Phylogenetic relationships and genetic population structure
inferred from nuclear genome
Among 595,163 de novocatalog loci generated with STACKS de novo pipeline and mapped to
the B. barbus genome 251,956 loci had multiple alignments,
322,820 had one alignment and 20,387 were unmapped.
The ‘stacks-integrate-alignments’
procedure filtered out 371,899 loci due to mapping quality, 97,561 due
to alignment coverage, and 12,020 due to percent identity, resulting in
93,296 loci retained for downstream analyses (detailed statistics on
each sample including raw reads is given in Supplementary material S10).
The phylogeny of Ethiopian Labeobarbus (Figure 6A) based on
15,820 SNPs is generally congruent with that based on mtDNA data (Levin
et al., 2020 and Figure 6A). Sympatric generalized and thick-lipped
ecomorphs clustered together and form monophyletic lineages with high
support for all studied basins/subbasins (90-100 bootstrap values)
except for the Gojeb (62). The Labeobarbus lineages subdivided
into two clades representing i) Eastern (L. gananensis from
Genale River, Indian Ocean basin) and ii) Western (L. cf.intermedius sensu lato from the Didessa, Gojeb, Sore, and Birbir
Rivers) parts of the Ethiopian Highlands (Fig. 6A). The сlade of the
Western Plateau is further subdivided for the Northern subclade (Didessa
River in the Blue Nile basin) and the Southern subclade that combines
the Gojeb (Omo-Turkana basin), Sore, and Birbir (White Nile basin)
populations. The Southern subclade is further subdivided into lineages
according to geographical basin belonging to the Gojeb (Omo-Turkana)
lineage and White Nile lineage comprising the Sore and Birbir
populations. Remarkably, the Sore and Birbir populations also form the
sister monophyletic sublineages within White Nile lineage (Fig. 6A).
An analysis of the population genetic structure revealed an optimum of
four (K ) clusters that correspond to the (i) Genale, (ii)
Didessa, (iii) Gojeb, and iv) White Nile populations from the Sore and
Birbir Rivers (Figure 6A). Five samples from the Gojeb River have a
little admixture (~10%) from the White Nile cluster.
When each basin with sympatric ecomorphs was analyzed independently,
only one river with subdivision by ecomorphs was revealed – the Didessa
in the Blue Nile basin (Fig. 6A). Individuals from White Nile basin are
further subdivided by geographical populations from the Sore and Birbir
Rivers (Fig. 6A). PCA of the 2,411 SNPs confirmed six well-defined
clusters that correspond to the phylogenetic and population genomics
results including subdivision of generalized and thick-lipped ecomorphs
in the Didessa (Fig. 6B).
All ReichF ST pairwise comparisons between inferred genetic
clusters were statistically significant with values ranging from 0.21
(0.18-0.25 95%CI) between Didessa generalized ecomorph and Didessa
thick-lipped ecomorph to 0.66 (0.63-0.68) between Sore and Genale
(Supplementary Data S11).F STpairwise comparisons of the pairs of sympatric ecomorphs within each
basin (Supplementary Data S12) was significant only for Didessa, where
ecomorphs constitute well segregated genetic pools.