scholarly journals Life History Effects on Neutral Diversity Levels of Autosomes and Sex Chromosomes

Genetics ◽  
2020 ◽  
Vol 215 (4) ◽  
pp. 1133-1142 ◽  
Author(s):  
Guy Amster ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Sex Chromosomes ◽  
Life Histories ◽  
Genetic Data ◽  
Mutation Rates ◽  
Female Ratio ◽  
Diversity Patterns ◽  
History Effects ◽  
Generation Times ◽  
Male To Female

Understanding the determinants of neutral diversity patterns on autosomes and sex chromosomes provides a bedrock for the interpretation of population genetic data; in particular, differences between the two informs our understanding of sex-specific demographic and mutation processes. While sex-specific age-structure and variation in reproductive success have long been known to affect neutral diversity, theoretical descriptions of these effects were complicated and lacking in generality, stymying attempts to relate diversity patterns of species with their life history. Here, we derive general yet simple expressions for these effects. In particular, we show that life history effects on X-to-autosome ratios of pairwise diversity levels (X:A diversity ratios) depend only on the male-to-female ratios of mutation rates, generation times, and reproductive variances. Our results reveal that changing the male-to-female ratio of generation times has opposite effects on X:A ratios of diversity and divergence. They also explain how sex-specific life histories modulate the response of X:A diversity ratios to changes in population size. More generally, they clarify that sex-specific life history—generation times in particular—should have marked effects on X:A diversity ratios in many taxa and enable further investigation of these effects.

scholarly journals Life history effects on neutral diversity levels of autosomes and sex chromosomes

2017 ◽  
Author(s):  
Guy Amster ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Sex Chromosomes ◽  
Life Histories ◽  
Marked Effect ◽  
Genetic Data ◽  
Mutation Rates ◽  
X Chromosomes ◽  
Diversity Patterns ◽  
History Effects ◽  
Generation Times

AbstractAll else being equal, the ratio of genetic diversity levels on X and autosomes at selectively neutral sites should mirror the ratio of their numbers in the population and thus equal ¾. Because X chromosomes spend twice as many generations in females as in males, however, the ratio of diversity levels is also affected by sex differences in life history. The effects of life history on diversity levels, notably those of sex-specific age structures and reproductive variances, have been studied for decades, yet existing theory relies on many parameters that are difficult to measure and lacks generality in ways that limit their applicability. We derive general yet simple expressions for these effects and show that life history effects on X-to-autosome (X:A) ratios of diversity levels depend only on sex-ratios of mutation rates, generation times, and reproductive variances. These results reveal that changing the sex-ratio of generation times has opposite effects on X:A ratios of polymorphism and divergence. They also explain how sex-specific life histories modulate the response of X:A polymorphism ratios to changes in population size. More generally, they clarify that sex-specific life history—generation times in particular—should have a marked effect on X:A polymorphism ratios in many taxa and enable the investigation of these effects.Significance StatementUnderstanding the determinants of neutral diversity patterns on autosomes and sex chromosomes provides a bedrock for our interpretation of population genetic data. Sex-specific age-structure and variation in reproductive success have long been thought to affect neutral diversity, but theoretical descriptions of these effects were complicated and/or lacked in generality, stymying attempts to relate diversity patterns of species with their life history. We derive general yet simple expressions for these effects, which clarify how they impact neutral diversity and should enable studies of relative diversity levels on the autosomes and sex chromosomes in many taxa.

scholarly journals Changes in life history and population size can explain the relative neutral diversity levels on X and autosomes in extant human populations

2020 ◽  
Vol 117 (33) ◽  
pp. 20063-20069
Author(s):  
Guy Amster ◽  
David A. Murphy ◽  
William R. Milligan ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Population Size ◽  
Mutation Rates ◽  
Human Populations ◽  
Effective Population ◽  
Mutation Bias ◽  
Female Ratio ◽  
Generation Times ◽  
Population Sizes ◽  
Male Mutation Bias

In human populations, the relative levels of neutral diversity on the X and autosomes differ markedly from each other and from the naïve theoretical expectation of 3/4. Here we propose an explanation for these differences based on new theory about the effects of sex-specific life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly longer generation times in males than in females, are expected to have had multiple effects on human X-to-autosome (X:A) diversity ratios, as a result of male-biased mutation rates, the equilibrium X:A ratio of effective population sizes, and the differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for male mutation bias results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal that X:A ratios of effective population sizes are considerably greater than previously appreciated. Finally, we find that the joint effects of historical changes in life history and population size can explain the observed X:A diversity ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous, that non-African populations experienced a substantial reduction in polygyny and/or increase in the male-to-female ratio of generation times around the Out-of-Africa bottleneck, and that current diversity levels were affected by fairly recent changes in sex-specific life history.

scholarly journals Life history effects on the molecular clock of autosomes and sex chromosomes

2015 ◽  
Author(s):  
Guy Amster ◽  
Guy Sella
Keyword(s):  
Molecular Clock ◽  
Life Histories ◽  
Age Of Onset ◽  
Mutation Rates ◽  
Molecular Evidence ◽  
History Effects ◽  
Rates Of Evolution ◽  
Generation Times ◽  
Human Mutation ◽  
Low X

One of the foundational results of molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic ?molecular clock?. We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in extant hominines (i.e., human, chimpanzee and gorilla), considering a model that approximates features of the mutational process in most mammals and birds and some other vertebrates. As we show, this model helps explain and reconcile a number of seemingly puzzling observations. In hominines, it can explain the puzzlingly low X-to-autosome ratios of substitution rates and how the ratios and rates of autosomal substitutions differ among lineages. Importantly, it suggests how to translate pedigree-based estimates of human mutation rates into split times among apes, given sex-specific life histories. In so doing, it helps bridge the gap between estimates of split times of apes based on fossil and molecular evidence. Finally, considering these effects can help to reconcile recent evidence that changes in generation times should have small effects on mutation rates in humans with classic studies suggesting that they have had major effects on rates of evolution in the mammalian phylogeny.

Studies on Gracilaria. 5. In vitro life history of Gracilaria sp. from the Maritime Provinces

1977 ◽  
Vol 55 (10) ◽  
pp. 1282-1290 ◽  
Author(s):  
N. Bird ◽  
J. McLachlan ◽  
D. Grund
Keyword(s):  
Life History ◽  
Vegetative Propagation ◽  
Reproductive Potential ◽  
Maritime Provinces ◽  
Female Ratio ◽  
Reproductive Maturation ◽  
History Of ◽  
Male To Female ◽  
Wound Tissue

The life history of Gracilaria sp. was completed in culture demonstrating a typical Polysiphonia-type life history. Carpospores released by plants collected in nature developed into tetrasporophytes and subsequent release and germination of tetraspores gave rise to a gametophytic generation morphologically similar to the tetrasporophyte. Development of tetrasporophytes from carpospores released by the carposporophytic generation completed the life history. A male to female ratio of 1:1 was found for plants originating from tetraspores and only female plants grown in the presence of male plants formed fertile cystocarps. Detached plants showed the greatest reproductive potential; reproductive maturation of these plants occurred in 8–10 weeks after spore germination. Vegetative propagation through rapid regeneration of adventitious branches from wound tissue was observed.

scholarly journals Life history effects on the molecular clock of autosomes and sex chromosomes

2016 ◽  
Vol 113 (6) ◽  
pp. 1588-1593 ◽  
Author(s):  
Guy Amster ◽  
Guy Sella
Keyword(s):  
Molecular Clock ◽  
Generation Time ◽  
Life Histories ◽  
Age Of Onset ◽  
Mutation Rates ◽  
Major Influence ◽  
Molecular Evidence ◽  
Substitution Rates ◽  
History Effects ◽  
Low X

One of the foundational results in molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic “molecular clock.” We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in hominids (great apes), considering a model that approximates features of the mutational process in mammals, birds, and some other vertebrates. As we show, this model can account for a number of seemingly disparate observations: notably, the puzzlingly low X-to-autosome ratios of substitution rates in humans and chimpanzees and differences in rates of autosomal substitutions among hominine lineages (i.e., humans, chimpanzees, and gorillas). The model further suggests how to translate pedigree-based estimates of human mutation rates into split times among extant hominoids (apes), given sex-specific life histories. In so doing, it largely bridges the gap reported between estimates of split times based on fossil and molecular evidence, in particular suggesting that the human–chimpanzee split may have occurred as recently as 6.6 Mya. The model also implies that the “generation time effect” should be stronger in short-lived species, explaining why the generation time has a major influence on yearly substitution rates in mammals but only a subtle one in human pedigrees.

scholarly journals Life history and production of pelagic mysids and decapods in the Oyashio region, Japan

Crustaceana ◽  
2013 ◽  
Vol 86 (4) ◽  
pp. 449-474
Author(s):  
Kana Chikugo ◽  
Atsushi Yamaguchi ◽  
Kohei Matsuno ◽  
Rui Saito ◽  
Ichiro Imai
Keyword(s):  
Life History ◽  
Life Histories ◽  
Dominant Species ◽  
Life Cycles ◽  
Annual Production ◽  
Juvenile Growth ◽  
High Biomass ◽  
Oyashio Region ◽  
Generation Times ◽  
High Production

Pelagic Mysidacea and Decapoda have important roles in marine ecosystems. However, information on their life histories is extremely limited. This study aimed to evaluate the life cycles of pelagic Mysidacea and Decapoda in the Oyashio region, Japan. Production of the four dominant species was estimated by combining body mass (DM) data and abundance data. Mysidacea belonging to 5 species from 5 genera occurred in the study area. Their abundance and biomass ranged between 11.7-50.1 ind. m−2 and 1.2-7.9 g wet mass (WM) m−2, respectively. Six species from 6 genera belonged to Decapoda, and their abundance and biomass ranged between 9.0-17.3 ind. m−2 and 3.0-17.3 g WM m−2, respectively. Based on body length histograms, there were two to four cohorts for the three dominant mysids and one dominant decapod on each sampling date. Life histories of the two numerically dominant mysids (Eucopia australis and Boreomysis californica) followed similar patterns: recruitment of young in May, strong growth from April to June, and a longevity of three years. Life cycles of the two minor species (the mysid Meterythrops microphthalma and the decapod Hymenodora frontalis) were not clear because of their low abundance. The timing of recruitment of the young and the strong juvenile growth for the two dominant mysids corresponds with the season when their prey is abundant. The annual production of the dominant mysid species was 14.0 mg DM m−2 (B. californica) and 191.8 mg DM m−2 (E. australis). Annual production/biomass () ratios ranged between 0.242 (H. frontalis) and 0.643 (M. microphthalma). Compared with other regions, the Oyashio region showed high production and low ratios. The high production in the Oyashio region may be related to the high biomass of these species. Because of the low temperature conditions (3°C), pelagic mysids and decapods in the Oyashio region may have slower growth, longer generation times and lower ratios than in other oceans.

scholarly journals Changes in life history and population size can explain relative neutral diversity levels on X and autosomes in extant human populations

2019 ◽  
Author(s):  
Guy Amster ◽  
David A. Murphy ◽  
William M. Milligan ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Population Size ◽  
Mutation Rates ◽  
Human Populations ◽  
Effective Population ◽  
Mutation Bias ◽  
Historical Changes ◽  
Generation Times ◽  
Population Sizes ◽  
Male Mutation Bias

AbstractIn human populations, relative levels of neutral polymorphism on the X and autosomes differ markedly from each other and from the naive theoretical expectation of ¾. These differences have attracted considerable attention, with studies highlighting several potential causes, including male biased mutation and reproductive variance, historical changes in population size, and selection at linked loci. We revisit this question in light of our new theory about the effects of life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly higher generation times in males than females, likely had multiple effects on human X-to-autosomes (X:A) polymorphism ratios, through the extent of male mutation bias, the equilibrium X:A ratios of effective population sizes, and differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for the male bias in mutation results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal X:A ratios of effective population sizes to be considerably greater than previously appreciated. We then show that the joint effects of historical changes in life history and population size can explain X:A polymorphism ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous; that non-African populations experienced a substantial reduction in polygyny and/or increase in male-biased generation times around the out of Africa bottleneck; and that extant diversity levels were affected by fairly recent changes in sex-specific life history.Significance StatementAll else being equal, the ratio of diversity levels on X and autosomes at selectively neutral sites should mirror the ratio of their numbers in the population and thus equal ¾. In reality, the ratios observed across human populations differ markedly from ¾ and from each other. Because from a population perspective, autosomes spend an equal number of generations in both sexes while the X spends twice as many generations in females, these departures from the naïve expectations likely reflect differences between male and female life histories and their effects on mutation processes. Indeed, we show that the ratios observed across human populations can be explained by demographic history, assuming plausible, sex-specific mutation rates, generation times and reproductive variances.

scholarly journals The Leukodystrophy Spectrum in Saudi Arabia: Epidemiological, Clinical, Radiological, and Genetic Data

2021 ◽  
Vol 9 ◽  
Author(s):  
Majid Alfadhel ◽  
Mohammed Almuqbil ◽  
Fuad Al Mutairi ◽  
Muhammad Umair ◽  
Mohammed Almannai ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Retrospective Chart Review ◽  
Genetic Data ◽  
Consecutive Series ◽  
Female Ratio ◽  
Peripheral Nerve Involvement ◽  
Novel Variants ◽  
The Central Nervous System ◽  
Pelizaeus Merzbacher Disease ◽  
Male To Female

Background: Leukodystrophies (LDs) are inherited heterogeneous conditions that affect the central nervous system with or without peripheral nerve involvement. They are individually rare, but collectively, they are common. Thirty disorders were included by the Global Leukodystrophy Initiative Consortium (GLIA) as LDs.Methods: We conducted a retrospective chart review of a consecutive series of patients diagnosed with different types of LD from four large tertiary referral centers in Riyadh, Saudi Arabia. Only those 30 disorders defined by GLIA as LDs were included.Results: In total, 83 children from 61 families were identified and recruited for this study. The male-to-female ratio was 1.5:1, and a consanguinity rate of 58.5% was observed. An estimated prevalence of 1:48,780 or 2.05/100,000 was observed based on the clinical cohort, whereas a minimum of 1:32,857 or 3.04/100,000 was observed based on the local genetic database. The central region of the country exhibited the highest prevalence of LDs (48.5%). The most common LD was metachromatic leukodystrophy (MLD), and it accounted for 25.3%. The most common disorder based on carrier frequency was AGS. Novel variants were discovered in 51% of the cases, but 49% possessed previously reported variants. Missense variants were high in number and accounted for 73% of all cases. Compared with other disorders, MLD due to saposin b deficiency was more common than expected, Pelizaeus-Merzbacher-like disease was more prevalent than Pelizaeus-Merzbacher disease, and X-linked adrenoleukodystrophy was less common than expected. The mortality rate among our patients with LD was 24%.Conclusion: To the best of our knowledge, this is the largest cohort of patients with LD from Saudi Arabia. We present epidemiological, clinical, radiological, and genetic data. Furthermore, we report 18 variants that have not been reported previously. These findings are of great clinical and molecular utility for diagnosing and managing patients with LD.

Hormones and Behavior

2019 ◽  
pp. 11-26
Author(s):  
Maren N. Vitousek ◽  
Laura A. Schoenle
Keyword(s):  
Life History ◽  
Life Histories ◽  
Life History Traits ◽  
Developmental Plasticity ◽  
Endocrine System ◽  
Phenotypic Traits ◽  
Social Environments ◽  
Trade Offs ◽  
And Behavior

Hormones mediate the expression of life history traits—phenotypic traits that contribute to lifetime fitness (i.e., reproductive timing, growth rate, number and size of offspring). The endocrine system shapes phenotype by organizing tissues during developmental periods and by activating changes in behavior, physiology, and morphology in response to varying physical and social environments. Because hormones can simultaneously regulate many traits (hormonal pleiotropy), they are important mediators of life history trade-offs among growth, reproduction, and survival. This chapter reviews the role of hormones in shaping life histories with an emphasis on developmental plasticity and reversible flexibility in endocrine and life history traits. It also discusses the advantages of studying hormone–behavior interactions from an evolutionary perspective. Recent research in evolutionary endocrinology has provided insight into the heritability of endocrine traits, how selection on hormone systems may influence the evolution of life histories, and the role of hormonal pleiotropy in driving or constraining evolution.

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