scholarly journals Demographic inference under the coalescent in a spatial continuum

2016 ◽  
Vol 111 ◽  
pp. 43-50 ◽  
Author(s):  
Stéphane Guindon ◽  
Hongbin Guo ◽  
David Welch
Keyword(s):  
Demographic Inference ◽  
Spatial Continuum

scholarly journals Demographic inference under the coalescent in a spatial continuum

2016 ◽  
Author(s):  
Stephane Guindon ◽  
Hongbin Guo ◽  
David Welch
Keyword(s):  
Genetic Diversity ◽  
Spatial Data ◽  
Null Model ◽  
Theoretical Work ◽  
Spatial Density ◽  
Recent Theoretical Work ◽  
The Usa ◽  
Demographic Inference ◽  
Two Parameters ◽  
Spatial Continuum

Understanding population dynamics from the analysis of molecular and spatial data requires sound statistical modeling. Current approaches assume that populations are naturally partitioned into discrete demes, thereby failing to be relevant in cases where individuals are scattered on a spatial continuum. Other models predict the formation of increasingly tight clusters of individuals in space, which, again, conflicts with biological evidence. Building on recent theoretical work, we introduce a new genealogy-based inference framework that alleviates these issues. This approach effectively implements a stochastic model in which the distribution of individuals is homogeneous and stationary, thereby providing a relevant null model for the fluctuation of genetic diversity in time and space. Importantly, the spatial density of individuals in a population and their range of dispersal during the course of evolution are two parameters that can be inferred separately with this method. The validity of the new inference framework is confirmed with extensive simulations and the analysis of influenza sequences collected over five seasons in the USA.

scholarly journals Correction to: The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure

Heredity ◽  
2021 ◽  
Vol 126 (4) ◽  
pp. 706-706
Author(s):  
Willy Rodríguez ◽  
Olivier Mazet ◽  
Simona Grusea ◽  
Armando Arredondo ◽  
Josué M. Corujo ◽  
...  
Keyword(s):  
Population Structure ◽  
Structured Coalescent ◽  
Demographic Inference

scholarly journals Means of Lexical Representation of Spatial Continuum in Early Stories of I. A. Bunin

2021 ◽  
pp. 191-212
Author(s):  
M. A. Dubova ◽  
N. A. Larina
Keyword(s):  
Cognitive Linguistics ◽  
Individual Characteristics ◽  
Lexical Representation ◽  
Wrong Side ◽  
The World ◽  
Representation Of Space ◽  
World Modeling ◽  
The Individual ◽  
Linguistic Material ◽  
Spatial Continuum

The question of ways of creating a spatial continuum in the early stories of I. A. Bunin “On the wrong side”, “On the farm” and “On the Donets”, united by a single principle of nomination and included in the first book of the writer’s prose “To the end of the world” (1897) is considered in the article. The semantics of the title actualizes the spatial component of the author’s linguistic picture of the world, which determined the path of linguistic and stylistic analysis of the linguistic material of stories. The authors pay special attention to the means of lexical representation of space as one of the basic linguo-cognitive categories. The novelty of the research lies in the fact that the language material has been identified, systematized and described, which makes it possible to determine the individual author's characteristics in the creation of the spatial continuum of I. A. Bunin’s early stories. The relevance of the study is due to the appeal to the problems of cognitive linguistics. On the basis of statistical, descriptive and linguo-cognitive methods of analysis, the authors identify and describe the means of lexical representation of the spatial model created in the stories of I. A. Bunin, which is characterized by a clear structuredness and individuality of the author’s approach. In the course of the study, the authors come to conclusions that make it possible to characterize the features of the construction of space in the early stories of the writer, taking into account the individual characteristics of the author's world modeling, and also to analyze the linguistic parameters of the idiostyle of I. A. Bunin.

scholarly journals Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Diversity ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 164 ◽  
Author(s):  
Peter Houde ◽  
Edward L. Braun ◽  
Lawrence Zhou
Keyword(s):  
Evolutionary Biology ◽  
Gene Tree ◽  
Difficult Problem ◽  
Gene Trees ◽  
Effective Population ◽  
Deep Time ◽  
Ecological Release ◽  
Population Sizes ◽  
Demographic Inference ◽  
Gene Tree Discordance

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

scholarly journals Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data

2020 ◽  
Vol 37 (7) ◽  
pp. 2124-2136
Author(s):  
Paul D Blischak ◽  
Michael S Barker ◽  
Ryan N Gutenkunst
Keyword(s):  
Puma Concolor ◽  
Demographic History ◽  
Random Mating ◽  
Simulated Data ◽  
Conservation Agriculture ◽  
Model Fit ◽  
Parameter Estimates ◽  
History Of ◽  
Demographic Inference ◽  
Inbred Populations

Abstract Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model’s ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.

scholarly journals Genetic structure and demographic inference of the regular sea urchin Sterechinus neumayeri (Meissner, 1900) in the Southern Ocean: The role of the last glaciation

PLoS ONE ◽  
2018 ◽  
Vol 13 (6) ◽  
pp. e0197611 ◽  
Author(s):  
Angie Díaz ◽  
Karin Gérard ◽  
Claudio González-Wevar ◽  
Claudia Maturana ◽  
Jean-Pierre Féral ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Southern Ocean ◽  
Sea Urchin ◽  
Sterechinus Neumayeri ◽  
Last Glaciation ◽  
Demographic Inference

scholarly journals Geometry of the Sample Frequency Spectrum and the Perils of Demographic Inference

Genetics ◽  
2018 ◽  
Vol 210 (2) ◽  
pp. 665-682 ◽  
Author(s):  
Zvi Rosen ◽  
Anand Bhaskar ◽  
Sebastien Roch ◽  
Yun S. Song
Keyword(s):  
Frequency Spectrum ◽  
Sample Frequency ◽  
Demographic Inference
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