Inbreeding avoidance in the Raute hunter–gatherers from Nepal Inez Derkx1,2,3, Gina Menn1, Begoña Dobon4, Sudarshan Subedi5, Prajwal Rajbhandari6, Anita Gyawali7, Mark Dyble8,9, Daniel Major-Smith9,10,11, Gul Deniz Salali9, Nikhil Chaudhary8,9, Lucio Vinicius1,9, Jaume Bertranpetit4 and Andrea Migliano1,9 1Institute of Evolutionary Anthropology, University of Zurich, Zürich 8057, Switzerland 2Swiss Tropical and Public Health Institute, Allschwil 4123, Switzerland 3University of Basel, Basel, Basel-Stadt 4001, Switzerland 4Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Barcelona 08003, Spain 5Department of Conflict, Peace and Development Studies, Tribhuvan University, Kirtipur 44600, Nepal 6Research Institute for Bioscience and Biotechnology, Lalitpur 44700, Nepal 7Committee to Study the Social, Cultural, Economic and Geographical Habitat of Raute Community, Birendranagar 21700, Nepal 8Department of Archaeology, Cambridge University, Cambridge CB2 3DZ, UK 9Department of Anthropology, University College London, London WC1H 0BW, UK 10Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK 11Department of the Study of Religion, Institute for Culture and Society, Aarhus Universitet, Aarhus 8000, Denmark ID, 0000-0002-6889-494X; PR, 0000-0003-3159-8263; MD, 0000-0001-6861-1631; DM-S, 0000-0001-6467-2023; GDS, 0000-0001-9538-3064; LV, 0000-0002-9396-3249; AM, 0000-0003-4364-2735 Inbreeding can reduce fitness and genetic diversity, posing significant challenges for small human populations. While mobility and exogamy are known mechanisms of inbreeding avoidance among hunter–gatherers, the effects of cultural systems in mitigating these risks have not been studied in detail. Here, we investigate inbreeding patterns and avoidance strategies in the Raute of Nepal in comparison with two other contemporary hunter–gatherer populations, the Agta of the Philippines and the Mbendjele BaYaka of the Republic of Congo, using genome-wide single nucleotide polymorphism data and kinship analysis. We find evidence for heightened levels of homozygosity and a general preference towards genetically dissimilar mates among these populations, despite wide variation in population structure and connectivity. In addition, our simulations also show that the Raute’s patrilineal clan-based exogamic marriage system reduces expected offspring inbreeding more effectively than random mating or close-kin avoidance. These results suggest that the Raute’s cultural rules may be a compensatory strategy for their demographic isolation. Our findings highlight the importance of social structure in shaping genetic outcomes and demonstrate how cultural practices can evolve as adaptive responses to the constraints of small population size. 1. Introduction Inbreeding, the mating between genetically close relatives, can profoundly affect demography by reducing genetic diversity, especially in small or isolated populations [1,2]. It arises through either consanguineous marriages or the fixation of genetic variants owing to genetic drift, leading to an increase in the proportion of homozygosity and higher genetic relatedness within a population [3,4]. Increased homozygosity can expose the effects © 2026 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. Research Cite this article: Derkx I et al. 2026 Inbreeding avoidance in the Raute hunter–gatherers from Nepal. Proc. R. Soc. B 293: 20260109. https://doi.org/10.1098/rspb.2026.0109 Received: 15 January 2026 Accepted: 9 March 2026 Subject Category: Evolution Subject Areas: evolution, genetics, behaviour Keywords: hunter–gatherers, Raute, inbreeding, inbreeding avoidance Author for correspondence: Inez Derkx e-mail: inez.derkx@swisstph.ch Electronic supplementary material is available online at https://doi.org/10.6084/ m9.figshare.c.8383190. Downloaded from http://royalsocietypublishing.org/rspb/article-pdf/doi/10.1098/rspb.2026.0109/6134863/rspb.2026.0109.pdf by University of Cambridge user on 26 May 2026 http://orcid.org/ http://orcid.org/0000-0002-6889-494X https://orcid.org/0000-0003-3159-8263 https://orcid.org/0000-0001-6861-1631 http://orcid.org/0000-0001-6467-2023 http://orcid.org/0000-0001-9538-3064 http://orcid.org/0000-0002-9396-3249 http://orcid.org/0000-0003-4364-2735 http://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by/4.0/ https://crossmark.crossref.org/dialog/?doi=10.1098/rspb.2026.0109&domain=pdf&date_stamp=2026-04-25 https://doi.org/10.1098/rspb.2026.0109 https://doi.org/10.6084/m9.figshare.c.8383190 https://doi.org/10.6084/m9.figshare.c.8383190 of deleterious alleles and reduce beneficial heterozygous traits, leading to inbreeding depression and a decline in overall fitness [3,4]. To mitigate such costs, sexually reproducing species, including humans, have developed various inbreeding avoidance mechanisms. In humans, hunter–gatherer (HG) populations may have relied on extensive kin networks and large-scale mobility to select genetically and physically distant mates[5] [6–8]. Female exogamy, whereby women mate outside their group, and diverse post-marital residence patterns likely helped to create such extensive networks among historical groups [9]. Palaeoge- netic evidence for these strategies has been found in the genomes of ancient European HGs and in Upper Palaeolithic remains in western Russia, the latter of which exhibited homozygosity patterns associated with high mobility and exogamy, as well as in the late Mesolithic sites of Téviec and Hoedic in Brittany, which suggest low relatedness among co-residents [10,11]. This evidence implies that past HG populations likely adopted inbreeding avoidance strategies reflecting their population size, demography, culture and lifestyle. Nevertheless, HGs may still perceive a general heightened drift-related vulnerability to inbreeding owing to their small band sizes [12]. Specifically, their inability to sustain large, dense populations as a result of resource constraints may have increased genetic drift and therefore inbreeding risk: the probability of relatedness between two randomly chosen mates [12,13]. Studies in the few remaining HG populations seem to confirm their higher exposure to inbreeding risk. Populations such as the Biaka from Central Africa, San from South Africa, Maniq and Punan Batu from Southeast Asia, and Raute from Nepal all exhibit higher levels of homozygosity compared with neighbouring non-foraging populations [14–18]. These findings suggest that HGs may indeed experience a higher inbreeding risk compared with non-foraging populations. Some HG populations may be particularly vulnerable to inbreeding owing to limited kin networks and regional connectivity. One such population is the Raute of Nepal, an HG group residing in the foothills of the Himalayas and exhibiting a very high inbreeding coefficient of 0.226 (FROH), meaning approximately 22.6% of their genome is homozygous [15,19]. This may partially result from recent historical population decline, further exacerbated by a current small population size, genetic isolation from other populations through group endogamy, and cultural isolation [15,20]. The Raute have therefore lacked recent dispersal and crossbreeding opportunities, potentially prompting alternative inbreeding avoidance strategies [15]. One possibility is stricter adherence to cultural marriage rules. For example, the Casiguran Agta and the Hanunoo of Mindoro prohibit marriage between kin, a custom that allows expansion of support networks while mitigating inbreeding risk [21]. In some populations, such rules are governed by a clan system. The BaYaka from Central Africa, for instance, check whether a potential couple is in breach of clan exogamy rules prior to allowing marriage [22]. The Raute rely on a patrilineal clan system that subdivides them into three sub-groups (patriclans), within which marriage is prohibited. Women permanently join their husbands’ clan upon marriage. However, it is still unclear whether their patriclan system has any effect on inbreeding avoidance. We hypothesize that higher levels of homozygosity among HG populations require more effective inbreeding avoidance strategies, which in the case of the highly inbred Raute population means an ever-closer adherence to strict marriage rules dictated by their patriclan system. Here, we compare genetic data from the Raute [15] with two geographically and demograph- ically distinct HG populations: the Mbendjele BaYaka from the Republic of Congo and the Palanan Agta from the Philippines [23]. This comparative study thereby contributes novel evidence on inbreeding in extant HGs and their cultural adaptations to inbreeding avoidance. 2. Results (a) The Agta, BaYaka and Raute show higher levels of homozygosity than their non-forager neighbours We first compared homozygosity levels in the Raute, other HG populations, and their nearby non-foraging populations. We used FROH—the proportion of the genome contained in runs of homozygosity (ROH), where a higher proportion indicates increased levels of inbreeding—as our estimate of inbreeding [24]. Homozygosity levels are higher in all three HG populations than in their nearby non-foraging neighbours (figure 1). This general trend was further supported by a Bayesian model, which predicted higher average FROH among HGs compared with nearby non-foraging populations (electronic supplementary material, figure S1). In addition, the Raute and the Agta differ more from their neighbouring populations than the BaYaka (see also the posterior predictions from the Bayesian model in electronic supplementary material, figure S1). The BaYaka, on the other hand, show the lowest levels of inbreeding among the three HG populations, which is likely linked to their demographic and genetic history. More specifically, this population is characterized by long-term connectivity to other HG populations from West and Central Africa, and a larger regional joint population size (over 30 000) and available gene pool [25,26]. Similarly, while the Palanan Agta sampled in this study comprise only around 1000 individuals, the overall Agta population in the Luzon province numbers around 10 000 people [27,28]. In contrast, the Raute’s lack of connectivity to other populations, endogamic marriage practices and cultural isolation mean their gene pool is limited to their population size of 150 individuals [15]. (b) Lower relatedness in hunter–gatherer couples suggests inbreeding avoidance The higher homozygosity levels in the HG populations, especially the Raute, suggest a necessity for effective inbreeding avoidance strategies. We thus compared spousal relatedness both with overall population relatedness and with the expected relatedness of the population subset, including only potential spouses or the available mating pool. Table 1 shows that average spousal relatedness is lowest in the BaYaka (r = 0.0053, n = 3), followed by the Agta (r = 0.0175, n = 25), and is highest in the 2 royalsocietypublishing.org/journal/rspb Proc. R. Soc. B 293: 20260109 Downloaded from http://royalsocietypublishing.org/rspb/article-pdf/doi/10.1098/rspb.2026.0109/6134863/rspb.2026.0109.pdf by University of Cambridge user on 26 May 2026 Raute (0.1240, n = 11). Given the total average population relatedness in the three populations (r = 0.0255, 0.0460 and 0.1410 for Agta, BaYaka and Raute, respectively), the results suggest a general preference for less genetically similar mates (figure 2A and table 1). Examining median relatedness further supports this conclusion, except for the Agta, where median spousal relatedness is slightly higher than in the total population. However, this comparison is limited because the total population pool contains unlikely potential couples such as parent– offspring dyads. To circumvent this issue, we also computed the expected relatedness of the subset of hypothetical potential couples (figure 2B and §4). Consistent with initial findings, the Raute showed the highest expected relatedness among potential partner dyads when compared with the Agta and BaYaka (figure 2B). Furthermore, the average relatedness among spouses in all three HG populations was lower than or equal to the first quartile of expected relatedness in the subset of possible partner dyads (electronic supplementary material, table S1). The expected relatedness outcomes significantly differed between all three populations, as illustrated by ANOVA (p < 0.0001) and subsequent post hoc analysis (least-squares means, p < 0.0001) for all population combinations (electronic supplementary material, figure S2). Overall, these findings strongly suggest that less genetically related individuals are chosen as spouses in all three HG populations. (c) Raute’s patriclan exogamy reduces inbreeding A potential strategy to reduce inbreeding in the Raute may be provided by their patriclan system. Beyond a general close-kin avoidance rule shared with many other populations (prohibiting mating among close relatives such as parents and offspring or siblings), the patriclan system additionally prohibits marriage between paternal parallel cousins (i.e. children of the father’s brother) [19]. We used permutation tests to compare the observed mean and median relatedness within and between clans with a null distribution obtained through random reassignment of clan membership over many permutations (electronic supplementary material, tables S2 and S3). The tests revealed a clear difference in mean relatedness between same-clan and different-clan dyads, with the observed mean difference (0.00425, p < 0.001) at the fair tail (<0.03%) of the permutation distribution (figure 3A, left). In contrast, no difference was detected in median relatedness (median difference = −0.00130, p = 0.126) (figure 3B, right). The results may be driven by highly related dyads within clans rather than general elevated relatedness in the population. This Figure 1. Relationship between subsistence style, region and inbreeding measured by FROH. Populations are represented on the y-axis, and the FROH of all individuals per population is shown on the x-axis, faceted by region and coloured by subsistence style. 3 royalsocietypublishing.org/journal/rspb Proc. R. Soc. B 293: 20260109 Downloaded from http://royalsocietypublishing.org/rspb/article-pdf/doi/10.1098/rspb.2026.0109/6134863/rspb.2026.0109.pdf by University of Cambridge user on 26 May 2026 finding thereby provides evidence for the role of the patriclan system as a way of ensuring individuals do not partner with closely related individuals. We further simulated how the Raute’s patriclan exogamy performed against three other mating strategies: panmixia (random mating, as the null hypothesis), close-kin avoidance (no marriages between first-degree relatives) and patriclan endogamy (opposite of exogamy, included to examine the effect of existing genetic variation within clans). We calculated the expected offspring inbreeding coefficient (EOIC), which accounts for both the relatedness of a couple and their individual inbreeding coefficients, as well as relatedness. Results showed that clan exogamy yields the lowest EOIC and relatedness values, closely followed by close-kin avoidance, random mating and finally clan endogamy (figure 3B). Close-kin avoidance significantly reduces EOIC compared with random mating and clan endogamy. However, clan exogamy results in even lower EOIC than close-kin avoidance, as confirmed by ANOVA (p < 0.0001), subsequent post hoc analysis (least-squares means, p < 0.0001) (electronic supplementary material, figure S3) and a Bayesian linear regression (electronic supplementary material, figure S4). Owing to overall limited genetic variation, high EOIC is observed regardless of the simulated mating system, especially when compared with the average population FROH of 0.226. Nonetheless, these findings indicate that patriclan exogamy may be a slightly more effective cultural mechanism for reducing future inbreeding in the Raute than close-kin avoidance alone. 3. Discussion We explored the dynamics of inbreeding and its avoidance in the Raute HGs, relying on comparisons with the Agta and BaYaka HGs. Our results indicate that all three populations exhibit higher homozygosity levels compared with neighbouring non-foraging populations. Previous studies of the Maniq and Punan Batu HGs from Southeast Asia had revealed similar results [16,18]. Together, these findings confirm that HGs generally exhibit higher levels of inbreeding than non-foraging neighbours, and more broadly that subsistence style may thus impact inbreeding risk [12,17]. However, inbreeding levels also varied between the Agta, BaYaka and Raute, likely reflecting their differences in population size, demographic history, social structure, cultural norms and network connectivity, among other factors. This was further demonstrated by their differences in population relatedness, with the Raute showing considerably higher average and median relatedness when compared with the Agta and BaYaka, and also by the substantially higher relatedness between spouses in Figure 2. Relatedness in the Agta, BaYaka and Raute. (A) Distribution of the (relatedness) estimated from all dyadic connections in each population (see §4). Vertical dashed lines: average observed spousal relatedness in each population. (B) Comparison of observed relatedness(ɸ) among spouses in each population (blue horizontal dashed line below each box plot) and distribution of expected relatedness (ɸ) between potential spouses (box plots). The horizontal orange lines represent the total population’s average relatedness. Table 1. Overview of mean and median relatedness and sample sizes for all spousal dyads and total population dyads in each of the three hunter–gatherer populations. Agta BaYaka Raute population no. couples population no. couples population no. couples N pairs 9615 25 166 3 6328 11 N individuals 141 50 19 6 113 22 mean r 0.0255 0.0175 0.0468 0.0053 0.1410 0.1240 median r 0.0168 0.0174 0.0080 0.0030 0.1340 0.1280 4 royalsocietypublishing.org/journal/rspb Proc. R. Soc. B 293: 20260109 Downloaded from http://royalsocietypublishing.org/rspb/article-pdf/doi/10.1098/rspb.2026.0109/6134863/rspb.2026.0109.pdf by University of Cambridge user on 26 May 2026 the Raute population. Nonetheless, the lower relatedness in the hypothetical subset of eligible mating partners compared with observed spousal relatedness potentially suggests some level of inbreeding avoidance in the three HG populations. Any putative inbreeding avoidance rules may vary across the three populations. For example, marriages are not allowed between unrelated in-laws in the Agta [21] or between members of the same clan among the BaYaka, and both populations generally favour partners from distant locations or different bands [22]. In addition, they can also rely on high (post-marital) dispersal or extensive social or kin networks [3,21,22,29–33]. Small and isolated populations such as the Raute may be less likely to avoid higher average relatedness owing to lacking similar dispersal opportunities and larger group sizes. Still, the Raute appear to be able to select less related partners than expected, potentially underscoring the role of their patriclan exogamy strategy, which prevents marriage among first-degree relatives as well as paternal parallel cousins. Our modelling of four mating scenarios in the Raute indeed suggests that patriclan exogamy engenders the lowest EOIC, highlight- ing the importance of cultural customs and systems as inbreeding avoidance mechanisms, particularly in extremely small and isolated societies. As mentioned above, many human populations have developed rules against close-kin marriage. The Casiguran Agta have an exogamy rule that prohibits marriage with anyone with whom they share a kin connection, while a relatedness study among the Palanan Agta found only 2 out of 80 couples to have any kind of pedigree relatedness [21,27]. Similarly, the San of Nyae Nyae in Namibia do not permit marriage with someone from the same residential camp and have specific kinship terms for various relatives that dictate whether marriage is permissible [34,35]. In addition to such rules, the BaYaka and the Raute may have created a clan-based marriage system to prevent certain marriages beyond merely those between close kin [19,22]. The limited sampling of the Agta and BaYaka as well as the potential fluidity in marriage partnerships and potentially incomplete record of spouses posed significant challenges to our study. Moreover, we cannot guarantee that our sampled populations are representative of the total Agta and BaYaka populations. These limitations were taken into account in Figure 3. Effect of mating strategies on offspring and overall relatedness in the Raute. (A) Differences in mean and median relatedness between same-clan and different-clan dyads. (B) Violin plots of the expected offspring inbreeding coefficient (EOIC) and relatedness distributions under four demographic scenarios among the Raute: patriclan exogamy, close-kin avoidance, random mating and patriclan endogamy. 5 royalsocietypublishing.org/journal/rspb Proc. R. Soc. B 293: 20260109 Downloaded from http://royalsocietypublishing.org/rspb/article-pdf/doi/10.1098/rspb.2026.0109/6134863/rspb.2026.0109.pdf by University of Cambridge user on 26 May 2026 our methodological choices, for instance, in our use of simulations. Moreover, there was no individual-level information available regarding clan membership or other mating preferences for the Agta and BaYaka, although ethnographic records have described inbreeding avoidance customs in these populations. Hence, further individual-level comparisons of potential inbreeding avoidance strategies in the Raute, Agta and BaYaka were not possible. Future studies of clan structure, function and individual membership in HG populations are required to allow generalization of our findings and conclusions. Together, our findings provide evidence for the existence of effective inbreeding avoidance strategies in three HG popu- lations. Isolated and small populations such as the Raute appear to face more stringent demographic challenges and may therefore rely on additional cultural inbreeding avoidance mechanisms such as their patriclan system to prevent marriages, even among non-close kin. While such cultural rules could mitigate inbreeding risks to a certain degree, they may not be sufficient to prevent genetic drift in these populations, as reflected in the Raute’s currently high levels of homozygosity and population relatedness. Future studies should therefore examine how external demographic and genetic pressures influence the long-term viability of such populations, and to what degree cultural interventions can circumvent resulting inbreeding effects. 4. Methods (a) Ethnographic background (i) The Agta The Palanan Agta are a sub-population of around 1000 individuals from the Luzon Agta population—an indigenous HG group of around 10 000 people living on the island of Luzon in the Philippines—who reside in the Palanan municipality of the Isabela province. The Agta are considered a largely mobile population who primarily rely on foraging and agricultural labour for subsistence. They live in camps of, on average, around 20 adults, with mostly fluid camp membership, meaning individuals may move camps often [27,36]. The Palanan Agta have been shown to reside with many unrelated individuals in camps, a finding that was linked to their multilevel social structure, as further evidenced by the relatively low estimated pedigree relatedness of 0.010 for adults in the whole sub-population and 0.074 for adult campmates [27,37]. Kinship terminology and practices for the Casiguran and Sierra Madre Agta were previously described by Early & Headland [38], Headland [21] and Minter [39], who highlight that Agta do not marry those whom they have a kinship term for, resulting in individuals often having partners from neighbouring areas. Such practices are in line with the low camp relatedness in the Palanan Agta, as detailed above, and the Casiguran Agta, whose camp relatedness was estimated to be 0.053 [7]. (ii) The Mbendjele BaYaka The Mbendjele are a sub-population of the BaYaka population who reside in the northern rainforests of the Republic of Congo and speak the Mbendjele language [22]. They are considered part of the larger meta-population of Central African HGs, who have been shown to have been connected via both historical and recent networks [25,26]. The BaYaka have an immediate-return economy, relying primarily on foraging and hunting for subsistence. The group lives in multifamily camps of approximately 10–60 individuals with varying degrees of sedentariness and permanency, although camps can be as big as 200 individuals [36,40]. Like in the Agta camps, relatedness between adults within these camps is low [36]. Additionally, the Mbendjele are divided into patrilineal clans, whose genealogies generally go back several generations and which are not limited to single territories. They practice clan exogamy, meaning that within-clan marriage is not allowed. This is enforced by fathers checking the rule of clan exogamy prior to two individuals marrying [22]. (iii) The Raute The Raute are a small population of approximately 150 individuals residing in the Karnali province of Nepal. They traditionally engaged in primarily hunting and gathering activities but have received financial and other aid in recent years to supplement this subsistence. The population has likely undergone a recent decline, explaining their current group size and the high levels of homozygosity found in its members [15,20]. The Raute do not permit marriage with individuals from other populations (population endogamy). However, all individuals in the population are divided into three patrilineal clans, and members of the same clan are not permitted to marry (clan exogamy). Upon marriage, females ‘move’ (not physically, as clans co-reside together in a single camp) to their husbands’ clan, and children will automatically be members of their fathers’ clan too [19]. The rule of clan exogamy, like in the BaYaka, may be seen as an extension of a general rule prohibiting marriage among close kin, as paternal parallel cousins are also not allowed to marry within this system. (b) Genetic data For the Raute, nearly all individuals above the age of 4 were included as study participants (n = 120). In addition, 47 individuals from surrounding agricultural villages also provided saliva samples (total n = 167), which were collected using Oragene DNA/ saliva kits and genotyped using the Affymetrix Axiom Genome-Wide Human Origins 1 Array. After genotyping and quality control (QC), 157 individuals were included in this study (113 Raute and 44 agriculturalists), with approximately 600 ooo single nucleotide polymorphisms (SNPs) (see [15] for more details on the sampling procedure and QC workflow). Saliva samples for 6 royalsocietypublishing.org/journal/rspb Proc. R. Soc. B 293: 20260109 Downloaded from http://royalsocietypublishing.org/rspb/article-pdf/doi/10.1098/rspb.2026.0109/6134863/rspb.2026.0109.pdf by University of Cambridge user on 26 May 2026 the Agta (n = 155) were collected in 2013 and 2014 across multiple camps over two field seasons, and for the BaYaka (n = 21) in 2014. Saliva collection and genotyping were performed using the same procedure as for the Raute, yielding a total of 617 063 samples and 141 Agta, 14 Palanan farmers and 19 BaYaka samples post QC. These data were combined with publicly available SNP data from 21 Mbo individuals from Cameroon [41]. PLINK v. 1.9 [42[43]] was employed to calculate ROH for each population using the homozyg option and using only autosomal SNPs. To eliminate shorter ROH resulting from linkage disequilibrium, the minimum segment length was set at ≥300 kb, and the minimum number of SNPs was set at 30, following the methods of Derkx et al. [15] and Ceballos et al. [14]. The ROH-based inbreeding coefficient (FROH) was calculated using only segments larger than 1.5 Mb with the R package detectRUNS. In addition to reporting the distributions of FROH per population, we used Bayesian models implemented in the brms package in R [44] to examine the effect of region and subsistence on FROH, using the leave-one-out method in the loo R package to find the best-fitting model: FROH ~ subsistence + (1 + subsistence | region) with a Beta family [45]. Kinship coefficients (ɸ) were used as a proxy for genetic relatedness and were calculated using IBIS with a minimum segment length of 7 cM for all three populations (see [15] for an overview of the procedures). Kinship coefficients, referred to throughout the manuscript as ‘relatedness’, provide a measure of genetic similarity between two individuals by calculating the probability that a pair of randomly sampled homologous alleles—one from each of two individuals—are identical by descent (i.e. they are inherited from a common ancestor) [46,47]. Compared with the relatedness coefficient r, which calculates the proportion of alleles shared that are identical by descent, the kinship coefficient appears to show lower relatedness values for the same sets of relatives (e.g. for parent–offspring relationship, ɸ = 0.25 and r = 0.5 or 2ɸ), but ultimately describes the same relationships [46,48]. (c) Relatedness in couples We examined whether relatedness between couples could give an indication of inbreeding avoidance in the Agta, BaYaka and Raute by comparing observed relatedness among spouses (n = 25, n = 3, n = 11, respectively) in each population with the distribution of dyadic relatedness between all possible combinations of individuals in the total sampled population (table 1). We then computed expected relatedness using a subset of pairs of the total population, containing only pairs of individuals who are hypothetically eligible to marry (electronic supplementary material, table S1). Two individuals are considered eligible when they are of different sex, are both above 16 years old and are not first-degree relatives (ɸ < 0.1768). While this subset does not perfectly represent each individual’s potential partners, it does create a more realistic image of potential mates compared with the total population. Expected relatedness was obtained by performing 10 000 permutations in which relatedness was randomly shuffled, without shuffling the information about which pairs are originally couples. We subsequently selected only the pairs labelled as ‘couples’, the number of which was kept equal to the original number of couples per population, to compute average relatedness per permutation. The distribution of the 10 000 mean and median relatedness values for couples per population was then visualized in R using ggplot2 [49] and compared against the observed average relatedness among the real couples. Lastly, we performed an ANOVA test (kinship ~ population) and used the R package emmeans [50] to calculate and compare least-squares means for post hoc analysis. (d) Demographic marriage models in the Raute To examine inbreeding and the effects of various potential inbreeding avoidance strategies in the Raute, we first compared the relatedness between all pairs of individuals within and between clans, grouped as either ‘same clan’ (i) or ‘different clan’ (ii) (electronic supplementary material, tables S2 and S3). We performed 50 000 permutations in which the clan membership of all 113 individuals was shuffled, and subsequent dyads (n = 6328) were labelled 1 or 2. The differences in mean and median relatedness between 1-dyads and 2-dyads were subsequently computed for each permutation, and p-values were taken as the proportion of instances in which the permuted mean and median differences were higher than the observed differences in mean and median relatedness for same- and different-clan dyads. We then examined four potential scenarios, each reflecting a different mating or marriage strategy, always assuming that individuals do not mate with same-sex individuals and are over 16 years old when married: (i) random mating (panmixia): individuals randomly choose a marriage partner; (ii) clan exogamy: individuals cannot marry other individuals inside their clan and do not marry close kin; (iii) clan endogamy: individuals can only marry other individuals inside their clan; and (iv) close-kin avoidance: individuals only avoid marrying first-degree relatives (r < 0.1768), irrespective of their clan membership. In each simulation, a data frame is created which includes all eligible males and females (given the demographic scenario) along with their relatedness (pairwise) and inbreeding (individual) measures. The ROH-based inbreeding coefficient (FROH) is used as a proxy for the degree of inbreeding in individuals. From this data frame, 11 pairs are randomly sampled to mimic the total sampled number of real Raute couples. For each pair, the EOIC of their offspring is calculated. This is done only once per pair but may be seen as the average of potential multiple offspring that a hypothetical couple could have. The EOIC is calculated as follows: F = ((FROH mother + FROH father)/2) + (ϕmother & father/2). The calculation is thus based on the inbreeding coefficients of both the father and mother as well as the relatedness of the pair. The resulting 11 EOICs and relatedness are then averaged. This whole process is repeated 100 000 times per scenario. The resulting four distributions are compared in a violin plot as well as an ANOVA test and post hoc analysis using least-squares means, as well as a simple linear regression model 7 royalsocietypublishing.org/journal/rspb Proc. R. Soc. B 293: 20260109 Downloaded from http://royalsocietypublishing.org/rspb/article-pdf/doi/10.1098/rspb.2026.0109/6134863/rspb.2026.0109.pdf by University of Cambridge user on 26 May 2026 (EOIC ~ mating scenario using a Gaussian family) implemented in brms to understand how each strategy impacts the expected offspring inbreeding coefficients (electronic supplementary material, figure S4) [44]. Ethics. This study received ethical approval from the Ethics Commission of the University of Zurich (ethics code no. 20.2.8), the Nepali Health Ministry (reference no. 1219) and the University College London Ethics Committee (ethics code 3086/003). Additionally, research permission was granted by the local government in the Philippines as well as community members of the Agta in Palanan, the Republic of Congo’s Ministry of Scientific Research, the Karnali provincial government (Nepal), and the three leaders of the Raute community. Before participating, all individuals gave informed consent, which was obtained after group and individual presentations outlining the research procedures and providing a thorough explanation of the study's objectives in either the indigenous language (Agta and BaYaka) or the local language (Raute), including how to withdraw consent. Raute participants were compensated with goods for their involvement. For a detailed explanation of consent procedures with the Agta study participants, see [23]. This study involves the combination of anthropological and genetic data, in some cases directly linked to pairs of individuals (relatedness between spouses). Given the size of the Agta, BaYaka, and especially the Raute populations, these data have been used with extreme caution to ensure the anonymity of research participants. We ask for the discretion of our readers when interpreting our findings and making generalized conclusions about either the populations at hand or the broader research implications of this paper. Data accessibility. All data and code necessary to reproduce the analyses and findings reported in this study are publicly available in an Open Science Framework (OSF) repository: [51][]. These data include runs of homozygosity data for all individuals and pairwise genetic relatedness for all pairs in the Agta, BaYaka and Raute populations. The sequenced genetic data for the Raute are available under controlled access at the European Genome-phenome Archive (EGA) under accession number EGA50000000714, subject to ethical restrictions and data access approval. The sequenced genetic data for the Agta and BaYaka populations are not publicly available owing to ethical restrictions and the terms of informed consent protecting the privacy of individual participants. Access to these data may be considered upon reasonable request and subject to appropriate ethical approvals and data-sharing agreements. The last author (A.M.) can be contacted for questions regarding genetic data access. The remaining publicly available data were obtained from [41] and can be found at https://reich.hms.harvard.edu/datasets. Supplementary material is available online [52]. Declaration of AI. The authors occasionally made use of GPT-4-turbo (OpenAI) in the editing of this work, which was subsequently carefully reviewed and edited by the authors. They take full responsibility for the final content of the publication. Authors’ contributions. I.D.: conceptualization, data curation, formal analysis, funding acquisition, methodology, visualization, writing—original draft, writing—review and editing; G.M.: data curation; B.D.: formal analysis, writing—review and editing; S.S.: data curation; P.R.: project administration; A.G.: data curation; M.D.: data curation, writing—review and editing; D.M.-S.: data curation, writing—review and editing; G.D.S.: data curation; N.C.: data curation; L.V.: supervision, writing—review and editing; J.B.: methodology, supervision, writing—original draft, writing—review and editing; A.M.: resources, supervision, writing—review and editing. All authors gave final approval for publication and agreed to be held accountable for the work performed herein. Conflict of interest declaration. We declare we have no competing interests. Funding. I.D. received funding from the Schultz Foundation (A. H. 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Introduction 2. Results (a) The Agta, BaYaka and Raute show higher levels of homozygosity than their non-forager neighbours (b) Lower relatedness in hunter–gatherer couples suggests inbreeding avoidance (c) Raute’s patriclan exogamy reduces inbreeding 3. Discussion 4. Methods (a) Ethnographic background (b) Genetic data (c) Relatedness in couples (d) Demographic marriage models in the Raute