Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample.
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.
Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy. pfrancalacci@uniss.it.
Paolo
P
Francalacci
Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy. darsanna@uniss.it.
Daria
D
Sanna
Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy. auseli@uniss.it.
Antonella
A
Useli
Center for Advanced Studies, Research and Development in Sardinia, Sassari, Italy. berutti@berutti.net.|Institut für Humangenetik, Helmholtz Zentrum, Munich, Germany. berutti@berutti.net.
Riccardo
R
Berutti
Cardiff School of Biosciences, Cardiff University, Cardiff, UK. barbatom@cardiff.ac.uk.
Mario
M
Barbato
Istituto di Ricerca Genetica e Biomedica CNR, Cagliari, Italy. whalenmb@hotmail.com.
Michael B
MB
Whalen
Istituto di Ricerca Genetica e Biomedica CNR, Cagliari, Italy. andrea.angius@irgb.cnr.it.
Andrea
A
Angius
Istituto di Ricerca Genetica e Biomedica CNR, Cagliari, Italy. scarlino81@gmail.com.
Carlo
C
Sidore
Departamento de Genética, Antropología Física y Fisiología Animal, Universidad del País Vasco, Bilbao, Spain. santos.alonso@ehu.es.
Santos
S
Alonso
Dipartimento di Biologia, Università d Pisa, Pisa, Italy. stofanelli@unipi.it.
Sergio
S
Tofanelli
Istituto di Ricerca Genetica e Biomedica CNR, Cagliari, Italy. fcucca@uniss.it.|Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy. fcucca@uniss.it.
Francesco
F
Cucca
D000328:Adult; D041322:Chromosomes, Human, Y / Q000235:genetics*; D005843:Geography; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D007558:Italy; D008297:Male; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*