scholarly journals STRIDE: Species Tree Root Inference from Gene Duplication Events

2017 ◽  
Vol 34 (12) ◽  
pp. 3267-3278 ◽  
Author(s):  
David M Emms ◽  
Steven Kelly
Keyword(s):  
Gene Duplication ◽  
Species Tree ◽  
Duplication Events

scholarly journals STRIDE: Species Tree Root Inference from Gene Duplication Events

2017 ◽  
Author(s):  
David M. Emms ◽  
Steven Kelly
Keyword(s):  
Probability Distribution ◽  
Gene Duplication ◽  
Probability Model ◽  
Duplication Event ◽  
Species Tree ◽  
The Novel ◽  
Gene Trees ◽  
Duplication Events ◽  
Genome Scale ◽  
Scale Data

AbstractThe correct interpretation of a phylogenetic tree is dependent on it being correctly rooted. A gene duplication event at the base of a clade of species is synapamorphic, and thus excludes the root of the species tree from that clade. We present STRIDE, a fast, effective, and outgroup-free method for species tree root inference from gene duplication events. STRIDE identifies sets of well-supported gene duplication events from cohorts of gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of the true root. We show that STRIDE infers the correct root of the species tree for a large range of simulated and real species sets. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for datasets where information is limited. Furthermore, application of STRIDE to inference of the origin of the eukaryotic tree resulted in a root probability distribution that was consistent with, but unable to distinguish between, leading hypotheses for the origin of the eukaryotes. In summary, STRIDE is a fast, scalable, and effective method for species tree root inference from genome scale data.

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.

Evolution of Placental Function in Mammals: The Molecular Basis of Gas and Nutrient Transfer, Hormone Secretion, and Immune Responses

2012 ◽  
Vol 92 (4) ◽  
pp. 1543-1576 ◽  
Author(s):  
Anthony M. Carter
Keyword(s):  
Gene Duplication ◽  
Convergent Evolution ◽  
Globin Gene ◽  
Hormone Secretion ◽  
Human Leukocyte ◽  
Amino Acid Transporters ◽  
Placental Lactogens ◽  
Wide Range ◽  
Duplication Events ◽  
Range Of Functions

Placenta has a wide range of functions. Some are supported by novel genes that have evolved following gene duplication events while others require acquisition of gene expression by the trophoblast. Although not expressed in the placenta, high-affinity fetal hemoglobins play a key role in placental gas exchange. They evolved following duplications within the beta-globin gene family with convergent evolution occurring in ruminants and primates. In primates there was also an interesting rearrangement of a cassette of genes in relation to an upstream locus control region. Substrate transfer from mother to fetus is maintained by expression of classic sugar and amino acid transporters at the trophoblast microvillous and basal membranes. In contrast, placental peptide hormones have arisen largely by gene duplication, yielding for example chorionic gonadotropins from the luteinizing hormone gene and placental lactogens from the growth hormone and prolactin genes. There has been a remarkable degree of convergent evolution with placental lactogens emerging separately in the ruminant, rodent, and primate lineages and chorionic gonadotropins evolving separately in equids and higher primates. Finally, coevolution in the primate lineage of killer immunoglobulin-like receptors and human leukocyte antigens can be linked to the deep invasion of the uterus by trophoblast that is a characteristic feature of human placentation.

scholarly journals Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates

2019 ◽  
Vol 36 (7) ◽  
pp. 1384-1404 ◽  
Author(s):  
Arthur Zwaenepoel ◽  
Yves Van de Peer
Keyword(s):  
Maximum Likelihood ◽  
Gene Duplication ◽  
Gene Tree ◽  
Probabilistic Approach ◽  
Species Tree ◽  
Rate Variation ◽  
Whole Genome ◽  
Tree Reconciliation ◽  
Gene Duplication And Loss ◽  
Loss Rates

Abstract Gene tree–species tree reconciliation methods have been employed for studying ancient whole-genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of interest in a reference species tree. Such approaches do not account for uncertainty in the gene tree and reconciliation, or do so only heuristically. The effects of these simplifications on the inference of ancient WGDs are unclear. In particular, the effects of variation in gene duplication and loss rates across the species tree have not been considered. Here, we developed a full probabilistic approach for phylogenomic reconciliation-based WGD inference, accounting for both gene tree and reconciliation uncertainty using a method based on the principle of amalgamated likelihood estimation. The model and methods are implemented in a maximum likelihood and Bayesian setting and account for variation of duplication and loss rates across the species tree, using methods inspired by phylogenetic divergence time estimation. We applied our newly developed framework to ancient WGDs in land plants and investigated the effects of duplication and loss rate variation on reconciliation and gene count based assessment of these earlier proposed WGDs.

Two gene duplication events in the human and primate dopamine D5 receptor gene family

Gene ◽  
1995 ◽  
Vol 154 (2) ◽  
pp. 153-158 ◽  
Author(s):  
Adriano Marchese ◽  
Timothy V. Beischlag ◽  
Tuan Nguyen ◽  
Hyman B. Niznik ◽  
Richard L. Weinshank ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Receptor Gene ◽  
Duplication Events ◽  
Dopamine D5 Receptor ◽  
Receptor Gene Family

scholarly journals In with the Old, in with the New: The Promiscuity of the Duplication Process Engenders Diverse Pathways for Novel Gene Creation

2012 ◽  
Vol 2012 ◽  
pp. 1-24 ◽  
Author(s):  
Vaishali Katju
Keyword(s):  
Gene Duplication ◽  
Population Size ◽  
Population Genetic ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Dna And Rna ◽  
Duplication Events ◽  
History Of ◽  
Theoretical Population ◽  
Novel Exon

The gene duplication process has exhibited far greater promiscuity in the creation of paralogs with novel exon-intron structures than anticipated even by Ohno. In this paper I explore the history of the field, from the neo-Darwinian synthesis through Ohno’s formulation of the canonical model for the evolution of gene duplicates and culminating in the present genomic era. I delineate the major tenets of Ohno’s model and discuss its failure to encapsulate the full complexity of the duplication process as revealed in the era of genomics. I discuss the diverse classes of paralogs originating from both DNA- and RNA-mediated duplication events and their evolutionary potential for assuming radically altered functions, as well as the degree to which they can function unconstrained from the pressure of gene conversion. Lastly, I explore theoretical population-genetic considerations of how the effective population size (Ne) of a species may influence the probability of emergence of genes with radically altered functions.

scholarly journals Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

2016 ◽  
Author(s):  
Kousuke Hanada ◽  
Ayumi Tezuka ◽  
Masafumi Nozawa ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Synonymous Substitution ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Highly Qualified ◽  
Duplication Events ◽  
Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

scholarly journals Patterns of gene evolution following duplications and speciations in vertebrates

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8813 ◽  
Author(s):  
Kyle T. David ◽  
Jamie R. Oaks ◽  
Kenneth M. Halanych
Keyword(s):  
Gene Duplication ◽  
Gene Evolution ◽  
Strong Support ◽  
Duplication Event ◽  
Gene Trees ◽  
Loss Of Function ◽  
Eukaryotic Genes ◽  
Gene Copies ◽  
Duplication Events ◽  
And Function

Background Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.

Sign in / Sign up

Export Citation Format

Share Document