scholarly journals The projection of a test genome onto a reference population and applications to humans and archaic hominins

2014 ◽  
Author(s):  
Melinda A Yang ◽  
Kelley Harris ◽  
Montgomery Slatkin
Keyword(s):  
Numerical Analysis ◽  
Population Size ◽  
Demographic History ◽  
Reference Population ◽  
Average Weight ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Test Genome ◽  
History Of ◽  
Past Population

We introduce a method for comparing a test genome with numerous genomes from a reference population. Sites in the test genome are given a weight w that depends on the allele frequency x in the reference population. The projection of the test genome onto the reference population is the average weight for each x, w(x). The weight is assigned in such a way that if the test genome is a random sample from the reference population, w(x)=1. Using analytic theory, numerical analysis, and simulations, we show how the projection depends on the time of population splitting, the history of admixture and changes in past population size. The projection is sensitive to small amounts of past admixture, the direction of admixture and admixture from a population not sampled (a ghost population). We compute the projection of several human and two archaic genomes onto three reference populations from the 1000 Genomes project, Europeans (CEU), Han Chinese (CHB) and Yoruba (YRI) and discuss the consistency of our analysis with previously published results for European and Yoruba demographic history. Including higher amounts of admixture between Europeans and Yoruba soon after their separation and low amounts of admixture more recently can resolve discrepancies between the projections and demographic inferences from some previous studies.

scholarly journals Introgression makes waves in inferred histories of effective population size

2017 ◽  
Author(s):  
John Hawks
Keyword(s):  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
History Of ◽  
Or Gene ◽  
Time Of Origin ◽  
Past Population

AbstractHuman populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.

scholarly journals Evidences of delayed size recovery in Araucaria angustifolia populations after post-glacial colonization of highlands in Southeastern Brazil

2008 ◽  
Vol 80 (3) ◽  
pp. 433-443 ◽  
Author(s):  
Valdir M. Stefenon ◽  
Hermann Behling ◽  
Oliver Gailing ◽  
Reiner Finkeldey
Keyword(s):  
Population Size ◽  
Demographic History ◽  
Southeastern Brazil ◽  
Effective Population ◽  
History Of ◽  
Natural Stands ◽  
Recovery Dynamics ◽  
The Relationship ◽  
Palynological Records ◽  
Small Effective Population Size

Up to date, little is known about the relationship between historical demography and the current genetic structure of A. Angus As a first effort towards overcoming this lack, microsatellite data scored in six populations and isozyme allele frequencies published for 11 natural stands of this species were analysed in order to assess molecular signatures of populations' demographic history. Signatures of genetic bottlenecks were captured in all analysed populations of southeastern Brazil. Among southern populations, signatures of small effective population size were observed in only three out of 13 populations. Southern populations likely experienced faster recovery of population size after migration onto highlands. Accordingly, current genetic diversity of the southern populations gives evidence of fast population size recovery. In general, demographic history of A. Angusmatches climatic dynamics of southern and southeastern Brazil during the Pleistocene and Holocene. Palynological records and reconstruction of the past climatic dynamics of southeastern and southern Brazil support the hypothesis of different population size recovery dynamics for populations from these regions.

scholarly journals Inferring number of populations and changes in connectivity under the n-island model

Heredity ◽  
2021 ◽  
Author(s):  
Armando Arredondo ◽  
Beatriz Mourato ◽  
Khoa Nguyen ◽  
Simon Boitard ◽  
Willy Rodríguez ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Demographic History ◽  
Simulated Data ◽  
Fixed Number ◽  
Ancestral Population ◽  
Demographic Model ◽  
History Of ◽  
Time Periods

AbstractInferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.

scholarly journals Exploring the Demographic History of Populations with Enhanced Lexis Surfaces

2019 ◽  
Author(s):  
Jorge Cimentada ◽  
Sebastian Klüsener ◽  
Tim Riffe
Keyword(s):  
Population Size ◽  
Demographic History ◽  
Cohort Size ◽  
Birth Cohorts ◽  
Demographic Development ◽  
Analytical Potential ◽  
R Shiny ◽  
History Of ◽  
Very High ◽  
Shiny Application

Lexis surfaces are widely used to analyze demographic trends across periods, ages, and birth cohorts. When used to visualize rates or similar, these plots usually do not convey information about population size. The failure to communicate population size in Lexis surfaces can lead to misinterpretations of the mortality conditions populations face because, for example, high mortality rates at very high ages have historically been experienced by only a small proportion of a population or cohort. We propose enhanced Lexis surfaces that include a visual representation of population size. The examples we present demonstrate how such plots can give readers a more intuitive understanding of the demographic development of a population over time. Visualizations are implemented using an R-Shiny application, building upon perception theories. We present example plots for enhanced Lexis surfaces that show trends in cohort mortality and first-order differences in cohort mortality developments. These plots illustrate how adding the cohort size dimension allows us to extend the analytical potential of standard Lexis surfaces. Our enhanced Lexis surfaces improve conventional depictions of period, age, and cohort trends in demographic developments of populations and cohorts. An online interactive visualization tool based on Human Mortality Database data allows users to generate and export enhanced Lexis surfaces for their research. The R code to generate the application (and a link to the deployed application) can be accessed at https://github.com/cimentadaj/lexis_plot.

scholarly journals Neutral genomic signatures of host-parasite coevolution

2019 ◽  
Author(s):  
Daniel Živković ◽  
Sona John ◽  
Mélissa Verin ◽  
Wolfgang Stephan ◽  
Aurélien Tellier
Keyword(s):  
Population Size ◽  
Demographic History ◽  
Analytical Framework ◽  
Parasite Population ◽  
Full Genome ◽  
Genome Data ◽  
Genomic Signatures ◽  
Population Sizes ◽  
History Of ◽  
Cyclic Changes

AbstractCoevolution is a selective process of reciprocal adaptation between antagonistic or mutualistic symbionts and their host. Classic population genetics theory predicts the signatures of selection at the interacting loci but not the neutral genome-wide polymorphism patterns. We here build a coevolutionary model with cyclic changes in the host and parasite population sizes. Using an analytical framework, we investigate if and when these population size changes can be observed in the neutral site frequency spectrum of the host and parasite full genome data. We show that polymorphism data sampled over time can capture the changes in the population size of the parasite but not of the host because genetic drift and mutations occur on different time scales in the coevolving species. This is due to the small parasite population size at the onset of the coevolutionary history subsequently undergoing a series of strong bottlenecks. We also show that tracking coevolutionary cycles is more likely for a small amount of parasite per host and for multiple parasite generations per host generation. Our results demonstrate that time sampling of host and parasite full genome data are crucial to infer the co-demographic history of interacting species.

scholarly journals Historical DNA reveals the demographic history of Atlantic cod ( Gadus morhua ) in medieval and early modern Iceland

2014 ◽  
Vol 281 (1777) ◽  
pp. 20132976 ◽  
Author(s):  
Guðbjörg Ásta Ólafsdóttir ◽  
Kristen M. Westfall ◽  
Ragnar Edvardsson ◽  
Snæbjörn Pálsson
Keyword(s):  
Early Modern ◽  
Population Size ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Demographic History ◽  
Ecosystem Change ◽  
Nucleotide Variation ◽  
Modern Times ◽  
History Of ◽  
Early Modern Times

Atlantic cod ( Gadus morhua ) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500–1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b ( cytb ) and Pantophysin I ( Pan I) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size ( N E ), a marked bottleneck event at 1400–1500 and a decrease in N E in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.

scholarly journals Diverse demographic histories in a guild of hymenopteran parasitoids

2019 ◽  
Author(s):  
William Walton ◽  
Graham N Stone ◽  
Konrad Lohse
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Demographic History ◽  
Whole Genome Sequence ◽  
Parasitoid Wasps ◽  
Effective Population ◽  
Glacial Cycles ◽  
Genome Wide ◽  
History Of ◽  
Hymenopteran Parasitoids

AbstractSignatures of changes in population size have been detected in genome-wide variation in many species. However, the causes of such changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely studied, little is known about the demographic history of refugial populations, and the extent and causes of demographic variation among codistributed species. We used whole genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). We find support for large changes in effective population size (Ne) through the Pleistocene that coincide with major climate change events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories are largely idiosyncratic. Our results are compatible with the idea that specialist parasitoids attacking a narrow range of hosts experience greater fluctuations in Ne than generalists.

scholarly journals Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management

2021 ◽  
Author(s):  
Leanne Faulks ◽  
Prashant Kaushik ◽  
Shoji Taniguchi ◽  
Masashi Sekino ◽  
Reiichiro Nakamichi ◽  
...  
Keyword(s):  
Population Size ◽  
Environmental Conditions ◽  
Wildlife Conservation ◽  
Demographic History ◽  
Population Decline ◽  
Anguilla Japonica ◽  
Japanese Eel ◽  
Population Declines ◽  
Effective Population ◽  
History Of

Assessing the status or population size of species is a key task for wildlife conservation and the sustainable management of harvested species. In particular, assessing historical changes in population size provides an evolutionary perspective on current population dynamics and can help distinguish between anthropogenic and natural causes for population decline. Japanese eel (Anguilla japonica) is an endangered yet commercially important catadromous fish species. Here we assess the demographic history of Japanese eel using the pairwise and multiple sequentially Markovian coalescent methods. The analyses indicate a reduction in effective population size (Ne) from 38 000 to 10 000 individuals between 4 and 1 Ma, followed by an increase to 80 000 individuals, between 1 Ma and 22-30 kya. Approximately 22-30 kya there is evidence for a reduction in Ne to approximately 60 000 individuals. These events are likely due to changes in environmental conditions, such as sea level and oceanic currents, especially around the last glacial maximum (19-33 kya). The results of this study suggest that Japanese eel has experienced at least two population bottlenecks, interspersed by a period of population growth. This pattern of demographic history may make Japanese eel sensitive to current and future population declines. Conservation management of Japanese eel should focus on practical ways to prevent further population decline and the loss of genetic diversity that is essential for the species to adapt to changing environmental conditions such as climate change.

scholarly journals Changes in Genetic Diversity and Demographic History of Jankowski’s Bunting (Emberiza Jankowskii), as Revealed by Mitochondrial DNA and Microsatellite Markers

2021 ◽  
Author(s):  
Long Huang ◽  
Guochen Feng ◽  
Dan Li ◽  
Weiping Shang ◽  
Lishi Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
Population Size ◽  
Demographic History ◽  
Effective Population ◽  
High Genetic Diversity ◽  
History Of ◽  
Eastern Inner Mongolia

Abstract The genetic variation and distribution of a population depend largely on the demographic history. For instance, populations that have recently experienced shrinkage usually have a lower genetic diversity. However, some endangered species with a narrow distribution have a high genetic diversity resulting from large historical population sizes and long generation times. In addition, very recent population bottlenecks may not be reflected in the population’s genetic information. In this study, we used a mitochondrial DNA marker and 15 microsatellite markers to reveal the genetic diversity, recent changes, inbreeding, and demographic history of a Jankowski’s bunting (Emberiza jankowskii) population in eastern Inner Mongolia. The results show that the genetic diversity of the population remained at a relatively stable and high level until recently. Severe population shrinkage did not result in a considerable lack of genetic variation because of the large historical population size and relatively short periods of human disturbance. In addition, introgression and gene flow among populations compensate for the loss of genetic variation to some extent. Considering the current small effective population size and the existence of inbreeding, we recommend that habitat protection be continued to maximize the genetic diversity of the Jankowski’s bunting population.

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