Genomics is an invaluable tool for conservation, particularly for endangered species impacted by wildlife trafficking. This study uses genomic data to provide new insights to aid conservation and management of endangered species, using as a case study the Yellow cardinal (Gubernatrix cristata), a bird endemic to southern South America severely affected by illegal trade and the transformation of its natural habitat. We explore population structure within the Yellow cardinal, delimiting management units and describing connectivity among them. Additionally, we develop and assess the accuracy of a panel of 189 informative SNPs, and demonstrate how these can reliably assign confiscated individuals to one of the management units established. Lastly, we assess hybridization between the Yellow cardinal and the Diuca finch (Diuca diuca), which is reported to occur in regions of sympatry. We confirm that hybridization occurs, although it is not as common as previously thought, and that hybrids might be fertile, as we found evidence of backcrossing with Yellow cardinals. We discuss the implications of this introgression for the evolution and conservation of Yellow cardinals. Our study provides new, valuable information that can guide conservation efforts, comprising a test case for the use of genomics in combating illegal trafficking, with potential application beyond the case of the Yellow cardinal.

The Major Histocompatibility Complex (MHC) is a central element in the vertebrate immune system. While MHC genes are a common target of conservation genomic studies, it has been challenging to reliably amplify locus-specific alleles, which is especially problematic when studying endangered lineages, like some Harbour porpoise (Phocoena phocoena) populations and subspecies. Here, we manually annotated all MHC II genes in the Harbour porpoise genome, and genotyped every exon 2 in 94 individuals spanning six geographical regions, including the endangered Black Sea porpoise subspecies (Phocoena phocoena relicta) and the endangered Proper Baltic Sea population of the North Atlantic subspecies (P. p. phocoena). We performed gene-wise analyses of diversity and selection, and put the results into perspective with 24 available Harbour porpoise genomes. Furthermore, we characterized all MHC II genes in 19 available long-read cetacean and terrestrial outgroups genomes to study the MHC II evolution across the cetacean diversification. From the 10 MHC II loci annotated in the Harbour porpoise genome, two (DRB1 and DQB) exhibited inflated allelic diversity and signatures of positive selection. Interestingly, DRB genes followed different evolutionary trajectories in mysticetes and odontocetes. Our results have significant conservation implications since we identified reduced MHC II diversity in the endangered Black Sea subspecies, and provide a case study for reliable MHC II genotyping in other species. Further, our study demonstrates the need for long-read genomes to understand the genomic architecture of MHC and to accurately assess its diversity and evolution.

The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species which primarily occurs in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes that vary broadly in salinity and temperature. Here we produced 74 whole genomes at intermediate coverage to study Harbour porpoise’s evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high quality SNPs sampled at 8 localities across the North Atlantic and adjacent waters, which we used for population structure, demographic, and genotype-environment association analyses. Our results support a genetic differentiation between three subspecies, and three distinct populations within the subspecies P.p. phocoena: Atlantic, Belt Sea and Proper Baltic Sea. Effective population size and Tajima’s D levels suggest a population contraction in both Black Sea and Iberian porpoises while a population expansion in the P.p. phocoena populations. Phylogenetic trees indicate a post-glacial colonization of Harbour porpoises from a southern refugium. Genotype-environment association analysis identified salinity as a major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity levels. Our study highlights the value of whole genome resequencing to unravel subtle population structure in highly mobile species and shows how strong environmental gradients and local adaptation may lead to population differentiation. The results have great conservation implications as we found major levels of inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.

Ecological speciation within the mormyrid genus Campylomormyrus resulted in sympatric species exhibiting divergence in their feeding apparatus and electric organ discharge (EOD). This study documents the overall diet of the genus Campylomormyrus and examines the hypothesis that Campylomormyrus radiation is caused by an adaptation to different food sources. We performed diet assessment of five sympatric Campylomormyrus species (C. alces, C. compressirostris, C. curvirostris, C. tshokwe, C. numenius) and their sister taxon Gnathonemus petersii with markedly different snout morphologies and EODs using hybrid capture/HTS DNA metabarcoding of their stomach contents. Our approach allowed for high taxonomic resolution of prey items, including benthic invertebrates, allochthonous invertebrates, and vegetation. Comparisons of the diet compositions using quantitative measures and diet overlap indices revealed that all species are able to exploit multiple food niches in their habitats, i.e., fauna at the bottom, the water surface, and the water column. Major part of the diet is larvae of aquatic insects, such as dipterans, coleopterans, and trichopterans, known to occur in holes and interstitial spaces of the substrate. The results showed that different snout morphologies and the associated divergence in the EOD translate into different prey spectra. This suggests that the diversification in EOD and the morphology of the feeding apparatus is under functional adaptation.

Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommuniy studies, we jointly examine active and dormant communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (I) spatial and temporal connectivity of the communities, (II) environmental factors influencing local communities, and (III) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples, but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity. Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (I) spatial and temporal connectivity of the communities, (II) environmental factors influencing local communities, and (III) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples, but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.    

Ecological speciation within the mormyrid genus Campylomormyrus resulted in sympatric species exhibiting divergence in their feeding apparatus and electric organ discharge (EOD). This study provides direct evidence to support the suggested ecological speciation scenario that Campylomormyrus radiation is caused by an adaptation to different food sources. We performed diet assessment of sympatric Campylomormyrus species with markedly different snout morphologies and EODs using hybrid capture/NGS DNA metabarcoding of their stomach contents. Our approach allowed for high taxonomic resolution of prey items, including benthic invertebrates, allochthonous invertebrates, and vegetation. Comparisons of the diet compositions using quantitative measures and diet overlap indices revealed that all species are able to exploit multiple food niches in their habitats, i.e. fauna at the bottom, the water surface, and the water column. The major part of the diet is larvae of aquatic insects, such as dipterans, coleopterans, and trichopterans, known to occur in holes and interstitial spaces of the substrate. The results showed that different snout morphologies and the associated divergence in the EOD translate into different prey spectra. This suggests that the diversification in EOD and the morphology of the feeding apparatus is under functional adaptation.

Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden, this decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after presumed illegal release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (as a proxy for fitness) of introgressed and non-introgressed populations, and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition. We observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency towards higher body weight, relative to regional non-introgressed populations. These differences were not observed among introgressed and non-introgressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than southern populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of struggling range margin populations without distortion of local adaptation.

Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modelled as random noise and linear reaction norms that assume simple one-to-one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and non-adaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directional climate change. Non-adaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, logistic, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (i) smaller phenotypic than genotypic variance in the population and the coexistence of polymorphisms, (ii) many-to-one genotype-phenotype map, and (iii) the maintenance of higher genetic variation – compared to linear reaction norms and genetic determinism – even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red noise stochasticity and was particularly important for life histories with low fecundity. Populations producing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.

A species’ response to thermal stress is an essential physiological trait that can determine occurrence and temporal succession in nature, including response to climate change. Environmental temperature affects zooplankton performance by altering life-spans and population growth rates, but the molecular mechanisms underlying these alterations are largely unknown. To compare temperature-related demography, we performed cross-temperature life-table experiments in closely related heat-tolerant and heat-sensitive Brachionus rotifer species that occur in sympatry. Within these same populations, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. We found significant cross-species and cross-temperature differences in heat response, with the heat-sensitive species adopting a strategy of high survival and low population growth, while the heat-tolerant followed an opposite strategy. Comparative transcriptomic analyses revealed both shared and opposing responses to heat. Most notably, expression of heat shock proteins (hsps) is strikingly different in the two species. In both species, hsp responses mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories such as energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to induction of meiotic division as well as genes responsible for post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.