This paper aims to integrate cytogenetic and ecological approaches into a phylogenetic framework to better understand the evolution and systematics of Senna series Aphyllae, an endemic group of arid and semi-arid regions of South America. We counted the chromosome numbers at the population level in three species of series Aphyllae using a conventional technique (GIEMSA) and in situ hybridization (FISH). Phylogenetic reconstructions and inference of chromosome evolution were based on four plastid DNA regions and one nuclear marker. A principal component analysis was carried out using environmental data. Finally, ecological niche models (ENM) were implemented: (1) to identify the abiotic factors that constraint the potential geographical distribution of series Aphyllae and (2) to understand the ecological drivers for species diversification. The basic chromosome number is x = 12. Senna aphylla showed three cytotypes with (2n = 24, 48 and 60) and S. pachyrrhiza has two cytotypes (2n = 24 and 48). Senna crassiramea appeared to be polyploid with 2n = 48. In diploid S. pachyrrhiza, two 45S and three 5S rDNA sites were reported. In tetraploid S. crassiramea, four 45S and four 5S rDNA sites were detected. The ENM and ecological speciation tests suggest that in series Aphyllae speciation was sometimes associated with conservatism and sometimes with niche divergence. Our results contribute to the evolutionary knowledge of Neotropical legumes and understanding of drivers of diversification in arid regions in South America.
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