We analysed the phylogeographic structure of five resident bird lineages distributed in the seasonally dry tropical forests (SDTF) of Mesoamerica to test whether they show patterns of synchronous and geographically coincident genetic divergence during the Quaternary. We generated phylogenetic trees, estimated divergence times and analysed the genetic structure of populations (based on sequences of mitochondrial genes), as well as estimating historical distributions (range extension and areas of long-term climate stability) during the Late Pleistocene. We tested and selected the phylogeographic divergence scenarios that best explain the current divergence patterns of taxa using the Approximate Bayesian Computation (ABC) approach. For most species, phylogenetic trees and haplotype networks showed a clear genetic structure associated with geographical distribution. Overall, the divergence times ranged from 0.29–2.0 Mya, suggesting that diversification of populations occurred at different times during the Pleistocene. The palaeodistribution models predicted at least two areas of climatic stability within the current SDTF that probably allowed glacial-interglacial persistence of isolated bird populations along the Mexican Pacific, thus promoting their genetic divergence. The results provide information relevant to the identification of diversification hotspots for the Mesoamerican SDTF avifauna.

Mammillaria parkinsonii and M. perbella are species endemic to the Queretano–Hidalguense Desert (QHD), a potential globose cacti Pleistocene refuge. We tested if the phylogeographic and genetic structures of these species are temporally consistent with the Pleistocene glacial refuge hypothesis. In this case, there would be high haplotype divergence associated with population contraction during the Last Glacial period (115-11.7 kya). Chloroplast DNA sequences and ISSR nuclear markers were used to estimate genetic diversity and structure, haplotype networks, and divergence times. Changes in paleodistribution were modeled using the Ecological Niche Model (MNE). cpDNA and ISSR markers revealed low-to-moderate genetic diversity in M. pakinsonii and M. perbella (π = 0.0004, 0.0044 respectively; H_S = 0.362–0.434, 0.293–0.400, respectively) and high population differentiation (G_ST = 1, 0.722, respectively; Φ_ST = 0.378, 0.3957, respectively), with no evidence of gene flow (Nm = 0, 0.29, respectively). The estimated divergence times and MNE showed that population divergence began during the Last Glacial in M. perbella and continued into the Holocene for both species. This divergence is associated with population contraction, geographic isolation, and disruption of gene flow. This joint evidence indicated that Pleistocene–Holocene glacial cycles may have driven the recent divergence of these Mammillaria species in the QHD.