DOI: 10.5061/dryad.jh9w0vtp9
title: Data from: Pleistocene transitions from the proto-Congo to adjacent rivers uncovered by phylogenetics and biogeography of <em>Bryconaethiops</em> (Teleostei: Alestidae)

description: African freshwater fishes serve as important biogeographical indicators of
 geomorphological and hydrological history across the continent. However,
 research focusing on the phylogeny, biogeography, and diversification of
 African fishes, particularly in central Africa, is relatively scarce.
 Here, we evaluate three geological hypotheses regarding the formation of
 the contemporary Congo basin: 1) the dominance of the Ogooué and Kouilou
 rivers along the western continental margin during the Cretaceous, 2) an
 eastward-flowing Congo-Zambezian system forming the Rufiji Delta during
 the Paleogene, and 3) river basin capture resulting in the formation of
 the Lower Congo River during the Pliocene. To do this, we reconstructed
 the phylogeny of featherfin tetras of the genus Bryconaethiops using their
 mitochondrial genomes, estimated diversification chronology, and detected
 biogeographic transitions in Central Africa. Analysis included a
 molecular matrix of complete mitochondrial genomes comprising 13
 protein-coding genes totaling 14,869 bp for 36 Bryconaethiops and related
 alestid taxa. Phylogenetic analyses included maximum likelihood, Bayesian
 fossil calibration, and parametric biogeographic reconstructions. Support
 for generic monophyly was evaluated using internal and external anatomy
 with microcomputed tomography (µCT) and conventional morphometric/meristic
 analyses. Data from museum specimens provided updated distributional
 ranges for each Bryconaethiops species. Time-calibrated
 phylogenetic and biogeographic analyses suggest initial diversification of
 Bryconaethiops occurred in Lower Guinea during the Oligocene (ca. 25 Ma),
 followed by transitions to the Nilo-Sudan and Middle Congo regions during
 the Early Miocene (ca. 19–17 Ma). Three distinct Pleistocene dispersal
 events to the Lower Congo (ca. 0.7–0.05 Ma) and three to the Upper Congo
 and Malagarasi of Tanganyika (ca. 1.5–0.1 Ma) were detected. Morphological
 analysis reveals four generic synapomorphies associated with modification
 of the upper and lower jaws, dentition, and elongation of dorsal-fin
 lepidotrichia, in addition to evidence for revalidation of B.
 mocquardianus (Thominot, 1886) from Atlantic coastal rivers of the eastern
 Gulf of Guinea.
description: # Dryad dataset Dataset DOI:
 [10.5061/dryad.jh9w0vtp9](10.5061/dryad.jh9w0vtp9) ## Description of the
 data and file structure Genomic DNA (gDNA) was extracted using Qiagen
 DNeasy Blood & Tissue kit. Libraries were pooled for sequencing in
 approximately equimolar ratios and sequenced on the Illumina NovaSeq 6000
 platform on a partial S4 PE150 lane to approximately 1 Gbp in total.
 Sixteen mitogenomes, including the outgroup taxa, were obtained from fastq
 reads generated from Illumina sequencing of ultraconserved elements
 (UCEs). ### Files and variables #### File: bryconaethiops.phy
 **Description:** Mitogenome matrix of 36 taxa and 14,869 bp, including 13
 protein-coding genes. #### File: bryconaethiops.xml **Description:** Input
 file generated by BEAUTi, including the matrix and all priors for time
 calibration. #### File: Supp-raxml.TRE **Description:** Original RAxML
 tree file. #### File: Supp-iqtree.tre **Description:** Original IQTREE
 tree file. #### File: Supp-MCC-beast.tre **Description:** Original maximum
 clade credibility tree file. ## Code/software Geneious v6.0.3 FigTree v1.4
 BEAST v2.4.8 ## Access information Other publicly accessible locations of
 the data: * There are no other publicly accessible locations of the data.
 Data was derived from the following sources: * Data is original and was
 generated from museum specimens and next-generation sequencing.