Volume 16 Supplement 10
Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics
Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer
 Ruth Davidson^{1},
 Pranjal Vachaspati^{2},
 Siavash Mirarab^{4, 5} and
 Tandy Warnow^{2, 3}Email author
DOI: 10.1186/1471216416S10S1
© Davidson et al. 2015
Published: 2 October 2015
Abstract
Background
Species tree estimation is challenged by gene tree heterogeneity resulting from biological processes such as duplication and loss, hybridization, incomplete lineage sorting (ILS), and horizontal gene transfer (HGT). Mathematical theory about reconstructing species trees in the presence of HGT alone or ILS alone suggests that quartetbased species tree methods (known to be statistically consistent under ILS, or under bounded amounts of HGT) might be effective techniques for estimating species trees when both HGT and ILS are present.
Results
We evaluated several publicly available coalescentbased methods and concatenation under maximum likelihood on simulated datasets with moderate ILS and varying levels of HGT. Our study shows that two quartetbased species tree estimation methods (ASTRAL2 and weighted Quartets MaxCut) are both highly accurate, even on datasets with high rates of HGT. In contrast, although NJst and concatenation using maximum likelihood are highly accurate under low HGT, they are less robust to high HGT rates.
Conclusion
Our study shows that quartetbased speciestree estimation methods can be highly accurate under the presence of both HGT and ILS. The study suggests the possibility that some quartetbased methods might be statistically consistent under phylogenomic models of gene tree heterogeneity with both HGT and ILS.
Keywords
phylogenomics HGT ILS summary methods concatenationBackground
A species phylogeny is a graphical model of the common evolutionary history of a group of species, and is most often represented as a phylogenetic tree or phylogenetic network [1]. A species phylogeny gives valuable information about protein functions [2–4], hostparasite relationships [5], etc.
However, species tree estimation is difficult, due to multiple biological processes, including recombination [6], duplication and loss [7], hybridization [8], incomplete lineage sorting (ILS) [9], and horizontal gene transfer (HGT) [10], that can cause a given genomic locus to have a tree that is different from the species tree. As a result, multiple loci are needed to estimate a species phylogeny with high accuracy.
Of the many sources of gene tree discord, the one that has received the greatest attention is ILS, which is modeled by the multispecies coalescent (MSC) model [11]. An MSC model tree has a rooted tree T , leaflabelled by a set of species, and is given with branch lengths in coalescent units. Gene trees evolve within the species tree, in a backwards process described by the MSC; thus, lineages "coalesce" on the branches of the tree, as they move from the leaves of the species tree towards the root. When two lineages fail to coalesce on the earliest branch in which they can coalesce, this can result in a gene tree having a different topology than the species tree.
Under the MSC model, each species tree defines a probability distribution on gene trees, and the species tree can be identified uniquely from this distribution. Hence, one type of technique (called a "summary method") for estimating species trees under the MSC operates by first estimating gene trees for a set of different loci, and then uses this estimated distribution on gene trees to estimate the species tree. A summary method is said to be statistically consistent under the MSC model if, as the number of loci and sites per locus go to infinity, the estimated species tree returned by the method will converge in probability to the true species tree [12]. Many statistically consistent summary methods have been developed for estimating species trees when gene discordance is due to ILS [13–19].
Despite advances in developing statistically consistent methods for species tree estimation that are robust to ILS, by far the most common technique for estimating a species tree is concatenation analysis, in which the sequence alignments for the different loci are combined into one large supermatrix, and then a phylogeny is estimated on the alignment using maximum likelihood [20, 21]. This type of approach, however, is sometimes not statistically consistent under the multispecies coalescent model [22, 12] in the presence of ILS. Hence, even though concatenation often has good accuracy (even under conditions with moderately high ILS levels) [23–25], a large effort has been made to develop alternative methods that are provably robust to ILS and have good accuracy on realistic conditions.
For very small datasets, Bayesian methods such as BEST [26], *BEAST [27] or BUCKypop [28] (the population tree from BUCKy) can provide excellent accuracy; however, these methods are too computationally intensive to use on even moderate sized datasets with hundreds to thousands of loci and 30 or more species [29, 30].
Of the currently available coalescentbased methods, ASTRAL2 [19], MPEST [13], and NJst [17] have emerged as the most accurate of the methods that can run on datasets with 50 or more species and hundreds to thousands of loci. However, the comparison among these methods shows that MPEST is typically not as accurate as NJst and ASTRAL2 and is also much slower than both [19]. Some newer statistically consistent methods have also been developed (e.g., SVDquartets [31]), but have not yet been sufficiently evaluated in terms of their accuracy and scalability in comparison to other coalescentbased methods.
Some of the most commonly used coalescentbased methods estimate species trees by encoding each gene tree as a set of quartet trees (i.e., unrooted 4leaf trees), and then estimate the species tree from the quartet tree frequencies. The mathematical basis of this approach is the following theorem, originally proved in [32]:
Theorem 1 Under the multispecies coalescent model, for every model species tree (T, θ) (where θ denotes the branch lengths of T in coalescent units) and for every set X of four leaves from T, the most probable unrooted gene tree topology on X is identical to the species tree T restricted to the leafset X.
Interestingly, nearly the same theorem was proven under two phylogenomic models that addressed horizontal gene transfer (HGT)! When HGT is present, the evolutionary history of the species is not really treelike, but rather requires a phylogenetic network [1]. Under HGT models, a phylogenetic network consists of an underlying species tree T with horizontal gene transfer edges (represented by directed edges) between branches in the tree, and each locus evolves down a tree (though not necessarily the species tree) within this network. Hence, while the species evolution is not purely treelike, the gene tree evolution is treelike. Furthermore, for this type of reticulate phylogeny, it is reasonable to ask whether the underlying species tree T can be reconstructed from gene trees estimated on the different loci.
This question has been partially answered for two models of HGT. The first models HGT events between lineages using a continuoustime Poisson process [33], and is called the stochastic HGT model. In a stochastic HGT model, the HGT events happen between contemporaneous lineages, either uniformly at random or with probability that depends on the distance between the lineages (so that events are less likely if the lineages are more distantly related). The second type of model assumes that there are HGT edges between specific pairs of branches in a species tree, commonly referred to as highways, along which HGT events are far more likely to occur than elsewhere in the tree; this is called the highways HGT model [34].
The theoretical framework for estimating the underlying species tree under these two HGT models was established in [35] (for estimating rooted species trees from rooted gene trees) and in [36] (for estimating unrooted species trees from unrooted gene trees). Specifically, [36] proved theorems that under both the stochastic HGT model and highways model, but with bounded amounts of HGT per gene, the most probable quartet tree would be topologically identical to the species tree. Note that these theorems are the equivalents of Theorem 1 under the two bounded HGT models.
Some species tree estimation methods operate by computing gene trees, encoding each computed gene tree as a set of quartet trees, and determining the dominant quartet tree for every four species (i.e., the quartet tree that appears the most frequently of the three possible unrooted quartet trees). Then, these dominant quartet trees are combined using a quartet amalgamation method (e.g., Quartets Max Cut [37] or QFM [38]). This type of species tree estimation method can be statistically consistent under the MSC model, and also under these bounded HGT models  depending on the quartet amalgamation method, as we now show.
Theorem 2 Let M be a summary method (i.e., a method that constructs a species tree from an input set of gene trees). Suppose that M has the property that it is guaranteed to return the unique tree compatible with the dominant quartet trees defined by its input set of gene trees, whenever the dominant quartet trees are compatible. Then M is statistically consistent under the MSC model, and also under the bounded HGT models given in [36].
Proof To establish statistical consistency, we only need to prove that as the number of sites per locus and the number of loci both increase, the tree returned by the method converges in probability to the species tree. As the number of sites per locus and the number of loci both increase, the dominant quartet tree converges to the most probable quartet tree on every set X of four species. Under the MSC model and also under the bounded HGT models in [36], the most probable quartet tree on any set X is topologically identical to the species tree. Hence, for a large enough number of loci and large enough number of sites per locus, with probability converging to 1, the input to the quartetbased methods will be a set of gene trees such that the dominant quartet trees are all compatible with the species tree. Furthermore, the species tree will be the unique such compatibility tree, and so the method will return the true species tree.
Similarly, we can prove the following:
Theorem 3 ASTRAL and ASTRAL2 are statistically consistent under the bounded HGT models of [36].
This proof uses Theorem 1, but is essentially identical to the proofs of statistical consistency for ASTRAL and ASTRAL2 under the MSC model [19]; see Methods for the proof of this theorem.
Very little is known about the theoretical guarantees of any species tree estimation methods under models in which both HGT and ILS can occur. In fact, to the best of our knowledge, no methods have yet been proven statistically consistent under these conditions. We also do not know much about the empirical performance of any species tree estimation methods under these conditions. As far as we know, the only simulation study to date of the impact of both ILS and HGT on the performance of species tree estimation methods is [39], which explored the performance of two coalescentbased methods, BUCKy and BEST, on data that evolved under both processes. However, both of these methods are computationally intensive, and cannot run on even moderately large datasets (e.g., BEST is slower than *BEAST, and *BEAST is too computationally intensive to use on datasets with more than about 100 loci) [30, 29].
We estimated gene trees on each locus using the FastTree2 maximum likelihood software [41], and then used the summary methods on these estimated gene trees to estimate the species tree. We also concatenated the sequence alignments and ran unpartitioned FastTree2 maximum likelihood on the concatenated superalignment. Finally, we analyzed a Cyanobacteria dataset with 11 species and 1128 genes [42], which is believed to have evolved under high levels of HGT and has been used to evaluate methods for inferring species trees in the presence of HGT [43, 40]. See Methods for additional details.
Results
We ran 28 experiments using ASTRAL2, NJst, wQMC, and an unpartitioned concatenated maximum likelihood analysis (CAML) using FastTree2 on 51taxon datasets that evolved under a moderate amount of ILS but with varying rates of HGT under the stochastic HGT model. In our analyses, all methods produced binary trees; hence, we report the normalized bipartition distance (also called the RobinsonFoulds [44] distance) between estimated species trees and true species trees. We report results for both true and estimated gene trees, with 10 to 1000 genes. To evaluate the relationship between topological accuracy and performance with respect to the optimization problem that ASTRAL2 and wQMC attempt to solve, we compared the quartet support scores and topological accuracy of trees computed by ASTRAL2 and wQMC.
Results on estimated gene trees
Results on true gene trees
Comparing quartet scores of trees produced by ASTRAL2 and wQMC
While the differences between ASTRAL2 and wQMC are often small, ASTRAL2 nearly always matches or improves on wQMC with respect to tree topology. Both ASTRAL2 and wQMC attempt to solve the Maximum Quartet Support Species Tree problem (MQSST, see Methods), but use very different techniques. In particular, ASTRAL2 constrains the search space based on the input gene trees, and then finds an optimal solution within that constrained space, but wQMC uses a greedy heuristic and does not constrain the search. One hypothesis for the improved topological accuracy of ASTRAL2 compared to wQMC is that ASTRAL2 finds better solutions to the MQSST optimization problem, and a competing hypothesis is that the higher topological accuracy achieved by ASTRAL2 is due in part to the constraint it imposes on the solution space.
We examined the quartet scores for wQMC and ASTRAL2 across the different model conditions. For 57.2% of all cases involving estimated gene trees, the species trees returned by the two methods had the same quartet support. ASTRAL2 returned a tree with a better quartet score than wQMC 29.8% of the time while wQMC returned a tree with a better quartet score 13.0% of the time. Thus, in general ASTRAL2 does a better job than wQMC of finding good solutions to MQSST. However, there are cases in which wQMC produces trees with better scores, and the cases are typically cases with high HGT levels (i.e., there are no cases with HGT rate (1), and more than half of the cases occurred for HGT rate (6)).
Cyanobacterial data
We analyzed a cyanobacterial data set from [42] using ASTRAL2 with multilocus bootstrapping (see Methods) to estimate a species tree. Two estimated species trees were reported in [42]: one is the "plurality tree", which has served as the reference tree for this dataset. The plurality tree is a supertree (computed using MRP [45]) on a set of quartet trees represented in a plurality of the gene trees that have high support. The other tree is a PhyML [46] maximum likelihood tree. The ASTRAL2 majority consensus tree (see Methods) has 100% bootstrap support on all its branches, and is identical to the plurality tree that has served as the reference tree for this dataset. The wQMC tree was previously reported for this dataset in [40], and is also topologically identical to the plurality tree.
Discussion
While all methods had very good accuracy on the simulated datasets under the lowest HGT rates, they were clearly differentiated on the higher HGT rates, especially when the number of genes was not too large. Specifically, on the higher HGT rates, concatenation using maximum likelihood and NJst were both less accurate than ASTRAL2 and wQMC. However, all summary methods we explored were impacted by gene tree estimation error. Furthermore, there are no proofs of convergence to the true species tree if the gene trees have estimation error for these or other standard summary methods [47, 12]. Since many of the lower HGT model conditions had substantial gene tree heterogeneity resulting from ILS, this study shows that many methods  and even unpartitioned concatenation using maximum likelihood can be highly accurate under these highly heterogeneous model conditions.
Results on the biological dataset showed that ASTRAL2 and wQMC both matched the reference "plurality tree", and hence may be correct. But this analysis is perhaps less helpful, since the reference tree is based on the MRP analysis of a set of quartet trees, and MRP on quartet trees is a heuristic for the unweighted version of the optimization problem addressed by wQMC and ASTRAL2. Thus, the three methods are closely related in terms of their optimality criteria, and this may explain why they produce the same tree on this input.
This experimental study evaluated the performance of these methods when HGT is also present, and demonstrated that wQMC and ASTRAL2 maintained good accuracy even in the presence of HGT, while NJst tended to be more impacted by high levels of HGT. The explanation as to why NJst is not as robust to high HGT levels as ASTRAL2 and wQMC is likely to be that the theoretical justification for NJst only applies to the MSC model, and not to the bounded HGT models. On the other hand, both ASTRAL2 and wQMC attempt to solve the MQSST problem, for which optimal solutions are statistically consistent under the MSC model, and also under the bounded HGT models discussed in [36].
Finally, the slight advantage ASTRAL2 had over wQMC in terms of topological accuracy is largely due to its better ability to find good solutions to the MQSST problem, but constraining the search space is also part of the reason that ASTRAL2 has good topological accuracy, even under conditions with very high rates of HGT.
Conclusions
This study evaluated ASTRAL2, NJst, wQMC, and concatenated analysis using unpartitioned maximum likelihood (CAML) on one biological and several simulated datasets in which ILS and HGT were both present. We observed that the quartetbased methods (ASTRAL2 and wQMC) generally had better accuracy than NJst, and that CAML could be more accurate than all methods under conditions with low HGT rates. In particular, ASTRAL2, a species tree estimation method that was initially designed to estimate species trees in the presence of ILS, had excellent accuracy and generally gave somewhat more accurate results than the other methods we explored. However, all methods were highly accurate under the low to moderate HGT levels, and were only differentiated under the two highest HGT levels. The methods based on quartets (i.e., wQMC and ASTRAL2) had the highest robustness to HGT. While the study is limited in scope, the results suggest that highly accurate species trees can be constructed, even in the presence of both HGT and ILS, using quartetbased methods.
As noted, ASTRAL2 and NJst are statistically consistent under the MSC model (in which only ILS occurs), and ASTRAL2 is also statistically consistent under the bounded HGT models addressed by [36]. However, NJst has not been shown to be statistically consistent under the bounded HGT models, and wQMC may not be statistically consistent under either model (because it is not guaranteed to solve its optimization problem exactly, even when all the dominant quartet trees are compatible). Because the proof of statistical consistency for ASTRAL2 depends only on the requirement that for all sets of four taxa, the most probable quartet tree is topologically identical to the induced species tree on the four taxa, we conjecture that ASTRAL2 will be statistically consistent under models in which both ILS and HGT occur but at bounded rates (where the bounds on one process will depend on the other's bounds).
Although the results in this study are encouraging, future work needs to evaluate the performance of species tree estimation methods under a broader set of conditions. In particular, we only evaluated performance under the stochastic HGT model; future work should evaluate methods under the highways model as well. Our datasets had only one level of ILS, and it is possible that under conditions with higher or lower levels of ILS, the effect of HGT would be different. This study was limited to gene trees in which heterogeneity was due only to ILS and HGT; future studies should examine other sources of discord, including gene duplication and loss, and/or orthology detection errors. Larger numbers of taxa, and/or gene trees with missing taxa, are also likely to present significant analytical challenges, and accurate estimation may not be as easily obtained. Hence, future studies should also evaluate accuracy on larger and more challenging datasets, in order to determine whether the good accuracy we saw for the quartetbased methods is maintained under more difficult conditions. Similarly, it is possible that some methods might provide highly accurate results on smaller numbers of species, and that the relative performance of methods could change on those conditions. Thus, performance on small datasets (with perhaps only 10 species) should also be explored.
This study was limited in terms of the methods that were explored, in that we restricted the analysis to reasonably fast methods, and of these fast methods we only explored those methods that had been shown to perform well under ILSonly scenarios. However, it is possible that some coalescentbased species tree estimation methods, such as MPEST, STAR, etc., might perform well under HGT+ILS scenarios. It is also likely some computationally intensive methods, such as BUCKypop, *BEAST, and BEST, might provide better accuracy than ASTRAL2 on datasets with HGT+ILS. There are also methods designed to infer species trees in the presence of gene tree discordance resulting from duplication and loss, and it is possible that some of these methods (e.g., PhylDog [48] and MixTreEM [49]) might have good accuracy under the MSC. Future work should also explore CAML using different ML heuristics (e.g., PhyML [46], nhPhyML [50], IQTree [51]) and under more complex sequence evolution models. In addition, it would be very interesting to explore fully partitioned ML analyses, since these have very different statistical properties than unpartitioned analyses [12].
Methods
Species tree estimation methods
Maximum Quartet Support Species Tree Problem
ASTRAL, ASTRAL2, and wQMC all address the same optimization problem, which we now explain. Given an input set $\phantom{\rule{0.25em}{0ex}}\mathcal{G}$ of gene trees on a species set S and a quartet tree q on four species from S, we let $n\left(\mathcal{G},\phantom{\rule{0.3em}{0ex}}q\right)$ denote the number of gene trees in $\phantom{\rule{0.25em}{0ex}}\mathcal{G}$ that induce the quartet tree q. Then, the quartet support of T given G, denoted $w\mathcal{G}\left(T\right)$, is ${\sum}_{q\in Q\left(T\right)}n\left(\mathcal{G},q\right)$, where Q(T ) denotes the set of all quartet trees in T . Hence, we can define the Maximum Quartet Support Species Tree Problem (MQSST), as follows.

Input: a set of gene trees $\phantom{\rule{0.25em}{0ex}}\mathcal{G}$ on a species set S.

Output: a tree T on the species set S maximizing $w\mathcal{G}\left(T\right)$, the quartet support of T given $\phantom{\rule{0.25em}{0ex}}\mathcal{G}$.
MQSST is NP hard when the input set of gene trees induce only one tree for each set of four taxa in S [52], and is of unknown computational complexity when all the gene trees are complete (i.e., have all the species in S).
Weighted Quartets MaxCut
The quartet amalgamation method wQMC [40] is a greedy heuristic for a weighted version of the MQSST problem, in which the input can have weights on each quartet tree. The wQMC heuristic uses a greedy strategy to find good solutions to its optimization problems, but is not guaranteed to solve its optimization problem (weighted MQSST) exactly. To use wQMC as a summary method, we define the weight of a quartet tree q to be the quartet support $n\left(\mathcal{G},\phantom{\rule{0.3em}{0ex}}q\right)$ of q in the input set of gene trees $\phantom{\rule{0.25em}{0ex}}\mathcal{G}$.
We wrote scripts (available in our supporting online material) that use a previously published code [53] to compute the weights of each quartet tree. After we calculate these weights (saving them in a file called <quartetscores>), we run wQMC version 3.1 using the following command:
./maxcuttree qrtt=<quartetscores> weights=on otre=<speciestree>
ASTRAL and ASTRAL2
ASTRAL [18] and its improved version, ASTRAL2 [19], also attempt to solve the MQSST problem. Both have exact versions that provably solve the MQSST problem but run in exponential time, and faster versions that constrain the search space (using the input set of gene trees), and then provably solve the constrained problem exactly. ASTRAL and ASTRAL2 differ in how they constrain the search space (ASTRAL2 searches a larger part of tree space than ASTRAL) and how they are implemented (ASTRAL2 is faster). Here we focus on ASTRAL2, since it is faster and more accurate than ASTRAL.
Given the input set of gene trees, ASTRAL2 defines a set X of bipartitions on the taxon set S; when all the gene trees are complete (i.e., have no missing taxa), then X will contain all the bipartitions from the input gene trees as well as potentially other bipartitions. ASTRAL2 runs in O(nkX^{2}) time, where n is the number of species and k is the number of genes, and thus can be fast whenever X is not too large. While X is not theoretically bounded by a polynomial in n and k, for many datasets X is not very large, so that ASTRAL2 is able to complete analyses within 24 hours on 1000 species and 1000 genes [19].
ASTRAL2 finds a globally optimal solution to the constrained optimization problem where we restrict the output species tree to draw its bipartitions from X. ASTRAL and ASTRAL2, run in their default versions (which use the constrained search), are both statistically consistent under the multispecies coalescent model when all the gene trees are complete (i.e., this restriction to the set X of bipartitions does not change their statistical guarantees) [19].
We now provide a proof for Theorem 3, establishing that ASTRAL and ASTRAL2, run in default mode, are statistically consistent under the MSC model and also under the bounded HGT models.
Proof for Theorem 3. As proved in [18, 19], ASTRAL and ASTRAL2 are guaranteed to find globally optimal solutions to the constrained MQSST problem. The default settings for the constraint set X of bipartitions allowed in the output species tree always includes all bipartitions from the input gene trees; hence, as the number of genes increases, with probability converging to 1, every bipartition from the species tree will be in the set X. Therefore, with probability converging to 1, the true species tree will be a feasible solution (i.e., within the constrained search space) as the number of loci and number of sites per locus both increase (as established in [18, 19]). Recall that the quartet support score of a tree T is the total, over all quartet trees in T, of the number of gene trees that contain that quartet tree. As shown in [36], under the bounded HGT models in [36], the most probable quartet tree on any four taxon set A is topologically identical to the quartet tree on X induced by the true species tree. Hence, with probability converging to 1, under these bounded HGT models, the most frequent quartet tree on any set A of four leaves will be the true species tree on A. Given any set of gene trees in which for all fourleaf sets A the most frequent quartet tree on A is the true species tree on A, the quartet support score of the true species tree T* will be the maximum possible quartet support score (since any other species tree T cannot have larger quartet support for any quartet tree). Furthermore, given any set of gene trees in which the most frequent quartet tree is unique for all four taxa and equal to the species tree on the four taxa, the true species tree T* will have the unique maximum quartet support score. Hence, as the number of loci and number of sites per locus both increase, the tree returned by an exact solution to the constrained MQSST problem, using default settings for X, will converge in probability to the true species tree T*. Therefore, ASTRAL and ASTRAL2 are statistically consistent under the bounded HGT models of [36].
We ran ASTRAL2 version 4.7.6 on the simulated data using the following command:
java jar astral.4.7.6.jar i <genetrees> o <speciestree>
where <genetrees> is a file containing the gene trees in newick format, and
<speciestree> is the output.
For the biological data, we used ASTRAL2 with multilocus bootstrapping (MLBS), using the following commands:
java jar astral.4.7.6.jar i < bootstrap replicates >
o <species replicate>
where <bootstrap replicates> is the collection of 1128 gene trees generated by taking the n^{ th } line of the gene tree file n = {1, ... , 100}, and <species replicate> is the n^{ th } bootstrap replicate species tree T_{ n }. To calculate the final species tree T with bootstrap support values, we computed the majority consensus tree using Dendropy version 3.12.2 [54].
NJst
NJst is a summary method that has two steps. In the first step, it computes a distance matrix on the species set, where D[x, y] is the average leaftoleaf topological distance between x and y among all the gene trees. In the second step, it runs neighbor joining [55], a popular distancebased phylogeny estimation method. NJst is statistically consistent under the MSC model because the distance matrix it computes converges in probability to an additive matrix defining the true species tree, and neighbor joining will return the true species tree once the computed distance matrix is sufficiently close to the additive matrix for the species tree; see [17] for this proof.
To run NJst, we used phybase version 1.4 [56] and custom scripts, available in our supplementary material.
Gene tree estimation
To compute gene trees, we ran FastTree2 version 2.1.4, using the following command:
fasttree nt gtr quiet nopr gamma n 1000 [input] > [output]
where [input] is a file that includes all the alignments of all 1000 genes and [output] will be one file with all 1000 estimated gene trees.
CAML
To perform the concatenated analyses under maximum likelihood, we ran FastTree2 version 2.1.4, with the following command:
fasttree nt gtr nopr [input] > [output]
Computing Error Rates
The coalescentbased methods ASTRAL2, wQMC, and NJst used in this study all return binary species trees. We also verified that all trees returned in our CAML analysis were binary, and all simulated data used in this study contained only binary model species trees. The RobinsonFoulds (RF) distance [44] between two trees T1 and T2 on the same set of n taxa measures the number of bipartitions that appear in only one of T1 or T2. Therefore, if T1 and T2 are identical, the RF distance is 0, and the maximum RF distance between T1 and T2 is 2n−6. The RF distance can be converted to an error rate by dividing by 2n − 6. When comparing only binary trees, false negative rates, false positive rates, and normalized RobinsonFoulds distances are all equivalent. Therefore, we computed missing branch rates to establish error rates, but we report RF rates. Error rates were computed by finding the missing branch rate using custom scripts available in our supporting online materials.
Measuring Quartet Support Scores of ASTRAL2 and wQMC
The command used to measure the quartet support score was
java jar astral.4.7.6.jar q <speciestreefile> I <genetreesfile>
Data
HGT+ILS Simulated Data The simulated dataset was simulated using SimPhy [57] version 1.0 (downloaded January 20, 2015). There are 6 data sets containing 50 replicates apiece: each replicate has its own 51taxon species tree. For every model species tree, one taxon is an outgroup, and so is actually a 50taxon rooted species tree. These model trees were simulated under a Yule process, with birth rates set to 0.000001 (per generation) and the maximum tree length set to 2 million generations.
Then, on each species tree, 1000 locus trees are simulated, where each can differ from the species tree due to HGT events, and we used HGT rates (1)(6) given by 0, 2 × 10^{−9}, 5 × 10^{−9}, 2 × 10^{−8}, 2 × 10^{−7}, and 5 × 10^{ −7 }. These values correspond to expected numbers of HGT events per gene of 0, 0.08, 0.2, 0.8, 8, and 20. Thus, HGT rate (1) is no HGT events, HGT rate (2) is 0.08 HGT events per gene, up to HGT rate (6) of 20 HGT events per gene. Note that in our simulations, for each HGT event, the probability of a branch being chosen as the receptor of the transfer is proportional to its distance from the donor.
Once locus trees are simulated, a gene tree is simulated for each locus tree according to the MSC model, with population size parameter set to 200,000. Thus, at the end, we have 1000 true genes that differ from the species tree due to both ILS and also potentially HGT (when the HGT rate is positive).
The SimPhy command used to generate a model replicate in the data sets is simphy rs 50 rl U:1000,1000 rg 1 st U:2000000,2000000 si U:1,1 sl U:50,50 sb U:0.000001,0.000001 cp U:200000,2000000 hs L:1.5,1 hl L:1.2,1 hg l:1.4,1 cu E:10000000 so U:1,1 od 1 or 0 v 3 cs 293745 o model.50.2000000.0.000001.<transferrate> lt U:<transferrate>,<transferrate> lk 1
On each simulated true gene tree, we used INDELible [58] v. 1.03 to simulate sequence alignments according to the GTR+Gamma model, with model parameters estimated from three different real datasets (these parameters are identical to those used in [19]). This simulation produces GTR parameters that vary from one gene to another, where the parameters are drawn for each gene from a distribution at random. See [19] for details about the simulation process. The alignment length is set to 1000 bp for all genes. After simulating gene alignments, we used FastTree2 [41] to estimate gene trees under the GTR model. Thus for each replicate, we have both true and estimated gene trees.
For HGT rate (1) (where all the discordance is due to ILS), the average RF [44] distance between true gene trees and the species tree is 30.4%. Therefore, the amount of ILS in these data sets is moderately high.
Cyanobacterial Data The cyanobacterial data set has 1128 genes on 11 taxa, and was first analyzed in [42], which suggested that the 11 genome sequences may have acquired between 9.5% and 16.6% of their genes through HGT. We obtained 100 bootstrap replicate gene trees for each of the 1128 genes from the first author of [43], and computed an ASTRAL2 tree on these data using multilocus bootstrapping.
Availability of supporting data
All data used in this study, and commands needed to regenerate the data, are available online at goo.gl/0p4IGD.
Abbreviations
 CAML:

concatenated analysis using maximum likelihood
 GTR+Gamma:

Generalized Time Reversible model of site evolution with Gamma distributed rates across sites
 HGT:

horizontal gene transfer
 ILS:

incomplete lineage sorting
 MSC:

multispecies coalescent
 ML:

maximum likelihood
 MLBS:

multilocus bootstrapping
 MQSST:

maximum quartet support species tree
 MSC:

multispecies coalescent
Declarations
Acknowledgements
RD was supported by NSF grant DMS1401591. PV was supported by the Roy J. Carver graduate fellowship from the UIUC College of Engineering. SM was supported by a Howard Hughes Medical Institute graduate fellowship and by NSF grant DBI1461364. TW was supported by NSF grant DBI1461364 and by a gift from the Grainger Foundation to the University of Illinois at UrbanaChampaign College of Engineering. The authors thank Mukul Bansal for sharing the data from [42].
Publication costs for this article were funded by the corresponding author's instutition.
This article has been published as part of BMC Genomics Volume 16 Supplement 10, 2015: Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/16/S10.
Authors’ Affiliations
References
 Morrison DA: Introduction to Phylogenetic Networks. 2011, RJR Productions, Uppsala, SwedenGoogle Scholar
 Sjölander K: Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics. 2004, 20 (2): 170179.View ArticleGoogle Scholar
 Eisen JA, Fraser CM: Phylogenomics: intersection of evolution and genomics. Science. 2003, 300 (5626): 17061707.View ArticleGoogle Scholar
 Engelhardt BE, Jordan MI, Repo ST, Brenner SE: Phylogenetic molecular function annotation. J Phys: Conf Ser. 2009, 180: 12024Google Scholar
 Thompson JN: The Geographic Mosaic of Coevolution. 2005, The University of Chicago Press, ChicagoGoogle Scholar
 Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walte P: Molecular Biology of the Cell. 2002, Garland Science, New York, 4Google Scholar
 Nussbaum R, McInnes RR, Willard HF: Genetics in Medicine. 2007, Saunders Elsevier, Philadelphia, PA, 7Google Scholar
 Arnold ML: Natural Hybridization and Evolution. 1997, Oxford University Press, OxfordGoogle Scholar
 Maddison W: Gene trees in species trees. Syst Biol. 1997, 46: 523536.View ArticleGoogle Scholar
 Woese C: On the evolution of cells. Proc Natl Acad Sci USA. 2002, 99: 87428747.View ArticleGoogle Scholar
 Kingman JFC: On the genealogy of large populations. J Appl Probab. 1982, 19A: 2743.View ArticleGoogle Scholar
 Warnow T: Concatenation analyses in the presence of incomplete lineage sorting. PLOS Currents: Tree of Life. 2015, 105: 1013718410131445951717.Google Scholar
 Liu L, Yu L, Edwards SV: A maximum pseudolikelihood approach for estimating species trees under the coalescent model. BMC Evol Biol. 2010, 10 (1): 302View ArticleGoogle Scholar
 Mossel E, Roch S: Incomplete lineage sorting: consistent phylogeny estimation from multiple loci. IEEE/ACM Trans Comput Biol Bioinformatics (TCBB). 2011, 7 (1): 166171.View ArticleGoogle Scholar
 Kubatko LS, Carstens BC, Knowles LL: STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 2009, 25 (7): 971973.View ArticleGoogle Scholar
 Liu L, Yu L, Pearl DK, Edwards SV: Estimating species phylogenies using coalescence times among sequences. Syst Biol. 2009, 58 (5): 468477.View ArticleGoogle Scholar
 Liu L, Yu L: Estimating species trees from unrooted gene trees. Syst Biol. 2011, 60: 661667.View ArticleGoogle Scholar
 Mirarab S, Reaz R, Bayzid MS, Zimmerman T, Swenson M, Warnow T: ASTRAL: genomescale coalescentbased species tree estimation. Bioinformatics. 2014, 30: 15411548.View ArticleGoogle Scholar
 Mirarab S, Warnow T: ASTRALII: coalescentbased species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics. 2015, 31: doi:10.1093/bioinformatics/btv234Google Scholar
 Jarvis ED, Mirarab S, et al: Whole genome analyses resolve early branches in the tree of life of modern birds. Science. 2014, 346 (6215): 13201331.View ArticleGoogle Scholar
 Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GKS, LeebensMack J: Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci USA. 2014, 111 (45): 48594868. doi:10.1073/pnas.1323926111, [http://www.pnas.org/content/111/45/E4859.full.pdf+html]View ArticleGoogle Scholar
 Roch S, Steel M: Likelihoodbased tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theoret Popul Biol. 2015, 100: 5662.View ArticleGoogle Scholar
 Gatesy J, Springer MS: Concatenation versus coalescence versus "concatalescence". Proc Natl Acad Sci USA. 2013, 110: doi:10.1073/Proc. Natl. Acad. Sci..1221121110Google Scholar
 Patel S, Kimball R, Braun E: Error in phylogenetic estimation for bushes in the tree of life. J Phylogen Evol Biol. 2013, 1 (110): 2Google Scholar
 Bayzid MS, Warnow T: Naive binning improves phylogenomic analyses. Bioinformatics. 2013, 28: 22772284.View ArticleGoogle Scholar
 Liu L: BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics. 2008, 24 (21): 25422543.View ArticleGoogle Scholar
 Heled J, Drummond AJ: Bayesian inference of species trees from multilocus data. Mol Biol Evol. 2010, 27 (3): 570580.View ArticleGoogle Scholar
 Larget BR, Kotha SK, Dewey CN, Ané C: BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics. 2010, 26: 29102911.View ArticleGoogle Scholar
 Zimmermann T, Mirarab S, Warnow T: BBCA: Improving the scalability of *BEAST using random binning. BMC Genomics. 2014, 15 (Suppl 6): 11View ArticleGoogle Scholar
 Yang J, Warnow T: Fast and accurate methods for phylogenomic analyses. BMC Bioinformatics. 2011, 12: 4View ArticleGoogle Scholar
 Chifman J, Kubatko L: Quartet inference from SNP data under the coalescent model. Bioinformatics. 2014, 530:Google Scholar
 Allman ES, Degnan JH, Rhodes JA: Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. J Math Biol. 2011, 62: 833862.View ArticleGoogle Scholar
 Galtier N: A model of horizontal gene transfer and the bacterial phylogeny problem. Syst Biol. 2007, 56: 633642.View ArticleGoogle Scholar
 Beiko RG, Harlow TJ, Ragan MA: Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA. 2005, 102: 1433214337.View ArticleGoogle Scholar
 Steel M, Linz S, Huson DH, Sanderson MJ: Identifying a species tree subject to random lateral gene transfer. J Theor Biol. 2013, 322: 8193.View ArticleGoogle Scholar
 Roch S, Snir S: Recovering the treelike trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis. J Comput Biol. 2013, 20: 93112.View ArticleGoogle Scholar
 Snir S, Rao S: Quartets MaxCut: A fast algorithm for amalgamating quartet trees. Mol Phylog Evol. 2012, 62: 18.View ArticleGoogle Scholar
 Reaz R, Bayzid MS, Rahman MS: Accurate phylogenetic tree reconstruction from quartets: A heuristic approach. PloS One. 2014, 9 (8): 104008View ArticleGoogle Scholar
 Chung Y, Ané C: Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer. Syst Biol. 2011, 60: 261275.View ArticleGoogle Scholar
 Avni E, Cohen R, Snir S: Weighted quartets phylogenetics. Syst Biol. 2015, 64: 233242.View ArticleGoogle Scholar
 Price MN, Dehal PS, Arkin AP: FastTree 2: approximately maximumlikelihood trees for large alignments. PLoS ONE. 2010, 5: 9490View ArticleGoogle Scholar
 Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT: Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res. 2006, 16: 10991108.View ArticleGoogle Scholar
 Bansal MS, Banay G, Gogarten JP, Harlow TJ, Shamir R: Systematic inference of highways of horizontal gene transfer in prokaryotes. Bioinformatics. 2013, 29: 571579.View ArticleGoogle Scholar
 Robinson DF, Foulds LR: Comparison of phylogenetic trees. Math Biosci. 1981, 53: 131147.View ArticleGoogle Scholar
 Baum BR, Ragan MA: The MRP method. Phylogenetic Supertrees: Combining Information to Reveal The Tree Of Life. Edited by: BinindaEmonds, O.R.P. 2004, Kluwer Academic, Dordrecht, the Netherlands, 1734.View ArticleGoogle Scholar
 Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696704.View ArticleGoogle Scholar
 Roch S, Warnow T: On the robustness to gene tree estimation error (or lack thereof) of coalescentbased species tree methods. Syst Biol. 2015, 101093016.Google Scholar
 Boussau B, Szöllőosi GJ, Duret L, Gouy M, Tannier E, Daubin V: Genomescale coestimation of species and gene trees. Genome Res. 2013, 23 (2): 323330.View ArticleGoogle Scholar
 Ullah L, Parviainen P, Lagergren J: Species tree inference using a mixture model. Mol Biol Evol. 2015, doi: 10.1093/molbev/msv115Google Scholar
 Boussau B, Gouy M: Efficient likelihood computations with nonreversible models of evolution. Syst Biol. 2006, 55 (5): 75668.View ArticleGoogle Scholar
 Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ: IQTREE: A fast and effective stochastic algorithm for estimating maximumlikelihood phylogenies. Mol Biol Evol. 2015, 32 (1): 268274.View ArticleGoogle Scholar
 Jiang T, Kearney P, Li M: A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM J Comput. 2001, 30: 19421961.View ArticleGoogle Scholar
 Johansen J: Computing triplet and quartet distances. PhD thesis, Aarhus University, Computer Science Department. 2013Google Scholar
 Sukumaran J, Holder MT: DendroPy: A Python library for phylogenetic computing. Bioinformatics. 2010, 26: 15691571.View ArticleGoogle Scholar
 Saitou N, Nei M: The neighborjoining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987, 4: 406425.Google Scholar
 Liu L: Phybase server. [https://faculty.franklin.uga.edu/lliu/content/phybase]
 Mallo D, Oliviera Martins L, Posada D: SimPhy: Comprehensive simulation of gene, locus and species trees at the genomewide level. [https://code.google.com/p/simphyproject/]
 Fletcher W, Yang Z: INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol. 2009, 26: 18791888.View ArticleGoogle Scholar
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