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  1. Article ; Online: Biological races in humans.

    Templeton, Alan R

    Studies in history and philosophy of biological and biomedical sciences

    2013  Volume 44, Issue 3, Page(s) 262–271

    Abstract: Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological ... ...

    Abstract Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race.
    MeSH term(s) Adaptation, Physiological ; Africa ; Animals ; Biological Evolution ; Continental Population Groups/genetics ; Genetic Variation ; Humans ; Pan troglodytes/genetics
    Language English
    Publishing date 2013-05-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1500765-0
    ISSN 1879-2499 ; 1369-8486
    ISSN (online) 1879-2499
    ISSN 1369-8486
    DOI 10.1016/j.shpsc.2013.04.010
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  2. Article ; Online: Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorder

    David Kainer / Alan R. Templeton / Erica T. Prates / Daniel Jacboson / Euan R.O. Allan / Sharlee Climer / Michael R. Garvin

    HGG Advances, Vol 4, Iss 1, Pp 100150- (2023)

    1480  

    Abstract: Summary: The heritability of autism spectrum disorder (ASD), based on 680,000 families and five countries, is estimated to be nearly 80%, yet heritability reported from SNP-based studies are consistently lower, and few significant loci have been ... ...

    Abstract Summary: The heritability of autism spectrum disorder (ASD), based on 680,000 families and five countries, is estimated to be nearly 80%, yet heritability reported from SNP-based studies are consistently lower, and few significant loci have been identified with genome-wide association studies. This gap in genomic information may reside in rare variants, interaction among variants (epistasis), or cryptic structural variation (SV) and may provide mechanisms that underlie ASD. Here we use a method to identify potential SVs based on non-Mendelian inheritance patterns in pedigrees using parent-child genotypes from ASD families and demonstrate that they are enriched in ASD-risk genes. Most are in non-coding genic space and are over-represented in expression quantitative trait loci, suggesting that they affect gene regulation, which we confirm with their overlap of differentially expressed genes in postmortem brain tissue of ASD individuals. We then identify an SV in the GRIK2 gene that alters RNA splicing and a regulatory region of the ACMSD gene in the kynurenine pathway as significantly associated with a non-verbal ASD phenotype, supporting our hypothesis that these currently excluded loci can provide a clearer mechanistic understanding of ASD. Finally, we use an explainable artificial intelligence approach to define subgroups demonstrating their use in the context of precision medicine.
    Keywords Genomic structural variation ; missing heritability ; autism spectrum disorder ; Mendelian inheritance ; artificial intelligence ; precision medicine ; Genetics ; QH426-470
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: PaCE Builds on the Tradition of Responsible Research Within NAPCRG.

    Haeme, Raymond / Felzien, Maret / Kelly, Kirk / Lowe, Susan / Martinez-Guijosa, Arturo / Mason, Kirk / Kaplan, David / LeMaster, Joseph / Westfall, John M / Pavilanis, Alan / Templeton, Anna / Haddad, Leyla / Ramsden, Vivian R

    Annals of family medicine

    2023  Volume 21, Issue 6, Page(s) 562–563

    MeSH term(s) Humans ; Family Practice ; Primary Health Care
    Language English
    Publishing date 2023-11-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2171425-3
    ISSN 1544-1717 ; 1544-1709
    ISSN (online) 1544-1717
    ISSN 1544-1709
    DOI 10.1370/afm.3063
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  4. Article ; Online: Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorder.

    Kainer, David / Templeton, Alan R / Prates, Erica T / Jacboson, Daniel / Allan, Euan R O / Climer, Sharlee / Garvin, Michael R

    HGG advances

    2022  Volume 4, Issue 1, Page(s) 100150

    Abstract: The heritability of autism spectrum disorder (ASD), based on 680,000 families and five countries, is estimated to be nearly 80%, yet heritability reported from SNP-based studies are consistently lower, and few significant loci have been identified with ... ...

    Abstract The heritability of autism spectrum disorder (ASD), based on 680,000 families and five countries, is estimated to be nearly 80%, yet heritability reported from SNP-based studies are consistently lower, and few significant loci have been identified with genome-wide association studies. This gap in genomic information may reside in rare variants, interaction among variants (epistasis), or cryptic structural variation (SV) and may provide mechanisms that underlie ASD. Here we use a method to identify potential SVs based on non-Mendelian inheritance patterns in pedigrees using parent-child genotypes from ASD families and demonstrate that they are enriched in ASD-risk genes. Most are in non-coding genic space and are over-represented in expression quantitative trait loci, suggesting that they affect gene regulation, which we confirm with their overlap of differentially expressed genes in postmortem brain tissue of ASD individuals. We then identify an SV in the GRIK2 gene that alters RNA splicing and a regulatory region of the
    MeSH term(s) Humans ; Autism Spectrum Disorder/genetics ; Genome-Wide Association Study/methods ; Artificial Intelligence ; Quantitative Trait Loci/genetics ; Inheritance Patterns/genetics
    Language English
    Publishing date 2022-10-06
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ISSN 2666-2477
    ISSN (online) 2666-2477
    DOI 10.1016/j.xhgg.2022.100150
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  5. Article ; Online: Coalescent-based, maximum likelihood inference in phylogeography.

    Templeton, Alan R

    Molecular ecology

    2010  Volume 19, Issue 3, Page(s) 431–435

    MeSH term(s) Computer Simulation ; Evolution, Molecular ; Geography ; Haplotypes ; Likelihood Functions ; Models, Statistical ; Phylogeny ; Sequence Analysis, DNA
    Language English
    Publishing date 2010-01-11
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/j.1365-294X.2009.04514.x
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  6. Article: Correcting approximate Bayesian computation.

    Templeton, Alan R

    Trends in ecology & evolution

    2010  Volume 25, Issue 9, Page(s) 488–9; author reply 490–1

    MeSH term(s) Algorithms ; Bayes Theorem ; Biostatistics ; Models, Biological ; Models, Statistical ; Probability
    Language English
    Publishing date 2010-07-07
    Publishing country England
    Document type Comment ; Letter ; Research Support, N.I.H., Extramural
    ZDB-ID 284965-3
    ISSN 1872-8383 ; 0169-5347
    ISSN (online) 1872-8383
    ISSN 0169-5347
    DOI 10.1016/j.tree.2010.06.009
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  7. Article ; Online: The diverse applications of cladistic analysis of molecular evolution, with special reference to nested clade analysis.

    Templeton, Alan R

    International journal of molecular sciences

    2010  Volume 11, Issue 1, Page(s) 124–139

    Abstract: The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This ... ...

    Abstract The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many ways in which clades (branches) of haplotype trees have been applied in recent years, including the study of genotype/phenotype associations at candidate loci and in genome-wide association studies, the phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species.
    MeSH term(s) Animals ; Evolution, Molecular ; Genetic Association Studies ; Haplotypes ; Humans ; Phylogeny ; Phylogeography ; Species Specificity
    Language English
    Publishing date 2010-01-08
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms11010124
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  8. Article ; Online: Network-based hierarchical population structure analysis for large genomic data sets.

    Greenbaum, Gili / Rubin, Amir / Templeton, Alan R / Rosenberg, Noah A

    Genome research

    2019  Volume 29, Issue 12, Page(s) 2020–2033

    Abstract: Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is ... ...

    Abstract Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is becoming increasingly possible to reveal many hierarchical levels of structure, including fine-scale genetic clusters. To analyze these data sets, methods need to be appropriately suited to the challenges of extracting multilevel structure from whole-genome data. Here, we present a network-based approach for constructing population structure representations from genetic data. The use of community-detection algorithms from network theory generates a natural hierarchical perspective on the representation that the method produces. The method is computationally efficient, and it requires relatively few assumptions regarding the biological processes that underlie the data. We show the approach by analyzing population structure in the model plant species
    MeSH term(s) Algorithms ; Databases, Nucleic Acid ; Genome, Human ; Genomics ; Humans ; Sequence Analysis, DNA
    Language English
    Publishing date 2019-11-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.250092.119
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    Zs.A 3729: Show issues Location:
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  9. Article: Has human evolution stopped?

    Templeton, Alan R

    Rambam Maimonides medical journal

    2010  Volume 1, Issue 1, Page(s) e0006

    Abstract: It has been argued that human evolution has stopped because humans now adapt to their environment via cultural evolution and not biological evolution. However, all organisms adapt to their environment, and humans are no exception. Culture defines much of ...

    Abstract It has been argued that human evolution has stopped because humans now adapt to their environment via cultural evolution and not biological evolution. However, all organisms adapt to their environment, and humans are no exception. Culture defines much of the human environment, so cultural evolution has actually led to adaptive evolution in humans. Examples are given to illustrate the rapid pace of adaptive evolution in response to cultural innovations. These adaptive responses have important implications for infectious diseases, Mendelian genetic diseases, and systemic diseases in current human populations. Moreover, evolution proceeds by mechanisms other than natural selection. The recent growth in human population size has greatly increased the reservoir of mutational variants in the human gene pool, thereby enhancing the potential for human evolution. The increase in human population size coupled with our increased capacity to move across the globe has induced a rapid and ongoing evolutionary shift in how genetic variation is distributed within and among local human populations. In particular, genetic differences between human populations are rapidly diminishing and individual heterozygosity is increasing, with beneficial health effects. Finally, even when cultural evolution eliminates selection on a trait, the trait can still evolve due to natural selection on other traits. Our traits are not isolated, independent units, but rather are integrated into a functional whole, so selection on one trait can cause evolution to occur on another trait, sometimes with mildly maladaptive consequences.
    Language English
    Publishing date 2010-07-02
    Publishing country Israel
    Document type Journal Article
    ZDB-ID 2573657-7
    ISSN 2076-9172
    ISSN 2076-9172
    DOI 10.5041/RMMJ.10006
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  10. Article ; Online: Coherent and incoherent inference in phylogeography and human evolution.

    Templeton, Alan R

    Proceedings of the National Academy of Sciences of the United States of America

    2010  Volume 107, Issue 14, Page(s) 6376–6381

    Abstract: A hypothesis is nested within a more general hypothesis when it is a special case of the more general hypothesis. Composite hypotheses consist of more than one component, and in many cases different composite hypotheses can share some but not all of ... ...

    Abstract A hypothesis is nested within a more general hypothesis when it is a special case of the more general hypothesis. Composite hypotheses consist of more than one component, and in many cases different composite hypotheses can share some but not all of these components and hence are overlapping. In statistics, coherent measures of fit of nested and overlapping composite hypotheses are technically those measures that are consistent with the constraints of formal logic. For example, the probability of the nested special case must be less than or equal to the probability of the general model within which the special case is nested. Any statistic that assigns greater probability to the special case is said to be incoherent. An example of incoherence is shown in human evolution, for which the approximate Bayesian computation (ABC) method assigned a probability to a model of human evolution that was a thousand-fold larger than a more general model within which the first model was fully nested. Possible causes of this incoherence are identified, and corrections and restrictions are suggested to make ABC and similar methods coherent. Another coalescent-based method, nested clade phylogeographic analysis, is coherent and also allows the testing of individual components of composite hypotheses, another attribute lacking in ABC and other coalescent-simulation approaches. Incoherence is a highly undesirable property because it means that the inference is mathematically incorrect and formally illogical, and the published incoherent inferences on human evolution that favor the out-of-Africa replacement hypothesis have no statistical or logical validity.
    MeSH term(s) Biological Evolution ; Humans ; Phylogeny ; Probability
    Language English
    Publishing date 2010-03-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.0910647107
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