Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species

Coral Reef Population Genomics in an Age of Global Change

Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.

Complementary evidence for small-scale spatial assemblages of the exploited grass emperor (Lethrinus laticaudis) in the Shark Bay World Heritage Area, Western Australia

Understanding the connectivity of exploited fish populations is critical to their management under both rapid and long-term environmental change. Patterns of connectivity are unknown for most fishes in the Shark Bay World Heritage Area (Western Australia), a large, shallow embayment in the eastern Indian Ocean, vulnerable to marine heatwaves. The composition of oxygen (δ¹⁸O) and carbon (δ¹³C) stable isotopes in whole otoliths of the recreationally-important reef fish Lethrinus laticaudis did not differ between Shark Bay's two large inner gulfs, separated by the Peron Peninsula. However, significant differences were found between pairs of locations with different salinities over a spatial scale of ∼60 km within each gulf. Misclassification of samples was greatest between locations mostly in different gulfs, but with similar salinities (15-41%), and rare between adjacent locations in the same gulf with different salinities (0-5%). This is influenced by the strong correlation (ρ = 0.93) between δ¹⁸O in otoliths and the salinity gradient of the two gulfs, and further supported by a lack of correlation in the similarities of isotope compositions and distances between locations (ρ = 0.16). Fish samples from each of the different locations were composed of multiple year-classes, yet the otolith chemistry distinguished them at a minimum distance of 16 km apart, indicating that small-scale connectivity of L. laticaudis is likely during the majority of their life cycle. Physical barriers to movement of post-settlement individuals (land masses, expansive seagrass and sand) between the small, isolated reefs of Shark Bay may reduce large scale connectivity, which instead would occur mostly by egg and larval dispersal. The probable scale of connectivity of post-settlement L. laticaudis indicates that this major recreational fishing target species may be vulnerable to localised over-exploitation and negative environmental effects on population sources and sinks within this shallow embayment. Maintaining sustainable spawning biomass at scales relevant to the extent of connectivity for such a species in a World Heritage Area is an important management consideration.

Coupled Source-Sink Habitats Produce Spatial and Temporal Variation of Cancer Cell Molecular Properties as an Alternative to Branched Clonal Evolution and Stem Cell Paradigms

Intratumoral molecular cancer cell heterogeneity is conventionally ascribed to the accumulation of random mutations that occasionally generate fitter phenotypes. This model is built upon the “mutation-selection” paradigm in which mutations drive ever-fitter cancer cells independent of environmental circumstances. An alternative model posits spatio-temporal variation (e.g., blood flow heterogeneity) drives speciation by selecting for cancer cells adapted to each different environment. Here, spatial genetic variation is the consequence rather than the cause of intratumoral evolution. In nature, spatially heterogenous environments are frequently coupled through migration. Drawing from ecological models, we investigate adjacent well-perfused and poorly-perfused tumor regions as “source” and “sink” habitats, respectively. The source habitat has a high carrying capacity resulting in more emigration than immigration. Sink habitats may support a small (“soft-sink”) or no (“hard-sink”) local population. Ecologically, sink habitats can reduce the population size of the source habitat so that, for example, the density of cancer cells directly around blood vessels may be lower than expected. Evolutionarily, sink habitats can exert a selective pressure favoring traits different from those in the source habitat so that, for example, cancer cells adjacent to blood vessels may be suboptimally adapted for that habitat. Soft sinks favor a generalist cancer cell type that moves between the environment but can, under some circumstances, produce speciation events forming source and sink habitat specialists resulting in significant molecular variation in cancer cells separated by small distances. Finally, sink habitats, with limited blood supply, may receive reduced concentrations of systemic drug treatments; and local hypoxia and acidosis may further decrease drug efficacy allowing cells to survive treatment and evolve resistance. In such cases, the sink transforms into the source habitat for resistant cancer cells, leading to treatment failure and tumor progression. We note these dynamics will result in spatial variations in molecular properties as an alternative to the conventional branched evolution model and will result in cellular migration as well as variation in cancer cell phenotype and proliferation currently described by the stem cell paradigm.

Genomic signatures of spatially divergent selection at clownfish range margins

Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.

Population Genetic Structure and Connectivity of the European Lobster Homarus gammarus in the Adriatic and Mediterranean Seas

Highly selective fishing has the potential to permanently change the characteristics within a population and could drive the decline of genetic diversity. European lobster is an intensively fished crustacean species in the Adriatic Sea which reaches high market value. Since knowledge of population structure and dynamics is important for effective fisheries management, in this study, we used 14 neutral microsatellites loci and partial mitochondrial COI region sequencing to explore population connectivity and genetic structure by comparing samples from the Adriatic Sea and the adjacent basins of the Mediterranean Sea. The obtained results suggest that neutral genetic diversity has not been significantly affected by decrease in population size due to overfishing, habitat degradation and other anthropogenic activities. Global genetic differentiation across all populations was low (F ST = 0.0062). Populations from the Adriatic Sea were panmictic, while genetic differentiation was found among populations from different Mediterranean basins. Observed gene flow for European lobster suggest that populations in the north eastern Adriatic act as a source for surrounding areas, emphasizing the need to protect these populations by establishing interconnected MPAs that will be beneficial for both fisheries and conservation management.

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

Reconciling differences in natural tags to infer demographic and genetic connectivity in marine fish populations

Processes regulating population connectivity are complex, ranging from extrinsic environmental factors to intrinsic individual based features, and are a major force shaping the persistence of fish species and population responses to harvesting and environmental change. Here we developed an integrated assessment of demographic and genetic connectivity of European flounder Platichthys flesus in the northeast Atlantic (from the Norwegian to the Portuguese coast) and Baltic Sea. Specifically, we used a Bayesian infinite mixture model to infer the most likely number of natal sources of individuals based on otolith near core chemical composition. Simultaneously, we characterised genetic connectivity via microsatellite DNA markers, and evaluated how the combined use of natural tags informed individual movement and long-term population exchange rates. Individual markers provided different insights on movement, with otolith chemistry delineating Norwegian and Baltic Sea sources, whilst genetic markers showed a latitudinal pattern which distinguished southern peripheral populations along the Iberian coast. Overall, the integrated use of natural tags resulted in outcomes that were not readily anticipated by individual movement or gene flow markers alone. Our ecological and evolutionary approach provided a synergistic view on connectivity, which will be paramount to align biological and management units and safeguard species' biocomplexity.