scholarly journals The Structured Coalescent and its Approximations

2016 ◽  
Author(s):  
Nicola F. Müller ◽  
David A. Rasmussen ◽  
Tanja Stadler
Keyword(s):  
Sequence Data ◽  
Large Datasets ◽  
Approximate Methods ◽  
Exact Numerical Solution ◽  
Migration Rates ◽  
Geographic Spread ◽  
Occurrence Data ◽  
Migration History ◽  
History Of ◽  
Structured Coalescent

Phylogenetics can be used to elucidate the movement of genes between populations of organisms, using phylogeographic methods. This has been widely done to quantify pathogen movement between different host populations, the migration history of humans, and the geographic spread of languages or the gene flow between species using the location or state of samples alongside sequence data. Phylogenies therefore offer insights into migration processes not available from classic epidemiological or occurrence data alone. Phylogeographic methods have however several known shortcomings. In particular, one of the most widely used methods treats migration the same as mutation, and therefore does not incorporate information about population demography. This may lead to severe biases in estimated migration rates for datasets where sampling is biased across populations. The structured coalescent on the other hand allows us to coherently model the migration and coalescent process, but current implementations struggle with complex datasets due to the need to infer ancestral migration histories. Thus, approximations to the structured coalescent, which integrate over all ancestral migration histories, have been developed. However, the validity and robustness of these approximations remain unclear. We present an exact numerical solution to the structured coalescent that does not require the inference of migration histories. While this solution is computationally unfeasible for large datasets, it clarifies the assumptions of previously developed approximate methods and allows us to provide an improved approximation to the structured coalescent. We have implemented these methods in BEAST2, and we show how these methods compare under different scenarios.

scholarly journals MASCOT: Parameter and state inference under the marginal structured coalescent approximation

2017 ◽  
Author(s):  
Nicola F. Müller ◽  
David A. Rasmussen ◽  
Tanja Stadler
Keyword(s):  
Migration Rate ◽  
Sequence Data ◽  
Source Code ◽  
Large Datasets ◽  
Population Size Estimates ◽  
Integration Techniques ◽  
Structured Coalescent ◽  
And Migration ◽  
State Inference ◽  
Size Estimates

AbstractMotivationThe structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many states, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states. We showed that our approximation provides unbiased migration rate and population size estimates across a wide parameter range.ResultsWe here extend this approach by providing a new algorithm to calculate the probability of the state of internal nodes that includes the information from the full phylogenetic tree. We show that this algorithm is able to increase the probability attributed to the true node states. Furthermore we use improved integration techniques, such that our method is now able to analyse larger datasets, including a H3N2 dataset with 433 sequences sampled from 5 different locations.AvailabilityThe here presented methods are combined into the BEAST2 package MASCOT, the Marginal Approximation of the Structured COalescenT. This package can be downloaded via the BEAUti package manager. The source code is available at https://github.com/nicfel/Mascot.git.

scholarly journals Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Nicola F Müller ◽  
Gytis Dudas ◽  
Tanja Stadler
Keyword(s):  
Population Dynamics ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Structured Populations ◽  
Model Parameters ◽  
Effective Population ◽  
Genetic Sequence ◽  
Migration Rates ◽  
Population Sizes ◽  
Structured Coalescent

Abstract Population dynamics can be inferred from genetic sequence data by using phylodynamic methods. These methods typically quantify the dynamics in unstructured populations or assume migration rates and effective population sizes to be constant through time in structured populations. When considering rates to vary through time in structured populations, the number of parameters to infer increases rapidly and the available data might not be sufficient to inform these. Additionally, it is often of interest to know what predicts these parameters rather than knowing the parameters themselves. Here, we introduce a method to  infer the predictors for time-varying migration rates and effective population sizes by using a generalized linear model (GLM) approach under the marginal approximation of the structured coalescent. Using simulations, we show that our approach is able to reliably infer the model parameters and its predictors from phylogenetic trees. Furthermore, when simulating trees under the structured coalescent, we show that our new approach outperforms the discrete trait GLM model. We then apply our framework to a previously described Ebola virus dataset, where we infer the parameters and its predictors from genome sequences while accounting for phylogenetic uncertainty. We infer weekly cases to be the strongest predictor for effective population size and geographic distance the strongest predictor for migration. This approach is implemented as part of the BEAST2 package MASCOT, which allows us to jointly infer population dynamics, i.e. the parameters and predictors, within structured populations, the phylogenetic tree, and evolutionary parameters.

scholarly journals Migration and World History: Reaching a New Frontier

2007 ◽  
Vol 52 (1) ◽  
pp. 89-96 ◽  
Author(s):  
Leo Lucassen
Keyword(s):  
Economic History ◽  
Western Europe ◽  
Human Life ◽  
Human Mobility ◽  
Structural Aspect ◽  
Labour Relations ◽  
Migration History ◽  
Significant Phenomenon ◽  
History Of ◽  
And Gender

Migration history has made some major leaps forward in the last fifteen years or so. An important contribution was Leslie Page Moch's Moving Europeans, published in 1992, in which she weaves the latest insights in migration history into the general social and economic history of western Europe. Using Charles Tilly's typology of migration patterns and his ideas on the process of proletarianization since the sixteenth century, Moch skilfully integrates the experience of human mobility in the history of urbanization, labour relations, (proto)industrialization, demography, family history, and gender relations. Her state-of-the-art overview has been very influential, not least because it fundamentally criticizes the modernization paradigm of Wilbur Zelinsky and others, who assumed that only in the nineteenth century, as a result of industrialization and urbanization, migration became a significant phenomenon. Instead, she convincingly argues that migration was a structural aspect of human life. Since then many new studies have proved her point and refined her model.

On the Trails of Free-Roaming Elephants

Transfers ◽  
2020 ◽  
pp. 1-21
Author(s):  
Paul G. Keil
Keyword(s):  
British Empire ◽  
Political History ◽  
Human Mobility ◽  
Human Agency ◽  
Northeast India ◽  
Mountain Ranges ◽  
Migration History ◽  
The Social ◽  
Elephant Population ◽  
History Of

Humans and elephants have historically shared the forested mountain ranges of Zomia, a geography defined by the regular movement of people and an ecology shaped by the movement of its elephant population. This article will examine how free-roaming elephant pathways facilitated human mobility in the highlands defining the Indo-Myanmar border. It will analyze the more-than-human agency that emerges when following elephant trails and the varying role this forest infrastructure might have played in the social and political history of the region. The article will explore two historical examples. First, the migration of a Lisu community in Upper Myanmar who utilized elephant paths to navigate their passage. Second, how the British Empire exploited a network of elephant-human tracks to subjugate the peoples living in Mizoram, northeast India. In these regions the patterns of migration, history of colonization, and identities and practices of communities must be understood in relation to wild elephants.

Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

2021 ◽  
Author(s):  
Sara Fuentes-Soriano ◽  
Elizabeth A. Kellogg
Keyword(s):  
Sequence Data ◽  
Plastid Dna ◽  
Sister Relationship ◽  
Data Set ◽  
Woody Perennial ◽  
History Of ◽  
Nuclear Its ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

scholarly journals The Principle of Least Interaction Action

1974 ◽  
Vol 3 ◽  
pp. 489-489
Author(s):  
M. W. Ovenden
Keyword(s):  
Solar System ◽  
Planetary System ◽  
Satellite System ◽  
Asteroid Belt ◽  
Correct Prediction ◽  
The Sun ◽  
Approximate Methods ◽  
Satellites Of Jupiter ◽  
History Of ◽  
Minimum Interaction

AbstractThe intuitive notion that a satellite system will change its configuration rapidly when the satellites come close together, and slowly when they are far apart, is generalized to ‘The Principle of Least Interaction Action’, viz. that such a system will most often be found in a configuration for which the time-mean of the action associated with the mutual interaction of the satellites is a minimum. The principle has been confirmed by numerical integration of simulated systems with large relative masses. The principle lead to the correct prediction of the preference, in the solar system, for nearly-commensurable periods. Approximate methods for calculating the evolution of an actual satellite system over periods ˜ 109 yr show that the satellite system of Uranus, the five major satellites of Jupiter, and the five planets of Barnard’s star recently discovered, are all found very close to their respective minimum interaction distributions. Applied to the planetary system of the Sun, the principle requires that there was once a planet of mass ˜ 90 Mθ in the asteroid belt, which ‘disappeared’ relatively recently in the history of the solar system.

Diaspora in the United States: Chinese and Indians Compared

2010 ◽  
Vol 6 (2) ◽  
pp. 286-310 ◽  
Author(s):  
Emily Skop ◽  
Wei Li
Keyword(s):  
United States ◽  
Racial Discrimination ◽  
20Th Century ◽  
The United States ◽  
Foreign Born ◽  
Migration Rates ◽  
China And India ◽  
History Of ◽  
Migrant Groups ◽  
The U.S

AbstractIn recent years, the migration rates from both China and India to the U.S. have accelerated. Since 2000 more than a third of foreign-born Chinese and 40% of foreign-born Indians have arrived in that country. This paper will document the evolving patterns of immigration from China and India to the U.S. by tracing the history of immigration and racial discrimination, the dramatic transitions that have occurred since the mid-20th century, and the current demographic and socioeconomic profiles of these two migrant groups.

scholarly journals Migration and Access to Welfare Benefits in the EU: The Interplay between Residence and Nationality

2020 ◽  
pp. 1-32
Author(s):  
Daniela Vintila ◽  
Jean-Michel Lafleur
Keyword(s):  
Social Protection ◽  
Analytical Framework ◽  
Welfare Regimes ◽  
Welfare Benefits ◽  
Migration History ◽  
The Social ◽  
History Of ◽  
Societal Dynamics ◽  
Social Protection Systems ◽  
The Eu

Abstract Increasing mobility to and from European Union (EU) countries has started to challenge the principles of territoriality and national citizenship through which European democracies traditionally conditioned access to social benefits. Existing typologies of immigrant social protection regimes do not seem to adequately capture (nor explain) the diverse repertoire of policy configurations through which European welfare regimes adapt to migration-driven societal dynamics. This introductory chapter provides a critical reflection on the link between migration and access to welfare in the EU. In doing so, it aims to propose a comprehensive analytical framework that allows for a systematic comparison of the inclusiveness of social protection systems towards mobile individuals. We argue that states’ responsiveness towards the social protection needs of their immigrant and emigrant populations has to be examined through a combination of factors, including the characteristics of these populations, the migration history of these countries, as well as the main features of their welfare state.

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