scholarly journals The impact of the fossils in molecular clocks: an example using chelid turtles

2015 ◽  
Author(s):  
Juan Alfredo Holley ◽  
Néstor Guillermo Basso ◽  
Juliana Sterli
Keyword(s):  
Molecular Clock ◽  
Information Source ◽  
Hierarchical Cluster ◽  
Molecular Data ◽  
Molecular Clocks ◽  
South American ◽  
Fossil Species ◽  
Early Diversification ◽  
Phylogenetic Hypotheses ◽  
The Impact

Background. The clade Chelidae (Testudines, Pleurodira) is a group of fresh water turtles with representatives in Australasia and South America. Its diversity of extant and fossil species is characterized by two recognized morphotypes: the long-necked and the short-necked chelids. So far, the phylogenies constructed over Chelidae differ depending on the information source. While morphology recovers one monophyletic group of long-necked chelids (with South American and Australasian species), the molecular data split the group into South American and Australasian chelids, both as monophyletic sister groups and containing long-necked species. The consequences of this conflict imply the emergence of long-necked chelids (i) one time before the final breakup of Southern Gondwana (≅ 35 Mya) or (ii) independently after this event. Methods. Using BEAST, a set of molecular clock analyses was performed. Seven of these analyses correspond to the molecular hypothesis and thirteen to the morphological hypothesis. So, ten fossils were used as calibration points in different combinations for each hypothesis. The results were statistically compared performing ANOVA and the global similarity was inspected by a hierarchical cluster analysis (HCA). Results. Molecular hypothesis: all the analyses produced an age of the origin of Chelidae, and rising of long neck, older than 35 Mys. Divergence times in the South American clade were generally older than the observed in the Australasian clade. The result of the HCA was: analyses 2, 4 and 5 form a group and the analyses 3, 6 and 7 form another group; the analysis 1 is close related to this last. Morphological hypothesis: the origin of the clade of long-necked chelids predated the 35 Mys in all the analyses except one; however the Chelodina group resulted younger than this age in all the analyses. The HCA yielded two main groups of molecular clock analyses (1, 3, 7, 8, 9, 13 and 2, 4, 6, 10, 11, 12) and one analysis (5) clearly separated of these two. The ANOVA resulted in significant differences for all estimated nodes in both phylogenetic hypotheses. Discussion. Our set of molecular clock analyses suggests an early diversification of the chelid turtles and the raising of the long-necked chelids before the final breakup of Southern Gondwana. However, the appearance of this trait one time or as evolutionary convergence still depends on which phylogenetic scenario is taken into account. Furthermore, our results indicate that the number of calibration points not necessarily improve the precision of estimated nodes. Instead the “quality” of the fossils used as calibrations and its position in the phylogeny, have appreciable impact not only over this parameter, but also over the global evolutionary rate along the tree.

scholarly journals The impact of the fossils in molecular clocks: an example using chelid turtles

2015 ◽  
Author(s):  
Juan Alfredo Holley ◽  
Néstor Guillermo Basso ◽  
Juliana Sterli
Keyword(s):  
Molecular Clock ◽  
Information Source ◽  
Hierarchical Cluster ◽  
Molecular Data ◽  
Molecular Clocks ◽  
South American ◽  
Fossil Species ◽  
Early Diversification ◽  
Phylogenetic Hypotheses ◽  
The Impact

Background. The clade Chelidae (Testudines, Pleurodira) is a group of fresh water turtles with representatives in Australasia and South America. Its diversity of extant and fossil species is characterized by two recognized morphotypes: the long-necked and the short-necked chelids. So far, the phylogenies constructed over Chelidae differ depending on the information source. While morphology recovers one monophyletic group of long-necked chelids (with South American and Australasian species), the molecular data split the group into South American and Australasian chelids, both as monophyletic sister groups and containing long-necked species. The consequences of this conflict imply the emergence of long-necked chelids (i) one time before the final breakup of Southern Gondwana (≅ 35 Mya) or (ii) independently after this event. Methods. Using BEAST, a set of molecular clock analyses was performed. Seven of these analyses correspond to the molecular hypothesis and thirteen to the morphological hypothesis. So, ten fossils were used as calibration points in different combinations for each hypothesis. The results were statistically compared performing ANOVA and the global similarity was inspected by a hierarchical cluster analysis (HCA). Results. Molecular hypothesis: all the analyses produced an age of the origin of Chelidae, and rising of long neck, older than 35 Mys. Divergence times in the South American clade were generally older than the observed in the Australasian clade. The result of the HCA was: analyses 2, 4 and 5 form a group and the analyses 3, 6 and 7 form another group; the analysis 1 is close related to this last. Morphological hypothesis: the origin of the clade of long-necked chelids predated the 35 Mys in all the analyses except one; however the Chelodina group resulted younger than this age in all the analyses. The HCA yielded two main groups of molecular clock analyses (1, 3, 7, 8, 9, 13 and 2, 4, 6, 10, 11, 12) and one analysis (5) clearly separated of these two. The ANOVA resulted in significant differences for all estimated nodes in both phylogenetic hypotheses. Discussion. Our set of molecular clock analyses suggests an early diversification of the chelid turtles and the raising of the long-necked chelids before the final breakup of Southern Gondwana. However, the appearance of this trait one time or as evolutionary convergence still depends on which phylogenetic scenario is taken into account. Furthermore, our results indicate that the number of calibration points not necessarily improve the precision of estimated nodes. Instead the “quality” of the fossils used as calibrations and its position in the phylogeny, have appreciable impact not only over this parameter, but also over the global evolutionary rate along the tree.

scholarly journals The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

2018 ◽  
Author(s):  
Brice A. J. Sarver ◽  
Matthew W. Pennell ◽  
Joseph W. Brown ◽  
Sara Keeble ◽  
Kayla M. Hardwick ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Parameter Estimates ◽  
Molecular Clocks ◽  
Estimation Of Parameters ◽  
Rate Heterogeneity ◽  
Diversification Rates ◽  
The Impact

AbstractComparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the selection of these priors has on the inference of comparative parameters has not been thoroughly investigated. Such uncertainty may systematically bias phylogenetic reconstruction and, subsequently, parameter estimation. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we use BEAST to simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation rates and extinction rates) from these trees. When substitution rate heterogeneity is large, parameter estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

scholarly journals Tips and nodes are complementary not competing approaches to the calibration of molecular clocks

2016 ◽  
Vol 12 (4) ◽  
pp. 20150975 ◽  
Author(s):  
Joseph E. O'Reilly ◽  
Philip C. J. Donoghue
Keyword(s):  
Molecular Clock ◽  
Divergence Time ◽  
Molecular Clocks ◽  
Fossil Species ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Fossil Evidence ◽  
Accuracy And Precision ◽  
Age Constraints ◽  
Age Estimates

Molecular clock methodology provides the best means of establishing evolutionary timescales, the accuracy and precision of which remain reliant on calibration, traditionally based on fossil constraints on clade (node) ages. Tip calibration has been developed to obviate undesirable aspects of node calibration, including the need for maximum age constraints that are invariably very difficult to justify. Instead, tip calibration incorporates fossil species as dated tips alongside living relatives, potentially improving the accuracy and precision of divergence time estimates. We demonstrate that tip calibration yields node calibrations that violate fossil evidence, contributing to unjustifiably young and ancient age estimates, less precise and (presumably) accurate than conventional node calibration. However, we go on to show that node and tip calibrations are complementary, producing meaningful age estimates, with node minima enforcing realistic ages and fossil tips interacting with node calibrations to objectively define maximum age constraints on clade ages. Together, tip and node calibrations may yield evolutionary timescales that are better justified, more precise and accurate than either calibration strategy can achieve alone.

scholarly journals Tectonic blocks and molecular clocks

2016 ◽  
Vol 371 (1699) ◽  
pp. 20160098 ◽  
Author(s):  
Kenneth De Baets ◽  
Alexandre Antonelli ◽  
Philip C. J. Donoghue
Keyword(s):  
New Zealand ◽  
Atlantic Ocean ◽  
Molecular Clock ◽  
Phylogenetic Trees ◽  
Molecular Clocks ◽  
Geological Data ◽  
Isthmus Of Panama ◽  
The Impact ◽  
Age Constraints

Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

scholarly journals The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6334 ◽  
Author(s):  
Brice A.J. Sarver ◽  
Matthew W. Pennell ◽  
Joseph W. Brown ◽  
Sara Keeble ◽  
Kayla M. Hardwick ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Molecular Clocks ◽  
Estimation Of Parameters ◽  
Rate Heterogeneity ◽  
Diversification Rates ◽  
The Impact

Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

Infoveillance based on Social Sensors to Analyze the impact of Covid19 in South American Population (Preprint)

2020 ◽  
Author(s):  
Josimar E. Chire Saire
Keyword(s):  
Text Mining ◽  
Electronic Communication ◽  
Spanish Speakers ◽  
South American ◽  
South American Population ◽  
The People ◽  
Data Source ◽  
The Impact ◽  
General Concern ◽  
Social Sensors

BACKGROUND Infoveillance is an application from Infodemiology field with the aim to monitor public health and create public policies. Social sensor is the people providing thought, ideas through electronic communication channels(i.e. Internet). The actual scenario is related to tackle the covid19 impact over the world, many countries have the infrastructure, scientists to help the growth and countries took actions to decrease the impact. South American countries have a different context about Economy, Health and Research, so Infoveillance can be a useful tool to monitor and improve the decisions and be more strategical. The motivation of this work is analyze the capital of Spanish Speakers Countries in South America using a Text Mining Approach with Twitter as data source. The preliminary results helps to understand what happens two weeks ago and opens the analysis from different perspectives i.e. Economics, Social. OBJECTIVE Analyze the behaviour of South American Capitals in front of covid19 pandemics and show the helpfulness of Text Mining Approach for Infoveillance tasks. METHODS Text Mining process RESULTS - Argentina and Venezuela capitals are the biggest number of post during this period, opposite with Bolivia, Ecuador and Uruguay. - Most relevant users are related to mass media like radio, television or newspapers. - There is a general concern about covid19 but every country talks about different areas: Economics, Health, Environmental Impact. CONCLUSIONS Infoveillance based on Social Sensors with data coming from Twitter can help to understand the trends on the population of the capitals. Besides, it is necessary to filter the posts for processing the text and get insights about frequency, top users, most important terms. This data is useful to analyse the population from different approaches. INTERNATIONAL REGISTERED REPORT RR2-https://doi.org/10.1101/2020.04.06.20055749

scholarly journals An Evaluation Methodology for Interactive Reinforcement Learning with Simulated Users

Biomimetics ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 13
Author(s):  
Adam Bignold ◽  
Francisco Cruz ◽  
Richard Dazeley ◽  
Peter Vamplew ◽  
Cameron Foale
Keyword(s):  
Reinforcement Learning ◽  
Information Source ◽  
Human Interaction ◽  
Evaluation Methodology ◽  
External Information ◽  
Preliminary Evaluation ◽  
Learning Agents ◽  
Learning Agent ◽  
Knowledge Bias ◽  
The Impact

Interactive reinforcement learning methods utilise an external information source to evaluate decisions and accelerate learning. Previous work has shown that human advice could significantly improve learning agents’ performance. When evaluating reinforcement learning algorithms, it is common to repeat experiments as parameters are altered or to gain a sufficient sample size. In this regard, to require human interaction every time an experiment is restarted is undesirable, particularly when the expense in doing so can be considerable. Additionally, reusing the same people for the experiment introduces bias, as they will learn the behaviour of the agent and the dynamics of the environment. This paper presents a methodology for evaluating interactive reinforcement learning agents by employing simulated users. Simulated users allow human knowledge, bias, and interaction to be simulated. The use of simulated users allows the development and testing of reinforcement learning agents, and can provide indicative results of agent performance under defined human constraints. While simulated users are no replacement for actual humans, they do offer an affordable and fast alternative for evaluative assisted agents. We introduce a method for performing a preliminary evaluation utilising simulated users to show how performance changes depending on the type of user assisting the agent. Moreover, we describe how human interaction may be simulated, and present an experiment illustrating the applicability of simulating users in evaluating agent performance when assisted by different types of trainers. Experimental results show that the use of this methodology allows for greater insight into the performance of interactive reinforcement learning agents when advised by different users. The use of simulated users with varying characteristics allows for evaluation of the impact of those characteristics on the behaviour of the learning agent.

scholarly journals Loose Ends in the Cortinarius Phylogeny: Five New Myxotelamonoid Species Indicate a High Diversity of These Ectomycorrhizal Fungi with South American Nothofagaceae

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 420
Author(s):  
María Eugenia Salgado Salomón ◽  
Carolina Barroetaveña ◽  
Tuula Niskanen ◽  
Kare Liimatainen ◽  
Matthew E. Smith ◽  
...  
Keyword(s):  
New Species ◽  
Current Knowledge ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Global Scale ◽  
South American ◽  
Edible Fungi ◽  
Rdna Its ◽  
Morphological And Molecular Data ◽  
High Diversity

This paper is a contribution to the current knowledge of taxonomy, ecology and distribution of South American Cortinarius (Pers.) Gray. Cortinarius is among the most widely distributed and species-rich basidiomycete genera occurring with South American Nothofagaceae and species are found in many distinct habitats, including shrublands and forests. Due to their ectomycorrhizal role, Cortinarius species are critical for nutrient cycling in forests, especially at higher latitudes. Some species have also been reported as edible fungi with high nutritional quality. Our aim is to unravel the taxonomy of selected Cortinarius belonging to phlegmacioid and myxotelamonioid species based on morphological and molecular data. After widely sampling Cortinarius specimens in Patagonian Nothofagaceae forests and comparing them to reference collections (including holotypes), we propose five new species of Cortinarius in this work. Phylogenetic analyses of concatenated rDNA ITS-LSU and RPB1 sequences failed to place these new species into known Cortinarius sections or lineages. These findings highlight our knowledge gaps regarding the fungal diversity of South American Nothofagaceae forests. Due to the high diversity of endemic Patagonian taxa, it is clear that the South American Cortinarius diversity needs to be discovered and described in order to understand the evolutionary history of Cortinarius on a global scale.

Impact of word-of-mouth, job attributes and relationship strength on employer attractiveness

2019 ◽  
Vol 42 (6) ◽  
pp. 721-739 ◽  
Author(s):  
Faiz Ahamad
Keyword(s):  
Social Media ◽  
Word Of Mouth ◽  
Information Source ◽  
Differential Impact ◽  
Content Type ◽  
Job Attributes ◽  
Relationship Strength ◽  
Job Information ◽  
Employer Attractiveness ◽  
The Impact

Purpose Job information through word-of-mouth (WOM) has a crucial impact on employer attractiveness. The phenomenal rise of social media offers alternate WOM platforms for sharing job information, which is quite different from traditional face-to-face WOM. The purpose of this paper is to examine the differential impact of traditional word-of-mouth (t-WOM) and social media word-of-mouth (s-WOM) on employer attractiveness along with the difference in the job attributes and relationship strength with the information source. Design/methodology/approach A 2 × 2 × 2 experiment was conducted to examine the impact of information source (t-WOM and s-WOM), job attributes (tangible and intangible) and relationship strength (strong and weak), on employer attractiveness. Source expertise and source trust were treated as the control variable. Findings The result shows the differential impact of t-WOM and s-WOM on employer attractiveness. Moreover, t-WOM from strong relation source found to have a high impact on employer attractiveness than s-WOM. No significant difference due to job attributes was found. Research limitations/implications Use of only positive WOM and not the negative one, student as the subjects, etc. Practical implications The present study suggests using t-WOM and s-WOM to attract talented job seekers. Originality/value This is the first study to analyze the differential impact of t-WOM and s-WOM on employer attractiveness.

Central and Peripheral Clock Control of Circadian Feeding Rhythms

2021 ◽  
pp. 074873042110458
Author(s):  
Carson V. Fulgham ◽  
Austin P. Dreyer ◽  
Anita Nasseri ◽  
Asia N. Miller ◽  
Jacob Love ◽  
...  
Keyword(s):  
Locomotor Activity ◽  
Circadian Clock ◽  
Feeding Behavior ◽  
Molecular Clock ◽  
Fat Body ◽  
Molecular Clocks ◽  
Central Brain ◽  
Feeding Rhythms ◽  
Free Running ◽  
The Brain

Many behaviors exhibit ~24-h oscillations under control of an endogenous circadian timing system that tracks time of day via a molecular circadian clock. In the fruit fly, Drosophila melanogaster, most circadian research has focused on the generation of locomotor activity rhythms, but a fundamental question is how the circadian clock orchestrates multiple distinct behavioral outputs. Here, we have investigated the cells and circuits mediating circadian control of feeding behavior. Using an array of genetic tools, we show that, as is the case for locomotor activity rhythms, the presence of feeding rhythms requires molecular clock function in the ventrolateral clock neurons of the central brain. We further demonstrate that the speed of molecular clock oscillations in these neurons dictates the free-running period length of feeding rhythms. In contrast to the effects observed with central clock cell manipulations, we show that genetic abrogation of the molecular clock in the fat body, a peripheral metabolic tissue, is without effect on feeding behavior. Interestingly, we find that molecular clocks in the brain and fat body of control flies gradually grow out of phase with one another under free-running conditions, likely due to a long endogenous period of the fat body clock. Under these conditions, the period of feeding rhythms tracks with molecular oscillations in central brain clock cells, consistent with a primary role of the brain clock in dictating the timing of feeding behavior. Finally, despite a lack of effect of fat body selective manipulations, we find that flies with simultaneous disruption of molecular clocks in multiple peripheral tissues (but with intact central clocks) exhibit decreased feeding rhythm strength and reduced overall food intake. We conclude that both central and peripheral clocks contribute to the regulation of feeding rhythms, with a particularly dominant, pacemaker role for specific populations of central brain clock cells.

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