Interview with the authors: Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges

In a recent paper in Molecular Ecology, Portinha et al. used population genomic data to analyse the speciation history of two closely related species of wood ants, Formica polyctena and F. aquilonia. Using a demographic modelling approach, the authors reconstruct the history of divergence for multiple heterospecific pairs of populations. In all cases, the authors found that there was evidence for divergence with gene flow. However, for a sympatric population pair sampled in Finland there was evidence for substantially elevated gene flow between the species. Their findings imply that population genomic analysis of speciation history may be geographically variable for particular species.

We sent some questions to Beatriz Portinha and Pierre Nouhaud, the corresponding authors of this work, to get more detail on this study.

Ant mound surface covered in ants. Photo credit: Jack Beresford

What led to your interest in this topic / what was the motivation for this study? 

Knowledge on the demographic and speciation histories is essential for understanding
contemporary genomic patterns in natural populations, which is why we wanted to
reconstruct it for the emerging Formica model system. Our study species, Formica polyctena
and F. aquilonia, are known to hybridize naturally in Southern Finland, where their hybrids
have been studied for over 10 years (Kulmuni et al., 2010; Martin-Roy et al. 2021). We
wanted to test whether a similar divergence history was consistently inferred across the
European ranges of both species, or whether the Finnish populations would stand apart,
possibly because of gene flow mediated by hybrid populations in the area.

What difficulties did you run into along the way? 

Formica polyctena and F. aquilonia had a limited genomic toolbox when we started the
project, and we initially relied on a distant and non-contiguous reference assembly.
Meanwhile, our group assembled a high quality reference genome (Nouhaud et al., 2022),
which improved the quality of our inferences.

The demographic modelling software we used, fastsimcoal2, can simulate a large panel of
evolutionary scenarios. When planning this study, we wanted to design models that
considered alternative scenarios for the divergence of the species which would be as
biologically meaningful as possible, while keeping the number of models low enough that the
project 1) would not be a huge computational burden and 2) would be executable in the
available time frame (Beatriz’s MSc. project, funded by Erasmus+ and Societas pro Fauna et
Flora Fennica). This was an especially important aspect as we used four distinct population
pairs to reconstruct the history of the two species, so each model had to be run, at least, four
different times.

What is the biggest or most surprising innovation highlighted in this study? 

We found that there was already bidirectional gene flow occurring in Finland before the
hybridization events that led to the present-day hybrid populations. This was not suspected
before, as there is no evidence in the literature, and it suggests that F. polyctena in Finland
may be admixed, which is supported by the fact that we have not found non-admixed F.
individuals in Finland.

Moving forward, what are the next steps in this area of research?

The divergence history we inferred between F. polyctena and F. aquilonia can be used to
run simulations about the evolution of the hybrid populations, which is what we did in a
subsequent work (Nouhaud et al. 2022). In the longer run, it would also be important to
extend this work by reconstructing the divergence history of the whole F. rufa species group,
which encompasses 5 species (including F. aquilonia and F. polyctena) and where gene flow
is prevalent (Seifert, 2021).

Describe the significance of this research for the general scientific community in one sentence.

Genomes from individuals sampled thousands of kilometers apart tell the same ancient
history, while their most recent history may be different.

Describe the significance of this research for your scientific community in one sentence.

The divergence history between two species can be reliably and consistently inferred from a
small number of individuals sampled across the species’ ranges.

Portinha, B., Avril, A., Bernasconi, C., Helanterä, H., Monaghan, J., Seifert, B., Sousa, V. C., Kulmuni, J., & Nouhaud, P. (2022). Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges. Molecular Ecology, 31, 3416– 3431.

Kulmuni, J., Seifert, B. & Pamilo, P. (2010). Segregation distortion causes large-scale
differences between male and female genomes in hybrid ants. Proceedings on the National
Academy of Sciences
, 107(16), 7371-7376.

Martin-Roy, R., Nygård, E., Nouhaud, P. & Kulmuni, J. (2021). Differences in thermal
tolerance between parental species could fuel thermal adaptation in hybrid wood ants.
American Naturalist, 198(2), 278-294.

Nouhaud, P., Beresford, J. & Kulmuni, J. (2022). Assembly of a hybrid Formica aquilonia× F.
ant genome from a haploid male. Journal of Heredity, esac019, 1-7.

Nouhaud, P., Martin, S. H., Portinha, B., Sousa, V. C. & Kulmuni, J. (2022). Rapid and
repeatable genome evolution across three hybrid ant populations. bioRxiv.

Seifert, B. (2021). A taxonomic revision of the Palaearctic members of the Formica rufa
group (Hymenoptera: Formicidae) – the famous mound-building red wood ants.
Myrmecological News, 31, 133-179.

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