The Tempo and Mode of Evolution of Acoustic Communication Signals of Felids

1998 ◽  
Vol 2 (2) ◽  
pp. 233-248 ◽  
Author(s):  
Gustav Peters ◽  
Barbara A. Tonkin-Leyhausen
Keyword(s):  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Acoustic Communication ◽  
Time Scale ◽  
Evolutionary Process ◽  
Time Frame ◽  
Evolutionary Change ◽  
Clock Model ◽  
Communication Signals ◽  
Molecular Clock Model

Based on the molecular clock model of evolution, molecular phylogenies represent reconstructions of the evolutionary process with a time scale. From these, inferences can be drawn about the evolution of other characters, including behaviour patterns. Mapping particular vocalization types in the Felidae (cats) on a published molecular phylogeny of this mammal family reveals that the distribution of these behavioural characters is fully congruent with it. Thence a time frame for the evolution of these vocalizations can be inferred, indicating large differences in their evolutionary age. Phylogenetic stasis for several million years in particular vocalization types refutes the hypothesis that behavioural characters are generally more susceptible to evolutionary change than morphological ones.

scholarly journals Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies

2020 ◽  
Vol 38 (1) ◽  
pp. 307-317
Author(s):  
Xavier Didelot ◽  
Igor Siveroni ◽  
Erik M Volz
Keyword(s):  
Molecular Clock ◽  
Real Data ◽  
Evolutionary Rates ◽  
Data Sets ◽  
Clock Rate ◽  
Clock Model ◽  
Genomic Epidemiology ◽  
Molecular Clock Model ◽  
Clock Models ◽  
Relaxed Clock

Abstract Phylogenetic dating is one of the most powerful and commonly used methods of drawing epidemiological interpretations from pathogen genomic data. Building such trees requires considering a molecular clock model which represents the rate at which substitutions accumulate on genomes. When the molecular clock rate is constant throughout the tree then the clock is said to be strict, but this is often not an acceptable assumption. Alternatively, relaxed clock models consider variations in the clock rate, often based on a distribution of rates for each branch. However, we show here that the distributions of rates across branches in commonly used relaxed clock models are incompatible with the biological expectation that the sum of the numbers of substitutions on two neighboring branches should be distributed as the substitution number on a single branch of equivalent length. We call this expectation the additivity property. We further show how assumptions of commonly used relaxed clock models can lead to estimates of evolutionary rates and dates with low precision and biased confidence intervals. We therefore propose a new additive relaxed clock model where the additivity property is satisfied. We illustrate the use of our new additive relaxed clock model on a range of simulated and real data sets, and we show that using this new model leads to more accurate estimates of mean evolutionary rates and ancestral dates.

scholarly journals Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

2017 ◽  
Vol 114 (35) ◽  
pp. E7282-E7290 ◽  
Author(s):  
Liang Liu ◽  
Jin Zhang ◽  
Frank E. Rheindt ◽  
Fumin Lei ◽  
Yanhua Qu ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Mass Extinction ◽  
Sensitivity Analyses ◽  
Divergence Times ◽  
Delayed Response ◽  
Clock Model ◽  
Molecular Clock Model ◽  
Shift Analysis ◽  
Continuous Radiation ◽  
Genome Scale

The timing of the diversification of placental mammals relative to the Cretaceous–Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.

scholarly journals Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

2012 ◽  
Vol 29 (9) ◽  
pp. 2157-2167 ◽  
Author(s):  
Guy Baele ◽  
Philippe Lemey ◽  
Trevor Bedford ◽  
Andrew Rambaut ◽  
Marc A. Suchard ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Model Comparison ◽  
Clock Model ◽  
Molecular Clock Model

scholarly journals Understanding the Overdispersed Molecular Clock

Genetics ◽  
2000 ◽  
Vol 154 (3) ◽  
pp. 1403-1417 ◽  
Author(s):  
David J Cutler
Keyword(s):  
Molecular Evolution ◽  
Molecular Clock ◽  
Time Scale ◽  
Population Parameter ◽  
Deleterious Mutations ◽  
Slow Time ◽  
Slow Time Scale ◽  
Key Population ◽  
Protein Encoding ◽  
Rates Of Molecular Evolution

Abstract Rates of molecular evolution at some protein-encoding loci are more irregular than expected under a simple neutral model of molecular evolution. This pattern of excessive irregularity in protein substitutions is often called the “overdispersed molecular clock” and is characterized by an index of dispersion, R(T) > 1. Assuming infinite sites, no recombination model of the gene R(T) is given for a general stationary model of molecular evolution. R(T) is shown to be affected by only three things: fluctuations that occur on a very slow time scale, advantageous or deleterious mutations, and interactions between mutations. In the absence of interactions, advantageous mutations are shown to lower R(T); deleterious mutations are shown to raise it. Previously described models for the overdispersed molecular clock are analyzed in terms of this work as are a few very simple new models. A model of deleterious mutations is shown to be sufficient to explain the observed values of R(T). Our current best estimates of R(T) suggest that either most mutations are deleterious or some key population parameter changes on a very slow time scale. No other interpretations seem plausible. Finally, a comment is made on how R(T) might be used to distinguish selective sweeps from background selection.

scholarly journals Testing the spatial and temporal framework of speciation in an ancient lake species flock: the leech genus <i>Dina</i> (Hirudinea: Erpobdellidae) in Lake Ohrid

2010 ◽  
Vol 7 (11) ◽  
pp. 3387-3402 ◽  
Author(s):  
S. Trajanovski ◽  
C. Albrecht ◽  
K. Schreiber ◽  
R. Schultheiß ◽  
T. Stadler ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Abiotic Factors ◽  
Time Frame ◽  
Recent Common Ancestor ◽  
Species Flock ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
Most Recent Common Ancestor ◽  
Extant Species

Abstract. Ancient Lake Ohrid on the Balkan Peninsula is considered to be the oldest ancient lake in Europe with a suggested Plio-/Pleistocene age. Its exact geological age, however, remains unknown. Therefore, molecular clock data of Lake Ohrid biota may serve as an independent constraint of available geological data, and may thus help to refine age estimates. Such evolutionary data may also help unravel potential biotic and abiotic factors that promote speciation events. Here, mitochondrial sequencing data of one of the largest groups of endemic taxa in the Ohrid watershed, the leech genus Dina, is used to test whether it represents an ancient lake species flock, to study the role of potential horizontal and vertical barriers in the watershed for evolutionary events, to estimate the onset of diversification in this group based on molecular clock analyses, and to compare this data with data from other endemic species for providing an approximate time frame for the origin of Lake Ohrid. Based on the criteria speciosity, monophyly and endemicity, it can be concluded that Dina spp. from the Ohrid watershed, indeed, represents an ancient lake species flock. Lineage sorting of its species, however, does not seem to be complete and/or hybridization may occur. Analyses of population structures of Dina spp. in the Ohrid watershed indicate a horizontal zonation of haplotypes from spring and lake populations, corroborating the role of lake-side springs, particularly the southern feeder springs, for evolutionary processes in endemic Ohrid taxa. Vertical differentiation of lake taxa, however, appears to be limited, though differences between populations from the littoral and the profundal are apparent. Molecular clock analyses indicate that the most recent common ancestor of extant species of this flock is approximately 1.99 ± 0.83 million years (Ma) old, whereas the split of the Ohrid Dina flock from a potential sister taxon outside the lake is estimated at 8.30 ± 3.60 Ma. Comparisons with other groups of endemic Ohrid species indicated that in all cases, diversification within the watershed started ≤2 Ma ago. Thus, this estimate may provide information on a minimum age for the origin of Lake Ohrid. Maximum ages are less consistent and generally less reliable. But cautiously, a maximum age of 3 Ma is suggested. Interestingly, this time frame of approximately 2–3 Ma ago for the origin of Lake Ohrid, generated based on genetic data, well fits the time frame most often used in the literature by geologists.

scholarly journals Eco-evolutionary dynamics

2009 ◽  
Vol 364 (1523) ◽  
pp. 1483-1489 ◽  
Author(s):  
F. Pelletier ◽  
D. Garant ◽  
A.P. Hendry
Keyword(s):  
Time Scale ◽  
Evolutionary Dynamics ◽  
Evolutionary Change ◽  
Ecological Change ◽  
Evolutionary Changes ◽  
Microevolutionary Change ◽  
Theoretical Developments ◽  
Rapid Evolutionary Change

Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.

Mate call as reward: Acoustic communication signals can acquire positive reinforcing values during adulthood in female zebra finches (Taeniopygia guttata).

2016 ◽  
Vol 130 (1) ◽  
pp. 36-43 ◽  
Author(s):  
Alexandra M. Hernandez ◽  
Emilie C. Perez ◽  
Hervé Mulard ◽  
Nicolas Mathevon ◽  
Clémentine Vignal
Keyword(s):  
Acoustic Communication ◽  
Taeniopygia Guttata ◽  
Zebra Finches ◽  
Communication Signals

scholarly journals Postmodernism, Postmodernist Fiction, Apocalypse and Fantasy

2019 ◽  
pp. 1-8
Author(s):  
Dr. S. Z. Abbas
Keyword(s):  
Temporal Logic ◽  
Time Scale ◽  
Historical Perspective ◽  
Time Frame ◽  
Experimental Techniques ◽  
Modern Literature ◽  
True Nature ◽  
Avant Garde

Terms like 'modern', 'postmodern' and 'contemporary' are subject-centered, and not based on any historical or objective phenomenon or personality. Everyone feels that something called 'Postmodernism' has happened, but, as regards its true nature and causes, opinion is divided; a few people say postmodernism is a fiction. There is also a problem with the nomenclature. What was referred to as 'contemporary', for example, in 1956 by the writers of that year will not be so to the generation of Y2K. All these terms tend to shift about what is known as PP in temporal logic, which itself keeps moving on the time scale. When we rename modern literature as the age of T.S. Eliot, we assign it a slot in the historical perspective. A further complication is created by the use of ‘modern’ and 'modernist', ‘postmodern’ and ‘postmodernist' as well as ‘contemporary.’ We may, perhaps, safely assume that its element in each case signifies the avant-garde, a group of authors in the respective period that is distinguished by experimentation and innovation. While attempts to accord the postmodern period a definitive time frame (which includes the postmodernist movement in arts and literature) remain in an inconclusive stage, let us assume that postmodernism encompasses the period from the fifties to the present time, which is open-endeded. It should also be noted that some postmodernist writers concentrate on new tones and new reality rather than experimental techniques.

scholarly journals Testing the spatial and temporal framework of speciation in an ancient lake species flock: the leech genus <i>Dina</i> (Hirudinea: Erpobdellidae) in Lake Ohrid

2010 ◽  
Vol 7 (4) ◽  
pp. 5011-5045 ◽  
Author(s):  
S. Trajanovski ◽  
C. Albrecht ◽  
K. Schreiber ◽  
R. Schultheiß ◽  
T. Stadler ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Abiotic Factors ◽  
Time Frame ◽  
Recent Common Ancestor ◽  
Species Flock ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
Most Recent Common Ancestor ◽  
Extant Species

Abstract. Ancient Lake Ohrid on the Balkan Peninsula is considered to be the oldest ancient lake in Europe with a suggested Plio-Pleistocene age. Its exact geological age, however, remains unknown. Therefore, molecular clock data of Lake Ohrid biota may serve as an independent constraint of available geological data, and may thus also help to refine age estimates. Such evolutionary data may also help unravel potential biotic and abiotic factors that promote speciation events. Here, mitochondrial sequencing data of one of the largest groups of endemic taxa in Lake Ohrid, the leech genus Dina, is used to test whether it represents an ancient lake species flock, to study the role of horizontal and vertical barriers in Lake Ohrid for evolutionary events, to estimate the onset of intralacustrine diversification in this group based on molecular clock analyses, and to compare this data with data from other endemic species for providing an approximate time frame for the origin of Lake Ohrid. Based on the criteria speciosity, monophyly and endemicity, it can be concluded that Lake Ohrid Dina, indeed, represents an ancient lake species flock. Lineage sorting of its species, however, does not seem to be complete. Analyses of population structures of Dina spp. in the Ohrid watershed indicate a horizontal zonation of haplotypes from spring and lake populations, corroborating the role of lake-side springs, particularly the southern feeder springs, for evolutionary processes in endemic Ohrid taxa. Vertical differentiation of lake taxa, however, appears to be limited, though differences between populations from the littoral and the profundal are apparent. Molecular clock analyses indicate that the most recent common ancestor of extant species of this flock is approximately 1.99±0.83 Ma old, whereas the split of the Lake Ohrid Dina flock from a potential sister taxon outside the lake is estimated at 8.30±3.60 Ma. Comparisons with other groups of endemic Ohrid species indicated that in all cases, intralacustrine diversification started ≤2 Ma ago. Thus, this estimate may provide information on a minimum age for the origin of Lake Ohrid. Maximum ages are less consistent and generally less reliable. But cautiously, a maximum age of 3 Ma is suggested. Interestingly, this time frame of approximately 2–3 Ma for the origin of Lake Ohrid, generated based solely on evolutionary data, well fits the time frame most often used in the literature by geologists. Future studies must show whether this concurrence holds true.

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