Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi

Abstract

Whole genome sequences are beginning to revolutionise our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic datasets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of SNPs extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomise the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than two million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the dataset to non-introgressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome datasets.

The genome of the pygmy right whale illuminates the evolution of rorquals

“…These ancient introgression events could also, together with the number of discordant trees caused by ILS, result in a false topology of bifurcating branches that cannot be resolved unless the entire history of introgression events could be unscrambled. Such an attempt to remove putative signals of introgression in a similar case of mbuna cichlids did not alter the distribution of conflicts for the problematic branches [ 81 ]. Therefore, choosing between one of the three possible topologies might not be possible, which supports our finding that the evolution of rorquals is best described as a hard polytomy.…”

Taxonomic investigation of the zooplanktivorous Lake Malawi cichlids Copadichromis mloto (Iles) and C. virginalis (Iles)

“…The strikingly long terminal branches observed in the NJ tree where withinindividual hetrozygosity is retained (Supplementary Figure 1) reflect that cross-sample coalescence in many regions of the genome pre-dates the estimated splits, indicating substantial shared ancestral variation and incomplete lineage sorting. This accurately reflects the challenge in constructing robust phylogenetic estimates in Malawian cichlids, even with full genome sequence information (Scherz et al, 2022). A factor influencing this pattern may be a rapid population expansion around the time of speciation, perhaps co-incident with colonisation of deep-water habitats (Genner et al, 2010), while extensive introgression among species is probable and will further confound phylogeny estimation (Scherz et al, 2022).…”

“…This accurately reflects the challenge in constructing robust phylogenetic estimates in Malawian cichlids, even with full genome sequence information (Scherz et al, 2022). A factor influencing this pattern may be a rapid population expansion around the time of speciation, perhaps co-incident with colonisation of deep-water habitats (Genner et al, 2010), while extensive introgression among species is probable and will further confound phylogeny estimation (Scherz et al, 2022).…”

Phylogenomic Analyses Show Repeated Evolution of Hypertrophied Lips Among Lake Malawi Cichlid Fishes

“…Four individuals were pooled per lane with the aim of generating an approximate genome coverage of 20× per individual. Our genomic dataset was supplemented with additional short-read WGS data for 60 individuals sequenced by Malinsky et al (2018) and seven individuals by Scherz et al (2022) ( supplementary table S1, Supplementary Material online ).…”