Biology subjects

Wasef, S.

Publications and source records attributed to Wasef, S..

5 recordsLinked to original sources

bioRxiv2025

Archaeological Bolivian maize genomes suggest Inca cultural expansion augmented maize diversity in South America

Previous archaeological and anthropological studies have demonstrated the myriad of ways that cultural and political systems shape access to food and food preferences. However, few studies have conducted a biocultural analysis linking specific genotypic/phenotypic traits as evidence of cultural selection in ancient contexts. Here, we provide insight into this topic through ancient genome data from Bolivian maize dating to [~]500-600 BP, included as an offering with the mummified remains of a young girl. These data are compared to 16 previously published archaeological maize samples spanning at least 5,000 years of evolution, and 226 modern maize samples. Our phylogenetic analysis showed that the archaeological Bolivian maize (aBM) has the closest genetic distance to the archaeological maize from ancient Peru, which in turn shared the most similarities with archaeological Peruvian maize. During the period of interaction between the Inca state and local polities in the central Andes and consequent interactions with local agricultural traditions, the genetic diversity of maize increased. Ovule development in modern maize was selected and compared to those in archaeological specimens, revealing evidence of targeted breeding strategies aimed at improving seed quality and yield. While the cultural origin of the maize - either Inca or local Aymara - is uncertain, we demonstrate that the samples are most similar to Peruvian maize and potential targeted selection strategies for enhanced growth were well established by the 15th century. Significance StatementMaize has been improved through selective breeding delivering desirable horticultural, agronomic, and cultural characteristics, related to environment, nutrition, etc. Inca culture was closely associated with maize diversity, but there is little evidence to show how and why culture influenced that diversity and modern maize biogeographic patterns in South America. We show that in the 15th century CE, maize diversity in the central Andes was enhanced through selection for specific traits associated with reproduction. We hypothesize that this may have contributed to maize becoming a staple under the Inca, as happened previously with expanding Tiwanaku interactions and influence during the Middle Horizon.

plant biology↗

bioRxiv2020

The Ancient DNA Insights into Aboriginal Australian Mortuary Practices

Paleogenetics is a relatively new and promising field that has the potential to provide new information about past Indigenous social systems, including insights into the complexity of burial practices. We present results of the first ancient DNA (aDNA) investigation into traditional mortuary practices among Australian Aboriginal people with a focus on North-East Australia. We recovered mitochondrial and Y chromosome sequences from five ancestral Aboriginal Australian remains that were excavated from the Flinders Island group in Cape York, Queensland. Two of these individuals were sampled from disturbed beach burials, while the other three were from bundle burials located in rock shelters. Genomic analyses showed that individuals from all three rock shelter burials and one of the two beach burials had a close genealogical relationship to contemporary individuals from communities from Cape York. In contrast the remaining male individual, found buried on the beach, had a mitochondrial DNA sequence that suggested that he was not from this location but that he was closely related to people from central Queensland or New South Wales. In addition, this individual was associated with a distinctive burial practice to the other four people. It has been suggested that traditionally non-locals or lower status individuals were buried on beaches. Our findings suggest that theories put forward about beach burials being non-local, or less esteemed members of the community, can potentially be resolved through analyses of uniparental genomic data. Generally, these results support the suggestion often derived from ethnohistoric accounts that inequality in Indigenous Australian mortuary practices might be based on the status, sex, and/or age of individuals and may instead relate to place of geographic origin. There is, however, some departure from the traditional ethnohistoric account in that complex mortuary internments were also offered to female individuals of the community, with genomic analyses helping to confirm that the gender of one of the rockshelter internments was that of a young female.

evolutionary biology↗

bioRxiv2019

Mitogenomic Diversity in Sacred Ibis Mummies sheds light on early Egyptian practices

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from [~]600BC. Although it is known that a very large number of these votive mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred [~]2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild Sacred Ibis for the ritual yearly demand.

evolutionary biology↗

bioRxiv2018

Fishing for Mitochondrial DNA in The Egyptian Sacred Ibis Mummies

The long-term preservation of DNA requires a number of optimal conditions, including consistent exposure to cool, dry, and dark environments. As a result, the successful recovery of ancient DNA from material from warmer climates such as those in Egypt has often been met with scepticism. Egypt has an abundance of ancient mummified animals and humans, whose genetic analyses would offer important insights into ancient cultural practices. To date, the retrieval of complete genomes from ancient Egyptian remains of humans or other animals has been largely unsuccessful. To test for the presence of even short DNA sequences in Egyptian material, we performed second-generation shotgun sequencing of DNA libraries constructed from ancient Sacred Ibis mummies. Since most of the resulting Illumina libraries were shown to contain extremely low levels (less than 0.06%) of endogenous mitochondrial DNA, we aimed to enrich these samples using targeted in-solution hybridisation methods. Using biotinylated RNA baits designed to Sacred Ibis complete mitochondrial sequences, we trialled a number of conditions and parameters and achieved up to 4705-fold enrichment. We also found that a combination of hybridisation temperature and the use of the polymerase KAPA HiFi significantly increased both the efficiency of targeted hybridisation and post-hybridisation amplification respectively. Furthermore, improved enrichment was accompanied with only minor increases in clonality. Our method enabled us to reconstruct the first complete mitochondrial genomes from ancient Egyptian sub-fossil material.

genomics↗

bioRxiv2018

Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

evolutionary biology↗