Combinatorial Speciation: Reassembling of old genetic variation facilitates rapid speciation and adaptive radiation

A fresh way of looking at the origin of species.

The origin of new species – or speciation – is a slow process that takes thousands to millions of years. In general, populations become geographically isolated and slowly accumulate incompatible mutations. There are numerous examples of such allopatric speciation events, see for example this blog post on hummingbirds and crombecs. But what about rapid speciation events and adaptive radiations where numerous species arise in the evolutionary blink of an eye? These scenarios seem incompatible with the slow accumulation of mutations. A recent paper in the journal Trends in Ecology & Evolution provides a possible solution to this paradox: combinatorial speciation!


Old Genetic Variants

The genomic approach to speciation has revealed that many genetic variants that underlie speciation events are often much older than the actual time when the species originated. Take, for instance, the apple maggot species complex (Rhagoletis pomonella). These species emerged in about 200 years, whereas the genomic variation responsible for their origin dates back to about 1.6 million years ago. Similarly, genetic variation associated with adaptation to different food sources predates the radiation of Darwin’s Finches on the Galapagos Islands.

But where did this genetic variation come from? David Marques, Joana Meier and Ole Seehausen propose two main sources: standing genetic variation and hybridization. In their paper, the authors provide several cases. I will complement their list with some examples from the Avian Hybrids blog.

darwin's finches.jpg

The genetic variation that fueled the diversification of Darwin’s Finches was already present (from: Grant 1991 – Scientific American)


Standing Genetic Variation

Standing genetic variation refers to ancestral variation that is already present in the population and can be utilized immediately. An example of using old genetic variants concerns the vinous-throated parrotbill (Sinosuthora webbiana). This small songbird occurs on the Asian mainland and the island of Taiwan. There, it lives up to 3100 meters above sea level. A recent genomic study compared island populations from the lowlands and the highlands to understand how these birds adapted to living at high altitude. The analyses revealed that most genetic variants under selection in the highland populations are also present in birds from the mainland. This suggests that these variants are not new mutations but represent old genetic variants that proved to be useful in a high altitude setting. In other words, adaptation from standing genetic variation. You can read the whole story in this blog post.

vinous-throated parrotbill

The vinous-throated parrotbill (from:


Introgressive Hybridization

The second source of old variants is introgressive hybridization. Gene flow between different species can fuel the rapid origin of new species. Indeed, I have written before about hybridization as the engine of adaptive radiation. The authors provide several reasons for why hybridization is a powerful source for rapid speciation.


Filtered Genetic Variation

Hybridization will immediately augment genetic variation, the fuel for adaptive evolution. A classical example is the radiation of cichlid fishes in the African lakes. Moreover, the genes that are acquired by hybridization have already been filtered by selection in the donor species. Hence, deleterious alleles are less likely to be exchanged between species. New mutations, on the other hand, are often (slightly) deleterious.

A nice example of this process concerns subspecies of the White Wagtail (Motacilla alba) which are characterized by different head patterns. Some ornithologists think that these patterns are the outcome of a few genes that are being shuffled around by hybridization. You can read more about this interesting system here.


Different head patterns of the White Wagtail (from:


Extreme Phenotypes

Interactions between divergent genes can result in transgressive segregation, namely extreme phenotypes that lie outside the range of the interacting species. These novel phenotypes can facilitate adaptation to particular ecological niches. The likelihood of transgressive segregation partly depends on the divergence between the hybridizing species. In highly divergent species, there are more ways in which old variants can be reordered into new combinations.

Hybridization between recently diverged taxa is less likely to drive the rapid origin of new species. However, it can facilitate parallel speciation, the recurrent evolution of similar species. This has been documented in threespine sticklebacks where marine populations have repeatedly colonized freshwater habitats. It might also explain the recurrent evolution of plumage patterns in Wheatears (see here for the complete story of these birds).


Male eastern black-eared wheatear at Ipsilou Monastery, Lesvos, Greece © Mark S Jobling | Wikimedia Commons


Sorting of incompatibilities

Incompatible mutations are unlikely to arise in a single population because they will be weeded out by selection. But these mutations could arise in separate lineages and consequently be brought together by hybridization, leading to the rapid origin of new species. This probably happened in the Italian Sparrow (Passer italiae), a hybrid species between House Sparrow (P. domesticus) and Spanish Sparrow (P. hispaniolensis). The title of this paper Hybrid speciation through sorting of parental incompatibilities in Italian sparrows – is quite clear about the underlying process. If you are interested in this case, you can read more about it here and here.

italian sparrow

The Italian Sparrow (from


Large Effects

Introgression can result in the transfer of large-effect haplotypes that contain multiple coadapted genes. These regions of large phenotypic or ecological effect can help populations respond quickly to new challenges. Inversions – regions in the DNA that have been flipped around and contain numerous genes – are a good example of such large-effect haplotypes. Classic examples of important inversions in birds include the Ruff (Calidris pugnax) and the White-throated Sparrow (Zonotrichia albicollis). See this blog post for an overview of inversions in avian evolution.


The three ruff phenotypes (faeder, satellite & territorial) are caused by an inversion (from:


Combining Views

In summary, the reassembly of old genetic variants into new combinations can facilitate adaptive radiation and rapid speciation. How common this combinatorial speciation is, remains to be determined. However, it seems like a plausible mechanism to explain numerous radiations.

While reading this paper, I remembered playing around with similar ideas during my PhD. Searching through my dusty PhD-archive, I came across this figure (which didn’t make it into the final version of the dissertation). I was on the right track but didn’t synthesize it into a common framework. To put it in Thomas Henry Huxley’s words when he read Darwin’s book On the Origin of Species: “How extremely stupid not to have thought of that.”

Adaptive Potential

Some thoughts from my PhD work…



Marques, D.A., Meier, J.I. & Seehausen, O. (2019) A Combinatorial View on Speciation and Adaptive Radiation. Trends in Ecology & Evolution.

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