TY - JOUR
T1 - High levels of copy number variation of ampliconic genes across major human Y haplogroups
AU - Ye, Danling
AU - Zaidi, Arslan A.
AU - Tomaszkiewicz, Marta
AU - Anthony, Kate
AU - Liebowitz, Corey
AU - DeGiorgio, Michael
AU - Shriver, Mark D.
AU - Makova, Kateryna D.
N1 - Funding Information:
The authors are grateful to Tomas Benjamin Gonzalez Zarzar for providing facial masculinity scores and to David Puts, PaulMedvedev, and Rahul Vegesna for helpful discussions. We also thank the ADAPT study participants, without whom this research would not have been possible. Funding for the project was provided by the Penn State Center for Human Evolution and Disease (CHED) seed grant, the Huck Institutes for the Life Sciences, the Eberly College of Sciences, the Institute of Cyberscience at Penn State, and by a grant from the Pennsylvania Department of Health using Tobacco Settlement Funds. The Department specifically disclaims responsibility for any analyses, interpretations, or conclusions.
Funding Information:
The authors are grateful to Tomas Benjamin Gonzalez Zarzar for providing facial masculinity scores and to David Puts, Paul Medvedev, and Rahul Vegesna for helpful discussions. We also thank the ADAPT study participants, without whom this research would not have been possible. Funding for the project was provided by the Penn State Center for Human Evolution and Disease (CHED) seed grant, the Huck Institutes for the Life Sciences, the Eberly College of Sciences, the Institute of Cyberscience at Penn State, and by a grant from the Pennsylvania Department of Health using Tobacco Settlement Funds. The Department specifically disclaims responsibility for any analyses, interpretations, or conclusions.
Publisher Copyright:
© The Author(s) 2018.
PY - 2018/5/1
Y1 - 2018/5/1
N2 - Because of its highly repetitive nature, the humanmale-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared bymales fromvery different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according tomajor Y haplogroups.Overall, only two gene families (RBMY and TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of a male could not be predicted based on his ampliconic gene copy numbers. Finally, we did not find significant correlations either between copy number variation and individual's height, or between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.
AB - Because of its highly repetitive nature, the humanmale-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared bymales fromvery different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according tomajor Y haplogroups.Overall, only two gene families (RBMY and TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of a male could not be predicted based on his ampliconic gene copy numbers. Finally, we did not find significant correlations either between copy number variation and individual's height, or between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.
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U2 - 10.1093/gbe/evy086
DO - 10.1093/gbe/evy086
M3 - Article
C2 - 29718380
AN - SCOPUS:85049665806
SN - 1759-6653
VL - 10
SP - 1333
EP - 1350
JO - Genome biology and evolution
JF - Genome biology and evolution
IS - 5
ER -