Statistical inconsistency of the unrooted minimize deep coalescence criterion

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.

The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization is NP-Hard

The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events. While the reconciliation problem is well-studied for species and gene trees subject to events such as duplication, transfer, loss, and deep coalescence, recent work has examined species phylogenies that incorporate hybridization and are thus represented by networks rather than trees. In this paper, we show that the problem of computing a maximum parsimony reconciliation for a gene tree and species network is NP-hard even when only considering deep coalescence. This result suggests that future work on maximum parsimony reconciliation for species networks should explore approximation algorithms and heuristics.

Phylogenomic terraces: presence and implication in species tree estimation from gene trees

Species tree estimation from multi-locus dataset is extremely challenging, especially in the presence of gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Summary methods have been developed which estimate gene trees and then combine the gene trees to estimate a species tree by optimizing various optimization scores. In this study, we have formalized the concept of “phylogenomic terraces” in the species tree space, where multiple species trees with distinct topologies may have exactly the same optimization score (quartet score, extra lineage score, etc.) with respect to a collection of gene trees. We investigated the presence and implication of terraces in species tree estimation from multi-locus data by taking ILS into account. We analyzed two of the most popular ILS-aware optimization criteria: maximize quartet consistency (MQC) and minimize deep coalescence (MDC). Methods based on MQC are provably statistically consistent, whereas MDC is not a consistent criterion for species tree estimation. Our experiments, on a collection of dataset simulated under ILS, indicate that MDC-based methods may achieve competitive or identical quartet consistency score as MQC but could be significantly worse than MQC in terms of tree accuracy – demonstrating the presence and affect of phylogenomic terraces. This is the first known study that formalizes the concept of phylogenomic terraces in the context of species tree estimation from multi-locus data, and reports the presence and implications of terraces in species tree estimation under ILS.

Mitochondrial DNA Polymorphisms of the Saisiyat Indigenous Group of Taiwan, Search for a Negrito Signature

The genetic profile of Negritos of the Philippines differs from the non-Negrito groups with mitochondrial DNA haplogroups B4b1a2, B5, D6a, M, M52a, and N11b. Although Negritos are not seen in Taiwan, the strong genetic affinity between the Philippines and Taiwan Mountain Tribe Aborigines (TwMtA), and Folks tales of TwMtA, Saisiyat and Atayal recounting past contacts with Negritos, warrant the search for a Negrito signature in Taiwan. Material and Method: Discriminant Analysis of Principal Component (DAPC) was used to determine the genetic relationship between TwMtA, Filipino and non-TwMtA groups. Results: The deep coalescence of B4b1a2 in the Philippine Negritos, Saisiyat, Atayal, Island Southeast Asia, and SEA (Southeast Asia) suggested a deeply rooted common ancestry, but could not support a past Negrito presence in Taiwan. Conversely, the sharing of cultural components and mtDNA (mitochondrial DNA) haplogroup D6a2 in Saisiyat, Atayal and Philippine Negritos may characterize a Negrito signature in Taiwan. Although the molecular variation of D6a2 determines its presence in Taiwan back to middle Neolithic, other markers, Y-SNP haplogroups C-M146 and K-M9, warrant further analysis. Conclusion: Most likely, the physical characteristics, languages, and the genetic makeup of the Negritos in Taiwan have been diluted as the result of heavy migration from the mainland in the last 400 years.

Minimizing the deep coalescence cost

Metagenomic studies identify the species present in an environmental sample usually by using procedures that match molecular sequences, e.g. genes, with the species taxonomy. Here, we first formulate the problem of gene-species matching in the parsimony framework using binary phylogenetic gene and species trees under the deep coalescence cost and the assumption that each gene is paired uniquely with one species. In particular, we solve the problem in the cases when one of the trees is a caterpillar. Next, we propose a dynamic programming algorithm, which solves the problem exactly, however, its time and space complexity is exponential. Next, we generalize the problem to include non-binary trees and show the solution for caterpillar trees. We then propose time and space-efficient heuristic algorithms for solving the gene-species matching problem for any input trees. Finally, we present the results of computational experiments on simulated and empirical datasets consisting of binary tree pairs.

De novo transcriptome assembly, annotation, and identification of low-copy number genes in the flowering plant genus Silene (Caryophyllaceae)

Phylogenetic methods that rely on information from multiple, unlinked genes have recently been developed for resolving complex situations where evolutionary relationships do not conform to bifurcated trees and are more adequately depicted by networks. Such situations arise when successive interspecific hybridizations in combination with genome duplications have shaped species phylogenies. Several processes such as homoeolog loss and deep coalescence can potentially hamper our ability to recover the historical signal correctly. Consequently the prospect of reconstructing accurate phylogenies lies in the combination of several low-copy nuclear markers that when, used in concert, can provide homoeologs for all the ancestral genomes and help to disentangle gene tree incongruence due to deep coalescence events. Expressed sequence tag (EST) databases represent valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. The genus Silene L. is a prime example of a plant group whose evolutionary history involves numerous events of hybridization and polyploidization. As for many groups there is currently a shortage of low-copy nuclear markers, for which phylogenetic usefulness has been demonstrated. Here, we present two EST libraries for two species of Silene that belong to large phylogenetic groups not previously investigated with next generation technologies. The assembled and annotated transcriptomes are used for identifying low copy nuclear regions, suitable for sequencing.