scholarly journals Reconciliation of Gene and Species Trees

2014 ◽  
Vol 2014 ◽  
pp. 1-22 ◽  
Author(s):  
L. Y. Rusin ◽  
E. V. Lyubetskaya ◽  
K. Y. Gorbunov ◽  
V. A. Lyubetsky
Keyword(s):  
Time Scales ◽  
Gene Evolution ◽  
Single Species ◽  
Species Tree ◽  
Gene Duplications ◽  
Species Trees ◽  
Evolutionary Scenario ◽  
Algorithmic Construction ◽  
Basic Ideas ◽  
Horizontal Transfers

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.

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 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.

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 Experimental Evolution of Legume Symbionts: What Have We Learnt?

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 339 ◽  
Author(s):  
Ginaini Grazielli Doin de Moura ◽  
Philippe Remigi ◽  
Catherine Masson-Boivin ◽  
Delphine Capela
Keyword(s):  
Experimental Evolution ◽  
Nitrogen Fixing ◽  
Plant Selection ◽  
Cell Infection ◽  
Symbiotic Gene ◽  
Symbiotic Plasmid ◽  
Evolutionary Scenario ◽  
Gene Acquisition ◽  
Regulatory Circuits ◽  
Horizontal Transfers

Rhizobia, the nitrogen-fixing symbionts of legumes, are polyphyletic bacteria distributed in many alpha- and beta-proteobacterial genera. They likely emerged and diversified through independent horizontal transfers of key symbiotic genes. To replay the evolution of a new rhizobium genus under laboratory conditions, the symbiotic plasmid of Cupriavidus taiwanensis was introduced in the plant pathogen Ralstonia solanacearum, and the generated proto-rhizobium was submitted to repeated inoculations to the C. taiwanensis host, Mimosa pudica L. This experiment validated a two-step evolutionary scenario of key symbiotic gene acquisition followed by genome remodeling under plant selection. Nodulation and nodule cell infection were obtained and optimized mainly via the rewiring of regulatory circuits of the recipient bacterium. Symbiotic adaptation was shown to be accelerated by the activity of a mutagenesis cassette conserved in most rhizobia. Investigating mutated genes led us to identify new components of R. solanacearum virulence and C. taiwanensis symbiosis. Nitrogen fixation was not acquired in our short experiment. However, we showed that post-infection sanctions allowed the increase in frequency of nitrogen-fixing variants among a non-fixing population in the M. pudica–C. taiwanensis system and likely allowed the spread of this trait in natura. Experimental evolution thus provided new insights into rhizobium biology and evolution.

scholarly journals Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

2020 ◽  
Author(s):  
Diego F Morales-Briones ◽  
Gudrun Kadereit ◽  
Delphine T Tefarikis ◽  
Michael J Moore ◽  
Stephen A Smith ◽  
...  
Keyword(s):  
Network Inference ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Species Tree ◽  
Data Sets ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Gene Tree Discordance

Abstract Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]

scholarly journals Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

2020 ◽  
Author(s):  
Matthew H Van Dam ◽  
James B Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Gene Tree ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

scholarly journals FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i57-i65 ◽  
Author(s):  
Erin K Molloy ◽  
Tandy Warnow
Keyword(s):  
Gene Duplication ◽  
Species Tree ◽  
Supplementary Information ◽  
Biological Research ◽  
Generic Model ◽  
Species Trees ◽  
Basic Part ◽  
Gene Duplication And Loss ◽  
Tree Estimation ◽  
Scalable Methods

Abstract Motivation Species tree estimation is a basic part of biological research but can be challenging because of gene duplication and loss (GDL), which results in genes that can appear more than once in a given genome. All common approaches in phylogenomic studies either reduce available data or are error-prone, and thus, scalable methods that do not discard data and have high accuracy on large heterogeneous datasets are needed. Results We present FastMulRFS, a polynomial-time method for estimating species trees without knowledge of orthology. We prove that FastMulRFS is statistically consistent under a generic model of GDL when adversarial GDL does not occur. Our extensive simulation study shows that FastMulRFS matches the accuracy of MulRF (which tries to solve the same optimization problem) and has better accuracy than prior methods, including ASTRAL-multi (the only method to date that has been proven statistically consistent under GDL), while being much faster than both methods. Availability and impementation FastMulRFS is available on Github (https://github.com/ekmolloy/fastmulrfs). Supplementary information Supplementary data are available at Bioinformatics online.

From population genetics to phylogeny: Uses and limits of mitochondrial DNA

1990 ◽  
Vol 3 (1) ◽  
pp. 111 ◽  
Author(s):  
RH Crozier
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Gene ◽  
Single Gene ◽  
Dna Amplification ◽  
Species Tree ◽  
Population Subdivision ◽  
Evolutionary Divergence ◽  
Gene Trees ◽  
Species Trees ◽  
Effective Population

Mitochondrial DNA (mtDNA) is clonally and maternally inherited in all animals and in most plants. Mitochondrial gene content is similar although not identical in all eukaryotes. Because of these characteristics, mtDNA has a number of features useful to systematists for all levels of evolutionary divergence. Clonal inheritance leads to unusual confidence in constructing gene trees which are useful in population-level studies, such as in the detection of population subdivision. Maternal inheritance presents the opportunity to distinguish paternal from maternal gene flow. The clonal, or single-gene, nature of mtDNA inheritance leads to consideration of the expected convergence between gene- and species-trees. For closely related populations or species, it is desirable to use several genes to be sure that the correct species-tree is discovered; this means that, although mtDNA will be the most precise guide to the species tree because of its lower effective population size, nuclear genes should also be used in such studies. Although restriction fragment length polymorphisms dominated the field until recently, sequencing following DNA amplification using the polymerase chain reaction is now easier and opens up the use of preserved specimens to molecular systematists. Because mitochondria1 genes evolve at different rates, one of appropriate rate can be selected for almost any phylogenetic problem.

POPULATION GROWTH MODELING WITH BOOM AND BUST PATTERNS: THE IMPULSIVE DIFFERENTIAL EQUATION FORMALISM

2015 ◽  
Vol 23 (supp01) ◽  
pp. S135-S149 ◽  
Author(s):  
FERNANDO CÓRDOVA-LEPE ◽  
GONZALO ROBLEDO ◽  
JAVIER CABRERA-VILLEGAS
Keyword(s):  
Differential Equation ◽  
Population Dynamics ◽  
Time Scales ◽  
Chaotic Dynamics ◽  
Impulsive Differential Equation ◽  
Dynamical Behavior ◽  
Single Species ◽  
Open Problems ◽  
Boom And Bust ◽  
Different Time Scales

This note gives an overview on basic mathematical models describing the population dynamics of a single species whose vital dynamics has different time scales. We present five cases combining two time–scales with Malthusian growth in at least one scale. The dynamical behavior shows a progressive complexity, from "naive" to chaotic dynamics (in the Li–Yorke's sense). In addition, some open problems and new results are presented.

scholarly journals Uprooting phylogenetic uncertainty in coalescent species delimitation: A meta-analysis of empirical studies

2015 ◽  
Vol 61 (5) ◽  
pp. 866-873 ◽  
Author(s):  
Itzue W. Caviedes-Solis ◽  
Nassima M. Bouzid ◽  
Barbara L. Banbury ◽  
Adam D. Leaché
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Species Tree ◽  
Species Trees ◽  
Posterior Probabilities ◽  
Guide Tree ◽  
Tree Topologies ◽  
Accurate Quantification

Abstract Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence data. Bayesian Phylogenetics and Phylogeography (BPP) is a coalescent-based method frequently used to delimit species; however, empirical studies suggest that the requirement of a user-specified guide tree biases the range of possible outcomes. We evaluate fifteen multi-locus datasets using the most recent iteration of BPP, which eliminates the need for a user-specified guide tree and reconstructs the species tree in synchrony with species delimitation (= unguided species delimitation). We found that the number of species recovered with guided versus unguided species delimitation was the same except for two cases, and that posterior probabilities were generally lower for the unguided analyses as a result of searching across species trees in addition to species delimitation models. The guide trees used in previous studies were often discordant with the species tree topologies estimated by BPP. We also compared species trees estimated using BPP and *BEAST and found that when the topologies are the same, BPP tends to give higher posterior probabilities.

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