The analysis of regional scale patterns of diversity allows insights into the processes that have shaped modern biodiversity at the macro‐scale. Previous analyses studying biogeographic regionalisation across different high‐level taxa have shown similar trends at a global scale. However, incorporating phylogenetic methods when comparing biogeographic regionalisation between subgroups facilitates identification of mechanisms leading to the biogeographic distribution of specific taxa. We analysed the spatial trends of phylogenetic diversity and phylogenetic endemism of 325 species of New World bats, using updated range maps of the modern distributions. These analyses showed phylogeographic signals that reflect the different evolutionary histories of these families. Zoogeographical zones were detected based on range‐weighted phylogenetic turnover. Values of high phylogenetic diversity and endemism were distributed differently across families, suggesting niche conservatism, but a general latitudinal trend of diversity was evident across taxa. Overall, two main bioregions were shared across New World bat taxa (Nearctic and Neotropical), with two additional subregions (Andean and La Platan). We found strong support for an additional transitional zone in the Pacific coast of South America for Emballonuridae and Molossidae. Differences in regionalisation across families indicate that niche conservatism, in situ diversification and dispersal ability are major drivers for the regionalisation of New World bats, within a dual‐centre of diversification scenario. We also found strong inter‐familial support for an independent Caribbean biogeographic region.
Phyllostomidae Rojas et al. (2016) phylogeny
Trimmed Rojas et al. (2016) phylogeny to match Phyllostomidae distribution data. This phylogeny was used to assess differences in our bioregionalisation results between Fritz et al. (2009)'s phylogeny and Rojas et al. (2016)'s phylogeny
PhyllostomidaeRojas.nex
Phyllostomidae Fritz et al. (2009) phylogeny
Trimmed Fritz et al. (2009) phylogeny to match Phyllostomidae distribution data. This phylogeny was used to assess differences in our bioregionalisation results between Fritz et al. (2009)'s phylogeny and Rojas et al. (2016)'s phylogeny
PhyllostomidaeFritz.nex
Phyllostomidae Rojas et al. (2018) occurrence data
Occurrence data of phyllostomid species based on distributional maps from Rojas et al. (2018) used to compare differences in our results between the IUCN (2016) distribution maps and Rojas et al. (2018) models.
PhyllostomidaeRojasOccurrence.csv
Phyllostomidae IUCN (2016) occurrence data
Occurrence data of phyllostomid species based on distributional maps from IUCN (2016) used to compare differences in our results between the IUCN (2016) distribution maps and Rojas et al. (2018) models.
PhyllostomidaeIUCNOccurrence.csv
Emballonuridae Fritz et al. (2009) phylogeny
Trimmed Fritz et al. (2009) phylogeny to match Emballonuridae distribution data. This phylogeny was used to quantify phylogenetic diversity and endemism.
EmballonuridaeFritz.NEX
Emballonuridae IUCN (2016) occurrence data
Occurrence data of emballonurid species based on distributional maps from IUCN (2016).
EmballonuridaeIUCNOccurrence.csv
Molossidae Fritz et al. (2009) phylogeny
Trimmed Fritz et al. (2009) phylogeny to match Molossidae distribution data. This phylogeny was used to quantify phylogenetic diversity and endemism.
MolossidaeFritz.NEX
Molossidae IUCN (2016) occurrence data
Occurrence data of molossid species based on distributional maps from IUCN (2016).
MolossidaeIUCNOccurrence.csv
Mormoopidae Fritz et al. (2009) phylogeny
Trimmed Fritz et al. (2009) phylogeny to match Mormoopidae distribution data. This phylogeny was used to quantify phylogenetic diversity and endemism.
MormoopidaeFritz.NEX
Mormoopidae IUCN (2016) occurrence data
Occurrence data of mormoopid species based on distributional maps from IUCN (2016).
MormoopidaeIUCNOccurrence.csv
Natalidae Fritz et al. (2009) phylogeny
Trimmed Fritz et al. (2009) phylogeny to match Natalidae distribution data. This phylogeny was used to quantify phylogenetic diversity and endemism.
NatalidaeFritz.NEX
Natalidae IUCN (2016) occurrence data
Occurrence data of emballonurid species based on distributional maps from IUCN (2016).
NatalidaeIUCNOccurrence.csv
Vespertilionidae Fritz et al. (2009) phylogeny
Trimmed Fritz et al. (2009) phylogeny to match Vespertilionidae distribution data. This phylogeny was used to quantify phylogenetic diversity and endemism.
VespertilionidaeFritz.NEX
Vespertilionidae IUCN (2016) occurrence data
Occurrence data of vespertilionid species based on distributional maps from IUCN (2016).
VespertilionidaeIUCNOccurrence.csv
