MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent

Schiffels, Stephan; Wang, Ke

doi:10.1007/978-1-0716-0199-0_7

Cited by 153 publications

(222 citation statements)

References 15 publications

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“…To infer historical changes in effective population size ( Ne ) and estimate the TMRCA in the P. vivax and P. vivax-like populations, we ran the MSMC program ( 75 ) on the core genome of all chromosomes. Homozygous SNPs present on each Plasmodium chromosome were considered as single phased haplotype.…”

Section: Methodsmentioning

confidence: 99%

Population genomic evidence of a Southeast Asian origin ofPlasmodium vivax

Daron

Boissière

Ngoubangoye

et al. 2020

Preprint

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20Plasmodium vivax is the most prevalent and widespread human malaria parasite, 21 with almost three billion people living at risk of infection. With the discovery of its closest 22 genetic relatives in African great apes (Plasmodium vivax-like), the origin of P. vivax has 23 been proposed to be located in the sub-Saharan African area. However, the limited number 24 of genetic markers and samples investigated questioned the robustness of this result. Here, 25 we examined the population genomic variation of 447 human P. vivax strains and 19 ape P. 26 vivax-like strains originating from 24 different countries across the world. We identified 27 2,005,455 high quality single-nucleotide polymorphism loci allowing us to conduct an 28 extensive characterization to date of P. vivax worldwide genetic variation. Phylogenetic 29 relationships between human and ape Plasmodium revealed that P. vivax is a sister clade of 30 P. vivax-like, not included within the radiation of P. vivax-like. By investigating a variety of 31 aspects of P. vivax variation, we identified several striking geographical patterns in summary 32 statistics as function of increasing geographic distance from Southeast Asia, suggesting that 33 P. vivax may derived from serial founder effects from a single origin located in Asia. 34 evolutionary selection partly due to known drug resistance genes. However, even though 62 they released hundreds of complete genomes, each of them restricted their investigation on 63 a sub-fraction of the worldwide P. vivax diversity, either located in Asia-Pacific or South 64America. Consequently, a comprehensive picture of the worldwide genetic diversity and 65 structure of P. vivax populations is still missing and its evolutionary history and how it spread 66 over the world is still poorly understood. Moreover, despite growing evidence suggesting an 67 underlying widespread presence of P. vivax across all malaria-endemic regions of Africa from this area. Thus, a key challenge is to provide a worldwide understanding of the genetic 70 variability of P. vivax at the genome level to bring insights on the past demographic history 71 and origin of this pathogen. 72The origin of current P. vivax in humans has stimulated passionate and exciting 73 debates for years. Certain studies placed the origin of the human P. vivax in Southeast Asia 74 ("out of Asia" hypothesis) based on its phylogenetic position in a clade of parasites infecting 75Asian monkeys (17)(18)(19). This scenario was also supported by genotyping data at 11 76 microsatellite markers collected across four continents, showing the highest microsatellite 77 diversity in Southeast Asia (20, 21). However, the Asian-origin has been challenged by an 78 "out of Africa" scenario, with the recent discovery of a closely related Plasmodium species 79 circulating in wild-living African great apes (chimpanzees and gorillas) (22). This new 80 lineage, hereafter referred to as P. vivax-like, was suggested to have given rise to P. vivax in 81 humans following the transfer of parasit...

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Section: Methodsmentioning

confidence: 99%

Population genomic evidence of a Southeast Asian origin ofPlasmodium vivax

Daron

Boissière

Ngoubangoye

et al. 2020

Preprint

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“…PSMC output was converted to effective population size assuming a mutation rate of 3.5x10 -9 bp -1 generation -1 and a generation time of 0.5 years, as described previously (Schumer et al, 2018). We note that although other methods such as MSMC allow for simultaneous inference of demographic history in multiple individuals, they also require phasing, which can introduce errors, especially in cases where high quality reference panels are not available (Schiffels & Wang, 2020).…”

Section: Psmc Demographic Inferencementioning

confidence: 99%

Two new hybrid zones expand the swordtail hybridization model system

Dl¹,

Moran²,

Kim

et al. 2020

Preprint

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Natural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here we characterize hybrid populations formed between the northern swordtail fish Xiphophorus cortezi and X. birchmanni from collection sites on two rivers. We develop sensitive and accurate local ancestry calling for this system based on low coverage whole genome sequencing. Strikingly, we find that hybrid populations on both rivers consist of two genetically distinct subpopulations: a cluster of nearly pure X. birchmanni individuals and one of phenotypically intermediate hybrids that derive ~85-90% of their genome from X. cortezi. Simulations and empirical data suggest that at both sites initial hybridization occurred ~150 generations ago, with little evidence for contemporary gene flow between subpopulations, likely due to strong assortative mating. The patterns of population structure uncovered here mirror those seen in hybridization between X. birchmanni and its sister species, X. malinche. Future comparisons will provide a window into the repeatability of the outcomes of hybridization not only across independent hybridization events between the same species but also across distinct species pairs.

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“…For endangered species for which fewer populations and individuals exist, if it is a priority to obtain their genetic parameters, new bioinformatics tools have been developed to estimate the demographic history based on fewer individuals sampled (Gronau et al, 2011;Schiffels and Wang, 2020). The problem is that these methods rely on large amounts of SNPs, which can be challenging to obtain if no reference genomes are available (Glenn, 2011).…”

Section: Tests Of Selection Using Bayescenvmentioning

confidence: 99%

“…In addition, the bioinformatic processing required for large samples can be limiting, making it difficult to obtain adequate genomic representation for enough individuals and populations. A solution has been to prioritize sequencing power to compensate for fewer individuals or populations (Schiffels and Wang, 2020). However, in the context of local adaptation, sampling populations in different parts of the distribution or different environments can affect the adequate estimation of genetic parameters (Meirmans, 2015).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize

et al. 2020

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Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For all datasets, we generated different subsampling designs by changing the number of loci, individuals, populations, and individuals per population to test for deviations in classic population genetics parameters (H S , F IS , F ST). For the empirical datasets we also analyzed the effect of sampling design on landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling a different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. F IS was particularly sensitive to a low sampling of individuals in the simulated, genomic, and microsatellite datasets. For the empirical and simulated genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For the empirical datasets, we found that increasing the number of populations sampled was important in obtaining precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.

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MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent

Cited by 153 publications

References 15 publications

Population genomic evidence of a Southeast Asian origin ofPlasmodium vivax

Population genomic evidence of a Southeast Asian origin ofPlasmodium vivax

Two new hybrid zones expand the swordtail hybridization model system

Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize

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