DOI: 10.5061/dryad.f3j6f8g
title: Data from: Hidden diversity of African yellow house bats (Vespertilionidae, Scotophilus): insights from multilocus phylogenetics and lineage delimitation

description: The genus Scotophilus contains 21 currently recognized species ranging
 throughout Africa and Southeast Asia. Among the 13 species recognized from
 continental Africa, systematic relationships remain poorly understood.
 Taxonomic uncertainty regarding names, suggestions of polytypic species
 complexes, and undescribed cryptic diversity all contribute to the current
 confusion. To gain insights into the systematics of this group, we
 inferred single locus and multi-locus phylogenies and conducted lineage
 delimitation analyses using seven unlinked genes for specimens from across
 Africa. Recent collections from Kenya allowed us to carry out
 population-level analyses for the diverse assemblage of East African
 Scotophilus. Multi-locus coalescent delimitation methods indicated strong
 support for three recently named lineages thought to be restricted to
 Kenya and Tanzania; it also uncovered two new distinctive lineages at
 present known only from Kenya. Subsequent taxonomic assessments that
 integrate these genetic data with phenotypic, distributional, and/or
 ecological traits are needed to establish these lineages as valid species.
 Nevertheless, as many as 15 Scotophilus species may occur in continental
 Africa, 10 of these in Kenya alone. Our analysis highlights the importance
 of population-level surveys for the detection of cryptic diversity in
 understudied regions such as the Afrotropics.
description: alignment_Scotophilus_cytb_233Nexus file containing 233 unique haplotypes of cytochrome b from African Scotophilus. This alignment was used to generate the gene tree in Fig. 1.Concatenated_alignment_cyt-b_+_6_intronsNexus file containing 31 concatenated sequences of cyt-b, ABHD, ACOX2, ACPT, COPS, ROGDI, and STAT5 from African Scotophilus. This alignment was used to generate the gene tree in Fig. 2A.Concatenated_alignment_6_intronsNexus file containing 31 concatenated sequences of ABHD, ACOX2, ACPT, COPS, ROGDI, and STAT5 from African Scotophilus. This alignment was used to generate the gene tree in Fig. 2B.alignment_cytb_31Nexus file containing 31 cyt-b sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3 and in species delimitation analyses.alignment_ABHD_phaseNexus file containing phased alleles from ABHD sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.alignment_ACOX2_phaseNexus file containing phased alleles from ACOX2 sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.alignment_ACPT_phaseNexus file containing phased alleles from ACPT sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.alignment_COPS_phaseNexus file containing phased alleles from COPS sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.alignment_ROGDI_phaseNexus file containing phased alleles from ROGDI sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.alignment_STAT5_phaseNexus file containing phased alleles from STAT5 sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.