To include or not to include: The impact of gene filtering on species tree estimation methods

Molloy, Erin K.; Warnow, Tandy

doi:10.1101/149120

Cited by 26 publications

(32 citation statements)

References 65 publications

(79 reference statements)

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“…The widespread adoption of methods accounting for incomplete lineage sorting is one of the major innovations made possible by phylogenomics [ 52 ], but its utility for phylogenetic inference in deep time remains a topic of discussion [ 53 , 54 ]. Simulations have demonstrated that genes with minimal phylogenetic information might produce unreliable gene trees, which in turn reduce the accuracy of species tree estimation using summary methods [ 55 , 56 ]. Our empirical analysis shows that rate heterogeneity among neognathostomate echinoids might be strong enough to bias some coalescent-based approaches, potentially by reducing the phylogenetic signal of individual genes and affecting gene tree accuracy (as recently found by other empirical studies, see [ 57 ] and references therein).…”

Section: Discussionmentioning

confidence: 99%

A phylogenomic resolution of the sea urchin tree of life

Koch¹,

Coppard²,

Lessios³

et al. 2018

BMC Evol Biol

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BackgroundEchinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved.ResultsWe performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We show that phylogenetic signal for novel resolutions of these lineages is strong and distributed throughout the genome, and fail to recover systematic biases as drivers of our results.ConclusionsOur investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1300-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

A phylogenomic resolution of the sea urchin tree of life

Koch¹,

Coppard²,

Lessios³

et al. 2018

BMC Evol Biol

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“…In addition, we also constructed a species tree with the same set of loci using SVDquartets (Chifman & Kubatko, ) in Paup* (Swofford, ). SVDquartets is expected to be more accurate than ASTRAL when there are few phylogenetically informative sites among loci, so we chose to use both of these two methods given possible biases in our loci (Molloy & Warnow, ).…”

Section: Methodsmentioning

confidence: 99%

Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny

Dam

Trautwein

Spicer

et al. 2019

Molecular Ecology Resources

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Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in‐silico by constructing a phylogeny using 13 existing Acari genomes, as well as 6 additional taxa from a variety of genomic sources. Our Acari‐specific probe kit improves the recovery of loci within mites over an existing general arachnid UCE probe set. Our initial phylogeny recovers the major mite lineages, yet finds mites to be non‐monophyletic overall, with Opiliones (harvestmen) and Ricinuleidae (hooded tickspiders) rendering Parasitiformes paraphyletic.

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“…Multispecies coalescence is increasingly prevalent in analyses using genomic data [34]. However, the reliability of species tree analyses can be reduced due to characteristics of individual genes such as length, missing data, and base heterogeneity that obstruct gene tree reconstruction and may increase gene tree error [35][36][37]. Gene trees are also useful for investigating discordance [38].…”

Section: Introductionmentioning

confidence: 99%

Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics

et al. 2021

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Background The most species-rich radiation of animal life in the 66 million years following the Cretaceous extinction event is that of schizophoran flies: a third of fly diversity including Drosophila fruit fly model organisms, house flies, forensic blow flies, agricultural pest flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these flies. We use protein encoding sequence data from transcriptomes, including 3145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge. Results Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea stat. rev. as successive sister groups to the remaining Schizophora. Ephydroidea, Drosophila’s superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroborated by morphological traits, the ‘Modified Oviscapt Clade’ containing Tephritoidea, Nerioidea, and other families, and the ‘Cleft Pedicel Clade’ containing Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multispecies coalescent approaches. Rogue taxon removal was effective in increasing support values compared with strategies that maximise gene coverage or minimise missing data. Conclusions Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.

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To include or not to include: The impact of gene filtering on species tree estimation methods

Cited by 26 publications

References 65 publications

A phylogenomic resolution of the sea urchin tree of life

A phylogenomic resolution of the sea urchin tree of life

Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny

Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics

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