Visualizing Speciation in Artificial Cichlid Fish

2006 ◽  
Vol 12 (2) ◽  
pp. 243-257 ◽  
Author(s):  
Ross Clement
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Cichlid Fish ◽  
Natural Consequence ◽  
Open Problems ◽  
Visualization System ◽  
Low Level ◽  
Wide Range ◽  
Level Information ◽  
History Of

The Cichlid Speciation Project (CSP) is an ALife simulation system for investigating open problems in the speciation of African cichlid fish. The CSP can be used to perform a wide range of experiments that show that speciation is a natural consequence of certain biological systems. A visualization system capable of extracting the history of speciation from low-level trace data and creating a phylogenetic tree has been implemented. Unlike previous approaches, this visualization system presents a concrete trace of speciation, rather than a summary of low-level information from which the viewer can make subjective decisions on how speciation progressed. The phylogenetic trees are a more objective visualization of speciation, and enable automated collection and summarization of the results of experiments. The visualization system is used to create a phylogenetic tree from an experiment that models sympatric speciation.

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

scholarly journals MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Mengni Liu ◽  
Jianyu Chen ◽  
Xin Wang ◽  
Chengwei Wang ◽  
Xiaolong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Cancer Evolution ◽  
Evolutionary Patterns ◽  
Evolutionary Trajectory ◽  
Wide Range ◽  
Heterogeneous Features ◽  
History Of ◽  
Somatic Alterations ◽  
Tumor Biopsies

Abstract Background Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches. Findings Here, we present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution. Conclusions In summary, MesKit is useful for interpreting ITH and tracing evolutionary trajectory based on MRS data. MesKit is implemented in R and available at https://bioconductor.org/packages/MesKit under the GPL v3 license.

scholarly journals Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

2021 ◽  
Author(s):  
Gil Yardeni ◽  
Juan Viruel ◽  
Margot Paris ◽  
Jaqueline Hess ◽  
Clara Groot Crego ◽  
...  
Keyword(s):  
Population Genetic ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
Rapid Radiation ◽  
Entire Family ◽  
Coding Regions ◽  
Target Capture ◽  
Wide Range ◽  
History Of ◽  
Evolutionary Radiations

Target capture emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family. However, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

scholarly journals Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae

2019 ◽  
Vol 8 (1) ◽  
pp. 32
Author(s):  
Manuel Villalobos-Cid ◽  
Francisco Salinas ◽  
Eduardo I. Kessi-Pérez ◽  
Matteo De Chiara ◽  
Gianni Liti ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Total Evidence ◽  
Sequence Information ◽  
Phylogenetic Cluster ◽  
History Of ◽  
Tree Topologies ◽  
Yeast Genomes

Massive sequencing projects executed in Saccharomyces cerevisiae have revealed in detail its population structure. The recent “1002 yeast genomes project” has become the most complete catalogue of yeast genetic diversity and a powerful resource to analyse the evolutionary history of genes affecting specific phenotypes. In this work, we selected 22 nitrogen associated genes and analysed the sequence information from the 1011 strains of the “1002 yeast genomes project”. We constructed a total evidence (TE) phylogenetic tree using concatenated information, which showed a 27% topology similarity with the reference (REF) tree of the “1002 yeast genomes project”. We also generated individual phylogenetic trees for each gene and compared their topologies, identifying genes with similar topologies (suggesting a shared evolutionary history). Furthermore, we pruned the constructed phylogenetic trees to compare the REF tree topology versus the TE tree and the individual genes trees, considering each phylogenetic cluster/subcluster within the population, observing genes with cluster/subcluster topologies of high similarity to the REF tree. Finally, we used the pruned versions of the phylogenetic trees to compare four strains considered as representatives of S. cerevisiae clean lineages, observing for 15 genes that its cluster topologies match 100% the REF tree, supporting that these strains represent main lineages of yeast population. Altogether, our results showed the potential of tree topologies comparison for exploring the evolutionary history of a specific group of genes.

scholarly journals Cloning and Characterization of Two Putative P-Type ATPases from the Marine Microalga Dunaliella maritima Similar to Plant H+-ATPases and Their Gene Expression Analysis under Conditions of Hyperosmotic Salt Shock

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2667
Author(s):  
Dmitrii A. Matalin ◽  
Dmitrii E. Khramov ◽  
Alexey V. Shuvalov ◽  
Vadim S. Volkov ◽  
Yurii V. Balnokin ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Low Level ◽  
Salt Shock ◽  
Freshwater Organisms ◽  
Marine Microalga ◽  
Wide Range ◽  
History Of ◽  
Na Ions ◽  
High Concentrations ◽  
P Type

The green microalga genus Dunaliella is mostly comprised of species that exhibit a wide range of salinity tolerance, including inhabitants of hyperhaline reservoirs. Na+ content in Dunaliella cells inhabiting saline environments is maintained at a fairly low level, comparable to that in the cells of freshwater organisms. However, despite a long history of studying the physiological and molecular mechanisms that ensure the ability of halotolerant Dunaliella species to survive at high concentrations of NaCl, the question of how Dunaliella cells remove excess Na+ ions entering from the environment is still debatable. For thermodynamic reasons it should be a primary active mechanism; for example, via a Na+-transporting ATPase, but the molecular identification of Na+-transporting mechanism in Dunaliella has not yet been carried out. Formerly, in the euryhaline alga D. maritima, we functionally identified Na+-transporting P-type ATPase in experiments with plasma membrane (PM) vesicles which were isolated from this alga. Here we describe the cloning of two putative P-type ATPases from D. maritima, DmHA1 and DmHA2. Phylogenetic analysis showed that both ATPases belong to the clade of proton P-type ATPases, but the similarity between DmHA1 and DmHA2 is not high. The expression of DmHA1 and DmHA2 in D. maritima cells under hyperosmotic salt shock was studied by qRT-PCR. Expression of DmHA1 gene decreases and remains at a relatively low level during the response of D. maritima cells to hyperosmotic salt shock. In contrast, expression of DmHA2 increases under hyperosmotic salt shock. This indicates that DmHA2 is important for overcoming hyperosmotic salt stress by the algal cells and as an ATPase it is likely directly involved in transport of Na+ ions. We assume that it is the DmHA2 ATPase that represents the Na+-transporting ATPase.

scholarly journals Distribution of COVID-19 and Phylogenetic Tree Construction of SARS-CoV-2 in Indonesia

2020 ◽  
Vol 14 (suppl 1) ◽  
pp. 1035-1042
Author(s):  
Dora Dayu Rahma Turista ◽  
Aesthetica Islamy ◽  
Viol Dhea Kharisma ◽  
Arif Nur Muhammad Ansori
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Case Fatality ◽  
Medical Personnel ◽  
Distribution Data ◽  
Cure Rate ◽  
Transmission Process ◽  
Tree Construction ◽  
The World ◽  
History Of

Coronavirus disease 2019 (COVID-19) is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has spread quickly across the world and has been declared a pandemic. Indonesia has many COVID-19 cases, with a high mortality rate. This study aimed to describe the distribution of COVID-19 in Indonesia and constructed the SARS-CoV-2 phylogenetic tree from Indonesian isolates and those from other countries, including other CoVs to determine their relationship. The distribution data of COVID-19 in Indonesia were obtained from the COVID-19 Management Handling Unit and descriptively analyzed. SARS-CoV-2 isolates were retrieved from the GenBank® (National Center of Biotechnology Information, USA) and GISAID EpiCoV™ databases and were used to construct phylogenetic trees using MEGA X software. Of the 37 provinces in Indonesia, five provinces with the highest case fatality rates were DKI Jakarta, Jawa Barat, Jawa Timur, and Banten, and the five provinces with the highest cure rate were Kepulauan Riau, Bali, Aceh, Gorontalo, and DI Yogyakarta. SARS-CoV-2 Indonesian isolates were closely related to SARS-CoV-2 isolates from other countries. The rapid and widespread distribution of SARS-CoV-2 in Indonesia was caused by the lack of compliance with territorial restrictions and dishonesty with medical personnel. These data revealed that mutations can occur during the transmission process, which can be caused by a history of travel and increased patient immunity.

Group Experiences and Individual Differences in Stuttering

2019 ◽  
Vol 62 (12) ◽  
pp. 4335-4350 ◽  
Author(s):  
Seth E. Tichenor ◽  
J. Scott Yaruss
Keyword(s):  
Individual Differences ◽  
Support Groups ◽  
Support Group ◽  
Affective States ◽  
Life Outcomes ◽  
Self Help ◽  
Wide Range ◽  
Group Experiences ◽  
History Of ◽  
Adults Who Stutter

Purpose This study explored group experiences and individual differences in the behaviors, thoughts, and feelings perceived by adults who stutter. Respondents' goals when speaking and prior participation in self-help/support groups were used to predict individual differences in reported behaviors, thoughts, and feelings. Method In this study, 502 adults who stutter completed a survey examining their behaviors, thoughts, and feelings in and around moments of stuttering. Data were analyzed to determine distributions of group and individual experiences. Results Speakers reported experiencing a wide range of both overt behaviors (e.g., repetitions) and covert behaviors (e.g., remaining silent, choosing not to speak). Having the goal of not stuttering when speaking was significantly associated with more covert behaviors and more negative cognitive and affective states, whereas a history of self-help/support group participation was significantly associated with a decreased probability of these behaviors and states. Conclusion Data from this survey suggest that participating in self-help/support groups and having a goal of communicating freely (as opposed to trying not to stutter) are associated with less negative life outcomes due to stuttering. Results further indicate that the behaviors, thoughts, and experiences most commonly reported by speakers may not be those that are most readily observed by listeners.

ROLE OF LIPID PROFILE IN OVARIAN CARCINOMA PATIENTS

2019 ◽  
Vol 3 (8) ◽  
Author(s):  
Dr. Manisha ◽  
Dr. Ruchi Jindal
Keyword(s):  
Ovarian Cancer ◽  
Lipid Profile ◽  
Cancer Patients ◽  
Ovarian Tumor ◽  
Ovarian Cancer Risk ◽  
Low Level ◽  
Medical College ◽  
Group I ◽  
History Of

Background: The term "ovarian cancer" includes several different types of cancer that  arise from cells of the ovary, most commonly, tumors arise from the epithelium or lining cells of the ovary.  Ovarian cancer risk is positively associated with higher consumption of dietary cholesterol and eggs, and inversely associated with a higher intake of vegetables. High consumption of fats may increase circulating estrogen levels, thus increasing the possibility of cell damage and proliferation that is responsible for cancerous growth. Material & Methods: The present study was conducted at Geetanjali Medical College and Hospital, Udaipur (Rajasthan). Total  100 cases (females) attending the obstetrics and gynecology department for some gynecological and other problem  were selected for this study between the age of 40-60 years, who were attending cancer centre at GEETANJALI MEDICAL COLLEGE AND  HOSPITAL, Udaipur (Rajasthan).                GROUP I: - It consisted of healthy females control subjects (n=50) .By routine examination and tests, we ensured that all the subjects were healthy and there were no signs and symptoms or history of ovarian tumor and diseases GROUP II: - It consisted of ovarian cancer females subjects (n=50) with a history of ovarian tumor. Results:   Higher level of cholesterol, LDL, VLDL and low level of HDL are found in ovarian cancer patients. Conclusion: The present study we highlights the importance and role of serum lipid profile in diagnosis, prognosis and recurrence of the disease. The study shows that serum level of cholesterol, LDL, VLDL was elevated in  patients of ovarian cancer while low level of HDL are found in ovarian cancer patients. Key words: lipid profile, ovarian cancer.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

Introduction: Emotion, History and the Arts

2018 ◽  
Vol 7 (2) ◽  
pp. 117-128 ◽  
Author(s):  
Erin Sullivan ◽  
Marie Louise Herzfeld-Schild
Keyword(s):  
Historical Change ◽  
Carson Mccullers ◽  
Emotional Life ◽  
Review Section ◽  
The Arts ◽  
Wide Range ◽  
War Correspondents ◽  
History Of ◽  
Johan Huizinga

This introduction surveys the rise of the history of emotions as a field and the role of the arts in such developments. Reflecting on the foundational role of the arts in the early emotion-oriented histories of Johan Huizinga and Jacob Burkhardt, as well as the concerns about methodological impressionism that have sometimes arisen in response to such studies, the introduction considers how intensive engagements with the arts can open up new insights into past emotions while still being historically and theoretically rigorous. Drawing on a wide range of emotionally charged art works from different times and places—including the novels of Carson McCullers and Harriet Beecher-Stowe, the private poetry of neo-Confucian Chinese civil servants, the photojournalism of twentieth-century war correspondents, and music from Igor Stravinsky to the Beatles—the introduction proposes five ways in which art in all its forms contributes to emotional life and consequently to emotional histories: first, by incubating deep emotional experiences that contribute to formations of identity; second, by acting as a place for the expression of private or deviant emotions; third, by functioning as a barometer of wider cultural and attitudinal change; fourth, by serving as an engine of momentous historical change; and fifth, by working as a tool for emotional connection across communities, both within specific time periods but also across them. The introduction finishes by outlining how the special issue's five articles and review section address each of these categories, while also illustrating new methodological possibilities for the field.

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