Ancestral Reconstruction of Karyotypes Reveals an Exceptional Rate of Nonrandom Chromosomal Evolution in Sunflower

Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here, we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package syntR. The syntR algorithm performs as well as previous ad hoc methods while being systematic, repeatable, and applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax. Using syntR, we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years, a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between one and three translocations involving only 8 of the 17 chromosomes. This nonrandom exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that Helianthus has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.

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Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution

10.1101/737155 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kate L. Ostevik ◽

Kieran Samuk ◽

Loren H. Rieseberg

Keyword(s):

Ad Hoc ◽

Hybrid Sterility ◽

Chromosomal Rearrangements ◽

Chromosomal Evolution ◽

R Package ◽

High Density ◽

Genetic Maps ◽

High Rate ◽

Ancestral Reconstruction ◽

Karyotypic Diversity

AbstractMapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous ad-hoc methods while being systematic, repeatable, and is applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax.Using syntR, and we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years – a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between 1 and 3 translocations involving only 8 of the 17 chromosomes. This non-random exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that Helianthus has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.

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Rapid speciation and karyotype evolution in Orthoptera

10.1101/2021.07.06.451348 ◽

2021 ◽

Author(s):

Octavio Manuel Palacios-Gimenez

Keyword(s):

Karyotype Evolution ◽

Evolutionary Model ◽

Chromosomal Evolution ◽

High Rate ◽

Recent Common Ancestor ◽

Extinction Rate ◽

Background Rate ◽

Speciation Rate ◽

Most Recent Common Ancestor ◽

Karyotypic Diversity

To test the hypothesis that high speciation rate in groups is coupled with high rate of karyotype evolution but also that younger groups having a higher rate of karyotypic diversity, I estimated rates of speciation and rates of karyotype evolution in 1,177 species belonging to 26 families in the insect order Orthoptera. Rates of karyotype evolution were estimated using the diploid number and the number of chromosome arms (fundamental number) from published karyotypes of Orthoptera. Rates of speciation were quantified considering the number of species examined karyotypically in each family, the most recent common ancestor of each family and the information about extinction rate. The rate of speciation was strongly correlated with rate of karyotype evolution and the average rates of speciation was nearly ~177 times higher than the background rate estimated for Orthoptera based on acoustic communication using phylogenomic data, as well as 8.4 and 35.6 times higher than the estimated speciation rate in vertebrates and bivalve mollusks respectively, indicating that Orthoptera has evolved very fast at chromosomal level. The findings supported the hypothesis of a high speciation rate in lineages with high rate of chromosomal evolution but there were not evidences that younger groups tended to have higher rate of karyotypic diversity. Furthermore, rates of karyotype evolution most closely fitted the punctuational evolutionary model indicating the existence of long periods of stasis of karyotype change with most karyotype change occurring quickly over short evolutionary times. I discussed genetic drift, divergent selection and meiotic drive as potential biological mechanisms to explain karyotype evolution allowing or impeding for the fixation of chromosomal rearrangements and in turn speciation in orthopterans lineages.

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Extensive Amplification of Telomeric Repeats in the Karyotypically Highly Diverse African Pygmy Mice

Cytogenetic and Genome Research ◽

10.1159/000478297 ◽

2017 ◽

Vol 152 (2) ◽

pp. 55-64 ◽

Cited By ~ 4

Author(s):

Victor Colomina ◽

Josette Catalan ◽

Janice Britton-Davidian ◽

Frédéric Veyrunes

Keyword(s):

Mammalian Species ◽

Chromosomal Rearrangements ◽

Replication Timing ◽

Pericentromeric Region ◽

Chromosomal Evolution ◽

Telomeric Repeats ◽

Telomeric Sequences ◽

Interstitial Telomeric Sequences ◽

Karyotypic Diversity ◽

The One

Telomeres are ribonucleoprotein structures protecting the physical ends of eukaryotic chromosomes. However, telomeric sequences can also occur at non-terminal regions of chromosomes, forming the so-called interstitial telomeric sequences (ITSs). Some ITSs are considered as relics of past chromosomal rearrangements and as such provide important insights into karyotype evolution. By FISH, we explored the distribution of telomeric motifs in the genome of a complex of mammalian species that has long been recognized for its extraordinary karyotypic diversity: the African pygmy mice. This survey involved 5 species, representing 10 highly diverse karyotypes with or without autosomal and sex-autosome robertsonian (Rb) fusions. The study revealed that in species with an ancestral-like karyotype (i.e., no fusions; Mus mattheyi and M. indutus), only terminal telomeres were observed, whereas in species experiencing intense chromosomal evolution (e.g., M. minutoides, M. musculoides), a large amplification of telomeric repeats was also identified in the pericentromeric region of acrocentrics and most metacentrics. We concluded that (i) the mechanism of Rb fusion in the African pygmy mice is different than the one highlighted in the house mouse; (ii) the intensity of the ITS hybridization signal could be a signature of the age of formation of the Rb fusion; (iii) the large amplification of pericentromeric telomeric sequences in acrocentrics may mediate the formation of Rb fusions, and (iv) the ITSs on the sex-autosome fusion Rb(X.1) may participate to the insulation buffer between the sexual and autosomal arms to prevent X inactivation from spreading and silencing autosomal genes and allow the independent regulation of replication timing of both segments.

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Extensive Sex Chromosome Polymorphism of Microtus thomasi/Microtus atticus Species Complex Associated with Cryptic Chromosomal Rearrangements and Independent Accumulation of Heterochromatin

Cytogenetic and Genome Research ◽

10.1159/000477114 ◽

2017 ◽

Vol 151 (4) ◽

pp. 198-207 ◽

Cited By ~ 3

Author(s):

Michail T. Rovatsos ◽

Juan A. Marchal ◽

Ismael Romero-Fernández ◽

Maria Arroyo ◽

Eva B. Athanasopoulou ◽

...

Keyword(s):

Sex Chromosomes ◽

Dna Sequences ◽

Sex Chromosome ◽

Chromosomal Rearrangements ◽

Chromosomal Evolution ◽

Chromosome Polymorphism ◽

Random Drift ◽

X Chromosomes ◽

Karyotypic Diversity ◽

Comparative Painting

The sibling species Microtus thomasi and M. atticus represent probably the highest karyotypic diversity within the genus Microtus and are an interesting model for chromosomal evolution studies. In addition to variation in autosomes, they show a high intraspecific variation in the size and morphology of both sex chromosomes. We analyzed individuals with different sex chromosome constitutions using 3 painting probes, 2 from Y chromosome variants and 1 from the small arm of the submetacentric X chromosome. Our comparative painting approach uncovered 12 variants of Y and 14 variants of X chromosomes, which demonstrates that the polymorphism of sex chromosomes is substantially larger than previously reported. We suggest that 2 main processes are responsible for this sex chromosome polymorphism: change of morphology from acrocentric to submetacentric or metacentric chromosomes and increase in size due to accumulation of repetitive DNA sequences, generating heterochromatic blocks. Strong genetic drift in small and fragmented populations of these 2 species could be related to the origin and maintenance of the large polymorphism of sex chromosomes. We proposed that a similar polymorphism variation combined with random drift fixing the biggest sex chromosomes could have occurred in the origin of some of the actual Microtus species with giant sex chromosomes.

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Noncontingent Nonreinforcement of a Response as the Aversive Event in a Cer Paradigm

Psychological Reports ◽

10.2466/pr0.1971.29.3f.1196 ◽

1971 ◽

Vol 29 (3_suppl) ◽

pp. 1196-1198 ◽

Cited By ~ 1

Author(s):

Richard S. Calef ◽

Richard A. Kaufman ◽

Ronald N. Bone ◽

Steven A. Werk

Keyword(s):

Reinforcement Schedule ◽

Present Experiment ◽

High Density ◽

High Rate ◽

Aversive Event ◽

Necessary Condition ◽

Facilitation Effect ◽

Response Facilitation ◽

Early Training ◽

Low Rate

The present experiment investigated the effects of noncontingent nonreinforcement as the aversive event in a CER paradigm. The results showed a significant response-facilitation effect during early training, but none during later training with a high rate-producing, high-density reinforcement schedule. The present results imply that a low rate-producing, high-density reinforcement schedule is not a necessary condition for response facilitation.

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Power analysis in a SMART design: sample size estimation for determining the best embedded dynamic treatment regime

Biostatistics ◽

10.1093/biostatistics/kxy064 ◽

2018 ◽

Vol 21 (3) ◽

pp. 432-448 ◽

Cited By ~ 2

Author(s):

William J Artman ◽

Inbal Nahum-Shani ◽

Tianshuang Wu ◽

James R Mckay ◽

Ashkan Ertefaie

Keyword(s):

Power Analysis ◽

Ad Hoc ◽

Treatment Effectiveness ◽

R Package ◽

Treatment Regime ◽

Size Estimation ◽

Dynamic Treatment Regime ◽

Dynamic Treatment ◽

The Individual ◽

Number Of Individuals

Summary Sequential, multiple assignment, randomized trial (SMART) designs have become increasingly popular in the field of precision medicine by providing a means for comparing more than two sequences of treatments tailored to the individual patient, i.e., dynamic treatment regime (DTR). The construction of evidence-based DTRs promises a replacement to ad hoc one-size-fits-all decisions pervasive in patient care. However, there are substantial statistical challenges in sizing SMART designs due to the correlation structure between the DTRs embedded in the design (EDTR). Since a primary goal of SMARTs is the construction of an optimal EDTR, investigators are interested in sizing SMARTs based on the ability to screen out EDTRs inferior to the optimal EDTR by a given amount which cannot be done using existing methods. In this article, we fill this gap by developing a rigorous power analysis framework that leverages the multiple comparisons with the best methodology. Our method employs Monte Carlo simulation to compute the number of individuals to enroll in an arbitrary SMART. We evaluate our method through extensive simulation studies. We illustrate our method by retrospectively computing the power in the Extending Treatment Effectiveness of Naltrexone (EXTEND) trial. An R package implementing our methodology is available to download from the Comprehensive R Archive Network.

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Identifying home locations in human mobility data: an open-source R package for comparison and reproducibility

10.31235/osf.io/k3jp2 ◽

2021 ◽

Author(s):

Qingqing Chen ◽

Ate Poorthuis

Keyword(s):

Software Package ◽

Ad Hoc ◽

Human Mobility ◽

Building Blocks ◽

R Package ◽

Location Based Services ◽

R Software ◽

Mobility Data ◽

Residential Population ◽

Research Goal

Identifying meaningful locations, such as home or work, from human mobility data has become an increasingly common prerequisite for geographic research. Although location-based services (LBS) and other mobile technology have rapidly grown in recent years, it can be challenging to infer meaningful places from such data, which - compared to conventional datasets – can be devoid of context. Existing approaches are often developed ad-hoc and can lack transparency and reproducibility. To address this, we introduce an R software package for inferring home locations from LBS data. The package implements pre-existing algorithms and provides building blocks to make writing algorithmic ‘recipes’ more convenient. We evaluate this approach by analyzing a de-identified LBS dataset from Singapore that aims to balance ethics and privacy with the research goal of identifying meaningful locations. We show that ensemble approaches, combining multiple algorithms, can be especially valuable in this regard as the resulting patterns of inferred home locations closely correlate with the distribution of residential population. We hope this package, and others like it, will contribute to an increase in use and sharing of comparable algorithms, research code and data. This will increase transparency and reproducibility in mobility analyses and further the ongoing discourse around ethical big data research.

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fullsibQTL: an R package for QTL mapping in biparental populations of outcrossing species

10.1101/2020.12.04.412262 ◽

2020 ◽

Author(s):

Rodrigo Gazaffi ◽

Rodrigo R. Amadeu ◽

Marcelo Mollinari ◽

João R. B. F. Rosa ◽

Cristiane H. Taniguti ◽

...

Keyword(s):

Qtl Mapping ◽

Open Source ◽

Qtl Analysis ◽

Source Code ◽

R Package ◽

Genetic Maps ◽

Linkage Phase ◽

Position Effects ◽

Genetic Features ◽

Outcrossing Species

ABSTRACTAccurate QTL mapping in outcrossing species requires software programs which consider genetic features of these populations, such as markers with different segregation patterns and different level of information. Although the available mapping procedures to date allow inferring QTL position and effects, they are mostly not based on multilocus genetic maps. Having a QTL analysis based in such maps is crucial since they allow informative markers to propagate their information to less informative intervals of the map. We developed fullsibQTL, a novel and freely available R package to perform composite interval QTL mapping considering outcrossing populations and markers with different segregation patterns. It allows to estimate QTL position, effects, segregation patterns, and linkage phase with flanking markers. Additionally, several statistical and graphical tools are implemented, for straightforward analysis and interpretations. fullsibQTL is an R open source package with C and R source code (GPLv3). It is multiplatform and can be installed from https://github.com/augusto-garcia/fullsibQTL.

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Associations Between Cellular Levels of ATP and Prodigiosin Pigment Throughout the Growth Cycle of Serratia marcescens

Canadian Journal of Microbiology ◽

10.1139/cjm-2020-0619 ◽

2021 ◽

Author(s):

Pryce L. Haddix

Keyword(s):

Stationary Phase ◽

Serratia Marcescens ◽

Stationary Phases ◽

Growth Cycle ◽

High Density ◽

High Rate ◽

Lag Phase ◽

Positive Role ◽

Atp Production ◽

Density Growth

ABSTRACT Serratia marcescens is a prolific producer of the red, membrane-associated pigment prodigiosin. Earlier work has established both a positive role for prodigiosin in ATP production during population lag phase and a negative role during high-rate, low cell density growth. This study uses the growth rate and growth phase modulation afforded by chemostat culture to extend prodigiosin functional analysis to the high density and stationary phases. Cellular levels of prodigiosin were positively associated with cellular levels of ATP during high-density growth, and artificial pigment induction during this phase increased cellular ATP. Following peak high density ATP per cell, early stationary phase enabled significant population growth while prodigiosin levels remained high and ATP declined. During late stationary phase, ATP per cell was positively associated with prodigiosin per cell while both declined during continued growth. These results provide correlational evidence for multiple effects of prodigiosin pigment on ATP production throughout the growth cycle. Earlier work and the data presented here enable formulation of a working model for the oscillating relationships between cellular levels of ATP and prodigiosin during batch culture.

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Analyzing the Effect of Node Density on the Performance of the LAR-1P Algorithm

International Journal of Information Technology and Web Engineering ◽

10.4018/jitwe.2012040102 ◽

2012 ◽

Vol 7 (2) ◽

pp. 16-29

Author(s):

Hussein Al-Bahadili ◽

Ali Maqousi ◽

Reyadh S. Naoum

Keyword(s):

Network Performance ◽

Ad Hoc ◽

High Density ◽

Low Density ◽

Probabilistic Algorithms ◽

Excellent Performance ◽

Node Density ◽

Simulation Results ◽

Mobile Ad Hoc ◽

Hoc Networks

The location-aided routing scheme 1 (LAR-1) and probabilistic algorithms are combined together into a new algorithm for route discovery in mobile ad hoc networks (MANETs) called LAR-1P. Simulation results demonstrated that the LAR-1P algorithm reduces the number of retransmissions as compared to LAR-1 without sacrificing network reachability. Furthermore, on a sub-network (zone) scale, the algorithm provides an excellent performance in high-density zones, while in low-density zones; it preserves the performance of LAR-1. This paper provides a detailed analysis of the performance of the LAR-1P algorithm through various simulations, where the actual numerical values for the number of retransmissions and reachability in high- and low-density zones were computed to demonstrate the effectiveness and significance of the algorithm and how it provides better performance than LAR-1 in high-density zones. In addition, the effect of the total number of nodes on the average network performance is also investigated.

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