DOI: 10.5061/dryad.kd51c5bgm
title: Data from: Phylogenomic and anatomical evidence for the Late Cretaceous diversification of African characiform fishes, including a new family, under the influence of the Trans-Saharan Seaway

description: Geological evidence supports the occurrence of an epicontinental
 Trans-Saharan Seaway bisecting the African continent during the Late
 Cretaceous to early Paleogene. The seaway formed a wide saltwater channel
 connecting the Neotethys with the South Atlantic, yet no previous study
 has investigated its impact on freshwater fish diversification.
 Phylogenomic data and time-calibrated trees indicate a Late Cretaceous
 signature for the appearance of three modern lineages of characiform
 fishes. Phylogenetic analyses using ultraconserved elements of 83
 characiforms reveals that Alestidae, Hepsetus, and Lepidarchidae fam. nov.
 originated during the Santonian-Campanian of the Late Cretaceous (84–77.5
 million years ago; Ma). Lepidarchidae consists of two monotypic taxa not
 previously recognized as sister species: the Niger tetra Arnoldichthys
 endemic to the lower Niger and Ogun rivers of Nigeria, and the dwarf
 jellybean tetra Lepidarchus from coastal rivers of Ghana, Côte
 d'Ivoire, Liberia, Sierra Leone, and Guinea. Microcomputed tomography
 scans (µCT) of 117 characiforms provide three novel morphological
 characters supporting Hepsetus and Lepidarchidae, four characters for
 monophyly of Lepidarchidae and five for a restricted Alestidae. The
 Santonian-Campanian divergence indicates allopatric speciation processes
 influenced by the Trans-Saharan Seaway, partitioning the African
 ichthyofauna in a west-east orientation. The timing for African
 characiform cladogenesis aligns with the Cenomanian fossil record and is
 circa 16–23 Ma younger than the earliest characiform-like fossils from
 Late Cretaceous outcrops of Morocco and Sudan. This study highlights the
 magnitude of Cretaceous transgression events shaping the freshwater biota
 and gaps in our understanding of the evolutionary history and
 paleobiogeography of ray-finned fishes across the African continent.
description: Total genomic DNA was extracted using the DNeasy tissue kit,
 quantified and enriched genomic libraries using the myBaits Ostariophysan
 2.7Kv1 probeset with an overnight hybridization, washes at 65ºC, and
 additional quantification with a spectrofluorimetric assay. Samples were
 sequenced on the Illumina NovaSeq 6000 platform on a partial S4 PE150 lane
 to approximately 14Gbp total for captured libraries.
 PHYLUCE v1.5.0 was used to perform all UCE data analysis,
 including removal of adapters and low-quality bases with Illumiprocessor
 and Trimmomatic, as well as assembling fasta contigs with Velvet v1.5.0.
 We searched for orthologous UCE loci using the myBaits Ostariophysan
 2.7Kv1 probeset and removed potential paralog regions with
 <em>phyluce_assembly_match_contigs_to_probes</em> in PHYLUCE
 v1.5.0. We extracted and aligned loci using an edge-trimming method
 implemented in MUSCLE and used three matrices: the 60% complete matrix
 (<em>i.e.</em> loci present in at least 51 terminals), the 70%
 complete matrix (<em>i.e.</em> loci present in at least 59
 terminals), and for calibration, the 80% complete matrix
 (<em>i.e.</em> loci present in at least 67
 terminals). Maximum likelihood (ML) were conducted in
 RAxML v8.2.11 with one thousand non-parametric bootstraps and individual
 gene trees were obtained using a coalescent-based analysis using ML trees
 for each UCE locus with RAxML-PTHREAD-SSE3 and species trees from the best
 likelihood trees using ASTRAL v5.6.1. Time calibration
 analyses were performed in BEAUTI and BEAST v2.4.8 using the 80% complete
 UCE matrix under the GTR+G+I evolutionary model and a relaxed lognormal
 clock model. The priors included a birth-death tree model, diversification
 rate, one root constraint, and four fossil calibrations.
 Specimens were µCT scanned using a GE Phoenix v|tome|x with a
 180kV Nano Tube at resolutions ranging from 6.2 to 27.8 μm, with beam
 energy set between 110–100 kV and 200–180 mA.
description: # Data from: Phylogenomic and anatomical evidence for the Late Cretaceous
 diversification of African characiform fishes, including a new family,
 under the influence of the Trans-Saharan Seaway
 [https://doi.org/10.5061/dryad.kd51c5bgm](https://doi.org/10.5061/dryad.kd51c5bgm) ## Description of the data and file structure Data was collected from museum specimens. Sequences were obtained from captures of ultraconserved elements of 84 taxa using Illumina approaches. Data was processed by Phyluce and analyses ran through RAxML, Astral, and BEAST.  ### Files and variables #### File: lepidarchidae-80.xml **Description:** Data file used for BEAST time-calibrated analysis. #### File: MCC-tree-all.tre **Description:** Maximum Clade Credibility timetree of Lepidarchidae and other characiforms. #### File: muscle-nexus-edge-trimmed-clean-80p.nex **Description:** Data matrix 80% complete of ultraconserved elements. #### File: muscle-nexus-edge-trimmed-clean-60p.phylip **Description:** Data matrix 60% complete of ultraconserved elements. #### File: muscle-nexus-edge-trimmed-clean-70p.phylip **Description:** Data matrix 70% complete of ultraconserved elements. ## Code/software PHYLUCE v1.5.0 RAxML v8.2.11 ASTRAL v5.6.1 BEAST v2.4.8