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 Neutral genomic signatures of host-parasite coevolution

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Daniel živković ◽  
Sona John ◽  
Mélissa Verin ◽  
Wolfgang Stephan ◽  
Aurélien Tellier
Keyword(s):  
Time Series ◽  
Evolutionary Model ◽  
Host Population ◽  
Full Genome ◽  
Relative Time ◽  
Genomic Changes ◽  
Genome Data ◽  
Genomic Signatures ◽  
Genome Wide ◽  
Cyclic Changes

Abstract Background Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations. Results We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time. Conclusions Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

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 Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192613 ◽  
Author(s):  
Elisa G. Dierickx ◽  
Simon Yung Wa Sin ◽  
H. Pieter J. van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Approaches To Study ◽  
Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

scholarly journals Stability of Corynosoma populations with fluctuating population densities of the seal definitive host

Parasitology ◽  
2004 ◽  
Vol 129 (5) ◽  
pp. 635-642 ◽  
Author(s):  
E. T. VALTONEN ◽  
E. HELLE ◽  
R. POULIN
Keyword(s):  
Population Size ◽  
Definitive Host ◽  
Paratenic Host ◽  
Mature Female ◽  
Host Population ◽  
Fish Host ◽  
Parasite Population ◽  
Natural Systems ◽  
Population Sizes ◽  
Bothnian Bay

In theory there should be a strong coupling between host and parasite population sizes. Here, we investigated population size and structure in 3 species of acanthocephalans, Corynosoma semerme, C. strumosum and C. magdaleni, in ringed seals (Phoca hispida) from the Bothnian Bay over a period of more than 20 years. During this period, seal numbers first decreased markedly and then increased steadily; at the same time, a paratenic fish host particularly important for C. strumosum has gradually disappeared from the bay due to decreasing salinity. We found no evidence that the mean abundance of any of the 3 acanthocephalan species changed significantly over time, nor was there any relationship between parasite abundance at any point in time and seal numbers in the corresponding year. Based on the proportion of sexually mature female worms per infrapopulation, and on relationships between the sex ratio of worms and infrapopulation size, both C. magdaleni and C. semerme appear to be doing well, independently of the population size of their seal definitive hosts. In contrast, perhaps because of the loss of its main paratenic host, C. strumosum appears more at risk in the Bothnian Bay. Our results show that in complex natural systems, there are not necessarily simple, direct links between definitive host population size or density, and parasite population dynamics.

scholarly journals An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241038
Author(s):  
Pita Sudrajad ◽  
Subiharta Subiharta ◽  
Yudi Adinata ◽  
Af’idatul Lathifah ◽  
Jun Heon Lee ◽  
...  
Keyword(s):  
Demographic History ◽  
Bos Indicus ◽  
Molecular Evidence ◽  
Effective Population ◽  
Genome Data ◽  
Bos Javanicus ◽  
History Of ◽  
Genome Data Analysis ◽  
Almost All ◽  
Insight Into

The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.

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 More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

2010 ◽  
Vol 365 (1556) ◽  
pp. 3277-3288 ◽  
Author(s):  
Anne C. Stone ◽  
Fabia U. Battistuzzi ◽  
Laura S. Kubatko ◽  
George H. Perry ◽  
Evan Trudeau ◽  
...  
Keyword(s):  
Demographic History ◽  
Time Estimation ◽  
Divergence Times ◽  
Effective Population ◽  
Founding Population ◽  
Time Estimates ◽  
Population Structures ◽  
Population Sizes ◽  
History Of ◽  
Mtdna Diversity

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees ( Pan troglodytes ) from each of the three established subspecies ( P. t. troglodytes , P. t. schweinfurthii and P. t. verus ) and the proposed fourth subspecies ( P. t. ellioti ). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human–chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1–1.5, 1.1–0.76 and 0.25–0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

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.

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