Background:

Polianthes cernua, P. geminiflora var. clivicola, P. geminiflora var. geminiflora, P. geminiflora var. pueblensis, P. graminifolia, P. multicolor, P. quilae, and P. zapopanensis represent a species complex.

Hypothesis:

A phylogeographic analysis would uncover different linages within Polianthes geminiflora complex.

Studied species:

Polianthes geminiflora complex.

Study site and dates:

Mexico, 2014-2025.

Methods:

We sequenced the ndhF-rpl32, rpl32-trnL, and 3’rps16-5’trnK intergenic regions of chloroplast DNA from 195 individuals, which pertains to 23 populations. The genealogy was estimated with a haplotype network and the genetic diversity with S, h, π, and Hd indexes. The genetic structure was inferred with F ST value of an analysis of molecular variance. The number of lineages was estimated with a spatial analysis of molecular variance (SAMOVA). The phylogeographic structure was estimated with N ST and G ST indexes. Lastly, the demographic history was described using the indexes F S, D, analysis of mismatch distribution (ADDP), and Bayesian skyline plot.

Results:

The data set contained 195 sequences with 1,552 bp each. The haplotype network showed 28 haplotypes and two haplogroups. It was incongruent with the SAMOVA which identified 19 lineages. The neutrality test was not statistically significant.

Conclusions:

The Polianthes geminiflora complex had genetic and phylogeographic structure. There is incongruence between genetic and morphological variation. The presence of lineages with low genetic variation results from a recent diversification, topographic variation, low dispersal capacity and the Pleistocene refugia formation.

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