Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

Abstract

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Fire coral clones demonstrate phenotypic plasticity among reef habitats

“…Millepora platyphylla is the only species of fire corals identified in French Polynesia (Dubé et al., ). However, corals of the Millepora genus can be found in all tropical coral reef regions (Lewis, ).…”

“…Genomic DNA was extracted using a QIAxtractor automated genomic DNA extraction instrument, according to manufacturer's instructions. Samples were amplified and genotyped at 12 microsatellite loci shown to be coral‐specific and polymorphic in M. platyphylla (Dubé, Planes, Zhou, Berteaux‐Lecellier, & Boissin, ). The primers used are (listed in Table ).…”

An integrated morpho-molecular approach to delineate species boundaries of Millepora from the Red Sea

“…Therefore, COI and 16S rDNA may be selected for future works aimed to evaluate the species 325 boundaries of Millepora throughout its entire geographic distribution. A potential additional marker could be the ITS 326 region that has been successfully used for the identification of Millepora from Japan (Takama et al 2018) The recently 327 developed set of 15 microsatellites Dubé et al (2017c) seemed, however, to be only valid for the Indo-Pacific species.…”

“…Mauritius, this may also concern specimens from this locality that were studied by Dubé et al (2017c), who did not 393 refer to Boschma's (1966) work. Our results remove the doubts expressed by Boschma (1966)…”

“…Recent outcomes of molecular phylogenetic analyses and DNA taxonomy have provided advantages for the understanding of Millepora systematics and connectivity (López et al 2015;, Hoeksema et al 2014;, de Souza et al 2017;, Dubé et al 2017c). The use of genetics has elucidated the identification and the geographic origin of fire corals in some isolated and remoted islands of the central and eastern Atlantic Ocean, including for example the Canaries, Capeo Verde Islands, and Ascension Island (López et al 2015;, Hoeksema et al 20142017 (Loya 1972(Loya , 1976, Benayahu and Loya 1977;, Perkol-Finkel and Benayahu 2004).…”