Demographic history

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Inferring sex-specific demographic history from SNP data

Inferring sex-specific demographic history from SNP data

For illustration purposes, we analyzed both cattle and human SNP genotyping data, provid- ing new insights into the sex-specific demographic history of these two species. We chose three cattle breeds (HOL, ANG and NDA) with contrasting breeding schemes (from a widespread use of artificial insemination in the HOL dairy cattle to mostly uncontrolled mating in the NDA cattle from West-Africa). These breeds are also representative of the post-domestication history, with HOL, ANG and NDA presumably originating from the same domestication cen- ter in the Middle East, ca. 10,000 YBP [ 56 ]. As expected, we found a strongly female-biased ESR in the commercial breeds (HOL and ANG), with less than two effective males for 100 effective females in both breeds. These ESR estimates integrate over the time of divergence between ANG and HOL, which has occurred ca. 2,000 YBP [ 57 ]. Since modern genetic improvement programs have been generalized only recently (in the past 70 years), the impact of increased selective pressure for beef (in ANG) or milk (in HOL) production on the ESR might thus be even higher than our estimate suggests. Before that, indeed, the ESR for commer- cial cattle breeds might have been only moderately female-biased, as we observe for the tradi- tionally raised NDA with about 36 effective males for 100 effective females. More interestingly, we found a strongly male-biased ESR (four effective females for 100 effective males) in the internal branch of the tree, which is ancestral to the ANG and HOL breeds. This result supports the hypothesis that around the period of cattle domestication, females were plausibly more eas- ily managed than males. Keeping and rearing preferentially female offspring would indeed tend to decrease the effective size for females. At the same time, preventing tamed females from breeding randomly with wild males would be a difficult task, which would result in turn in an increased effective size for males (see [ 58 ], p. 2218), and therefore in a male-biased ESR. Alternatively, introgression of wild auroch males into domesticated cattle [ 59 , 60 ] may have increased the male effective population size. Deciphering between these two non-mutually exclusive hypotheses would require further investigations.
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Demographic history and genomics of local adaptation in blue tit populations

Demographic history and genomics of local adaptation in blue tit populations

2.5 | Analysis of demographic history Alternative models of divergence history including the effects of se- lection at linked sites affecting Ne and of differential introgression (m) were compared using an ABC framework modified from Roux et al. (2016). Linked selection either under the form of hitchhiking of neutral loci linked to a selective sweep (Maynard Haigh & Smith, 1974) or under the form of background selection (Charlesworth, Morgan, & Charlesworth, 1993) has strong effects in regions of low recombina- tion and have been shown to influence model choice and parameter estimates (Ewing & Jensen, 2016; Schrider, Shanku, & Kern, 2016). The same is true when populations accumulate reproductive incompat- ibilities during the divergence process: The resulting barrier to gene flow reduces the effective migration rate along the genome (Barton & Bengtsson, 1986) and not accounting for it can affect demographic model choice and parameter estimates (Roux, Tsagkogeorga, Bierne, & Galtier, 2013; Sousa, Carneiro, Ferrand, & Hey, 2013). Moreover, in- cluding selected loci in demographic inferences can reveal the deeper origins of population divergence (Bierne et al., 2013). Six scenarios were compared for the four pairs of deciduous and evergreen popula- tions in order to test whether the divergence between different habi- tats was not due to a divergence in different historical refugia but to a contemporary ecological divergence. We included a model of panmixia (PAN), a model of equilibrium corresponding to the island model with two populations (EQ), a model of isolation with migration (IM), a model of SC, a model of divergence with migration during the first genera- tions, that is, ancestral migration (AM), and a model of strict isolation (SI). The prior and details of the simulation pipeline are fully described in the Note S1. The PAN model assumes that the two focal populations descent from a single panmictic population characterized by its effec- tive size (Ne). The EQ model (equivalent to the island model) assumes that the population is subdivided into two discrete populations of sizes
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Ancient genomes from present-day France unveil 7,000 years of its demographic history

Ancient genomes from present-day France unveil 7,000 years of its demographic history

Ancient genomes from present-day France unveil 7,000 years of its demographic history. Samantha Brunel 1 , E. Andrew Bennett 1 , Laurent Cardin 1,2 , Damien Garraud 1,2 , Hélène Barrand Emam 3,4 , Alexandre Beylier 5,6 , Bruno Boulestin 7 , Fanny Chenal 4,8 , Elsa Ciesielski 6 , Fabien Convertini 6,8 , Bernard Dedet 6 , Stéphanie Desbrosse-Degobertiere 8 , Sophie Desenne 8,9 , Jerôme Dubouloz 9 , Henri Duday 7 , Gilles Escalon 6,8 , Véronique Fabre 6,8 , Eric Gailledrat 6 , Muriel Gandelin 8,10 , Yves Gleize 7,8 , Sébastien Goepfert 3 , Jean Guilaine 11,12 , Lamys Hachem 8,9 , Michael Ilett 9 , François Lambach 7 , Florent Maziere 6,8 , Bertrand Perrin 3,4 , Suzanne Plouin 4 , Estelle Pinard 8,9 , Ivan Praud 8,9 , Isabelle Richard 8,12 , Vincent Riquier 8,9 , Réjane Roure 5 , Benoit Sendra 6,8 , Corinne Thevenet 8,9 , Sandrine Thiol 8 , Elisabeth Vauquelin 8 , Luc Vergnaud 3,4 , Thierry Grange 1,* , Eva-Maria Geigl 1,* , Melanie Pruvost 1,7,*
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Joint inference of adaptive and demographic history from temporal population genomic data

Joint inference of adaptive and demographic history from temporal population genomic data

Navascu´ es (INRA, UM, UU) Joint inference of adaptive and demographic history 7/10/2019 11 / 12.. Conclusions & Perspectives[r]

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The role of topography in structuring the demographic history of the pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

The role of topography in structuring the demographic history of the pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Sampling the entire range would allow one to test whether all the Mediterranean refugia of montane pines, especially P. nigra, correspond to differentiation centres of the moth, and if the major dispersal centres are associated with expansions of the lowland pines. Rather than showing that mountains acted as physical barriers to dispersal, our results suggest that topography played a major role in shaping the distribution of maternal lineages through the demographic history of its main host plants. Most mid-elevation regions served as glacial refugia, and the moth later expanded into lowlands from these bottlenecked populations, following its relatively thermophilic pine hosts. Mountains offered suitable environmental conditions along the slopes that permitted the persistence of this oligophagous insect during the glacial and interglacial periods. The rest of the species' range could be recurrently recolonized by spatial expansions from these refugia.
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Inferring sex-specific demographic history from SNP data

Inferring sex-specific demographic history from SNP data

For illustration purposes, we analyzed both cattle and human SNP genotyping data, provid- ing new insights into the sex-specific demographic history of these two species. We chose three cattle breeds (HOL, ANG and NDA) with contrasting breeding schemes (from a widespread use of artificial insemination in the HOL dairy cattle to mostly uncontrolled mating in the NDA cattle from West-Africa). These breeds are also representative of the post-domestication history, with HOL, ANG and NDA presumably originating from the same domestication cen- ter in the Middle East, ca. 10,000 YBP [ 56 ]. As expected, we found a strongly female-biased ESR in the commercial breeds (HOL and ANG), with less than two effective males for 100 effective females in both breeds. These ESR estimates integrate over the time of divergence between ANG and HOL, which has occurred ca. 2,000 YBP [ 57 ]. Since modern genetic improvement programs have been generalized only recently (in the past 70 years), the impact of increased selective pressure for beef (in ANG) or milk (in HOL) production on the ESR might thus be even higher than our estimate suggests. Before that, indeed, the ESR for commer- cial cattle breeds might have been only moderately female-biased, as we observe for the tradi- tionally raised NDA with about 36 effective males for 100 effective females. More interestingly, we found a strongly male-biased ESR (four effective females for 100 effective males) in the internal branch of the tree, which is ancestral to the ANG and HOL breeds. This result supports the hypothesis that around the period of cattle domestication, females were plausibly more eas- ily managed than males. Keeping and rearing preferentially female offspring would indeed tend to decrease the effective size for females. At the same time, preventing tamed females from breeding randomly with wild males would be a difficult task, which would result in turn in an increased effective size for males (see [ 58 ], p. 2218), and therefore in a male-biased ESR. Alternatively, introgression of wild auroch males into domesticated cattle [ 59 , 60 ] may have increased the male effective population size. Deciphering between these two non-mutually exclusive hypotheses would require further investigations.
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Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield

Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield

Abstract How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such pro- cesses. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum-likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contrac- tion, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demo- graphic events, with a trend towards the increase in frequency of light-demanding, dis- turbance-associated species.
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The Migraine project : A user- friendly software for likelihood-based inferences of spatial structure and demographic history from genetic data

The Migraine project : A user- friendly software for likelihood-based inferences of spatial structure and demographic history from genetic data

Intro Algorithms Mut & Demo Models Software Demo Simulation studies Future Conclusions A realistic setting Demographic estimate D e σ e 2 =555 ind (D ˆ e =0.003 ind.m ˆ −2 , σ e =125 m) ˆ Genetic regression estimate D e σ e =753 ind (CI 319 – 3162). ˆ

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Extending Approximate Bayesian Computation with Supervised Machine Learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest

Extending Approximate Bayesian Computation with Supervised Machine Learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest

4  |  DISCUSSION Population genetics is now poised for an explosion in the use of SML approaches (Schrider & Kern, 2018). In this context, any effort to create self- contained, efficient, and user- friendly software packages capable of performing the entire workflow associated to SML meth- ods would streamline such methods and make them more accessible to researchers, especially for nonspecialist users. For this purpose, we developed the package DIYABC Random Forest v1.0 which inte- grates, within a user- friendly interface, a set of methods to simulate training sets for various types of molecular data under custom evo- lutionary scenarios, encode both the simulated and observed (tar- get) data as large size feature vectors (summary statistics), train RF algorithms, apply them on observed data point(s), and assess their performance in term of prediction (using various metrics to evaluate error and accuracy). We illustrate the main potentialities and func- tionalities of DIYABC Random Forest v1.0 through the treatments of pseudo- observed and real data sets corresponding to PoolSeq and IndSeq SNP data sets. Our results indicate that SML methods such as RF show great promise in scenario selection and demographic es- timation using genetic data and we argue that they may soon be the preferred choice over alternative methods based on traditional ABC.
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French Guiana Amerindian demographic history as revealed by autosomal and Y-chromosome STRs.

French Guiana Amerindian demographic history as revealed by autosomal and Y-chromosome STRs.

find clear geographic or linguistic patterns among Amazonian Amerindians. Indeed, no correlation has been detected in our data between the D a and geographic distances (Table S7) (Mantel test, r ¼ 2 0.012; p ¼ 0.48). The result indicating a recent genetic bottleneck in the Emerillon agrees with our previous findings (Mazie`res et al. 2007) and is undoubtedly related to the demographic decrease that occurred among Amerindians during the last century (Hurault 1965; Mazie`res et al. 2009). Genetic and demographic bottlenecks (i.e. reduction of the effective and census sizes of the population, respectively) are not automatically linked (Luikart et al. 1998b). The former can occur without reduction of the total population size if the next generation descends from a few mating pairs or a few breeders of one sex (Low 1988; Kittles et al. 1999; Wilder et al. 2004; Hammer et al. 2008). Conversely, a demographic reduction does not always lead to a severe loss of genetic diversity (Allendorf 1986). Central African Pygmies present an enlightening illustration of these phenomena. These hunter-gatherers show more variability for the HVS-I mtDNA (haplotype diversity above 0.80, Destro-Bisol et al. 2004), ASTRs (mean heterozygosity ¼ 0.76, Destro-Bisol et al. 2000) and YSTRs (gene diversity ¼ 0.56, Coia et al. 2004) than South Amerindians (mean values for HVS-I ¼ 0.77, Mazie`res et al. 2008; ASTRs ¼ 0.68; YSTRs ¼ 0.34, Table I), but no signs of population expansion (Excoffier and Schneider 1999) or substantial population decrease (Patin et al. 2009).
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Demographic history of Abies alba Mill. in the French Pyrenees

Demographic history of Abies alba Mill. in the French Pyrenees

Bruno Fady, Thomas Boivin, Brigitte Musch, Ivan Scotti, Marie Suez, Caroline Scotti-Saintagne.. To cite this version:.[r]

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Digest: Demographic inferences accounting for selection at linked sites

Digest: Demographic inferences accounting for selection at linked sites

may confound the detection of local adaptation. A scenario of secondary contacts was favored both between and within Ameri- can and European Atlantic salmon populations, providing strong evidence for a reticulated demographic history. This work empha- sizes the importance of identifying a null model of demographic history for a given species that accounts for both population struc- ture and selection at linked sites. Future studies seeking to identify signatures of divergent selection in natural populations will need to take into account variation in effective population size both in time and along the genome. Finally, this study illustrates the flexibility of ABC demographic inferences to account for dataset particularities such as the ascertainment bias in SNP chip arrays,
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Demographic inference through approximate-Bayesian-computation skyline plots

Demographic inference through approximate-Bayesian-computation skyline plots

The main appeal of skyline plots is to depict demographic trajectories not bounded by a mathematical function, thus potentially reflecting more realistically the demography of natural populations. However, our results show that plotted trajectories only loosely reflect the true demography, particularly for contracting populations. The match between the true and inferred demographic trajectory was good for constant size populations and for some expanding populations. Ancestral and current population sizes (the extremes of the skyline plot) were also retrieved accurately for favourable scenarios. Nevertheless, the shape of the curve representing the transition between population sizes was a poor representation of the true demographic trajectory in many cases. While this conclusion is specific for the implementation presented in this work, it calls to caution for the interpretation of results from other methods yielding smooth skyline plots (e.g., Heled & Drummond, 2008 ; Gill et al., 2013 ; Nikolic & Chevalet, 2014 ). The key for a smooth skyline plot is the prior on the effective-size autocorrelation through time. The demographic history consists of several demographic periods. Within each period the effective size at consecutive generations is correlated through some mathematical function (often a constant). Between consecutive periods, population size can be independent (our approach) or correlated by different sets of priors. Drummond et al. (2005) proposed using an exponential prior for the effective size ( θ i ) at period i with mean equal to the previous period effective size (θ i− 1 ). In the Bayesian
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Transnational History - Introduction

Transnational History - Introduction

Transnational history is an approach that emphasise what works between and through the units that humans have set up to organize their collective life, rather than what has been happening within these units taken as monads. It is a relational approach that focuses on relations and formations, circulations and connections, between, across and through these units, and how they have been made, not made and unmade. To appraise its tentative nature, it needs to be remembered that the phrase ‘transnational history’ is still young and its definition remains fluid. Chapter 1 will replace this idea in the wider context of the social sciences, picture this diversity, and connect it to the trajectory of the term since its appearance in 1842. Just as ‘transnational’ as an adjective is being used to specify a certain class of phenomena, or a
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Making History Work

Making History Work

The resuit was the first course of its kind in Canada. Stretching over the entire academie year, Applied Studies in History is divided into three components. In Pre-Practicum Seminars (Sept.-Oct.), students address the conceptual, methodological and ethical issues raised by the application of history outside the university classroom, drawing upon the established literature on applied history, along with other historical products (such as film, ‘ living muséums’, etc.). During the Practicum period (Nov.-March), students spend eight hours per week in a local company or organisation, acquiring the day-to-day skills required in that environment, and working toward a Final Project which is the crowning achievement of the practicum. Each practicum is regularly monitored both at the
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Making History Work

Making History Work

My answer to each of these inquiries has been to say that I plan to survive, one way or another! But the point is, the demand for good, but useable history is as great as it has ever been. I am reminded of the rise in the 1920s of Gebrauchsmusik, music designed to be socially useful and relevant, for example, music for film, radio, learners, and amateurs. It was sometimes called “community music, ” and at first attracted the attention of few professional composers. Paul Hindemith, especially after his émi ­ gration to the United States, wrote quantifies of music and textbooks that embodied the very best practices of professional composition, but in forms and in circumstances that invited whole new communities to do music, to make music, and to enjoy music as never before.
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Impact of Demographic Changes on Inflation and the Macroeconomy

Impact of Demographic Changes on Inflation and the Macroeconomy

Considerable difficulty lies in choosing appropriate variables for capturing demographic changes. In a representative-agent model of growth, population growth is a clean exogenous component that is to be used for empirical analysis. However, in a model with heterogeneous agents—typically in the setting of overlapping generations—there are compositional changes in demographics. Callen et al. (2004) uses the share of working-age population and the share of elderly population as two independent variables; other papers, including Muto, Oda, and Sudo (2012), capture the growth and the composition of population via the fertility rate and the longevity rate. While changes in fertility or mortality are key drivers of demographic changes, they might not be an adequate indicator for analyzing the macroeconomic impact of demographic changes, considering the long lag with which their changes affect the population structure and therefore the economy. For this reason,
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Demographic and ethnographic changes in Transcaucasia, 1897-1956

Demographic and ethnographic changes in Transcaucasia, 1897-1956

We lack data to analyze the relative fertility of the principal national groups, but the rate of population growth over the whole period suggests that the Armenian[r]

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LA SOURCE DÉMOGRAPHIQUE DES ELECTIONS [The demographic source of elections]

LA SOURCE DÉMOGRAPHIQUE DES ELECTIONS [The demographic source of elections]

ll est conforme aux missions des d6partements qui consistent pour une grande part i s'occuper des personnes (personnes 6g6es, handicap6s, aide sociale i I'enfance, personnes [r]

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Demographic inference using skyline plots on approximate bayesian computation

Demographic inference using skyline plots on approximate bayesian computation

Bayesian Skyline Plots are representations of the posterior probability density of the effective population size in function of time. A model with[r]

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