Big data and small brown birds: how whole-genome sequencing can inform conservation of the threatened aquatic warbler?
- luisamarins19
- 19 hours ago
- 5 min read
The ERGA-BGE case study led by Dr Justyna Kubacka of Museum and Institute of Zoology, Polish Academy of Sciences, is drawing to an end. You can read about the project here. In a nutshell, the study relied upon available DNA extracts to carry out whole-genome re-sequencing of – ultimately – 60 individuals of the aquatic warbler. This small brown songbird is a threatened habitat specialist breeding in central-European fens, a vanishing wetland habitat. The aquatic warbler went through a steep decline – especially within the past 150-200 years – caused by destruction of its breeding sites.
Aquatic warblers were sampled in two geographical populations with hardly any breeding habitat in between. The first one was the Biebrza Valley, located in north-eastern Poland, a stable, large and well-connected population. It was sampled in 1997 and 2018, enabling temporal comparisons. The second one, located about 600 km westwards as the crow flies, was West Pomerania in Poland, a moderate-sized, isolated and steeply declining population. There, samples were obtained in 1999, allowing spatial analysis. With the whole-genome sequences at hand, thanks to ERGA-BGE funding, and supported by colleagues Dr Wiktor Kuśmirek and Dr Krystyna Nadachowska-Brzyska, Dr Kubacka set out to evaluate inbreeding, effective population size and genetic bottlenecks, as well as population structure between the two distant populations. Importantly, the team relied on the recently published, high-quality chromosome-level reference genome of the aquatic warbler.
Results paint a worrisome picture. Genomic diversity was low in both populations and compared to that found in some passerines endemic to islands. The only good news was that no temporal trend was detected in Biebrza. The low diversity could compromise the ability of the aquatic warbler to adapt to changing conditions, such as increasing drought, emergence of new diseases or lowered abundance of preferred arthropod prey on the marsh, all of which are expected under global warming. This is concerning especially because – unlike in many other birds – it is only female aquatic warblers that incubate eggs and feed young. With this pattern of parental care, raising young successfully under environmental change could present a challenge. Hence, depleted adaptive potential could compromise population growth more in the aquatic warbler than in species in which both parents raise their offspring.
The team then looked at inbreeding rates with a powerful tool, runs of homozygosity (ROHs) – stretches within a genome that originate from one ancestor. This kind of inbreeding results not only through mating of closely related individuals, but also when a population is small and so more strongly affected by genetic drift (random loss of genetic diversity) compared to a large population. Long ROHs (above 1 million base pairs) are indicative of inbreeding within the recent 10-50 generations (20-100 years in the aquatic warbler) and form a strong proxy of extinction risk. The pattern of long ROHs showed increased inbreeding in West Pomerania, compared to Biebrza, and no temporal shift in the latter. This means that over the 20-100 years before sampling, West Pomerania had faced enhanced genetic drift and accelerated loss of genomic diversity. On top of this, average relatedness between individuals was clearly elevated in this population, relative to Biebrza.
Genomic diversity was similar across all the studied populations. However, this amount of genomic variation is shown by endemic island passerines with small populations. Recent inbreeding - identified with long runs of homozygosity (ROHs) was elevated in West Pomerania, indicating enhanced genetic drift in the last 20-100 years before sampling. Aquatic warblers from West Pomerania were more interrelated than the Biebrza birds, pointing to lack of immigration and low population size in the former.
With the dense genomic data, the team was also able to do detective work and track back historical changes in effective population size. This parameter shows how strong the work of genetic drift is, which depends mostly on population size. The results were consistent with the decline in numbers and showed a recent genetic bottleneck around the industrial era in the mid-1800s, when wetland destruction accelerated. This result was especially clear for the Biebrza samples. For West Pomerania, the effective population size was much lower over the examined period than in Biebrza. A picture of a founding event, followed by expansion in the mid-1800s and then a steep drop was revealed. Therefore, genomic diversity of West Pomerania could have been depleted at least twice.
Finally, the team checked whether the two populations bear signs of genetic divergence. Results indicated only very week genetic differentiation and no clear evidence for two separate genetic populations. Apparently, either insufficient time has passed for genetic change to accumulate between West Pomerania and Biebrza, or some weak connectivity had been maintained. Nevertheless, it was too little to stop genomic erosion in West Pomerania.
While the analysis relied on historical samples, it brings an important insight for present day conservation efforts. A large-scale translocation project is being carried out to restore the nearly lost West Pomerania population. The results of the ERGA-BGE project indicate that genetic drift and inbreeding could have contributed to its swift decline. To restore this population through translocation while avoiding the genomic history repeating itself, it is crucial to improve the breeding habitat and extend its area. It is also fundamental to enlarge or create stepping-stone habitats between West Pomerania and the nearest large and stable populations, to restore gene exchange.
The work could not have been performed without the collectors, Prof. Andrzej Dyrcz, Dr Benedikt Giessing, Dr Jarosław Krogulec and Grzegorz Kiljan. For a quarter of century, the samples were curated by Prof. Michael Wink at the Heidelberg University and by Dr Martin Päckert at the Senckenberg Natural History Collections in Dresden, Germany. The project received funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government. The bioinformatic analysis was conducted with the support of the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw, Poland (ICM UW).
About the Author
Dr Justyna Kubacka is an evolutionary ecologist and ornithologist and is constantly gaining skills in population genomics. She works at the Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw. She belongs to the aquatic warbler genome team of the ERGA Pilot reference genome project. In her free time, she loves doing cross-country skiing and gardening.
