scholarly journals Direct evidence of an increasing mutational load in humans

2018 ◽  
Author(s):  
Stéphane Aris-Brosou
Keyword(s):  
Population Dynamics ◽  
Direct Evidence ◽  
Human Populations ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
Evolutionary Trajectory ◽  
Local Adaptations ◽  
The Past ◽  
Risk Alleles ◽  
Diabetes And Obesity

AbstractThe extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. While the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations, but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.

scholarly journals Direct Evidence of an Increasing Mutational Load in Humans

2019 ◽  
Vol 36 (12) ◽  
pp. 2823-2829 ◽  
Author(s):  
Stéphane Aris-Brosou
Keyword(s):  
Population Dynamics ◽  
Direct Evidence ◽  
Human Populations ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
Evolutionary Trajectory ◽  
Local Adaptations ◽  
The Past ◽  
Risk Alleles ◽  
Diabetes And Obesity

Abstract The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. Although the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes, and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.

scholarly journals Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

2015 ◽  
Vol 113 (4) ◽  
pp. E440-E449 ◽  
Author(s):  
Brenna M. Henn ◽  
Laura R. Botigué ◽  
Stephan Peischl ◽  
Isabelle Dupanloup ◽  
Mikhail Lipatov ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Allele Frequencies ◽  
Sub Saharan Africa ◽  
Human Populations ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
High Coverage ◽  
Deleterious Alleles ◽  
Out Of Africa ◽  
Sub Saharan

The Out-of-Africa (OOA) dispersal ∼50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

scholarly journals Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes

2015 ◽  
Author(s):  
Brenna M. Henn ◽  
Laura R Botigue ◽  
Stephan Peischl ◽  
Isabelle Dupanloup ◽  
Mikhail Lipatov ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Allele Frequencies ◽  
Sub Saharan Africa ◽  
Human Populations ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
High Coverage ◽  
Deleterious Alleles ◽  
Out Of Africa ◽  
Sub Saharan

The Out-of-Africa (OOA) dispersal ~50,000 years ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from 7 geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

scholarly journals Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions

2020 ◽  
Vol 37 (9) ◽  
pp. 2691-2698 ◽  
Author(s):  
Xiaoming Liu
Keyword(s):  
Population Dynamics ◽  
Population Expansion ◽  
Future Research ◽  
Human Populations ◽  
Neolithic Revolution ◽  
Cpg Sites ◽  
Hunting And Gathering ◽  
Genome Wide ◽  
Polymorphic Pattern ◽  
Improved Model

Abstract The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.

scholarly journals 3D Insights into the Effects of Captivity on Wolf Mastication and Their Tooth Marks; Implications in Ecological Studies of Both the Past and Present

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2323
Author(s):  
Lloyd A. Courtenay ◽  
Darío Herranz-Rodrigo ◽  
José Yravedra ◽  
José Mª Vázquez-Rodríguez ◽  
Rosa Huguet ◽  
...  
Keyword(s):  
Data Science ◽  
Surface Modifications ◽  
Human Populations ◽  
Ecological Studies ◽  
The Past ◽  
Carnivore Species ◽  
Different Populations ◽  
Complex Relationships ◽  
As Stress ◽  
Tooth Marks

Human populations have been known to develop complex relationships with large carnivore species throughout time, with evidence of both competition and collaboration to obtain resources throughout the Pleistocene. From this perspective, many archaeological and palaeontological sites present evidence of carnivore modifications to bone. In response to this, specialists in the study of microscopic bone surface modifications have resorted to the use of 3D modeling and data science techniques for the inspection of these elements, reaching novel limits for the discerning of carnivore agencies. The present research analyzes the tooth mark variability produced by multiple Iberian wolf individuals, with the aim of studying how captivity may affect the nature of tooth marks left on bone. In addition to this, four different populations of both wild and captive Iberian wolves are also compared for a more in-depth comparison of intra-species variability. This research statistically shows that large canid tooth pits are the least affected by captivity, while tooth scores appear more superficial when produced by captive wolves. The superficial nature of captive wolf tooth scores is additionally seen to correlate with other metric features, thus influencing overall mark morphologies. In light of this, the present study opens a new dialogue on the reasons behind this, advising caution when using tooth scores for carnivore identification and contemplating how elements such as stress may be affecting the wolves under study.

The Origins of Domestic Sheep and Goats: a Reconsideration in the Light of the Fossil Evidence

1969 ◽  
Vol 34 ◽  
pp. 368-384 ◽  
Author(s):  
Sebastian Payne
Keyword(s):  
Direct Evidence ◽  
Present Situation ◽  
Wild Relatives ◽  
The Other ◽  
Domestic Sheep ◽  
Sheep And Goats ◽  
Animal Domestication ◽  
The Past ◽  
The One ◽  
And Control

In recent discussions of the origins and process of animal domestication (Reed, 1961, Zeuner, 1963), both authors rely on two kinds of evidence: on the one hand, the present distributions and characteristics of the different breeds of whatever animal is being discussed, together with its feral and wild relatives, and, on the other hand, the past record, given by literary and pictorial sources and the bones from archaeological and geological sites. Increased recognition of the limitations of the past record, whether in the accuracy of the information it appears to give (as in the case of pictorial sources), or in the certainty of the deductions we are at present capable of drawing from it (this applies especially to the osteological record), has led these authors to argue mainly from the present situation, using the past record to confirm or amplify the existing picture.Arguing from the present, many hypotheses about the origins and process of domestication are available. The only test we have, when attempting to choose between these, lies in the direct evidence of the past record. The past record, it is freely admitted, is very fragmentary: the information provided by the present situation is more exact, ranges over a much wider field, and is more open to test and control. Nevertheless, the past record, however imperfect it is, is the only direct evidence we have about the process of domestication.

Measuring the Selective Utilization of Animal Species by Prehistoric Human Populations

1979 ◽  
Vol 44 (1) ◽  
pp. 155-160 ◽  
Author(s):  
Bruce D. Smith
Keyword(s):  
Animal Species ◽  
Human Populations ◽  
Relative Importance ◽  
The Past

To determine the pattern of selective utilization of animal species by prehistoric human populations, it is first necessary to quantify the relative importance of species of animals in the diet of prehistoric human groups through analysis of archaeologically recovered faunal samples. These values are then compared with estimates of the relative availability of different species of animals in the environment. Such estimates of the relative availability of animal species in prehistoric habitat situations, usually quantified in terms of biomass, are obtained by projecting data from modern analog situations into the past. When attempting to reconstruct prehistoric biotic communities in this manner, it is important to be aware of a number of possible sources of bias and to evaluate and apply modern wildlife data according to a set of interrelated principles. Sources of bias and criteria for selecting modern wildlife analog data are discussed.

scholarly journals Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations

2017 ◽  
Vol 284 (1861) ◽  
pp. 20170706 ◽  
Author(s):  
Valentin Thouzeau ◽  
Philippe Mennecier ◽  
Paul Verdu ◽  
Frédéric Austerlitz
Keyword(s):  
Central Asia ◽  
Linguistic Diversity ◽  
Past History ◽  
Genetic Data ◽  
Human Populations ◽  
Language Diversity ◽  
Methodological Framework ◽  
The Past ◽  
Approximate Bayesian ◽  
Future Work

Linguistic and genetic data have been widely compared, but the histories underlying these descriptions are rarely jointly inferred. We developed a unique methodological framework for analysing jointly language diversity and genetic polymorphism data, to infer the past history of separation, exchange and admixture events among human populations. This method relies on approximate Bayesian computations that enable the identification of the most probable historical scenario underlying each type of data, and to infer the parameters of these scenarios. For this purpose, we developed a new computer program PopLingSim that simulates the evolution of linguistic diversity, which we coupled with an existing coalescent-based genetic simulation program, to simulate both linguistic and genetic data within a set of populations. Applying this new program to a wide linguistic and genetic dataset of Central Asia, we found several differences between linguistic and genetic histories. In particular, we showed how genetic and linguistic exchanges differed in the past in this area: some cultural exchanges were maintained without genetic exchanges. The methodological framework and the linguistic simulation tool developed here can be used in future work for disentangling complex linguistic and genetic evolutions underlying human biological and cultural histories.

scholarly journals Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and patterns of mutation accumulation

2021 ◽  
Author(s):  
Moisès Coll Macià ◽  
Laurits Skov ◽  
Benjamin Marco Peter ◽  
Mikkel Heide Schierup
Keyword(s):  
Fragment Length ◽  
Human Populations ◽  
Female Age ◽  
Generation Interval ◽  
The Past ◽  
Geographical Regions ◽  
Neanderthal Admixture ◽  
Rate Of Decay ◽  
Out Of Africa ◽  
Insight Into

AbstractAfter the main out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today1,2. Here we investigate the size distribution of these fragments in non-African genomes3. We find consistent differences in fragment length distributions across Eurasia with 11% longer fragments in East Asians than in West Eurasians. By comparing extant populations and ancient samples, we show that these differences are due to a different rate of decay in length by recombination since the Neanderthal admixture. In line with this, we observe a strong correlation between the average fragment length and the accumulation of derived mutations, similar to what is expected by changing the ages at reproduction as estimated from trio studies4. Altogether, our results suggest consistent differences in the generation interval across Eurasia, by up to 20% (e.g. 25 versus 30 years), over the past 40,000 years. We use sex-specific accumulations of derived alleles to infer how these changes in generation intervals between geographical regions could have been mainly driven by shifts in either male or female age of reproduction, or both. We also find that previously reported variation in the mutational spectrum5 may be largely explained by changes to the generation interval and not by changes to the underlying mutational mechanism. We conclude that Neanderthal fragment lengths provide unique insight into differences of a key demographic parameter among human populations over the recent history.

scholarly journals Ecology of the Anthropocene signals hope for consciously managing the planetary ecosystem

2021 ◽  
Vol 118 (28) ◽  
pp. e2024150118
Author(s):  
Clarence Lehman ◽  
Shelby Loberg ◽  
Michael Wilson ◽  
Eville Gorham
Keyword(s):  
Population Growth ◽  
Cultural Evolution ◽  
Human Population ◽  
Human Populations ◽  
Present Moment ◽  
Minimal Set ◽  
The Past ◽  
Food Species ◽  
Large Predators ◽  
Population Numbers

Human populations have grown to such an extent that our species has become a dominant force on the planet, prompting geologists to begin applying the term Anthropocene to recognize the present moment. Many approaches seek to explain the past and future of human population growth, in the form of narratives and models. Some of the most influential models have parameters that cannot be precisely known but are estimated by expert opinion. Here we apply a unified model of ecology to provide a macroscale summary of the net effects of many microscale processes, using a minimal set of parameters that can be known. Our models match estimates of historic and prehistoric global human population numbers and provide predictions that correspond to some of the more complicated current models. In addition to fitting the data well they reveal that, amidst enormous complexity in our human and prehuman past, three key ecological discontinuities have occurred in turn: 1) becoming dominant competitors of large predators rather than their prey, 2) becoming mutualists with food species rather than acting as predators upon them, and 3) changing from a regime of uncontrolled population growth to one of controlled fertility instead. All three processes have been interlinked with cultural evolution and all three ushered in developments of the Anthropocene. Understanding the trajectories that have delivered us to this stage can help guide prudent paths into the future.

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