A genome Tree of Life for the Fungi kingdom

Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information–based trees (“gene trees”), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes. Within the last decade, a large number of whole-genome sequences of fungi have become publicly available, which represent, at present, the most fundamental and complete information about each fungal organism. This presents an opportunity to infer kinship among fungi using a whole-genome information-based tree (“genome tree”). The method we used allows comparison of whole-genome information without MSA, and is a variation of a computational algorithm developed to find semantic similarities or plagiarism in two books, where we represent whole-genomic information of an organism as a book of words without spaces. The genome tree reveals several significant and notable differences from the gene trees, and these differences invoke new discussions about alternative narratives for the evolution of some of the currently accepted fungal groups.

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Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽

10.1093/genetics/164.4.1645 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1645-1656 ◽

Cited By ~ 3

Author(s):

Bruce Rannala ◽

Ziheng Yang

Keyword(s):

Dna Sequences ◽

Gene Tree ◽

Species Tree ◽

Bayes Estimation ◽

Ancestral Population ◽

Divergence Times ◽

Gene Trees ◽

Species Divergence ◽

Multiple Loci ◽

Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

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Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

10.1101/181115 ◽

2017 ◽

Author(s):

Matthew Parks ◽

Teofil Nakov ◽

Elizabeth Ruck ◽

Norman J. Wickett ◽

Andrew J. Alverson

Keyword(s):

Whole Genome Duplication ◽

Large Scale ◽

Genome Duplication ◽

Gene Tree ◽

Genomic Diversity ◽

Phylogenomic Analysis ◽

Whole Genome ◽

Gene Trees ◽

Angiosperm Evolution ◽

Polyploid Formation

ABSTRACTPremise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.MethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.Key resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.ConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.

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Whole-Proteome Tree of Arthropods: An “alignment-free” phylogeny of proteome “books”

10.21203/rs.3.rs-46859/v1 ◽

2020 ◽

Author(s):

Sung-Hou Kim ◽

JaeJin Choi ◽

Byung-Ju Kim

Keyword(s):

Text Analysis ◽

Gene Tree ◽

Whole Genome ◽

Gene Trees ◽

View Point ◽

Analysis Method ◽

Genome Sequences ◽

Alignment Free ◽

Grouping Pattern ◽

Almost All

Abstract Background: An “organism tree” of a group of extant-organisms can be considered as a conceptual tree to capture a simplified narrative of the evolutionary course among the organisms. Due to the difficulties of whole-genome sequencing for many organisms, the most common approach has been to construct a “gene tree” by selecting a group of genes common among the organisms, “align” each gene family and estimate evolutionary distances. Despite broad acceptance of the gene trees as the surrogates for the organism trees, there are important limitations and confounding issues with the approach. During last decades, whole-genome sequences of many extant-arthropods became available, providing an opportunity to construct a “whole-proteome tree” of the arthropods, the largest and most species-diverse group of all living animals. Results: An “alignment-free” whole-proteome tree of the arthropods shows that (a) the demographic grouping-pattern is similar to those in the gene trees, but there are notable differences in the branching orders of the groups and the sisterhood relationships between pairs of the groups; and (b) almost all the “founders” of the groups have emerged in an “explosive burst” near the root of the tree. Conclusion: Since the whole-proteome sequence of an organism can be considered as a “book” of amino-acid alphabets, a tree of the books can be constructed, without alignment of sequences, using a text analysis method of Information Theory, which allows comparing the information content of whole-proteomes. Such tree provides another view-point to consider in telling the narrative of kinship among the arthropods.

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Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

Systematic Biology ◽

10.1093/sysbio/syz019 ◽

2019 ◽

Vol 68 (6) ◽

pp. 937-955 ◽

Cited By ~ 21

Author(s):

Alison Cloutier ◽

Timothy B Sackton ◽

Phil Grayson ◽

Michele Clamp ◽

Allan J Baker ◽

...

Keyword(s):

Sequence Data ◽

Incomplete Lineage Sorting ◽

Estimation Error ◽

Gene Tree ◽

Species Tree ◽

Tree Topology ◽

Whole Genome ◽

Gene Trees ◽

Lineage Sorting ◽

Genome Analyses

Abstract Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

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The Multispecies Coalescent in Space and Time

10.1101/2020.08.02.233395 ◽

2020 ◽

Author(s):

Patrick F. McKenzie ◽

Deren A. R. Eaton

Keyword(s):

Gene Tree ◽

Species Tree ◽

Gene Trees ◽

Effective Population ◽

Sliding Windows ◽

Multispecies Coalescent ◽

A Genome ◽

Tree Inference ◽

Rate Of Decay ◽

Coalescent Time

AbstractA key distinction between species tree inference under the multi-species coalescent model (MSC), and the inference of gene trees in sliding windows along a genome, is in the effect of genetic linkage. Whereas the MSC explicitly assumes genealogies to be unlinked, i.e., statistically independent, genealogies located close together on genomes are spatially auto-correlated. Here we use tree sequence simulations with recombination to explore the effects of species tree parameters on spatial patterns of linkage among genealogies. We decompose coalescent time units to demonstrate differential effects of generation time and effective population size on spatial coalescent patterns, and we define a new metric, “phylogenetic linkage,” for measuring the rate of decay of phylogenetic similarity by comparison to distances among unlinked genealogies. Finally, we provide a simple example where accounting for phylogenetic linkage in sliding window analyses improves local gene tree inference.

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Genome Tree of Life: Deep Burst of Organism Diversity

10.1101/756155 ◽

2019 ◽

Cited By ~ 2

Author(s):

JaeJin Choi ◽

Sung-Hou Kim

Keyword(s):

Genome Sequence ◽

Tree Of Life ◽

Whole Genome Sequence ◽

Whole Genome ◽

A Genome ◽

Living Organisms ◽

Life On Earth ◽

Large Groups ◽

Emergence Of Life ◽

Genome Tree

AbstractAn organism Tree of Life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms of today. Such tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the extant organisms. Since the whole genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a genome Tol can be an empirically derivable surrogate for the organism ToL. However, a genome ToL has been impossible to construct because of the practical reasons that experimentally determining the whole genome sequences of a large number of diverse organisms was technically impossible. Thus, for several decades, gene ToLs, based on selected genes, have been commonly used as a surrogate for the organisms ToL. This situation changed dramatically during the last several decades due to rapid advances in DNA sequencing technology. Here we describe the main features of a genome ToL that are different from those of the broadly accepted gene ToLs: (a) the first two organism groups to emerge are the founders of prokarya and eukarya, (b) they diversify into six large groups and all the founders of the groups have emerged in a “Deep Burst” at the very beginning period of the emergence of Life on Earth and (c) other differences are notable in the order of emergence of smaller groups.Significance StatementTree of Life is a conceptual and metaphorical tree that captures a simplified narrative of the evolutionary course and kinship among all living organisms of today. Since the whole genome sequence information of an organism is, at present, the most comprehensive description of the organism, we reconstructed a Genome Tree of Life using the proteome information from the whole genomes of over 4000 different living organisms on Earth. It suggests that (a) the first two primitive organism groups to emerge are the founders of prokarya and eukarya, (b) they diversify into six large groups, and (c) all the founders of the groups have emerged in a “Deep Burst” at the very beginning period of the emergence of Life on Earth.

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Whole-Proteome Tree of Insects: An Information-theory-based “alignment-free” phylogeny and grouping of “proteome books”

10.1101/2020.07.11.198689 ◽

2020 ◽

Author(s):

JaeJin Choi ◽

Byung-Ju Kim ◽

Sung-Hou Kim

Keyword(s):

Information Theory ◽

Text Analysis ◽

Gene Tree ◽

Alternative View ◽

Whole Genome ◽

Gene Trees ◽

Analysis Method ◽

Genome Sequences ◽

Alignment Free ◽

Grouping Pattern

AbstractBackgroundAn “organism tree” of insects, the largest and most species-diverse group of all living animals, can be considered as a metaphorical and conceptual tree to capture a simplified narrative of the complex and unpredictable evolutionary courses of the extant insects. Currently, the most common approach has been to construct a “gene tree”, as a surrogate for the organism tree, by selecting a group of highly alignable regions of each of the select genes/proteins to represent each organism. However, such selected regions account for a small fraction of all genes/proteins and even smaller fraction of whole genome of an organism. During last decades, whole-genome sequences of many extant insects became available, providing an opportunity to construct a “whole-genome or whole-proteome tree” of insects using Information Theory without sequence alignment (alignment-free method).ResultsA whole-proteome tree of the insects shows that (a) the demographic grouping-pattern is similar to those in the gene trees, but there are notable differences in the branching orders of the groups, thus, the sisterhood relationships between pairs of the groups; and (b) all the founders of the major groups have emerged in an “explosive burst” near the root of the tree.ConclusionSince the whole-proteome sequence of an organism can be considered as a “book” of amino-acid alphabets, a tree of the books can be constructed, without alignment of sequences, using a text analysis method of Information Theory. Such tree provides an alternative view-point of constructing a narrative of evolution and kinship among the extant insects.

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Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya

PeerJ ◽

10.7717/peerj.5254 ◽

2018 ◽

Vol 6 ◽

pp. e5254 ◽

Cited By ~ 4

Author(s):

James M. Wainaina ◽

Elijah Ateka ◽

Timothy Makori ◽

Monica A. Kehoe ◽

Laura M. Boykin

Keyword(s):

Coat Protein ◽

Sweet Potato ◽

Field Isolate ◽

Gene Tree ◽

Evolutionary Relationship ◽

Sub Saharan Africa ◽

Whole Genome ◽

Gene Trees ◽

Species Trees ◽

Potato Viruses

Sweet potato is a major food security crop within sub-Saharan Africa where 90% of Africa production occurs. One of the major limitations of sweet potato production are viral infections. In this study, we used a combination of whole genome sequences from a field isolate obtained from Kenya and those available in GenBank. Sequences of four sweet potato viruses: Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato chlorotic fleck virus (SPCFV) were obtained from the Kenyan sample. SPFMV sequences both from this study and from GenBank were found to be recombinant. Recombination breakpoints were found within the Nla-Pro, coat protein and P1 genes. The SPCSV, SPVC, and SPCFV viruses from this study were non-recombinant. Bayesian phylogenomic relationships across whole genome trees showed variation in the number of well-supported clades; within SPCSV (RNA1 and RNA2) and SPFMV two well-supported clades (I and II) were resolved. The SPCFV tree resolved three well-supported clades (I–III) while four well-supported clades were resolved in SPVC (I–IV). Similar clades were resolved within the coalescent species trees. However, there were disagreements between the clades resolved in the gene trees compared to those from the whole genome tree and coalescent species trees. However the coat protein gene tree of SPCSV and SPCFV resolved similar clades to the genome and coalescent species tree while this was not the case in SPFMV and SPVC. In addition, we report variation in selective pressure within sites of individual genes across all four viruses; overall all viruses were under purifying selection. We report the first complete genomes of SPFMV, SPVC, SPCFV, and a partial SPCSV from Kenya as a mixed infection in one sample. Our findings provide a snap shot on the evolutionary relationship of sweet potato viruses (SPFMV, SPVC, SPCFV, and SPCSV) from Kenya as well as assessing whether selection pressure has an effect on their evolution.

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Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1421385112 ◽

2015 ◽

Vol 112 (33) ◽

pp. 10139-10146 ◽

Cited By ~ 61

Author(s):

Chuan Ku ◽

Shijulal Nelson-Sathi ◽

Mayo Roettger ◽

Sriram Garg ◽

Einat Hazkani-Covo ◽

...

Keyword(s):

Gene Transfer ◽

Single Gene ◽

Gene Tree ◽

Eukaryotic Cell ◽

Specific Gene ◽

Gene Trees ◽

Endosymbiotic Gene Transfer ◽

Evolutionary Innovation ◽

Eukaryotic Genes ◽

A Genome

Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners—the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)—and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic—and plant and algal—lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller’s ratchet—the origin of eukaryotic recombination, or sex—might have required surprisingly little evolutionary innovation.

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Testing morphology-based delimitation of Vulpicida juniperinus and V. tubulosus (Parmeliaceae) using three molecular markers

The Lichenologist ◽

10.1017/s0024282912000448 ◽

2012 ◽

Vol 44 (6) ◽

pp. 757-772 ◽

Cited By ~ 7

Author(s):

Kristiina MARK ◽

Lauri SAAG ◽

Andres SAAG ◽

Arne THELL ◽

Tiina RANDLANE

Keyword(s):

Molecular Markers ◽

Dna Sequences ◽

Gene Tree ◽

Single Locus ◽

Gene Trees ◽

Nuclear Its

AbstractThe delimitation of two morphologically similar and not easily separable Vulpicida species, V. juniperinus and V. tubulosus, is analyzed using nuclear ITS and Mcm7, and mitochondrial SSU DNA sequences. Seventy-nine Vulpicida specimens, most from the two focal taxa, are included in the three-locus gene tree. The results from Bayesian and parsimony analyses are presented. There are strong conflicts between the single locus gene trees. Vulpicida juniperinus and V. tubulosus are divided into two clearly distinguished groups in the ITS and concatenated B/MCMC tree. However, these species are mixed in both clades, appearing polyphyletic. Currently accepted V. juniperinus and V. tubulosus are not distinct according to the loci studied. Vulpicida pinastri appears monophyletic based on the available sequences.

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