Inferring human population size and separation history from multiple genome sequences

Schiffels, Stephan; Durbin, Richard

doi:10.1101/005348

Cited by 170 publications

(313 citation statements)

References 54 publications

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“…With a detailed recombination map, equations relating the recombination fraction to expectations of LD can be used to estimate the recent history of N e , for example, SNeP (Barbato et al, 2015) and Hollenbeck et al (2016). Finally, with dense, phased genotype data, powerful new methods allow inference of complex demographic histories, including N e , for example, the multiple sequentially markovian coalescent (Schiffels and Durbin, 2014) and diCal (Sheehan et al, 2013), but these data are not yet available for most species.…”

Section: Related Approachesmentioning

confidence: 99%

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

2016

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Contemporary effective population size (N e ) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these N e estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause N e estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based N e estimates (N e ). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r 2 values, simply removing large r 2 values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias inN e is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision ofN e is much lower than expected based on the assumption that each pair of loci provides completely independent information. Heredity (Wright, 1931), which determines the rate of evolutionary change due to genetic drift and informs the equilibrium level of genetic variation and the effectiveness of selection. N e is often much lower than census size (Frankham, 1995), demonstrating that simply counting individuals is insufficient to predict rates of evolutionary change. In addition to the number of mating individuals, N e is affected by sex ratio, variation in reproductive success, age structure, migration and other demographic factors. It is an extremely relevant metric in conservation biology, with low N e leading to inbreeding and reduced genetic diversity (Ellstrand and Elam, 1993). See Charlesworth (2009) for a primer on N e , and Wang (2005) for a review of estimation methods.Populations with smaller N e undergo more genetic drift than larger populations. This genetic drift randomly generates associations between alleles at different loci, known as linkage (or gametic) disequilibrium (LD) at a rate inversely proportional to N e . As a result, measures of LD between independently-segregating loci can be used to provide an estimate of N e (Sved, 1971;Hill, 1981;Waples, 1991). Over the past decades, many studies have leveraged data sets consisting of a few dozen loci for genetic estimates of N e (Luikart et al., 2010). While these studies continue to be useful, especially for long-running

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Section: Related Approachesmentioning

confidence: 99%

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

2016

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“…Retrophylogenomics. We inferred past effective population sizes separately for the thylacine and Tasmanian devil using the PSMCʹ method as implemented in the program MSMC 92 .…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

“…MSMC gave the scaled mutation rate as θ d = 6.69107 × 10 −5 and θ t = 2.6563 × 10 −5 for the Tasmanian devil and the thylacine, respectively. Provided the "-fixedRecombination" parameter is not used, MSMC estimates ρ during each Baum-Welch iteration, which is very accurate after 50 iterations 92 . MSMC gave the scaled recombination rate at the 50th iteration as ρ d = 2.34114 × 10 −4 and ρ t = 5.78165 × 10 −5 for the Tasmanian devil and the thylacine, respectively.…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

et al. 2017

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The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.

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“…I constructed five simple branching models (without migration) based on the split times described in Pagani et al 16 All models used a scaling of 2N generations ¼ 1 million years and, when possible, assumed that the median genetic split times as estimated from MSMC 19 are actual population split times. Models 1-3 are simple branching models ( Figure 3A) with a split time between Europeans and East Asians of 30 Kya, a split time between Eurasians and Papuans of 40 Kya, and a split time between Eurasians and West Africans of 75 Kya.…”

Section: Simulations Modeled After Pagani Et Almentioning

confidence: 99%

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

Wall

2017

The American Journal of Human Genetics

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Inferring human population size and separation history from multiple genome sequences

Cited by 170 publications

References 54 publications

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

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