The frequency and topology of pseudoorthologs

Smith, Megan L.; Hahn, Matthew W.

doi:10.1101/2021.02.17.431499

Cited by 4 publications

(9 citation statements)

References 44 publications

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“…Hidden paralogs, biological or artifactual, are not typically accounted for in phylogenomic datasets (Smith and Hahn, 2021a; 2021b), but they are a potential source of inaccurate signal and additional conflict in datasets for which gene tree discordance is already high. This is especially true in herbariomic datasets and systems for which little is known about the history of gene or genome duplication in the system, a common limitation in plant groups (Li and Barker 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Bipartition support was calculated against an ASTRAL-III tree (Zhang et al 2018) inferred from the best maximum likelihood (ML) topologies of 314 gene trees. With the assumption that coalescent methods are robust enough to noise to produce an approximate species tree from all supposed orthologous loci (Markin and Eulenstein 2020; Legried et al 2021; Smith and Hahn 2021b; Yan et al 2021), we expect that truly single-copy gene trees should be more similar to the species tree than trees for cryptic multi-copy genes. For the first level of filtering, gene trees with average and above bipartition support were selected.…”

Section: Methodsmentioning

confidence: 99%

“…While methods have been available to extract orthologs from transcriptomes (Yang and Smith 2014), genomes (Emms and Kelly 2015), and proteomes (Cosentino and Iwasaki 2019; Emms and Kelly 2019), adequate detection of paralogs is required in target capture datasets to filter orthologs (Morales-Briones et al 2020). This can be difficult if the region has undergone differential loss (Smith and Hahn 2021a, 2021b), resulting in pseudo-orthologs, in which a single copy of the locus is present in each sample despite non-orthology (Koonin 2005). This difficulty can be further exacerbated by artifacts of data collection and assembly that may increase the number of loci with an undetected history of GDL (i.e., cryptic paralogs).…”

mentioning

confidence: 99%

“…Problems may be further increased if using a universal bait set, as lower specificity of probes for the focal system leads to a higher proportion of off-target amplicons, including additional copies of target genes (Hart et al 2016; Johnson et al 2016, 2019; Liu et al 2019; Gardner et al 2020). Hidden paralogs are increasingly acknowledged as a source of error in genomic datasets (Smith and Hahn 2021a, 2021b). While coalescent methods that model ILS appear robust to pseudo-orthologs (Markin and Eulenstein 2020; Legried et al 2021; Smith and Hahn 2021b; Yan et al 2021), the effect of cryptic paralogs, which do not represent any biological process, is unknown.…”

mentioning

confidence: 99%

“…Hidden paralogs are increasingly acknowledged as a source of error in genomic datasets (Smith and Hahn 2021a, 2021b). While coalescent methods that model ILS appear robust to pseudo-orthologs (Markin and Eulenstein 2020; Legried et al 2021; Smith and Hahn 2021b; Yan et al 2021), the effect of cryptic paralogs, which do not represent any biological process, is unknown. As the number of herbariomic target sequence capture datasets continues to rapidly rise and we begin to explore the utility of multi-copy genes for phylogenetic inference (Gardner et al 2020), we should be careful that the benefit of known paralogs is not lost in the noise of cryptic paralogs.…”

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confidence: 99%

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Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Lagomarsino

2021

Preprint

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The Andes mountains in South America are a biodiversity hotspot within a hotspot, the New World Tropics, for seed plants. Much of this diversity is concentrated at middle-elevations in cloud forests, yet the evolutionary patterns underlying this extraordinary diversity remain poorly understood. This is partially due to a paucity of resolved phylogenies for cloud forest plant lineages: the young age of the Andes and generally high diversification rates among Andean systems precludes robust phylogenetic inference, and remote populations, few genomic resources, and generally understudied organisms make acquiring high-quality data difficult. We present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation with potential to provide insight into some of the abiotic and extrinsic factors that promote the highest diversity observed on the globe. Our dataset, representing data for 50 of the ca. 75 spp. obtained almost entirely from herbarium specimens via hybrid-enriched target sequence capture with the universal bait set Angiosperms353, included a proportion of poorly assembled loci likely representing multi-copy genes, but with insufficient data to be flagged by paralog filters: cryptic paralogs. These cryptic paralogs likely result from limitations in data collection that are common in herbariomics combined with a history of genome duplication and are likely common in other plant phylogenomic datasets. Standard empirical metrics for identifying poor-quality genes, which typically focus on filtering for genes with high phylogenetic informativeness, failed to identify problematic loci in our dataset where strong but inaccurate signal was a greater problem. Filtering by bipartition support was the most successful method for selecting genes and resulted in a species tree with lower discordance, higher support, and a more accurate topology relative to a consensus tree. Using known paralogs, we investigate the utility of multi-copy genes in phylogenetic inference and find a role for paralogs in resolving deep nodes and major clades, though at the expense of gene tree concordance and support. With the first phylogeny, we infer the biogeographic history of Freziera and identify the northern Andes as a source region. We also identify distinct modes of diversification in the northern and central Andes, highlighting the importance of fine-scale biogeographic study in Andean cloud forest systems.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Lagomarsino

2021

Preprint

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Using all gene families vastly expands data available for phylogenomic inference

Smith

Vanderpool

Hahn

2021

Preprint

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Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs by using clustering approaches and retaining families with a single sequence from each species. However, this approach can severely limit the amount of data available by excluding larger families. Recent methodological advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several popular methods for species tree inference appear to be robust to the inclusion of paralogs, and hence could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference using genomes from 26 primate species. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data (i.e., including orthologs and paralogs). We explore several species tree inference methods, finding that across all nodes of the tree except one, identical trees are returned across nearly all datasets and methods. As in previous studies, the relationships among Platyrrhini remain contentious; however, the tree inference methods matter more than the dataset used. We also assess the effects of each dataset on branch length estimates, measures of phylogenetic uncertainty and concordance, and in detecting introgression. Our results demonstrate that using data from larger gene families drastically increases the number of genes available for phylogenetic inference and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression.

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Enriching for orthologs increases support for Xenacoelomorpha and Ambulacraria sister relationship

Mulhair

McCarthey

Siu-Ting

et al. 2021

Preprint

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Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum, or within Deuterostomia, sister to Ambulacraria. While their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral Bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. More recently, further studies have brought into question whether Deuterostomia should be considered monophyletic at all. Hidden paralogy presents a major challenge for reconstructing species phylogenies. Here we assess whether hidden paralogy has contributed to the conflict over the placement of Xenacoelomorpha. Our approach assesses previously published datasets, enriching for orthogroups whose gene trees support well resolved clans elsewhere in the animal tree of life. We find that the majority of constituent genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy is rife at this depth. We demonstrate that enrichment for genes with orthologous signal alters the final topology that is inferred, whilst simultaneously improving fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our orthology enriched set of genes. At a time when we are steadily progressing towards sequencing all of life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modelled adequately.

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The frequency and topology of pseudoorthologs

Cited by 4 publications

References 44 publications

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Strong phylogenetic signal despite high phylogenomic complexity in an Andean plant radiation (Freziera,Pentaphylacaceae)

Using all gene families vastly expands data available for phylogenomic inference

Enriching for orthologs increases support for Xenacoelomorpha and Ambulacraria sister relationship

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