Estimating pairwise relatedness between individuals with different levels of ploidy

Huang, Kang; Ritland, Kermit; Guo, Songtao; Dunn, Derek W.; Chen, Dan; Ren, Yi; Xin, Qi; Zhang, Pei; He, Gang; Li, Baoguo

doi:10.1111/1755-0998.12351

Cited by 13 publications

(22 citation statements)

References 46 publications

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“…Allele frequencies and expected heterozygosity ( H exp ) were estimated for all 15 study loci from 113 mother queens and 109 of their male mates using GENEPOP ON THE WEB 4.2 [ 79 , 80 ]. Pairwise genetic relatedness coefficients ( r ) between each progeny-yielding mother queen and her mate(s), as well as between pairs of nestmate queens, were estimated by the maximum likelihood method of Huang et al [ 81 ] using the program POLYRELATEDNESS V1.5 and excluding the three supergene-linked loci; means and 95% confidence intervals (CIs) for r were obtained from 1000 bootstrap replicates over all pairs, a procedure adopted in light of the absence of colony-level effects on queen relatedness (Additional file 6 : Text S2). Associations between r and congruence in deviations from Mendelian ratios at the supergene were examined for pairs of nestmate queens using a resampling method combined with non-parametric Spearman correlation tests (Additional file 2 : Text S1); congruence in queens’ segregation ratios was represented by the difference in their k values (∆ k ), with k the proportion of gametes with the supergene-linked allele represented in a progeny.…”

Section: Methodsmentioning

confidence: 99%

Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta

Ross

Shoemaker

2018

BMC Genet

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BackgroundThe Sb supergene in the fire ant Solenopsis invicta determines the form of colony social organization, with colonies whose inhabitants bear the element containing multiple reproductive queens and colonies lacking it containing only a single queen. Several features of this supergene — including suppressed recombination, presence of deleterious mutations, association with a large centromere, and “green-beard” behavior — suggest that it may be a selfish genetic element that engages in transmission ratio distortion (TRD), defined as significant departures in progeny allele frequencies from Mendelian inheritance ratios. We tested this possibility by surveying segregation ratios in embryo progenies of 101 queens of the “polygyne” social form (3512 embryos) using three supergene-linked markers and twelve markers outside the supergene.ResultsSignificant departures from Mendelian ratios were observed at the supergene loci in 3–5 times more progenies than expected in the absence of TRD and than found, on average, among non-supergene loci. Also, supergene loci displayed the greatest mean deviations from Mendelian ratios among all study loci, although these typically were modest. A surprising feature of the observed inter-progeny variation in TRD was that significant deviations involved not only excesses of supergene alleles but also similarly frequent excesses of the alternate alleles on the homologous chromosome. As expected given the common occurrence of such “drive reversal” in this system, alleles associated with the supergene gain no consistent transmission advantage over their alternate alleles at the population level. Finally, we observed low levels of recombination and incomplete gametic disequilibrium across the supergene, including between adjacent markers within a single inversion.ConclusionsOur data confirm the prediction that the Sb supergene is a selfish genetic element capable of biasing its own transmission during reproduction, yet counterselection for suppressor loci evidently has produced an evolutionary stalemate in TRD between the variant homologous haplotypes on the “social chromosome”. Evidence implicates prezygotic segregation distortion as responsible for the TRD we document, with “true” meiotic drive the most likely mechanism. Low levels of recombination and incomplete gametic disequilibrium across the supergene suggest that selection does not preserve a single uniform supergene haplotype responsible for inducing polygyny.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0685-9) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta

Ross

Shoemaker

2018

BMC Genet

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“…For the microsatellite typing obtained from 229 baker yeasts, Ritland relatedness coefficient [51] was estimated using PolyRelatedness, a software able to estimating pairwise relatedness between individuals with different levels of ploidy [81]. A neighbor joining tree was obtained using the nj function from the ape R package.…”

Section: Phylogenetic Tree Imputationmentioning

confidence: 99%

Evidence for two main domestication trajectories inSaccharomyces cerevisiaelinked to distinct bread-making processes

Bigey

Segond

Friedrich

et al. 2020

Preprint

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Keywords yeast, tetraploid, Saccharomyces, sourdough, bread 1 2 3 4 5 6 7 8 9 10 11 12 13 14 SummaryDespite bread being one of the most historically and culturally important fermented products, its history and influence on the evolution of associated microbial species remains largely unknown. The first evidence of leavened bread dates to the second millenium BCE in Egypt and since, the art of bread-making developed and spread worldwide. Nowadays, leavened bread is made either by using a pure commercial culture of the yeast Saccharomyces cerevisiae or by propagating a sourdough, which is a mix of flour and water spontaneously fermented by yeast and bacteria. We studied the domestication of S. cerevisiae populations originating from industry and sourdough and tested whether these different bread-making processes led to population divergence. We found that the origin of S. cerevisiae bakery strains is polyphyletic with 67 % of strains clustering in two main clades: most commercial strains were tetraploid and clustered with strains having diverse origins, including beer. By contrast, most sourdough strains were diploids and found in a second clade of strains having mosaic genomes and diverse origins including fruits, or clinical and wild environments. When compared to the others, sourdough strains harboured in average a higher copy number of genes involved in maltose utilization, a common sugar produced from dough starch. Overall, a high level of gene flow from multiple contributors was detected. Phenotyping of bakery and non bakery strains further showed that sourdough and industrial bakery populations have undergone human selection for rapidly starting fermentations and for high CO 2 production. Interestingly, sourdough strains also showed a better adaptation to a sourdough mimicking environment, suggesting that natural selection occurred as well. In summary, our results revealed that the domestication of bakery yeast populations has been accompanied by dispersion, hybridization and divergent selection through industrial and artisanal bakery processes. In addition, they unveiled for the first time a case of fungus domestication where species divergence occurred through autotetraploidisation.

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“…基因型亲缘度 Genotypic relatedness 与基因型相异度相反, 指一个种群中两两基因型间亲缘程度的平均值。对于植物微卫星分子标记数据, 二倍体可以用STORM软件 (Frasier, 2008)或者R程序包"related" (Pew et al, 2015), 多倍体用P OLY R ELATEDNESS 计算基因型亲缘度 (Huang et al, 2015)。 The average value of relatedness between two genotypes in a population, which is contrary to genotypic dissimilarity. For plant microsatellite marker data, genotypic relatedness of diploids can be calculated with STORM software (Frasier, 2008) or R package "related" (Pew et al, 2015), and genotypic relatedness of polyploids can be calculated with P OLY R ELATEDNESS (Huang et al, 2015).…”

Section: 基因型 Genotype 一个个体在指定数量的位点上等位基因的组成。mentioning

confidence: 99%

A review on the relationships between plant genetic diversity and ecosystem functioning

Zhang¹

2018

Chinese Journal of Plant Ecology

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The loss of genetic diversity is accelerating due to habitat loss and population reduction caused by global change and anthropologenic activities. For species-poor ecosystems, the effect of genetic diversity on ecosystem functioning may not be smaller than that of species diversity. Therefore, understanding the relationship between genetic diversity and ecosystem functioning (GD-EF) and its underlying mechanisms is important for biodiversity conservation, responses of ecosystems to environmental change and ecological restoration. Here, we reviewed the studies on the effects of plant genetic diversity on ecosystem structures (community structure of the higher tropic level) and ecosystem functions (primary production, nutrient cycling and ecosystem stability), and the mechanisms underlying these relationships. We also discussed the influence of functional diversity on GD-EF, the comparison of effects of the genetic and species diversity on ecosystem functioning, and the application of GD-EF in the ecological restorations. We finally pointed out the limitations in current studies to provide references for the future: (1) further studies on the mechanisms of GD-EF are needed; (2) no study has evaluated the influence of genetic diversity on maltifunctinarity; (3) the impacts of different measurements of genetic diversity on ecosystem functioning are unclear; (4) there are lack of long-time GD-EF studies and GD-EF studies conducted at multidimensional scales; (5) the relative importance of genetic diversity and other factors on ecosystem functioning in the nature is unclear.

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Estimating pairwise relatedness between individuals with different levels of ploidy

Cited by 13 publications

References 46 publications

Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta

Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta

Evidence for two main domestication trajectories inSaccharomyces cerevisiaelinked to distinct bread-making processes

A review on the relationships between plant genetic diversity and ecosystem functioning

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