scholarly journals Phylogenetic Comparative Methods: A User’s Guide for Paleontologists

2020 ◽  
Author(s):  
Laura Soul ◽  
David Wright
Keyword(s):  
Evolutionary Dynamics ◽  
Comparative Methods ◽  
Model Fit ◽  
Phylogenetic Comparative Methods ◽  
Sources Of Uncertainty ◽  
History Of ◽  
Statistical Approaches ◽  
Evolutionary Tempo And Mode ◽  
Fossil Data ◽  
Analytical Tools

Recent advances in statistical approaches called Phylogenetic Comparative Methods (PCMs) have provided paleontologists with a powerful set of analytical tools for investigating evolutionary tempo and mode in fossil lineages. However, attempts to integrate PCMs with fossil data often present workers with practical challenges or unfamiliar literature. In this paper, we present guides to the theory behind, and application of, PCMs with fossil taxa. Based on an empirical dataset of Paleozoic crinoids, we present example analyses to illustrate common applications of PCMs to fossil data, including investigating patterns of correlated trait evolution, and macroevolutionary models of morphological change. We emphasize the importance of accounting for sources of uncertainty, and discuss how to evaluate model fit and adequacy. Finally, we discuss several promising methods for modelling heterogenous evolutionary dynamics with fossil phylogenies. Integrating phylogeny-based approaches with the fossil record provides a rigorous, quantitative perspective to understanding key patterns in the history of life.

scholarly journals A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes)

2019 ◽  
Vol 286 (1910) ◽  
pp. 20190122 ◽  
Author(s):  
Jenna M. McCullough ◽  
Robert G. Moyle ◽  
Brian T. Smith ◽  
Michael J. Andersen
Keyword(s):  
Evolutionary Dynamics ◽  
Species Tree ◽  
Old World ◽  
Avian Order ◽  
History Of ◽  
The Tropics ◽  
Fossil Data ◽  
Old World Tropics ◽  
New Framework

The evolution of pantropically distributed clades has puzzled palaeo- and neontologists for decades regarding the different hypotheses about where they originated. In this study, we explored how a pantropical distribution arose in a diverse clade with a rich fossil history: the avian order Coraciiformes. This group has played a central role in the debate of the biogeographical history of Neoaves. However, the order lacked a coherent species tree to inform study of its evolutionary dynamics. Here, we present the first complete species tree of Coraciiformes, produced with 4858 ultraconserved elements, which supports two clades: (1) Old World-restricted bee-eaters, rollers and ground-rollers; and (2) New World todies and motmots, and cosmopolitan kingfishers. Our results indicated two pulses of diversification: (1) major lineages of Coraciiformes arose in Laurasia approximately 57 Ma, followed by independent dispersals into equatorial regions, possibly due to tracking tropical habitat into the lower latitudes—the Coracii (Coraciidae + Brachypteraciidae) into the Afrotropics, bee-eaters throughout the Old World tropics, and kingfishers into the Australasian tropics; and (2) diversification of genera in the tropics during the Miocene and Pliocene. Our study supports the important role of Laurasia as the geographical origin of a major pantropical lineage and provides a new framework for comparative analyses in this charismatic bird radiation.

scholarly journals Phylogenetic Comparative Methods can Provide Important Insights into the Evolution of Toxic Weaponry

Toxins ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 518 ◽  
Author(s):  
Kevin Arbuckle
Keyword(s):  
Interdisciplinary Approach ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Perspective ◽  
Venom Composition ◽  
Wide Range ◽  
Ecological View ◽  
Evolutionary View ◽  
Post Hoc ◽  
Analytical Tools

The literature on chemical weaponry of organisms is vast and provides a rich understanding of the composition and mechanisms of the toxins and other components involved. However, an ecological or evolutionary perspective has often been lacking and is largely limited to (1) molecular evolutionary studies of particular toxins (lacking an ecological view); (2) comparisons across different species that ignore phylogenetic relatedness (lacking an evolutionary view); or (3) descriptive studies of venom composition and toxicology that contain post hoc and untested ecological or evolutionary interpretations (a common event but essentially uninformative speculation). Conveniently, comparative biologists have prolifically been developing and using a wide range of phylogenetic comparative methods that allow us to explicitly address many ecological and evolutionary questions relating to venoms and poisons. Nevertheless, these analytical tools and approaches are rarely used and poorly known by biological toxinologists and toxicologists. In this review I aim to (1) introduce phylogenetic comparative methods to the latter audience; (2) highlight the range of questions that can be addressed using them; and (3) encourage biological toxinologists and toxicologists to either seek out adequate training in comparative biology or seek collaboration with comparative biologists to reap the fruits of a powerful interdisciplinary approach to the field.

scholarly journals Evolutionary history of quadrupedal walking gaits shows mammalian release from locomotor constraint

2021 ◽  
Vol 288 (1957) ◽  
pp. 20210937
Author(s):  
Alexa N. Wimberly ◽  
Graham J. Slater ◽  
Michael C. Granatosky
Keyword(s):  
Evolutionary History ◽  
Evolutionary Rate ◽  
Strong Support ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Limb Movements ◽  
Comprehensive Understanding ◽  
Origin And Evolution ◽  
History Of ◽  
Quadrupedal Walking

Vertebrates employ an impressive range of strategies for coordinating their limb movements while walking. Although this gait variation has been quantified and hypotheses for its origins tested in select tetrapod lineages, a comprehensive understanding of gait evolution in a macroevolutionary context is currently lacking. We used freely available internet videos to nearly double the number of species with quantitative gait data, and used phylogenetic comparative methods to test key hypotheses about symmetrical gait origin and evolution. We find strong support for an ancestral lateral-sequence diagonal-couplet gait in quadrupedal gnathostomes, and this mode is remarkably conserved throughout tetrapod phylogeny. Evolutionary rate analyses show that mammals overcame this ancestral constraint, resulting in a greater range of phase values than any other tetrapod lineage. Diagonal-sequence diagonal-couplet gaits are significantly associated with arboreality in mammals, though this relationship is not recovered for other tetrapod lineages. Notably, the lateral-sequence lateral-couplet gait, unique to mammals among extant tetrapods, is not associated with any traditional explanations. The complex drivers of gait diversification in mammals remain unclear, but our analyses suggest that their success was due, in part, to release from a locomotor constraint that has probably persisted in other extant tetrapod lineages for over 375 Myr.

The evolutionary trends of grammatical gender in Indo-Aryan languages

2020 ◽  
pp. 1-30
Author(s):  
Marc Allassonnière-Tang ◽  
Michael Dunn
Keyword(s):  
Historical Linguistic ◽  
Evolutionary Dynamics ◽  
Grammatical Gender ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Trends ◽  
Personal Pronouns ◽  
Demonstrative Pronouns ◽  
Feature Values ◽  
Prior Analysis

Abstract This paper infers the processes of development and change of grammatical gender in Indo-Aryan languages using phylogenetic comparative methods. 48 Indo-Aryan languages are coded based on 44 presence-absence features relating to gender marking on the verbs, adjectives, personal pronouns, demonstrative pronouns, and possessive pronouns. A Bayesian Reverse Jump Hyper Prior analysis, which infers the evolutionary dynamics of changes between feature values, gives results that are consistent with historical linguistic and typological studies on gender systems in Indo-Aryan languages and predicts the evolutionary trends of the features included in the dataset.

scholarly journals Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 808
Author(s):  
Laura Pérez-Lago ◽  
Teresa Aldámiz-Echevarría ◽  
Rita García-Martínez ◽  
Leire Pérez-Latorre ◽  
Marta Herranz ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Evolutionary Dynamics ◽  
Viral Evolution ◽  
Special Focus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
New Variant ◽  
History Of ◽  
Evolution Dynamics ◽  
The Uk

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.

scholarly journals Optimizing Consistency and Coverage in Configurational Causal Modeling

2021 ◽  
pp. 004912412199555
Author(s):  
Michael Baumgartner ◽  
Mathias Ambühl
Keyword(s):  
Model Selection ◽  
Causal Inference ◽  
Comparative Methods ◽  
Causal Models ◽  
Causal Modeling ◽  
Model Fit

Consistency and coverage are two core parameters of model fit used by configurational comparative methods (CCMs) of causal inference. Among causal models that perform equally well in other respects (e.g., robustness or compliance with background theories), those with higher consistency and coverage are typically considered preferable. Finding the optimally obtainable consistency and coverage scores for data [Formula: see text], so far, is a matter of repeatedly applying CCMs to [Formula: see text] while varying threshold settings. This article introduces a procedure called ConCovOpt that calculates, prior to actual CCM analyses, the consistency and coverage scores that can optimally be obtained by models inferred from [Formula: see text]. Moreover, we show how models reaching optimal scores can be methodically built in case of crisp-set and multi-value data. ConCovOpt is a tool, not for blindly maximizing model fit, but for rendering transparent the space of viable models at optimal fit scores in order to facilitate informed model selection—which, as we demonstrate by various data examples, may have substantive modeling implications.

A New Approach to the Modeling of Magnetorheological Dampers and Application to Resonance Control

2021 ◽  
Author(s):  
Dennis A. Siginer ◽  
Mario Letelier ◽  
Juan Sebastián Stockle Henríquez
Keyword(s):  
Flow Pattern ◽  
Yield Stress ◽  
A Priori ◽  
Time History ◽  
Magnetorheological Damper ◽  
Mr Fluid ◽  
Variable Resistance ◽  
History Of ◽  
Displacement Pattern ◽  
Analytical Tools

Abstract A predetermined flow pattern in a magnetorheological damper providing continuously variable resistance to flow is required for efficient damping of a given load. The required predetermined flow pattern rests on the a priori determination of the constitutive properties of the magnetorheological (MR) fluid determined to generate variable resistance to flow. The inverse problem of constructing the predetermined response of the damper with a specific displacement pattern of the piston in the damper for efficient damping of a given load is solved. The magnetorheological (MR) fluid in the damper is modeled as a Bingham phase change material with time dependent yield stress offering continuously variable resistance to the flow in the piston to achieve the required specific displacement pattern. The governing equations are solved for any time history of the dimensionless yield stress of the fluid which in turn is determined from the imposed response of the damper. Analytical tools developed can be used in optimizing damper performance. The application of the method to resonance mitigation is illustrated.

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