Microsatellite-assisted identification and comparative population genetics of Malagasy olive species (Noronhia spp., Oleaceae)

ABSTRACT

An exhaustive inventory of Madagascar’s native flora is necessary to optimize its conservation, particularly for highly diversified endemic groups of plants whose many habitats are threatened with short-term loss. The Malagasy olive (Noronhia spp., Oleaceae), with at least 80 species, is recognized as one of the highly diversified tree genera of the SW Indian Ocean Flora. Field identification of Noronhia species is, however, often a challenge and numerous sterile samples need posterior identification. As molecular tools may assist this task, we tested cross-species amplification of 13 nuclear microsatellite loci (ie SSRs) among a large sample of Noronhia taxa (60 of the 82 described species in Madagascar). Eight species were also investigated at the population level with 13 nuclear and 15 plastid SSRs. A high cross-species transferability of markers was demonstrated, although three nuclear loci showed evidence of null alleles in some species. Based on the amount of genetic diversity observed within eight diploid species, we showed that putative polyploids could be efficiently detected using nuclear SSRs. Our markers thus allowed revealing one polyploid taxon (N. louvelii), but their relatively low frequency suggests that whole-genome duplication was not a major process involved in the high diversification of Noronhia as previously hypothesized. Finally, plastid lineages as well as genetic clusters identified with nuclear SSRs allowed distinguishing all six species collected at Andohahela and Marojejy. These results demonstrate that microsatellites can assist Noronhia identification in their diversity hotspots, as well as reveal contrasting genetic diversity patterns (such as isolation by distance) between sympatric taxa.

KEYWORDS:

• Biodiversity inventory and conservation
• IBD
• Madagascar
• Noronhia
• polyploidy
• population genetics
• species identification
• tsilaitra

Acknowledgments

We thank the Direction Générale du Ministère de l’Environnement et des Forêts de Madagascar, Madagascar’s Ad Hoc Committee for Fauna and Flora, and Organizational Committee for Environmental Research (CAFF/CORE) for permission to perform this study (permit number: [232/11]/MEF/SG/DGF/DCB.SAP/SCB), and for their support. We thank the local communities of Andohahela, Ankafobe and Marojejy for their warm reception and support. We are grateful to the Get-Plage sequencing platform for genotyping services. We thank particularly S. Fourre, M. A. Naranjo Arcos, A. Staquet, U. Suescun, C. Verbeke, and C. Vignes for lab assistance, as well as the KMCC team, J. Razanatsoa, Anicet, Barbara, Bat, Jordi, and Mino for their enthusiasm during field trips. We also thank J. Corrège and B. Fougeron for their support in informatics. Lab work was funded through an ERA-NET BiodivERsA project: INFRAGECO (Inference, Fragmentation, Genomics, and Conservation, ANR-16-EBI3-0014). We also thank the LIA BEEG-B (Laboratoire International Associé – Bioinformatics, Ecology, Evolution, Genomics and Behaviour, CNRS), the LABEX TULIP (ANR-10-LABX-0041) and CEBA (ANR-10-LABX-25-01).

Supplementary material

Supplemental data for this article can be accessed here.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

All samples information and genotyping data are provided in Supplemental Data.

Author contributions

Océane Gorrilliot performed data analyses and co-wrote the paper.

Cynthia Hong-Wa secured and identified plant material, and edited the final text.

Franck Rakotonasolo secured plant material and obtained research permit.

Guillaume Besnard conceived the study, performed lab work and data analyses, and wrote the paper with the help of all authors.

Additional information

Funding

This work was supported by the LabEx CEBA [ANR-10-LABX-25-01]; ERA-NET BiodivERsA INFRAGECO [ANR-16-EBI3-0014]; LabEx TULIP [ANR-10-LABX-0041]; LIA BEEG-B (CNRS).