[12] In 2007, Strouhal would characterize the physical features of ancient A-Group Nubians as being "Caucasoid" which were "not distinguishable from the contemporary Predynastic Upper Egyptians of the Badarian and Naqadian cultures", based in reference to previous anthropological studies from 1975 and 1985.

Moreover, Keita criticised the methodology of the 1993 Brace study for excluding "the Maghreb, Sudan, and the Horn of Africa" from the designated Sub-Saharan group samples which he argued was nearly categorised and "(incorrectly)" as monolithic".

He also concluded that more material was needed to make a firm conclusion about the relationship between the early Holocene Nile valley populations and later ancient Egyptians.

[20] Kanya Godde in a 2009 study evaluated population relationships by comparing cranial traits in twelve Nubian and Egyptian groups which included skeletal remains from the Badarian period.

She also cited previous anthropological studies and archaeological evidence which indicated close affinities between the Badarians and other southernly, African populations.

[22] In 2023, Christopher Ehret wrote that the physical anthropological findings from the "major burial sites of those founding locales of ancient Egypt in the fourth millennium BCE, notably El-Badari as well as Naqada, show no demographic indebtedness to the Levant".

[23] Some researchers have critiqued the reliability of craniology—the study of skull shapes and sizes—in drawing definitive conclusions about the biological relationships and identities of ancient populations.

Keita, relying solely on cranial measurements without considering broader archaeological and environmental contexts can lead to oversimplified or misleading interpretations.

Researchers such as Ron Pinhasi and Jay T. Stock strongly advocate for integrating craniometric data with genetic, archaeological, and environmental evidences to offer a more comprehensive understanding of population history and biological relationships.

[26] They argue that conclusions drawn strictly from craniological or other morphological analyses about cultural or ancestral relationships should be approached with caution and supported by multiple lines of evidence.

Advancements in ancient DNA analysis and other bioarchaeological methodologies have provided more precise tools for investigating genetic relationships and migration patterns.

[29] Dental trait analysis of Badarian fossils conducted in a thesis study found that they were closely related to other Afroasiatic-speaking populations inhabiting Northeast Africa and the Maghreb.

[30]: 231–2 While dental trait analysis has been a useful tool in bioarchaeology for assessing biological relationships among ancient populations, recent scholarship highlights its limitations.

Bioanthropologist Christy G. Turner II and colleagues have emphasized that "dental morphology alone may not provide a complete picture of population relationships and must be integrated with other lines of evidence."

[31] Sonia Zakrzewski (2003), found that samples from the Badarian to the Middle Kingdom in Upper Egypt had "tropical body plans", but that their proportions were actually "super-negroid" (i.e. the limb indices are relatively longer than in many "African" populations).

She proposed that the apparent development of an increasingly African body plan over time may also be due to Nubian mercenaries being included in the Middle Kingdom sample.

Zakrzewski concluded that the "results must remain provisional due to the relatively small sample sizes and the lack of skeletal material that cross-cuts all social and economic groups within each time period".

[32] In 2011, Michelle Raxter examined the changes in limb proportions and body sizes in ancient Egyptians in a worldwide and regional comparative thesis study.

Overall, the study found that "Ancient Egyptians have more tropically adapted limbs in comparison to body breadths, which tend to be intermediate when plotted against higher and lower latitude populations.

Raxter also acknowledged that a larger sample collection from the early and late predynastic groups would have enabled "closer examination of biological changes in the transition to agriculture".

[33] Limb proportion analysis has been utilized in physical anthropology to study climatic adaptations and infer aspects of population history among ancient groups.

Measurements such as the brachial index (upper arm to forearm ratio) and crural index (thigh to lower leg ratio) have been used to assess thermoregulatory adaptations according to Allen's rule, which posits that populations in warmer climates tend to have longer limbs to dissipate heat, while those in colder climates have shorter limbs to conserve heat.

[35][36] Anthropologist Tenton W. Holliday further cautions that "while limb proportions can provide insights into broad patterns of climatic adaptation, they are not definitive indicators of genetic relationships or cultural affiliations among ancient populations."