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The authors explored the effects of nonindependent mate pairing across breeding seasons on Ne. Two results have particular relevance for understanding human demography: nonindependent mate pairing has no effect in monogamous mating systems, but can have a strong effect in polygynous systems. In the latter scenario, nonindependent mating across breeding seasons leads to a relatively reduced male Ne.
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16• Evans, B.J., Charlesworth, B., The effect of nonindependent mate pairing on the effective population size. Genetics 193 (2013), 545–556 The authors explored the effects of nonindependent mate pairing across breeding seasons on Ne. Two results have particular relevance for understanding human demography: nonindependent mate pairing has no effect in monogamous mating systems, but can have a strong effect in polygynous systems. In the latter scenario, nonindependent mating across breeding seasons leads to a relatively reduced male Ne.
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19 Kong, A., Frigge, M.L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., Gudjonsson, S.A., Sigurdsson, A., Jonasdottir, A., Jonasdottir, A., et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature 488 (2012), 471–475.
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20 Francioli, L.C., Polak, P.P., Koren, A., Menelaou, A., Chun, S., Renkens, I., van Duijn, C.M., Swertz, M., Wijmenga, C., van Ommen, G., et al. Genome-wide patterns and properties of de novo mutations in humans. Nat Genet 47 (2015), 822–826.
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This study incorporates generation time into models of mutation bias to better understand patterns of substitution among the great apes. The authors show that sex differences in generation time can affect mutation and substitution in complex ways.
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21• Amster, G., Sella, G., Life history effects on the molecular clock of autosomes and sex chromosomes. Proc Natl Acad Sci U S A 113 (2016), 1588–1593 This study incorporates generation time into models of mutation bias to better understand patterns of substitution among the great apes. The authors show that sex differences in generation time can affect mutation and substitution in complex ways.
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In this paper, the authors show that how patterns of migration affect genetic diversity, particularly in regards to isolation and reconnection events. They show that a reconnection event after complete isolation can cause an unexpectedly abrupt increase in within-population diversity, with a peak much higher than equilibrium values. This increased diversity can last for a very long time, occur under a wide range of parameter values, and be indistinguishable from a range of demographic and selective forces using common population genetic measures.
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22• Alcala, N., Streit, D., Goudet, J., Vuilleumier, S., Peak and persistent excess of genetic diversity following an abrupt migration increase. Genetics 193 (2013), 953–971 In this paper, the authors show that how patterns of migration affect genetic diversity, particularly in regards to isolation and reconnection events. They show that a reconnection event after complete isolation can cause an unexpectedly abrupt increase in within-population diversity, with a peak much higher than equilibrium values. This increased diversity can last for a very long time, occur under a wide range of parameter values, and be indistinguishable from a range of demographic and selective forces using common population genetic measures.
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Alcala, N.1
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23 Wilkins, J.F., Marlowe, F.W., Sex-biased migration in humans: what should we expect from genetic data?. Bioessays 28 (2006), 290–300.
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24 Schraiber, J.G., Akey, J.M., Methods and models for unravelling human evolutionary history. Nat Rev Genet 16 (2015), 727–740.
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The authors modeled the effects of admixture on the autosomes and X chromosome. For a single event, admixture on the X chromosome varies in a way that, by comparing it to admixture on the autosomes, one is able to identify initial sex-specific contributions from each source population. In the case of constant admixture, admixture measures on the X and autosomes cannot be used to identify specific sex-biased contributions; rather, it is only possible to produce a range of estimates.
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25• Goldberg, A., Rosenberg, N.A., Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome. Genetics 201 (2015), 263–279 The authors modeled the effects of admixture on the autosomes and X chromosome. For a single event, admixture on the X chromosome varies in a way that, by comparing it to admixture on the autosomes, one is able to identify initial sex-specific contributions from each source population. In the case of constant admixture, admixture measures on the X and autosomes cannot be used to identify specific sex-biased contributions; rather, it is only possible to produce a range of estimates.
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Goldberg, A.1
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26 Lippold, S., Xu, H., Ko, A., Li, M., Renaud, G., Butthof, A., Schröder, R., Stoneking, M., Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. Investig Genet 5 (2014), 1–17.
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27 Aimé, C., Heyer, E., Austerlitz, F., Inference of sex-specific expansion patterns in human populations from Y-chromosome polymorphism. Am J Phys Anthr 157 (2015), 217–225.
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28
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This was one of the first attempts to use genome-scale data to understand the effects of sex-biased processes on neutral diversity. Notably, they found higher than expected X/A diversity ratios in a geographically diverse sample of populations and conclude that a greater variance in reproductive sex in males than females might be a phenomenon common among many human societies.
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28• Hammer, M.F., Mendez, F.L., Cox, M.P., Woerner, A.E., Wall, J.D., Sex-biased evolutionary forces shape genomic patterns of human diversity. PLOS Genet, 4, 2008, e1000202 This was one of the first attempts to use genome-scale data to understand the effects of sex-biased processes on neutral diversity. Notably, they found higher than expected X/A diversity ratios in a geographically diverse sample of populations and conclude that a greater variance in reproductive sex in males than females might be a phenomenon common among many human societies.
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29
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29 Emery, L.S., Felsenstein, J., Akey, J.M., Estimators of the human effective sex ratio detect sex biases on different timescales. Am J Hum Genet 87 (2010), 848–856.
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30
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This is one of the first studies to jointly analyze diversity across the autosomes, X chromosome, Y chromosome, and mtDNA from whole genomes, identifying significantly reduced Y-linked diversity relative to neutral equilibrium expectations in humans. They showed that models of extreme variance in male reproductive success, together with population-specific estimates of demography in African and European populations, were not sufficient to explain this observation. They instead showed that models including natural selection acting on the non-recombining Y chromosome were consistent with genome-wide diversity.
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30•• Wilson Sayres, M.A., Lohmueller, K.E., Nielsen, R., Natural selection reduced diversity on human Y chromosomes. PLoS Genet, 10, 2014, e1004064 This is one of the first studies to jointly analyze diversity across the autosomes, X chromosome, Y chromosome, and mtDNA from whole genomes, identifying significantly reduced Y-linked diversity relative to neutral equilibrium expectations in humans. They showed that models of extreme variance in male reproductive success, together with population-specific estimates of demography in African and European populations, were not sufficient to explain this observation. They instead showed that models including natural selection acting on the non-recombining Y chromosome were consistent with genome-wide diversity.
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Wilson Sayres, M.A.1
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31
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31 Rodriguez-Flores, J.L., Fakhro, K., Agosto-Perez, F., Ramstetter, M.D., Arbiza, L., Vincent, T.L., Robay, A., Malek, J.A., Suhre, K., Chouchane, L., et al. Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome Res 26 (2016), 151–162.
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32
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32 Batini, C., Hallast, P., Zadik, D., Delser, P.M., Benazzo, A., Ghirotto, S., Arroyo-Pardo, E., Cavalleri, G.L., de Knijff, P., Dupuy, B.M., et al. Large-scale recent expansion of European patrilineages shown by population resequencing. Nat Commun, 6, 2015, 7152.
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33
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This study analyzed genetic diversity on across a global sample of 456 geographically distinct Y chromosome and mtDNA and used Bayesian skyline plots to infer temporal changes in historical population sizes for these paternally inherited and maternally inherited loci. Both markers showed evidence of an expansion approximately 40–60 thousand years ago, though Y-linked diversity was consistently lower than mtDNA diversity. Further, the Y chromosome, but not the mtDNA, showed evidence of a contraction between 4 and 8 thousand years ago, depending on the population, which correlates with changes in human culture after the onset of agriculture.
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33•• Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M.A., Järve, M., Talas, U.G., Rootsi, S., Ilumäe, A.-M.-.M., Mägi, R., Mitt, M., et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res 25 (2015), 459–466 This study analyzed genetic diversity on across a global sample of 456 geographically distinct Y chromosome and mtDNA and used Bayesian skyline plots to infer temporal changes in historical population sizes for these paternally inherited and maternally inherited loci. Both markers showed evidence of an expansion approximately 40–60 thousand years ago, though Y-linked diversity was consistently lower than mtDNA diversity. Further, the Y chromosome, but not the mtDNA, showed evidence of a contraction between 4 and 8 thousand years ago, depending on the population, which correlates with changes in human culture after the onset of agriculture.
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Genome Res
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Karmin, M.1
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34
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Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
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The authors analyzed a sample of 1244 Y chromosomes sequenced as part of the 1000 genomes project. They identified more than 65 000 mutations (most of them single nucleotide polymorphisms) and discovered strong signals of both tremendous variance in male reproductive success and strong purifying selection.
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34• Poznik, G.D., Xue, Y., Mendez, F.L., Willems, T.F., Massaia, A., Wilson Sayres, M.A., Ayub, Q., McCarthy, S.A., Narechania, A., Kashin, S., et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet 48 (2016), 593–599 The authors analyzed a sample of 1244 Y chromosomes sequenced as part of the 1000 genomes project. They identified more than 65 000 mutations (most of them single nucleotide polymorphisms) and discovered strong signals of both tremendous variance in male reproductive success and strong purifying selection.
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Poznik, G.D.1
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35
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Female and male perspectives on the Neolithic Transition in Europe: clues from ancient and modern genetic data
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35 Rasteiro, R., Chikhi, L., Female and male perspectives on the Neolithic Transition in Europe: clues from ancient and modern genetic data. PLOS ONE, 8, 2013, e60944.
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Rasteiro, R.1
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Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia
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36 Aimé, C., Verdu, P., Ségurel, L., Martinez-Cruz, B., Hegay, T., Heyer, E., Austerlitz, F., Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia. Eur J Hum Genet 22 (2014), 1201–1207.
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Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming
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37 Aimé, C., Laval, G., Patin, E., Verdu, P., Ségurel, L., Chaix, R., Hegay, T., Quintana-Murci, L., Heyer, E., Austerlitz, F., Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming. Mol Biol Evol 30 (2013), 2629–2644.
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38 Wen, S.-Q., Tong, X.-Z., Li, H., Y-chromosome-based genetic pattern in East Asia affected by Neolithic transition. Quat Int, 2016 (in press).
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Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African pygmies and non-pygmies
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39 Verdu, P., Becker, N.S., Froment, A., Georges, M., Grugni, V., Quintana-Murci, L., Hombert, J.-M-.M., Van der Veen, L., Le Bomin, S., Bahuchet, S., et al. Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African pygmies and non-pygmies. Mol Biol Evol 30 (2013), 918–937.
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40
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