scholarly journals Evolution of degrees of carnivory and dietary specialization across Mammalia and their effects on speciation

2021 ◽  
Author(s):  
Matthew D. Pollard ◽  
Emily E. Puckett
Keyword(s):  
Information Loss ◽  
Food Resources ◽  
Continuous Variables ◽  
Dietary Specialization ◽  
Speciation Rate ◽  
Speciation Rates ◽  
The Continuum ◽  
Continuous Traits

ABSTRACTConflation between omnivory and dietary generalism limits ecological and evolutionary analyses of diet, including estimating contributions to speciation and diversification. Additionally, categorizing species into qualitative dietary classes leads to information loss in these analyses. Here, we constructed two continuous variables – degree of carnivory (i.e., the position along the continuum from complete herbivory to complete carnivory) and degree of dietary specialization (i.e., the number and variety of food resources utilized) – to elucidate their histories across Mammalia, and to tease out their independent contributions to mammalian speciation. We observed that degree of carnivory significantly affected speciation rate across Mammalia, whereas dietary specialization did not. We further considered phylogenetic scale in diet-dependent speciation and saw that degree of carnivory significantly affected speciation in ungulates, carnivorans, bats, eulipotyphlans, and marsupials, while the effect of dietary specialization was only significant in carnivorans. Across Mammalia, omnivores had the lowest speciation rates. Our analyses using two different categorical diet variables led to contrasting signals of diet-dependent diversification, and subsequently different conclusions regarding diet’s macroevolutionary role. We argue that treating variables such as diet as continuous instead of categorical reduces information loss and avoids the problem of contrasting macroevolutionary signals caused by differential discretization of biologically continuous traits.

scholarly journals What affects power to estimate speciation rate shifts?

2018 ◽  
Author(s):  
Ullasa Kodandaramaiah ◽  
Gopal Murali
Keyword(s):  
Evolutionary Biology ◽  
Ecological Factors ◽  
Tree Age ◽  
Character State ◽  
Speciation Rate ◽  
Relative Age ◽  
Rate Shift ◽  
Rate Asymmetry ◽  
Bias Ratio ◽  
Speciation Rates

The development of methods to estimate rates of speciation and extinction from time- calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.

scholarly journals Consequences of the COVID-19 pandemic on the continuum of the care in a cohort of people living with HIV followed in a single center of Northern Italy

2020 ◽  
Author(s):  
Eugenia Quiros-Roldan ◽  
Paola Magro ◽  
Canio Carriero ◽  
Annacarla Chiesa ◽  
Issa El Hamad ◽  
...  
Keyword(s):  
Antiretroviral Drugs ◽  
Hiv Care ◽  
Categorical Variables ◽  
People Living With Hiv ◽  
Continuous Variables ◽  
Hiv Diagnosis ◽  
Missed Visits ◽  
Hiv Continuum Of Care ◽  
Living With Hiv ◽  
The Continuum

Abstract Introduction: During the COVID-19 pandemic, hospitals faced increasing pressure, where people living with HIV risked to either acquire SARS-CoV-2 and to interrupt the HIV continuum of care.Methods: this is a retrospective, observational study. We compared the numbers of medical visits performed, antiretroviral drugs dispensed and the number of new HIV diagnosis and of hospitalizations in a cohort of people living with HIV (PLWH) followed by the Spedali Civili of Brescia between the bimester of the COVID-19 pandemic peak and the bimester of October-November 2019. Data were retrieved from administrative files and from paper and electronic clinical charts. Categorical variables were described using frequencies and percentages, while continuous variables were described using mean, median, and interquartile range (IQR) values. Means for continuous variables were compared using Student’s t-tests and the Mann-Whitney test. Proportions for categorical variables were compared using the χ2 test.Results: As of December 31st, 2019, a total of 3875 PLWH were followed in our clinic. Mean age was 51,4 ±13 years old, where 28% were females and 18.8% non-Italian. Overall, 98.9% were on ART (n=3834), 93% were viro-suppressed. A total of 1217 and 1162 patients had their visit scheduled at our out-patient HIV clinic during the two bimesters of 2019 and 2020, respectively. Comparing the two periods, we observed a raise of missed visits from 5% to 8% (p<0.01), a reduction in the number of new HIV diagnosis from 6.4 in 2019 to 2.5 per month in 2020 (p=0.01), a drop in ART dispensation and an increase of hospitalized HIV patients due to COVID-19. ART regimens including protease inhibitors (PIs) had a smaller average drop than ART not including PIs (16,6% vs 21,6%, p<0.05). Whether this may be due to the perception of a possible efficacy of PIs on COVID19 is not known. Conclusions: Our experience highlights the importance of a resilient healthcare system and the need to implement new strategies in order to guarantee the continuum of HIV care even in the context of emergency.

scholarly journals Positive association between population genetic differentiation and speciation rates in New World birds

2017 ◽  
Vol 114 (24) ◽  
pp. 6328-6333 ◽  
Author(s):  
Michael G. Harvey ◽  
Glenn F. Seeholzer ◽  
Brian Tilston Smith ◽  
Daniel L. Rabosky ◽  
Andrés M. Cuervo ◽  
...  
Keyword(s):  
Population Differentiation ◽  
New World ◽  
Bird Species ◽  
Positive Association ◽  
Tropical Species ◽  
Implicit Assumption ◽  
Speciation Rate ◽  
Population Genetic Differentiation ◽  
Evolutionary Diversification ◽  
Speciation Rates

An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from 173 New World bird species (>17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity.

scholarly journals Tree size and relative clade age influence estimation of speciation rate shifts

2017 ◽  
Author(s):  
Ullasa Kodandaramaiah ◽  
Gopal Murali
Keyword(s):  
Evolutionary Biology ◽  
Ecological Factors ◽  
Diversification Rate ◽  
Tree Age ◽  
Speciation Rate ◽  
Rate Shift ◽  
Rate Asymmetry ◽  
Speciation Rates ◽  
Estimate Rate ◽  
Type Ii Errors

The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. We use rigorous simulations to evaluate the statistical performance of three widely used modelling approaches - BiSSE, BAMM and MEDUSA - in relation to detection of speciation rates shifts. We simulated sets of trees with each tree having a single increase in speciation rate. We varied the location of shifts, the degree of increase in speciation rate and the total age of the tree. We then used BiSSE, BAMM and MEDUSA to estimate rate shifts. For BiSSE, we assigned different character states for the lineages with different simulated speciation rates. We show that all methods are better at detecting rate shifts when the change in speciation rate is higher, but had high Type II errors (non-detection of rate shifts). While the algorithms more accurately identified rate shifts close to the root of the tree, both perform poorly when the rate shift occurred more recently. All methods performed better with increase in the overall number of tips and the number of tips in the clade with rate shift, both of which are correlated with tree age and speciation rate asymmetry. We discuss the implications of this study for the use and development of methods for hypothesis testing based on diversification rate shifts.

Clinical Pathways for the Continuum of Rehabilitation

2014 ◽  
Author(s):  
Karen Hoffman ◽  
Amanda Thomas ◽  
Stephen Brett
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Clinical Pathways ◽  
Information Loss ◽  
System Failure ◽  
Nursing Support ◽  
Serious Illness ◽  
Intensive Care Patients ◽  
Major Illness ◽  
The Continuum

People who experience major illness or injury commonly are admitted to an intensive care unit, yet it is important to recognize that the intensive care unit is merely one part of a journey from the onset of illness or injury to recovery and subsequent rebuilding of life. This journey is characterized by a number of changes in the level of medical and nursing support, location, team, and often focus of care. These ‘way points’ on this journey to recovery represent opportunities for system failure and loss of key pieces of information. The patient-centred focus on treatment and recovery can be compromised by organizational deficits. What is recognized in many clinical fields is the requirement to assemble a continuum of care which anticipates these way points and minimizes the chances of information loss. These organized processes are termed clinical pathways and can be applied to patients recovering from serious illness or injury characterized by a stay in an intensive care unit. This chapter outlines the rationale and background of this concept and how it might be applied in practice for the benefit of recovering intensive care patients.

scholarly journals Ecological causes of uneven speciation and species richness in mammals

2019 ◽  
Author(s):  
Nathan S. Upham ◽  
Jacob A. Esselstyn ◽  
Walter Jetz
Keyword(s):  
Species Richness ◽  
Species Turnover ◽  
Rate Variation ◽  
Ecological Traits ◽  
Ecological Opportunity ◽  
Diversification Rates ◽  
Speciation Rate ◽  
Diversity Gradient ◽  
Speciation Rates

ABSTRACTBiodiversity is distributed unevenly from the poles to the equator, and among branches of the tree of life, yet how those enigmatic patterns are related is unclear. We investigated global speciation-rate variation across crown Mammalia using a novel time-scaled phylogeny (N=5,911 species, ~70% with DNA), finding that trait- and latitude-associated speciation has caused uneven species richness among groups. We identify 24 branch-specific shifts in net diversification rates linked to ecological traits. Using time-slices to define clades, we show that speciation rates are a stronger predictor of clade richness than age. Speciation is slower in tropical than extra-tropical lineages, but only at the level of clades not species tips, consistent with fossil evidence that the latitudinal diversity gradient may be a relatively young phenomenon in mammals. In contrast, species tip rates are fastest in mammals that are low dispersal or diurnal, consistent with models of ephemeral speciation and ecological opportunity, respectively. These findings juxtapose nested levels of diversification, suggesting a central role of species turnover gradients in generating uneven patterns of modern biodiversity.

scholarly journals Asymmetrical reliability of the Alda Score favours a dichotomous representation of lithium responsiveness

2019 ◽  
Author(s):  
Abraham Nunes ◽  
Thomas Trappenberg ◽  
Martin Alda
Keyword(s):  
Bipolar Disorder ◽  
Theoretical Analysis ◽  
Ground Truth ◽  
Continuous Variable ◽  
Generative Model ◽  
Continuous Variables ◽  
Rater Reliability ◽  
Using Data ◽  
The Relationship ◽  
The Continuum

AbstractThe Alda score is commonly used to quantify lithium responsiveness in bipolar disorder. Most often, this score is dichotomized into “responder” and “non-responder” categories, respectively. This practice is often criticized as inappropriate, since continuous variables are thought to invariably be “more informative” than their dichotomizations. We therefore investigated the degree of informativeness across raw and dichotomized versions of the Alda score, using data from a published study of the scale’s inter-rater reliability (n=59 raters of 12 standardized vignettes each). After learning a generative model for the relationship between observed and ground truth scores (the latter defined by a consensus rating of the 12 vignettes), we show that the dichotomized scale is more robust to inter-rater disagreement than the raw 0-10 scale. Further theoretical analysis shows that when a measure’s reliability is stronger at one extreme of the continuum—a scenario which has received little-to-no statistical attention, but which likely occurs for the Alda score ≥ 7—dichotomization of a continuous variable may be more informative concerning its ground truth value, particularly in the presence of noise. Our study suggests that research employing the Alda score of lithium responsiveness should continue using the dichotomous definition, particularly when data are sampled across multiple raters.

scholarly journals What affects power to estimate speciation rate shifts?

2018 ◽  
Author(s):  
Ullasa Kodandaramaiah ◽  
Gopal Murali
Keyword(s):  
Evolutionary Biology ◽  
Ecological Factors ◽  
Tree Age ◽  
Character State ◽  
Speciation Rate ◽  
Relative Age ◽  
Rate Shift ◽  
Rate Asymmetry ◽  
Bias Ratio ◽  
Speciation Rates

The development of methods to estimate rates of speciation and extinction from time- calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal ecological factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rates, and three modelling methods – BiSSE, MEDUSA and BAMM – have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide some suggestions to users of these methods.

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