GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data

Noskova, Ekaterina; Ulyantsev, Vladimir; Koepfli, Klaus Peter; O’Brien, Stephen J.; Dobrynin, Pavel

doi:10.1093/gigascience/giaa005

Cited by 50 publications

(40 citation statements)

References 44 publications

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“…The expected and observed 2D‐SFS were compared with gadma v1.0.0 (Noskova et al, 2020 ), using the Powell's conjugate direction method implemented in moments v1.0.2 (Jouganous et al, 2017 ) and four repeats with default parameters. The examined models were restricted to a structure with two changes each before and after the population split without gene flow.…”

Section: Methodsmentioning

confidence: 99%

The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes

et al. 2021

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Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole‐genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome‐wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for ‘molecular pre‐adaptation’ in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome‐wide factors underlying the propensity for these cichlid fishes to adaptively radiate.

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Section: Methodsmentioning

confidence: 99%

The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes

et al. 2021

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“…Glacial periods have influenced sea level through time and have had a significant effect on the demography of coral reef fishes through the Indo‐West Pacific (Avise, 2009 ; Hewitt, 2004 ; Hickerson et al, 2010 ). To determine whether these events have influenced the evolutionary history of P. leopardus in the Coral Sea and the GBR, we inferred the demographic histories of populations using a modified diffusion approximation of the Wright‐Fischer population model implemented in the program GADMA (Noskova et al, 2020 ). GADMA infers the joint demographic history of up to three populations from genetic data and has benefits over other programs because it does not require the user to specify the large number of possible demographic histories that may characterize a group of populations.…”

Section: Methodsmentioning

confidence: 99%

“…Moments was selected as the software to simulate allele frequency spectra from demographic models because it has shown to produce robust results and is computationally more efficient than alternatives (Noskova et al, 2020 ). Initial model structure was set to one time interval before the population split and one after (1,1).…”

Section: Methodsmentioning

confidence: 99%

Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Payet

Pratchett

Saenz‐Agudelo

et al. 2022

Evolutionary Applications

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Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology, since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10 -120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

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“…We used easySFS ( https://github.com/isaacovercast/easySFS ) to estimate the site frequency spectrum (sfs), which was the input file for the demographic analysis using GADMA ( Noskova et al 2020 ). The GADMA approximation software tool was used to compare the expected allele frequency and the observed allele frequency spectrum over the parameter value space by computing a composite-likelihood score for the best plausible evolutionary scenarios.…”

Section: Methodsmentioning

confidence: 99%

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Zhang

Yang

et al. 2021

Molecular Biology and Evolution

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Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We re-sequenced 80 Eurasian pigs from 9 different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene-flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y-chromosomes.

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GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data

Cited by 50 publications

References 44 publications

The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes

The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes

Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

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