Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises.

Lorises are a group of globally threatened strepsirrhine primates that exhibit many unusual physiological and behavioral features, including a low metabolic rate, slow movement, and hibernation. Here, we assembled a chromosome-level genome sequence of the pygmy loris (Xanthonycticebus pygmaeus) and resequenced whole genomes from 50 pygmy lorises and 6 Bengal slow lorises (Nycticebus bengalensis). We found that many gene families involved in detoxification have been specifically expanded in the pygmy loris, including the GSTA gene family, with many newly derived copies functioning specifically in the liver. We detected many genes displaying evolutionary convergence between pygmy loris and koala, including PITRM1. Significant decreases in PITRM1 enzymatic activity in these two species may have contributed to their characteristic low rate of metabolism. We also detected many evolutionarily convergent genes and positively selected genes in the pygmy loris that are involved in muscle development. Functional assays demonstrated the decreased ability of one positively selected gene, MYOF, to up-regulate the fast-type muscle fiber, consistent with the lower proportion of fast-twitch muscle fibers in the pygmy loris. The protein product of another positively selected gene in the pygmy loris, PER2, exhibited weaker binding to the key circadian core protein CRY, a finding that may be related to this species' unusual circadian rhythm. Finally, population genomics analysis revealed that these two extant loris species, which coexist in the same habitat, have exhibited an inverse relationship in terms of their demography over the past 1 million years, implying strong interspecies competition after speciation.

Integrative Omics Reveals Rapidly Evolving Regulatory Sequences Driving Primate Brain Evolution.

Although the continual expansion of the brain during primate evolution accounts for our enhanced cognitive capabilities, the drivers of brain evolution have scarcely been explored in these ancestral nodes. Here, we performed large-scale comparative genomic, transcriptomic, and epigenomic analyses to investigate the evolutionary alterations acquired by brain genes and provide comprehensive listings of innovatory genetic elements along the evolutionary path from ancestral primates to human. The regulatory sequences associated with brain-expressed genes experienced rapid change, particularly in the ancestor of the Simiiformes. Extensive comparisons of single-cell and bulk transcriptomic data between primate and nonprimate brains revealed that these regulatory sequences may drive the high expression of certain genes in primate brains. Employing in utero electroporation into mouse embryonic cortex, we show that the primate-specific brain-biased gene BMP7 was recruited, probably in the ancestor of the Simiiformes, to regulate neuronal proliferation in the primate ventricular zone. Our study provides a comprehensive listing of genes and regulatory changes along the brain evolution lineage of ancestral primates leading to human. These data should be invaluable for future functional studies that will deepen our understanding not only of the genetic basis of human brain evolution but also of inherited disease.

Male-Male Mounting Behaviour in Free-Ranging Golden Snub-Nosed Monkeys (Rhinopithecus roxellana).

An all-male band of golden snub-nosed monkeys (Rhinopithecus roxellana) was observed for 3 months in the Qinling Mountains of China, in order to collect data on the frequencies and contextual significance of male-male mounting behaviour. Mounts occurred in a variety of affiliative, dominance-related and sexual contexts, which differed depending upon the ages of the males involved. Mounting behaviour in this group was mainly initiated by adults. Juveniles mounted each other in affiliative contexts (during play and prior to grooming). Adult males mounted subadult and juvenile partners in a greater variety of sociosexual contexts (dominance/rank-related interactions; reconciliation following agonistic encounters, and sometimes as a prelude to receiving grooming). However, subadults and juveniles were never observed to mount adults. In one dyad, involving an adult male and a subadult partner, mounting was more frequent and prolonged, and included bouts of deep pelvic thrusting. Two mounts resulted in anal intromissions and, in 1 case, the subadult partner exhibited seminal emission. Given that the study took place during the annual mating peak period of R. roxellana, it is possible that this unusual male-male sexual activity was related to the absence of mating opportunities for those adults that were excluded from 1-male units.

Male cooperation for breeding opportunities contributes to the evolution of multilevel societies.

A small number of primate species including snub-nosed monkeys (colobines), geladas (papionins) and humans live in multilevel societies (MLSs), in which multiple one-male polygamous units (OMUs) coexist to form a band, and non-breeding males associate in bachelor groups. Phylogenetic reconstructions indicate that the papionin MLS appears to have evolved through internal fissioning of large mixed-sex groups, whereas the colobine MLS evolved through the aggregation of small, isolated OMUs. However, how agonistic males maintain tolerance under intensive competition over limited breeding opportunities remains unclear. Using a combination of behavioural analysis, satellite telemetry and genetic data, we quantified the social network of males in a bachelor group of golden snub-nosed monkeys. The results show a strong effect of kinship on social bonds among bachelors. Their interactions ranged from cooperation to agonism, and were regulated by access to mating partners. We suggest that an 'arms race' between breeding males' collective defence against usurpation attempts by bachelor males and bachelor males' aggregative offence to obtain reproductive opportunities has selected for larger group size on both sides. The results provide insight into the role that kin selection plays in shaping inter-male cohesion which facilities the evolution of multilevel societies. These findings have implications for understanding human social evolution, as male-male bonds are a hallmark of small- and large-scale human societies.

Age- and sex-based patterns of positional behavior and substrate utilization in the golden snub-nosed monkey (Rhinopithecus roxellana).

Body mass plays an important role in primate positional behavior and in sexually dimorphic arboreal primate species may influence how immature and adult individuals travel through the forest canopy and access food resources. In this study, we examined age- and sex-based patterns of positional behavior and substrate utilization in wild golden snub-nosed monkeys (Rhinopithecus roxellana), an endangered species of Asian colobine. Our results indicated that among all age and sex classes, sitting was the most common feeding and resting posture and during travel, quadrupedal walking was the dominant locomotor behavior. Despite the fact that adult male R. roxellana are reported to exhibit a body mass nearly two times that of adult females, we found no significant sex differences in the positional repertoire during feeding and traveling. In addition, we found that while infants and juveniles used similar postural and locomotor behaviors as their adult counterparts, younger golden snub-nosed monkeys more frequently engaged in risky or escape-oriented behaviors such as climbing, running, leaping, and forelimb suspension. With increasing age, the use of quadrupedal walking and dropping (downward in-air displacement of body mass that does not require hindlimb propulsion) increased and the use of leaping, suspensory postures, and bridging decreased. Finally, given differences in the positional repertoire of adult and immature golden snub-nosed monkeys, we argue that studies of ontogenetic patterns of positional behavior should emphasize what it takes to survive at each life stage rather than what it takes to match an adult repertoire.

Postconflict Conciliation within One-Male Breeding Units in Sichuan Snub-Nosed Monkeys in the Qinling Mountains, China.

This study analyzed conflict and postconflict (PC) conciliation between males and females within one-male breeding units in Sichuan snub-nosed monkeys (Rhinopithecus roxellana) in the Qinling Mountains, China. The PC matched-control and time rule methods were used to collect and analyze data recorded from September 2013 to June 2014. The conciliatory tendency among individuals following conflict was 82.07%, and affiliation occurred within a few minutes after the conflict, which was not significantly different between mating and nonmating seasons. The PC conciliation scenarios were different from those reported from captivity. Lumbar hold and grooming were the most common expressions in reconciliation. In addition, bystander affiliation was uniquely found, which may be associated with the more terrestrial locomotion of R. roxellana, compared with other colobines.

Combinatorial efficiency evaluation: the knapsack problem in data envelopment analysis.

The traditional data envelopment analysis (DEA) literatures generally concentrated on the efficiency evaluation of single decision making unit (DMU). However, in many practical problems, the decision makers are required to choose a number of DMUs instead of a single one from the DMUs set. Therefore, it is necessary to study the combinatorial efficiency evaluation problem which can be illustrated as a knapsack problem naturally. It is indicated that the basic model proposed by Cook and Green may have some drawbacks and a modified model, which is combined with the super efficiency model, is proposed in this paper. What is more, our proposed model is more persuasive to the decision makers because it is able to provide a unique best combination of DMUs. An adapted local search algorithm is developed as a solver of this problem. Finally, numerical examples are provided to examine the validity of our proposed model and the adapted local search algorithm.

Dynamic foraging strategy adaptation to heterogeneous environments contributes to social aggregation in snub-nosed monkeys.

The dynamics of animal social structures are heavily influenced by environmental patterns of competition and cooperation. In folivorous colobine primates, prevailing theories suggest that larger group sizes should be favored in rainforests with a year-round abundance of food, thereby reducing feeding competition. Yet, paradoxically, larger groups are frequently found in high-altitude or high-latitude montane ecosystems characterized by a seasonal scarcity of leaves. This contradiction is posited to arise from cooperative benefits in heterogeneous environments. To investigate this hypothesis, we carried out a six-year field study on two neighboring groups of golden snub-nosed monkey ( Rhinopithecus roxellana), a species representing the northernmost distribution of colobine primates. Results showed that the groups adjusted their movement and habitat selection in response to fluctuating climates and spatiotemporal variability of resources, indicative of a dynamic foraging strategy. Notably, during the cold, resource-scarce conditions in winter, the large group occupied food-rich habitats but did not exhibit significantly longer daily travel distances than the smaller neighboring group. Subsequently, we compiled an eco-behavioral dataset of 52 colobine species to explore their evolutionary trajectories. Analysis of this dataset suggested that the increase in group size may have evolved via home range expansion in response to the cold and heterogeneous climates found at higher altitudes or latitudes. Hence, we developed a multi-benefits framework to interpret the formation of larger groups by integrating environmental heterogeneity. In cold and diverse environments, even smaller groups require larger home ranges to meet their dynamic survival needs. The spatiotemporal distribution of high-quality resources within these expanded home ranges facilitates more frequent interactions between groups, thereby encouraging social aggregation into larger groups. This process enhances the benefits of collaborative actions and reproductive opportunities, while simultaneously optimizing travel costs through a dynamic foraging strategy.

Adaptations to a cold climate promoted social evolution in Asian colobine primates.

The biological mechanisms that underpin primate social evolution remain poorly understood. Asian colobines display a range of social organizations, which makes them good models for investigating social evolution. By integrating ecological, geological, fossil, behavioral, and genomic analyses, we found that colobine primates that inhabit colder environments tend to live in larger, more complex groups. Specifically, glacial periods during the past 6 million years promoted the selection of genes involved in cold-related energy metabolism and neurohormonal regulation. More-efficient dopamine and oxytocin pathways developed in odd-nosed monkeys, which may have favored the prolongation of maternal care and lactation, increasing infant survival in cold environments. These adaptive changes appear to have strengthened interindividual affiliation, increased male-male tolerance, and facilitated the stepwise aggregation from independent one-male groups to large multilevel societies.

Comparative genomics reveals the hybrid origin of a macaque group.

Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions exhibited equal contributions from each parental lineage, suggesting that they were less affected by subsequent backcrossing and hence could have played an important role in maintaining hybrid integrity. We identified many reproduction-associated genes that could have contributed to the development of the mixed sexual phenotypes characteristic of the fascicularis group. The phylogeny within the silenus group was also resolved, and functional experimentation confirmed that all extant Western silenus species are susceptible to HIV-1 infection. Our study provides novel insights into macaque evolution and reveals a hybrid speciation event that has occurred only very rarely in primates.

Phylogenomic analyses provide insights into primate evolution.

Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.

Sexual interference in the Golden snub-nosed monkey (Rhinopithecus roxellana): a test of the sexual competition hypothesis in a polygynous species.

Sexual interference (SI), which is defined as any disturbance directed to a mating pair by other individuals, has been reported in several primate species. It is widely suggested that successful harassers experience improved mating success by increasing their access to reproductive partners as well as by reducing the mating success of rivals. Although theories of primate sexual conflict highlight male intra-sexual mating competition, females also are reported to actively disrupt copulations between mating partners. In this study, we investigated SI in a multilevel troop of Golden snub-nosed monkeys (Rhinopithecus roxellana) inhabiting the Qinling Mountains, China. Behavioral observations of 11 one-male units (OMU) that comprised the multilevel troop were conducted from September 2007 to May 2008. During this period 17.1% of 652 documented intra-OMU sexual encounters were characterized either by mild or aggressive forms of harassment. Sexual harassment was typically performed by a single individual (91.9%), and in 75.7% of cases the harasser was an adult or sub-adult female. The frequency of female harassment was positively correlated with the number of adult and sub-adult females residing in an OMU, and resulted in a significant decrease in matings ending in ejaculation. We found that the amount of SI a female received was not a significant predictor of her reproductive success. However, females who conceived during the mating season directed higher levels of harassment at other females than females who did not conceive. We evaluate the strength of the sexual competition hypothesis and the hormonally modulated aggression hypothesis in explaining patterns of SI in female Golden snub-nosed monkeys.

Bachelor groups in primate multilevel society facilitate gene flow across fragmented habitats.

In the face of ongoing habitat fragmentation, many primate species have experienced reduced gene flow resulting in a reduction of genetic diversity, population bottlenecks, and inbreeding depression, including golden snub-nosed monkeys Rhinopithecus roxellana. Golden snub-nosed monkeys live in a multilevel society composed of several 1 male harem units that aggregate to form a cohesive breeding band, which is followed by one or more bachelor groups composed of juvenile, subadult, and adult male members. In this research, we examine the continuous landscape resistance surface, the genetic diversity and patterns of gene flow among 4 isolated breeding bands and 1 all-male band in the Qinling Mountains, China. Landscape surface modeling suggested that human activities and ecological factors severely limit the movement of individuals among breeding bands. Although these conditions are expected to result in reduced gene flow, reduced genetic diversity, and an increased opportunity for a genetic bottleneck, based on population genetic analyses of 13 microsatellite loci from 188 individuals inhabiting 4 isolated breeding bands and 1 all-male band, we found high levels of genetic diversity but low levels of genetic divergence, as well as high rates of gene flow between males residing in the all-male band and each of the 4 breeding bands. Our results indicate that the movement of bachelor males across the landscape, along with their association with several different breeding bands, appears to provide a mechanism for promoting gene flows and maintaining genetic diversity that may counteract the otherwise isolating effects of habitat fragmentation.

Correction to: Review of GPS collar deployments and performance on nonhuman primates.

In the original publication of the article, figure 1 was wrongly published as a duplication.

Review of GPS collar deployments and performance on nonhuman primates.

Over the past 20 years, GPS collars have emerged as powerful tools for the study of nonhuman primate (hereafter, "primate") movement ecology. As the size and cost of GPS collars have decreased and performance has improved, it is timely to review the use and success of GPS collar deployments on primates to date. Here we compile data on deployments and performance of GPS collars by brand and examine how these relate to characteristics of the primate species and field contexts in which they were deployed. The compiled results of 179 GPS collar deployments across 17 species by 16 research teams show these technologies can provide advantages, particularly in adding to the quality, quantity, and temporal span of data collection. However, aspects of this technology still require substantial improvement in order to make deployment on many primate species pragmatic economically. In particular, current limitations regarding battery lifespan relative to collar weight, the efficacy of remote drop-off mechanisms, and the ability to remotely retrieve data need to be addressed before the technology is likely to be widely adopted. Moreover, despite the increasing utility of GPS collars in the field, they remain substantially more expensive than VHF collars and tracking via handheld GPS units, and cost considerations of GPS collars may limit sample sizes and thereby the strength of inferences. Still, the overall high quality and quantity of data obtained, combined with the reduced need for on-the-ground tracking by field personnel, may help defray the high equipment cost. We argue that primatologists armed with the information in this review have much to gain from the recent, substantial improvements in GPS collar technology.

Social dynamics of the golden snub-nosed monkey (Rhinopithecus roxellana): female transfer and one-male unit succession.

Among primates that form multilevel societies, understanding factors and mechanisms associated with the movement of individuals between groups, clans, and one-male social units offers important insight into primate reproductive and social strategies. In this research we present data based on an 8-year field study of a multilevel troop of Sichuan snub-nosed monkeys (Rhinopithecus roxellana) in the Qinling Mountains of China. Our study troop contained 78-126 individuals, and was usually organized into 6-8 one-male units (OMU). The majority of OMUs were composed of networks of unrelated females and their offspring. We found that 59.7% (43/72) of subadult and adult females in our study troop transferred between OMUs (n=66) or disappeared (n=7) from the troop. In the majority of cases, two or more females transferred together into new OMUs or troops. In R. roxellana, new OMUs formed in several ways. During 2001-2008, 16 adult males appeared in the study troop. Over this period, we observed 13 different males who became harem leaders either by taking over an existing harem or by attracting females from other OMUs into their harem. We also observed four OMUs from a neighboring troop to successfully immigrate into the study troop. The number of individuals in these newly immigrated OMUs was significantly smaller than that number of individuals in resident OMUs. During harem formation, fighting between adult males was rarely observed, and female mate choice appeared to play a crucial role in harem male recruitment and replacement. These results suggest that golden snub-nosed monkeys are organized in a nonmatrilineal social system. Female mate choice and possibly incest avoidance appear to play important roles in female transfer, male tenure, and OMU stability.

A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana).

BACKGROUND: The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered colobine species endemic to China, which has several distinct traits including a unique social structure. Although a genome assembly for R. roxellana is available, it is incomplete and fragmented because it was constructed using short-read sequencing technology. Thus, important information such as genome structural variation and repeat sequences may be absent. FINDINGS: To obtain a high-quality chromosomal assembly for R. roxellana qinlingensis, we used 5 methods: Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, BioNano optical maps, 10X Genomics link-reads, and high-throughput chromosome conformation capture. The assembled genome was ∼3.04 Gb, with a contig N50 of 5.72 Mb and a scaffold N50 of 144.56 Mb. This represented a 100-fold improvement over the previously published genome. In the new genome, 22,497 protein-coding genes were predicted, of which 22,053 were functionally annotated. Gene family analysis showed that 993 and 2,745 gene families were expanded and contracted, respectively. The reconstructed phylogeny recovered a close relationship between R. rollexana and Macaca mulatta, and these 2 species diverged ∼13.4 million years ago. CONCLUSION: We constructed a high-quality genome assembly of the Qinling golden snub-nosed monkey; it had superior continuity and accuracy, which might be useful for future genetic studies in this species and as a new standard reference genome for colobine primates. In addition, the updated genome assembly might improve our understanding of this species and could assist conservation efforts.

Female choice impacts residential male takeover in golden snub-nosed monkeys (Rhinopithecus roxellana).

In primate species with social systems consisting of one-male breeding units (OMUs), resident male takeover represents a major challenge to individual reproductive success and mating strategies. The golden snub-nosed monkey (Rhinopithecus roxellana) is characterized by large multilevel societies (MLS) comprised of several OMUs and all-male units (AMUs); however, the factors and mechanisms associated with resident male takeover, which offer important insight into primate reproduction and social strategies, are still poorly understood. Based on 5-year monitoring data from a free-ranging herd of golden monkeys from the Qinling Mountains in China, we categorized three phases of an OMU, that is, a rising phase, developing phase, and declining phase. The rising and declining phases were unstable periods in which male takeover in an OMU might occur. Factors causing takeover, such as leader male rank, fighting ability, reproduction rate, and affiliation (proximity, allogrooming), were analyzed for males and females and for different OMUs. Results indicated that the new resident male's fighting ability was lower than that of the former resident male in 23 cases. After replacement, the rank order of the new resident male significantly declined. Females involved in a takeover increased their distance from the resident male and decreased mating frequency during the three months prior to takeover. Females with infants under one-year-old had a marked effect on the specific time of takeover occurrence. These results suggested that female choice was the main factor deciding whether a takeover attempt was successful. Furthermore, rather than male conflict, females more often initiated and affected takeover and outcome, implying that the social status and competitive ability of the males played lesser roles during takeover.

Preliminary report on Sichuan golden snub-nosed monkeys (Rhinopithecus roxellana roxellana) at Laohegou Nature Reserve, Sichuan, China.

Comparative studies of subspecies under different ecological environments offer insights into intraspecies evolutionary adaptive mechanisms. Golden snub-nosed monkeys (Rhinopithecus roxellana) include three subspecies in China classified mainly by their morphological variations: R. r. roxellana (Sichuan and Gansu province), R. r. qinlingensis (Shaanxi province) and R. r. hubeiensis (Hubei province). These three subspecies live in three isolated area with different environments. Past works focused on the last two subspecies, but little information of habitat and behaviors of the nominated subspecies (R. r. roxellana) is available to date. We conducted a two-year study on the diet, activity budget, home range and social organization of 4 herds of R. r. roxellana, based on a total of 106 days' observation in Laohegou (LHG) Nature Reserve, Sichuan province. By using scan sampling method, our results suggest that the R. r roxellana feeds predominantly on leaves (77.5%), and spends more time feeding (40.0%) and resting (27.0%) while compared to the other two subspecies. Kernel Density Estimation Method based on GPS technology confirms that R. r roxellana has relatively larger home ranges (49.1 km2). The unit size (8.3 ± 3.5 individuals) of R. r roxellana is also smaller. Therefore, it is possible that differences in food availability in relation to habitats have important impacts on the feeding strategy and social system of the golden snub-nosed monkey. These results provide data to further explore intraspecific adaptations of living primates.