Replication data for : DNA-based monitoring of bushmeat trade dynamics and hotspots across western and central Africa

For COI and Cytb, we checked for the presence of potential pseudogenes (or NUMTS; Lopez et al., 1994), by screening for the disruption of their reading frame in Geneious prime v. 2023.3.1 (Kearse et al., 2012). For 12S and 16S, due to the absence of a reading frame, potential pseudogenes were screened for through long-branch and aberrant phylogenetic branching patterns (Triant & DeWoody, 2007). The sequences representative of 12S and 16S were first aligned with Muscle (Edgar, 2004) in Mega v.11 (Tamura et al., 2021) under default settings.

Second, we used Gblock (phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks), with both relaxed and default settings depending on the levels of divergence within orders, to remove poorly aligned positions, resulting in final alignments of 288-331 bp for 12S and 322-485 bp for 16S. Neighbour Joining (NJ) trees (Saitou & Nei, 1987) were generated with MEGA under the K2P (Kimura, 1980) model and the option “pairwise deletion”.

Node robustness was assessed through 500 bootstrap (Felsenstein, 1985) replicates. The same NJ tree approach was used for COI and Cytb as a secondary assessment of sequence quality, as pseudogenes do not necessarily translate into reading frame disruption. The data is organized as four distinct FASTA alignments of nucleotide sequences, representing different mitochondrial DNA markers: Cytochrome c oxidase I (COI; 658 bp), Cytochrome b (Cytb; 402 bp), and 12S (167 - 404 bp) and 16S (210 - 528 bp).

Together with associated metadata, the FASTA files can be downloaded for local BLAST analyses.