Uncorrelated change produces the apparent dependence of evolutionary rate on interval

An intriguing phenomenon in the study of evolutionary rates of morphological change measured from fossil lineages has been the dependence of these rates on the inverse of the measurement interval. This effect has been reported across wide ranges of species as well as within single lineages, and has been interpreted as representing a smooth extension of evolutionary rate from generational timescales to paleontological timescales, suggesting that macroevolution may be simply microevolution extended over longer intervals. There has been some debate about whether this inverse dependence is a real feature of evolutionary change, or a mathematical or psychological artifact associated with the interpretation of data.Our analysis indicates that the strong inverse dependence of rate on interval is an artifact produced by the phenomenon of spurious self-correlation. Spurious self-correlation can appear in any calculation when a ratio is plotted against its denominator, as is done in plotting rate versus interval, and when these two quantities are not well correlated with one another. We demonstrate that the effect of spurious self-correlation appears in seven published data sets of evolutionary rate that range from taxonomically broad compendia to studies of single families. The effect obscures the underlying information about the dependence of evolutionary change on interval that is present in the data sets. In five of the seven data sets examined there is no significant correlation between the extent of evolutionary change and elapsed time. Where such a correlation does exist, the inverse dependence of rate on interval length is weakened. We describe the role played by taxonomic, dynamic, and character inhomogeneity in producing the lack of correlation of change with interval in each of these data sets. This lack of correlation of change with interval, and the accompanying inverse correlation of rate with interval, most likely arises from discontinuous modes of evolutionary change in which a distinct long-term dynamic dominates net change over geological time spans. It is poorly explained by the extrapolationary microevolutionary models that have been said to account for this phenomenon.

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The Sampling Distribution of Disease-Associated Alleles

Genetics ◽

10.1093/genetics/147.4.1855 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1855-1861 ◽

Cited By ~ 1

Author(s):

Montgomery Slatkin ◽

Bruce Rannala

Keyword(s):

Low Frequency ◽

Null Model ◽

Sampling Distribution ◽

Death Process ◽

Published Data ◽

Data Sets ◽

Likelihood Functions ◽

Alternative Hypotheses ◽

Size Standard ◽

Birth Death

Abstract A theory is developed that provides the sampling distribution of low frequency alleles at a single locus under the assumption that each allele is the result of a unique mutation. The numbers of copies of each allele is assumed to follow a linear birth-death process with sampling. If the population is of constant size, standard results from theory of birth-death processes show that the distribution of numbers of copies of each allele is logarithmic and that the joint distribution of numbers of copies of k alleles found in a sample of size n follows the Ewens sampling distribution. If the population from which the sample was obtained was increasing in size, if there are different selective classes of alleles, or if there are differences in penetrance among alleles, the Ewens distribution no longer applies. Likelihood functions for a given set of observations are obtained under different alternative hypotheses. These results are applied to published data from the BRCA1 locus (associated with early onset breast cancer) and the factor VIII locus (associated with hemophilia A) in humans. In both cases, the sampling distribution of alleles allows rejection of the null hypothesis, but relatively small deviations from the null model can account for the data. In particular, roughly the same population growth rate appears consistent with both data sets.

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Relative testis size and mating systems in anurans: large testis in multiple-male mating in foam-nesting frogs

Animal Biology ◽

10.1163/157075511x570312 ◽

2011 ◽

Vol 61 (2) ◽

pp. 225-238 ◽

Cited By ~ 15

Author(s):

Wen Bo Liao ◽

Zhi Ping Mi ◽

Cai Quan Zhou ◽

Ling Jin ◽

Xian Han ◽

...

Keyword(s):

Sperm Competition ◽

Published Data ◽

Male Mating ◽

Data Sets ◽

Testis Size ◽

Data Set ◽

Monogamous Species ◽

Large Testis ◽

Testes Size ◽

Testis Mass

AbstractComparative studies of the relative testes size in animals show that promiscuous species have relatively larger testes than monogamous species. Sperm competition favours the evolution of larger ejaculates in many animals – they give bigger testes. In the view, we presented data on relative testis mass for 17 Chinese species including 3 polyandrous species. We analyzed relative testis mass within the Chinese data set and combining those data with published data sets on Japanese and African frogs. We found that polyandrous foam nesting species have relatively large testes, suggesting that sperm competition was an important factor affecting the evolution of relative testes size. For 4 polyandrous species testes mass is positively correlated with intensity (males/mating) but not with risk (frequency of polyandrous matings) of sperm competition.

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Children with 5′-end NF1 gene mutations are more likely to have glioma

Neurology Genetics ◽

10.1212/nxg.0000000000000192 ◽

2017 ◽

Vol 3 (5) ◽

pp. e192 ◽

Cited By ~ 12

Author(s):

Corina Anastasaki ◽

Stephanie M. Morris ◽

Feng Gao ◽

David H. Gutmann

Keyword(s):

Gene Mutation ◽

Statistical Significance ◽

Gene Mutations ◽

Neurofibromatosis Type ◽

Published Data ◽

Data Sets ◽

Nonsense Mutations ◽

Data Set ◽

Nf1 Gene ◽

The Relationship

Objective:To ascertain the relationship between the germline NF1 gene mutation and glioma development in patients with neurofibromatosis type 1 (NF1).Methods:The relationship between the type and location of the germline NF1 mutation and the presence of a glioma was analyzed in 37 participants with NF1 from one institution (Washington University School of Medicine [WUSM]) with a clinical diagnosis of NF1. Odds ratios (ORs) were calculated using both unadjusted and weighted analyses of this data set in combination with 4 previously published data sets.Results:While no statistical significance was observed between the location and type of the NF1 mutation and glioma in the WUSM cohort, power calculations revealed that a sample size of 307 participants would be required to determine the predictive value of the position or type of the NF1 gene mutation. Combining our data set with 4 previously published data sets (n = 310), children with glioma were found to be more likely to harbor 5′-end gene mutations (OR = 2; p = 0.006). Moreover, while not clinically predictive due to insufficient sensitivity and specificity, this association with glioma was stronger for participants with 5′-end truncating (OR = 2.32; p = 0.005) or 5′-end nonsense (OR = 3.93; p = 0.005) mutations relative to those without glioma.Conclusions:Individuals with NF1 and glioma are more likely to harbor nonsense mutations in the 5′ end of the NF1 gene, suggesting that the NF1 mutation may be one predictive factor for glioma in this at-risk population.

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Structure in parasite component communities in wild rodents: predictability, stability, associations and interactions .... or pure randomness?

Parasitology ◽

10.1017/s0031182008000334 ◽

2008 ◽

Vol 135 (7) ◽

pp. 751-766 ◽

Cited By ~ 42

Author(s):

J. M. BEHNKE

Keyword(s):

Species Richness ◽

Published Data ◽

Data Sets ◽

Wild Rodents ◽

Heligmosomoides Polygyrus ◽

Wood Mice ◽

Core Species ◽

Helminth Communities ◽

Immune Mediated ◽

Concurrent Infections

SUMMARYExperimental data establish that interactions exist between species of intestinal helminths during concurrent infections in rodents, the strongest effects being mediated through the host's immune responses. Detecting immune-mediated relationships in wild rodent populations has been fraught with problems and published data do not support a major role for interactions in structuring helminth communities. Helminths in wild rodents show predictable patterns of seasonal, host age-dependent and spatial variation in species richness and in abundance of core species. When these are controlled for, patterns of co-infection compatible with synergistic interactions can be demonstrated. At least one of these, the positive relationship betweenHeligmosomoides polygyrusand species richness of other helminths has been demonstrated in three totally independent data-sets. Collectively, they explain only a small percentage of the variance/deviance in abundance data and at this level are unlikely to play a major role in structuring helminth communities, although they may be important in the more heavily infected wood mice. Current worm burdens underestimate the possibility that earlier interactions through the immune system have taken place, and therefore interactions may have a greater role to play than is immediately evident from current worm burdens. Longitudinal studies are proposed to resolve this issue.

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Systematic and ontology-based approach to interoperable cross-domain open government data services

Transforming Government People Process and Policy ◽

10.1108/tg-08-2021-0132 ◽

2021 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Hadi Masoumi ◽

Bahar Farahani ◽

Fereidoon Shams Aliee

Keyword(s):

Social Innovation ◽

Open Government ◽

Published Data ◽

Data Sets ◽

Full Potential ◽

Top Down ◽

Content Type ◽

Data Services ◽

Open Government Data ◽

Government Data

Purpose Open government data (OGD) has emerged as a radical paradigm shift and endeavor among government administrations across the world mainly due to its promises of transparency, accountability, public-private collaboration, civic participation, social innovation and data-driven value creation. Complexity, cross-cutting nature, diversity of data sets, interoperability and quality issues usually hamper unlocking the full potential value of data. To tackle these challenges, this paper aims to provide a novel solution using a top-down approach. Design/methodology/approach In this paper, the authors propose a systematic ontology-based approach combined with a novel architecture and its corresponding processes enabling organizations to carry out all the steps in the OGD value chain. In addition, an OGD Platform including a portal (www.iranopendata.ir) and a data management system (www.ogdms.iranopendata.ir) are developed to showcase the proposed solution. Findings The efficiency and the applicability of the solution are evaluated by a real-life use case on energy consumption of the buildings of the city of Tehran, Iran. Finally, a comparison was made with existing solutions, and the results show the proposed approach is able to address the existing gaps in the literature. Originality/value The results imply that modeling and designing the data model, as well as exploiting an ontology-based approach are critical pillars to create rich, relevant and well-described OGD data sets. Moreover, clarity on processes, roles and responsibilities are the key factors influencing the quality of the published data services. Thus, to the best of the knowledge, this is the first study that exploits and considers an ontology-based approach in a top-down manner to create OGD data sets.

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Emerging Evidences for an Implication of the Neurodegeneration-Associated Protein TAU in Cancer

Brain Sciences ◽

10.3390/brainsci10110862 ◽

2020 ◽

Vol 10 (11) ◽

pp. 862

Author(s):

Stéphanie Papin ◽

Paolo Paganetti

Keyword(s):

Neurodegenerative Disorders ◽

Neurodegenerative Disorder ◽

Inverse Correlation ◽

Epidemiologic Studies ◽

Point Of View ◽

Published Data ◽

Cancer Resistance ◽

Microtubule Network ◽

Mapt Gene

Neurodegenerative disorders and cancer may appear unrelated illnesses. Yet, epidemiologic studies indicate an inverse correlation between their respective incidences for specific cancers. Possibly explaining these findings, increasing evidence indicates that common molecular pathways are involved, often in opposite manner, in the pathogenesis of both disease families. Genetic mutations in the MAPT gene encoding for TAU protein cause an inherited form of frontotemporal dementia, a neurodegenerative disorder, but also increase the risk of developing cancer. Assigning TAU at the interface between cancer and neurodegenerative disorders, two major aging-linked disease families, offers a possible clue for the epidemiological observation inversely correlating these human illnesses. In addition, the expression level of TAU is recognized as a prognostic marker for cancer, as well as a modifier of cancer resistance to chemotherapy. Because of its microtubule-binding properties, TAU may interfere with the mechanism of action of taxanes, a class of chemotherapeutic drugs designed to stabilize the microtubule network and impair cell division. Indeed, a low TAU expression is associated to a better response to taxanes. Although TAU main binding partners are microtubules, TAU is able to relocate to subcellular sites devoid of microtubules and is also able to bind to cancer-linked proteins, suggesting a role of TAU in modulating microtubule-independent cellular pathways associated to oncogenesis. This concept is strengthened by experimental evidence linking TAU to P53 signaling, DNA stability and protection, processes that protect against cancer. This review aims at collecting literature data supporting the association between TAU and cancer. We will first summarize the evidence linking neurodegenerative disorders and cancer, then published data supporting a role of TAU as a modifier of the efficacy of chemotherapies and of the oncogenic process. We will finish by addressing from a mechanistic point of view the role of TAU in de-regulating critical cancer pathways, including the interaction of TAU with cancer-associated proteins.

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Mobile Robotic Sensors for Environmental Monitoring using Gaussian Markov Random Field

Robotica ◽

10.1017/s026357472000079x ◽

2020 ◽

pp. 1-23

Author(s):

Linh Nguyen ◽

Sarath Kodagoda ◽

Ravindra Ranasinghe ◽

Gamini Dissanayake

Keyword(s):

Random Field ◽

Markov Random Field ◽

Adaptive Sampling ◽

Published Data ◽

Data Sets ◽

Independence Property ◽

Gaussian Markov Random Field ◽

Markov Random ◽

Sampling Optimization ◽

Robotic Sensors

SUMMARY This paper addresses the issue of monitoring spatial environmental phenomena of interest utilizing information collected by a network of mobile, wireless, and noisy sensors that can take discrete measurements as they navigate through the environment. It is proposed to employ Gaussian Markov random field (GMRF) represented on an irregular discrete lattice by using the stochastic partial differential equations method to model the physical spatial field. It then derives a GMRF-based approach to effectively predict the field at unmeasured locations, given available observations, in both centralized and distributed manners. Furthermore, a novel but efficient optimality criterion is then proposed to design centralized and distributed adaptive sampling strategies for the mobile robotic sensors to find the most informative sampling paths in taking future measurements. By taking advantage of conditional independence property in the GMRF, the adaptive sampling optimization problem is proven to be resolved in a deterministic time. The effectiveness of the proposed approach is compared and demonstrated using pre-published data sets with appealing results.

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Dive times for foraging dugongs in the Northern Territory.

Australian Mammalogy ◽

10.1071/am01167 ◽

2001 ◽

Vol 23 (2) ◽

pp. 167 ◽

Cited By ~ 4

Author(s):

SD Whiting

Keyword(s):

Northern Territory ◽

Published Data ◽

Data Sets ◽

Dive Behaviour ◽

Direct Observations ◽

In The Wild ◽

Observer Effects

THERE are few published studies of dive times of dugongs (Dugong dugon). Direct observations are problematic because D. dugon are shy and difficult to observe in the wild from boats without creating observer effects. Time Depth Recorders (TDR?s) can record dive and surface times during dive behaviour, but there are no published data as yet for D. dugon using this technology. Although studies on dive times using Time Depth Recorders (TDR?s) result in larger data sets, their results are difficult to relate to particular behaviours such as foraging. This paper provides submergence and surface interval times for D. dugon obtained by direct observations in Darwin Harbour. Direct observations, although time consuming, can produce important information related to the ecology of D. dugon.

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RUNX1-mutated families show phenotype heterogeneity and a somatic mutation profile unique to germline predisposed AML

Blood Advances ◽

10.1182/bloodadvances.2019000901 ◽

2020 ◽

Vol 4 (6) ◽

pp. 1131-1144 ◽

Cited By ~ 8

Author(s):

Anna L. Brown ◽

Peer Arts ◽

Catherine L. Carmichael ◽

Milena Babic ◽

Julia Dobbins ◽

...

Keyword(s):

Somatic Mutations ◽

Published Data ◽

Data Sets ◽

Gene Deletions ◽

Phenotypic Differences ◽

Recurrent Mutations ◽

Platelet Disorder ◽

Related Transcription Factor ◽

Phenotype Heterogeneity ◽

Familial Platelet Disorder

Abstract First reported in 1999, germline runt-related transcription factor 1 (RUNX1) mutations are a well-established cause of familial platelet disorder with predisposition to myeloid malignancy (FPD-MM). We present the clinical phenotypes and genetic mutations detected in 10 novel RUNX1-mutated FPD-MM families. Genomic analyses on these families detected 2 partial gene deletions, 3 novel mutations, and 5 recurrent mutations as the germline RUNX1 alterations leading to FPD-MM. Combining genomic data from the families reported herein with aggregated published data sets resulted in 130 germline RUNX1 families, which allowed us to investigate whether specific germline mutation characteristics (type, location) could explain the large phenotypic heterogeneity between patients with familial platelet disorder and different HMs. Comparing the somatic mutational signatures between the available familial (n = 35) and published sporadic (n = 137) RUNX1-mutated AML patients showed enrichment for somatic mutations affecting the second RUNX1 allele and GATA2. Conversely, we observed a decreased number of somatic mutations affecting NRAS, SRSF2, and DNMT3A and the collective genes associated with CHIP and epigenetic regulation. This is the largest aggregation and analysis of germline RUNX1 mutations performed to date, providing a unique opportunity to examine the factors underlying phenotypic differences and disease progression from FPD to MM.

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Spatial Differences in the Chemical Composition of Surface Water in the Hornsund Fjord Area: A Statistical Analysis with A Focus on Local Pollution Sources

Water ◽

10.3390/w12020496 ◽

2020 ◽

Vol 12 (2) ◽

pp. 496

Author(s):

Krystyna Koziol ◽

Marek Ruman ◽

Filip Pawlak ◽

Stanisław Chmiel ◽

Żaneta Polkowska

Keyword(s):

Chemical Composition ◽

Surface Water ◽

Human Activity ◽

Principal Component ◽

Inverse Correlation ◽

Published Data ◽

Pollution Transport ◽

Local Pollution ◽

Water Composition ◽

Spatial Differences

Surface catchments in Svalbard are sensitive to external pollution, and yet what is frequently considered external contamination may originate from local sources and natural processes. In this work, we analyze the chemical composition of surface waters in the catchments surrounding the Polish Polar Station in Svalbard, Hornsund fjord area. We have pooled unpublished and already published data describing surface water composition in 2010, related to its pH, electrical conductivity (EC), metals and metalloids, total organic carbon (TOC) and selected organic compound concentrations, including persistent organic pollutants (POPs) and surfactants. These data were statistically analyzed for spatial differences, using Kruskal–Wallis ANOVA and principal component analysis (PCA), with distance from the station in the PCA approximating local human activity impact. The geological composition of the substratum was found to be a strong determinant of metal and metalloid concentrations, sufficient to explain significant differences between the studied water bodies, except for the concentration of Cr. The past and present human activity in the area may have contributed also to some of the polycyclic aromatic hydrocarbons (PAHs), although only in the case of naphthalene can such an effect be confirmed by an inverse correlation with distance from the station. Other likely factors contributing to the chemical concentrations in the local waters are marine influence, long-range pollution transport and release from past deposition in the environment.

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