Mitochondrial genome skimming
Iterative rounds of genome skimming on 48 specimens allowed us to
reconstruct the entire maternally-inherited mitogenome for Coelaturini
from the Malawi Basin. This mitogenome contains 15,664 bp, and
annotation included the 37 expected genes (Boore, 1999): 2 for rRNA, 22
for tRNAs, which encode components in the mitochondrial translational
machinery, and 13 other genes that encode protein components of the
respiratory chain and ATP synthase (Fig. 4). On average
~40% of the mitogenome was recovered per individual
(range 0-100%), with consistent recovery of several gene regions across
most individuals, which would enable integration of mitogenomic data in
phylogenetic and population genetic analyses.
Macroevolutionary
analyses
All 95 Coelaturini specimens were
included in our phylogenetic analyses. Selection of loci with
>50% taxon-completeness resulted in a dataset that
contained 1,109 ORF supercontigs with a mean and total alignment length
of 2,118 bp and 2,348,614 bp, respectively. For UCEs, the cleaned and
trimmed dataset contained 276 loci with a mean and total alignment
length of 432 bp and 119,105 bp, respectively. For these, 515,219
(21.9%) and 11,001 (9.24%) sites, respectively, were phylogenetically
informative. Additional data on
specimen representation, alignment length, and the proportion of
informative and missing sites for each ORF and UCE locus are given in
Ortiz-Sepulveda et al. (2022). The partition analysis resulted in a
402–partition scheme with 45 unique substitution models for ORFs, and a
155-partition scheme and 51 unique substitution models for UCEs
(Ortiz-Sepulveda et al., 2022). The phylogenetic trees reconstructed
from the ORF and UCE datasets separately are highly congruent (Fig. 5,
S3, S4). Whereas the ORF tree is fully supported, except for at
population-level branches within the ‘Malawi’ clade, some uncertainty
exists as to terminal branches in the UCE tree, as evidenced by
decreasing support and some branch re-arrangements at very shallow
levels of divergence (Fig. 5, S3, S4).