Recent demographic histories of temperate deciduous trees inferred from microsatellite markers

Abstract Background Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing microsatellite data assume a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation does not follow SMM. Results This study aims to reconstruct the recent demographic histories of five cool-temperate tree species in Eastern Asia, Quercus mongolica, Q. liaotungensis, Juglans cathayensis, J. mandshurica and J. ailantifolia, by using 19 microsatellite markers with two methods considering generalized stepwise mutation model (GSM) (MIGRAINE and VarEff). Both programs revealed that all the five species experienced expansions after the Last Glacial Maximum (LGM). Within butternuts, J. cathayensis experienced a more serious bottleneck than the other species, and within oaks, Q. mongolica showed a moderate increase in population size and remained stable after the expansion. In addition, the point estimates of the multistep mutation proportion in the GSM model (pGSM) for all five species were between 0.50 and 0.65, indicating that when inferring population demographic history of the cool-temperate forest species using microsatellite markers, it is better to assume a GSM rather than a SMM. Conclusions This study provides the first direct evidence that five cool-temperate tree species in East Asia have experienced expansions after the LGM with microsatellite data. Considering the mutation model of microsatellite has a vital influence on demographic inference, combining multiple programs such as MIGRAINE and VarEff can effectively reduce errors caused by inappropriate model selection and prior setting.

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Recent demographic histories of temperate deciduous trees inferred from microsatellite markers

10.21203/rs.3.rs-119096/v1 ◽

2020 ◽

Author(s):

Yu Cao ◽

Da-Yong Zhang ◽

Yan-Fei Zeng ◽

Wei-Ning Bai

Keyword(s):

Microsatellite Markers ◽

Tree Species ◽

Demographic History ◽

Stepwise Mutation Model ◽

Moderate Increase ◽

Effective Population ◽

Mutation Model ◽

Cool Temperate ◽

Stepwise Mutation ◽

Population Demographic

Abstract Background Accurate inference of demographic histories of temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for reflecting recent historical events due to their high mutation rates. However, most programs analyze microsatellite data following a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation is not according with SMM. Results This study aims to reconstruct the recent demographic histories of five cool-temperate tree species, Quercus mongolica, Q. liaotungensis, Juglans cathayensis, J. mandshurica and J. ailantifolia, in eastern Asia by using 19 microsatellite markers and two methods considering generalized stepwise mutation model (GSM) (MIGRAINE and VarEff). Both types of software revealed that all populations experienced expansions after the Last Glacial Maximum (LGM). In particular, J. cathayensis experienced a more serious bottleneck in its history than the other species, leading to a smaller effective population of ancestors, while Q. mongolica showed only a moderate increase in population size and remained stable after the expansion. In addition, the point estimates of the multistep mutation proportion in the generalized stepwise mutation model (pGSM) in all populations were between 0.50 and 0.65, which indicates that when inferring population demographic history of the above forest species using microsatellite molecular markers, it is better to assume a GSM rather than a SMM. Conclusions This study provides the first direct evidence that five cool-temperate tree species in East Asia have experienced expansions after the LGM using microsatellites data. Moreover, since the mutation model of microsatellite have a vital influence on demographic inference, combining multiple software programs such as MIGRAINE and VarEff can effectively reduce unnecessary errors caused by inappropriate model selection and prior setting.

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An evaluation of genetic distances for use with microsatellite loci.

Genetics ◽

10.1093/genetics/139.1.463 ◽

1995 ◽

Vol 139 (1) ◽

pp. 463-471 ◽

Cited By ~ 22

Author(s):

D B Goldstein ◽

A Ruiz Linares ◽

L L Cavalli-Sforza ◽

M W Feldman

Keyword(s):

Microsatellite Loci ◽

Phylogenetic Reconstruction ◽

Genetic Distances ◽

Stepwise Mutation Model ◽

Mutation Model ◽

Stepwise Mutation ◽

The Difference ◽

Nei's Distance ◽

Infinite Alleles Model ◽

Overall Reliability

Abstract Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

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BOTTLENECK EFFECTS ON AVERAGE HETEROZYGOSITY AND GENETIC DISTANCE WITH THE STEPWISE MUTATION MODEL

Evolution ◽

10.1111/j.1558-5646.1977.tb01017.x ◽

1977 ◽

Vol 31 (2) ◽

pp. 347-356 ◽

Cited By ~ 162

Author(s):

Ranajit Chakraborty ◽

Masatoshi Nei

Keyword(s):

Genetic Distance ◽

Stepwise Mutation Model ◽

Average Heterozygosity ◽

Mutation Model ◽

Stepwise Mutation

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Measures of Variation at DNA Repeat Loci under a General Stepwise Mutation Model

Theoretical Population Biology ◽

10.1006/tpbi.1996.0035 ◽

1996 ◽

Vol 50 (3) ◽

pp. 345-367 ◽

Cited By ~ 58

Author(s):

Marek Kimmel ◽

Ranajit Chakraborty

Keyword(s):

Stepwise Mutation Model ◽

Mutation Model ◽

Dna Repeat ◽

Stepwise Mutation

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Simulation results with stepwise mutation model and their interpretations

Journal of Molecular Evolution ◽

10.1007/bf01796093 ◽

1977 ◽

Vol 9 (4) ◽

pp. 313-322 ◽

Cited By ~ 5

Author(s):

Ranajit Chakraborty

Keyword(s):

Stepwise Mutation Model ◽

Mutation Model ◽

Stepwise Mutation ◽

Simulation Results

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THE STEPWISE MUTATION MODEL: AN EXPERIMENTAL EVALUATION UTILIZING HEMOGLOBIN VARIANTS

Genetics ◽

10.1093/genetics/94.1.185 ◽

1980 ◽

Vol 94 (1) ◽

pp. 185-201

Author(s):

Paul A Fuerst ◽

Robert E Ferrell

Keyword(s):

Amino Acid ◽

Electrophoretic Mobility ◽

Tertiary Structure ◽

Stepwise Mutation Model ◽

Starch Gel Electrophoresis ◽

Human Hemoglobin ◽

Net Charge ◽

Mutation Model ◽

Stepwise Mutation ◽

Hemoglobin Variants

ABSTRACT The stepwise mutation model of OHTA and KIMURA (1973) was proposed to explain patterns of genetic variability revealed by means of electrophoresis. The assumption that electrophoretic mobility was principally determined by unit changes in net molecular charge has been criticized by JOHNSON (1974, 1977). This assumption has been tested directly using hemoglobin. Twenty-seven human hemoglobin variants with known amino acid substitutions, and 26 nonhuman hemoglobins with known sequences were studied by starch gel electrophoresis. Of these hemoglobin% 60 to 70% had electrophoretic mobilities that could be predicted solely on the basis of net charge calculated from the amino acid composition alone, ignoring tertiary structure. Only four hemoglobins showed a mobility that was clearly different from an expected mobility calculated using only the net charge of the molecule. For the remaining 30% of hemoglobins studied, mobility was determined by a combination. of net charge and other unidentified components, probably reflecting changes in ionization of some amino acid residues as a result of small alterations in tertiary structure due to the amino acid substitution in the variant. For the nonhuman hemoglobins, the deviation of a sample from its expected mobility increased with increasing amino acid divergence from human hemoglobin A.—It is concluded that the net electrostatic charge of a molecule is the principal determinant of electrophoretic mobility under the conditions studied. However, because of the significant deviation from strict stepwise mobility detected for 30 to 40% of the variants studied, it is further concluded that the infinite-allele model of KIMURA and CROW (1964) or a "mixed model" such as that proposed by LI (1976) may be more appropriate than the stepwise mutation model for the analysis of much of the available electrophoretic data from natural populations.

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Stepwise Mutation Model (SMM)

Encyclopedia of Genetics, Genomics, Proteomics and Informatics ◽

10.1007/978-1-4020-6754-9_16166 ◽

2008 ◽

pp. 1881-1881

Keyword(s):

Stepwise Mutation Model ◽

Mutation Model ◽

Stepwise Mutation

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Variabilidade genética de larvas e alevinos de piracanjuba (Brycon orbignyanus)

Arquivo Brasileiro de Medicina Veterinária e Zootecnia ◽

10.1590/1678-4162-10312 ◽

2019 ◽

Vol 71 (2) ◽

pp. 696-702

Author(s):

P.L. Castro ◽

V. Lewandowski ◽

F.P. Souza ◽

C. Sary ◽

N.G. Leite ◽

...

Keyword(s):

Stepwise Mutation Model ◽

Mutation Model ◽

Stepwise Mutation

RESUMO O objetivo do presente trabalho foi avaliar a variabilidade genética de larvas e alevinos de piracanjuba em programa de repovoamento. Foram coletadas 180 larvas de piracanjuba de três dias e 90 alevinos de três meses de idade. Foram avaliados cinco loci microssatélites, os quais produziram 19 alelos. Não houve presença de alelos raros nem perdas de alelos ao longo do período. A heterozigosidade observada foi superior nas larvas em relação aos alevinos. Houve desvio no equilíbrio de Hardy-Weinberg na maioria dos loci em ambos os grupos. O coeficiente de endogamia foi positivo em ambos os grupos, sendo a média dos alevinos superior em relação às larvas. O excesso de heterozigotos foi significativo no modelo Stepwise Mutation Model para os alevinos, indicando a possibilidade de efeito gargalo recente. Conclui-se que, apesar da adequada variabilidade genética encontrada, os valores do coeficiente de endogamia e a possibilidade de efeito gargalo nos alevinos atentam para a necessidade de constante monitoramento genético desses estoques antes da liberação no ambiente.

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