Primate Evolution Research Articles

Transcriptome of the Southern Muriqui Brachyteles arachnoides (Primates:Platyrrhini), a Critically Endangered New World Monkey: Evidence of Adaptive Evolution.

The southern muriqui (Brachyteles arachnoides) is the largest neotropical primate. This species is endemic to Brazil and is currently critically endangered due to its habitat destruction. The genetic basis underlying adaptive traits of New World monkeys has been a subject of interest to several investigators, with significant concern about genes related to the immune system. In the absence of a reference genome, RNA-seq and de novo transcriptome assembly have proved to be valuable genetic procedures for accessing gene sequences and testing evolutionary hypotheses. We present here a first report on the sequencing, assembly, annotation and adaptive selection analysis for thousands of transcripts of B. arachnoides from two different samples, corresponding to 13 different blood cells and fibroblasts. We assembled 284,283 transcripts with N50 of 2,940 bp, with a high rate of complete transcripts, with a median high scoring pair coverage of 88.2%, including low expressed transcripts, accounting for 72.3% of complete BUSCOs. We could predict and extract 81,400 coding sequences with 79.8% of significant BLAST hit against the Euarchontoglires SwissProt dataset. Of these 64,929 sequences, 34,084 were considered homologous to Supraprimate proteins, and of the remaining sequences (30,845), 94% were associated with a protein domain or a KEGG Orthology group, indicating potentially novel or specific protein-coding genes of B. arachnoides. We use the predicted protein sequences to perform a comparative analysis with 10 other primates. This analysis revealed, for the first time in an Atelid species, an expansion of APOBEC3G, extending this knowledge to all NWM families. Using a branch-site model, we searched for evidence of positive selection in 4,533 orthologous sets. This evolutionary analysis revealed 132 amino acid sites in 30 genes potentially evolving under positive selection, shedding light on primate genome evolution. These genes belonged to a wide variety of categories, including those encoding the innate immune system proteins (APOBEC3G, OAS2, and CEACAM1) among others related to the immune response. This work generated a set of thousands of complete sequences that can be used in other studies on molecular evolution and may help to unveil the evolution of primate genes. Still, further functional studies are required to provide an understanding of the underlying evolutionary forces modeling the primate genome.

Conserved mammalian modularity of quantitative trait loci revealed human functional orthologs in blood pressure control.

Genome-wide association studies (GWAS) have routinely detected human quantitative trait loci (QTLs) for complex traits. Viewing that most GWAS single nucleotide polymorphisms (SNPs) are found in non-coding regions unrelated to the physiology of a polygenic trait of interest, a vital question to answer is whether or not any of these SNPs can functionally alter the phenotype with which it is associated. The study of blood pressure (BP) is a case in point. Conserved mechanisms in controlling BP by modularity is now unifying differing mammalian orders in that understanding mechanisms in rodents is tantamount to revealing the same in humans, while overcoming experimental limitations imposed by human studies. As a proof of principle, we used BP QTLs from Dahl salt-sensitive rats (DSS) as substitutes to capture distinct human functional orthologs. 3 DSS BP QTLs are located into distinct genome regions and correspond to several human GWAS genes. Each of the QTLs independently exerted a major impact on BP in vivo. BP was functionally changed by normotensive alleles from each of these QTLs, and yet, the human GWAS SNPs do not exist in the rat. They cannot be responsible for physiological alterations in BP caused by these QTLs. These SNPs are genome emblems for QTLs nearby, rather than being QTLs per se, since they only emerged during primate evolution after BP-regulating mechanisms have been established. We then identified specific mutated coding domains that are conserved between rodents and humans and that may implicate different steps of a common pathway or separate pathways.

The landscape of tooth shape: Over 20 years of dental topography in primates.

Diet plays an incontrovertible role in primate evolution, affecting anatomy, growth and development, behavior, and social structure. It should come as no surprise that a myriad of methods for reconstructing diet have developed, mostly utilizing the element that is not only most common in the fossil record but also most pertinent to diet: teeth. Twenty years ago, the union of traditional, anatomical analyses with emerging scanning and imaging technologies led to the development of a new method for quantifying tooth shape and reconstructing the diets of extinct primates. This method became known as dental topography.

Human Endogenous Retrovirus K (HML-2) in Health and Disease.

Human endogenous retroviruses (HERVs) are derived from exogenous retrovirus infections in the evolution of primates and account for about 8% of the human genome. They were considered as silent passengers within our genomes for a long time, however, reactivation of HERVs has been associated with tumors and autoimmune diseases, especially the HERV-K (HML-2) family, the most recent integration groups with the least number of mutations and the most biologically active to encode functional retroviral proteins and produce retrovirus-like particles. Increasing studies are committed to determining the potential role of HERV-K (HML-2) in pathogenicity. Although there is still no evidence for HERV-K (HML-2) as a direct cause of diseases, aberrant expression profiles of the HERV-K (HML-2) transcripts and their regulatory function to their proximal host-genes were identified in different diseases. In this review, we summarized the advances between HERV-K (HML-2) and diseases to provide basis for further studies on the causal relationship between HERV-K (HML-2) and diseases. We recommended more attention to polymorphic integrated HERV-K (HML-2) loci which could be genetic causative factors and be associated with inter-individual differences in tumorigenesis and autoimmune diseases.

Baboons (Papio anubis) living in larger social groups have bigger brains

The evolutionary origin of Primates' exceptionally large brains is still highly debated. Two competing explanations have received much support: the ecological hypothesis and the social brain hypothesis (SBH). We tested the SBH in (n = 82) baboons (Papio anubis) belonging to the same research centre but housed in groups with size ranging from 2 to 63 individuals. We found that baboons living in larger social groups had larger brains. This effect was driven mainly by white matter volume and to a lesser extent by grey matter volume but not by the cerebrospinal fluid. In comparison, the size of the enclosure, an ecological variable, had no such effect. In contrast to the current re-emphasis on potential ecological drivers of primate brain evolution, the present study provides renewed support for the social brain hypothesis and suggests that the social brain plastically responds to group size. Many factors may well influence brain size, yet accumulating evidence suggests that the complexity of social life might be an important determinant of brain size in primates.

Characterization of the primate TRIM gene family reveals the recent evolution in primates.

The tripartite motif (TRIM) gene family encodes diverse distinct proteins that play important roles in many biological processes. However, the molecular evolution and phylogenetic relationships of TRIM genes in primates are still elusive. We performed a genomic approach to identify and characterize TRIM genes in human and other six primate genomes. In total, 537 putative functional TRIM genes were identified and TRIM members varied among primates. A neighbor joining (NJ) tree based on the protein sequences of 82 human TRIM genes indicates seven TRIM groups, which is consistent with the results based on the architectural motifs. Many TRIM gene duplication events were identified, indicating a recent expansion of TRIM family in primate lineages. Interestingly, the chimpanzee genome shows the greatest TRIM gene expansion among the primates; however, its congeneric species, bonobo, has the least number of TRIM genes and no duplication event. Moreover, we identified a ~ 200kb deletion on chromosome 11 of bonobos that results in a loss of cluster3 TRIM genes. The loss of TRIM genes might have occurred within the last 2 mys. Analysis of positive selection recovered 9 previously reported and 21 newly identified positively selected TRIM genes. In particular, most positive selected sites are located in the B30.2 domains. Our results have provided new insight into the evolution of primate TRIM genes and will broaden our understanding on the functions of the TRIM family.

Human-specific ARHGAP11B increases size and folding of primate neocortex in the fetal marmoset.

The neocortex has expanded during mammalian evolution. Overexpression studies in developing mouse and ferret neocortex have implicated the human-specific gene ARHGAP11B in neocortical expansion, but the relevance for primate evolution has been unclear. Here, we provide functional evidence that ARHGAP11B causes expansion of the primate neocortex. ARHGAP11B expressed in fetal neocortex of the common marmoset under control of the gene's own (human) promoter increased the numbers of basal radial glia progenitors in the marmoset outer subventricular zone, increased the numbers of upper-layer neurons, enlarged the neocortex, and induced its folding. Thus, the human-specific ARHGAP11B drives changes in development in the nonhuman primate marmoset that reflect the changes in evolution that characterize human neocortical development.

Evolution of a splice variant that acts as an endogenous antagonist of the original INSL3 in primates.

Alu sequences are the most abundant repetitive elements in the human genome, and have proliferated to more than one million copies in the human genome. Primate-specific Alu sequences account for ~10% of the human genome, and their spread within the genome has the potential to generate new exons. The new exons produced by Alu elements appear in various primate genes, and their functions have been elucidated. Here, we identified a new exon in the insulin-like 3 gene (INSL3), which evolved ~50 million years ago, and led to a splicing variant with 31 extra amino acid residues in addition to the original 95 nucleotides (NTs) of INSL3. The Alu-INSL3 isoform underwent diverse changes during primate evolution; we identified that human Alu-INSL3 might be on its way to functionality and has potential to antagonize LGR8-INSL3 function. Therefore, the present study is designed to provide an example of the evolutionary trajectory of a variant peptide hormone antagonist that caused by the insertion of an Alu element in primates.

A single mutation in the ACTR8 gene associated with lineage-specific expression in primates

BackgroundAlternative splicing (AS) generates various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel AluSz6-exonized ACTR8 transcript of the crab-eating monkey (Macaca fascicularis). In the present study, we sought to determine the molecular mechanism of AluSz6 exonization of the ACTR8 gene and investigate its evolutionary and functional consequences in the crab-eating monkey.ResultsWe performed RT-PCR and genomic PCR to analyze AluSz6 exonization in the ACTR8 gene and the expression of the AluSz6-exonized transcript in nine primate samples, including prosimians, New world monkeys, Old world monkeys, and hominoids. AluSz6 integration was estimated to have occurred before the divergence of simians and prosimians. The Alu-exonized transcript obtained by AS was lineage-specific and expressed only in Old world monkeys and apes, and humans. This lineage-specific expression was caused by a single G duplication in AluSz6, which provides a new canonical 5′ splicing site. We further identified other alternative transcripts that were unaffected by the AluSz6 insertion. Finally, we observed that the alternative transcripts were transcribed into new isoforms with C-terminus deletion, and in silico analysis showed that these isoforms do not have a destructive function.ConclusionsThe single G duplication in the TE sequence is the source of TE exonization and AS, and this mutation may suffer a different fate of ACTR8 gene expression during primate evolution.

Invariant Synapse Density and Neuronal Connectivity Scaling in Primate Neocortical Evolution.

Synapses are involved in the communication of information from one neuron to another. However, a systematic analysis of synapse density in the neocortex from a diversity of species is lacking, limiting what can be understood about the evolution of this fundamental aspect of brain structure. To address this, we quantified synapse density in supragranular layers II-III and infragranular layers V-VI from primary visual cortex and inferior temporal cortex in a sample of 25 species of primates, including humans. We found that synapse densities were relatively constant across these levels of the cortical visual processing hierarchy and did not significantly differ with brain mass, varying by only 1.9-fold across species. We also found that neuron densities decreased in relation to brain enlargement. Consequently, these data show that the number of synapses per neuron significantly rises as a function of brain expansion in these neocortical areas of primates. Humans displayed the highest number of synapses per neuron, but these values were generally within expectations based on brain size. The metabolic and biophysical constraints that regulate uniformity of synapse density, therefore, likely underlie a key principle of neuronal connectivity scaling in primate neocortical evolution.

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome.

Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.

Biometric Pilot-Studies Reveal the Arrangement and Shape of Windows on a Traditional Façade to be Implicitly “Engaging”, Whereas Contemporary Façades are Not

The human brain evolved to implicitly approach or avoid objects in its surroundings. Requisite for survival, this behavior happens without conscious awareness or control, honed over 60 million years of primate evolution. Biometric technologies, including eye tracking, reveal these unconscious behaviors at work and allow us to predict the initial response of a design experience. This paper shows how a biometric tool, 3M-VAS (Visual Attention Software), can be effectively used in architecture. This tool aggregates 30 years of eye-tracking data, and is commonly applied in website and signage design. A pilot-study uses simplified drawings of building elevations to show 3M-VAS’s predictive power in revealing implicit human responses of engagement and disengagement to buildings. The implications on the impact of a structure in creating the public realm suggest recommendations for approving new architecture.

The Genetics of Encephalization in Eight Inbred Mouse Strains and their F1 Crosses

Increased relative brain size (encephalization) is an important feature of primate and human evolution that has been associated with increased intelligence. Although the heritability of brain size is known to be high, the extent to which different genetic factor types (e.g., additive genotype, maternal genotype, sex, nonadditive genetic interactions) contribute to measured brain size and encephalization are not as well understood. Endocast measures from a large normative sample of genetically diverse mouse lines were estimated to quantify 1) how increased encephalization impacts neurocranial shape and 2) the contribution of various genetic factors towards determining encephalization. Digital endocasts were estimated for 1182 mice representing the eight Collaborative Cross mouse inbred founder lines and 62 reciprocal F1 crosses. Endocasts were estimated by applying a single atlas image endocast segmentation to micro‐computed tomography (μCT) images of each specimen’s skull, based on the nonlinear volumetric image registration of each μCT to the representative atlas image. This method was validated by comparison of automatically extracted endocasts to endocasts that were manually segmented (using Endex software) for a large subset of the specimens. Measures of endocast volume, length, width, and height represent different aspects of endocast size. Ratios of volume over cranial base length (IRE) and volume over body weight (V2W) represent encephalization relative to cranial size and body size, respectively. Diallel analysis (BayesDiallel in R) was used to estimate the genetic influence of multiple additive and nonadditive genetic factors on each measure. The total heritability of each size and encephalization measure is between 0.82 and 0.87, with additive founder strain genotype effects accounting for the vast majority of this heritability. There are also significant inbreeding, sex, maternal genotype, and founder strain cross‐specific effects. The additive effects of founder genotypes were more pronounced for V2W than for IRE, with some of the strains showing opposite directions of effect between these encephalization measures. Care must be taken in the measure of overall size used to estimate encephalization. While inbred mice tend to have smaller overall size, they tend to have a higher encephalization, likely because the impact of inbreeding on brain volume is not as severe as the impact on skull size or body weight. In addition to the strength of genotypic effects, we quantified the influence of increased encephalization on overall cranial vault shape. As encephalization increases, endocasts display more substantial increases in cranial vault height than either length or width. Variation in the mouse cranial base size appears limited, while the shape of later ossifying vault bones strongly covaries with relative brain size. These results support the conclusion that encephalization is highly heritable and indicate which types of genetic factors contribute most strongly. Additionally, relatively large mouse brains are accommodated primarily through variation in cranial vault height, leading to a round cranial vault shape that is analogous to globular vault of modern humans.Support or Funding InformationFinancial support provided by Stony Brook University Startup Funds to CJP

Comparative genomic analysis of the 3' UTR of human MDM2 identifies multiple transposable elements, an RLP24 pseudogene and a cluster of novel repeat sequences that arose during primate evolution.

The MDM2 oncogene is a negative regulator of the p53 tumour suppressor. This relationship appears to have originated over a billion years ago. The human MDM2 gene encodes a variety of mRNAs with exceptionally long 3'UTRs (up to 5.7kb); however, it was unclear whether MDM2 3'UTRs from other species are similarly long or conserved at the sequence level. Here, we report that all but one of the primate species most closely related to humans (greater and lesser apes) have similarly long 3'UTRs with high sequence similarity across their entire length. More distantly related species (Old world monkeys and new world monkeys) tend to have shorter MDM2 3'UTRs homologous to the corresponding position of the human MDM2 3'UTR while non-primate species exhibit little similarity at all. Remarkably, DNA sequences downstream of the shorter primate 3'UTRs are syntenic with distal regions in the human and other ape MDM2 3'UTRs. These homologous non-transcribed intergenic and transcribed 3'UTR-encoding regions are comprised of a variety of transposable elements, an RLP24 pseudogene and a cluster of novel repeat sequences suggestive of another unknown transposable element. Our analysis suggests that the primary difference between long and short MDM2 3'UTRs is a switch in polyA site usage to include conserved transposable elements that remain intergenic in more distantly related primates. It will be important to determine the relative contribution of these elements to post-transcriptional and translational regulation of MDM2 and hence p53-mediated tumour suppression.

Functional Captures of Multiple Human Quantitative Trait Loci Regulating Blood Pressure with the Use of Orthologs in Genetically Defined Rat Models

BackgroundMost signals from human genome-wide association studies (GWAS) for blood pressure (BP) are single-nucleotide polymorphisms (SNPs). It was unknown if such SNPs can functionally affect BP. Because BP is similar between humans and rodents, unraveling basic mechanisms from rodents can reveal the same BP-modulating mechanisms in humans originating from their common ancestors while overcoming limitations in human epidemiology. MethodsFor the first time, we used quantitative trait loci (QTLs) from Dahl salt-sensitive (DSS) rats as functional surrogates to capture human BP QTLs. ResultsA total of 107 human GWAS genes may be classified into 2 common pathways of hypertension pathogeneses. Among them, 4 DSS BP QTLs correspond to 4 human GWAS genes. Each of them independently showed a major impact on BP in vivo and thus functional redundancy. BP was altered by each of these 4 QTLs, but human GWAS SNPs marking these QTLs do not exist in the rat. They cannot be responsible for physiological changes in BP caused by these QTLs and are genome signposts marking positions of the QTLs nearby, rather than being QTLs themselves. These SNPs appeared during primate evolution, independently of BP regulation. Because the functional dosage of QTLs, not their gene dose, determined hypertension pathogenesis, a role for the noncoding GWAS SNPs in BP via regulating gene expressions can be discounted. ConclusionsThe human QTLs may function in a common pathway, with each involved in a different step in the pathway leading to BP control. These results may be conceptually paradigm shifting.

Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates.

Epigenetic mechanisms influence the development and maintenance of complex phenotypes and may also contribute to the evolution of species-specific phenotypes. With respect to skeletal traits, little is known about the gene regulation underlying these hard tissues or how tissue-specific patterns are associated with bone morphology or vary among species. To begin exploring these topics, this study evaluates one epigenetic mechanism, DNA methylation, in skeletal tissues from five nonhuman primate species which display anatomical and locomotor differences representative of their phylogenetic groups. First, we test whether intraspecific variation in skeletal DNA methylation is associated with intraspecific variation in femur morphology. Second, we identify interspecific differences in DNA methylation and assess whether these lineage-specific patterns may have contributed to species-specific morphologies. Specifically, we use the Illumina Infinium MethylationEPIC BeadChip to identify DNA methylation patterns in femur trabecular bone from baboons (n = 28), macaques (n = 10), vervets (n = 10), chimpanzees (n = 4), and marmosets (n = 6). Significant differentially methylated positions (DMPs) were associated with a subset of morphological variants, but these likely have small biological effects and may be confounded by other variables associated with morphological variation. Conversely, several species-specific DMPs were identified, and these are found in genes enriched for functions associated with complex skeletal traits. Overall, these findings reveal that while intraspecific epigenetic variation is not readily associated with skeletal morphology differences, some interspecific epigenetic differences in skeletal tissues exist and may contribute to evolutionarily distinct phenotypes. This work forms a foundation for future explorations of gene regulation and skeletal trait evolution in primates.

Ontogeny of locomotion in mouse lemurs: Implications for primate evolution

The environment of juvenile primates is very challenging. They have to forage and move on the same substrates as adults do and escape the same predators, despite their immature state. In this study, we explore the developmental strategies that may provide effective locomotor abilities early in life. This could provide new insights into the selective pressures acting on juvenile primates and into evolution of primate locomotion. We conducted an ontogenetic study of 36 arboreal gray mouse lemurs from birth to adulthood (6 months of age). The investigated parameters were, for both limbs, (1) grasping behavior during locomotion (i.e., grip postures), (2) grasping performance (i.e., pull strength), and (3) motor coordination (i.e., rotarod test). Our results show that 8-day-old babies are able to climb substrates of various slopes and diameters outside of their nest. Although juveniles cannot successfully complete a motor coordination test before 30 days of age, young individuals display relative pull strengths that are very high or even on par with adults, guaranteeing stability on narrow substrates. These powerful grasps highlight the importance of the grasping function for these juveniles that are not carried and move independently on arboreal substrates shortly after their first week of life. Moreover, the pedal grasping provides a secure grasp on all substrates across ontogeny; however, manual secure grasps decrease during development, being highly used only shortly after birth on vertical and narrow substrates. These results first suggest different functional roles of the hands and feet, with the hind limbs ensuring body balance on the substrates, freeing the upper limbs for manipulation. They further show vertical and narrow branches to be especially challenging, requiring strong grasps, which suggests that they may drive the evolution of strong grasping abilities in primates.

The Central Role of Small Vertical Substrates for the Origin of Grasping in Early Primates.

The manual and pedal grasping abilities of primates, characterized by an opposable hallux, flat nails, and elongated digits, constitute a unique combination of features that likely promoted their characteristic use of arboreal habitats. These hand and foot specificities are central for understanding the origins and early evolution of primates and have long been associated with foraging in a fine-branch milieu. However, other arboreal mammals occupy similar niches, and it remains unclear how substrate type may have exerted a selective pressure on the acquisition of nails and a divergent pollex/hallux in primates or in what sequential order these traits evolved. Here, we video-recorded 14,564 grasps during arboreal locomotion in 11 primate species (6 strepsirrhines and 5 platyrrhines) and 11 non-primate arboreal species (1 scandentian, 3 rodents, 3 carnivorans, and 4 marsupials). We quantified our observations with 19 variables to analyze the effect of substrate orientation and diameter on hand and foot postural repertoire. We found that hand and foot postures correlate with phylogeny. Also, primates exhibited high repertoire diversity, with a strong capability for postural adjustment compared to the other studied groups. Surprisingly, nails do not confer an advantage in negotiating small substrates unless the animal is large, but the possession of a grasping pollex and hallux is crucial for climbing small vertical substrates. We propose that the divergent hallux and pollex may have resulted from a frequent use of vertical plants in early primate ecological scenarios, although nails may not have resulted from a fundamental adaptation to arboreal locomotion.

Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools.

In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.

Environmental fluctuation impacted the evolution of Early Pleistocene non-human primates: Biomarker and geochemical evidence from Mohui Cave (Bubing, Guangxi, southern China)

Quaternary climate variability, profoundly impacting the evolution and distribution of plants and animals across the globe, has been reconstructed by many sediment archives. Here, we track past changes of temperature, rainfall and plant type by using the n-alkane and glycerol dialkyl glycerol tetraethers (GDGTs), as well as weathering and pedogenesis by mineralogical and geochemical proxies from a 250 cm deep soil sediment profile from the Early Pleistocene deposits in Mohui Cave, southern China. Indices for weathering intensity such as mineral composition (quartz, feldspar and calcite), major element proxies (Ti/Na, Al/Na, Al/Mg, Ti/Mg, CIW, PIA, CPA, CIA), trace element proxies (Ba/Sr and Rb/Sr), and biomarker proxies (OEP, LSR and CPI) show similar secular trends, revealing a three-stage historical accumulation. The high long-chain n-alkane ratios (C31/C29 and (C31+C33)/(C27+C29)) indicate that the vegetation in the region had increases in percentage of woody plants and decreases in herbs during periods of relatively lower temperature and less precipitation, which evidenced from GDGTs, consistent with a weak weathering process influenced by summer monsoon strength. Further, we compared the distribution of these plant types with the taxonomic variation in the vertebrate paleontological fossils excavated from the same profile in Mohui Cave. The distribution of Lufengpithecus appears in only one interval but Gigantopithecus blacki appears throughout the profile, despite an environment that experienced transitional stages from grassland to woodland in relatively cooler and drier conditions. We infer that in face of these climatic changes Lufengpithecus may have preferred to emigrate from the region, while Gigantopithecus blacki may have stayed given that it was limited to staying in its core area.