New Approaches for Inferring Phylogenies in the Presence of Paralogs

Smith, Megan L.; Hahn, Matthew W.

doi:10.1016/j.tig.2020.08.012

Cited by 61 publications

(66 citation statements)

References 116 publications

(130 reference statements)

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“…Recently developed methods based on quartet similarity ( Zhang et al 2020a ), Robinson–Foulds distances ( Molloy and Warnow 2020 ), or maximum likelihood ( Morel et al 2021 ) can directly estimate a species tree that is consistent with the MSC from multicopy genes without inferring orthologs (for a recent review, see Smith and Hahn 2021 ). However, their behavior on complex data sets using archival materials is yet to be explored.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)

et al. 2021

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Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here we used an automated approach for orthology inference in a target enrichment data set of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested ancient WGDs in the group. However, both the phylogenetic location and putative parental lineages of these WGD events remain unknown. By taking paralogs into consideration and inferring orthologs from target enrichment data, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach we established the autopolyploid origin of the entire Alchemilla s.l. and the nested allopolyploid origin of four major clades within the group. Here we showed the utility of automated tree-based orthology inference methods, previously designed for genomic or transcriptomic data sets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment data sets.

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Section: Discussionmentioning

confidence: 99%

Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae)

et al. 2021

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“…Given that most phylogenomic methods cannot take into account polyploid SNP genotypes [ 82 ], our initial phylogenies were instead built using an alignment-free method that computes distances from the intersection of k -mer distributions in unaligned reads [ 83 , 84 ]. Matrices of k -mer distances were then used to infer a phylogenetic tree with branch lengths using [ 85 ].…”

Section: Methodsmentioning

confidence: 99%

Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout

et al. 2021

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The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological ‘ecotypes’ observed in polyploid snowtrout (Cyprinidae: Schizothorax ). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq ( N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples ( N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational ‘ecotypes’ were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively ‘masks’ previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.

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“…This includes the relatively young history of divergence for some OTUs, taxon sampling, choosing marker types or identification of orthologous/paralogous genes (single-copy vs. gene duplicates) in trout. As paralogs impede investigations in salmonids (Lecaudey et al, 2018), databases (Pasquier et al, 2016;Samy et al, 2017) and tools providing guidelines for de novo or graph-based inference methods for orthologous gene identification have been developed (Kapli et al, 2020;Smith & Hahn, 2020).…”

Section: The Futurementioning

confidence: 99%