Demographic inference

Marchi, Nina; Schlichta, Flávia; Excoffier, Laurent

doi:10.1016/j.cub.2021.01.053

Cited by 43 publications

(40 citation statements)

References 9 publications

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“…This migration gradually reduced the genetic diversity of these populations because of their distance from Africa (76). At the micro-evolutionary scale of fewer than 20 generations, Quebec demography may serve as an example of how human populations evolved, assisting interpretation of models of demographic inference attempting to reconstruct demographic histories (1).…”

Section: Québec Population History and Founder Eventsmentioning

confidence: 99%

“…It relies on likelihoods using demographic models that assume long-term equilibria. To reveal populations' genetic past and demographic history, we routinely model populations' ascending genealogical trees (1). However, "the history of the human species and of particular populations suggests that long-term equilibria, an assumption of many genetic models, is only a convenient mathematical fiction" (2, 3) (and see also (4)).…”

Section: Introductionmentioning

confidence: 99%

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The effective family size of immigrant founders predicts their long-term demographic outcome: from Québec settlers to their 20th-century descendants

Labuda

Harding

Milot

et al. 2021

Preprint

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Human evolution involves population splits, size fluctuations, founder effects, and admixture. Population history reconstruction based on genetic diversity data routinely relies on simple demographic models while projecting the past. Yet, no specific demographic assumptions are needed to understand the genetic structure of the founder population of Quebec. Because genealogy and genetics are intimately related, we used descending genealogies of this population to pursue the fate of its founder lineages. Maternal and paternal lines reflect the transmission of mtDNA and the Y-chromosome, respectively. We followed their transmission in real-time, from the 17th century down to its 20th-century population. We counted the number of married children of immigrants (i.e., their effective family size, EFS), estimated the proportion of successful immigrants in terms of their survival ratio, and assessed net growth rates and extinction. Likewise, we evaluated the same parameters for their Quebec-born descendants. The survival ratio of the first immigrants was the highest and declined over time in association with the decreasing immigrants EFS. Parents with high EFS left plentiful married progeny, putting EFS as the most important variable determining the parental demographic success throughout time for generations ahead. The 17th and 18th-century immigrants bear the most remarkable demographic and genetic impact on the 20th-century population of Quebec. Lessons learned from Quebec genealogies can teach us about the consequences of founder effects and migrations through real peoples history. The effective family size of immigrant founders predicts their long-term demographic outcome.

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Section: Québec Population History and Founder Eventsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The effective family size of immigrant founders predicts their long-term demographic outcome: from Québec settlers to their 20th-century descendants

Labuda

Harding

Milot

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…pool-seq data and Site Frequency Spectrums (SFSs), that are increasingly available for a broad range of organisms. Existing methods to infer migration pulses would typically use individual genome sequences or haplotypes to detect repeated admixture events, and exploit neutral variation only (Marchi et al ., 2021). The approach we have sketched here could thus provide a way to improve our methodological arsenal to infer the occurrence of pulsed migration from genomic data.…”

Section: Discussionmentioning

confidence: 99%

Migration pulsedness alters patterns of allele fixation and local adaptation in a mainland-island model

Aubree

Calcagno

et al. 2021

Preprint

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Gene flow, through allele migration and spread, is critical in determining patterns of population genetic structure, divergence and local adaptation. While evolutionary theory has typically envisioned gene flow as a continuous connection among populations, many processes can render it fluctuating and intermittent. We analyze mathematically a stochastic mainland-island model in continuous time, in which migration occur as recurrent “pulses”. We derive simple analytical approximations regarding how migration pulsedness affects the effective migration rates across a range of selection and dominance scenarios. Predictions are validated with stochastic simulations and summarized with graphical interpretations in terms of fixation probabilities. We show that migration pulsedness can decrease or increase gene flow, respectively above or below a selection threshold that is for additive alleles and lower for recessive deleterious alleles. We propose that pulsedness may leave a genomic detectable signature, by differentially affecting the fixation rates of loci subjected to different selection regimes. The additional migration created by pulsedness is called a “pulsedness” load. Our results indicate that migration pulsedness, and more broadly temporally variable migration, is important to consider for evolutionary and population genetics predictions. Specifically, it would overall be detrimental to the local adaptation and persistence of small peripheral populations.

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“…Demographic inference using site-frequency spectra (quantifying the relative frequency of alleles at different rarities present in a population) reliant on genome-wide data allows for the estimation of gene flow and effective population sizes across populations of interest (Marchi et al 2021 ). These have been previously shown to lead to accurate population size estimates in simulations (Nunziata and Weisrock 2018 ) and empirically in salamanders (Nunziata et al 2017 ), and are a promising tool for assessing population sizes of cryptic species.…”

Section: Conservation Of Rare and Cryptic Cave-obligate Tetrapodsmentioning

confidence: 99%

From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods

Recknagel

Trontelj

2021

BioScience

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Throughout most of the kingdom Animalia, evolutionary transitions from surface life to a life permanently bound to caves and other subterranean habitats have occurred innumerous times. Not so in tetrapods, where a mere 14 cave-obligate species—all plethodontid and proteid salamanders—are known. We discuss why cave tetrapods are so exceptional and why only salamanders have made the transition. Their evolution follows predictable and convergent, albeit independent pathways. Among the many known changes associated with transitions to subterranean life, eye degeneration, starvation resistance, and longevity are especially relevant to human biomedical research. Recently, sequences of salamander genomes have become available opening up genomic research for cave tetrapods. We discuss new genomic methods that can spur our understanding of the evolutionary mechanisms behind convergent phenotypic change, the relative roles of selective and neutral evolution, cryptic species diversity, and data relevant for conservation such as effective population size and demography.

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Demographic inference

Cited by 43 publications

References 9 publications

The effective family size of immigrant founders predicts their long-term demographic outcome: from Québec settlers to their 20th-century descendants

The effective family size of immigrant founders predicts their long-term demographic outcome: from Québec settlers to their 20th-century descendants

Migration pulsedness alters patterns of allele fixation and local adaptation in a mainland-island model

From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods

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