Cross-cousin marriage among Tsimane forager-horticulturalists during demographic transition and market integration

Although still prevalent in many human societies, the practice of cousin marriage has precipitously declined in populations undergoing rapid demographic and socioeconomic change. However, it is still unclear whether changes in the structure of the marriage pool or changes in the fitness-relevant consequences of cousin marriage more strongly influence the frequency of cousin marriage. Here, we use genealogical data collected by the Tsimane Health and Life History Project to show that there is a small but measurable decline in the frequency of first cross-cousin marriage since the mid-twentieth century. Such changes are linked to concomitant changes in the pool of potential spouses in recent decades. We find only very modest differences in fitness-relevant demographic measures between first cousin and non-cousin marriages. These differences have been diminishing as the Tsimane have become more market integrated. The factors that influence preferences for cousin marriage appear to be less prevalent now than in the past, but cultural inertia might slow the pace of change in marriage norms. Overall, our findings suggest that cultural changes in marriage practices reflect underlying societal changes that shape the pool of potential spouses.

Modelling animal network data in R using STRAND

There have been recent calls for wider application of generative modelling approaches in applied social network analysis. At present, however, it remains difficult for typical end users-for example, field researchers-to implement generative network models, as there is a dearth of openly available software packages that make application of such models as simple as other, permutation-based approaches. Here, we outline the STRAND R package, which provides a suite of generative models for Bayesian analysis of animal social network data that can be implemented using simple, base R syntax. To facilitate ease of use, we provide a tutorial demonstrating how STRAND can be used to model proportion, count or binary network data using stochastic block models, social relation models or a combination of the two modelling frameworks. STRAND facilitates the application of generative network models to a broad range of data found in the animal social networks literature.

Women's subsistence strategies predict fertility across cultures, but context matters

While it is commonly assumed that farmers have higher, and foragers lower, fertility compared to populations practicing other forms of subsistence, robust supportive evidence is lacking. We tested whether subsistence activities-incorporating market integration-are associated with fertility in 10,250 women from 27 small-scale societies and found considerable variation in fertility. This variation did not align with group-level subsistence typologies. Societies labeled as "farmers" did not have higher fertility than others, while "foragers" did not have lower fertility. However, at the individual level, we found strong evidence that fertility was positively associated with farming and moderate evidence of a negative relationship between foraging and fertility. Markers of market integration were strongly negatively correlated with fertility. Despite strong cross-cultural evidence, these relationships were not consistent in all populations, highlighting the importance of the socioecological context, which likely influences the diverse mechanisms driving the relationship between fertility and subsistence.

Women's subsistence networks scaffold cultural transmission among BaYaka foragers in the Congo Basin

In hunter-gatherer societies, women's subsistence activities are crucial for food provisioning and children's social learning but are understudied relative to men's activities. To understand the structure of women's foraging networks, we present 230 days of focal-follow data in a BaYaka community. To analyze these data, we develop a stochastic blockmodel for repeat observations with uneven sampling. We find that women's subsistence networks are characterized by cooperation between kin, gender homophily, and mixed age-group composition. During early childhood, individuals preferentially coforage with adult kin, but those in middle childhood and adolescence are likely to coforage with nonkin peers, providing opportunities for horizontal learning. By quantifying the probability of coforaging ties across age classes and relatedness levels, our findings provide insights into the scope for social learning during women's subsistence activities in a real-world foraging population and provide ground-truth values for key parameters used in formal models of cumulative culture.

Reproductive inequality in humans and other mammals

To address claims of human exceptionalism, we determine where humans fit within the greater mammalian distribution of reproductive inequality. We show that humans exhibit lower reproductive skew (i.e., inequality in the number of surviving offspring) among males and smaller sex differences in reproductive skew than most other mammals, while nevertheless falling within the mammalian range. Additionally, female reproductive skew is higher in polygynous human populations than in polygynous nonhumans mammals on average. This patterning of skew can be attributed in part to the prevalence of monogamy in humans compared to the predominance of polygyny in nonhuman mammals, to the limited degree of polygyny in the human societies that practice it, and to the importance of unequally held rival resources to women's fitness. The muted reproductive inequality observed in humans appears to be linked to several unusual characteristics of our species-including high levels of cooperation among males, high dependence on unequally held rival resources, complementarities between maternal and paternal investment, as well as social and legal institutions that enforce monogamous norms.

Automatic entry and coding of social networks and dyadic peer ratings

In small-scale communities, social-scientists can use photo-rosters to collect social network and dyadic peer-ratings data. In past work, we introduced an R package to automate photo-standardization, survey construction, and data-entry. This R package, however, lacked two key features required for fully-unsupervised data-entry. First, respondent IDs needed to be manually linked to cellphone photographs of the photo-roster before DieTryin could process the data; second, users needed to identify the locations of the photo-roster in each cellphone photograph using a point-and-click interface. To address the first shortcoming, we introduce a new Android application, DieTryinCam, which facilitates annotation of cell-phone photographs with respondent, question, and panel IDs. To address the second shortcoming, we add new functionality to the DieTryin R package, which allows for the precise location of the photograph roster to be automatically identified. Automated data entry in DieTryin now requires no user input beyond a single function call from R.

Reliable network inference from unreliable data: A tutorial on latent network modeling using STRAND

Social network analysis provides an important framework for studying the causes, consequences, and structure of social ties. However, standard self-report measures-for example, as collected through the popular "name-generator" method-do not provide an impartial representation of such ties, be they transfers, interactions, or social relationships. At best, they represent perceptions filtered through the cognitive biases of respondents. Individuals may, for example, report transfers that did not really occur, or forget to mention transfers that really did. The propensity to make such reporting inaccuracies is both an individual-level and item-level characteristic-variable across members of any given group. Past research has highlighted that many network-level properties are highly sensitive to such reporting inaccuracies. However, there remains a dearth of easily deployed statistical tools that account for such biases. To address this issue, we provide a latent network model that allows researchers to jointly estimate parameters measuring both reporting biases and a latent, underlying social network. Building upon past research, we conduct several simulation experiments in which network data are subject to various reporting biases, and find that these reporting biases strongly impact fundamental network properties. These impacts are not adequately remedied using the most frequently deployed approaches for network reconstruction in the social sciences (i.e., treating either the union or the intersection of double-sampled data as the true network), but are appropriately resolved through the use of our latent network models. To make implementation of our models easier for end-users, we provide a fully documented R package, STRAND, and include a tutorial illustrating its functionality when applied to empirical food/money sharing data from a rural Colombian population. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Fitness consequences of cousin marriage: a life-history assessment in two populations

Cousin marriage, a spousal union between close kin, occurs at high frequencies in many parts of the world. The rates of cousin marriage in humans are concordant with empirical studies that challenge the traditionally held view that reproduction with kin is generally avoided in animals. Similarly, some theoretical models in animal behaviour show that inbreeding avoidance is more constrained than previously thought. Such studies highlight the importance of quantifying the costs and benefits of reproduction among close kin over the whole life-course. Here, we use genealogical data from two human populations with high frequencies of cousin marriage (the Dogon from Mali, and the Ancien Régime nobility from Europe) to estimate these potential costs and benefits. We compare age-specific fertility and survival curves, as well as the projected growth rates, of subpopulations of each marriage type. Fitness costs of cousin marriage are present in terms of reduced child survival (in both populations), while benefits exist as increased fertility for men (in the Dogon) and for women (in the Ancien Régime nobility). We also find some differences in the projected growth rates of lineages as a function of marriage type. Finally, we discuss the trade-offs that might shape marriage decisions in different ecological conditions.

Distinguishing Intergroup and Long-Distance Relationships

Intergroup and long-distance relationships are both central features of human social life, but because intergroup relationships are emphasized in the literature, long-distance relationships are often overlooked. Here, we make the case that intergroup and long-distance relationships should be studied as distinct, albeit related, features of human sociality. First, we review the functions of both kinds of relationship: while both can be conduits for difficult-to-access resources, intergroup relationships can reduce intergroup conflict whereas long-distance relationships are especially effective at buffering widespread resource shortfalls. Second, to illustrate the importance of distinguishing the two relationship types, we present a case study from rural Bolivia. Combining ethnography and two different experimental techniques, we find that the importance of intergroup relationships-and the salience of group membership itself-varies across populations and across methods. Although ethnography revealed that participants often rely on long-distance relationships for resource access, we were unable to capture participant preferences for these relationships with a forced-choice technique. Taken together, our review and empirical data highlight that (1) intergroup and long-distance relationships can have different functions and can be more or less important in different contexts and (2) validating experimental field data with ethnography is crucial for work on human sociality. We close by outlining future directions for research on long-distance relationships in humans.

Games and enculturation: A cross-cultural analysis of cooperative goal structures in Austronesian games

While most animals play, only humans play games. As animal play serves to teach offspring important life-skills in a safe scenario, human games might, in similar ways, teach important culturally relevant skills. Humans in all cultures play games; however, it is not clear whether variation in the characteristics of games across cultural groups is related to group-level attributes. Here we investigate specifically whether the cooperativeness of games covaries with socio-ecological differences across cultural groups. We hypothesize that cultural groups that engage in frequent inter-group conflict, cooperative sustenance acquisition, or that have less stratified social structures, might more frequently play cooperative games as compared to groups that do not share these characteristics. To test these hypotheses, we gathered data from the ethnographic record on 25 ethnolinguistic groups in the Austronesian language family. We show that cultural groups with higher levels of inter-group conflict and cooperative land-based hunting play cooperative games more frequently than other groups. Additionally, cultural groups with higher levels of intra-group conflict play competitive games more frequently than other groups. These findings indicate that games are not randomly distributed among cultures, but rather relate to the socio-ecological settings of the cultural groups that practice them. We argue that games serve as training grounds for group-specific norms and values and thereby have an important function in enculturation during childhood. Moreover, games might server an important role in the maintenance of cultural diversity.

Functional 3-Dimensional Retinal Organoids: Technological Progress and Existing Challenges

Stem cell scientists have developed methods for the self-formation of artificial organs, often referred to as organoids. Organoids can be used as model systems for research in multiple biological disciplines. Yoshiki Sasai’s innovation for deriving mammalian retinal tissue from in vitro stem cells has had a large impact on the study of the biology of vision. New developments in retinal organoid technology provide avenues for in vitro models of human retinal diseases, studies of pathological mechanisms, and development of therapies for retinal degeneration, including electronic retinal implants and gene therapy. Moreover, these innovations have played key roles in establishing models for large-scale drug screening, studying the stages of retinal development, and providing a human model for personalized therapeutic approaches, like cell transplants to replace degenerated retinal cells. Here, we first discuss the importance of human retinal organoids to the biomedical sciences. Then, we review various functional features of retinal organoids that have been developed. Finally, we highlight the current limitations of retinal organoid technologies.

Cofeeding tolerance in chimpanzees depends on group composition: a longitudinal study across four communities

Social tolerance is generally treated as a stable, species-specific characteristic. Recent research, however, has questioned this position and emphasized the importance of intraspecific variation. We investigate the temporal stability of social tolerance in four groups of sanctuary-housed chimpanzees over eight years using a commonly employed measure: experimental cofeeding tolerance. We then draw on longitudinal data on the demographic composition of each group to identify the factors associated with cofeeding tolerance. We find appreciable levels of variation in cofeeding tolerance across both groups and years that correspond closely to changes in group-level demographic composition. For example, cofeeding tolerance is lower when there are many females with young infants. These results suggest that social tolerance may be a "responding trait" of chimpanzee sociality, reflecting individual-level behavioral responses to social changes. Additional, experimental research is needed to better model the causal drivers of social tolerance within and among species.

The multinomial index: a robust measure of reproductive skew

Inequality or skew in reproductive success (RS) is common across many animal species and is of long-standing interest to the study of social evolution. However, the measurement of inequality in RS in natural populations has been challenging because existing quantitative measures are highly sensitive to variation in group/sample size, mean RS, and age-structure. This makes comparisons across multiple groups and/or species vulnerable to statistical artefacts and hinders empirical and theoretical progress. Here, we present a new measure of reproductive skew, the multinomial index, M, that is unaffected by many of the structural biases affecting existing indices. M is analytically related to Nonacs’ binomial index, B, and comparably accounts for heterogeneity in age across individuals; in addition, M allows for the possibility of diminishing or even highly nonlinear RS returns to age. Unlike B, however, M is not biased by differences in sample/group size. To demonstrate the value of our index for cross-population comparisons, we conduct a reanalysis of male reproductive skew in 31 primate species. We show that a previously reported negative effect of group size on mating skew was an artefact of structural biases in existing skew measures, which inevitably decline with group size; this bias disappears when using M. Applying phylogenetically controlled, mixed-effects models to the same dataset, we identify key similarities and differences in the inferred within- and between-species predictors of reproductive skew across metrics. Finally, we provide an R package, SkewCalc, to estimate M from empirical data.

Racial Disparities in Police Use of Deadly Force Against Unarmed Individuals Persist After Appropriately Benchmarking Shooting Data on Violent Crime Rates

Cesario et al. argue that benchmarking the relative counts of killings by police on relative crime rates, rather than relative population sizes, generates a measure of racial disparity in the use of lethal force that is unbiased by differential crime rates. Their publication, however, lacked any formal derivation showing that their benchmarking methodology has the statistical properties required to establish such a claim. We use the causal model of lethal force by police conditional on relative crime rates implicit in their analyses and prove that their benchmarking methodology does not, in general, remove the bias introduced by crime rate differences. Instead, it creates strong statistical biases that mask true racial disparities, especially in the killing of unarmed noncriminals by police. Reanalysis of their data using formally derived criminality-correcting benchmarks shows that there is strong and statistically reliable evidence of anti-Black racial disparities in the killing of unarmed Americans by police in 2015–2016.

Preferences and constraints: the value of economic games for studying human behaviour

As economic games have spread from experimental economics to other social sciences, so too have critiques of their usefulness for drawing inferences about the 'real world'. What these criticisms often miss is that games can be used to reveal individuals' private preferences in ways that observational and interview data cannot; furthermore, economic games can be designed such that they do provide insights into real-world behaviour. Here, we draw on our collective experience using economic games in field contexts to illustrate how researchers can strategically alter the framing or design of economic games to draw inferences about private-world or real-world preferences. A detailed case study from coastal Colombia provides an example of the subtleties of game design and how games can be combined fruitfully with self-report data. We close with a list of concrete recommendations for how to modify economic games to better match particular research questions and research contexts.

Unpacking mating success and testing Bateman's principles in a human population

Human marriage systems, characterized by long-term partnerships and extended windows of parental care, differ from the mating systems of pulsed or seasonally breeding non-human animals in which Bateman’s principles were originally tested. These features, paradigmatic of but not unique to humans, complicate the accurate measurement of mating success in evaluating Bateman’s three principles. Here, we unpack the concept of mating success into distinct components: number of partners, number of years partnered, the timing of partnerships, and the quality of partners. Drawing on longitudinal records of marriage and reproduction collected in a natural-fertility East African population over a 20-year period, we test and compare various models of the relationship between mating success and reproductive success (RS), and show that an accurate assessment of male and female reproductive behaviour requires consideration of all major components of mating success. Furthermore, we demonstrate that while Bateman’s third principle holds when mating success is defined in terms of years married, women’s fitness increases whereas men’s fitness decreases from an increase in the number of marriage partners, holding constant the total effective duration of marriages. We discuss these findings in terms of the distinct, sex-specific pathways through which RS can be optimized, and comment on the contribution of this approach to the broader study of sexual selection.

Kinship ties across the lifespan in human communities

A hypothesis for the evolution of long post-reproductive lifespans in the human lineage involves asymmetries in relatedness between young immigrant females and the older females in their new groups. In these circumstances, inter-generational reproductive conflicts between younger and older females are predicted to resolve in favour of the younger females, who realize fewer inclusive fitness benefits from ceding reproduction to others. This conceptual model anticipates that immigrants to a community initially have few kin ties to others in the group, gradually showing greater relatedness to group members as they have descendants who remain with them in the group. We examine this prediction in a cross-cultural sample of communities, which vary in their sex-biased dispersal patterns and other aspects of social organization. Drawing on genealogical and demographic data, the analysis provides general but not comprehensive support for the prediction that average relatedness of immigrants to other group members increases as they age. In rare cases, natal members of the community also exhibit age-related increases in relatedness. We also find large variation in the proportion of female group members who are immigrants, beyond simple traditional considerations of patrilocality or matrilocality, which raises questions about the circumstances under which this hypothesis of female competition are met. We consider possible explanations for these heterogenous results, and we address methodological considerations that merit increased attention for research on kinship and reproductive conflict in human societies. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.

Evidence for encounter-conditional, area-restricted search in a preliminary study of Colombian blowgun hunters

Active search for prey is energetically costly, so understanding how foragers optimize search has been central to foraging theory. Some theoretical work has suggested that foragers of randomly distributed prey should search using Lévy flights, while work on area-restricted and intermittent search strategies has demonstrated that foragers can use the information provided by prey encounters to more effectively adapt search direction and velocity. Previous empirical comparisons of these search modes have tended to rely on distribution-level analyses, due to the difficulty of collecting event-level data on encounters linked to the GPS tracks of foragers. Here we use a preliminary event-level data-set (18.7 hours of encounter-annotated focal follows over 6 trips) to show that two Colombian blowgun hunters use adaptive encounter-conditional heuristics, not non-conditional Lévy flights, when searching for prey. Using a theoretically derived Bayesian model, we estimate changes in turning-angle and search velocity as a function of encounters with prey at lagged time-steps, and find that: 1) hunters increase average turning-angle in response to encounters, producing a more tortuous search of patches of higher prey density, but adopt more efficient uni-directional, inter-patch movement after failing to encounter prey over a sufficient period of time; and, 2) hunters reduce search velocity in response to encounters, causing them to spend more of their search time in patches with demonstrably higher prey density. These results illustrate the importance of using event-level data to contrast encounter-conditional, area-restricted search and Lévy flights in explaining the search behavior of humans and other organisms.

Greater wealth inequality, less polygyny: rethinking the polygyny threshold model

Monogamy appears to have become the predominant human mating system with the emergence of highly unequal agricultural populations that replaced relatively egalitarian horticultural populations, challenging the conventional idea-based on the polygyny threshold model-that polygyny should be positively associated with wealth inequality. To address this polygyny paradox, we generalize the standard polygyny threshold model to a mutual mate choice model predicting the fraction of women married polygynously. We then demonstrate two conditions that are jointly sufficient to make monogamy the predominant marriage form, even in highly unequal societies. We assess if these conditions are satisfied using individual-level data from 29 human populations. Our analysis shows that with the shift to stratified agricultural economies: (i) the population frequency of relatively poor individuals increased, increasing wealth inequality, but decreasing the frequency of individuals with sufficient wealth to secure polygynous marriage, and (ii) diminishing marginal fitness returns to additional wives prevent extremely wealthy men from obtaining as many wives as their relative wealth would otherwise predict. These conditions jointly lead to a high population-level frequency of monogamy.

The Origins and Maintenance of Female Genital Modification across Africa : Bayesian Phylogenetic Modeling of Cultural Evolution under the Influence of Selection

We present formal evolutionary models for the origins and persistence of the practice of Female Genital Modification (FGMo). We then test the implications of these models using normative cross-cultural data on FGMo in Africa and Bayesian phylogenetic methods that explicitly model adaptive evolution. Empirical evidence provides some support for the findings of our evolutionary models that the de novo origins of the FGMo practice should be associated with social stratification, and that social stratification should place selective pressures on the adoption of FGMo; these results, however, are tempered by the finding that FGMo has arisen in many cultures that have no social stratification, and that forces operating orthogonally to stratification appear to play a more important role in the cross-cultural distribution of FGMo. To explain these cases, one must consider cultural evolutionary explanations in conjunction with behavioral ecological ones. We conclude with a discussion of the implications of our study for policies designed to end the practice of FGMo.

Frequency-Dependent Social Transmission and the Interethnic Transfer of Female Genital Modification in the African Diaspora and Indigenous Populations of Colombia

We present a quantitative account based on ethnographic and documentary research of the prevalence of female genital modification (FGMo) in the African diaspora and indigenous populations of Colombia. We use these data to test hypotheses concerning the cultural evolutionary drivers of costly trait persistence, attenuation, and intergroup transmission. The uptake of FGMo by indigenous populations in Colombia is consistent with frequency-dependent hypotheses for the social transmission of the FGMo trait from the African diaspora population in the period following the era of slavery in Colombia. The prevalence and severity of practices related to FGMo decline with level of sociocultural integration into mainstream Colombian culture. Our results provide empirical support for the cultural evolutionary models proposed by Ross et al. (2015) to describe the transmission dynamics of FGMo and other costly traits. Analysis of costly trait dynamics contributes knowledge useful to applied anthropology and may be of interest in policy design and human rights monitoring in Colombia and elsewhere.

A Multi-Level Bayesian Analysis of Racial Bias in Police Shootings at the County-Level in the United States, 2011-2014

A geographically-resolved, multi-level Bayesian model is used to analyze the data presented in the U.S. Police-Shooting Database (USPSD) in order to investigate the extent of racial bias in the shooting of American civilians by police officers in recent years. In contrast to previous work that relied on the FBI’s Supplemental Homicide Reports that were constructed from self-reported cases of police-involved homicide, this data set is less likely to be biased by police reporting practices. County-specific relative risk outcomes of being shot by police are estimated as a function of the interaction of: 1) whether suspects/civilians were armed or unarmed, and 2) the race/ethnicity of the suspects/civilians. The results provide evidence of a significant bias in the killing of unarmed black Americans relative to unarmed white Americans, in that the probability of being {black, unarmed, and shot by police} is about 3.49 times the probability of being {white, unarmed, and shot by police} on average. Furthermore, the results of multi-level modeling show that there exists significant heterogeneity across counties in the extent of racial bias in police shootings, with some counties showing relative risk ratios of 20 to 1 or more. Finally, analysis of police shooting data as a function of county-level predictors suggests that racial bias in police shootings is most likely to emerge in police departments in larger metropolitan counties with low median incomes and a sizable portion of black residents, especially when there is high financial inequality in that county. There is no relationship between county-level racial bias in police shootings and crime rates (even race-specific crime rates), meaning that the racial bias observed in police shootings in this data set is not explainable as a response to local-level crime rates.

Evolutionary distance of amino acid sequence orthologs across macaque subspecies: identifying candidate genes for SIV resistance in Chinese rhesus macaques

We use the Reciprocal Smallest Distance (RSD) algorithm to identify amino acid sequence orthologs in the Chinese and Indian rhesus macaque draft sequences and estimate the evolutionary distance between such orthologs. We then use GOanna to map gene function annotations and human gene identifiers to the rhesus macaque amino acid sequences. We conclude methodologically by cross-tabulating a list of amino acid orthologs with large divergence scores with a list of genes known to be involved in SIV or HIV pathogenesis. We find that many of the amino acid sequences with large evolutionary divergence scores, as calculated by the RSD algorithm, have been shown to be related to HIV pathogenesis in previous laboratory studies. Four of the strongest candidate genes for SIVmac resistance in Chinese rhesus macaques identified in this study are CDK9, CXCL12, TRIM21, and TRIM32. Additionally, ANKRD30A, CTSZ, GORASP2, GTF2H1, IL13RA1, MUC16, NMDAR1, Notch1, NT5M, PDCD5, RAD50, and TM9SF2 were identified as possible candidates, among others. We failed to find many laboratory experiments contrasting the effects of Indian and Chinese orthologs at these sites on SIVmac pathogenesis, but future comparative studies might hold fertile ground for research into the biological mechanisms underlying innate resistance to SIVmac in Chinese rhesus macaques.

A large-scale SNP-based genomic admixture analysis of the captive rhesus macaque colony at the California National Primate Research Center

Some breeding facilities in the United States have crossbred Chinese and Indian rhesus macaque (Macaca mulatta) founders either purposefully or inadvertently. Genetic variation that reflects geographic origins among research subjects has the potential to influence experimental outcomes. The use of animals from different geographic regions, their hybrids, and animals of varying degrees of kinship in an experiment can obscure treatment effects under study because high interanimal genetic variance can increase phenotypic variance among the research subjects. The intent of this study, based on a broad genomic analysis of 2,808 single nucleotide polymorphisms (SNPs), is to ensure that only animals estimated to be of pure Indian or Chinese ancestry, based on both demographic and genetic information, are used as sources of infants for derivation and expansion of the California National Primate Research Center's (CNPRC) super-Specific Pathogen Free (SSPF) rhesus macaque colony. Studies of short tandem repeats (STRs) in Indian and Chinese rhesus macaques have reported that heterozygosity of STRs is higher in Chinese rhesus macaques than in Indian rhesus macaques. The present study shows that heterozygosity of SNPs is actually higher in Indian than in Chinese rhesus macaques and that the Chinese SSPF rhesus macaque colony is far less differentiated from their founders compared to the Indian-origin animals. The results also reveal no evidence of recent gene flow from long-tailed and pig-tailed macaques into the source populations of the SSPF rhesus macaques. This study indicates that many of the long-tailed macaques held in the CNPRC are closely related individuals. Most polymorphisms shared among the captive rhesus, long-tailed, and pig-tailed macaques likely predate the divergence among these groups.

An empirical comparison of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) for relatedness estimation in Chinese rhesus macaques (Macaca mulatta)

We compare the effectiveness of short tandem repeat (STR) and single nucleotide polymorphism (SNP) genotypes for estimating pairwise relatedness, using molecular data and pedigree records from a captive Chinese rhesus macaque population at the California National Primate Research Center. We find that a panel of 81 SNPs is as effective at estimating first-order kin relationships as a panel of 14 highly polymorphic STRs. We note, however, that the selected STRs provide more precise predictions of relatedness than the selected SNPs, and may be preferred in contexts that require the discrimination of kin related more distantly than first-order relatives. Additionally, we compare the performance of three commonly used relatedness estimation algorithms, and find that the Wang [2002] algorithm outperforms other algorithms when analyzing STR data, while the Queller & Goodnight [1989] algorithm outperforms other algorithms when analyzing SNP data. Future research is needed to address the number of SNPs required to reach the discriminatory power of a standard STR panel in relatedness estimation for primate colony management.

Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes

We genotyped a Chinese and an Indian-origin rhesus macaque using the Affymetrix Genome-Wide Human SNP Array 6.0 and cataloged 85,473 uniquely mapping heterospecific SNPs. These SNPs were assigned to rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus reference sequences. The conserved gene order (synteny) revealed by heterospecific SNP maps is in concordance with that of the published human and rhesus macaque genomes. Using these SNPs' original human rs numbers, we identified 12,328 genes annotated in humans that are associated with these SNPs, 3674 of which were found in at least one of the two rhesus macaques studied. Due to their density, the heterospecific SNPs allow fine-grained comparisons, including approximate boundaries of intra- and extra-chromosomal rearrangements involving gene orthologs, which can be used to distinguish rhesus macaque chromosomes from human chromosomes.