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Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

View ORCID ProfileErin K. Molloy, John Gatesy, Mark S. Springer
doi: https://doi.org/10.1101/2020.09.29.319038
Erin K. Molloy
1Department of Computer Science, University of Maryland, College Park, College Park, 20742, USA
2Institute for Advanced Computer Studies, Univ. of Maryland, College Park, College Park, MD 20740
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  • For correspondence: ekmolloy@umd.edu springer@ucr.edu
John Gatesy
3Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, 10024, USA
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Mark S. Springer
4Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, 92521, USA
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  • For correspondence: ekmolloy@umd.edu springer@ucr.edu
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Abstract

A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e. local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study, provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100 000 parsimony-informative RIs. We found that, when given just 1 000 parsimony-informative RIs as input, ASTRAL BP successfully reconstructed major clades (i.e clades separated by branches > 0.3 CUs) with high support and identified rapid radiations (i.e. shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • We have extended our simulation study by varying the number of retroelement insertions from 100 to 100,000. This enabled us to discuss the impact of data quantity on species tree estimation, including the utility of branch support for controlling false positive edges. We have added an in-depth analysis of data sets with just a few thousand retroelement insertions, simulated from the Palaeognathae model species tree (this model tree is based on the tree estimated by Cloutier et al. 2019 by running ASTRAL given >20,000 estimated gene trees as input). This enables us to discuss the utility of our proposed methods for reconstructing major clades and identifying rapid radiations under more realistic model conditions. We have largely rewritten the introduction/discussion sections, fixing many typos in this process.

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Posted August 20, 2021.
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Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
Erin K. Molloy, John Gatesy, Mark S. Springer
bioRxiv 2020.09.29.319038; doi: https://doi.org/10.1101/2020.09.29.319038
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Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
Erin K. Molloy, John Gatesy, Mark S. Springer
bioRxiv 2020.09.29.319038; doi: https://doi.org/10.1101/2020.09.29.319038

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