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Inferring human neutral genetic variation from craniodental phenotypes

Rathmann, H, Perretti, S, Porcu, V, Hanihara, T, Scott, GR, Irish, JD, Reyes-Centeno, H, Ghirotto, S and Harvati, K (2023) Inferring human neutral genetic variation from craniodental phenotypes. PNAS Nexus, 2 (7).

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There is a growing consensus that global patterns of modern human cranial and dental variation are shaped largely by neutral evolutionary processes, suggesting that craniodental features can be used as reliable proxies for inferring population structure and history in bioarchaeological, forensic, and paleoanthropological contexts. However, there is disagreement on whether certain types of data preserve a neutral signature to a greater degree than others. Here we address this unresolved question and systematically test the relative neutrality of four standard metric and non-metric craniodental data types employing an extensive computational genotype-phenotype comparison across modern populations from around the world. Our computation draws on the largest existing datasets currently available, while accounting for geographically structured environmental variation, population sampling uncertainty, disparate numbers of phenotypic variables, and stochastic variation inherent to a neutral model of evolution. Our results reveal that the four data types differentially capture neutral genomic variation, with highest signals preserved in dental non-metric and cranial metric data, followed by cranial non-metric and dental metric data. Importantly, we demonstrate that combining all four data types together maximizes the neutral genetic signal compared to using them separately, even with a limited number of phenotypic variables. We hypothesize that this reflects a lower level of genetic integration through pleiotropy between, compared to within, the four data types, effectively forming four different modules associated with relatively independent sets of loci. Therefore, we recommend that future craniodental investigations adopt holistic combined data approaches, allowing for more robust inferences about underlying neutral genetic variation.

Item Type: Article
Subjects: Q Science > QM Human anatomy
Q Science > QP Physiology
Divisions: Biological & Environmental Sciences (from Sep 19)
Publisher: Oxford University Press (OUP)
SWORD Depositor: A Symplectic
Date Deposited: 07 Jul 2023 14:48
Last Modified: 31 Jul 2023 14:15
DOI or ID number: 10.1093/pnasnexus/pgad217
URI: https://researchonline.ljmu.ac.uk/id/eprint/20272
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