1. Evolutionary Biology

A multispecies coalescent model for quantitative traits

  1. Fábio K Mendes  Is a corresponding author
  2. Jesualdo A Fuentes-González
  3. Joshua G Schraiber
  4. Matthew W. Hahn
  1. Indiana University, United States
  2. Temple University, United States
https://doi.org/10.7554/eLife.36482
Share this article
Cite this article
  1. Fábio K Mendes
  2. Jesualdo A Fuentes-González
  3. Joshua G Schraiber
  4. Matthew W. Hahn
(2018)
A multispecies coalescent model for quantitative traits
eLife 7:e36482.
https://doi.org/10.7554/eLife.36482
  2. Download BibTeX
  3. Download .RIS

Abstract

We present a multispecies coalescent model for quantitative traits that allows for evolutionary inferences at micro- and macroevolutionary scales. A major advantage of this model is its ability to incorporate genealogical discordance underlying a quantitative trait. We show that discordance causes a decrease in the expected trait covariance between more closely related species relative to more distantly related species. If unaccounted for, this outcome can lead to an overestimation of a trait's evolutionary rate, to a decrease in its phylogenetic signal, and to errors when examining shifts in mean trait values. The number of loci controlling a quantitative trait appears to be irrelevant to all trends reported, and discordance also affected discrete, threshold traits. Our model and analyses point to the conditions under which different methods should fare better or worse, in addition to indicating current and future approaches that can mitigate the effects of discordance.

Data availability

Simulated data can be found at: https://doi.org/10.5061/dryad.m2s1735

The following data sets were generated

Article and author information

Author details

  1. Fábio K Mendes

    Department of Biology, Indiana University, Bloomington, United States
    For correspondence
    fkmendes@indiana.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6204-7208

  2. Jesualdo A Fuentes-González

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Joshua G Schraiber

    Department of Biology, Temple University, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Matthew W. Hahn

    Department of Biology, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5731-8808

Funding

National Science Foundation (DBI-1564611)

  • Matthew W. Hahn

National Institutes of Health (R35 GM124745)

  • Joshua G Schraiber

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Antonis Rokas, Vanderbilt University, United States

Version history

  1. Received: March 7, 2018
  2. Accepted: July 2, 2018
  3. Accepted Manuscript published: July 3, 2018 (version 1)
  4. Version of Record published: August 14, 2018 (version 2)

Copyright

© 2018, Mendes et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,691
    views
  • 316
    downloads
  • 43
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Fábio K Mendes
  2. Jesualdo A Fuentes-González
  3. Joshua G Schraiber
  4. Matthew W. Hahn
(2018)
A multispecies coalescent model for quantitative traits
eLife 7:e36482.
https://doi.org/10.7554/eLife.36482

Share this article

https://doi.org/10.7554/eLife.36482

Categories and tags

Further reading

    1. Computational and Systems Biology
    2. Evolutionary Biology

    CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA

    Ryan T Bell, Harutyun Sahakyan ... Eugene V Koonin
    Research Article

    A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote coiled-coil nuclease tandems (CoCoNuTs) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with three distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.

    1. Evolutionary Biology
    2. Neuroscience

    Large-scale deorphanization of Nematostella vectensis neuropeptide G protein-coupled receptors supports the independent expansion of bilaterian and cnidarian peptidergic systems

    Daniel Thiel, Luis Alfonso Yañez Guerra ... Gáspár Jékely
    Research Article

    Neuropeptides are ancient signaling molecules in animals but only few peptide receptors are known outside bilaterians. Cnidarians possess a large number of G protein-coupled receptors (GPCRs) – the most common receptors of bilaterian neuropeptides – but most of these remain orphan with no known ligands. We searched for neuropeptides in the sea anemone Nematostella vectensis and created a library of 64 peptides derived from 33 precursors. In a large-scale pharmacological screen with these peptides and 161 N. vectensis GPCRs, we identified 31 receptors specifically activated by 1 to 3 of 14 peptides. Mapping GPCR and neuropeptide expression to single-cell sequencing data revealed how cnidarian tissues are extensively connected by multilayer peptidergic networks. Phylogenetic analysis identified no direct orthology to bilaterian peptidergic systems and supports the independent expansion of neuropeptide signaling in cnidarians from a few ancestral peptide-receptor pairs.

    1. Evolutionary Biology

    Circadian Rhythms: Cnidarians are CLOCKing in

    Erica R Kwiatkowski, Patrick Emery
    Insight

    Studies of the starlet sea anemone provide important insights into the early evolution of the circadian clock in animals.