Dataset Information

Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.

ABSTRACT:

Background

In phylogenetics, we often seek to reconcile gene trees with species trees within the framework of an evolutionary model. While the most popular models for eukaryotic species allow for only gene duplication and gene loss or only multispecies coalescence, recent work has combined these phenomena through a reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes the duplication-loss and coalescent history of a gene family. However, the LCT makes the simplifying assumption that only one individual is sampled per species whereas, with advances in gene sequencing, we now have access to multiple samples per species.

Results

We demonstrate that with these additional samples, there exist gene tree topologies that are impossible to reconcile with any species tree. In particular, the multiple samples enforce new constraints on the placement of duplications within a valid reconciliation. To model these constraints, we extend the LCT to a new structure, the partially labeled coalescent tree (PLCT) and demonstrate how to use the PLCT to evaluate the feasibility of a gene tree topology. We apply our algorithm to two clades of apes and flies to characterize possible sources of infeasibility.

Conclusion

Going forward, we believe that this model represents a first step towards understanding reconciliations in duplication-loss-coalescence models with multiple samples per species.

SUBMITTER: Rogers J

PROVIDER: S-EPMC5460407 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Publications

Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.

Rogers Jennifer J Fishberg Andrew A Youngs Nora N Wu Yi-Chieh YC

BMC bioinformatics 20170605 1

<h4>Background</h4>In phylogenetics, we often seek to reconcile gene trees with species trees within the framework of an evolutionary model. While the most popular models for eukaryotic species allow for only gene duplication and gene loss or only multispecies coalescence, recent work has combined these phenomena through a reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes the duplication-loss and coalescent history of a gene family. However, the LCT makes ...[more]

PMID: 28583091

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Project description:Whole-genome duplication (WGD) occurs broadly and repeatedly across the 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 identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few 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 degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree 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 genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.].

Dataset Information

Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.

Background

Results

Conclusion

Publications

Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.

Similar Datasets

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