Developing evolutionary anthropology in local ecosystems.

The traditional regional focus of evolutionary anthropology-typically defined as places where hominin fossils, nonhuman primates, and non-western populations reside-forms the basis of much evolutionary anthropological research. Using the highly biodiverse temperate region of Appalachia as an example, we suggest that evolutionary anthropologists have much to gain by stepping outside of this traditional geographic area. Being purposely provocative, we argue that evolutionary anthropologists might also benefit from conducting research in Appalachia and other temperate ecosystems. We briefly discuss multiple areas of study-including studies of seed dispersal, functional redundancy, convergent evolution, human behavioral ecology, and conservation-and how they can be considered within the purview of integrative and evolutionary anthropology. We also highlight broader impacts to higher education that evolutionary anthropologists can help promote by working in local ecosystems.

Getting it right: Teaching undergraduate biology to undermine racial essentialism.

How we teach human genetics matters for social equity. The biology curriculum appears to be a crucial locus of intervention for either reinforcing or undermining students' racial essentialist views. The Mendelian genetic models dominating textbooks, particularly in combination with racially inflected language sometimes used when teaching about monogenic disorders, can increase middle and high school students' racial essentialism and opposition to policies to increase equity. These findings are of particular concern given the increasing spread of racist misinformation online and the misappropriation of human genomics research by white supremacists, who take advantage of low levels of genetics literacy in the general public. Encouragingly, however, teaching updated information about the geographical distribution of human genetic variation and the complex, multifactorial basis of most human traits, reduces students' endorsement of racial essentialism. The genetics curriculum is therefore a key tool in combating misinformation and scientific racism. Here, we describe a framework and example teaching materials for teaching students key concepts in genetics, human evolutionary history, and human phenotypic variation at the undergraduate level. This framework can be flexibly applied in biology and anthropology classes and adjusted based on time availability. Our goal is to provide undergraduate-level instructors with varying levels of expertise with a set of evidence-informed tools for teaching human genetics to combat scientific racism, including an evolving set of instructional resources, as well as learning goals and pedagogical approaches. Resources can be found at https://noto.li/YIlhZ5. Additionally, we hope to generate conversation about integrating modern genetics into the undergraduate curriculum, in light of recent findings about the risks and opportunities associated with teaching genetics.

The long lives of primates and the 'invariant rate of ageing' hypothesis.

Is it possible to slow the rate of ageing, or do biological constraints limit its plasticity? We test the 'invariant rate of ageing' hypothesis, which posits that the rate of ageing is relatively fixed within species, with a collection of 39 human and nonhuman primate datasets across seven genera. We first recapitulate, in nonhuman primates, the highly regular relationship between life expectancy and lifespan equality seen in humans. We next demonstrate that variation in the rate of ageing within genera is orders of magnitude smaller than variation in pre-adult and age-independent mortality. Finally, we demonstrate that changes in the rate of ageing, but not other mortality parameters, produce striking, species-atypical changes in mortality patterns. Our results support the invariant rate of ageing hypothesis, implying biological constraints on how much the human rate of ageing can be slowed.

Comparative genomic analysis of sifakas (Propithecus) reveals selection for folivory and high heterozygosity despite endangered status.

Sifakas (genus Propithecus) are critically endangered, large-bodied diurnal lemurs that eat leaf-based diets and show corresponding anatomical and microbial adaptations to folivory. We report on the genome assembly of Coquerel's sifaka (P. coquereli) and the resequenced genomes of Verreaux's (P. verreauxi), the golden-crowned (P. tattersalli), and the diademed (P. diadema) sifakas. We find high heterozygosity in all sifakas compared with other primates and endangered mammals. Demographic reconstructions nevertheless suggest declines in effective population size beginning before human arrival on Madagascar. Comparative genomic analyses indicate pervasive accelerated evolution in the ancestral sifaka lineage affecting genes in several complementary pathways relevant to folivory, including nutrient absorption and xenobiotic and fatty acid metabolism. Sifakas show convergent evolution at the level of the pathway, gene family, gene, and amino acid substitution with other folivores. Although sifakas have relatively generalized diets, the physiological challenges of habitual folivory likely led to strong selection.

Maternal death and offspring fitness in multiple wild primates.

Primate offspring often depend on their mothers well beyond the age of weaning, and offspring that experience maternal death in early life can suffer substantial reductions in fitness across the life span. Here, we leverage data from eight wild primate populations (seven species) to examine two underappreciated pathways linking early maternal death and offspring fitness that are distinct from direct effects of orphaning on offspring survival. First, we show that, for five of the seven species, offspring face reduced survival during the years immediately preceding maternal death, while the mother is still alive. Second, we identify an intergenerational effect of early maternal loss in three species (muriquis, baboons, and blue monkeys), such that early maternal death experienced in one generation leads to reduced offspring survival in the next. Our results have important implications for the evolution of slow life histories in primates, as they suggest that maternal condition and survival are more important for offspring fitness than previously realized.

Age-associated epigenetic change in chimpanzees and humans.

Methylation levels have been shown to change with age at sites across the human genome. Change at some of these sites is so consistent across individuals that it can be used as an 'epigenetic clock' to predict an individual's chronological age to within a few years. Here, we examined how the pattern of epigenetic ageing in chimpanzees compares with humans. We profiled genome-wide blood methylation levels by microarray for 113 samples from 83 chimpanzees aged 1-58 years (26 chimpanzees were sampled at multiple ages during their lifespan). Many sites (greater than 65 000) showed significant change in methylation with age and around one-third (32%) of these overlap with sites showing significant age-related change in humans. At over 80% of sites showing age-related change in both species, chimpanzees displayed a significantly faster rate of age-related change in methylation than humans. We also built a chimpanzee-specific epigenetic clock that predicted age in our test dataset with a median absolute deviation from known age of only 2.4 years. However, our chimpanzee clock showed little overlap with previously constructed human clocks. Methylation at CpGs comprising our chimpanzee clock showed moderate heritability. Although the use of a human microarray for profiling chimpanzees biases our results towards regions with shared genomic sequence between the species, nevertheless, our results indicate that there is considerable conservation in epigenetic ageing between chimpanzees and humans, but also substantial divergence in both rate and genomic distribution of ageing-associated sites. This article is part of the theme issue 'Evolution of the primate ageing process'.

Genetic population structure of endangered ring-tailed lemurs (Lemur catta) from nine sites in southern Madagascar.

Madagascar's ring-tailed lemurs (Lemur catta) are experiencing rapid population declines due to ongoing habitat loss and fragmentation, as well as increasing exploitation for bushmeat and the illegal pet trade. Despite being the focus of extensive and ongoing behavioral studies, there is comparatively little known about the genetic population structuring of the species. Here, we present the most comprehensive population genetic analysis of ring-tailed lemurs to date from across their likely remaining geographic range. We assessed levels of genetic diversity and population genetic structure using multilocus genotypes for 106 adult individuals from nine geographically representative localities. Population structure and F ST analyses revealed moderate genetic differentiation with localities being geographically partitioned into northern, southern, western and also potentially central clusters. Overall genetic diversity, in terms of allelic richness and observed heterozygosity, was high in the species (AR = 4.74, H O = 0.811). In fact, it is the highest among all published lemur estimates to date. While these results are encouraging, ring-tailed lemurs are currently affected by ongoing habitat fragmentation and occur at lower densities in poorer quality habitats. The effects of continued isolation and fragmentation, coupled with climate-driven environmental instability, will therefore likely impede the long-term viability of the species.

Epigenetic Clocks.

Recent research has revealed clock-like patterns of epigenetic change across the life span in humans. Models describing these epigenetic changes have been dubbed "epigenetic clocks," and they can not only predict chronological age but also reveal biological age, which measures physiological homeostasis and deterioration over the life span. Comparative studies of the epigenetic clocks of different primate species are likely to provide insights into the evolution of life history schedules, as well as shed light on the physiological and genetic bases of aging and aging-related diseases. Chronological age estimation using clock-based calculators may also offer biological anthropologists a useful tool for applying to forensic and demographic studies.

Novel opsin gene variation in large-bodied, diurnal lemurs.

Some primate populations include both trichromatic and dichromatic (red-green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity pattern, are hypothesized to play a role. Limited data on X-linked opsin variation in lemurs make such hypotheses difficult to evaluate. We provide the first detailed examination of X-linked opsin variation across a lemur clade (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal and largest extant lemur, Indri indri, and nine species of smaller, generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister taxon to Propithecus) lacks a polymorphism, at least eight species of diurnal indriids have two or more X-linked opsin alleles. Four rainforest-living taxa-I. indri and the three largest Propithecus species-have alleles not previously documented in lemurs. Moreover, we identified at least three opsin alleles in Indri with peak spectral sensitivities similar to some New World monkeys.

Non-human primates avoid the detrimental effects of prenatal androgen exposure in mixed-sex litters: combined demographic, behavioral, and genetic analyses.

Producing single versus multiple births has important life history trade-offs, including the potential benefits and risks of sharing a common in utero environment. Sex hormones can diffuse through amniotic fluid and fetal membranes, and females with male littermates risk exposure to high levels of fetal testosterone, which are shown to have masculinizing effects and negative fitness consequences in many mammals. Whereas most primates give birth to single offspring, several New World monkey and strepsirrhine species regularly give birth to small litters. We examined whether neonatal testosterone exposure might be detrimental to females in mixed-sex litters by compiling data from long-term breeding records for seven primate species (Saguinus oedipus; Varecia variegata, Varecia rubra, Microcebus murinis, Mirza coquereli, Cheirogaleus medius, Galago moholi). Litter sex ratios did not differ from the expected 1:2:1 (MM:MF:FF for twins) and 1:2:2:1 (MMM:MMF:MFF:FFF for triplets). Measures of reproductive success, including female survivorship, offspring-survivorship, and inter-birth interval, did not differ between females born in mixed-sex versus all-female litters, indicating that litter-producing non-human primates, unlike humans and rodents, show no signs of detrimental effects from androgen exposure in mixed sex litters. Although we found no evidence for CYP19A1 gene duplications-a hypothesized mechanism for coping with androgen exposure-aromatase protein evolution shows patterns of convergence among litter-producing taxa. That some primates have effectively found a way to circumvent a major cost of multiple births has implications for understanding variation in litter size and life history strategies across mammals.

Paternity in wild ring-tailed lemurs (Lemur catta): Implications for male mating strategies.

In group-living species with male dominance hierarchies where receptive periods of females do not overlap, high male reproductive skew would be predicted. However, the existence of female multiple mating and alternative male mating strategies can call into question single-male monopolization of paternity in groups. Ring-tailed lemurs (Lemur catta) are seasonally breeding primates that live in multi-male, multi-female groups. Although established groups show male dominance hierarchies, male dominance relationships can break down during mating periods. In addition, females are the dominant sex and mate with multiple males during estrus, including group residents, and extra-group males-posing the question of whether there is high or low male paternity skew in groups. In this study, we analyzed paternity in a population of wild L. catta from the Bezà Mahafaly Special Reserve in southwestern Madagascar. Paternity was determined with 80-95% confidence for 39 offspring born to nine different groups. We calculated male reproductive skew indices for six groups, and our results showed a range of values corresponding to both high and low reproductive skew. Between 21% and 33% of offspring (3 of 14 or three of nine, counting paternity assignments at the 80% or 95% confidence levels, respectively) were sired by extra-troop males. Males siring offspring within the same group during the same year appear to be unrelated. Our study provides evidence of varying male reproductive skew in different L. catta groups. A single male may monopolize paternity across one or more years, while in other groups, >1 male can sire offspring within the same group, even within a single year. Extra-group mating is a viable strategy that can result in extra-group paternity for L. catta males.

Primate genotyping via high resolution melt analysis: rapid and reliable identification of color vision status in wild lemurs.

Analyses of genetic polymorphisms can aid our understanding of intra- and interspecific variation in primate sociality, ecology, and behavior. Studies of primate opsin genes are prime examples of this, as single nucleotide variants (SNVs) in the X-linked opsin gene underlie variation in color vision. For primate species with polymorphic trichromacy, genotyping opsin SNVs can generally indicate whether individual primates are red-green color-blind (denoted homozygous M or homozygous L) or have full trichromatic color vision (heterozygous ML). Given the potential influence of color vision on behavior and fitness, characterizing the color vision status of study subjects is becoming commonplace for many primate field projects. Such studies traditionally involve a multi-step sequencing-based method that can be costly and time-consuming. Here we present a new reliable, rapid, and relatively inexpensive method for characterizing color vision in primate populations using high resolution melt analysis (HRMA). Using lemurs as a case study, we characterized variation at exons 3 and/or 5 of the X-linked opsin gene for 87 individuals representing nine species. We scored opsin genotypes and color vision status using both traditional sequencing-based methods as well as our novel melting-curve based HRMA protocol. For each species, the melting curves of varying genotypes (homozygous M, homozygous L, heterozygous ML) differed in melting temperature and/or shape. Melting curves for each sample were consistent across replicates, and genotype-specific melting curves were consistent across DNA sources (blood vs. feces). We show that opsin genotypes can be quickly and reliably scored using HRMA once lab-specific reference curves have been developed based on known genotypes. Although the protocol presented here focuses on genotyping lemur opsin loci, we also consider the larger potential for applying this approach to various types of genetic studies of primate populations.

Genetic Evidence for Male and Female Dispersal in Wild Lemur catta.

Lemur catta has traditionally been considered a species with male-biased dispersal; however, occasional female dispersal occurs. Using molecular data, we evaluated dispersal patterns in 2 L. catta populations in southwestern Madagascar: Tsimanampesotse National Park (TNP) and Bezà Mahafaly Special Reserve (BMSR). We also investigated the genetic differentiation between the populations and dispersal partner relatedness. Results showed minor genetic differentiation between the populations (Ï´(ST) = 0.039), which may indicate gene flow historically occurring in this region, made possible by the presence of L. catta groups between the sites. Different patterns of sex-biased dispersal were found between the sites using corrected assignment indices: male-biased dispersal in TNP, and a lack of sex-biased dispersal in BMSR. Observational evidence of female dispersal in BMSR supports these results and may imply intense female resource competition in and around BMSR, because small groups of 2-3 females have been observed dispersing within BMSR and entering the reserve from outside. These dispersing groups largely consisted of mothers transferring with daughters, although we have an aunt-niece pair transferring together. Genetic data suggest that males also transfer with relatives. Our data demonstrate that dispersal partners consist of same-sexed kin for L. catta males and females, highlighting the importance of kin selection.

Model selection, zero-inflated models, and predictors of primate abundance in Korup National Park, Cameroon.

Determining the ecological and anthropogenic factors that shape the abundance and distribution of wild primates is a critical component of primate conservation research. Such research is complicated, however, whenever the species under study are encountered infrequently, a characteristic of many taxa that are threatened with extinction. Typically, the resulting data sets based on surveys of such species will have a high frequency of zero counts which makes it difficult to determine the predictor variables that are associated with species abundance. In this study, we test various statistical models using survey data that was gathered on seven species of primate in Korup National Park, Cameroon. Predictor variables include hunting signs and aspects of habitat structure and floristic composition. Our statistical models include zero-inflated models that are tailored to deal with a high frequency of zero counts. First, using exploratory data analysis we found the most informative set of models as ranked by Δ-AIC (Akaike's information criterion). On the basis of this analysis, we used five predictor variables to construct several regression models including Poisson, zero-inflated Poisson, negative binomial, and zero-inflated negative binomial. Total basal area of all trees, density of secondary tree species, hunting signs, and mean basal area of all trees were significant predictors of abundance in the zero-inflated models. We discuss the statistical logic behind zero-inflated models and provide an interpretation of parameter estimates. We recommend that researchers explore a variety of models when determining the factors that correlate with primate abundance.

Evaluating ring-tailed lemurs (Lemur catta) from southwestern Madagascar for a genetic population bottleneck.

In light of historical and recent anthropogenic influences on Malagasy primate populations, in this study ring-tailed lemur (Lemur catta) samples from two sites in southwestern Madagascar, Beza Mahafaly Special Reserve (BMSR) and Tsimanampetsotsa National Park (TNP), were evaluated for the genetic signature of a population bottleneck. A total of 45 individuals (20 from BMSR and 25 from TNP) were genotyped at seven microsatellite loci. Three methods were used to evaluate these populations for evidence of a historical bottleneck: M-ratio, mode-shift, and heterozygosity excess tests. Three mutation models were used for heterozygosity excess tests: the stepwise mutation model (SMM), two-phase model (TPM), and infinite allele model (IAM). M-ratio estimations indicated a potential bottleneck in both populations under some conditions. Although mode-shift tests did not strongly indicate a population bottleneck in the recent historical past when samples from all individuals were included, a female-only analysis indicated a potential bottleneck in TNP. Heterozygosity excess was indicated under two of the three mutation models (IAM and TPM), with TNP showing stronger evidence of heterozygosity excess than BMSR. Taken together, these results suggest that a bottleneck may have occurred among L. catta in southwestern Madagascar in the recent past. Given knowledge of how current major stochastic climatic events and human-induced change can negatively impact extant lemur populations, it is reasonable that comparable events in the historical past could have caused a population bottleneck. This evaluation additionally functions to highlight the continuing environmental and anthropogenic challenges faced by lemurs in southwestern Madagascar.

Linking genotypes, phenotypes, and fitness in wild primate populations.

In the decade since the first draft of the human genome was announced, genome sequencing projects have been initiated for an additional twenty-some primate species. Within the next several years, genome sequence data will likely become available for all primate genera and for most individuals within some primate populations. At the same time, gene mapping and association studies of humans and other organisms are rapidly advancing our understanding of the genetic bases of behavioral and morphological traits. Primatologists are especially well-placed to take advantage of this coming flood of genetic data. Here we discuss what this new era of primate genomics means for field primatology and highlight some of the unprecedented opportunities it will afford, particularly with regard to examining the genetic basis of primate adaptation and diversity.

Demographic concepts and research pertaining to the study of wild primate populations.

Demography is the study of individuals as members of a population. The dynamics of a population are determined by collectively analyzing individual schedules of survival, growth, and reproduction. Together, these schedules are known as the vital rates of the population. The vital rates, along with dispersal, contribute to population structure, which refers to how the population is organized by age, sex, density, and social groups. I briefly review the history of anthropological demography as it pertains to wild primates and then I discuss basic demographic concepts and approaches for studying wild primate populations. I then turn to demographic studies of wild primate demography. Primates are generally characterized by high adult survival probabilities relative to survival at other age/stage classes and most primate populations have population growth rates near equilibrium. Changes in adult survival have the greatest impact on population growth rate (i.e., fitness) relative to other demographic traits such as juvenile/yearling survival or age at first reproduction. I discuss how these demographic patterns, and others, connect to topics and issues in behavioral ecology, life history theory, population genetics, and conservation biology. These connections help reaffirm the fact that the vital rates are both targets and agents of evolutionary change. In this regard, demographic studies of wild primates provide a critical link between the proximate socioecological processes that operate in a species and the long-term phylogenetic patterns that characterize a species.

Demography of Verreaux's sifaka in a stochastic rainfall environment.

In this study, we use deterministic and stochastic models to analyze the demography of Verreaux's sifaka (Propithecus verreauxi verreauxi) in a fluctuating rainfall environment. The model is based on 16 years of data from Beza Mahafaly Special Reserve, southwest Madagascar. The parameters in the stage-classified life cycle were estimated using mark-recapture methods. Statistical models were evaluated using information-theoretic techniques and multi-model inference. The highest ranking model is time-invariant, but the averaged model includes rainfall-dependence of survival and breeding. We used a time-series model of rainfall to construct a stochastic demographic model. The time-invariant model and the stochastic model give a population growth rate of about 0.98. Bootstrap confidence intervals on the growth rates, both deterministic and stochastic, include 1. Growth rates are most elastic to changes in adult survival. Many demographic statistics show a nonlinear response to annual rainfall but are depressed when annual rainfall is low, or the variance in annual rainfall is high. Perturbation analyses from both the time-invariant and stochastic models indicate that recruitment and survival of older females are key determinants of population growth rate.