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Background  The Micronycterinae form a subfamily of leaf-nosed bats (Phyllostomidae) that contains the genera  Lampronycteris  Sanborn, 1949, and  Micronycteris  Gray, 1866 ( stricto  sensu), and is characterized by marked karyotypic variability and discrepancies in the phylogenetic relationships suggested by the molecular versus morphological data. In the present study, we investigated the chromosomal evolution of the Micronycterinae using classical cytogenetics and multidirectional chromosome painting with whole-chromosomes probes of  Phyllostomus hastatus  and  Carollia brevicauda . Our goal was to perform comparative chromosome mapping between the genera of this subfamily and explore the potential for using chromosomal rearrangements as phylogenetic markers.    Results  The Micronycterinae exhibit great inter- and intraspecific karyotype diversity, with large blocks of telomere-like sequences inserted within or adjacent to constitutive heterochromatin regions. The phylogenetic results generated from our chromosomal data revealed that the Micronycterinae hold a basal position in the phylogenetic tree of the Phyllostomidae. Molecular cytogenetic data confirmed that there is a low degree of karyotype similarity between  Lampronycteris  and  Micronycteris  specimens analyzed, indicating an absence of synapomorphic associations in Micronycterinae.    Conclusions  We herein confirm that karyotypic variability is present in subfamily Micronycterinae. We further report intraspecific variation and describe a new cytotype in  M. megalotis . The cytogenetic data show that this group typically has large blocks of interstitial telomeric sequences that do not appear to be correlated with chromosomal rearrangement events. Phylogenetic analysis using chromosome data recovered the basal position for Micronycterinae, but did not demonstrate that it is a monophyletic lineage, due to the absence of common chromosomal synapomorphy between the genera. These findings may be related to an increase in the rate of chromosomal evolution during the time period that separates  Lampronycteris  from  Micronycteris .    Electronic supplementary material  The online version of this article (10.1186/s12862-019-1421-4) contains supplementary material, which is available to authorized users.

Karyotype, evolution and phylogenetic reconstruction in Micronycterinae bats with implications for the ancestral karyotype of Phyllostomidae