversification of bird species.

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Crombecs

Now, let’s cross the Atlantic Ocean to have a look on the African continent. Here, Jerry Huntley and Gary Voelker studied the evolutionary history of Crombecs (genus Sylvietta), a group of nine species that are spread across tropical and arid regions of Africa.

The genetic analysis of this group revealed a southern origin (South Africa and Zambia) with a split into two groups some 6 million years ago. The first group consists of four species that are adapted to arid habitats, whereas the second group is comprised of three forest species and two arid-adapted species. Similar to the Hummingbirds discussed above climatic changes during the Pliocene and Pleistocene probably instigated the diversification of these species.

Long-billed Crombec (from http://www.hbw.com/)

 

A Dry Corridor

Around 2.3 million years ago the retraction of tropical forests from East Africa resulted in a corridor that connected arid regions in the north and the south. This might have driven the expansion and evolution of the arid-adapted species of the first group, such as Red-capped Crombec (S. ruficapilla) and Somali Crombec (S. isabellina).

The two arid-adapted species from the second group, Philippa’s Crombec (S. philippae) and Northern Crombec (S. brachyura), probably shifted from forest to arid habitats during the contraction of tropical forests. These results show how the fragmentation of Plio-Pleistocene forest in Africa impacted the evolution of birds.

 

Different, but the same

These two studies indicate how the same climatic event (the Pliocene-Pleistocene transition) led to different processes – origin of rivers vs. expansion of arid regions – that ultimately resulted in a similar outcome: the diversification of bird species.

 

References

Araújo‐Silva, LE, LS Miranda, L Carneiro, A Aleixo (2017) Phylogeography and diversification of an Amazonian understory hummingbird: paraphyly and evidence for widespread cryptic speciation in the Plio‐Pleistocene. Ibis, 159:778-791.  http://onlinelibrary.wiley.com/doi/10.1111/ibi.12500/abstract

Huntley, JW, G Voelker (2017) A tale of the nearly tail‐less: the effects of Plio‐Pleistocene climate change on the diversification of the African avian genus Sylvietta. Zoologica Scripta, 46:523-535. http://onlinelibrary.wiley.com/doi/10.1111/zsc.12240/full

 

Avian hybridization in Asia: Venturing into the (relatively) unknown

Two recent studies explore hybridization in Asian Tit-species.

I came across two avian hybrid papers that have several things in common. First, both studies sampled extensively in Asia. Hybridization studies on Asian birds are relatively rare. Most research is still situated in Western Europe and North America, but luckily the other continents are catching up. Second, both studies concern tits (I considered the title “Asian Tits” for this post, but I was afraid it would have attracted the wrong audience). One study focuses on Penduline Tits (genus Remiz), while the other involves Long-tailed Tits (genus Aegithalos).

 

Penduline Tits

Most European birders (like me) are familiar with the Eurasian Penduline Tit (R. pendulinus). Cheeky little bastards that jump around in the reed beds and are practically impossible to catch on camera. Their black mask contributes to their naughty behavior. There are, however, three other species across Eurasia: the Black-headed Penduline Tit (R. macronyx), the White-crowned Penduline Tit (R. coronatus) and the Chinese Penduline Tit (R. consobrinus).

 

The four Remiz species: (1) White-crowned Penduline Tit, (2) Chinese Penduline Tit, (3) Eurasian Penduline Tit, and (4) Black-headed Penduline Tit.

 

 

Three Lineages

Despite being well-studied by behavioral ecologists, there is no proper phylogeny (i.e. evolutionary tree) for this genus. So, Hossein Barani-Biranvand and his colleagues sampled all species and sequenced the mitochondrial cytochrome-b gene along with ten microsatellites to solve this phylogenetic conundrum. The genetic analyses uncovered three distinct evolutionary lineages. White-crowned and Chinese Penduline Tit are clearly separate species, but there was little genetic differentiation between Eurasian and Black-headed Penduline Tit.

 

Recent Speciation

The genetic similarity between Eurasian and Black-headed Tit is rather surprising when you consider their morphology. They certainly look very different. This result can be explained by very recent speciation or hybridization (or both). Observations of birds with intermediate morphology near Topar (Kazakhstan) suggests that these species are interbreeding. The authors indicate that further genomic studies are needed. Exciting!

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Long-tailed Tits

The second study starts where the first one ended: with genomic data. Dezhi Zhang and colleagues RAD-sequenced two closely related species: Black-browed Bushtit (A. bonvaloti) and Sooty Bushtit (A. fuliginosus). These small fuzzy balls are mostly allopatric but meet in a narrow contact zone in central China. The ideal setting to study hybridization.

Black-browed Bushtit (left) and Sooty Bushtit

 

A Genomic Landscape

The genomic analysis revealed bi-directional gene flow, mostly going from Black-browed into Sooty Bushtit. But the main focus of the paper was the genomic landscape, a concept that is heavily debated these days. If you align two genomes and calculate divergence statistics for each region as you slide along the genome, you would uncover a landscape with peaks of high differentiation and valleys with no genetic differences. This genomic landscape has been found for many species (starting with Ficedula Flycatchers), but the processes that shape these landscapes are currently being investigated (you can read more about this in my recent Avian Research paper). With regard to these Bushtits, the authors suggest that linked selection (i.e. selection on certain genomic regions and their neighbors) may account for differentiation in allopatry, but not in the hybrid zone.

The genomic landscape of Bushtits. A divergence statistic (here Fst) is calculated for regions across the genome. Each dot represents one such region. Different shades of blue correspond to different chromosomes (from: Zhang et al. 2017, Molecular Ecology).

 

These two studies make me feel like travelling east to explore the avifauna there. How about you?

 

References

Barani‐Beiranvand, H, M Aliabadian, M Irestedt, Y Qu, J Darvish, T Székely, RE Van Dijk, PG Ericson. (2017). Phylogeny of penduline tits inferred from mitochondrial and microsatellite genotyping. Journal of Avian Biology, 48:932-940. http://onlinelibrary.wiley.com/doi/10.1111/jav.01163/full

Zhang, D, G Song, B Gao, Y Cheng, Y Qu, S Wu, S Shao, Y Wu, P Alström, F Lei. (2017). Genomic differentiation and patterns of gene flow between two long‐tailed tit species (Aegithalos). Molecular Ecology, 00:1-12.  http://onlinelibrary.wiley.com/doi/10.1111/mec.14383/full

 

These papers have been added to the Aegithalidae and brand new Remizidae pages.

You Go, Girl! Females determine direction of gene flow in Tree Finches

Female choice drives asymmetrical introgression in Tree Finches.

On Floreana Island (Galapagos archipelago) two species of Tree Finch (genus Camarhynchus) are interbreeding. The Medium Tree Finch (C. pauper) is critically endangered while the Small Tree Finch (C. parvulus) is more common on the island.

 

The Desperation Hypothesis

This situation – hybridization between a common and a rare species – sets the scene to test an interesting hypothesis known as Hubb’s Principle. This idea – which was coined by ichthyologist Carl Leavitt Hubbs in 1955 – predicts that mating with an individual from another species is more likely when the chances of finding a mate of your own species are low. In other words, when a bird cannot find a proper partner, it becomes so ‘desperate’ that it chooses a partner from another species (hence the other term for this idea: ‘Desperation Hypothesis’). From a gene flow perspective, you would expect genetic material to flow from the rare into the common species. With regard to the Tree Finches, this means gene flow from Medium into Small Tree Finch.

A Small Tree Finch female on the lookout (from http://www.hbw.com)

 

Choosy Females

And this is exactly what Katharina Peters and her colleagues found. Using microsatellites, they showed asymmetric introgression (i.e. interspecific gene flow) from the rare Medium Tree Finch into the more common Small Tree Finch. Further analyses revealed that female choice is probably the main driver of this pattern. Small Tree Finch females never paired with a Medium Tree Finch male, whereas Medium Tree Finch females often choose a Small Tree Finch as their partner.

A previous study (which you can read about here) already indicated that Small Tree Finches and hybrids sing similar songs. Darwin’s Finches learn songs from their fathers, which in the case of hybrids is a Small Tree Finch. So, Small Tree Finch females – which prefer males that sing the songs of their species – are more likely to pair with hybrids. Backcrossing is thus biased towards Small Tree Finches, resulting in gene flow into this species. Sounds logical, right? You might have to read this paragraph a couple of times to get the mechanism, so I made this scheme to visualize the process.

 

References

Peters, KJ, SA Myers, RY Dudaniec, JA O’Connor, S Kleindorfer. (2017). Females drive asymmetrical introgression from rare to common species in Darwin’s tree finches. Journal of Evolutionary Biology. 30:1940-1952.

Full paper: http://onlinelibrary.wiley.com/doi/10.1111/jeb.13167/full

 

This paper has been added to the Thraupidae page.

Hybridization in Birds: The Trilogy

My three PhD-chapters on avian hybrids have found their way into scientific journals. The trilogy is complete!

If you have read my PhD thesis (which you probably didn’t, but luckily you can find it here), you would notice that it was divided into two parts, each consisting of three chapters. Two trilogies, if you will. The first trilogy, focusing on hybridization in geese, was completed some months ago when I published the final part in BMC Evolutionary Biology. You can read more about the goose trilogy here. The second trilogy, which concerns avian hybridization in general, was finished this week with a publication in the ornithological journal Avian Research. Let’s have a closer look at these three papers.

 

Part 1: How many bird species hybridize?

Scientists familiar with the literature on avian hybridization would immediately respond to this question with “roughly 10%”. In 1992, Peter and Rosemary Grant (yes, those from the Darwin’s Finches) estimated that about 1 in 10 bird species has hybridized with at least one other species. But a lot of new data has accumulated since the beginning of the 1990’s. So, I decided to redo the analyses (using data from the Bird Hybrids Database). It turns out that the percentage has risen to 16% (and even as high as 22% if you include captive hybrids). And this estimate is probably too low given our ignorance of tropical birds.

In addition to this analysis I introduced the Avian Hybrids Project (the website you are currently reading). During the first months of my PhD, I read a lot on hybridization in birds (and other organisms). While I was plowing my way through this literature and writing small summaries per bird group, I thought “why not share this information with the world?” So, I started the Avian Hybrids Project and announced it with a publication in the journal Ibis: “The Avian Hybrids Project: gathering the scientific literature on avian hybridization.”

An overview of hybridization in birds. Green = no hybrids, Blue = wild hybrids, Red = captive hybrids. The size of the circles if proportional to the number of species in the bird order.

 

Part 2: From trees to bushes

The second part of the trilogy revolves around the implications of hybridization for phylogenetic research. Phylogenetics is the study of the evolutionary history and relationships between species. Traditionally, these relationships are depicted in bifurcating trees. But with the increasing amount of genome-wide data, it turned out that different genes often result in different phylogenetic trees. This phenomenon is known as gene tree discordance or phylogenetic incongruence. For example, an phylogenetic analysis of humans, chimps and gorillas showed that 30% of the genomic positions resulted in a different gene tree compared to the classical species tree (in which humans are most closely related to chimps).

There are many computational and biological processes that can explain these patterns. And hybridization is one possibility. When species interbreed, they might exchange genetic material, as process known as introgression. Analyses of these exchanged genetic regions often result in gene trees that conflict with the general species tree. It becomes difficult to capture these patterns in the traditional bifurcating phylogenetic tree. Therefore, I advocated for the use of phylogenetic networks. From trees to bushes!

You can read more about this in the paper “Birds in a Bush: Towards an Avian Phylogenetic Network“, which was published in The Auk.

 

A network of geese (from Ottenburghs et al. 2017 BMC Evol Biol)

 

Part 3: Genomics

And that brings us to part three, which was published this week in Avian Research. In this review paper, entitled “Avian Introgression in the Genomic Era“, I discuss the use of genomic data to study introgression in birds. In short, I introduce the following topics:

• Detecting hybrids
• Phylogenetic discordance (see also Part 2 of the trilogy)
• Hybrid Zones
• The Genomic Landscape

And here is the abstract:

Introgression, the incorporation of genetic material from one (sub)species into the gene pool of another by means of hybridization and backcrossing, is a common phenomenon in birds and can provide important insights into the speciation process. In the last decade, the toolkit for studying introgression has expanded together with the development of molecular markers. In this review, we explore how genomic data, the most recent step in this methodological progress, impacts different aspects in the study of avian introgression. First, the detection of hybrids and backcrosses has improved dramatically. The most widely used software package is STRUCTURE. Phylogenetic discordance (i.e. different loci resulting in discordant gene trees) is another means for the detection of introgression, although it should be regarded as a starting point for further analyses, not as a definitive proof of introgression. Specifically, disentangling introgression from other biological processes, such as incomplete lineage sorting, remains a challenging endeavour, although new techniques, such as the D-statistic, are being developed. In addition, phylogenetics might require a shift from trees to networks. Second, the study of hybrid zones by means of geographical or genomic cline analysis has led to important insights into the complex interplay between hybridization and speciation. However, because each hybrid zone study is just a single snapshot of a complex and continuously changing interaction, hybrid zones should be studied across different temporal and/or spatial scales. A third powerful tool is the genome scan. The debate on which evolutionary processes underlie the genomic landscape is still ongoing, as is the question whether loci involved in reproductive isolation cluster together in ‘islands of speciation’ or whether they are scattered throughout the genome. Exploring genomic landscapes across the avian tree of life will be an exciting field for further research. Finally, the findings from these different methods should be incorporated into specific speciation scenarios, which can consequently be tested using a modelling approach. All in all, this genomic perspective on avian hybridization and speciation will further our understanding in evolution in general.

Different aspects of studying introgression with genomic data. I propose to use the outcomes from these methods to better inform modelling exercises.

 

I guess you know what to read this weekend…

 

References

Ottenburghs, J., Ydenberg, R.C., van Hooft, P., Van Wieren, S.E., & Prins, H.H.T. (2015). The Avian Hybrids Project: gathering the scientific literature on avian hybridization. Ibis, 157 (4), 892-894 DOI: 10.1111/ibi.12285

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 doi: http://dx.doi.org/10.1642/AUK-16-53.1

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 https://doi.org/10.1186/s40657-017-0088-z