scholarly journals More genes underwent positive selection in chimpanzee evolution than in human evolution

2007 ◽  
Vol 104 (18) ◽  
pp. 7489-7494 ◽  
Author(s):  
Margaret A. Bakewell ◽  
Peng Shi ◽  
Jianzhi Zhang
Keyword(s):  
Positive Selection ◽  
Human Evolution ◽  
Nonsynonymous Substitution ◽  
Evolutionary Divergence ◽  
Common Belief ◽  
Human Origins ◽  
Effective Population ◽  
Darwinian Selection ◽  
Sequencing Errors ◽  
Nonsynonymous Substitution Rate

Observations of numerous dramatic and presumably adaptive phenotypic modifications during human evolution prompt the common belief that more genes have undergone positive Darwinian selection in the human lineage than in the chimpanzee lineage since their evolutionary divergence 6–7 million years ago. Here, we test this hypothesis by analyzing nearly 14,000 genes of humans and chimps. To ensure an accurate and unbiased comparison, we select a proper outgroup, avoid sequencing errors, and verify statistical methods. Our results show that the number of positively selected genes is substantially smaller in humans than in chimps, despite a generally higher nonsynonymous substitution rate in humans. These observations are explainable by the reduced efficacy of natural selection in humans because of their smaller long-term effective population size but refute the anthropocentric view that a grand enhancement in Darwinian selection underlies human origins. Although human and chimp positively selected genes have different molecular functions and participate in different biological processes, the differences do not ostensibly correspond to the widely assumed adaptations of these species, suggesting how little is currently known about which traits have been under positive selection. Our analysis of the identified positively selected genes lends support to the association between human Mendelian diseases and past adaptations but provides no evidence for either the chromosomal speciation hypothesis or the widespread brain-gene acceleration hypothesis of human origins.

Biology and Behaviour in Human Evolution

1991 ◽  
Vol 1 (2) ◽  
pp. 207-226 ◽  
Author(s):  
Phyllis C. Lee
Keyword(s):  
Human Evolution ◽  
Human Behaviour ◽  
Archaeological Record ◽  
Human Origins ◽  
Biological Perspective ◽  
Patterns And Processes ◽  
Reductionist Approach

Of the diverse approaches to understanding patterns and processes in human evolution, a focus on the biology of behaviour using principles derived from the non-human primates may have some utility for archaeologists. This article seeks to outline some biologically-based areas that could prove fruitful in exploring the origins of human behaviour within the archaeological record. It attempts to initiate a dialogue between biologists, even with their limited understanding of the problems facing those working with human origins, and archaeologists, in the hope that this dialogue will move beyond a simple reductionist approach towards the goal of integrating behaviour into a more sophisticated biological perspective.

Woman the Gatherer

2018 ◽  
pp. 133-142
Author(s):  
Erika Lorraine Milam
Keyword(s):  
Human Evolution ◽  
Animal Behavior ◽  
Field Research ◽  
Human Origins ◽  
Male Authority

This chapter considers the research of women anthropologists during this period. It shows how many anthropologists had fought to refute the picture of universal male authority implied by common narratives of human evolution were women, often at the very beginning of what turned out to be long, notable careers. Their research gave fuller form to a rhetorically powerful alternative to Man the Hunter in reconstructions of human origins—Woman the Gatherer. Like her partner, Woman the Gatherer found intellectual support in research on long-extinct human ancestors, studies of human cultures today, and animal behavior, with a new emphasis on field research among primates.

From population genetics to phylogeny: Uses and limits of mitochondrial DNA

1990 ◽  
Vol 3 (1) ◽  
pp. 111 ◽  
Author(s):  
RH Crozier
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Gene ◽  
Single Gene ◽  
Dna Amplification ◽  
Species Tree ◽  
Population Subdivision ◽  
Evolutionary Divergence ◽  
Gene Trees ◽  
Species Trees ◽  
Effective Population

Mitochondrial DNA (mtDNA) is clonally and maternally inherited in all animals and in most plants. Mitochondrial gene content is similar although not identical in all eukaryotes. Because of these characteristics, mtDNA has a number of features useful to systematists for all levels of evolutionary divergence. Clonal inheritance leads to unusual confidence in constructing gene trees which are useful in population-level studies, such as in the detection of population subdivision. Maternal inheritance presents the opportunity to distinguish paternal from maternal gene flow. The clonal, or single-gene, nature of mtDNA inheritance leads to consideration of the expected convergence between gene- and species-trees. For closely related populations or species, it is desirable to use several genes to be sure that the correct species-tree is discovered; this means that, although mtDNA will be the most precise guide to the species tree because of its lower effective population size, nuclear genes should also be used in such studies. Although restriction fragment length polymorphisms dominated the field until recently, sequencing following DNA amplification using the polymerase chain reaction is now easier and opens up the use of preserved specimens to molecular systematists. Because mitochondria1 genes evolve at different rates, one of appropriate rate can be selected for almost any phylogenetic problem.

scholarly journals Long-Term Persistence of Infection in Chimpanzees Inoculated with an Infectious Hepatitis C Virus Clone Is Associated with a Decrease in the Viral Amino Acid Substitution Rate and Low Levels of Heterogeneity

2004 ◽  
Vol 78 (18) ◽  
pp. 9782-9789 ◽  
Author(s):  
Javier Fernandez ◽  
Deborah Taylor ◽  
Duncan R. Morhardt ◽  
Kathleen Mihalik ◽  
Montserrat Puig ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Substitution Rate ◽  
Selective Pressure ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Nonsynonymous Substitution Rate ◽  
Over Time

ABSTRACT Two chimpanzees, 1535 and 1536, became persistently infected following inoculation with RNA transcripts from cDNA clones of hepatitis C virus (HCV). Analysis of the HCV genomes from both animals showed an accumulation of amino acid substitutions over time. The appearance of substitutions in the envelope genes was associated with increased antienvelope antibody titers. However, extensive mutations were not incorporated into hypervariable region 1 (HVR1). A comparison of the nonsynonymous substitution rate/synonymous substitution rate was made at various time points to analyze selective pressure. The highest level of selective pressure occurred during the acute phase and decreased as the infection continued. The nonsynonymous substitution rate was initially higher than the synonymous substitution rate but decreased over time from 3.3 × 10−3 (chimpanzee 1535) and 3.2 × 10−3 (chimpanzee 1536) substitutions/site/year at week 26 to 1.4 × 10−3 (chimpanzee 1535) and 1.7 × 10−3 (chimpanzee 1536) at week 216, while the synonymous substitution rate remained steady at ∼1 × 10−3 substitutions/site/year. Analysis of PCR products using single-stranded conformational polymorphism indicated a low level of heterogeneity in the viral genome. The results of these studies confirm that the persistence of infection is not solely due to changes in HVR1 or heterogeneity and that the majority of variants observed in natural infections could not arise simply through mutation during the time period most humans and chimpanzees are observed. These data also indicate that immune pressure and selection continue throughout the chronic phase.

scholarly journals Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 938 ◽  
Author(s):  
Islam ◽  
Li ◽  
Liu ◽  
Berihulay ◽  
Abied ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Positive Selection ◽  
Candidate Genes ◽  
Runs Of Homozygosity ◽  
Selection Signatures ◽  
Effective Population ◽  
Signature Of Selection ◽  
Genomic Regions ◽  
Insight Into

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

Human Evolution: A new molecular view of human origins

1994 ◽  
Vol 4 (7) ◽  
pp. 651-652 ◽  
Author(s):  
John F.Y. Brookfield
Keyword(s):  
Human Evolution ◽  
Human Origins

Inventing Homo gardarensis: Prestige, Pressure, and Human Evolution in Interwar Scandinavia

2014 ◽  
Vol 27 (2) ◽  
pp. 359-383 ◽  
Author(s):  
Peter C. Kjærgaard
Keyword(s):  
Human Evolution ◽  
Human Remains ◽  
International Competition ◽  
Evolutionary Explanation ◽  
Human Origins ◽  
Missing Link ◽  
Explanatory Framework ◽  
National Pride ◽  
Fossil Evidence

ArgumentIn the 1920s there were still very few fossil human remains to support an evolutionary explanation of human origins. Nonetheless, evolution as an explanatory framework was widely accepted. This led to a search for ancestors in several continents with fierce international competition. With so little fossil evidence available and the idea of a Missing Link as a crucial piece of evidence in human evolution still intact, many actors participated in the scientific race to identify the human ancestor. The curious case of Homo gardarensis serves as an example of how personal ambitions and national pride were deeply interconnected as scientific concerns were sometimes slighted in interwar palaeoanthropology.

Alternative models of Pleistocene biocultural evolution: a response to Foley

Antiquity ◽  
1989 ◽  
Vol 63 (238) ◽  
pp. 153-159 ◽  
Author(s):  
G. A. Clark
Keyword(s):  
Human Evolution ◽  
Modern Human ◽  
Human Populations ◽  
Human Origins ◽  
Single Source ◽  
Recent Discussion ◽  
Garden Of Eden ◽  
Biocultural Evolution ◽  
History Of ◽  
Origins Research

Human origins research has had a long history of vigorous debate. Recent discussion has been no exception, the more so perhaps as the strands of evidence — anthropological, archaeological, and now molecular-biological — are sufficiently diverse that not many can be well placed to deal fairly with them all. Here issue is taken with Foley's cladistic view of human evolution, and with the ‘Garden of Eden’ hypothesis of a single source in Africa for modern human populations.

scholarly journals Soft sweeps are the dominant mode of adaptation in the human genome

2016 ◽  
Author(s):  
Daniel R. Schrider ◽  
Andrew D. Kern
Keyword(s):  
Positive Selection ◽  
Human Evolution ◽  
System Development ◽  
Dominant Mode ◽  
Nervous System Development ◽  
Human Populations ◽  
Beneficial Mutation ◽  
Recent Positive Selection ◽  
Machine Learning Approach

ABSTRACTThe degree to which adaptation in recent human evolution shapes genetic variation remains controversial. This is in part due to the limited evidence in humans for classic “hard selective sweeps,” wherein a novel beneficial mutation rapidly sweeps through a population to fixation. However, positive selection may often proceed via “soft sweeps” acting on mutations already present within a population. Here we examine recent positive selection across six human populations using a powerful machine learning approach that is sensitive to both hard and soft sweeps. We found evidence that soft sweeps are widespread and account for the vast majority of recent human adaptation. Surprisingly, our results also suggest that linked positive selection affects patterns of variation across much of the genome, and may increase the frequencies of deleterious mutations. Our results also reveal insights into the role of sexual selection, cancer risk, and central nervous system development in recent human evolution.

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