Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample Evolutionary Biology

Paolo Francalacci, Daria Sanna, Antonella Useli, Riccardo Berutti, Mario Barbato, Michael B. Whalen, Andrea Angius, Carlo Sidore, Santos Alonso, Sergio Tofanelli, Francesco Cucca

Risultato della ricerca: Contributo in rivistaArticolo in rivista

Abstract

Background: Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions. Methods: DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software. Results: From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region. Conclusions: The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.
Lingua originaleEnglish
pagine (da-a)1-13
Numero di pagine13
RivistaBMC Research Notes
Volume8
DOI
Stato di pubblicazionePubblicato - 2015

Keywords

  • Adult
  • Biochemistry, Genetics and Molecular Biology (all)
  • Chromosomes, Human, Y
  • Geography
  • Haplotypes
  • Human evolutionary genetics
  • Humans
  • Italy
  • Male
  • Medicine (all)
  • Molecular phylogeny
  • Next Generation Sequencing
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Single nucleotide polymorphisms

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