Gone but not forgotten: entire radiation retains genomic fragments from their lost sister species

Despite the extinction of a whitefish species, fragments of its genome survived due to hybridization with all species of the extant radiation during eutrophication-induced speciation reversal.

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Human action resulted in worldwide degradation of ecosystems and biodiversity is lost at an unprecedented rate. To better understand the long-term influence of anthropogenic environmental change on biodiversity, we need a better mechanistic understanding of extinction processes and their effects on surviving species. Species can go extinct when their populations decline (due to e.g. habitat loss) until there are not enough individuals anymore to maintain a population. Another process leading to extinction is speciation reversal through introgressive hybridization: When reproductive isolation between species is mediated by the environment and the environment changes, this can result in the breakdown of reproductive isolation. In consequence, species start to interbreed. Hybridization can finally lead to extinction when the original parental species is completely replaced by hybrids.

Anthropogenic eutrophication of Swiss lakes during the 20th century led to the loss of around one third of all described Alpine whitefish species. Eutrophication resulted in the loss of well oxygenated deep-water spawning habitats, and it changed the composition of the small prey items whitefish feed on (mainly zooplankton and/or benthic invertebrates, depending on the species). Thereby, eutrophication had dual consequences on reproductive isolation between Alpine whitefish species: It decreased the available reproductive niche space and it relaxed divergent selection between whitefish species. The result was speciation reversal through introgressive hybridization, which, together with demographic decline, resulted in the extinction of numerous whitefish species within only few generations. In Lake Constance, a large lake at the borders of Switzerland, Germany and Austria, the extinction of Coregonus gutturosus was documented during the peak of the anthropogenic eutrophication period in the 1970-1980’s. C. gutturosus was an endemic deep-water specialist that was locally known as “Kilch” (Fig. 1).

Fig. 1: Taxonomically described Lake Constance whitefish species.

Extinct biodiversity can only be studied when samples of the lost species have been collected in natural history collections. However, complex evolutionary processes like speciation reversal often affect multiple species or even complete radiations. Thus, studying such processes is often limited by sample availability, as samples of the extinct species are crucial. Fisheries authorities of Lake Constance started already at the beginning of the 20th century with systematic monitoring and sampling of whitefish populations. One type of samples that have been taken are fish scale samples. Scale samples were collected in order to determine the age and growth rates of indivdual fish by analyzing growth rings, similar to growth rings of trees (Fig. 2). On a regular basis, fisheries wardens collected scale samples of all four described Lake Constance whitefish species (including the now extinct C. gutturosus). To determine the age of an individual under a microscope (Fig. 2), the scales have to be cleaned. However, as only few scales per individual are sufficient for this purpose, many of these historical samples had not been cleaned. These scale samples still have residual tissue attached that allows to extract DNA of whitefish that lived in Lake Constance almost a hundred years ago. Many of these samples stored in paper bags at room temperature survived until today and are still stored by fisheries authorities around the lake.

Fig. 2: A) Paper bags with preserved whitefish scale samples, collected in 1946. B) Cleaned whitefish scale under a microscope.

By using historical scale sample as source of DNA, we could compare the genomes of the historical population to the contemporary population of each of the four whitefish species of Lake Constance,  which has at least partially recovered from its past eutrophication. This approach allows to look at the genomic consequences of speciation reversal and helps to understand the C. gutturosus extinction and its effects on contemporary relatives.

In our project we sequenced the genomes of eleven individuals of the extinct C. gutturosus to compare it with genomes of the three other whitefish species living in Lake Constance. For the three surviving whitefish species, we sequenced data from almost hundred years back (before the eutrophication period started), but we also generated sequence data from fish that were sampled (Fig. 3) in 2015 (after the eutrophication period ended). By comparing genomes from before and after the eutrophication period of the lake, we could study the genomic change associated with the changed environment and identify the fragments of the genome of the extinct species that have been retained in the contemporary whitefish species in consequence to speciation reversal through introgressive hybridization.

Fig. 3: Setting nets for the sampling of contemporary whitefish species, used for the genomic comparison with historical populations.

By sequencing whole-genome data of pre- and post-eutrophication samples of all species in the radiation, we demonstrated that the now extinct species interbred with all three surviving whitefish species during the eutrophication period. We showed that the directionality of gene flow was consistent with the sequence of loss of reproductive niche space, as well as major changes in the selective regime during the eutrophic phase of the lake. As a result of hybridization, fragments of the genome of the extinct species can still be found in the contemporary whitefish species, including genomic variation shaped by positive selection in the extinct C. gutturosus before eutrophication.

While Lake Constance lost one whitefish species due to anthropogenic lake eutrophication, parts of its characteristic genomic variation survived in contemporary species due to speciation reversal. Hence, while species richness and species differentiation both declined, potential for future adaptability might have increased in the surviving species of the radiation. As Lake Constance has by today recovered from eutrophication, it will be interesting to see if and how this retained genomic variation will influence the future evolution of the whitefish radiation in Lake Constance.

Our study was funded as part of a large collaborative project called “SeeWandel: Life in Lake Constance – the past, present and future” as one of 13 projects across 7 research institutes, all addressing important questions regarding the resilience of the Lake Constance ecosystem. Funding for our study was provided by our research institute, the Swiss Federal Institute of Aquatic Science and Technology (Eawag), the Swiss Federal Office for the Environment (FOEN), and the European Fund for Regional Development – within the framework of the Interreg V programme “Alpenrhein-Bodensee-Hochrhein (Germany/Austria/Switzerland/Liechtenstein)” - with support of the Swiss Confederation and cantons.

The paper in Nature Ecology & Evolution can be found here.

David Frei

PhD Student, Eawag