Regulations surrounding destructive sampling and sample export for aDNA research projects vary widely and are enforced at different levels within governmental cultural or heritage institutions (Marquez-Grant and Fibiger, 2013). Regulatory bodies within these institutions are usually tasked with evaluating formal written requests to access collections and perform sampling and assure compliance with final reporting requirements. Besides institutions that enforce federal and/or state heritage regulations, in countries such as the United States and Canada, some Indigenous communities have their own regulations for genetic research studies (Claw et al., 2018, 2021; Begay et al., 2019; Wagner et al., 2020).

However, the reality in the Global South can be very different. Institutions tasked with regulating access to heritage or archaeological collections may lack or have unclear regulations and requirements, insufficient budgets or enforcement strategies to enact these regulations, or a combination thereof (e.g. (Abarca Labra et al., 2018)). This ambiguity can also affect local institutions or individuals (e.g. archaeologists leading excavations) who first receive research proposals for destructive analysis and where the sampling process itself may not be clearly defined nor accountability or follow-up measures outlined, leaving important decisions about sampling and research practices in the hands of a few.

Within Latin America, there is large variation in regulations for destructive sampling and few that are particularly dedicated to aDNA. For example, both Mexico and Chile have specific institutions dedicated to the research, conservation and protection of anthropological, archaeological, historical, and cultural heritage (National Institute of Anthropology and History (INAH) and National Monuments Council, respectively). INAH’s Archaeology Council regulates access to archaeological samples for all destructive and non-destructive analyses following institutional guidelines (Instituto Nacional de Antropología e Historia, 2019). Although the council has clear requirements for ancient bio-molecular research, some of them are not ready to be implemented (e.g., lack of infrastructure to store aDNA extracts, libraries, or genetic data). In some countries from this region, cultural artifacts and human bodies recovered from archaeological contexts are subject to a heritage process where there is a centralized entity managing their fate. This process primarily involves legal protection against destruction and variable levels of regulations for research settings, particularly if samples are leaving the country. Albeit necessary, there are some troubling assumptions under this model that are rarely discussed by aDNA researchers, particularly in relation to regulatory and state recognition of Indigenous identities, which we discuss in following sections.

In India, the Archaeological Survey of India (ASI) serves as the premier national governmental institution that oversees the cultural heritage of the country, including regulating the export of materials abroad for research. Additionally, state government archaeological departments have the autonomy to carry out the role of heritage conservation and conduct archaeological excavations in their respective jurisdictions. These institutions are well suited to implement and oversee a best-practice regulatory framework for sampling of human bodies from archaeological contexts for aDNA research (Jamir, 2022b; Pappu, 2022; Rai, 2022; Taher, 2022).

Historically unequal power relations can also shape heritage management in ways that have consequences for aDNA research as seen in Puerto Rico, which as a U.S. territory without federally recognized Indigenous nations, is excluded from NAGPRA (Rodríguez López, 2009b; d’Alpoim Guedes et al., 2021). While artifacts and human bodies recovered from archaeological contexts are considered the patrimony of all Puerto Ricans under local legislation, such laws are superseded by federal regulations (Pagán-Jiménezand Rodriguez Ramos, 2008; Rodríguez López, 2009a;, 2009b; Llorens-Liboy and Núñez, 2011). Indeed, many archaeological remains excavated in Puerto Rico were exported to the US mainland soon after the American invasion (Pagán Jiménez, 2000); well before Puerto Ricans could vote for their own government or enact modern heritage legislation. Now curated in museums and collections abroad (DaRos and Colten, 2009; Françozo and Strecker, 2017), these remains can be legally sampled for aDNA research without passing through the permitting process required by Puerto Rican authorities or consulting with island stakeholder communities.

Recommendation: Support efforts to improve local cultural and heritage management regulations and involve these institutions in the research process. Researchers can aid communities, permitting agencies, and ethical and regulatory boards seeking to develop better frameworks and guidelines for destructive aDNA analyses by holding open discussions with board members about the process, risks and potential benefits of aDNA research, and by providing detailed reports and inventories of the remaining DNA products and data files after research is concluded. Furthermore, engaging with local museums or other heritage management institutions may facilitate contacts with communities for consultations prior to study start and assist with dissemination of research results to the general public, local museums, universities or schools.

Although building local capacities for research is an essential first step towards ensuring sustainability, equity and inclusion within paleogenomics, many Global South nations face significant challenges in setting up training programs and maintaining research facilities. These challenges include economic austerity measures that underfund public education and scientific investment, small or nonexistent research funding streams, lack of support for research capacity building, and limited access to, or structural disparities in, higher education (Reidpath and Allotey, 2019; Reidpath and Allotey, 2020; Viera et al., 2020; Carter and Hujo, 2021).

In Latin America and the Caribbean, for example, enrollments in higher education have increased over the last decade but other inequities persist, such as patterned access to higher education based on income and low availability of coursework or degree programs in science fields (Ferreyra et al., 2017). For example, despite being a US territory, Puerto Rico’s universities are under-funded and about 42.9% of undergraduate students live below the poverty line (Nazario, 2014; Trines, 2018). As of this writing, there are limited opportunities for local undergraduate training in anthropology (Pagán Jiménez, 2000; Pagán-Jiménezand Rodriguez Ramos, 2008), and no formal graduate degree programs focused on biological anthropology, bioarchaeology, ancient DNA, or genomic science. While such programs can be pursued abroad, they often charge high tuition rates, making them unaffordable for many families, or limiting access just to high-income students. In Mexico, where a few degree programs in anthropology and genomics provide training in paleogenomics methods, severe budget cuts and government divestment threaten to reduce offerings and shutter educational institutions (Santos Cid, 2022). In India and Chile, degree programs in anthropology, archaeology, and genomics exist; however, there is currently only one functional aDNA lab in each country to train and conduct all local paleogenomics research.

Altogether, these factors make it difficult for local students to access and complete degree programs, reduce local job opportunities for scientific professionals, and accelerate brain-drain emigration patterns (Mishra, 2006; Weinberg, 2011; Docquier, 2014). In such contexts, local students may understandably see Global North countries as the only options for training, and local researchers may choose to export aDNA samples to these locations for processing and analyses. However, this creates a vicious cycle, as export means no local research is conducted, no training of students takes place, and local capacity for research remains underdeveloped.

Recommendation: Provide training opportunities to strengthen local research capacity. Researchers from Global North institutions can fund bilateral trainee exchanges with local institutions and provide wet lab and bioinformatics training in their labs. As shown by the success of the SING consortium workshops in the United states, Canada, Australia and Aotearoa (Malhi and Bader, 2015; Wade, 2018), short courses and training events can also become spaces to discuss multiple aspects of genomics research, including sampling strategies, data analyses or interpretations, and ethical considerations with local students and community members.

Ancient DNA research requires sterile conditions for data generation and high data quality standards. This calls for an entirely separate facility dedicated to low copy number DNA processing that complies with strict criteria (Knapp et al., 2012; Fulton and Shapiro, 2019), and uses sterile molecular grade reagents and consumables (Champlot et al., 2010; Llamas et al., 2017). In the last 5–6 years, paleogenomics data generation has been overtaken by the ‘1240k’ capture panel, costing nearly $250 per reaction without accounting for shipping and other export regulatory costs. Despite its early branding as “democratizing” paleogenomics (Pickrell and Reich, 2014), the capture panel remains out of reach for many laboratories in the Global South and may become yet another means of unequitable foreign collaborations (Argüelles et al., 2022).

Altogether, the cost of establishing, maintaining, and day-to-day running of a paleogenomics facility is not an easy feat, often requiring institutional and/or governmental commitment to infrastructure (e.g., lab space, equipment) and sustenance (e.g., hiring, reagents, consumables, maintenance). Not surprisingly, paleogenomics is not a high priority research avenue in most countries battling more pressing challenges, such as health crises or economic insecurity (Maher et al., 2012; Lebel and McLean, 2018; Liverpool, 2021). This often translates to little to no support for local researchers interested in developing this field in their countries, as reflected in the current distribution of global aDNA laboratories ² . For countries in the Global South that have aDNA laboratories, upkeep is often difficult with issues ranging from power shortages to infrastructural and maintenance limitations such as limited space and scope for expansion, delayed and pricey access to equipment and parts, lack of expertise to diagnose and repair breakdown of proprietary equipment, and so on. Moreover, sourcing and ordering reagents that are easily obtained in the Global North is time-consuming and often several fold more expensive elsewhere (Table 1) (Ciocca and Delgado, 2017; Valenzuela-Toro and Viglino, 2021). When adding publication and conference fees, and the US dollar advantage, the cost of conducting research becomes disproportionately higher in the Global South vis-à-vis available budgets. Ultimately, these disparities in resource availability for executing scientific programs creates opportunities for ‘grab-and-go’ strategies that further research inequity and helicopter science practices (Adame, 2021; Haelewaters et al., 2021).

Recommendation: Foster equitable collaborations by supporting local research capacity and involving knowledgeable local collaborators and researchers as equal partners at all stages. Researchers based at Global North institutions can do this at different levels, from sharing equipment and reagents to local laboratories to formally collaborating with local researchers on projects and international grants. If collaborating in countries that already have aDNA facilities, additional ways to support capacity are to write research grants together with local collaborators, and budget for both reagents and consumables to be ordered to the local lab and travel to process samples jointly in the local laboratory and plans to contribute to training. The expertise and experience of local researchers and institutions can contribute nuanced insights and guide research goals to focus on locally relevant questions. Local collaborators are likely to have a better understanding of the regional history, current socio-political situation, regulations and, importantly, ethical implications of research for local communities. Partnerships with local collaborators and institutions can also aid in developing culturally responsive materials (Judd and McKinnon, 2021), in their language, for dissemination of research results to the public via news sources or other venues. This is important as genetics papers are often loaded with scientific jargon and assumptions that may be hard to interpret and open to misinterpretation by those far from the research (Harmon, 2018; Reich, 2018; Gannon, 2019; Wolinsky, 2019; Panofsky et al., 2021).

In the United States, NAGPRA legally requires researchers to identify affiliated tribal nations for consultation about research with ancestral remains. Meanwhile, in many Global South countries, in addition to the lack of legal mandates for community consultation, there are other issues surrounding unclear regulations on heritage management (discussed above), Indigenous identities, and heterogeneity in the state-Indigenous dynamics across and within regions that should be considered while enacting nuanced, community-sensitive consultation and engagement strategies.

Ethnic identity and belonging are fluid sociocultural constructs with definitions that vary over time and between populations. In some Indigenous communities, these constructs can be tied to connections with land or ancestors, and with spiritual, cultural, religious and linguistic traits, while others may invoke biological (phenotypic) features. Insights from genetic ancestry studies, if not framed sensitively and acknowledging existing identity structures, could impose upon the process of identity construction for both individuals and communities (Egorova, 2009; Gibbon et al., 2011; TallBear, 2013; Wade et al., 2015; Benn Torres and Torres Colón, 2020; Crellin and Harris, 2020). Genetic insights can sometimes conflict with community and individual beliefs or reproduce nationalistic or essentialized notions of identity that suppress the existence of Indigenous peoples.

In some Latin American countries, including Mexico and Chile, the institutional de-indigenization processes put in practice by the state emphasize that most of the population is mestizo, trivializing and legally neglecting the inherent value of Indigenous ancestry (Vasconcelos, 1997; García Deister, 2014; Manrique, 2016; Wade, 2017). While Indigenous peoples have some legal recognition in these countries, the discourse of a majority mestizo nation erases Indigenous rights over ancestral lands and heritage under the illusion that all mestizos have equal rights over Pre-Hispanic cultural heritage (Endere and Ayala, 2012; Silva et al., 2022). Afrodescendant communities, who have faced historical marginalization and invisibility in Latin American countries, encounter similar challenges because national identity in these countries is so strongly tied to mestizaje (Arocha and Maya, 2008; Weltman-Cisneros and Tello, 2013; Agren, 2020). To illustrate how this misconception can permeate scholarship, a recent piece on global guidelines for aDNA research (Alpaslan-Roodenberg et al., 2021) wrongfully claimed that mestizos in many Latin American countries “embraced their Indigenous roots”, hence the request to consult with Indigenous peoples in this region was “paternalistic” and “colonialist”. By reproducing such harmful narratives that relegate Indigenous peoples to legacies that should be considered a matter of the past and only embedded in the present-day mestizo national identity, such statements reproduce a long history of institutional discrimination and Indigenous erasure in Latin America. While consultation with Indigenous peoples for aDNA research outside the United States is a complex subject, for which NAGPRA protocols cannot be directly applied, stating that it is not needed because Indigenous identity is well represented by the mestizo population and State institutions is a fallacy and a continuation of historical harms.

In India and other parts of South Asia, the dynamics and recognition of Indigenous identities and rights in heritage management may differ from other places discussed above and even display vast intra-regional heterogeneity but, ultimately, result in a similar undermining of Indigenous engagement and involvement that are, to our knowledge, not currently mandated in archaeological (Jamir, 2022a) or aDNA research.

In this context, from an aDNA researcher’s perspective, identifying Indigenous populations that could be affiliated to individuals found in a given archaeological site or museum collection is not straightforward. In places like Mexico, where ancient empires like the Mexica invaded many territories and where multiple cultures could coexist in a single place (Mata-Míguez et al., 2012; Manzanilla, 2017), an additional layer of complexity emerges. Even if these connections can be made, challenges can surface if present-day Indigenous communities do not hold spiritual affiliation to ancestors from many generations ago (Cucina, 2013; Whittaker, 2020), if they have never been consulted about research participation before or face other more immediate challenges to their sovereignty or livelihoods (Castellanos, 2020; Hesketh, 2021; Rodriguez Aguilera, 2021). Because of the high levels of poverty and injustice most Indigenous communities in the Global South face (Hall and Patrinos, 2012; Hall and Gandolfo, 2016), an aDNA researcher can be hesitant of whether bringing yet another issue to consult and decide upon (especially one that has never been considered before) is correct or if it is invasive or imposed.

Recommendation: Prioritize community engagement as an integral part of the research design. As outlined above and elsewhere (Wagner et al., 2020), there is no one-size-fits-all set of guidelines. Instead of foregoing the engagement process entirely because of the inherent complexity, the subject of community consultation needs to be discussed thoroughly and applied to each circumstance, while including Indigenous scholars and other stakeholders in deciding the most ethical approach for each place, regardless of whether local legislation requires consultation or Indigenous approval to carry out the project. This requires dedicated time and resources to research the history and present situation of the region and communities one wants to work with, and then preparing to engage with and involve them in horizontal discussion before, during and after the project. Integrating descendant community perspectives into research should not be seen as a burden or checkboxing an outreach step (Muller and Dortch, 2020). Instead, such discussions acknowledge and respect the richness of community-based knowledge that can additionally significantly enrich the research process (Wagner et al., 2020).