Dating with different techniques: Consilience of divergence times between Bean Goose species

Several methods suggest that Taiga and Tundra Bean Goose diverged about 2.5 million years ago.

One of the strongest arguments for evolution is consilience, the principle that evidence from independent, unrelated sources converges upon the same conclusions. Numerous lines of evidence, from genetic analyses and comparative morphology to biogeography and embryology, all point to the same unescapable conclusion: life on Earth evolved over billions of years. Doubting evolution would just be silly.

The principle of consilience can also be applied to smaller questions. In my own work on the evolution of geese, I uncovered a nice example of consilience: the divergence between Taiga Bean Goose (Anser fabalis) and Tundra Bean Goose (A. serrirostris). Using different dating techniques, I always converged upon the same answer: these species diverged around 2.5 million years ago.

mtDNA vs. Genomics

Before we delve into my goose work, we start with a study in the Journal of Evolutionary Biology. In 2000, Minna Ruokonen and her colleagues compared about 1000 base pairs of the mitochondrial DNA for seven goose species. Although they only included a sample of the Tundra Bean Goose (and not the Taiga Bean Goose), we can still compare this species with other closely related goose species, such as the Pink-footed Goose (A. brachyrhynchus). Based on the level of genetic divergence in the mtDNA, the researchers provided “a rough estimate for the timing of speciation events of Anser species […] within approximately 2–2.5 million years.”

More than 15 years later, during my PhD at Wageningen University, I used genomic data to unravel the evolutionary history of these goose species. After constructing a phylogenetic tree (based on 6,630,626 base pairs), I ran a molecular clock analysis with the software MCMCtree. First, I estimated a mean substitution rate based on previous studies. Next, the split between the two goose genera – Anser and Branta – was constrained between 4 and 20 million years, the time period for which we have reliable goose fossils. And finally, the MCMCtree analyses were run multiple times to check for convergence of the results. Using this approach, the divergence between Taiga Bean Goose and Tundra Bean Goose was estimated ca. 2.5 million years ago. Very similar to the mitochondrial result by Minna Ruokonen and her colleagues.

Genomic data suggested that the Taiga Bean Goose (in green) and the Tundra Bean Goose (in orange) diverged around 2.5 million years ago. From: Ottenburghs et al. (2016).

Demographic Models

So, now we have two independent lines of evidence for the divergence time between Taiga Bean Goose and Tundra Bean Goose. But it gets even better. During my postdoc at Uppsala University, I focused on the evolution of these two species (and later adding the Pink-footed Goose to the mix). To understand their evolutionary dynamics, I opted for a demographic modelling approach with genomic data. Using the software package DADI, I compared different demographic scenarios, ranging from strict isolation to secondary contact with asymmetrical gene flow.

DADI simulates the change in allele frequencies using a diffusion equation, similar to gas molecules moving through a room. Depending on the interplay of genetic drift, selection and migration, genetic variants spread through a population at different speeds. The end result can be visualized in a square with different populations on the horizontal and vertical axes (in my case, the two Bean Goose species). Genetic variants that are unique for one of the species can be found in the lower left corner, whereas variants shared by both species are found in the top right corner. Gene flow between the populations mixes things up. Different demographic models lead to different squares which can be compared to the actual data.

My genomic analyses pointed to a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Another independent line of evidence for the divergence time between Taiga Bean Goose and Tundra Bean Goose.

DADI uses a diffusion equation to simulate how genetic variants spread through a population. The result can be visualized in a square and compared with the actual data. For the Bean Geese, the close match between the data and the model suggested a scenario of allopatric divergence with secondary contact. From: Ottenburghs et al. (2020).

Consilience

And there you have it. Three independent analyses that all converge upon the same conclusion. It does not matter if you use a simple calculation based on mitochondrial divergence, a molecular clock calibrated with fossils, or a demographic model using diffusion equations. The conclusion is always the same: Taiga Bean Goose and Tundra Bean Goose diverged ca. 2.5 million years ago. Now, that is consilience.

References

Ottenburghs, J., Megens, H. J., Kraus, R. H., Madsen, O., van Hooft, P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. T. (2016). A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese. Molecular Phylogenetics and Evolution, 101, 303-313.

Ottenburghs, J., Honka, J., Müskens, G. J., & Ellegren, H. (2020). Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation. Heredity, 125(1-2), 73-84.

Ruokonen, M., Kvist, L., & Lumme, J. (2000). Close relatedness between mitochondrial DNA from seven Anser goose species. Journal of Evolutionary Biology, 13(3), 532-540.

Featured image: Taiga Bean Goose (Anser fabalis) © Marton Berntsen | Wikimedia Commons