scholarly journals Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8271
Author(s):  
Drew J. Duckett ◽  
Tara A. Pelletier ◽  
Bryan C. Carstens
Keyword(s):  
Posterior Distribution ◽  
Incomplete Lineage Sorting ◽  
R Package ◽  
Predictive Distribution ◽  
Species Trees ◽  
Lineage Sorting ◽  
Posterior Predictive Distribution ◽  
Coalescent Model ◽  
Multispecies Coalescent ◽  
Phylogenetic Estimation

Phylogenetic estimation under the multispecies coalescent model (MSCM) assumes all incongruence among loci is caused by incomplete lineage sorting. Therefore, applying the MSCM to datasets that contain incongruence that is caused by other processes, such as gene flow, can lead to biased phylogeny estimates. To identify possible bias when using the MSCM, we present P2C2M.SNAPP. P2C2M.SNAPP is an R package that identifies model violations using posterior predictive simulation. P2C2M.SNAPP uses the posterior distribution of species trees output by the software package SNAPP to simulate posterior predictive datasets under the MSCM, and then uses summary statistics to compare either the empirical data or the posterior distribution to the posterior predictive distribution to identify model violations. In simulation testing, P2C2M.SNAPP correctly classified up to 83% of datasets (depending on the summary statistic used) as to whether or not they violated the MSCM model. P2C2M.SNAPP represents a user-friendly way for researchers to perform posterior predictive model checks when using the popular SNAPP phylogenetic estimation program. It is freely available as an R package, along with additional program details and tutorials.

scholarly journals MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R

2020 ◽  
Author(s):  
John A Rhodes ◽  
Hector Baños ◽  
Jonathan D Mitchell ◽  
Elizabeth S Allman
Keyword(s):  
Network Inference ◽  
Incomplete Lineage Sorting ◽  
R Package ◽  
Species Tree ◽  
Supplementary Information ◽  
Species Trees ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent ◽  
Tree Inference

Abstract Summary MSCquartets is an R package for species tree hypothesis testing, inference of species trees, and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. Availability MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets. Supplementary information Supplementary materials, including example data and analyses, are incorporated into the package.

scholarly journals MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R

2020 ◽  
Author(s):  
John A. Rhodes ◽  
Hector Baños ◽  
Jonathan D. Mitchell ◽  
Elizabeth S. Allman
Keyword(s):  
Network Inference ◽  
Incomplete Lineage Sorting ◽  
R Package ◽  
Species Tree ◽  
Species Trees ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
Species Tree Inference

AbstractMSCquartets is an R package for species tree hypothesis testing, inference of species trees, and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package includes the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model.

scholarly journals Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

2022 ◽  
Author(s):  
XiaoXu Pang ◽  
Da-Yong Zhang
Keyword(s):  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
Tree Methods ◽  
The Impact

The species studied in any evolutionary investigation generally constitute a very small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has been rarely studied and is thus poorly understood. In this study, we use mathematical analysis and simulations to examine the robustness of species tree methods based on a multispecies coalescent model under gene flow sourcing from an extant or ghost lineage. We found that very low levels of extant or ghost introgression can result in anomalous gene trees (AGTs) on three-taxon rooted trees if accompanied by strong incomplete lineage sorting (ILS). In contrast, even massive introgression, with more than half of the recipient genome descending from the donor lineage, may not necessarily lead to AGTs. In cases involving an ingroup lineage (defined as one that diverged no earlier than the most basal species under investigation) acting as the donor of introgression, the time of root divergence among the investigated species was either underestimated or remained unaffected, but for the cases of outgroup ghost lineages acting as donors, the divergence time was generally overestimated. Under many conditions of ingroup introgression, the stronger the ILS was, the higher was the accuracy of estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

scholarly journals A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

2019 ◽  
Vol 37 (4) ◽  
pp. 1211-1223 ◽  
Author(s):  
Tomáš Flouri ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent

Abstract Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

scholarly journals The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution

2020 ◽  
Author(s):  
Qiuyi Li ◽  
Celine Scornavacca ◽  
Nicolas Galtier ◽  
Yao-Ban Chan
Keyword(s):  
Gene Family ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Gene Family Evolution ◽  
Gene Copy ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
New Model ◽  
Multispecies Coalescent

Abstract Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently, but in reality, ILS can affect gene copy number polymorphism, i.e., interfere with DTL. This has been previously recognised, but not treated in a satisfactory way, mainly because DTL events are naturally modelled forward-in-time, while ILS is naturally modelled backwards-in-time with the coalescent. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent (MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.

scholarly journals ILS-Aware Analyses of Retroelement Insertions in the Anomaly Zone

2020 ◽  
Author(s):  
Erin K. Molloy ◽  
John Gatesy ◽  
Mark S. Springer
Keyword(s):  
Dna Sequences ◽  
Incomplete Lineage Sorting ◽  
Species Tree ◽  
Species Trees ◽  
Lineage Sorting ◽  
Short Branch ◽  
Multispecies Coalescent ◽  
Branch Lengths ◽  
Tree Estimation ◽  
Infinite Sites Model

AbstractA major shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting (ILS). Coalescence methods explicitly 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 coalescence methods, retroelement insertions have emerged as powerful phylogenomic markers for species tree estimation. We show that two recently proposed methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the species tree under the multispecies coalescent model, with retroelement insertions following a neutral infinite sites model of mutation. The accuracy of these and other methods for inferring species trees with retroelements has not been assessed in simulation studies. We simulate retroelements for four different species trees, including three with short branch lengths in the anomaly zone, and assess the performance of eight different methods for recovering the correct species tree. We also examine whether ASTRAL_BP recovers accurate internal branch lengths for internodes of various lengths (in coalescent units). Our results indicate that two recently proposed ILS-aware methods, ASTRAL_BP and SDPquartets, as well as the newly proposed ASTRID_BP, always recover the correct species tree on data sets with large numbers of retroelements even when there are extremely short species-tree branches in the anomaly zone. Dollo parsimony performed almost as well as these ILS-aware methods. By contrast, unordered parsimony, polymorphism parsimony, and MDC recovered the correct species tree in the case of a pectinate tree with four ingroup taxa in the anomaly zone, but failed to recover the correct tree in more complex anomaly-zone situations with additional lineages impacted by extensive incomplete lineage sorting. Camin-Sokal parsimony always reconstructed an incorrect tree in the anomaly zone. ASTRAL_BP accurately estimated branch lengths when internal branches were very short as in anomaly zone situations, but branch lengths were upwardly biased by more than 35% when species tree branches were longer. We derive a mathematical correction for these distortions, assuming the expected number of new retroelement insertions per generation is constant across the species tree. We also show that short branches do not need to be corrected even when this assumption does not hold; therefore, the branch lengths estimates produced by ASTRAL_BP may provide insight into whether an estimated species tree is in the anomaly zone.

scholarly journals Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent

2021 ◽  
Author(s):  
Elizabeth S Allman ◽  
Jonathan D Mitchell ◽  
John A Rhodes
Keyword(s):  
Incomplete Lineage Sorting ◽  
Hypothesis Test ◽  
Statistical Tests ◽  
Gene Tree ◽  
Complex Model ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent

Abstract A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data are not in accord with the MSC, and thus that either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees is in accord with the MSC, the plots reveal when substantial incomplete lineage sorting is present. Applications to both simulated and empirical multilocus data sets illustrate the insights provided. [Gene tree discordance; hypothesis test; multispecies coalescent model; quartet concordance factor; simplex plot; species tree].

scholarly journals The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution

2020 ◽  
Author(s):  
Qiuyi Li ◽  
Celine Scornavacca ◽  
Nicolas Galtier ◽  
Yao-Ban Chan
Keyword(s):  
Gene Family ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Gene Family Evolution ◽  
Gene Copy ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
New Model ◽  
Multispecies Coalescent

AbstractIncomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently, but in reality, ILS can affect gene copy number polymorphism, i.e., interfere with DTL. This has been previously recognised, but not treated in a satisfactory way, mainly because DTL events are naturally modelled forward-in-time, while ILS is naturally modelled backwards-in-time with the coalescent. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent (MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.

scholarly journals Statistical inconsistency of the unrooted minimize deep coalescence criterion

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251107
Author(s):  
Ayed A. R. Alanzi ◽  
James H. Degnan
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Species Tree ◽  
Evolutionary Relationships ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Input Gene ◽  
Multispecies Coalescent ◽  
Deep Coalescence

Species trees, which describe the evolutionary relationships between species, are often inferred from gene trees, which describe the ancestral relationships between sequences sampled at different loci from the species of interest. A common approach to inferring species trees from gene trees is motivated by supposing that gene tree variation is due to incomplete lineage sorting, also known as deep coalescence. One of the earliest methods motivated by deep coalescence is to find the species tree that minimizes the number of deep coalescent events needed to explain discrepancies between the species tree and input gene trees. This minimize deep coalescence (MDC) criterion can be applied in both rooted and unrooted settings. where either rooted or unrooted gene trees can be used to infer a rooted species tree. Previous work has shown that MDC is statistically inconsistent in the rooted setting, meaning that under a probabilistic model for deep coalescence, the multispecies coalescent, for some species trees, increasing the number of input gene trees does not make the method more likely to return a correct species tree. Here, we obtain analogous results in the unrooted setting, showing conditions leading to inconsistency of the MDC criterion using the multispecies coalescent model with unrooted gene trees for four taxa and five taxa.

scholarly journals How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

2022 ◽  
Vol 12 ◽  
Author(s):  
Martha Kandziora ◽  
Petr Sklenář ◽  
Filip Kolář ◽  
Roswitha Schmickl
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Species Tree ◽  
Secondary Contact ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Phylogenetic Discordance ◽  
Gene Tree Discordance ◽  
High Degree

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.

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