The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In non-allopatric speciation, the genomes may remain undifferentiated to a large extent. In this paper, we analysed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used Amplified Fragment Length Polymorphisms (AFLPs) to characterise the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using Divergence Outlier Analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (FST=0.35), and FST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of non-allopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterised by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.

Heliotropium_AFLP_DataAFLP data in genpop formatMcheza table AFLP Heliotropium.txtSpecies tree of Heliotropium sect. CochraneaSpecies tree of Heliotropium sect. Cochranea generated with star-BEASTAdditional DNA sequences of Heliotropium sect. CochraneaGenBank accession numbers KF301622:KF301628. These sequences were added to the dataset of Luebert & Wen (Syst. Bot. 33:390–402, 2008) and used for the species tree analysis in star-BEAST.NCBI_Heliotropium_DEC2013