Ultraconserved elements resolve phylogenetic relationships and biogeographic history of African-Malagasy bent-winged bats (Miniopterus)

Terrence C Demos; Paul W Webala; Steven M Goodman; Julian C Kerbis Peterhans; Holly L Lutz; Bernard R Agwanda; Natalia Cortés-Delgado; Stefania Briones; Richard H Ree; Bruce D Patterson

doi:10.1016/j.ympev.2023.107890

Ultraconserved elements resolve phylogenetic relationships and biogeographic history of African-Malagasy bent-winged bats (Miniopterus)

Mol Phylogenet Evol. 2023 Nov:188:107890. doi: 10.1016/j.ympev.2023.107890. Epub 2023 Jul 28.

Affiliations

¹ Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA. Electronic address: tdemos@fieldmuseum.org.
² Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya.
³ Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA; Association Vahatra, BP 3972, Antananarivo 101, Madagascar.
⁴ Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA; College of Arts & Sciences, Roosevelt University, Chicago, IL, USA.
⁵ Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA; Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA.
⁶ Mammalogy Section, National Museums of Kenya, Nairobi, Kenya.
⁷ Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA; Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA.
⁸ Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA.

PMID: 37517508
DOI: 10.1016/j.ympev.2023.107890

Abstract

African-Malagasy species of the bat genus Miniopterus are notable both for the dramatic increase in the number of newly recognized species over the last 15 years, as well as for the profusion of new taxa from Madagascar and the neighboring Comoros. Since 2007, seven new Malagasy Miniopterus species have been described compared to only two new species since 1936 from the Afrotropics. The conservative morphology of Miniopterus and limited geographic sampling in continental Africa have undoubtedly contributed to the deficit of continental species. In addition to uncertainty over species limits, phylogenetic relationships of Miniopterus remain mostly unresolved, particularly at deeper backbone nodes. Previous phylogenetic studies were based on limited taxon sampling and/or limited genetic sampling involving no more than five loci. Here, we conduct the first phylogenomic study of the Afrotropical Miniopteridae by analyzing up to 3772 genome-wide ultraconserved elements (UCEs) from historic and modern samples of 70 individuals from 25 Miniopterus species/lineages. We analyze multiple datasets of varying degrees of completeness (70, 90, and 100 percent complete) using partitioned concatenated maximum likelihood and multispecies coalescent methods. Our well-supported, species-level phylogenies resolved most (6/8 or 7/8) backbone nodes and strongly support for the first time the monophyly of the Malagasy radiation. We inferred the crown age of African Miniopteridae in the late Miocene (10.4 Ma), while the main lineages of Miniopterus appear to have contemporaneously diversified in two sister radiations in the Afrotropics and Madagascar. Species-level divergence of 23 of 25 African + Malagasy Miniopterus were estimated to have 95 % HPDs that overlap with the late Miocene (5.3-10.4 Ma). We present ancestral range estimates that unambiguously support a continental African radiation that originated in the Zambezian and Somalian/Ethiopian biogeographic regions, but we cannot rule out back colonization of Africa from Madagascar. The phylogeny indicates genetic support for up to seven new species.

Keywords: Chiroptera; Chronogram; Madagascar; Miniopteridae; Museomics; Phylogenomics.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Africa
Animals
Chiroptera* / genetics
Humans
Madagascar
Phylogeny