scholarly journals MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers

2017 ◽  
Author(s):  
Cédric Chauve ◽  
Akbar Rafiey ◽  
Adrián A. Davín ◽  
Celine Scornavacca ◽  
Philippe Veber ◽  
...  
Keyword(s):  
Significant Proportion ◽  
Time Consistency ◽  
Confidence Score ◽  
Species Tree ◽  
Time Constraints ◽  
Gene Trees ◽  
Transfer Event ◽  
Maximum Time ◽  
Wide Range ◽  
History Of

AbstractLateral gene transfers between ancient species contain information about the relative timing of species diversification. Specifically, the ancestors of a donor species must have existed before the descendants of the recipient species. Hence, the detection of a transfer event can be translated into a time constraint between nodes of a phylogeny if the donor and recipient can be identified. When a set of transfers is detected by interpreting the phylogenetic discordance between gene trees and a species tree, the set of all deduced time constraints can be used to rank the species tree,i.e.order totally its internal nodes. Unfortunately lateral gene transfer detection is challenging and current methods produce a significant proportion of false positives. As a result, often, no ranking of the species tree is compatible with the full set of time constraints deduced from predicted transfers. Here we propose a method, implemented in a software called MaxTiC (Maximum Time Consistency), which takes as input a species tree and a series of (possibly inconsistent) time constraints between its internal nodes, weighted by confidence scores. MaxTiC outputs a ranked species tree compatible with a subset of constraints with maximum cumulated confidence score. We extensively test the method on simulated datasets, under a wide range of conditions that we compare to measures on biological datasets. In most conditions the obtained ranked tree is very close to the real one, confirming the potential of dating the history of life with transfers by maximizing time consistency. MaxTiC is freely available, distributed along with a documentation and several examples:https://github.com/ssolo/ALE/tree/master/maxtic.

scholarly journals Reconstruction of time-consistent species trees

2020 ◽  
Author(s):  
Manuel Lafond ◽  
Marc Hellmuth
Keyword(s):  
Time Complexity ◽  
Gene Tree ◽  
Time Consistency ◽  
Gene Families ◽  
Time Algorithm ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Evolutionary Event ◽  
History Of

Abstract Background: The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way.Results: In this contribution, we consider event-labeled gene trees that contain speciations, duplications as well as horizontal gene transfer (HGT) and we assume that the species tree is unknown. Although many problems become NP-hard as soon as HGT and time-consistency are involved, we show, in contrast, that the problem of finding a time-consistent species tree for a given event-labeled gene can be solved in polynomial-time. We provide a cubic-time algorithm to decide whether a "time-consistent" species for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity.

scholarly journals Quantifying the risk of hemiplasy in phylogenetic inference

2018 ◽  
Author(s):  
Rafael F. Guerrero ◽  
Matthew W. Hahn
Keyword(s):  
Risk Factor ◽  
Convergent Evolution ◽  
Phylogenetic Inference ◽  
Species Tree ◽  
New Method ◽  
Gene Trees ◽  
Arbitrary Length ◽  
Wide Range

AbstractConvergent evolution is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely— or more likely—than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a new method to calculate the ratio of these two probabilities (the “hemiplasy risk factor”) along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree in order to identify when and where incongruent traits may be more likely to be due to hemiplasy than homoplasy.

scholarly journals Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

2020 ◽  
Author(s):  
Dan Vanderpool ◽  
Bui Quang Minh ◽  
Robert Lanfear ◽  
Daniel Hughes ◽  
Shwetha Murali ◽  
...  
Keyword(s):  
World Monkey ◽  
Gene Tree ◽  
Species Tree ◽  
Molecular Dating ◽  
Macaca Nemestrina ◽  
Gene Trees ◽  
Individual Gene ◽  
Black And White ◽  
Fossil Evidence ◽  
History Of

AbstractOur understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here we present new reference genome assemblies for three Old World Monkey species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.

scholarly journals Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009095
Author(s):  
Thomas C. Nelson ◽  
Angela M. Stathos ◽  
Daniel D. Vanderpool ◽  
Findley R. Finseth ◽  
Yao-wu Yuan ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Tree ◽  
Nuclear Gene ◽  
Evolutionary Genetics ◽  
Species Tree ◽  
Pollination Syndrome ◽  
Gene Trees ◽  
Genome Wide ◽  
Hummingbird Pollination ◽  
History Of

Inferences about past processes of adaptation and speciation require a gene-scale and genome-wide understanding of the evolutionary history of diverging taxa. In this study, we use genome-wide capture of nuclear gene sequences, plus skimming of organellar sequences, to investigate the phylogenomics of monkeyflowers in Mimulus section Erythranthe (27 accessions from seven species). Taxa within Erythranthe, particularly the parapatric and putatively sister species M. lewisii (bee-pollinated) and M. cardinalis (hummingbird-pollinated), have been a model system for investigating the ecological genetics of speciation and adaptation for over five decades. Across >8000 nuclear loci, multiple methods resolve a predominant species tree in which M. cardinalis groups with other hummingbird-pollinated taxa (37% of gene trees), rather than being sister to M. lewisii (32% of gene trees). We independently corroborate a single evolution of hummingbird pollination syndrome in Erythranthe by demonstrating functional redundancy in genetic complementation tests of floral traits in hybrids; together, these analyses overturn a textbook case of pollination-syndrome convergence. Strong asymmetries in allele-sharing (Patterson’s D-statistic and related tests) indicate that gene-tree discordance reflects ancient and recent introgression rather than incomplete lineage sorting. Consistent with abundant introgression blurring the history of divergence, low-recombination and adaptation-associated regions support the new species tree, while high-recombination regions generate phylogenetic evidence for sister status for M. lewisii and M. cardinalis. Population-level sampling of core taxa also revealed two instances of chloroplast capture, with Sierran M. lewisii and Southern Californian M. parishii each carrying organelle genomes nested within respective sympatric M. cardinalis clades. A recent organellar transfer from M. cardinalis, an outcrosser where selfish cytonuclear dynamics are more likely, may account for the unexpected cytoplasmic male sterility effects of selfer M. parishii organelles in hybrids with M. lewisii. Overall, our phylogenomic results reveal extensive reticulation throughout the evolutionary history of a classic monkeyflower radiation, suggesting that natural selection (re-)assembles and maintains species-diagnostic traits and barriers in the face of gene flow. Our findings further underline the challenges, even in reproductively isolated species, in distinguishing re-use of adaptive alleles from true convergence and emphasize the value of a phylogenomic framework for reconstructing the evolutionary genetics of adaptation and speciation.

scholarly journals Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)

2020 ◽  
Author(s):  
Thomas C. Nelson ◽  
Angela M. Stathos ◽  
Daniel D. Vanderpool ◽  
Findley R. Finseth ◽  
Yao-wu Yuan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Species Tree ◽  
Sister Species ◽  
Pollination Syndrome ◽  
Gene Trees ◽  
Trait Evolution ◽  
Genome Wide ◽  
Hummingbird Pollination ◽  
History Of

AbstractInferences about past processes of adaptation and speciation require a gene-scale and genome-wide understanding of the evolutionary history of diverging taxa. In this study, we use genome-wide capture of nuclear gene sequences, plus skimming of organellar sequences, to investigate the phylogenomics of monkeyflowers in Mimulus section Erythranthe (27 accessions from seven species). Taxa within Erythranthe, particularly the parapatric and putatively sister species M. lewisii (bee-pollinated) and M. cardinalis (hummingbird-pollinated), have been a model system for investigating the ecological genetics of speciation and adaptation for over five decades. Across >8000 nuclear loci, multiple methods resolve a predominant species tree in which M. cardinalis groups with other hummingbird-pollinated taxa (37% of gene trees), rather than being sister to M. lewisii (32% of gene trees). We independently corroborate a single evolution of hummingbird pollination syndrome in Erythranthe by demonstrating functional redundancy in genetic complementation tests of floral traits in hybrids; together, these analyses overturn a textbook case of pollination-syndrome convergence. Strong asymmetries in allele-sharing (Patterson’s D-statistic and related tests) indicate that gene-tree discordance reflects ancient and recent introgression rather than incomplete lineage sorting. Consistent with abundant introgression blurring the history of divergence, low-recombination and adaptation-associated regions support the new species tree, while high-recombination regions generate phylogenetic evidence for sister status for M. lewisii and M. cardinalis. Population-level sampling of core taxa also revealed two instances of chloroplast capture, with Sierran M. lewisii and Southern Californian M. parishii each carrying organelle genomes nested within respective sympatric M. cardinalis clades. A recent organellar transfer from M. cardinalis, an outcrosser where selfish cytonuclear dynamics are more likely, may account for the unexpected cytoplasmic male sterility effects of selfer M. parishii organelles in hybrids with M. lewisii. Overall, our phylogenomic results reveal extensive reticulation throughout the evolutionary history of a classic monkeyflower radiation, suggesting that natural selection (re-)assembles and maintains species-diagnostic traits and barriers in the face of gene flow. Our findings further underline the challenges, even in reproductively isolated species, in distinguishing re-use of adaptive alleles from true convergence and emphasize the value of a phylogenomic framework for reconstructing the evolutionary genetics of adaptation and speciation.Author SummaryAdaptive radiations, which involve both divergent evolution of new traits and recurrent trait evolution, provide insight into the processes that generate and maintain organismal diversity. However, rapid radiations also generate particular challenges for inferring the evolutionary history and mechanistic basis of adaptation and speciation, as multiple processes can cause different parts of the genome to have distinct phylogenetic trees. Thus, inferences about the mode and timing of divergence and the causes of parallel trait evolution require a fine-grained understanding of the flow of genomic variation through time. In this study, we used genome-wide sampling of thousands of genes to re-construct the evolutionary histories of a model plant radiation, the monkeyflowers of Mimulus section Erythranthe. Work over the past half-century has established the parapatric and putatively sister species M. lewisii (bee-pollinated) and M. cardinalis (hummingbird-pollinated, as are three other species in the section) as textbook examples of both rapid speciation via shifts in pollination syndrome and convergent evolution of floral syndromes. Our phylogenomic analyses re-write both of these stories, placing M. cardinalis in a clade with other hummingbird-pollinated taxa and demonstrating that abundant introgression between ancestral lineages as well as in areas of current sympatry contributes to the real (but misleading) affinities between M. cardinalis and M. lewisii. This work illustrates the pervasive influence of gene flow and introgression during adaptive radiation and speciation, and underlines the necessity of a gene-scale and genome-wide phylogenomics framework for understanding trait divergence, even among well-established species.

Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae)

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1750-1759 ◽  
Author(s):  
LACEY L. KNOWLES ◽  
PAVEL B. KLIMOV
Keyword(s):  
Phylogenetic Relationships ◽  
Species Interactions ◽  
Sequence Data ◽  
Species Group ◽  
Species Tree ◽  
Terminal Branch ◽  
Gene Trees ◽  
Species Trees ◽  
Feather Mites ◽  
History Of

SUMMARYWith the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference – species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates – a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.

scholarly journals Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

PLoS Biology ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. e3000954
Author(s):  
Dan Vanderpool ◽  
Bui Quang Minh ◽  
Robert Lanfear ◽  
Daniel Hughes ◽  
Shwetha Murali ◽  
...  
Keyword(s):  
World Monkey ◽  
Gene Tree ◽  
Species Tree ◽  
Molecular Dating ◽  
Macaca Nemestrina ◽  
Gene Trees ◽  
Individual Gene ◽  
Black And White ◽  
Fossil Evidence ◽  
History Of

Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.

scholarly journals Quantifying the risk of hemiplasy in phylogenetic inference

2018 ◽  
Vol 115 (50) ◽  
pp. 12787-12792 ◽  
Author(s):  
Rafael F. Guerrero ◽  
Matthew W. Hahn
Keyword(s):  
Risk Factor ◽  
Convergent Evolution ◽  
Phylogenetic Inference ◽  
Species Tree ◽  
Character State ◽  
Gene Trees ◽  
Arbitrary Length ◽  
Wide Range

Convergent evolution—the appearance of the same character state in apparently unrelated organisms—is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely—or more likely—than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a method to calculate the ratio of these two probabilities (the “hemiplasy risk factor”) along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree to identify when and where incongruent traits may be due to hemiplasy.

scholarly journals The genomic view of diversification

2018 ◽  
Author(s):  
Julie Marin ◽  
Guillaume Achaz ◽  
Anton Crombach ◽  
Amaury Lambert
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Molecular Data ◽  
Species Tree ◽  
Data Sets ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Parameters Tuning ◽  
History Of ◽  
New Framework

AbstractEvolutionary relationships between species are traditionally represented in the form of a tree, the species tree. Its reconstruction from molecular data is hindered by frequent conflicts between gene genealogies. Usually, these disagreements are explained by incomplete lineage sorting (ILS) due to random coalescences of gene lineages inside the edges of the species tree. This paradigm, the multi-species coalescent (MSC), is constantly violated by the ubiquitous presence of gene flow, leading to incongruences between gene trees that cannot be explained by ILS alone. Here we argue instead in favor of a vision acknowledging the importance of gene flow and where gene histories shape the species tree rather than the opposite. We propose a new framework for modeling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees. We implement this framework in two mathematical models called the gene-based diversification models (GBD): 1) GBD-forward following all evolving genomes and 2) GBD-backward based on coalescent theory. They feature four parameters tuning colonization, gene flow, genetic drift and genetic differentiation. We propose a quick inference method based on differences between gene trees. Applied to two empirical data-sets prone to gene flow, we find a better support for the GBD model than for the MSC model. Along with the increasing awareness of the extent of gene flow, this work shows the importance of considering the richer signal contained in genomic histories, rather than in the mere species tree, to better apprehend the complex evolutionary history of species.

scholarly journals Kharkov Classical University and Kharkiv Institute of Public Education: problems of heredity (historiographical subjects)

2020 ◽  
Vol 3 (1) ◽  
pp. 16
Author(s):  
Olena Bohdashyna ◽  
Serhii Kudelko
Keyword(s):  
Public Education ◽  
Significant Proportion ◽  
100Th Anniversary ◽  
Theoretical Research ◽  
Practical Significance ◽  
Teaching Staff ◽  
Material Base ◽  
Wide Range ◽  
History Of ◽  
The University

The aim of the article is to highlight the evolution of ideas in Soviet and modern historiography on (non)perception of scientific traditions of the Kharkiv Imperial University by the Institute of Public Education named after O. O. Potebnya (KhIPE). Research methods: problematic-historiographic, historical-chronological, comparative-historical; principles of systematicity and objectivity. Main results and scientific novelty: for the first time it has been considered in detail how researchers assessments have changed from denying the necessity of mastering the old principles of higher education to the perception of the Kharkiv Institute of Public Education named after O. O. Potebnia as the heir of the pre-revolutionary university with partial preservation of traditions. The coverage in the historical thought of the 20s of the 20th and the beginning of the 19th century of problematic issues related to the establishment and operation of the KhIPE is analyzed. Particular attention is paid to the diversity of opinions and assessments of the KhIPE perceptions of the traditions of the Kharkiv Imperial University. The authors concludes that the traditions of the Kharkiv University were partially preserved in the work of the KhIPE, thanks to the inherited material base, and most importantly, the preserve of the main teaching staff, employees and part of the pre-revolutionary students. In the latter case, the years of 1921–1924 are meant, when some of students who had studied before the university closed in 1919 returned to study and non the latter case, the years of 1921–1924 are meant, when some of students who had studied before the university closed in 1919 returned to study and non-proletarian youth made up a significant proportion of the student contingent. In historical science the KhIPE’s estimation as successor to the Kharkiv University is unstable. Soviet authors focused mainly on the refusal of the leadership of the People’s Commissar of Education of the USRR and the IPE on the forms of the liquidated imperial university. Meanwhile, the contemporary authors, on the one hand, emphasize the voluntarism and failure of the educational reform and 1933 forced restoration of universities by the Soviet power. On the other hand, the idea that the tradition of the Imperial University was more than accepted until recently was considered to be in keeping with the KhIPE traditions. The article is dedicated to the 100th anniversary of the most radical reform in the history of domestic universities, the consequences and historical significance of which cause lively discussions among experts. The practical significance of the article is to change the priorities in teaching and promoting the history of the V. N. Karazin Kharkiv National University. The originality of the study is due to the unbiased consideration of a wide range of used historiographical sources (scientific works and journalism). Type of article: theoretical research.

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