From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals

Differential effects of nutrients and consumer pressure on sympatric cryptic coral species (Pocillopora spp.)

Cryptic species (evolutionarily distinct lineages that do not align with morphologically defined species) are being increasingly discovered but are poorly integrated into ecological theory. In particular, we still lack a useful understanding of if and how cryptic species differ in ways that affect community recovery from disturbances and responses to anthropogenic stressors, such as the removal of consumers and pollution from nutrients. On coral reefs, nutrient pollution increases the growth of macroalgae that displace corals. Reductions in herbivorous fishes reduce the suppression of macroalgae, while reductions in coralivorous fishes reduce predation on corals. An unresolved question is if and how cryptic coral species respond differently to these impacts, thereby differing in their ability to influence coral community dynamics and maintain coral dominance. Therefore, we assessed how the response of cryptic Pocillopora species over a period of three years following a simulated disturbance from a cyclone depended on the experimental reduction of fish consumer pressure and nutrient addition. After three years, five morphologically cryptic, but genetically distinct, Pocillopora species recruited to the reef. However, recruitment was dominated by two species: Pocillopora tuahiniensis (46%) and Pocillopora meandrina (43%). Under ambient conditions, recruitment of P. tuahiniensis and P. meandrina was similar, but experimentally reducing consumer pressure increased recruitment of P. tuahiniensis by up to 73% and reduced recruitment of P. meandrina by up to 49%. In both species, nutrient enrichment increased recruitment and colony growth rates equally, but colonies of P. tuahiniensis grew faster and were up to 25% larger after three years than those of P. meandrina, and growth was unaffected by reduced consumer pressure. Predation by excavating corallivorous fish was higher for P. meandrina than for P. tuahiniensis, especially under nutrient enrichment. In contrast, polyp extension (an indicator of elevated heterotrophic feeding as well as susceptibility and attractiveness to corallivores) was lower for P. meandrina than for P. tuahiniensis, especially under low to medium consumer pressure. Overall, we uncovered ecological differences in the response of morphologically cryptic foundation species to two pervasive stressors on coral reefs. Our results demonstrate how cryptic species respond differently to key anthropogenic stressors, which may contribute to response diversity that can support ecological resilience or increase extinction risk.

A genomic approach to Porites (Anthozoa: Scleractinia) megadiversity from the Indo-Pacific

Porites corals are vital components of tropical reef ecosystems worldwide, serving as ecosystem engineers and hubs of biodiversity in shallow water coral reefs. Despite their ecological significance and the widespread use of Porites spp. as models for research, the richness and evolutionary relationships of species within the genus remain elusive. In this study, we analyzed genomic data from 330 colonies of Porites from 17 localities across the Indo-Pacific region based on the reduced representation genomic approach ezRAD. We retrieved 25,163 SNPs and provided a phylogenomic hypothesis for 29 nominal species and 10 unknown morphologies, recovering 15 deeply rooted molecular clades. Among these, 12 clades included samples corresponding to single distinct morphospecies. One did not match any nominal species. The remaining two clades comprised species complexes, which included various massive and encrusting morphologies commonly used in experimental biology. Within these complexes, we observed additional geographic or morphological structure, indicating complex evolutionary dynamics, possibly reflecting distinct species, isolated populations or hybridization. Additionally, a series of divergent samples underscored the importance of more sampling to define species boundaries and refine phylogenomic relationships. We also integrated our findings with previous phylogenetic datasets and their respective sampling localities, challenging traditional notions about Porites species geographic distributions. Overall, our findings indicate a need to revise past synonymies and to formally establish new species. A precise understanding of Porites species and their diversity and distributions is necessary for effective reef conservation and management.

Symbiodiniaceae diversity in Pocillopora corals in different environments of the Colombian Eastern Pacific: symbiont specificity in spite of coral-host flexibility

Reef-building corals live in close mutualism with dinoflagellate algae (family Symbiodiniaceae), which play key roles in coral physiological performance and survival. Association patterns between host species and endosymbiont algae and their significance are still not fully understood, but they seem to affect the ability of hosts to inhabit different environments and their resilience to climate change. In this work, we used next-generation sequencing of the Internal Transcribed Spacer 2 region of ribosomal DNA to determine the diversity and composition of the Symbiodiniaceae community in Pocillopora corals from Colombia, in the Eastern Tropical Pacific (ETP). We sampled 243 colonies from four localities characterized by distinct sea surface temperature, turbidity, and proximity to the coast. Two genera of Symbiodiniaceae, Durusdinium and Cladocopium were found associated with Pocillopora mitochondrial Open Reading Frame (mtORF) types. Cladocopium latusorum was highly specific to Pocillopora mtORF type 1, while C. pacificum was found exclusively associated with Pocillopora mtORF type 3. In contrast, Durusdinium glynnii was found in both Pocillopora mtORF types. Furthermore, a Cladocopium-dominated symbiont community occurred in cooler and less turbid localities, while a Durusdinium- dominated community was found in localities with high sea surface temperature and high water turbidity, irrespective of mtORF type. These results suggest that Pocillopora mtORF lineages associate with different Symbiodiniaceae genera in response to local environmental conditions. The ability to associate with a different partner under particular environmental conditions (Pocillopora-Durusdinium combination), and also maintain a specific partnership (Cladocopium species and Pocillopora mtORF types) may be key to understanding the resilience of the genus Pocillopora on ETP coral reefs.

Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts

While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co-occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 Pocillopora corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of Pocillopora, most of which cannot be reliably identified based on morphology: P. meandrina (42.9%), P. tuahiniensis (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and P. cf. effusa (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used psbA ncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of Pocillopora species differed across habitats within the reef. Sister taxa P. verrucosa and P. tuahiniensis had similar niche breadths and hosted the same specialist symbiont species (mostly Cladocopium pacificum) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa P. meandrina and P. grandis had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly C. latusorum). Pocillopora acuta had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, Durusdinium gynnii. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth-Pocillopora species with a broader habitat niche also had a broader symbiont niche. Our results show how fine-scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated.

Latitudinal variation in thermal performance of the common coral Pocillopora spp

Understanding how tropical corals respond to temperatures is important to evaluating their capacity to persist in a warmer future. We studied the common Pacific coral Pocillopora over 44° of latitude, and used populations at three islands with different thermal regimes to compare their responses to temperature using thermal performance curves (TPCs) for respiration and gross photosynthesis. Corals were sampled in the local autumn from Moorea, Guam and Okinawa, where mean±s.d. annual seawater temperature is 28.0±0.9°C, 28.9±0.7°C and 25.1±3.4°C, respectively. TPCs for respiration were similar among latitudes, the thermal optimum (Topt) was above the local maximum temperature at all three islands, and maximum respiration was lowest at Okinawa. TPCs for gross photosynthesis were wider, implying greater thermal eurytopy, with a higher Topt in Moorea versus Guam and Okinawa. Topt was above the maximum temperature in Moorea, but was similar to daily temperatures over 13% of the year in Okinawa and 53% of the year in Guam. There was greater annual variation in daily temperatures in Okinawa than Guam or Moorea, which translated to large variation in the supply of metabolic energy and photosynthetically fixed carbon at higher latitudes. Despite these trends, the differences in TPCs for Pocillopora spp. were not profoundly different across latitudes, reducing the likelihood that populations of these corals could better match their phenotypes to future more extreme temperatures through migration. Any such response would place a premium on high metabolic plasticity and tolerance of large seasonal variations in energy budgets.

Investigating the potential roles of intra-colonial genetic variability in Pocillopora corals using genomics

Intra-colonial genetic variability (IGV), the presence of more than one genotype in a single colony, has been increasingly studied in scleractinians, revealing its high prevalence. Several studies hypothesised that IGV brings benefits, but few have investigated its roles from a genetic perspective. Here, using genomic data (SNPs), we investigated these potential benefits in populations of the coral Pocillopora acuta from Reunion Island (southwestern Indian Ocean). As the detection of IGV depends on sequencing and bioinformatics errors, we first explored the impact of the bioinformatics pipeline on its detection. Then, SNPs and genes variable within colonies were characterised. While most of the tested bioinformatics parameters did not significantly impact the detection of IGV, filtering on genotype depth of coverage strongly improved its detection by reducing genotyping errors. Mosaicism and chimerism, the two processes leading to IGV (the first through somatic mutations, the second through fusion of distinct organisms), were found in 7% and 12% of the colonies, respectively. Both processes led to several intra-colonial allelic differences, but most were non-coding or silent. However, 7% of the differences were non-silent and found in genes involved in a high diversity of biological processes, some of which were directly linked to responses to environmental stresses. IGV, therefore, appears as a source of genetic diversity and genetic plasticity, increasing the adaptive potential of colonies. Such benefits undoubtedly play an important role in the maintenance and the evolution of scleractinian populations and appear crucial for the future of coral reefs in the context of ongoing global changes.

Pocillopora tuahiniensis: a new species of scleractinian coral (Scleractinia, Pocilloporidae) from French Polynesia

Pocillopora tuahiniensis sp. nov. is described based on mitochondrial and nuclear genomic data, algal symbiont genetic data, geographic isolation, and its distribution pattern within reefs that is distinct from other sympatric Pocillopora species (Johnston et al. 2022a, b). Mitochondrial and nuclear genomic data reveal that P. tuahiniensis sp. nov. is a unique species, sister to P. verrucosa, and in a clade different from that of P. meandrina (Johnston et al. 2022a). However, the gross in situ colony appearance of P. tuahiniensis sp. nov. cannot easily be differentiated from that of P. verrucosa or P. meandrina at Moorea. By sequencing the mtORF region, P. tuahiniensis sp. nov. can be easily distinguished from other Pocillopora species. Pocillopora tuahiniensis sp. nov. has so far been sampled in French Polynesia, Ducie Island, and Rapa Nui (Armstrong et al. 2023; Edmunds et al. 2016; Forsman et al. 2013; Glin et al. 2017; Mayfield et al. 2015; Oury et al. 2021; Voolstra et al. 2023). On the fore reefs of Moorea, P. tuahiniensis sp. nov. is very abundant 10 m and is one of the most common Pocillopora species at these depths (Johnston et al. 2022b). It can also be found at a much lower abundance at shallow depths on the fore reef and back reef lagoon. The holotype is deposited at the Smithsonian Institution as USNM-SI 1522390 and the mtORF Genbank accession number is OP418359.

Dominance of the coral Pocillopora acuta around Phuket Island in the Andaman Sea, Thailand

Pocillopora damicornis (Linnaeus, 1758), a species complex, consists of several genetic lineages, some of which likely represent reproductively isolated species, including the species Pocillopora acuta Lamarck, 1816. Pocillopora acuta can exhibit similar morphological characteristics as P. damicornis, thus making it difficult to identify species-level taxonomic units. To determine whether the P. damicornis-like colonies on the reefs in the Andaman Sea (previously often identified as P. damicornis) consist of different species, we sampled individual colonies at five sites along a 50 km coastal stretch at Phuket Island and four island sites towards Krabi Province, Thailand. We sequenced 210 coral samples for the mitochondrial open reading frame and identified six distinct haplotypes, all belonging to P. acuta according to the literature. Recently, P. acuta was observed to efficiently recolonize heat-damaged reefs in Thailand as well as globally, making it a potentially important coral species in future reefs. Specifically in the light of global change, this study underscores the importance of high-resolution molecular species recognition, since taxonomic units are important factors for population genetic studies, and the latter are crucial for management and conservation efforts.

Species Diversity of Amanita Section Vaginatae in Eastern China, with a Description of Four New Species

Species of Amanita sect. Vaginatae (Fr.) Quél. are challenging to delimitate due to the morphological similarity or morphostasis among different taxa. In this study, a multi-locus (nuc rDNA region encompassing the internal transcribed spacers 1 and 2 with the 5.8S rDNA, the D1-D3 domains of nuc 28S rDNA, partial sequences of translation elongation factor 1-a, and the second largest subunit of RNA polymerase II) phylogeny was employed to investigate the species diversity of the section in eastern China. Sixteen species were recognized, including four new species; namely, A. circulata, A. multicingulata, A. orientalis, and A. sinofulva. They were documented with illustrated descriptions, ecological evidence, and comparisons with similar species. A key to the species of the section from eastern China is provided.

Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016-2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals-Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla-across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean

Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming.