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Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa. [ABSTRACT FROM AUTHOR]

Animal reproductive phenology varies from strongly seasonal to nonseasonal, sometimes among closely related or sympatric species. While the extent of reproductive seasonality is often attributed to environmental seasonality, this fails to explain many cases of nonseasonal breeding in seasonal environments. We investigated the evolutionary determinants of nonseasonal breeding in a wild primate, the chacma baboon (Papio ursinus), living in a seasonal environment with high climatic unpredictability. We tested three hypotheses proposing that nonseasonal breeding has evolved in response to (1) climatic unpredictability, (2) reproductive competition between females favoring birth asynchrony, and (3) individual, rank-dependent variations in optimal reproductive timing. We found strong support for an effect of reproductive asynchrony modulated by rank: (i) birth synchrony is costly to subordinate females, lengthening their interbirth intervals; (ii) females alter their reproductive timings (fertility periods and conceptions) in relation to previous conceptions in the group; and (iii) the reported effect of birth synchrony on interbirth intervals weakens the intensity of reproductive seasonality at the population level. This study emphasizes the importance of sociality in mediating the evolution of reproductive phenology in group-living organisms, a result of broad significance for understanding key demographic parameters driving population responses to increasing climatic fluctuations. [ABSTRACT FROM AUTHOR]

Mechanistic models suggest that individuals' memories could shape home range patterns and dynamics, and how neighbors share space. In social species, such dynamics of home range overlap may be affected by the pre-dispersal memories of immigrants. We tested this "immigrant knowledge hypothesis" in a wild population of chacma baboons (Papio ursinus). We predicted that overlap dynamics with a given neighboring troop's home range should reflect males' adaptive interests in overlap when the alpha male had immigrated from this neighboring troop but less so when the alpha male originated from elsewhere. We used data collected between 2005 and 2013 on two neighboring troops in Namibia, comprising GPS records of daily ranges, male natal origins, daily females' reproductive status, and a satellite index of vegetation growth. We found support for our prediction in line with male reproductive strategies but not in line with foraging conditions. In periods with a higher relative number of fertile females over adult males in the focal troop, male baboons would benefit from reducing overlap with their neighbors to mitigate the costs of between-troop mating competition. This was indeed observed but only when the alpha male of the focal troop was an immigrant from that neighboring troop, and not with alpha males of other origins, presumably due to their different knowledge of the neighboring troop. Our findings highlight the role of reproductive competition in the range dynamics of social groups, and suggest that spatial segregation between groups could increase through the combination of dispersal and memory. [ABSTRACT FROM AUTHOR]

The evolutionary benefits of reproductive seasonality are often measured by a single-fitness component, namely offspring survival. Yet different fitness components may be maximized by different birth timings. This may generate fitness trade-offs that could be critical to understanding variation in reproductive timing across individuals, populations and species. Here, we use long-term demographic and behavioural data from wild chacma baboons (Papio ursinus) living in a seasonal environment to test the adaptive significance of seasonal variation in birth frequencies. We identify two distinct optimal birth timings in the annual cycle, located four-month apart, which maximize offspring survival or minimize maternal interbirth intervals (IBIs), by respectively matching the annual food peak with late or early weaning. Observed births are the most frequent between these optima, supporting an adaptive trade-off between current and future reproduction. Furthermore, infants born closer to the optimal timing favouring maternal IBIs (instead of offspring survival) throw more tantrums, a typical manifestation of mother–offspring conflict. Maternal trade-offs over birth timing, which extend into mother–offspring conflict after birth, may commonly occur in long-lived species where development from birth to independence spans multiple seasons. Our findings therefore open new avenues to understanding the evolution of breeding phenology in long-lived animals, including humans. [ABSTRACT FROM AUTHOR]

The evolution of paternal care is rare in promiscuous mammals, where it is hampered by low paternity confidence. However, recent evidence indicates that juveniles whose fathers are present experience accelerated maturation in promiscuous baboon societies. The mechanisms mediating these paternal effects remain unclear. Here, we investigated whether father–offspring associations might facilitate offspring access to resources in wild desert baboons (Papio ursinus). We combined paternity analyses and behavioral observations of juveniles that had started feeding autonomously to show that (1) offspring associate more often with their genetic father than with any other male, and actively manage such associations, (2) offspring associate more closely with their father when another adult male is in sight, and when their mother is out of sight, (3) father–offspring associations are more frequent when juveniles are feeding (relative to other activities), and these associations enable juveniles to access richer food patches, and (4) father–offspring associations are stronger among subordinate males and their offspring. Taken together, these findings indicate that fathers may buffer the social and ecological environment faced by their offspring. In addition to mitigating risks of attacks by predators or conspecifics, paternal presence improves offspring access to food in wild baboons, highlighting a new mechanism through which fathers may impact offspring fitness in promiscuous primate societies. [ABSTRACT FROM PUBLISHER]

Host parasite diversity plays a fundamental role in ecological and evolutionary processes, yet the factors that drive it are still poorly understood. A variety of processes, operating across a range of spatial scales, are likely to influence both the probability of parasite encounter and subsequent infection. Here, we explored eight possible determinants of parasite richness, comprising rainfall and temperature at the population level, ranging behavior and home range productivity at the group level, and age, sex, body condition, and social rank at the individual level. We used a unique dataset describing gastrointestinal parasites in a terrestrial subtropical vertebrate (chacma baboons, Papio ursinus), comprising 662 fecal samples from 86 individuals representing all age-sex classes across two groups over two dry seasons in a desert population. Three mixed models were used to identify the most important factor at each of the three spatial scales (population, group, individual); these were then standardized and combined in a single, global, mixed model. Individual age had thestrongest influence on parasite richness, in a convex relationship. Parasite richness was also higher in females and animals in poor condition, albeit at a lower order of magnitude than age. Finally, with a further halving of effect size, parasite richness was positively correlated to day range and temperature. These findings indicate that a range of factors influence host parasite richness through both encounter and infection probabilities but that individual-level processes may be more important than those at the group or population level. Am J Phys Anthropol, 2012. © 2011 Wiley-Liss,Inc. [ABSTRACT FROM AUTHOR]

Multimale–multifemale groups, where both sexes mate promiscuously and the operational sex ratio is male biased, represent a classical mammalian society. Theory predicts low mating competition between females in such societies, but this is inconsistent with the frequent occurrence of female sexual signals. This study explores the determinants of female competition under such conditions by testing 3 hypotheses relating to patterns of aggression over the reproductive cycle in wild chacma baboons (Papio ursinus). Primarily, we expect the frequency of aggression to be highest among 1) lactating and pregnant females, who experience the greatest energetic demands, if females compete mainly over food, 2) lactating females, if females compete mainly over paternal care of infants, or 3) sexually active (swollen) females, if females compete mainly over mates. Data were collected from 27 females in 2 groups over 18 months and analyzed using mixed models. Our results provide most support for the mating competition hypothesis: aggression increases with the number of swollen females in a group, swollen females receive the most aggression, and mate-guarded swollen females receive more aggression than when unguarded. However, our analyses further indicate that such aggression rather than arising from direct mating competition, most likely reflects reproductive suppression and/or an increased exposure of swollen females to incidental aggression. These findings reveal the importance of sex in shaping social relationships among females in large primate groups where they were traditionally considered to be determined primarily by access to resources. Aggression associated with access to mates represents an extra cost of sociality to females. [ABSTRACT FROM PUBLISHER]

Many long-lived plant and animal species have nondiscrete overlapping generations. Although numerous models have been developed to predict the effective sizes ( Ne) of populations with overlapping generations, they are extremely difficult to apply to natural populations because of the large array of unknown and elusive life-table parameters involved. Unfortunately, little work has been done to estimate the Ne of populations with overlapping generations from marker data, in sharp contrast to the situation of populations with discrete generations for which quite a few estimators are available. In this study, we propose an estimator (EPA, estimator by parentage assignments) of the current Ne of populations with overlapping generations, using the sex, age, and multilocus genotype information of a single sample of individuals taken at random from the population. Simulations show that EPA provides unbiased and accurate estimates of Ne under realistic sampling and genotyping effort. Additionally, it yields estimates of other interesting parameters such as generation interval, the variances and covariances of lifetime family size, effective number of breeders of each age class, and life-table variables. Data from wild populations of baboons and hihi (stitchbird) were analyzed by EPA to demonstrate the use of the estimator in practical sampling and genotyping situations. [ABSTRACT FROM AUTHOR]

The assessment of relatedness may be crucial in the evolution of socio-sexual behaviour, because it can be associated with fitness benefits mediated by both nepotism and inbreeding avoidance. In this context, one proposed mechanism for kin recognition is 'phenotype matching'; animals might compare phenotypic similarities between themselves and others in order to assess the probability that they are related. Among cues potentially used for kin discrimination, body odours constitute interesting candidates that have been poorly investigated in anthropoid primates so far, because of a mixture of theoretical considerations and methodological/experimental constraints. In this study, we used an indirect approach to examine the similarity in odour signals emitted by related individuals from a natural population of chacma baboons (Paplo ursinus). For that purpose, we designed an innovative behavioural tool using mice olfactory abilities in a habituation-discrimination paradigm. We show that: (i) mice can detect odour differences between individuals of same sex and age class in another mammal species, and (ii) mice perceive a higher odour similarity between related baboons than between unrelated baboons. These results suggest that odours may play a role in both the signalling of individual characteristics and of relatedness among individuals in an anthropoid primate. The 'biological olfactometer' developed in this study offers new perspectives to the exploration of olfactory signals from a range of species. [ABSTRACT FROM AUTHOR]

General patterns of organization in the major histocompatibility complex (MHC) have been successfully explained by the model of birth-and-death evolution, but understanding why certain MHC genes are maintained together into specific haplotypes remains challenging. The haplotype configurations of the functionally important class II DR region have been described in few primates and display important interspecific variability with respect to the extent of allelic variation, the number of loci and/or combinations of loci present. Understanding the evolutionary mechanisms driving such variation is conditional upon characterizing haplotypes in new species and identifying the selective pressures acting on haplotypes. This study explores the variability of haplotype configurations in the Mhc-DRB region (exon 2) for the first time in wild non-human primates, chacma baboons ( Papio ursinus). Paur-DRB haplotypes were characterized through segregation studies and linkage disequilibrium. 23 Paur-DRB sequences and 15 haplotype configurations were identified in 199 animals. The Paur-DRB exon 2 is shown to be subjected to intense positive selection and frequent recombination. An approach recently developed for human vaccine studies was used to classify Paur-DRB sequences into supertypes, based on the physico-chemical properties of amino acids that are positively selected, thus most probably involved in antigen recognition. Sequences grouped into the same supertype (thus presumably sharing antigen-binding affinities) are non-randomly distributed within haplotypes, leading to an increased individual diversity of supertypes. Our results suggest that selection favoring haplotypes with complementary sets of DRB supertypes shapes functionally tuned haplotypes in this natural baboon population. [ABSTRACT FROM AUTHOR]

Summary Sexual violence occurring in the context of long-term heterosexual relationships, such as sexual intimidation, is widespread across human populations [ 1–3 ]. However, its evolutionary origins remain speculative because few studies have investigated the existence of comparable forms of sexual coercion in animals [ 4, 5 ], in which repeated male aggression toward a female provides the aggressor with delayed mating benefits [ 6 ]. Here, we test whether male aggression toward females functions as sexual coercion in wild chacma baboons ( Papio ursinus ). We found support for all three main predictions of the sexual coercion hypothesis [ 7 ]: male aggression (1) is greatest against cycling females, (2) is costly and represents the main source of injuries for cycling females, and (3) increases male mating success with their victims in the future. Detailed analysis of chronological sequences between aggression and matings ruled out other coercive mechanisms, such as short-term harassment and punishment, by showing that aggression and matings are temporally decoupled. This decoupling may explain why some forms of sexual violence have been largely overlooked in well-studied animal populations despite their likely impact on the fitness of both sexes. Finally, we found no support for alternative hypotheses such as a female preference for aggressive males [ 8, 9 ]. This new, detailed study of the forms and intensity of sexual intimidation in a wild primate suggests that it may be widespread across mammalian societies, with important implications for understanding the evolution of mate choice and sexual conflict in mammals, as well as the origins of human sexual violence. [ABSTRACT FROM AUTHOR]

Recent research reveals that female reproductive competition is common and may shape the social and reproductive strategies of female mammals. This study explores the determinants and intensity of female intrasexual conflicts in a wild promiscuous primate, the chacma baboon, Papio ursinus . We tested a suite of hypotheses to assess whether female–female aggression was primarily driven by instantaneous competition for food, mates or paternal care, or aimed at reducing future competition among offspring via reproductive suppression. Behavioural data were gathered from 53 females in two groups over two contrasting 2-year periods (2005–2006, 2013–2014): the first characterized by stability in the male dominance hierarchies, the second by instability induced by several immigration events and male take-overs. In both periods, we found that sexually receptive females received high levels of aggression from other sexually receptive females, consistent with competition over mating opportunities. In the unstable period, females exchanged higher rates of aggression than in the stable period, regardless of reproductive state, but lactating females received most aggression, consistent with higher competition over social access to male partners in response to increased infanticide risk. There was no evidence that aggression between females reflected either competition over food or reproductive suppression. These findings indicate that patterns of aggression between females fluctuate with sociodemographic factors affecting sexual and social access to males and reflect reproductive competition more closely than resource competition in this promiscuous primate society. [ABSTRACT FROM AUTHOR]

In monotocous mammals (i.e. where females produce one offspring at a time), most juveniles will experience the birth of a younger sibling in their life. Transition to siblinghood (TTS) has rarely been studied in primates, although it reflects the last step in the shift of maternal investment from one offspring to the next and could thus represent a critical moment for mother–offspring conflict and sibling competition. Here, we used behavioural data on juvenile primates that had recently experienced, or not, the birth of a younger sibling to investigate changes in mother–juvenile relationships during TTS in a wild population of chacma baboons, Papio ursinus. We show that (1) mother–juvenile spatial associations remained stable; (2) mothers did not decrease their probability of initiating proximity or affiliation with their juvenile; and (3) juveniles initiated proximity and affiliation more frequently towards their mothers, and showed more signs of anxiety, after the birth of their younger sibling. Taken together, these findings suggest that juveniles with a younger sibling solicit their mother more often and seek more maternal attention than juveniles without. Overall, mother–offspring conflict could extend into the postweaning period, during which more subtle maternal resources, such as maternal attention, could be at stake in competitive sibling relationships. • We examine the transition to siblinghood in wild chacma baboons. • Maternal behaviour does not change following the birth of a younger sibling. • But juveniles solicit their mother more often, and show more signs of anxiety. • These results suggest that weaned siblings may compete for maternal attention. [ABSTRACT FROM AUTHOR]

Maternal strategies reflect the trade-off between offspring needs and maternal ability to invest, a concept described by the evolutionary theory of parent–offspring conflict. In mammals this conflict has often been investigated by studying weaning, the transition from maternal milk consumption to dietary independence. An investigation of individual variation in weaning can provide information on the adaptive significance of maternal strategies in relation to social and biological variables. We analysed stable nitrogen isotopes of hair samples collected from 22 mother–infant dyads in a wild population of chacma baboons, Papio ursinus , in conjunction with behavioural data on suckling, to explore the temporal dynamics of weaning, as well as the extent and determinants of individual variation in these dynamics. The weaning pattern suggested by isotope values and behavioural data were congruent. The difference between infant and mother stable nitrogen isotope values decreased faster with age in infants of low-ranking mothers, which suggests a faster progression towards weaning, perhaps due to subordinate females experiencing lower resource availability and so being less able to bear the costs of lactation over prolonged periods. Additionally, within-infant variation in stable nitrogen isotope values showed an increase with age (which was not detectable between infants), potentially highlighting the nutritional costs that weaning imposes on offspring. Our combination of isotope analysis and behavioural data from a wild population provides insight into the evolution of maternal strategies. In particular, it suggests that the quantity of care a mother can provide is affected by her rank, with subordinate females possibly not able to lactate for as long and perhaps benefiting from weaning earlier. • Time to weaning may depend on maternal and offspring characteristics • Stable isotope signatures can characterize the weaning process • In baboons, offspring of low-ranked mothers moved towards weaning more quickly • Stable isotope analysis may show signs of nutritional stress in weaning infants • Social environment can influence the weaning process and maternal strategies [ABSTRACT FROM AUTHOR]

Reconciliation, or postconflict (PC) affiliation between former opponents, is a widespread conflict management strategy in animal societies, so-named for its relationship repair function. However, another possibility is that PC affiliation reflects a submissive response of victims towards aggressors to limit conflict escalation when the power imbalance between the opponents is large. Here we investigated this hypothesis in a highly asymmetric relationship context: heterosexual wild chacma baboon, Papio ursinus , dyads involving sexually receptive females, where sexual coercion by males is common. We found several lines of support for the submissive hypothesis in the context of sexual coercion. First, rates of sexual and nonsexual PC affiliative interactions in these dyads exhibited significant and comparable increases compared to baseline conditions (ca. three-fold). Second, the baseline strength of the heterosexual social bond (outside of an aggressive context) did not predict the likelihood of sexual and nonsexual PC affiliation. Third, mate-guarded females, who could not escape the proximity of their aggressor (and faced high risks of renewed aggression), exhibited the most PC affiliation with males. Finally, most PC affiliation sequences contained at least one sexual act, and the first sexual affiliative act was primarily initiated by females via presenting. This suggests that female victims affiliate in a submissive way by displaying sexual compliance to aggressive males. Nevertheless, we cannot exclude the co-occurrence of 'true' reconciliation: a quarter of PC affiliations between males and receptive females were exclusively nonsexual, and the first general affiliative act was equally initiated by males and females. Overall, our results suggest a mixed PC affiliation strategy in which submission may play an important role in highly asymmetric relationships and indicate that the function of PC affiliation may vary from submission to reconciliation depending on the species, dyads, individuals and conflicts under consideration. Future research on PC interactions would usefully consider this full spectrum. • Males and fertile females show increased affiliation after aggression. • The strength of the dyadic social bond does not predict postconflict affiliation. • Postconflict affiliations are most frequent in dyads involving coerced females. • A majority of postconflict affiliations are sexual, and mostly initiated by females. • Postconflict affiliation can be submissive in asymmetric relationships. [ABSTRACT FROM AUTHOR]