Biology subjects

Nanaei, H. A.

Publications and source records attributed to Nanaei, H. A..

3 recordsLinked to original sources

bioRxiv2026

No genetic evidence yet for hinnies at Mazongshan (400-160 BCE), northwestern China

In their recent study entitled "Ancient DNA reveals the co-existence of domestic horses, donkeys and their hybrids in the prehistorical northwestern China", Li and colleagues (2026) report the genetic identification of three horses, three donkeys and four first-generation hinny hybrids dating to 400-160 BCE from the Mazongshan jade mining site in northwestern China. While a re-analysis of their ancient DNA sequence data confirms the horse and donkey identifications, it indicates that the four putative hinny specimens were, in fact, donkeys. This revision removes the primary evidence originally shown for the presence of hinnies at this site. Therefore, new data from the Mazongshan bone assemblage are required to support the proposed role of hinny hybrids as integral components of trans-regional trade networks during the Late Warring States and Early Han periods.

evolutionary biology↗

bioRxiv2021

The first sheep graph pan-genome reveals the spectrum of structural variations and their effects on different tail phenotypes

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here, we assembled 26 haplotype-resolved genome assemblies from 13 genetically diverse sheep using PacBio HiFi sequencing. We constructed a graph-based ovine pan-genome and discovered 142,422 biallelic insertions and deletions, 7,028 divergent alleles and 13,419 multiallelic variations. We then used a graph-based approach to genotype the biallelic SVs in 684 individuals from 45 domestic breeds and two wild species. Integration with RNA-seq data allows to identify candidate expression-associated SVs. We demonstrate a direct link of SVs and phenotypes by localizing the putative causative insertion in HOXB13 gene responsible for the long-tail trait and identifying multiple large SVs associated with the fat-tail. Beyond generating a benchmark resource for ovine structural variants, our study highlights that animal genetic research will greatly benefit from using a pan-genome graph rather than a single reference genome.

genomics↗

bioRxiv2016

Evolutionary history of the brown rat: out of southern East Asia and selection

The brown rat (Rattus norvegicus) is found wherever humans live and transmits many diseases, and its breeding produced the laboratory rat used widely in medical research. Here, we sequenced whole genomes from 118 rats to explore the origin and dispersal routes of the brown rat and the domestication of the laboratory rat. We showed that brown rats migrated about 3600 years ago from southern East Asia, rather than Northern Asia as formerly suggested, to the Middle East and then to Europe and Africa. Many genes involved in the immune system experienced positive selection in the wild brown rat, while genes involved in the nervous system and energy metabolism showed evidence of artificial selection during the domestication of laboratory strains. Our findings demystify the puzzling origin and migration of brown rats and reveal the impact of evolution and domestication on this animal.

evolutionary biology↗