Detecting interregionally diversifying natural selection on modern human cranial form by using matched molecular and morphometric data

The spatiotemporal distribution of recent human adaptation is a long standing question. We developed a new coalescent-based method that collectively assigned human genome regions to modes of neutrality or to positive, negative, or balancing selection. Most importantly, the selection times were estimated for all positive selection signals, which ranged over the last half million years, penetrating the emergence of anatomically modern human (AMH). These selection time estimates were further supported by analyses of the genome sequences from three ancient AMHs and the Neanderthals. A series of brain function-related genes were found to carry signals of ancient selective sweeps, which may have defined the evolution of cognitive abilities either before Neanderthal divergence or during the emergence of AMH. Particularly, signals of brain evolution in AMH are strongly related to Alzheimer's disease pathways. In conclusion, this study reports a chronological atlas of natural selection in Human.

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Were neandertal and modern human cranial differences produced by natural selection or genetic drift?

Journal of Human Evolution ◽

10.1016/j.jhevol.2007.03.001 ◽

2007 ◽

Vol 53 (2) ◽

pp. 135-145 ◽

Cited By ~ 120

Author(s):

T WEAVER ◽

C ROSEMAN ◽

C STRINGER

Keyword(s):

Natural Selection ◽

Genetic Drift ◽

Modern Human

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Signatures of natural selection in the drug metabolizing enzyme genes: Opportunity for developing personalized and precision medicine

10.1101/113514 ◽

2017 ◽

Author(s):

Sheikh Nizamuddin ◽

K. Thangaraj

Keyword(s):

Natural Selection ◽

Drug Response ◽

Modern Human ◽

Beta Agonist ◽

P Value ◽

Q Value ◽

Drug Metabolizing Enzyme ◽

Comprehensive Information ◽

Other World ◽

Metabolizing Enzyme

AbstractModern human experienced various selective pressures; including range of xenobiotics which contributed to heterogeneity of drug response. Many genes involve in pharmacokinetics and dynamics of drug, have been reported under natural selection. However, none of the studies have utilized comprehensive information of drug-centered PharmGKB pathways. We have extended this work and aimed to investigate sweep signals, using 1,798 subjects, from 53 Indian and 15 other world populations. We observed that modifiers which alters the biochemical function of other genes, have excess of natural selection (median std-z score=0.033±0.95; p-value=1.7×10−9-3.7×10−3). Taxane and statin primarily used for chemotherapy and lowering cholesterol level, respectively; and well known for heterogeneous drug response. We observed that pharmacokinetic pathway of taxane and statins are under natural selection (p-value=2.53×10−9and 2.73×10−9-1.09×10−4; q-value=1.28×10−7 and 6.91×10−6-1.1×10−3). We also observed signal of selection in Ibuprofen pharmacokinetics (p-value=1.76×10−5; q-value =2.22×10−4), beta-agonist/beta-blocker pharmacodynamics (p-value=4.79×10−4; q-value =4.04×10−4) and Zidovudin pharmacokinetics/dynamic pathway (p-value=7.0×10−4; q-value =5.06×10−4). Hard sweeps signals were observed in a total of 322 loci. Of which, 53 affect mRNA expression (p-value<0.001) and 16 were already reported with therapeutic response. Interestingly, we observed that Africans have experience 2 phases of natural selection, one at ~30,000 another at ~10,000 years before present.

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Ancient Genomics of Modern Humans: The First Decade

Annual Review of Genomics and Human Genetics ◽

10.1146/annurev-genom-083117-021749 ◽

2018 ◽

Vol 19 (1) ◽

pp. 381-404 ◽

Cited By ~ 47

Author(s):

Pontus Skoglund ◽

Iain Mathieson

Keyword(s):

Genetic Diversity ◽

Natural Selection ◽

Phenotypic Diversity ◽

Modern Human ◽

Modern Humans ◽

Human Genomes ◽

African Populations ◽

History Of ◽

Out Of Africa ◽

Genomic Basis

The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent—in particular the effect of agricultural expansions in Africa, Europe, and Oceania—and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.

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From 48 to 46 Chromosomes: Origin of Modern Man

Journal of Molecular Biology Research ◽

10.5539/jmbr.v7n1p80 ◽

2017 ◽

Vol 7 (1) ◽

pp. 80

Author(s):

A. I. Ibraimov

Keyword(s):

Natural Selection ◽

East Africa ◽

Chromosome Rearrangement ◽

Modern Human ◽

Climatic Conditions ◽

Very High Frequency ◽

Single Chromosome ◽

Ecological Zones ◽

The Common ◽

Very High

It is old-established that the chromosome number in the chimpanzee, gorilla and orangutan was 48 and not 46 as in man. However, cause and effect of such chromosome rearrangement is unknown. A hypothesis has been proposed that natural selection caused merger of two pairs of autosomes into one chromosome. In the changed climate of the East Africa individuals with less amount of chromosomal Q-heterochromatin regions (Q-HRs) in genome were the most adapted. Two pairs of acrocentrics in the genome the common ancestor, which merged into a single chromosome, apparently, carried on their short arms of Q-HRs with a very high frequency, preventing the birth of individuals with a low number Q-heterochromatin. With the merger of these two pairs of acrocentrics into one, the number of autosomes bearing the Q-HRs reduced from nine to seven pairs, as in the modern human. Such chromosome rearrangement resulted in two important consequences: а) chromosomal Q-HRs distributed into seven Q-polymorphic autosomes, so that it was possible to give birth to the individuals with different, including the low, number of Q-heterochromatin; b) in the population individuals with low number of Q-HRs appeared, able to adapt to new, harsher climatic conditions. With the lapse of time, these individuals formed a new population in the new territory, where individuals with a number of chromosomal Q-HRs like the modern natives of Africa, and with the number of 46 chromosomes in the genome began to dominate. Thus, the cause of the origin of the 46 chromosome karyotype from an ancestral 48 chromosome line was natural selection, and an effect was adaptation, i.e. individuals with different, including the low, number of Q-HRs, got the advantage to open up and to colonize new ecological zones of the East Africa.

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Extraordinary Claims, Extraordinary Proof

Darwin's Roadmap to the Curriculum ◽

10.1093/oso/9780190624965.003.0005 ◽

2019 ◽

pp. 61-96

Author(s):

Thomas G. Nolen

Keyword(s):

Natural Selection ◽

Evolutionary Theory ◽

Modern Human ◽

Human Condition ◽

Human Origins ◽

Origin Of Species ◽

The Past ◽

Adaptive Value ◽

Overwhelming Evidence ◽

Human Characteristic

In 1859, Darwin proposed an extraordinary claim that natural selection could explain both the origin of species and why organisms were so well adapted to their environments. In the past 160 years, through thousands of studies, an enormous body of evidence has been compiled supporting Darwin’s extraordinary claims. This chapter explores both the critiques of current skeptics who contend that evolutionary theory has little utility for the modern human condition and presents research that has tested the now “un-extraordinary” claims about human origins. Further, utilizing the assumption that humans are animals, the author argues that when testing the possible adaptive value of a human characteristic, the standard fall back should no longer be that the trait is “cultural” but that, on the basis of overwhelming evidence, it is biological. If this happened to not be the case, then that would require extraordinary proof.

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