Reproductive isolation, evolutionary distinctiveness and setting conservation priorities: the case of European lake whitefish and the endangered North Sea houting (Coregonus spp.)

An integrated system to assess marine extinctions

More than 20 global marine extinctions and over 700 local extinctions have reportedly occurred during the past 500 years. However, available methods to determine how many of these species can be confidently declared true disappearances tend to be data-demanding, time-consuming, and not applicable to all taxonomic groups or scales of marine extinctions (global [G] and local [L]). We developed an integrated system to assess marine extinctions (ISAME) that can be applied to any taxonomic group at any geographic scale. We applied the ISAME method to 10 case studies to illustrate the possible ways in which the extinction status of marine species can be categorized as unverified, possibly extinct, or extinct. Of the 10 case studies we assessed, the ISAME method concludes that 6 should be categorized as unverified extinctions due to problems with species' identity and lack of reliable evidence supporting their disappearance (periwinkle-Littoraria flammea [G], houting-Coregonus oxyrinchus [G], long-spined urchin-Diadema antillarum [L], smalltooth sawfish-Pristis pectinata [L], and largetooth sawfish-P. pristis [L]). In contrast, ISAME classified the Guadalupe storm-petrel (Oceanodroma macrodactyla [G]) and the lost shark (Carcharhinus obsolerus [G]) as possibly extinct because the available evidence indicates that their extinction is plausible-while the largetooth sawfish [L] and Steller's sea cow (Hydrodamalis gigas [G]) were confirmed to be extinct. Determining whether a marine population or species is actually extinct or still extant is needed to guide conservation efforts and prevent further biodiversity losses.

Complex and divergent histories gave rise to genome-wide divergence patterns amongst European whitefish (Coregonus lavaretus)

Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion impacted contemporary biodiversity in complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish species on mainland Europe, but in Britain it has only seven native populations, all of which are found on the western extremes of the island. The origins and colonization routes of the species into Britain are unknown but likely contributed to contemporary genetic patterns and regional uniqueness. Here, we used up to 25,751 genome‐wide polymorphic loci to reconstruct the history and to discern the demographic and evolutionary forces underpinning divergence between British populations. Overall, we found lower genetic diversity in Scottish populations but high differentiation (F_ST = 0.433–0.712) from the English/Welsh and other European populations. Differentiation was elevated genome‐wide rather than in particular genomic regions. Demographic modelling supported a postglacial colonization into western Scotland from northern refugia and a separate colonization route for the English/Welsh populations from southern refugia, with these two groups having been separated for more than ca. 50 Ky. We found cyto‐nuclear discordance at a European scale, with the Scottish populations clustering closely with Baltic population in the mtDNA analysis but not in the nuclear data, and with the Norwegian and Alpine populations displaying the same mtDNA haplotype but being distantly related in the nuclear tree. These findings suggest that neutral processes, primarily drift and regionally distinct pre‐glacial evolutionary histories, are important drivers of genomic divergence in British populations of European whitefish. This sheds new light on the establishment of the native British freshwater fauna after the last glacial maximum.

Geographic hierarchical population genetic structuring in British European whitefish (Coregonus lavaretus) and its implications for conservation

The European whitefish Coregonus lavaretus complex represents one of the most diverse radiations within salmonids, with extreme morphological and genetic differentiation across its range. Such variation has led to the assignment of many populations to separate species. In Great Britain, the seven native populations of C. lavaretus (two in Scotland, four in England, one in Wales) were previously classified into three species, and recent taxonomic revision resurrected the previous nomenclature. Here we used a dataset of 15 microsatellites to: (1) investigate the genetic diversity of British populations, (2) assess the level of population structure and the relationships between British populations. Genetic diversity was highest in Welsh (HO = 0.50, AR = 5.29), intermediate in English (HO = 0.41–0.50, AR = 2.83–3.88), and lowest in Scottish populations (HO = 0.28–0.35, AR = 2.56–3.04). Population structure analyses indicated high genetic differentiation (global FST = 0.388) between all populations but for the two Scottish populations (FST = 0.063) and two English populations (FST = 0.038). Principal component analysis and molecular ANOVA revealed separation between Scottish, English, and Welsh populations, with the Scottish populations being the most diverged. We argue that the data presented here are not sufficient to support a separation of the British European whitefish populations into three separate species, but support the delineation of different ESUs for these populations.

Testing the devil's impact on southern Baltic and North Sea basins whitefish (Coregonus spp.) diversity

Background

The diversity and phylogeny of whitefish of the genus Coregonus is complex, and includes many endemic species of high conservation concern. However, because of commercial importance of whitefish fisheries, stockings and translocations have occurred repeatedly, which challenges the identification of local populations as conservation units. This study analyses the phylogenetic relationships of 15 contemporary and two historical populations of lake-resident and anadromous whitefish (Coregonus spp.) from the southern Baltic and North Sea basins. We elucidated the complex history of Lake Schaal (northern Germany) whitefish, for which a local tale suggests that the devil threw whitefish from the Central European Lake Constance into this lake. Studies from the early twentieth century indeed suggested numerous stocking events for Lake Schaal from Lake Constance, from Estonian/Russian Lake Peipsi and from the anadromous whitefish of the Baltic Sea.

Results

Analyses of 13 microsatellite markers showed that Lake Constance whitefish are unrelated to any northern Germany whitefish population, including the contemporary whitefish population from Lake Schaal. Comparison with four historical specimens further showed that the native Lake Schaal whitefish (C. holsatus) vanished from the lake, but has survived as a non-native population in the north German Lake Drewitz. The whitefish currently occurring in Lake Schaal and three adjacent lakes are identified as C. maraenoides, introduced from Lake Peipsi. The contemporary anadromous whitefish populations from the Baltic (German and Finnish coast) and the German River Treene (North Sea basin, stocked from Danish River Vida) grouped together, but showed significant genetic differentiation. The 14 historical specimens of C. oxyrinchus from Rivers Rhine and Schelde were assigned to several contemporary whitefish populations, but among them only one specimen was assigned to the contemporary River Treene population. Therefore, we do not support the view that the whitefish from River Vida/Treene are identical with the historical C. oxyrinchus.

Conclusions

Our study demonstrates that lake and anadromous whitefish in the Baltic and North Sea basins reflect a complex phylogeography, which is further blurred by the effects of repeated stocking and translocations. To identify conservation units, the genetic identity of each population has to be scrutinized.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1339-2) contains supplementary material, which is available to authorized users.

Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.)

Several studies have recently reported evidence for positive selection acting on the mitochondrial genome (mitogenome), emphasizing its potential role in adaptive divergence and speciation. In this study we searched 107 full mitogenomes of recently diverged species and lineages of whitefish (Coregonus ssp.) for signals of positive selection. These salmonids show several distinct morphological and ecological differences that may be associated with energetics and therefore potentially positive selection at the mitogenome level. We found that purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, the NADH dehydrogenase 2 gene (ND2) showed a highly elevated dN/dS ratio compared to the other mitochondrial genes, which was significantly higher in whitefish compared to other salmonids. We therefore further examined nonsynonymous evolution in ND2 by (i) mapping amino acid changes to a protein model structure which showed that they were located away from key functional residues of the protein, (ii) locating them in the sequences of other species of fish (Salmonidae, Anguillidae, Scombridae and Percidae) only to find pronounced overlap of nonsynonymous regions. We thus conclude that relaxed purifying selection is driving the evolution of ND2 by affecting mostly regions that have lower functional relevance.

Anthropogenic hybridization between endangered migratory and commercially harvested stationary whitefish taxa (Coregonus spp.)

Natural hybridization plays a key role in the process of speciation. However, anthropogenic (human induced) hybridization of historically isolated taxa raises conservation issues. Due to weak barriers to gene flow and the presence of endangered taxa, the whitefish species complex is an excellent study system to investigate the consequences of hybridization in conservation. We focused on three naturally reproductively isolated whitefish taxa in Germany: the endangered, anadromous North Sea houting (NSH) and Baltic houting (BH), which were reintroduced after local extinction, and the commercially stocked European whitefish (EW). To evaluate the genetic integrity of each taxon, source and reintroduced populations of NSH and BH, and EW populations were characterized based on two mitochondrial and 17 microsatellite loci. Additionally, we investigated gill raker counts as an adaptive phenotypic trait. Even though clear genetic and phenotypic differentiation confirmed the houtings as separate evolutionarily significant units, admixture analyses revealed an extensive hybrid zone. Hybridizations were introgressive, positively correlated with genetic diversity, and were reflected in the gill raker counts. The BH distribution range showed higher heterogeneity and stronger admixture than the NSH range. Erroneous stocking with non-native genotypes best explained these patterns, which pose challenges for the conservation of the endangered NSH and BH.

Are phenotypic traits useful for differentiating among a priori Coregonus taxa?

A key for three putative species apparently found in three geographic areas, i.e. Coregonus clupeoides (in Scotland), Coregonus stigmaticus (in England), and Coregonus pennantii (in Wales) given in a recent review was tested quantitatively using 544 individuals from nine populations. The classification success of the key was very low (27%). It was concluded that there is currently no robust evidence for the recognition of the three putative species. Furthermore, the use of phenotypic characters alone to distinguish putative species in postglacial fish species such as those of the genus Coregonus that show homoplasy in many of these traits is questioned. In the absence of further evidence, it was concluded that a single highly variable species best describes the pattern of phenotypic variation in these U.K. populations. On this basis it is argued that taxonomic subdivision of U.K. European coregonids is inappropriate and that Coregonus lavaretus should prevail as the species name applicable to all populations.

Expression of interest: transcriptomics and the designation of conservation units

An important task within conservation genetics consists in defining intraspecific conservation units. Most conceptual frameworks involve two steps: (i) identifying demographically independent units, and (ii) evaluating their degree of adaptive divergence. Whereas a plethora of methods are available for delineating genetic population structure, assessment of functional genetic divergence remains a challenge. In this issue, Tymchuk et al. (2010) study Atlantic salmon (Salmo salar) populations using both microsatellite markers and analysis of global gene expression. They show that important gene expression differences exist that can be interpreted in the context of different ecological conditions experienced by the populations, along with the populations' histories. This demonstrates an important potential role of transcriptomics for designating conservation units.

How robust are "isolation with migration" analyses to violations of the im model? A simulation study

Methods developed over the past decade have made it possible to estimate molecular demographic parameters such as effective population size, divergence time, and gene flow with unprecedented accuracy and precision. However, they make simplifying assumptions about certain aspects of the species' histories and the nature of the genetic data, and it is not clear how robust they are to violations of these assumptions. Here, we use simulated data sets to examine the effects of a number of violations of the "Isolation with Migration" (IM) model, including intralocus recombination, population structure, gene flow from an unsampled species, linkage among loci, and divergent selection, on demographic parameter estimates made using the program IMA. We also examine the effect of having data that fit a nucleotide substitution model other than the two relatively simple models available in IMA. We find that IMA estimates are generally quite robust to small to moderate violations of the IM model assumptions, comparable with what is often encountered in real-world scenarios. In particular, population structure within species, a condition encountered to some degree in virtually all species, has little effect on parameter estimates even for fairly high levels of structure. Likewise, most parameter estimates are robust to significant levels of recombination when data sets are pared down to apparently nonrecombining blocks, although substantial bias is introduced to several estimates when the entire data set with recombination is included. In contrast, a poor fit to the nucleotide substitution model can result in an increased error rate, in some cases due to a predictable bias and in other cases due to an increase in variance in parameter estimates among data sets simulated under the same conditions.