Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata

Genomic data reveals habitat partitioning in massive Porites on Guam, Micronesia

Corals in marginal reef habitats generally exhibit less bleaching and associated mortality compared to nearby corals in more pristine reef environments. It is unclear, however, if these differences are due to environmental differences, including turbidity, or genomic differences between the coral hosts in these different environments. One particularly interesting case is in the coral genus Porites, which contains numerous morphologically similar massive Porites species inhabiting a wide range of reef habitats, from turbid river deltas and stagnant back reefs to high-energy fore reefs. Here, we generate ddRAD data for 172 Porites corals from river delta and adjacent (<0.5 km) fore reef populations on Guam to assess the extent of genetic differentiation among massive Porites corals in these two contrasting environments and throughout the island. Phylogenetic and population genomic analyses consistently identify seven different clades of massive Porites, with the two largest clades predominantly inhabiting either river deltas or fore reefs, respectively. No population structure was detected in the two largest clades, and Cladocopium was the dominant symbiont genus in all clades and environments. The perceived bleaching resilience of corals in marginal reefs may therefore be attributed to interspecific differences between morphologically similar species, in addition to potentially mediating environmental differences. Marginal reef environments may therefore not provide a suitable refuge for many reef corals in a heating world, but instead host additional cryptic coral diversity.

Integrating cryptic diversity into coral evolution, symbiosis and conservation

Understanding how diversity evolves and is maintained is critical to predicting the future trajectories of ecosystems under climate change; however, our understanding of these processes is limited in marine systems. Corals, which engineer reef ecosystems, are critically threatened by climate change, and global efforts are underway to conserve and restore populations as attempts to mitigate ocean warming continue. Recently, sequencing efforts have uncovered widespread undescribed coral diversity, including 'cryptic lineages'-genetically distinct but morphologically similar coral taxa. Such cryptic lineages have been identified in at least 24 coral genera spanning the anthozoan phylogeny and across ocean basins. These cryptic lineages co-occur in many reef systems, but their distributions often differ among habitats. Research suggests that cryptic lineages are ecologically specialized and several examples demonstrate differences in thermal tolerance, highlighting the critical implications of this diversity for predicting coral responses to future warming. Here, we draw attention to recent discoveries, discuss how cryptic diversity affects the study of coral adaptation and acclimation to future environments, explore how it shapes symbiotic partnerships, and highlight challenges and opportunities for conservation and restoration efforts.

Small-scale genetic structure of coral populations in Palau based on whole mitochondrial genomes: Implications for future coral resilience

The ability of local populations to adapt to future climate conditions is facilitated by a balance between short range dispersal allowing local buildup of adaptively beneficial alleles, and longer dispersal moving these alleles throughout the species range. Reef building corals have relatively low dispersal larvae, but most population genetic studies show differentiation only over 100s of km. Here, we report full mitochondrial genome sequences from 284 tabletop corals (Acropora hyacinthus) from 39 patch reefs in Palau, and show two signals of genetic structure across reef scales from 1 to 55 km. First, divergent mitochondrial DNA haplotypes exist in different proportions from reef to reef, causing Phi_ST values of 0.02 (p = 0.02). Second, closely related sequences of mitochondrial Haplogroups are more likely to be co-located on the same reefs than expected by chance alone. We also compared these sequences to prior data on 155 colonies from American Samoa. In these comparisons, many Haplogroups in Palau were disproportionately represented or absent in American Samoa, and inter-regional Phi_ST = 0.259. However, we saw three instances of identical mitochondrial genomes between locations. Together, these data sets suggest two features of coral dispersal revealed by occurrence patterns in highly similar mitochondrial genomes. First, the Palau-American Samoa data suggest that long distance dispersal in corals is rare, as expected, but that it is common enough to deliver identical mitochondrial genomes across the Pacific. Second, higher than expected co-occurrence of Haplogroups on the same Palau reefs suggests greater retention of coral larvae on local reefs than predicted by many current oceanographic models of larval movement. Increased attention to local scales of coral genetic structure, dispersal, and selection may help increase the accuracy of models of future adaptation of corals and of assisted migration as a reef resilience intervention.

A decade of population genetics studies of scleractinian corals: A systematic review

Coral reefs are the most diverse marine ecosystems. However, coral cover has decreased worldwide due to natural disturbances, climate change, and local anthropogenic drivers. In recent decades, various genetic methods and molecular markers have been developed to assess genetic diversity, structure, and connectivity in different coral species to determine the vulnerability of their populations. This review aims to identify population genetic studies of scleractinian corals in the last decade (2010-2020), and the techniques and molecular markers used. Bibliometric analysis was conducted to identify journals and authors working in this field. We then calculated the number of genetic studies by species and ecoregion based on data obtained from 178 studies found in Scopus and Web of Science. Coral Reefs and Molecular Ecology were the main journals published population genetics studies, and microsatellites are the most widely used molecular markers. The Caribbean, Australian Barrier Reef, and South Kuroshio in Japan are among the ecoregions with the most population genetics data. In contrast, we found limited information about the Coral Triangle, a region with the highest biodiversity and key to coral reef conservation. Notably, only 117 (out of 1500 described) scleractinian coral species have genetic studies. This review emphasizes which coral species have been studied and highlights remaining gaps and locations where such data is critical for coral conservation.

Genetic patterns in Montipora capitata across an environmental mosaic in Kāne'ohe Bay, O'ahu, Hawai'i

Spatial genetic structure (SGS) is important to a population's ability to adapt to environmental change. For species that reproduce both sexually and asexually, the relative contribution of each reproductive mode has important ecological and evolutionary implications because asexual reproduction can have a strong effect on SGS. Reef-building corals reproduce sexually, but many species also propagate asexually under certain conditions. To understand SGS and the relative importance of reproductive mode across environmental gradients, we evaluated genetic relatedness in almost 600 colonies of Montipora capitata across 30 environmentally characterized sites in Kāne'ohe Bay, O'ahu, Hawaii, using low-depth restriction digest-associated sequencing. Clonal colonies were relatively rare overall but influenced SGS. Clones were located significantly closer to one another spatially than average colonies and were more frequent on sites where wave energy was relatively high, suggesting a strong role of mechanical breakage in their formation. Excluding clones, we found no evidence of isolation by distance within sites or across the bay. Several environmental characteristics were significant predictors of the underlying genetic variation (including degree heating weeks, time spent above 30°C, depth, sedimentation rate and wave height); however, they only explained 5% of this genetic variation. Our results show that asexual fragmentation contributes to the ecology of branching corals at local scales and that genetic diversity is maintained despite strong environmental gradients in a highly impacted ecosystem, suggesting potential for broad adaptation or acclimatization in this population.

Genetic differentiation and phylogeography of rotifer Polyarthra dolichoptera and P. vulgaris populations between Southeastern China and eastern North America: High intercontinental differences

Genetic differentiations and phylogeographical patterns of small organisms may be shaped by spatial isolation, environmental gradients, and gene flow. However, knowledge about genetic differentiation of rotifers at the intercontinental scale is still limited. Polyarthra dolichoptera and P. vulgaris are cosmopolitan rotifers that are tolerant to environmental changes, offering an excellent model to address the research gap. Here, we investigated the populations in Southeastern China and eastern North America and evaluated the phylogeographical patterns from their geographical range sizes, geographic–genetic distance relationships and their responses to spatial‐environmental factors. Using the mitochondrial cytochrome c oxidase subunit I gene as the DNA marker, we analyzed a total of 170 individuals. Our results showed that some putative cryptic species, also known as entities were widely distributed, but most of them were limited to single areas. The divergence of P. dolichoptera and P. vulgaris indicated that gene flow between continents was limited while that within each continent was stronger. Oceanographic barriers do affect the phylogeographic pattern of rotifers in continental waters and serve to maintain genetic diversity in nature. The genetic distance of P. dolichoptera and P. vulgaris populations showed significant positive correlation with geographic distance. This might be due to the combined effects of habitat heterogeneity, long‐distance colonization, and oceanographic barriers. Furthermore, at the intercontinental scale, spatial distance had a stronger influence than environmental variables on the genetic differentiations of both populations. Wind‐ and animal‐mediated transport and even historical events of continental plate tectonics are potential factors for phylogeography of cosmopolitan rotifers.

Barriers and corridors of gene flow in an urbanized tropical reef system

Information about the distribution of alleles among marine populations is critical for determining patterns of genetic connectivity that are essential in modern conservation planning. To estimate population connectivity in Singapore's urbanized equatorial reef system, we analysed single nucleotide polymorphisms (SNPs) from two species of reef-building corals with distinct life histories. For Porites sp., a broadcast-spawning coral, we found cryptic lineages that were differentially distributed at inshore and central-offshore sites that could be attributed to contemporary surface current regimes. Near panmixia was observed for Pocillopora acuta with differentiation of colonies at the farthest site from mainland Singapore, a possible consequence of the brooding nature and relatively long pelagic larval duration of the species. Furthermore, analysis of recent gene flow showed that 60-80% of colonies in each population were nonmigrants, underscoring self-recruitment as an important demographic process in this reef system. Apart from helping to enhance the management of Singapore's coral reef ecosystems, findings here pave the way for better understanding of the evolution of marine populations in South-East Asia.

Physiological and molecular responses of lobe coral indicate nearshore adaptations to anthropogenic stressors

Corals in nearshore marine environments are increasingly exposed to reduced water quality, which is the primary local threat to Hawaiian coral reefs. It is unclear if corals surviving in such conditions have adapted to withstand sedimentation, pollutants, and other environmental stressors. Lobe coral populations from Maunalua Bay, Hawaii showed clear genetic differentiation between the 'polluted, high-stress' nearshore site and the 'less polluted, lower-stress' offshore site. To understand the driving force of the observed genetic partitioning, reciprocal transplant and common-garden experiments were conducted to assess phenotypic differences between these two populations. Physiological responses differed significantly between the populations, revealing more stress-resilient traits in the nearshore corals. Changes in protein profiles highlighted the inherent differences in the cellular metabolic processes and activities between the two; nearshore corals did not significantly alter their proteome between the sites, while offshore corals responded to nearshore transplantation with increased abundances of proteins associated with detoxification, antioxidant defense, and regulation of cellular metabolic processes. The response differences across multiple phenotypes between the populations suggest local adaptation of nearshore corals to reduced water quality. Our results provide insight into coral’s adaptive potential and its underlying processes, and reveal potential protein biomarkers that could be used to predict resiliency.

Asexual reproduction in bad times? The case of Cladocora caespitosa in the eastern Mediterranean Sea

We analysed the patterns of genetic variability of eastern Mediterranean populations of the scleractinian coral Cladocora caespitosa, from the Aegean and Levantine seas, using 19 polymorphic microsatellite loci, 11 of which were newly characterized. The observed genetic pattern reflects a scenario of isolation by environment: F _ST comparisons showed a higher degree of genetic differentiation between the two Cypriot populations that are separated by only 11 km than between these two Levantine populations and the Aegean population in Greece, which are separated by 1300 km. We hypothesize that local-scale oceanographic factors influenced the dispersal of planulae between the geographically close populations, playing a crucial role in the genetic structure of this coastal coral. Yet, despite being characterized as a species with limited dispersal and high self-recruitment, large-scale migration does eventually occur as first-generation migrants were identified between the most distant populations. In line with previous findings of reproductive plasticity in C. caespitosa, we also found localized differences in reproduction mode (sexual vs. asexual) within a geographically limited context. Several individuals were identified as clones, indicating the predominance of asexual reproduction in one of the Cypriot populations. We interpret this predominance either as a direct response to or as an indirect consequence of perturbations suffered by this C. caespitosa population. These perturbations are caused by unfavourable environmental conditions that threatened local survival, in particular water temperature changes and windstorm swells. Asexual reproduction may be a mechanism used by C. caespitosa to counteract mortality events and recolonize devastated areas, and likely accounts for the occasional high levels of clonality and low levels of genetic diversity. Local adaptations such as these should therefore be considered in conservation and management strategies to maintain and preserve the gene pool of this endangered species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at (10.1007/s00338-020-02040-3).

Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

The 'species' is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The 'Porites lobata species complex' consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāne'ohe Bay Hawai'i during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

BACKGROUND

As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis).

RESULTS

Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus.

CONCLUSION

The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.