The pantropical Caesalpinia group includes 225 species in 27 monophyletic genera, and the group has undergone recent phylogenetic, taxonomic and biogeographic revisions. Previous works have reported a diverse pattern of heterochromatin distribution related to ecological niche/geographic distribution, and variation in genome size also correlated with environmental variables. In order to investigate the relationship between cytogenetic and ecological traits using the Caesalpinia group as a model, new cytomolecular data (chromosome number and morphology, CMA/DAPI staining and number and position of 5S and 35S rDNA sites) for 14 species in six genera were generated. These data were analysed by phylogenetic comparative methods. All species studied have 2n = 24 (16 M/SM + 8A), and most of them just have one pair of 5S rDNA sites and two to five pairs of 35S rDNA sites. Three heterochromatic patterns were observed on the chromosomes: (i) proximal CMA+/DAPI− bands, (ii) proximal CMA0/DAPI− bands and (iii) proximal CMA0/DAPI0 bands. The “Coulteria + Tara” and “Arquita + Balsamocarpon + Erythrostemon + Pomaria” clades (except for E. gilliesii, E. hughesii and E. mexicanus) independently showed CMA0/DAPI− bands associated with larger genomes and geographic distributions at higher latitudes. We statistically demonstrate that heterochromatin (CMA/DAPI intensity along the chromosome), genome size and latitude are autocorrelated in the Caesalpinia group. On the other hand, we found a non-significant correlation between genome size and amount of heterochromatin. We argue that environmental factors associated with different latitude may have played a role in contributing to the diversification of the heterochromatin in Caesalpinia group.
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