Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate

Multi-generational dispersal and dynamic patch occupancy reveals spatial and temporal stability of seascapes

The success of non-native species (NNS) invasions depends on patterns of dispersal and connectivity, which underpin genetic diversity, population establishment and growth. In the marine environment, both global environmental change and increasing anthropogenic activity can alter hydrodynamic patterns, leading to significant inter-annual variability in dispersal pathways. Despite this, multi-generational dispersal is rarely explicitly considered in attempts to understand NNS spread or in the design of management interventions. Here, we present a novel approach to quantifying species spread that considers range expansion and network formation across time using the non-native Pacific oyster, Magallana gigas (Thunberg 1793), as a model. We combined biophysical modelling, dynamic patch occupancy models, consideration of environmental factors, and graph network theory to model multi-generational dispersal in northwest Europe over 13 generations. Results revealed that M. gigas has a capacity for rapid range expansion through the creation of an ecological network of dispersal pathways that remains stable through time. Maximum network size was achieved in four generations, after which connectivity patterns remained temporally stable. Multi-generational connectivity could therefore be divided into two periods: network growth (2000-2003) and network stability (2004-2012). Our study is the first to examine how dispersal trajectories affect the temporal stability of ecological networks across biogeographic scales, and provides an approach for the assignment of site-based prioritisation of non-native species management at different stages of the invasion timeline. More broadly, the framework we present can be applied to other fields (e.g. Marine Protected Area design, management of threatened species and species range expansion due to climate change) as a means of characterising and defining ecological network structure, functioning and stability.

Sea anemone (Anthozoa, Actiniaria) diversity in Mo'orea (French Polynesia)

Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo'orea (French Polynesia) with the use of a dataset from the Mo'orea Biocode's "BioBlitz" initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo'orea's diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera Andvakia and Aiptasiomorpha. This research unveils the diverse sea anemone ecosystem in Mo'orea, spotlighting the area's ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.

Some reef-building corals only disperse metres per generation

Understanding the dispersal potential of different species is essential for predicting recovery trajectories following local disturbances and the potential for adaptive loci to spread to populations facing extreme environmental changes. However, dispersal distances have been notoriously difficult to estimate for scleractinian corals, where sexually (as gametes or larvae) or asexually (as fragments or larvae) derived propagules disperse through vast oceans. Here, we demonstrate that generational dispersal distances for sexually produced propagules can be indirectly inferred for corals using individual-based isolation-by-distance (IbD) analyses by combining reduced-representation genomic sequencing with photogrammetric spatial mapping. Colonies from the genus Agaricia were densely sampled across plots at four locations and three depths in Curaçao. Seven cryptic taxa were found among the three nominal species (Agaricia agaricites, Agaricia humilis and Agaricia lamarcki), with four taxa showing generational dispersal distances within metres (two taxa within A. agaricites and two within A. humilis). However, no signals of IbD were found in A. lamarcki taxa and thus these taxa probably disperse relatively longer distances. The short distances estimated here imply that A. agaricites and A. humilis populations are reliant on highly localized replenishment and demonstrate the need to estimate dispersal distances quantitatively for more coral species.

Rampant asexual reproduction and limited dispersal in a mangrove population of the coral Porites divaricata

Corals are critical to marine biodiversity. Reproduction and dispersal are key to their resilience, but rarely quantified in nature. Exploiting a unique system-a fully censused, longitudinally characterized, semi-isolated population inhabiting mangroves-we used 2bRAD sequencing to demonstrate that rampant asexual reproduction most likely via parthenogenesis and limited dispersal enable the persistence of a natural population of thin-finger coral (Porites divaricata). Unlike previous studies on coral dispersal, knowledge of colony age and location enabled us to identify plausible parent-offspring relationships within multiple clonal lineages and develop tightly constrained estimates of larval dispersal; the best-fitting model indicates dispersal is largely limited to a few metres from parent colonies. Our results explain why this species is adept at colonizing mangroves but suggest limited genetic diversity in mangrove populations and limited connectivity between mangroves and nearby reefs. As P. divaricata is gonochoristic, and parthenogenesis would be restricted to females (whereas fragmentation, which is presumably common in reef and seagrass habitats, is not), mangrove populations likely exhibit skewed sex ratios. These findings suggest that coral reproductive diversity can lead to distinctly different demographic outcomes in different habitats. Thus, coral conservation will require the protection of the entire coral habitat mosaic, and not just reefs.

Investigating population dynamics from parentage analysis in the highly endangered fan mussel Pinna nobilis

Understanding dispersal patterns is a major focus for conservation biology as it influences local survival and resilience in case of local disturbance, particularly for sessile species. Dispersal can be assessed through parentage analyses by estimating family structure and self-recruitment. This study documents the family structure of a pelagic spawner, Pinna nobilis, which is facing a major crisis that threatens its survival as most of its populations have been decimated by a parasite, Haplosporidium pinnae. In this context, we focused on a single population (Peyrefite, Banyuls-sur-mer, France) where 640 individuals were sampled in 2011, 2015, and 2018 and genotyped for 22 microsatellite markers. Genetic diversity was high and homogeneous among years, with mean allele numbers ranging between 13.6 and 14.8 and observed heterozygosities (H o) between 0.7121 and 0.7331. Low, but significant, genetic differentiations were found between 2011-2015 and 2015-2018. A parentage analysis described 11 clusters, including one prevailing, and revealed that 46.9% of individuals were involved in half-sib relationships, even between years, suggesting that source populations were recurrent year after year. There were few individuals resampled between years (30 in 2015 and 14 in 2018), indicating a rapid turnover. Considering the large number of half-sib relationships but the low number of relations per individual, we conclude that P. nobilis exhibit homogeneous reproductive success. Self-recruitment was not detected, making this population highly vulnerable as replenishment only relies on connectivity from neighboring populations. In the context of the pandemic caused by H. pinnae, these results will have to be considered when choosing a location to reintroduce individuals in potential future rescue plans.

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

Development of the first microsatellite markers using high-throughput sequencing for a hexaploid coastal species, Tournefortia argentea L. f. (Boraginaceae)

BACKGROUD

Tournefortia argentea L. f. is a hexaploid shrub or tree species with ecological and evolutionary significances, which forms the fringe of vegetation closest to the sea on tropical coral islands. Previous studies have never addressed on genetic information, and thus genomic resources remain scarce.

METHODS AND RESULTS

We used nine individuals from different islands to identify polymorphic microsatellites of T. argentea by Illumina high-throughput sequencing. Thirty-five polymorphic microsatellite markers were developed. Characteristics of each locus were tested using 48 individuals collected from three populations of T. argentea. A total of 320 alleles were found across the 35 microsatellite loci. The number of alleles per locus ranged from 5 to 15, with an average of 9.1. Observed and expected heterozygosities in each locus per population varied from 0.000 to 1.000 and from 0.000 to 0.893, respectively.

CONCLUSIONS

In this study, we report the development of 35 polymorphic microsatellite markers based on Illumina high-throughput sequencing. These markers will facilitate the investigations of genetic diversity, population structures and evolutionary history of T. argentea.

Molecular approaches reveal weak sibship aggregation and a high dispersal propensity in a non-native fish parasite

Inferring parameters related to the aggregation pattern of parasites and to their dispersal propensity are important for predicting their ecological consequences and evolutionary potential. Nonetheless, it is notoriously difficult to infer these parameters from wildlife parasites given the difficulty in tracking these organisms. Molecular-based inferences constitute a promising approach that has yet rarely been applied in the wild. Here, we combined several population genetic analyses including sibship reconstruction to document the genetic structure, patterns of sibship aggregation, and the dispersal dynamics of a non-native parasite of fish, the freshwater copepod ectoparasite Tracheliastes polycolpus. We collected parasites according to a hierarchical sampling design, with the sampling of all parasites from all host individuals captured in eight sites spread along an upstream-downstream river gradient. Individual multilocus genotypes were obtained from 14 microsatellite markers, and used to assign parasites to full-sib families and to investigate the genetic structure of T. polycolpus among both hosts and sampling sites. The distribution of full-sibs obtained among the sampling sites was used to estimate individual dispersal distances within families. Our results showed that T. polycolpus sibs tend to be aggregated within sites but not within host individuals. We detected important upstream-to-downstream dispersal events of T. polycolpus between sites (modal distance: 25.4 km; 95% CI [22.9, 27.7]), becoming scarcer as the geographic distance from their family core location increases. Such a dispersal pattern likely contributes to the strong isolation-by-distance observed at the river scale. We also detected some downstream-to-upstream dispersal events (modal distance: 2.6 km; 95% CI [2.2-23.3]) that likely result from movements of infected hosts. Within each site, the dispersal of free-living infective larvae among hosts likely contributes to increasing genetic diversity on hosts, possibly fostering the evolutionary potential of T. polycolpus.

Depth-dependent parental effects create invisible barriers to coral dispersal

Historically, marine populations were considered to be interconnected across large geographic regions due to the lack of apparent physical barriers to dispersal, coupled with a potentially widely dispersive pelagic larval stage. Recent studies, however, are providing increasing evidence of small-scale genetic segregation of populations across habitats and depths, separated in some cases by only a few dozen meters. Here, we performed a series of ex-situ and in-situ experiments using coral larvae of three brooding species from contrasting shallow- and deep-water reef habitats, and show that their settlement success, habitat choices, and subsequent survival are substantially influenced by parental effects in a habitat-dependent manner. Generally, larvae originating from deep-water corals, which experience less variable conditions, expressed more specific responses than shallow-water larvae, with a higher settlement success in simulated parental-habitat conditions. Survival of juvenile corals experimentally translocated to the sea was significantly lower when not at parental depths. We conclude that local adaptations and parental effects alongside larval selectivity and phenotype-environment mismatches combine to create invisible semipermeable barriers to coral dispersal and connectivity, leading to habitat-dependent population segregation.

Tom Shlesinger and Yossi Loya use ex-situ and in-situ experiments with coral larvae of three brooding species from contrasting shallow- and deep-water habitats and show that larvae originating from deep-water corals have narrower tolerances and higher habitat-specificity in simulated parental-habitat conditions. They also show that survival of juvenile corals experimentally translocated to the sea was significantly lower when not at parental depths. Together these results demonstrate that local adaptations and parental effects interact with larval selectivity and phenotype-environment mismatches to create semipermeable barriers to coral dispersal and connectivity.

Genetic relatedness in social groups of the emerald coral goby Paragobiodon xanthosoma creates potential for weak kin selection

Animals forming social groups that include breeders and nonbreeders present evolutionary paradoxes; why do breeders tolerate nonbreeders? And why do nonbreeders tolerate their situation? Both paradoxes are often explained with kin selection. Kin selection is, however, assumed to play little or no role in social group formation of marine organisms with dispersive larval phases. Yet, in some marine organisms, recent evidence suggests small-scale patterns of relatedness, meaning that this assumption must always be tested. Here, we investigated the genetic relatedness of social groups of the emerald coral goby, Paragobiodon xanthosoma. We genotyped 73 individuals from 16 groups in Kimbe Bay, Papua New Guinea, at 20 microsatellite loci and estimated pairwise relatedness among all individuals. We found that estimated pairwise relatedness among individuals within groups was significantly higher than the pairwise relatedness among individuals from the same reef, and pairwise relatedness among individuals from the same reef was significantly higher than the pairwise relatedness among individuals from different reefs. This spatial signature suggests that there may be very limited dispersal in this species. The slightly positive relatedness within groups creates the potential for weak kin selection, which may help to resolve the paradox of why breeders tolerate subordinates in P. xanthosoma. The other paradox, why nonbreeders tolerate their situation, is better explained by alternative hypotheses such as territory inheritance, and ecological and social constraints. We show that even in marine animals with dispersive larval phases, kin selection needs to be considered to explain the evolution of complex social groups.

Comparison of microsatellite distribution patterns in twenty-nine beetle genomes

Simple sequence repeats (SSRs) represent an important source of genetic variation that provides a basis for adaptation to different environments in organisms. In this study, we examined the distribution patterns of SSRs in twenty-nine beetle genomes and carried out Gene Ontology (GO) analysis of CDSs embedded with perfect SSRs (P-SSRs). The results demonstrated that imperfect SSRs (I-SSRs) represented the most abundant SSR category in beetle genomes and in different genomic regions (CDS, exon, and intron regions). The numbers of P-SSRs, I-SSRs, compound SSRs, and variable number tandem repeats were positively correlated with beetle genome size, whereas neither the frequency nor the density of the SSRs was correlated with genome size. Moreover, our results demonstrated that common genomic features of P-SSRs within the same suborder or family of Coleoptera were rare. Mono-, di-, tri-, or tetranucleotide SSRs were the most abundant P-SSR categories in beetle genomes. The preferred predominant repeat motif among the mononucleotide P-SSRs was (A)n, but the most frequent repeat motifs for other length classes varied differentially among these genomes. Furthermore, the P-SSR type with the highest GC content differed in the beetle genomes and in different genomic regions. CV (coefficient of variability) analysis demonstrated that the repeat copy numbers of P-SSRs presented relatively higher variation in introns than in CDSs and exons. The GO terms of CDSs containing P-SSRs for molecular functions were mainly enriched in "binding" and "transcription". Our findings will be useful for studying the functional roles of microsatellite heterogeneity in beetle adaptation.