DNA taxonomy in the timber genus Milicia: evidence of unidirectional introgression in the West African contact zone
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DNA-based techniques are helpful in characterising hybridisation patterns in plant species. To be efficient in disentangling species boundaries and interspecific gene flow, it is recommended to combine various methodologies and types of markers. Here, we used different analytical tools (algorithms implemented in Structure, Tess, NewHybrids and HIest, and the haploweb approach) and three nuclear genetic markers (7 nuclear simple sequence repeat loci (SSRs), 62 single-nucleotide polymorphism loci (SNPs) and a single-copy gene region, At103) to revisit hybridisation patterns in the commercially important African tree genus Milicia. Samples were collected in the natural ranges of Milicia regia and Milicia excelsa in West Africa. Using real data sets, simulated purebreds and hybrid genotypes, we found that SNPs yielded results more consistent than SSRs; outputs from the Bayesian and maximum-likelihood analyses differed significantly using the SSRs, whereas they were perfectly congruent using SNPs. A proportion of 12.4% hybrids were detected amongst the SNP genotype samples. A haploweb analysis of At103 gene sequences confirmed the existence of interspecific hybrids. There was also a clear evidence of advanced generations of hybrids (backcrossed individuals) but only towards M. regia. Although more investigation is required for understanding the mechanisms responsible for this asymmetric introgression, we suggest that it may be due to the differences in flowering time between species and between sexes, combined with a maternal inheritance of flowering time.
KeywordsHybridisation Introgression Haploweb Tropical forests Milicia sp.
The development of the SNP markers was carried out with the financial support of the International Tropical Timber Organization (ITTO) through the project PD 620/11 Rev.1 (M): “Development and implementation of species identification and timber tracking in Africa with DNA fingerprints and stable isotopes”. SNP genotyping was performed at the Genomic and Sequencing Facility of Bordeaux (grants from the Conseil Regional d’Aquitaine No. 20030304002FA and 20040305003FA, the European Union, FEDER No. 2003227 and “Investissements d’avenir, Convention attributive d’aide” No. ANR-10-EQPX-16-01). SSR genotyping and DNA sequencing were funded by the Belgian Fund for Scientific Research (F.R.S-FNRS, grant T0163.13). We would like also to thank the Associate Editor Felix Gugerli, two anonymous reviewers and Armel S. L. Donkpegan for their comments, corrections and suggestions that highly contributed in improving the manuscript.
Data archiving statement
The phased Milicia sequences of the nuclear gene At103 were deposited in GenBank under the accession numbers MF541241-MF541316. The At103 chromatograms of the length-variant heterozygotes were deposited in Dryad together with the nuclear SSR and SNP data at http://dx.doi.org/10.5061/dryad.m457d.
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