Additional file 1 of Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group)
Creators: name: Onditi, Kenneth Otieno
name: Demos, Terrence C.
name: Peterhans, Julian Kerbis
name: Zhong-Zheng Chen
name: Bryja, Josef
name: Lavrenchenko, Leonid A.
name: Musila, Simon
name: Verheyen, Erik
name: Van De Perre, Frederik
name: Akaibe, Benjamin Dudu
name: De La Sancha, Noé U.
name: Xue-Long Jiang
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. The phylogeny of the genus Lophuromys inferred from the Cytochrome b gene using Bayesian Inference in MrBayes. There were a total of 238 sequences in the analysis, representing all unique haplotypes from the initial alignment of 803 sequences. The numbers above branches represent the percentage posterior probability values. Figure S2. Map showing the type localities (red, green outlined crosses '+') of the non-Ethiopian L. flavopunctatus members, with the corresponding species names labeled in red fonts. The sampling points of samples used in the study are also shown, outlined to illustrate their distribution extents. Figure S3. A Maximum likelihood phylogeny of the non-Ethiopian L. flavopunctatus members inferred from the concatenated mitochondrial genes (Cytochrome b gene + cytochrome oxidase subunit 1) in IQ-TREE. The taxa labels represent the consensus species identities of main OTUs identified by species delimitation. Values above branches represent percentage Ultrafast Bootstrap support values. Figure S4. A maximum likelihood phylogeny of species in the L. flavopunctatus group inferred from the Interphotoreceptor retinol binding protein gene in IQ-TREE. Taxa labels indicate the samples ID _ Locality _ species names. Similar label font colors represent the same clades. All taxa with 'FMNH' and 'KE' in their IDs were sequenced from the current study, the rest were downloaded from GenBank. Values above branches are the ultrafast bootstrap support percentages. Figure S5. Haplotype network structure in selected non-Ethiopian L. flavopunctatus members inferred from Cytochrome b using the Median Joining Network algorithm in PopART. The networks show genealogical relationships between sampling locality in the L. zena, L. machangui, and L. zena clades which were selected for being sampled from broader areas and more localities. The number of base substitutions between haplotypes is shown as branch hatch marks. The node sizes correspond to the haplotype frequency (number of samples per haplotype) and branch lengths are relative to the number of mutations between haplotypes. Figure S6. Time calibrated maximum clade credibility tree of evolutionary relationships and divergence times in the genus Lophuromys reconstructed from Cytochrome b, Cytochrome oxidase subunit 1, and Interphotoreceptor retinoid binding protein using secondary most recent common ancestor calibrations. Branch labels show the posterior probability support values, node labels illustrate the median divergence height (age), and node bars show the highest posterior density interval. Figure S7. Classification results following discriminant analysis in using linear and geometric craniodental datasets of the non-Ethiopian L. flavopunctatus members. Values indicate cross-validated (leave-one-our bootstrapping) percentage success by which samples were classified into a priori and predicted species groups. The shaded diagonal values indicate the success by which samples were predicted into their groups which correspond to distinct Cytochrome b clades. N = number of samples. See Fig. 6 in the main manuscript for clade-stratified classification results. Figure S8. Cranial landmarks used in geometric morphometric analyses of the non-Ethiopian L. flavopunctatus members. Figure S9. Principal component analysis (PCA) of linear measurements used in the study. The plots show how samples cluster based on the first and second component scores. The top left scatter plot shows samples do not cluster in a distinct pattern consistent with the taxonomic units currently acknowledged in literature (top right). The bottom left plot shows the variances accounted for by all the component loadings.