Dataset Information

Complex patterns of sex-biased demography in canines.

ABSTRACT: The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and multiple paternity, have been observed in wolves, recent breeding practices could have led to female-biased mating patterns in breed dogs. For example, breed dogs are thought to have experienced a popular sire effect, where a small number of males father many offspring with a large number of females. Here we use genetic variation data to test how widespread sex-biased mating practices in canines are during different evolutionary time points. Using whole-genome sequence data from 33 dogs and wolves, we show that patterns of diversity on the X chromosome and autosomes are consistent with a higher number of reproducing males than females over ancient evolutionary history in both dogs and wolves, suggesting that mating practices did not change during early dog domestication. By contrast, since breed formation, we found evidence for a larger number of reproducing females than males in breed dogs, consistent with the popular sire effect. Our results confirm that canine demography has been complex, with opposing sex-biased processes occurring throughout their history. The signatures observed in genetic data are consistent with documented sex-biased mating practices in both the wild and domesticated populations, suggesting that these mating practices are pervasive.

SUBMITTER: Phung TN

PROVIDER: S-EPMC6545087 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Complex patterns of sex-biased demography in canines.

Phung Tanya N TN Wayne Robert K RK Wilson Melissa A MA Lohmueller Kirk E KE

Proceedings. Biological sciences 20190501 1903

The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and multiple paternity, have been observed in wolves, recent breeding practices could have led to female-biased mating patterns in breed dogs. For exampl ...[more]

PMID: 31113325

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Project description:Sex-biased demographic events ("sex-bias") involve unequal numbers of females and males. These events are typically inferred from the relative amount of X-chromosomal to autosomal genetic variation and have led to conflicting conclusions about human demographic history. Though population size changes alter the relative amount of X-chromosomal to autosomal genetic diversity even in the absence of sex-bias, this has generally not been accounted for in sex-bias estimators to date. Here, we present a novel method to identify sex-bias from genetic sequence data that models population size changes and estimates the female fraction of the effective population size during each time epoch. Compared to recent sex-bias inference methods, our approach can detect sex-bias that changes on a single population branch without requiring data from an outgroup or knowledge of divergence events. When applied to simulated data, conventional sex-bias estimators are biased by population size changes, especially recent growth or bottlenecks, while our estimator is unbiased. We next apply our method to high-coverage exome data from the 1000 Genomes Project and estimate a male bias in Yorubans (47% female) and Europeans (44%), possibly due to stronger background selection on the X chromosome than on the autosomes. Finally, we apply our method to the 1000 Genomes Project Phase 3 high-coverage Complete Genomics whole-genome data and estimate a female bias in Yorubans (63% female), Europeans (84%), Punjabis (82%), as well as Peruvians (56%), and a male bias in the Southern Han Chinese (45%). Our method additionally identifies a male-biased migration out of Africa based on data from Europeans (20% female). Our results demonstrate that modeling population size change is necessary to estimate sex-bias parameters accurately. Our approach gives insight into signatures of sex-bias in sexual species, and the demographic models it produces can serve as more accurate null models for tests of selection.

Project description:BackgroundMale and female vertebrates typically differ in a range of characteristics, from morphology to physiology to behavior, which are influenced by factors such as the social environment and the internal hormonal and genetic milieu. However, sex differences in gene expression profiles in the brains of vertebrates are only beginning to be understood. Fishes provide a unique complement to studies of sex differences in mammals and birds given that fish show extreme plasticity and lability of sexually dimorphic characters and behaviors during development and even adulthood. Hence, teleost models can give additional insight into sexual differentiation. The goal of this study is to identify neurotranscriptomic mechanisms for sex differences in the brain.ResultsIn this study we examined whole-brain sex-biased gene expression through RNA-sequencing across four strains of zebrafish. We subsequently conducted systems level analyses by examining gene network dynamics between the sexes using weighted gene coexpression network analysis. Surprisingly, only 61 genes (approximately 0.4% of genes analyzed) showed a significant sex effect across all four strains, and 48 of these differences were male-biased. Several of these genes are associated with steroid hormone biosynthesis. Despite sex differences in a display of stress-related behaviors, basal transcript levels did not predict the intensity of the behavioral display. WGCNA revealed only one module that was significantly associated with sex. Intriguingly, comparing intermodule dynamics between the sexes revealed only moderate preservation. Further we identify sex-specific gene modules.ConclusionsDespite differences in morphology, physiology, and behavior, there is limited sex-biased neural gene expression in zebrafish. Further, genes found to be sex-biased are associated with hormone biosynthesis, suggesting that sex steroid hormones may be key contributors to sexual behavioral plasticity seen in teleosts. A possible mechanism is through regulating specific brain gene networks.

Dataset Information

Complex patterns of sex-biased demography in canines.

Publications

Complex patterns of sex-biased demography in canines.

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