DOI: 10.5061/dryad.prr4xgxmr
title: Data from: Species tree estimation and the impact of gene loss following whole-genome duplication

description: Whole-genome duplication (WGD) has been demonstrated to occur broadly and
 repeatedly in the evolutionary history of eukaryotes, and is recognized as
 a prominent evolutionary force, especially in plants. Immediately
 following WGD, most genes are present in two copies as paralogs. Due to
 this redundancy, one copy of a paralog pair commonly undergoes
 pseudogenization and is eventually lost. When speciation occurs shortly
 after WGD, however, differential loss of paralogs may lead to spurious
 phylogenetic inference resulting from the inclusion of pseudoorthologs –
 paralogous genes mistakenly identify as orthologs because they are present
 in single copes within each sampled species. The influence and impact of
 including pseudoorthologs versus true orthologs as result of gene
 extinction (or incomplete laboratory sampling) in a phylogenetic context
 is only recently starting to gain empirical attention. Moreover, few of
 these studies have yet to investigate this phenomenon in an explicit
 coalescent framework. Here, using mathematical models, numerous simulated
 data sets, and two newly assembled empirical data sets, we assess the
 effect of pseudoorthologs on species tree estimation under varying levels
 of incomplete lineage sorting (ILS) and different patterns of gene loss
 following WGD. When gene loss occurs in the terminal branches of the
 species tree, the alignment-based (BPP) and gene-tree-based (ASTRAL,
 MP-EST, and STAR) coalescent methods are adversely affected as the level
 of ILS increases. This can be greatly improved by sampling a sufficiently
 large number of genes. Under the same circumstances, however,
 concatenation methods consistently estimate incorrect species trees as the
 number of sampled genes increases. Furthermore, pseudoorthologs can
 mislead species tree inference if gene loss occurs in the internal
 branches of the species tree, where both coalescent and concatenation
 methods are prone to produce inconsistent results. However,
 pseudoorthologs are problematic when filtering only for single-copy genes
 in phylogenomic data sets. Pruning orthologs or even randomly selecting a
 copy from multi-copy genes can avoid most of those pseudoorthologs. These
 results underscore the importance of understanding the influence of
 pseudoorthologs in the phylogenomics era.
description: DNA sequences were simulated on four 5-taxon species trees with
 two different topologies (i.e., pectinate species trees S1 and S3, and
 symmetrical species trees S2 and S4; see Fig. 2 in the paper) under the
 multispecies coalescent model. Next, we generated differential loss of
 paralogs on each simulated gene according to one of 14 patterns described
 in the paper. In the simulation, the four terminal lineages in the
 genealogical tree of the eight gene copies are removed according to the
 loss probabilities. 
description: <strong>S1.tar.gz: </strong>DNA sequences simulated
 from the species tree S1 under the multispecies coalescent model with gene
 loss <strong>S2.tar.gz: </strong>DNA
 sequences simulated from the species tree S2 under the multispecies
 coalescent model with gene loss
 <strong>S3.tar.gz: </strong>DNA sequences simulated
 from the species tree S3 under the multispecies coalescent model with gene
 loss <strong>S4.tar.gz</strong>: DNA
 sequences simulated from the species tree S4 under the multispecies
 coalescent model with gene loss