scholarly journals Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits

2010 ◽  
Vol 365 (1559) ◽  
pp. 3903-3912 ◽  
Author(s):  
Thomas E. Currie ◽  
Simon J. Greenhill ◽  
Ruth Mace
Keyword(s):  
Cultural Evolution ◽  
Horizontal Transmission ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Ancestral State ◽  
Regression Analyses ◽  
Trait Evolution ◽  
Phylogenetic Methods ◽  
Cultural Traits ◽  
Future Work

Phylogenetic comparative methods (PCMs) provide a potentially powerful toolkit for testing hypotheses about cultural evolution. Here, we build on previous simulation work to assess the effect horizontal transmission between cultures has on the ability of both phylogenetic and non-phylogenetic methods to make inferences about trait evolution. We found that the mode of horizontal transmission of traits has important consequences for both methods. Where traits were horizontally transmitted separately , PCMs accurately reported when trait evolution was not correlated even at the highest levels of horizontal transmission. By contrast, linear regression analyses often incorrectly concluded that traits were correlated. Where simulated trait evolution was not correlated and traits were horizontally transmitted as a pair , both methods inferred increased levels of positive correlation with increasing horizontal transmission. Where simulated trait evolution was correlated, increasing rates of separate horizontal transmission led to decreasing levels of inferred correlation for both methods, but increasing rates of paired horizontal transmission did not. Furthermore, the PCM was also able to make accurate inferences about the ancestral state of traits. These results suggest that under certain conditions, PCMs can be robust to the effects of horizontal transmission. We discuss ways that future work can investigate the mode and tempo of horizontal transmission of cultural traits.

scholarly journals Realistic scenarios of missing taxa in phylogenetic comparative methods and their effects on model selection and parameter estimation

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7917 ◽  
Author(s):  
Rafael S. Marcondes
Keyword(s):  
Parameter Estimation ◽  
Model Selection ◽  
Phylogenetic Signal ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Trait Evolution ◽  
Continuous Trait ◽  
Starting Point ◽  
Almost All ◽  
Future Work

Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree’s terminal taxa, but rarely do a tree and dataset include all taxa within a clade. Because the probability that a taxon is included in a dataset depends on ecological traits that have phylogenetic signal, missing taxa in real datasets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but the problem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work.

scholarly journals The Uses and Abuses of Tree Thinking in Cultural Evolution

2021 ◽  
Author(s):  
Cara Evans ◽  
Simon J. Greenhill ◽  
Joseph Watts ◽  
Johann-Mattis List ◽  
Carlos A. Botero ◽  
...  
Keyword(s):  
Best Practices ◽  
Cultural Evolution ◽  
Cross Cultural ◽  
Tree Thinking ◽  
Phylogenetic Methods ◽  
Cultural Research ◽  
Cross Cultural Research ◽  
Cultural Traits ◽  
Lines Of Evidence ◽  
Over Time

Modern phylogenetic methods are increasingly being used to address questions about macro-level patterns in cultural evolution. These methods can illuminate the unobservable histories of cultural traits and identify the evolutionary drivers of trait-change over time, but their application is not without pitfalls. Here we outline the current scope of research in cultural tree thinking, highlighting a toolkit of best practices to navigate and avoid the pitfalls and ‘abuses’ associated with their application. We emphasise two principles that support the appropriate application of phylogenetic methodologies in cross-cultural research: researchers should (1) draw on multiple lines of evidence when deciding if and which types of phylogenetic methods and models are suitable for their cross-cultural data, and (2) carefully consider how different cultural traits might have different evolutionary histories across space and time. When used appropriately phylogenetic methods can provide powerful insights into the processes of evolutionary change that have shaped the broad patterns of human history.

scholarly journals The uses and abuses of tree thinking in cultural evolution

2021 ◽  
Vol 376 (1828) ◽  
Author(s):  
Cara L. Evans ◽  
Simon J. Greenhill ◽  
Joseph Watts ◽  
Johann-Mattis List ◽  
Carlos A. Botero ◽  
...  
Keyword(s):  
Best Practices ◽  
Cultural Evolution ◽  
Cross Cultural ◽  
Theme Issue ◽  
Tree Thinking ◽  
Phylogenetic Methods ◽  
Cultural Research ◽  
Cross Cultural Research ◽  
Cultural Traits ◽  
Lines Of Evidence

Modern phylogenetic methods are increasingly being used to address questions about macro-level patterns in cultural evolution. These methods can illuminate the unobservable histories of cultural traits and identify the evolutionary drivers of trait change over time, but their application is not without pitfalls. Here, we outline the current scope of research in cultural tree thinking, highlighting a toolkit of best practices to navigate and avoid the pitfalls and ‘abuses' associated with their application. We emphasize two principles that support the appropriate application of phylogenetic methodologies in cross-cultural research: researchers should (1) draw on multiple lines of evidence when deciding if and which types of phylogenetic methods and models are suitable for their cross-cultural data, and (2) carefully consider how different cultural traits might have different evolutionary histories across space and time. When used appropriately phylogenetic methods can provide powerful insights into the processes of evolutionary change that have shaped the broad patterns of human history. This article is part of the theme issue ‘Foundations of cultural evolution'.

scholarly journals Beyond Brownian motion and the Ornstein-Uhlenbeck process: Stochastic diffusion models for the evolution of quantitative characters

2016 ◽  
Author(s):  
Simon Phillip Blomberg
Keyword(s):  
Brownian Motion ◽  
Stochastic Processes ◽  
Comparative Methods ◽  
Diffusion Models ◽  
Mathematical Framework ◽  
Phylogenetic Comparative Methods ◽  
Uhlenbeck Process ◽  
Trait Evolution ◽  
Ornstein Uhlenbeck Process ◽  
Non Gaussian

AbstractGaussian processes such as Brownian motion and the Ornstein-Uhlenbeck process have been popular models for the evolution of quantitative traits and are widely used in phylogenetic comparative methods. However, they have drawbacks which limit their utility. Here I describe new, non-Gaussian stochastic differential equation (diffusion) models of quantitative trait evolution. I present general methods for deriving new diffusion models, and discuss possible schemes for fitting non-Gaussian evolutionary models to trait data. The theory of stochastic processes provides a mathematical framework for understanding the properties of current, new and future phylogenetic comparative methods. Attention to the mathematical details of models of trait evolution and diversification may help avoid some pitfalls when using stochastic processes to model macroevolution.

scholarly journals A variable-rate quantitative trait evolution model using penalized-likelihood

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11997
Author(s):  
Liam J. Revell
Keyword(s):  
Brownian Motion ◽  
Quantitative Trait ◽  
Penalized Likelihood ◽  
Comparative Methods ◽  
Character Trait ◽  
Likelihood Method ◽  
Rate Variation ◽  
Phylogenetic Comparative Methods ◽  
Trait Evolution ◽  
Rate Of Evolution

In recent years it has become increasingly popular to use phylogenetic comparative methods to investigate heterogeneity in the rate or process of quantitative trait evolution across the branches or clades of a phylogenetic tree. Here, I present a new method for modeling variability in the rate of evolution of a continuously-valued character trait on a reconstructed phylogeny. The underlying model of evolution is stochastic diffusion (Brownian motion), but in which the instantaneous diffusion rate (σ2) also evolves by Brownian motion on a logarithmic scale. Unfortunately, it’s not possible to simultaneously estimate the rates of evolution along each edge of the tree and the rate of evolution of σ2 itself using Maximum Likelihood. As such, I propose a penalized-likelihood method in which the penalty term is equal to the log-transformed probability density of the rates under a Brownian model, multiplied by a ‘smoothing’ coefficient, λ, selected by the user. λ determines the magnitude of penalty that’s applied to rate variation between edges. Lower values of λ penalize rate variation relatively little; whereas larger λ values result in minimal rate variation among edges of the tree in the fitted model, eventually converging on a single value of σ2 for all of the branches of the tree. In addition to presenting this model here, I have also implemented it as part of my phytools R package in the function multirateBM. Using different values of the penalty coefficient, λ, I fit the model to simulated data with: Brownian rate variation among edges (the model assumption); uncorrelated rate variation; rate changes that occur in discrete places on the tree; and no rate variation at all among the branches of the phylogeny. I then compare the estimated values of σ2 to their known true values. In addition, I use the method to analyze a simple empirical dataset of body mass evolution in mammals. Finally, I discuss the relationship between the method of this article and other models from the phylogenetic comparative methods and finance literature, as well as some applications and limitations of the approach.

scholarly journals Trait Evolution with Jumps: Illusionary Normality

2017 ◽  
Author(s):  
Krzysztof Bartoszek
Keyword(s):  
Stochastic Process ◽  
Weak Convergence ◽  
Comparative Methods ◽  
The Other ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Models ◽  
Trait Evolution ◽  
Other Hand ◽  
Extinction Component

ABSTRACTPhylogenetic comparative methods for real-valued traits usually make use of stochastic process whose trajectories are continuous. This is despite biological intuition that evolution is rather punctuated than gradual. On the other hand, there has been a number of recent proposals of evolutionary models with jump components. However, as we are only beginning to understand the behaviour of branching Ornstein–Uhlenbeck (OU) processes the asymptotics of branching OU processes with jumps is an even greater unknown. In this work we build up on a previous study concerning OU with jumps evolution on a pure birth tree. We introduce an extinction component and explore via simulations, its effects on the weak convergence of such a process. We furthermore, also use this work to illustrate the simulation and graphic generation possibilities of the mvSLOUCH package.

scholarly journals Does horizontal transmission invalidate cultural phylogenies?

2009 ◽  
Vol 276 (1665) ◽  
pp. 2299-2306 ◽  
Author(s):  
Simon J. Greenhill ◽  
Thomas E. Currie ◽  
Russell D. Gray
Keyword(s):  
Cultural Evolution ◽  
Horizontal Transmission ◽  
Cultural Groups ◽  
Phylogenetic Methods ◽  
Tree Topologies ◽  
Divergence Dates ◽  
Linguistic Evolution

Phylogenetic methods have recently been applied to studies of cultural evolution. However, it has been claimed that the large amount of horizontal transmission that sometimes occurs between cultural groups invalidates the use of these methods. Here, we use a natural model of linguistic evolution to simulate borrowing between languages. The results show that tree topologies constructed with Bayesian phylogenetic methods are robust to realistic levels of borrowing. Inferences about divergence dates are slightly less robust and show a tendency to underestimate dates. Our results demonstrate that realistic levels of reticulation between cultures do not invalidate a phylogenetic approach to cultural and linguistic evolution.

Analogies are powerful and dangerous things

2006 ◽  
Vol 29 (4) ◽  
pp. 350-351 ◽  
Author(s):  
Monique Borgerhoff Mulder ◽  
Richard McElreath ◽  
Kari Britt Schroeder
Keyword(s):  
Cultural Evolution ◽  
Horizontal Transmission ◽  
Evolutionary Approach ◽  
Genetic Evolution ◽  
Cultural Inheritance ◽  
Cultural Traits ◽  
Strongly Agree

The analogy between biological and cultural evolution is not perfect. Yet, as Mesoudi et al. show, many of the vaunted differences between cultural and genetic evolution (for example, an absence of discrete particles of cultural inheritance, and the blurred distinction between cultural replicators and cultural phenotypes) are, on closer inspection, either illusory or peripheral to the validity of the analogy. But what about horizontal transmission? We strongly agree with the authors that the potential for horizontal transmission of cultural traits does not invalidate an evolutionary approach to culture. We suggest, however, that it does require a different evolutionary treatment.

scholarly journals Self-Organized Cultural Cycles and the Uncertainty of Archaeological Thought

2022 ◽  
Author(s):  
Aleksandr Diachenko ◽  
Iwona Sobkowiak-Tabaka
Keyword(s):  
Material Culture ◽  
Cultural Evolution ◽  
Culture Change ◽  
Horizontal Transmission ◽  
Complex Relationship ◽  
Replication Rate ◽  
Complex Dynamic ◽  
Self Organized ◽  
Cultural Traits ◽  
Punctuated Evolution

AbstractContributing to the issue of complex relationship between social and cultural evolution, this paper aims to analyze repetitive patterns, or cycles, in the development of material culture. Our analysis focuses on culture change associated with sociopolitical and economic stasis. The proposed toy model describes the cyclical character of the quantitative and qualitative composition of archaeological assemblages, which include hierarchically organized cultural traits. Cycles sequentially process the stages of unification, diversity, and return to unification. This complex dynamic behavior is caused by the ratio between cultural traits’ replication rate and the proportion of traits of the higher taxonomic order’s related unit. Our approach identifies a shift from conformist to anti-conformist transmission, corresponding with open and closed phases in cultural evolution in respect to the introduction of innovations. The model also describes the dependence of a probability for horizontal transmission upon orders of taxonomic hierarchy during open phases. The obtained results are indicative for gradual cultural evolution at the low orders of taxonomic hierarchy and punctuated evolution at its high orders. The similarity of the model outcomes to the patters of material culture change reflecting societal transformations enables discussions around the uncertainty of explanation in archaeology and anthropology.

scholarly journals Epistasis between cultural traits causes paradigm shifts in cultural evolution

2020 ◽  
Vol 7 (2) ◽  
pp. 191813 ◽  
Author(s):  
Ignacio Pascual ◽  
Jacobo Aguirre ◽  
Susanna Manrubia ◽  
José A. Cuesta
Keyword(s):  
Cultural Evolution ◽  
Fitness Landscape ◽  
Horizontal Transmission ◽  
Paradigm Shifts ◽  
Cultural Paradigm ◽  
Population Dynamics Model ◽  
Emergent Feature ◽  
Cultural Traits ◽  
Cultural Shifts ◽  
Irreversible Nature

Every now and then the cultural paradigm of a society changes. While current models of cultural shifts usually require a major exogenous or endogenous change, we propose that the mechanism underlying many paradigm shifts may just be an emergent feature of the inherent congruence among different cultural traits. We implement this idea through a population dynamics model in which individuals are defined by a vector of cultural traits that changes mainly through cultural contagion, biased by a ‘cultural fitness’ landscape, between contemporary individuals. Cultural traits reinforce or hinder each other (through a form of cultural epistasis) to prevent cognitive dissonance. Our main result is that abrupt paradigm shifts occur, in response to weak changes in the landscape, only in the presence of epistasis between cultural traits, and regardless of whether horizontal transmission is biased by homophily. A relevant consequence of this dynamics is the irreversible nature of paradigm shifts: the old paradigm cannot be restored even if the external changes are undone. Our model puts the phenomenon of paradigm shifts in cultural evolution in the same category as catastrophic shifts in ecology or phase transitions in physics, where minute causes lead to major collective changes.

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