Going with the flow: Gene flow from Chinese Spot-billed Ducks into Mallards

Genetic analyses show that Spot-billed Duck and Mallard diverged recently and hybridized in the process.

Telling male and female Mallards (Anas platyrhynchos) apart is not difficult. The male has an obvious fluorescent-green head, while the female is…well…brown (but nonetheless very beautiful). But did you know that most species in the Mallard complex are monochromatic (i.e. males and females have the same color)? Just have a look at the American Black Duck (A. rubripes) or the Hawaiian Duck (A. wyvilliana).

Most waterbird researchers argue that these monochromatic species originated from a dichromatic Mallard-like ancestor (see for example Omland 1997). A recent study in Current Zoology explored the evolutionary history of another monochromatic duck, the Spot-billed Duck (A. zonorhyncha).

mallard couple.jpg

Mallard couples are dichromatic: the brown female and the colorful male (from: http://www.wikipedia.com/).


Mixed Signals

Mallards and Spot-billed Ducks are difficult to separate with genetic data. When you construct a family tree for these duck species, you will arrive at clusters that contain both species. In technical terms, they do not form monophyletic groups. This pattern can be the outcome of two processes: recent divergence or hybridization.

Previous work in Russia suggested that hybridization was the main cause for this non-monophyly. Wenjuan Wang and colleagues expanded the sampling to China and reconstructed the evolutionary history of the Spot-billed Duck in more detail.


Mallards (black squares) and Spot-billed Ducks (white circles) do not form separate groups when you construct their family tree. They are not monophyletic (from: Kulikova et al. 2004 The Auk)


Too Little Time

The genetic analyses revealed that the non-monophyly between Mallard and Spot-billed Duck can be explained by both recent divergence and hybridization. Both species went their own evolutionary ways about 40,000 years ago. There has been too little time for the genetic variation to sort among the lineages.

In addition, hybridization between both species prevented faster differentiation. Isolation-with-migration analyses of mitochondrial DNA (mtDNA) indicated that gene flow was mainly from Spot-billed Ducks into Mallards. Given that mtDNA is maternally inherited, this suggests that female Spot-billed Ducks mostly mated with male Mallards.

This study nicely shows that ducks are a goldmine for those who want to understand the dynamics of hybridization.

spot-billed duck.jpg

A couple of Spot-billed Ducks (from: https://www.hbw.com)



Wang, W., Wang, Y., Lei, F., Wang, H. & Chen, J. (2018) Incomplete lineage sorting and introgression in the diversification of Chinese spot-billed ducks and mallards. Current Zoology

This paper has been added to the Anseriformes page.

Studying sperm success: A possible reproductive barrier between subspecies of the Long-tailed Finch

Interactions between sperm and egg might act as a reproductive barrier between two subspecies of an Australian finch.

Life as a sperm cell is not easy. In order to reach your goal (i.e. fertilizing the egg), you need to overcome numerous barriers. In birds, this includes among others passing the vagina, enter the female sperm storage tubules and reaching the site of fertilization. These obstacles can be especially problematic when you are a sperm cell in the body of a female from another species.


The different barriers a sperm cell has to cross before fertilizing an egg (from Birkhead & Brillard, 2007 Trends in Ecology and Evolution).

The challenges between copulation and fertilization of the egg are called postmating prezygotic barriers and might lead to reproductive isolation between two species. Because this process is difficult to study, it has been largely overlooked in birds. A recent study in Ecology and Evolution explored this reproductive barrier between subspecies of the Long-tailed Finch (Phoephila acuticauda).

Bill Colors

The Long-tailed Finch is endemic to Northern Australia. Based on bill color, you can distinguish between two subspecies: the red-billed hecki and the yellow-billed acuticauda. Interestlingly, hybrids between both subspecies have orange bills. A survey of bill color across their range indicated that there is selection against hybrids. Could this selection be due to postmating prezygotic barriers?


The two subspecies of Long-tailed Finch: the yellow-billed acuticauda and the red-billed hecki (from: https://griffithecology.com/research/long-tailed-finch/)

Sperm-Egg Interactions

To answer this question, Laura Hurley (Macquarie University) and her colleagues created captive crosses between the subspecies. They collected the eggs and extracted the perivitelline layer (PVL) of each egg. Next, they counted the number of sperm cells that managed to reach this layer. In birds, successful fertilization requires multiple sperm cells to penetrate the PVL. So, the number of sperm in the extracted PVL can be used as a proxy for fertilization success.


There was no significant difference in the number of sperm between pure crosses and hybrid pairs. However, when backcrossing hybrids with one of the parental species less sperm reached the PVL. This suggests that first generation hybrids have lower fertilization success. Similar results have been documented in gamefowl (order Galliformes) where later generation hybrids and backcrosses showed fertility problems. The authors indicate that their study “supports the role of [postmating prezygotic barriers] in avian specation, even in recently diverged taxa, that may not yet be fully genetically incompatible.”


A red-billed Long-tailed Finch (from: http://www.wikipedia.com/)


Griffith, S.C. & Hooper, D.M. (2017) Geographical variation in bill colour in the Long-tailed Finch: evidence for a narrow zone of admixture between sub-species. Emu – Austral Ornithology, 117: 141-150.

Hurley, L.L., Rowe, M. & Griffith, S.C. (2018) Differential sperm-egg interactions in experimental pairings between two subspecies and their hybrids in a passerine bird. Ecology and Evolution.

The papers have been added to the Estrildidae page.

Exploring the genomic landscape of wood-warblers

A more technical story on the evolution of genomic landscapes in wood-warblers.

Any birdwatcher can list the morphological characters that he or she uses to discriminate between closely related species. But how is this variation reflected on the genetic level? The possibility to sequence the entire genome of an individual has allowed biologists to explore this question. In general, they scan across the genome looking for differentiated regions (based on a collection of summary statistics). These ‘genomic landscapes’ hold to key to understand how bird species diversify. A recent study in the journal Molecular Ecology applied this approach to several members of the Parulidae family (New World warblers or wood-warblers).


Townsend’s Warbler (from: https://www.allaboutbirds.org/)


Some Summary Statistics

Darren Irwin (University of British Columbia) and his colleagues used three summary statistics: Fst, π(between) and π(within). What do these statistics actually represent?


The American geneticist Sewall Wright introduced Fst to explore how genetic variation is structured between populations by comparing the genetic variation within and between these populations. Fst ranges from 0 to 1, where zero implies that the two populations are freely interbreeding and where one implies that all genetic variation is explained by the population structure. This statistic can also be used to pinpoint genomic regions that are different between two populations.


This statistic is also known as Dxy and indicates the absolute genetic distance between two populations (in contrast to Fst, which is a relative measure). It counts the number of differences between two DNA sequences from distinct populations. For example, the sequences AATTCC and AATTGG differ in two positions. You can calculate π(between) by dividing the number of differences and the total sequence length: 2/6 = 1/3 or 33%.


The last summary statistic is similar to π(between) but instead of comparing individuals of two populations, you calculate it between individuals from the same population.


Mourning Warbler (from https://www.allaboutbirds.org/)


Four Models

By studying these three summary statistics, you can infer the evolutionary history of bird populations. For example, if two species diverged with some gene flow, you would expect that genomic regions that contribute to reproductive isolation – and are thus not exchanged between species – become different over time. So, both Fst and π(between) should be higher in these regions.

If, on the other hand, the species diverged without gene flow but were subject to different selection pressures, regions of high Fst are expected to show lower π(within), because selection tends to lower the genetic variation within a population.

Another pattern that is commonly observed in regions of high Fst and low π(between). This can be explained by a ‘recurrent selection’ model where these divergent genomic regions experienced strong selection before the species split, followed by recurrent selection after the split.

The authors of this study introduce a fourth model – ‘geographic-sweep-before-selective-differentiation’ – in which advantageous genetic variants spread through a geographically structured species complex. The outcome would be reduced π(between) and π(within) in regions of high Fst.

I can imagine that the four models and their predictions make your head spin. Luckily, the researchers provided a graphical representation of these models. Take your time to study this figure and see if you understand the expected patterns.


The four models and their predictions (From: Irwin et al. 2018, Molecular Ecology)


Three Species Pairs

The authors calculated the summary statistics for three species pairs in the Parulidae family:

  • MacGillivray’s Warbler (Geothlypis tolmiei) and Mourning Warbler (G. philadelphia)
  • Townsend’s Warbler (Setophaga townsendi) and Black-throated Green Warbler (S. virens)
  • Audubon’s Warbler (S. auduboni) and Myrtle Warbler (S. coronata)

In all three comparisons, the genetic patterns point to a model of recurrent selection or sweep-before-differentiation (models c and d in the figure). A more thorough modelling study will be needed to discriminate between these two models.

Interestingly, most of the genomes show little differentiation, only a small fraction is different. This suggests that reproductive isolation is caused by a few highly divergent regions, a pattern that has been observed in several other bird species, such as Wagtails and Nightingales. Moreover, these highly divergent regions – or ‘islands of differentiation’ –  were not shared between the species pairs, indicating that the causes of genomic differentiation are specific to each speciation event.


Myrtle Warbler (from http://www.wikipedia.com/)



Irwin, D.E., Mila, B., Toews, D.P.L., Brelsford, A., Kenyon, H.L., Porter, A.N., Grossen, C., Delmore, K.E., Alcaide, M. & Irwin, J.H. (2018) A comparison of genomic islands of differentiation across three young avian species pairs. Molecular Ecology.


This paper has been added to the Parulidae page.