Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology.

International audienceSix variable sequence markers are developed and analyzed to find out species boundaries in Hawaiian corals of the genus Pocillopora: the putative mitochondrial control region; a recently discovered, hypervariable mitochondrial open reading frame; the internal transcribed spacer 2 (ITS2), located in the nuclear ribosomal DNA; three nuclear introns of calmodulin, elongation factor-1alpha and the ATP synthase beta subunit. Using the first two markers, we identify five distinct mitochondrial lineages and these lineages are compatible with morphology. The situation is more complex with nuclear markers since more than two haplotypes are observed in some individuals. To detect clusters of individuals, haplotype networks are constructed with additional connections drawn between co-occurring haplotypes to delineate potential fields for recombination: few clusters of nuclear haplotypes are found to correspond to clusters of individuals, but those that are detected (mostly in the ITS2 dataset) are also compatible with morphology

Alteration of pathogenicity-linked life-history traits by resistance of its host Solanum tuberosum impacts sexual reproduction of the plant pathogenic oomycete Phytophthora infestans.

International audienceAlthough sexual reproduction implies a cost, it represents an evolutionary advantage for the adaptation and survival of facultative sexual pathogens. Understanding the maintenance of sex in pathogens requires to analyse how host resistance will impact their sexual reproduction through the alteration of their life-history traits. We explored this experimentally using potato (Solanum tuberosum) and one of its pathogens, the heterothallic oomycete Phytophthora infestans. Sexual reproduction was highest on hosts favouring asexual multiplication of the pathogen, suggesting similar nutritional requirements for both sexual and asexual sporulation. Sexual reproduction was also highest on hosts decreasing the latent period, probably because of a trade-off between growth and reproduction. Distinguishing host effects on each pathogenic trait remains however uneasy, as most life-history traits linked to pathogenicity were not independent of each other. We argue that sexual reproduction of P. infestans is an adaptation to survive when the host is susceptible and rapidly destroyed

Specific detection and quantification of virulent/avirulent Phytophthora infestans isolates using a real-time PCR assay that targets polymorphisms of the Avr3a gene.

Equipe 6International audienceMolecular tools that allow intraspecific quantification and discrimination of pathogen isolates are useful to assess fitness of competitors during mixed infections. However, methods that were developed for quantifying Phytophthora infestans are only specific at the species level. Here, we reported a TaqMan-based real-time PCR assay allowing, according to the specificity of the used probes, an accurate quantification of different proportions of two genetically distinct clones of P. infestans in mixed fractions. Indeed, in addition to a primer specific to P. infestans, two primers and two TaqMan(®) probes that target single-nucleotide polymorphisms located in the Avr3a/avr3a virulence gene sequence were designed. The reliability of the method was tested on serially diluted fractions containing plasmid DNA with either the Avr3a or the avr3a sequences at concentrations ranging from 10(2) to 10(8) copies per μl. Based on its specificity, sensitivity and repeatability, the proposed assay allowed a quantification of the targeted DNA sequence in fractions with a Avr3a/avr3a ratio in the range 1/99 to 99/1. The reliability of the test was also checked for counting zoospores. Applications for future research in P. infestans/host quantitative interactions were also discussed

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

Abstract 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

Molecular identification of symbiotic dinoflagellates in Pacific corals in the genus Pocillopora

info:eu-repo/semantics/publishe

High connectivity within restricted distribution range in Pocillopora corals

Aim Convergence, stasis and plasticity can frequently confound our understanding of species distributions in the seas. Yet delimiting species and understanding population connectivity across marine environments is mandatory for establishing appropriate management of coral reefs, which are experiencing critical declines. We test whether morphospecies from Pocillopora corals found on outer reef slopes are unique species or species complexes, in order to correctly define their respective distributions and consequently to accurately assess their population connectivity. Location Archipelagos and islands of the Western Indian Ocean and the Southern Pacific (New Caledonia, Tonga, French Polynesia). Taxon Pocillopora eydouxi/meandrina and Pocillopora verrucosa morphospecies (Scleractinia). Methods We analysed the 13‐microsatellite genotypes of 4837 colonies from six understudied ecoregions in the southern part of the genus distribution, to first explore the genetic partitioning within morphospecies. We then characterized the spatial distribution of each delimited species and analysed patterns of genetic diversity and connectivity for each species separately. Results Both morphospecies are complexes of species, each found almost exclusively in the Indian or the Pacific Oceans. Moreover, some of these cryptic species are found in sympatry over their whole distribution, which sometimes was very restricted. However, within each species, genetic diversity and connectivity were relatively high, although some populations were found differentiated for some species, while not for others. Main conclusions A weak connectivity was found between the Indian and Pacific Oceans, but high connectivity within both oceans, supporting the existence of a barrier impeding gene flow between both ocean basins in Pocillopora. Although constrained by the same geography and current patterns, some sympatric species present different connectivity patterns, demonstrating the importance of multi‐species connectivity models to set up appropriate management plans

Same places, same stories? Genomics reveals similar structuring and demographic patterns for four Pocillopora coral species in the southwestern Indian Ocean

Aim Efficiently protecting species requires knowing their ecological, life‐history and reproductive traits. This is particularly decisive for scleractinian corals, key components of coral reefs, which are experiencing critical declines. Yet their connectivity remains insufficiently documented. Here, we focused on four distinct species of the coral genus Pocillopora found in diverse habitats of the southwestern Indian Ocean and presenting various reproductive strategies. We aimed to understand whether these traits affect species connectivity. LocationArchipelagos and islands of the southwestern Indian Ocean. TaxonPocillopora spp. Methods We used target capture to collect single‐nucleotide polymorphisms (SNPs) from over a thousand colonies sampled across nine localities. From the ca. 1400 SNPs retained per species, Bayesian clustering methods, networks and demographic inferences were applied to first infer the population genetic structure and connectivity of each species, then the demographic history of each population. Results All four Pocillopora species exhibited almost the same genetic structuring pattern, reflecting the sampled ecoregions (Madagascar and surrounding islands vs. Mascarene Islands). However, the genetic differentiation was stronger (FST about 10 times higher) for P. acuta, the species inhabiting more enclosed habitats, such as lagoons and shallow waters, and reproducing mainly asexually. Similarly, all populations, except those from P. acuta, showed a signature of population expansion ca. 100,000 years ago, following the penultimate glacial period. Main Conclusions These results indicate reduced gene flow between Madagascar and the Mascarene Islands, probably linked to currents, suggesting distinct connectivity networks that should be considered independently when setting up conservation plans. In addition, shared demographic histories reflect that populations from these species have probably met the same environmental constraints and reacted similarly, something that should be considered in light of the ongoing rapid climate change

Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific

Studying population genetic connectivity (i.e., identifying gene flow among populations and understanding their impacts on the genetic structure and diversity of populations) is first a matter of knowing what we work on, that is, accurately delimiting evolutionary units. Here, we focused on Pocillopora damicornis sensu stricto (or Pocillopora PSH04 sensu Gélin et al. in Mol Phylogenet Evol 109:430–446. http://dx.doi.org/10.1016/j.ympev.2017.01.018PANIST, 2017). From 458 colonies sampled within the tropical southwestern Pacific [Chesterfield Islands and New Caledonia (Grande Terre and Loyalty Islands)], Bayesian assignments and network analyses were conducted with 11-microsatellite loci to first evaluate the genetic partitioning of the colonies in distinct Secondary Species Hypotheses (SSHs), then in distinct clusters. Population genetic connectivity was then assessed for each cluster separately. Pocillopora PSH04 was partitioned into two highly differentiated SSHs (SSH04a and SSH04b), regularly found in sympatry. Furthermore, SSH04a was subdivided into two clusters (SSH04a-1 and SSH04a-2). This pattern of genetic structuring seems not related to clonality, but rather to the establishment of reproductive barriers. Nevertheless, considering each cluster separately, the populations appeared highly differentiated, suggesting relatively weak gene flow. This low connectivity among populations, coupled with the existence of cryptic species, brings new insights to the connectivity pattern of this understudied Pacific region