Identity of freshwater shrimp populations (Palaemon Weber, 1795) from northern Mexico: genetic variation at local and regional scales

The freshwater genus Palaemon is widely distributed in north-eastern Mexico, where six species have been recognized. Of special interest is the area of the Cuatro Cienegas Valley (CCV) and the Salado and Bravo Rivers basins in central and northern Coahuila, where interconnections, ancient and contemporary, have created a mosaic of populations of species belonging to Palaemon that cannot unequivocally be assigned to one species. We seek to encompass the species determination in a phylogenetic framework by reconstructing phylogenetic relationships of the aforementioned populations and 4 of the species occurring in México. We collected information of three genetic fragments (COI, 12S, and H3) and performed maximum likelihood and Bayesian inference phylogenetic analyses. Also, through the analysis of a partial sequence of the cytochrome oxidase subunit I gene (COI) from individuals coming from 22 populations, we explored phylogeographic patterns from the three basins. Relaxed molecular clock were carried out focused on dating the cladogenesis of all species, while mismatch and Bayesian Skyline Plots analyses were used to test for possible demographic changes in populations from CCV. Gene-separated and concatenated phylogenetic analyses supported the monophyly of the species described from Mexico, but did not show their inclusion in one monophyletic clade, rather depicting a structure congruent with multiple invasions to freshwater. Dating analysis provided long-term temporal framework for cladogenesis. Three different lineages were found in the CCV, confirming the high diversity of this region. One of them is identified with P. sutkussi, and two are possible new species to science. Haplotype analyses provided insight from recent population processes and are congruent with a scenario where despite keeping signatures of past cladogenesis, more recent genetic structure reveals surprisingly higher connectivity between basins associated to the Bravo river system and CCV.