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Wilson D, Rogers JD. Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting. J Comput Biol 2023; 30:250-260. [PMID: 36848254 DOI: 10.1089/cmb.2022.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
This study assesses characteristics of the normalized compression distance (NCD) technique for building phylogenetic trees from molecular data. We examined results from a mammalian biological data set as well as a collection of simulated data with varying levels of incomplete lineage sorting. The implementation of NCD we analyze is a concatenation-based, distance-based, alignment-free, and model-free phylogeny estimation method, which takes concatenated unaligned sequence data as input and outputs a matrix of distances. We compare the NCD phylogeny estimation method with various other methods, including coalescent- and concatenation-based methods.
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Affiliation(s)
- Deangelo Wilson
- School of Computing, DePaul University, Chicago, Illinois, USA
| | - John D Rogers
- School of Computing, DePaul University, Chicago, Illinois, USA
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Avni E, Snir S. A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality. J Comput Biol 2018; 26:27-37. [PMID: 30422680 DOI: 10.1089/cmb.2018.0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extracting the strength of the tree signal that is encompassed by a collection of gene trees is an exceptionally challenging problem in phylogenomics. Often, this problem not only involves the construction of individual phylogenies based on different genes, which may be a difficult endeavor on its own, but is also exacerbated by many factors that create conflicts between the evolutionary histories of different gene families, such as duplications or losses of genes; hybridization events; incomplete lineage sorting; and horizontal gene transfer, the latter two play central roles in the evolution of eukaryotes and prokaryotes, respectively. In this work, we tackle the aforementioned problem by focusing on quartet trees, which are the most basic unit of information in the context of unrooted phylogenies. In the first part, we show how a theorem of Janson that generalizes the classical Hoeffding inequality can be used to develop a statistical test involving quartets. In the second part, we study real and simulated data using this theoretical advancement, thus demonstrating how the significance of the differences between sets of quartets can be assessed. Our results are particularly intriguing since they nonstandardly require the analysis of dependent random variables.
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Affiliation(s)
- Eliran Avni
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
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Davidson R, Lawhorn M, Rusinko J, Weber N. Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1010-1015. [PMID: 28113327 DOI: 10.1109/tcbb.2016.2638911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all displayed quartets in many practical problems with large numbers of taxa. We introduce the notion of an Efficient Quartet System (EQS) to represent a phylogenetic tree with a subset of the quartets displayed by the tree. We show mathematically that the set of quartets obtained from a tree via an EQS contains all of the combinatorial information of the tree itself. Using performance tests on simulated datasets, we also demonstrate that using an EQS to reduce the number of quartets in both summary method pipelines for species tree inference as well as methods for supertree inference results in only small reductions in accuracy.
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Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. ISME JOURNAL 2015; 9:2191-205. [PMID: 25756680 DOI: 10.1038/ismej.2015.31] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/08/2015] [Accepted: 01/28/2015] [Indexed: 11/09/2022]
Abstract
Methanogenic archaea are genotypically and phenotypically diverse organisms that are integral to carbon cycling in anaerobic environments. Owing to their genetic tractability and ability to be readily cultivated, Methanosarcina spp. have become a powerful model system for understanding methanogen biology at the cellular systems level. However, relatively little is known of how genotypic and phenotypic variation is partitioned in Methanosarcina populations inhabiting natural environments and the possible ecological and evolutionary implications of such variation. Here, we have identified how genomic and phenotypic diversity is partitioned within and between Methanosarcina mazei populations obtained from two different sediment environments in the Columbia River Estuary (Oregon, USA). Population genomic analysis of 56 M. mazei isolates averaging <1% nucleotide divergence revealed two distinct clades, which we refer to as 'mazei-T' and 'mazei-WC'. Genomic analyses showed that these clades differed in gene content and fixation of allelic variants, which point to potential differences in primary metabolism and also interactions with foreign genetic elements. This hypothesis of niche partitioning was supported by laboratory growth experiments that revealed significant differences in trimethylamine utilization. These findings improve our understanding of the ecologically relevant scales of genomic variation in natural systems and demonstrate interactions between genetic and ecological diversity in these easily cultivable and genetically tractable model methanogens.
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Nesbø CL, S Swithers K, Dahle H, Haverkamp THA, Birkeland NK, Sokolova T, Kublanov I, Zhaxybayeva O. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments. ISME JOURNAL 2014; 9:1532-42. [PMID: 25500512 DOI: 10.1038/ismej.2014.238] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 11/09/2022]
Abstract
Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the 'burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development.
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Affiliation(s)
- Camilla L Nesbø
- 1] Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway [2] Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Kristen S Swithers
- 1] Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, USA [2] Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Håkon Dahle
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway
| | - Nils-Kåre Birkeland
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Tatiana Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Zhaxybayeva
- 1] Department of Biological Sciences, Dartmouth College, Hanover, NH, USA [2] Department of Computer Science, Dartmouth College, Hanover, NH, USA
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Williams D, Gogarten JP, Papke RT. Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol 2013; 4:1223-44. [PMID: 23160063 PMCID: PMC3542582 DOI: 10.1093/gbe/evs098] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In vitro studies of the haloarchaeal genus Haloferax have demonstrated
their ability to frequently exchange DNA between species, whereas rates of homologous
recombination estimated from natural populations in the genus Halorubrum
are high enough to maintain random association of alleles between five loci. To quantify
the effects of gene transfer and recombination of commonly held (relaxed core) genes
during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history
of 21 genomes representing all major groups. Using a novel algorithm and a concatenated
ribosomal protein phylogeny as a reference, we created a directed horizontal genetic
transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed
that 90% of testable HGTs were by direct homologous replacement, rather than
nonhomologous integration followed by a loss. Network analysis revealed an inverse
log-linear relationship between HGT frequency and ribosomal protein evolutionary distance
that is maintained across the deepest divergences in Halobacteria. We use this
mathematical relationship to estimate the total transfers and amino acid substitutions
delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core
genes of each genome, we conservatively estimate that 11–20% of their
evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer
and homologous recombination of relaxed core genes between members of the class
Halobacteria disrupts the coevolution of genes; however, the generation of new
combinations of divergent but functionally related genes may lead to adaptive phenotypes
not available through cumulative mutations and recombination within a single
population.
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Affiliation(s)
- David Williams
- Department of Molecular and Cell Biology, University of Connecticut, CT, USA
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