Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships

Abstract

<jats:p>Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of <jats:italic>Coregonus</jats:italic> and (3) placement of <jats:italic>Parahucho</jats:italic>. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of <jats:italic>Coregonus</jats:italic>, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of <jats:italic>Parahucho</jats:italic> is as sister lineage of <jats:italic>Salmo</jats:italic>.</jats:p>

Phylogenomic resolution of the monotypic and enigmatic Amarsipus, the Bagless Glassfish (Teleostei, Amarsipidae)

“…A series of rapid, successive divergence events among major lineages early in pelagiarian history create a phylogenetic scenario that is difficult to resolve with the simple addition of more loci and analysed in traditional concatenated or coalescent species tree analytical frameworks (e.g. Campbell et al., 2017, 2020). This is reflected in the relatively high levels of gene tree discordance, low node support and inferred topologies that are inconsistent with regard to the relationships among the oldest nodes within the pelagiarian phylogeny (Figure 2).…”

Genomic Hatchery Introgression in Brown Trout (Salmo trutta L.): Development of a Diagnostic SNP Panel for Monitoring the Impacted Mediterranean Rivers

“…Another explanation could be that this SNP was a bioinformatic artefact, the consequence of over-merged loci (i.e., paralogous), being the diagnostic polymorphism in another region of the genome. Despite brown trout being a species of tetraploid origin [ 70 ], the coverage obtained with this marker from 2b-RADseq (12.46× ± 4.63× across 248 genotyped individuals) make the latter explanation unlikely. Nonetheless, TRU08 could be replaced by another diagnostic SNPs from the 2b-RADseq catalog ( Supplementary Table S1 ) or even by the SNP responsible for the distinct electrophoretic pattern between LDH-C * 100 and * 90 alleles [ 43 ].…”

“…Filtered reads were aligned to the brown trout genome with Bowtie 1.3.0 [ 67 ] using the −v alignment mode (v = number of allowed mismatches; −v 3). To limit artifactual SNPs from the tetraploid origin of the salmonids [ 68 , 69 , 70 ], reads with more than one alignment with the same quality were discarded (—best —strata m 1). Individuals with less than 900,000 aligned reads (Q1 aligned reads—IQR) were removed, since individuals with a low number of reads might act as a burden to obtaining a robust SNP panel (see Table 1 ).…”

The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution

“…With so many fully sequenced genomes/transcriptomes available, the proportion of one-to-one orthologs in typical multi-gene, multi-species data sets will become smaller and smaller, and most of the information about the history of genomes and organisms must be extracted from multi-copy gene families. This is particularly true of organisms having large, complex genomes and undergoing frequent hybridisation and large-scale duplications, such as the economically important angiosperms (Glémin et al, 2019;Stull et al, 2020) and fish (Alda et al, 2019;Campbell et al, 2020), to name just a few.…”