Local Adaptation in Marine Foundation Species at Microgeographic Scales

Unraveling Adaptive Evolutionary Divergence at Microgeographic Scales

AbstractStriking examples of local adaptation at fine geographic scales are increasingly being documented in natural populations. However, the relative contributions made by natural selection, phenotype-dependent dispersal (when individuals disperse with respect to a habitat preference), and mate preference in generating and maintaining microgeographic adaptation and divergence are not well studied. Here, we develop quantitative genetics models and individual-based simulations (IBSs) to uncover the evolutionary forces that possibly drive microgeographic divergence. We also perform Bayesian estimation of the parameters in our IBS using empirical data on habitat-specific variation in bill morphology in the island scrub-jay (Aphelocoma insularis) to apply our models to a natural system. We find that natural selection and phenotype-dependent dispersal can generate the patterns of divergence we observe in the island scrub-jay. However, mate preference for a mate with similar bill morphology, even though observed in the species, does not play a significant role in driving divergence. Our modeling approach provides insights into phenotypic evolution occurring over small spatial scales relative to dispersal ranges, suggesting that adaptive divergence at microgeographic scales may be common across a wider range of taxa than previously thought. Our quantitative genetic models help to inform future theoretical and empirical work to determine how selection, habitat preference, and mate preference contribute to local adaptation and microgeographic divergence.

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.

Partial Clonality Expands the Opportunity for Spatial Adaptation

AbstractReproductive mode may strongly impact adaptation in spatially varying populations linked by dispersal, especially when sexual and clonal offspring differ in dispersal. We determined how spatial structure affects adaptation in populations with mixed clonal and sexual reproduction. In a source-sink quantitative genetic deterministic model (with stabilizing selection around different optima), greater clonal reproduction or parent-offspring association (a measure of the part of the parent's phenotype other than the additive genetic component inherited by clonal offspring) increased the selective difference (difference between phenotypic optima) allowing sink populations to adapt. Given dispersal differences between clonally and sexually produced juveniles, adaptation increased with an increasing fraction of clonal dispersers. When considering migrational meltdown, partially clonal reproduction reduced cases where dispersal caused habitat loss. Stochastic individual-based simulations support these results, although the effect of differential dispersal was reversed, with decreased clonal dispersal allowing greater adaptation. These results parallel earlier findings that for an instantaneous shift in phenotypic optimum, increasing clonality allowed population persistence for a greater shift; here, selective change is spatial rather than temporal. These results may help explain the success of many partially clonal organisms in invading new habitats, complementing traditional explanations based on avoiding Allee effects.

Insights into the divergent evolution of the oceanic squid Sthenoteuthis oualaniensis (Cephalopoda: Ommastrephidae) from the Indian Ocean

Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms (viz. middle-sized, dwarf, and giant forms) whose taxonomic status has been disputed for decades. This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species. Molecular analyses employing mitochondrial (COI, ND2) and nuclear (H3) markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean, representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean. The mitochondrial-based phylograms revealed two distinct clades in the species: "dwarf forms + giant form" and "middle-sized forms," which further branch into geographically structured evolutionary units. Species delimitation analyses recovered five distinct clades, namely, the Arabian Sea giant and dwarf forms, Equatorial, Eastern Typical, and Other Middle-sized forms, representing the consensus molecular operational taxonomic units. H3 being heterozygous could not resolve the phylogeny. Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes, whereas these outputs and PCA results were incongruent with the morphological grouping. Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes. The giant form was genetically close to the dwarf forms, contradicting the earlier notion that it descended from the middle-sized form. It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters, while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.

A temporal and spatial study of genetic structure in four species of bladed Bangiales (Rhodophyta) from the southeastern Pacific coast of Chile

The coastline is a heterogeneous and highly dynamic environment influenced by abiotic and biotic variables affecting the temporal stability of genetic diversity and structure of marine organisms. The aim of this study was to determine how much the genetic structure of four species of marine Bangiales vary in time and space. Partial sequences of the cytochrome oxidase I (COI) gene obtained from two Pyropia (Py. sp. CHJ and Py. orbicularis) and two Porphyra (P. mumfordii and P. sp. FIH) species were used to compare the effect of the 40° S/41° S biogeographic break (spatial-regional scale) and the one of the Valdivia River discharges (spatial-local scale) and determine their temporal stability. Four seasonal samplings were taken during 1 year at five sites, one site located in Melinka (Magallanes province) and four sites along the coast of Valdivia (Intermediate area), on both sides of the river mouth. Results showed a strong genetic spatial structure at regional scale (ΦST > 0.4) in Py. sp. CHJ, Py. orbicularis, and P. mumfordii, congruent with the 41° S/42° S biogeographic break. A potential barrier to gene flow, related to the Valdivia River discharge, was detected only in P. mumfordii. In P. sp. FIH, spatial genetic structure was not detected at any scale. The genetic structure of all four species is stable throughout the year. The potential effect of main currents and river discharge in limiting the transport of Bangiales spores are discussed. We propose that both a restricted propagule dispersal and the formation potential for persistent banks of microscopic stages could lead to a temporally stable spatial partitioning of genetic variation in bladed Bangiales.

Intraspecific variation in a predator changes intertidal community through effects on a foundation species

Intraspecific variation is an important form of biodiversity that can alter community and ecosystem properties. Recent work demonstrates the community effects of intraspecific variation in predators via altering prey communities and in foundation species via shaping habitat attributes. However, tests of the community effects of intraspecific trait variation in predators acting on foundation species are lacking despite the fact that consumption of foundation species can have strong community effects by shaping habitat structure. Here, we tested the hypothesis that intraspecific foraging differences among populations of mussel-drilling dogwhelk predators (Nucella) differentially alter intertidal communities through effects on foundational mussels. We conducted a 9-month field experiment where we exposed intertidal mussel bed communities to predation from three Nucella populations that exhibit differences in size-selectivity and consumption time for mussel prey. At the end of the experiment, we measured mussel bed structure, species diversity, and community composition. While exposure to Nucella originating from different populations did not significantly alter overall community diversity, we found that differences in Nucella mussel selectivity significantly altered foundational mussel bed structure, which in turn altered the biomass of shore crabs and periwinkle snails. Our study extends the emerging paradigm of the ecological importance of intraspecific variation to include the effects of intraspecific variation on predators of foundation species.

A Pleistocene legacy structures variation in modern seagrass ecosystems

Sustaining biodiversity and ecosystems in the long term depends on their adjustment to a rapidly changing climate. By characterizing the structure of the marine plant eelgrass and associated communities at 50 sites across its broad range, we found that eelgrass growth form and biomass retain a legacy of Pleistocene range shifts and genetic bottlenecks that in turn affect the biomass of algae and invertebrates that fuel coastal food webs. The ecosystem-level effects of this ancient evolutionary legacy are comparable to or stronger than effects of current environmental forcing, suggesting that this economically important ecosystem may be unable to keep pace with rapid global change.

Distribution of Earth’s biomes is structured by the match between climate and plant traits, which in turn shape associated communities and ecosystem processes and services. However, that climate–trait match can be disrupted by historical events, with lasting ecosystem impacts. As Earth’s environment changes faster than at any time in human history, critical questions are whether and how organismal traits and ecosystems can adjust to altered conditions. We quantified the relative importance of current environmental forcing versus evolutionary history in shaping the growth form (stature and biomass) and associated community of eelgrass (Zostera marina), a widespread foundation plant of marine ecosystems along Northern Hemisphere coastlines, which experienced major shifts in distribution and genetic composition during the Pleistocene. We found that eelgrass stature and biomass retain a legacy of the Pleistocene colonization of the Atlantic from the ancestral Pacific range and of more recent within-basin bottlenecks and genetic differentiation. This evolutionary legacy in turn influences the biomass of associated algae and invertebrates that fuel coastal food webs, with effects comparable to or stronger than effects of current environmental forcing. Such historical lags in phenotypic acclimatization may constrain ecosystem adjustments to rapid anthropogenic climate change, thus altering predictions about the future functioning of ecosystems.

Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora

Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.