Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions

<p>Abstract</p> <p>Background</p> <p>Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. To address this gap, a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers. In addition, haplotypic diversity for its most prominent J1-M267 lineage was estimated using a set of 17 Y-specific STR loci.</p> <p>Results</p> <p>Saudi Arabia differentiates from other Arabian Peninsula countries by a higher presence of J2-M172 lineages. It is significantly different from Yemen mainly due to a comparative reduction of sub-Saharan Africa E1-M123 and Levantine J1-M267 male lineages. Around 14% of the Saudi Arabia Y-chromosome pool is typical of African biogeographic ancestry, 17% arrived to the area from the East across Iran, while the remainder 69% could be considered of direct or indirect Levantine ascription. Interestingly, basal E-M96* (n = 2) and J-M304* (n = 3) lineages have been detected, for the first time, in the Arabian Peninsula. Coalescence time for the most prominent J1-M267 haplogroup in Saudi Arabia (11.6 ± 1.9 ky) is similar to that obtained previously for Yemen (11.3 ± 2) but significantly older that those estimated for Qatar (7.3 ± 1.8) and UAE (6.8 ± 1.5).</p> <p>Conclusion</p> <p>The Y-chromosome genetic structure of the Arabian Peninsula seems to be mainly modulated by geography. The data confirm that this area has mainly been a recipient of gene flow from its African and Asian surrounding areas, probably mainly since the last Glacial maximum onwards. Although rare deep rooting lineages for Y-chromosome haplogroups E and J have been detected, the presence of more basal clades supportive of the southern exit route of modern humans to Eurasian, were not found.</p

The IGF1 small dog haplotype is derived from Middle Eastern grey wolves

<p>Abstract</p> <p>Background</p> <p>A selective sweep containing the insulin-like growth factor 1 (<it>IGF1</it>) gene is associated with size variation in domestic dogs. Intron 2 of <it>IGF1 </it>contains a SINE element and single nucleotide polymorphism (SNP) found in all small dog breeds that is almost entirely absent from large breeds. In this study, we surveyed a large sample of grey wolf populations to better understand the ancestral pattern of variation at <it>IGF1 </it>with a particular focus on the distribution of the small dog haplotype and its relationship to the origin of the dog.</p> <p>Results</p> <p>We present DNA sequence data that confirms the absence of the derived small SNP allele in the intron 2 region of <it>IGF1 </it>in a large sample of grey wolves and further establishes the absence of a small dog associated SINE element in all wild canids and most large dog breeds. Grey wolf haplotypes from the Middle East have higher nucleotide diversity suggesting an origin there. Additionally, PCA and phylogenetic analyses suggests a closer kinship of the small domestic dog <it>IGF1 </it>haplotype with those from Middle Eastern grey wolves.</p> <p>Conclusions</p> <p>The absence of both the SINE element and SNP allele in grey wolves suggests that the mutation for small body size post-dates the domestication of dogs. However, because all small dogs possess these diagnostic mutations, the mutations likely arose early in the history of domestic dogs. Our results show that the small dog haplotype is closely related to those in Middle Eastern wolves and is consistent with an ancient origin of the small dog haplotype there. Thus, in concordance with past archeological studies, our molecular analysis is consistent with the early evolution of small size in dogs from the Middle East.</p> <p>See associated opinion by Driscoll and Macdonald: <url>http://jbiol.com/content/9/2/10</url></p

Genetic Diversity of Southeast African Bantus and African Americans using the PowerPlex Y23 System

The aim of this investigation is to determine the capacity of the newly available Y-STR multiplex system, PowerPlex® Y23, to discriminate between populations of similar ancestry, specifically of African descent. Using network analysis, the partitioning of the 23-loci haplotypes was assessed in relation to Y-specific haplogroups. In the network projection, a number of Bantu haplogroups including E1b1a1a1a-M58, B2a1a-M109 and E2b-M98 as well as non-Bantu African haplogroups such as B2b2-M115 and A1b1b2b1-M118 segregate differentially based on Y-STR haplotypes. Further, we contrast population genetics parameters of the Bantu Southeast African and African American populations. Also, the genetic distance values illustrate the robust capacity of the PowerPlex® Y23 system to discriminate among populations. Noteworthy, we demonstrate that the two populations of African ancestry are as genetically different from each other as the African American population is from the Caucasian, Hispanic and Native American groups. For the first time, allelic and genotypic frequencies for the 23 Y-STR loci included in the PowerPlex® Y23 forensic system are provided for a continental Southeast African population, the Bantu from the Maputo Province