Primate Family Research Articles

A hybrid genome assembly of the endangered aye-aye (Daubentonia madagascariensis).

The aye-aye (Daubentonia madagascariensis) is the only extant member of the Daubentoniidae primate family. Although several reference genomes exist for this endangered strepsirrhine primate, the predominant usage of short-read sequencing has resulted in limited assembly contiguity and completeness, and no protein-coding gene annotations have yet been released. Here, we present a novel, fully annotated, chromosome-level hybrid de novo assembly for the species based on a combination of Oxford Nanopore Technologies long reads and Illumina short reads and scaffolded using genome-wide chromatin interaction data-a community resource that will improve future conservation efforts as well as primate comparative analyses.

Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites

Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.

Interspecific variation in the diet of Symphalangussyndactylus and Macacanemestrina at Genting Highlands, Pahang, Peninsular Malaysia.

Primate communities in the Genting Highlands consist of a single species of Hylobatidae and four species of Cercopithecidae, which are known to exhibit social interaction behaviour. Thus, a study on the diets of Symphalangussyndactylus (siamang; family Hylobatidae) and Macacanemestrina (pig-tailed macaque; family Cercopithecidae) was carried out at Genting Highlands, in order to compare the dietary preferences and interspecific competition between the two primate families. A DNA metabarcoding approach was used to analyse diet intake using non-invasive samples based on the trnL region. Based on the 140 amplicon sequence variants (ASVs) generated, 26 plant orders, 46 different families, 60 genera and 49 species were identified from 23 different plant classes. Fabaceae and Moraceae were classified as the most preferred plants at the family level for S.syndactylus; meanwhile, Piperaceae and Arecaceae were classified as the most preferred for M.nemestrina. Only six out of the 60 different plant genera classified in this study, were found to be consumed by both species. Therefore, the low similarity of preferred plants in the diets between the two families suggests that there is little interspecific competition. These findings are important for future conservation management of highland primates, especially in the Genting Highlands.

Invited Session III: Diversity in chromatic processing across the animal kingdom: Comparative connectomics reveals noncanonical wiring for color vision in human foveal retina.

The Old World macaque monkey and New World common marmoset provide fundamental models for human visual processing, yet the human ancestral lineage diverged from these monkey lineages over 25 Mya. We therefore asked whether fine-scale synaptic wiring in the nervous system is preserved across these three primate families, despite long periods of independent evolution. We applied connectomic electron microscopy to the specialized foveal retina where circuits for highest acuity and color vision reside. Synaptic motifs arising from the cone photoreceptor type sensitive to short (S) wavelengths and associated with "blue-yellow" (S-ON and S-OFF) color-coding circuitry were reconstructed. We found that distinctive circuitry arises from S cones for each of the three species. The S cones contacted neighboring L and M (long- and middle-wavelength sensitive) cones in humans, but such contacts were rare or absent in macaques and marmosets. We discovered a major S-OFF pathway in the human retina and established its absence in marmosets. Further, the S-ON and S-OFF chromatic pathways make excitatory-type synaptic contacts with L and M cone types in humans, but not in macaques or marmosets. Our results predict that early-stage chromatic signals are distinct in the human retina and imply that solving the human connectome at the nanoscale level of synaptic wiring will be critical for fully understanding the neural basis of human color vision.

A Rab-bit hole: Rab40 GTPases as new regulators of the actin cytoskeleton and cell migration.

The regulation of machinery involved in cell migration is vital to the maintenance of proper organism function. When migration is dysregulated, a variety of phenotypes ranging from developmental disorders to cancer metastasis can occur. One of the primary structures involved in cell migration is the actin cytoskeleton. Actin assembly and disassembly form a variety of dynamic structures which provide the pushing and contractile forces necessary for cells to properly migrate. As such, actin dynamics are tightly regulated. Classically, the Rho family of GTPases are considered the major regulators of the actin cytoskeleton during cell migration. Together, this family establishes polarity in the migrating cell by stimulating the formation of various actin structures in specific cellular locations. However, while the Rho GTPases are acknowledged as the core machinery regulating actin dynamics and cell migration, a variety of other proteins have become established as modulators of actin structures and cell migration. One such group of proteins is the Rab40 family of GTPases, an evolutionarily and functionally unique family of Rabs. Rab40 originated as a single protein in the bilaterians and, through multiple duplication events, expanded to a four-protein family in higher primates. Furthermore, unlike other members of the Rab family, Rab40 proteins contain a C-terminally located suppressor of cytokine signaling (SOCS) box domain. Through the SOCS box, Rab40 proteins interact with Cullin5 to form an E3 ubiquitin ligase complex. As a member of this complex, Rab40 ubiquitinates its effectors, controlling their degradation, localization, and activation. Because substrates of the Rab40/Cullin5 complex can play a role in regulating actin structures and cell migration, the Rab40 family of proteins has recently emerged as unique modulators of cell migration machinery.

Group densities of endangered small apes (Hylobatidae) in two adjacent forest reserves in Merapoh, Pahang, Malaysia

Small ape habitat is rapidly declining due to anthropogenic activities but the current population status of this endangered primate family in Malaysia remains unknown. Group densities of Hylobates lar and Symphalangus syndactylus in two adjacent forest reserves across the Sungai Yu Ecological Corridor (SYEC) in Merapoh, a critical connectivity area of the Central Forest Spine, were assessed. Vegetation assessment and satellite imagery were used to identify habitat characteristics and fixed-point active acoustic triangulation at six listening areas was conducted to estimate small ape group densities. Small ape habitat quality was high in the forested areas of the SYEC. The mean group density of H. lar across these six areas was 3.55 ± 0.9 groups km-² while the mean group density of S. syndactylus was 2.75 ± 1.0 groups km-². The mean group densities of small apes at SYEC were moderately high, compared with densities at other sites in the region, which suggests that the forests here constitute good habitat for both species, despite some observed anthropogenic disturbances. Both species occurred in all listening areas. A nationwide population census for small apes and regular monitoring to inform conservation planning are recommended. Further improvement to connectivity across the SYEC by installing artificial canopy bridges for arboreal animals is important to support the movement of small apes across habitat fragments in Merapoh.

Two waves of evolution in the rodent pregnancy-specific glycoprotein (Psg) gene family lead to structurally diverse PSGs

BackgroundThe evolution of pregnancy-specific glycoprotein (PSG) genes within the CEA gene family of primates correlates with the evolution of hemochorial placentation about 45 Myr ago. Thus, we hypothesized that hemochorial placentation with intimate contact between fetal cells and maternal immune cells favors the evolution and expansion of PSGs. With only a few exceptions, all rodents have hemochorial placentas thus the question arises whether Psgs evolved in all rodent genera.ResultsIn the analysis of 94 rodent species from 4 suborders, we identified Psg genes only in the suborder Myomorpha in three families (characteristic species in brackets), namely Muridae (mouse), Cricetidae (hamster) and Nesomyidae (giant pouched rat). All Psgs are located, as previously described for mouse and rat, in a region of the genome separated from the Cea gene family locus by several megabases, further referred to as the rodent Psg locus. In the suborders Castorimorpha (beaver), Hystricognatha (guinea pig) and Sciuromorpha (squirrel), neither Psg genes nor so called CEA-related cell adhesion molecule (Ceacam) genes were found in the Psg locus. There was even no evidence for the existence of Psgs in any other genomic region. In contrast to the Psg-harboring rodent species, which do not have activating CEACAMs, we were able to identify Ceacam genes encoding activating CEACAMs in all other rodents studied. In the Psg locus, there are genes encoding three structurally distinct CEACAM/PSGs: (i) CEACAMs composed of one N- and one A2-type domain (CEACAM9, CEACAM15), (ii) composed of two N domains (CEACAM11-CEACAM14) and (iii) composed of three to eight N domains and one A2 domain (PSGs). All of them were found to be secreted glycoproteins preferentially expressed by trophoblast cells, thus they should be considered as PSGs.ConclusionIn rodents Psg genes evolved only recently in the suborder Myomorpha shortly upon their most recent common ancestor (MRCA) has coopted the retroviral genes syncytin-A and syncytin-B which enabled the evolution of the three-layered trophoblast. The expansion of Psgs is limited to the Psg locus most likely after a translocation of a CEA-related gene – possibly encoding an ITAM harboring CEACAM. According to the expression pattern two waves of gene amplification occurred, coding for structurally different PSGs.

The potential for zoonotic malaria transmission in five areas of Indonesia inhabited by non-human primates

BackgroundIndonesia is home to many species of non-human primates (NHPs). Deforestation, which is still ongoing in Indonesia, has substantially reduced the habitat of NHPs in the republic. This has led to an intensification of interactions between NHPs and humans, which opens up the possibility of pathogen spillover. The aim of the present study was to determine the prevalence of malarial parasite infections in NHPs in five provinces of Indonesia in 2022. Species of the genus Anopheles that can potentially transmit malarial pathogens to humans were also investigated.MethodsAn epidemiological survey was conducted by capturing NHPs in traps installed in several localities in the five provinces, including in the surroundings of a wildlife sanctuary. Blood samples were drawn aseptically after the NHPs had been anesthetized; the animals were released after examination. Blood smears were prepared on glass slides, and dried blood spot tests on filter paper. Infections with Plasmodium spp. were determined morphologically from the blood smears, which were stained with Giemsa solution, and molecularly through polymerase chain reaction and DNA sequencing using rplU oligonucleotides. The NHPs were identified to species level by using the mitochondrial cytochrome c oxidase subunit I gene and the internal transcribed spacer 2 gene as barcoding DNA markers. Mosquito surveillance included the collection of larvae from breeding sites and that of adults through the human landing catch (HLC) method together with light traps.ResultsAnalysis of the DNA extracted from the dried blood spot tests of the 110 captured NHPs revealed that 50% were positive for Plasmodium, namely Plasmodium cynomolgi, Plasmodium coatneyi, Plasmodium inui, Plasmodium knowlesi and Plasmodium sp. Prevalence determined by microscopic examination of the blood smears was 42%. Species of the primate genus Macaca and family Hylobatidae were identified by molecular analysis. The most common mosquito breeding sites were ditches, puddles and natural ponds. Some of the Anopheles letifer captured through HLC carried sporozoites of malaria parasites that can cause the disease in primates.ConclusionsThe prevalence of malaria in the NHPs was high. Anopheles letifer, a potential vector of zoonotic malaria, was identified following its collection in Central Kalimantan by the HLC method. In sum, the potential for the transmission of zoonotic malaria in several regions of Indonesia is immense.Graphical

Comparative connectomics reveals noncanonical wiring for color vision in human foveal retina

The Old World macaque monkey and New World common marmoset provide fundamental models for human visual processing, yet the human ancestral lineage diverged from these monkey lineages over 25 Mya. We therefore asked whether fine-scale synaptic wiring in the nervous system is preserved across these three primate families, despite long periods of independent evolution. We applied connectomic electron microscopy to the specialized foveal retina where circuits for highest acuity and color vision reside. Synaptic motifs arising from the cone photoreceptor type sensitive to short (S) wavelengths and associated with "blue-yellow" (S-ON and S-OFF) color-coding circuitry were reconstructed. We found that distinctive circuitry arises from S cones for each of the three species. The S cones contacted neighboring L and M (long- and middle-wavelength sensitive) cones in humans, but such contacts were rare or absent in macaques and marmosets. We discovered a major S-OFF pathway in the human retina and established its absence in marmosets. Further, the S-ON and S-OFF chromatic pathways make excitatory-type synaptic contacts with L and M cone types in humans, but not in macaques or marmosets. Our results predict that early-stage chromatic signals are distinct in the human retina and imply that solving the human connectome at the nanoscale level of synaptic wiring will be critical for fully understanding the neural basis of human color vision.

Timing of the luteal-placental shift is delayed with additional fetuses in litter-bearing callitrichid monkeys, Saguinus oedipus and Callithrix jacchus

The luteal-placental shift is an important milestone of mammalian pregnancy signifying when endocrine control of pregnancy shifts from the corpus luteum of the ovary to the placenta. The corpus luteum is maintained by chorionic gonadotropin (CG). Upon sufficient placental maturation, CG production wanes, the corpus luteum involutes, and control is shifted to the placenta, one consequence of which is a midgestational rise in glucocorticoid production, especially cortisol and cortisone, by both mother and fetus. Glucocorticoids are involved in initiating parturition, prenatal programming of offspring phenotype, and maturing fetal organs. Limited evidence from human pregnancy suggests that the timing of this shift is delayed in twin pregnancies, but little is known about the timing of the luteal-placental shift in litter-bearing monkeys from the primate family Callitrichidae. Here we provide evidence from cotton-top tamarins (Saguinus oedipus) and common marmosets (Callithrix jacchus) of longer duration of elevated CG associated with multiple infant births compared to single births. Urinary profiles from cotton-top tamarins demonstrate that the decline of the extended elevation of CG precedes the onset of the midpregnancy sustained rise in glucocorticoids; this shift occurs later with an increase from one to two fetuses carried to term. In the common marmoset, the onset of the sustained rise of glucocorticoids in maternal urine is also delayed with an increase in infant number. Total urinary glucocorticoid levels during the last half of gestation increase monthly but do not differ by infant number. The significant delay in the luteal-placental shift suggests a longer period of placental maturation is needed to support a greater number of fetuses.

Breaking the constraint on the number of cervical vertebrae in mammals: On homeotic transformations in lorises and pottos.

Mammals almost always have seven cervical vertebrae. The strong evolutionary constraint on changes in this number has been broken in sloths and manatees. We have proposed that the extremely low activity and metabolic rates of these species relax the stabilizing selection against changes in the cervical count. Our hypothesis is that strong stabilizing selection in other mammals is largely indirect and due to associated pleiotropic effects, including juvenile cancers. Additional direct selection can occur due to biomechanical problems (thoracic outlet syndrome). Low metabolic and activity rates are thought to diminish these direct and indirect effects. To test this hypothesis within the primates, we have compared the number of cervical vertebrae of three lorisid species with particularly low activity and metabolic rates with those of more active primate species, including with their phylogenetically closest active relatives, the galagids (bushbabies). In support of our hypothesis, we found that 37.6% of the lorisid specimens had an abnormal cervical count, which is a higher percentage than in the other nine primate families, in which the incidence varied from zero to 2.2%. We conclude that our data support the importance of internal selection in constraining evolvability and of a relaxed stabilizing selection for increasing evolvability. Additionally, we discuss that there is no support for a role of the muscularized diaphragm in the evolutionary constraint.

Diet disparity and diversity predict extinction risk in primates

AbstractSpecies vary in their vulnerability to extinction according to their biology, ecology, environmental factors and threats to which they are exposed. Diet is an important ecological trait that affects many aspects of a species' biology, including its vulnerability to extinction. Despite the importance of diet as a species' trait, its influence on extinction risk has only been studied in a coarse way, in part due to a lack of detailed diet data covering a large breadth of species or geographic areas. We examined the association between diet and extinction risk in primates, using a high‐resolution dataset covering all major primate lineages and habitats on a global scale. The resolution of the dataset allowed us to calculate multiple biologically informative metrics for diet composition and diversity, allowing us to tease apart what aspects of diet were most important for predicting the risk of extinction, whilst accounting for phylogeny, body mass and geographic range size. Our results showed that both diet disparity and diet diversity predict primate extinction risk, showing that primates that are able to consume more types of items, and items that are more disparate from one another, are less prone to extinction. Furthermore, we found that although closely related species tend to have similar dietary diversity and disparity, these metrics vary widely amongst primate families. Primates with a high diet diversity and disparity may be able to cope better with fluctuations in food availability than species with homogeneous diet items, through a portfolio effect. Understanding the degree of dietary specialization of the species may help guide new studies relating to extinction risk and threats and be useful in future species assessments.

Skull variation in Afro-Eurasian monkeys results from both adaptive and non-adaptive evolutionary processes

Afro-Eurasian monkeys originated in the Miocene and are the most species-rich modern primate family. Molecular and fossil data have provided considerable insight into their evolutionary divergence, but we know considerably less about the evolutionary processes that underlie these differences. Here, we apply tests developed from quantitative genetics theory to a large (n > 3000) cranio-mandibular morphometric dataset, investigating the relative importance of adaptation (natural selection) and neutral processes (genetic drift) in shaping diversity at different taxonomic levels, an approach applied previously to monkeys of the Americas, apes, hominins, and other vertebrate taxa. Results indicate that natural selection, particularly for differences in size, plays a significant role in diversifying Afro-Eurasian monkeys as a whole. However, drift appears to better explain skull divergence within the subfamily Colobinae, and in particular the African colobine clade, likely due to habitat fragmentation. Small and declining population sizes make it likely that drift will continue in this taxon, with potentially dire implications for genetic diversity and future resilience in the face of environmental change. For the other taxa, many of whom also have decreasing populations and are threatened, understanding adaptive pressures similarly helps identify relative vulnerability and may assist with prioritising scarce conservation resources.

Evolution of host-microbe cell adherence by receptor domain shuffling.

Stable adherence to epithelial surfaces is required for colonization by diverse host-associated microbes. Successful attachment of pathogenic microbes to host cells via adhesin molecules is also the first step in many devastating infections. Despite the primacy of epithelial adherence in establishing host-microbe associations, the evolutionary processes that shape this crucial interface remain enigmatic. Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) encompass a multifunctional family of vertebrate cell surface proteins which are recurrent targets of bacterial adhesins at epithelial barriers. Here, we show that multiple members of the primate CEACAM family exhibit evidence of repeated natural selection at protein surfaces targeted by bacteria, consistent with pathogen-driven evolution. Divergence of CEACAM proteins between even closely related great apes is sufficient to control molecular interactions with a range of bacterial adhesins. Phylogenetic analyses further reveal that repeated gene conversion of CEACAM extracellular domains during primate divergence plays a key role in limiting bacterial adhesin host tropism. Moreover, we demonstrate that gene conversion has continued to shape CEACAM diversity within human populations, with abundant human CEACAM1 variants mediating evasion of adhesins from pathogenic Neisseria. Together this work reveals a mechanism by which gene conversion shapes first contact between microbes and animal hosts.

Attack of an infant by a female in a troop of howler monkeys (<i>Alouatta pigra</i>)


 
 
 Within the New World primate family of Atelidae, infanticidal attacks are most commonly reported in howler monkeys (Alouatta spp., Crockett, 2003; Knopff et al., 2004; Aguiar et al., 2005; Agoramoorthy and Rudran, 2009; Van Belle et al., 2010; Pavé et al., 2012). The howler monkey species that have been observed to exhibit this behaviour are black and gold howler monkeys (Alouatta caraya, Crockett, 2003; Pavé et al., 2012); Colombian red howler monkeys (A. seniculus, Agoramoorthy and Rudran, 1995; Beltrán and Stevenson, 2012); mantled howler monkeys (A. palliata, Crockett, 2003); brown howler monkeys (Martins et al., 2015); and Yucatán black howler monkeys (A. pigra, Crockett, 2003; Van Belle et al., 2010). In these documented attacks there is a lack of detail regarding the involvement of females, as the male is usually identified as the aggressor. These attacks are likely to occur following the immigration of a new male to a troop (Van Belle et al., 2010; Beltrán and Stevenson, 2012), up to five months after taking over a troop (Agoramoorthy and Rudran, 2009). A majority of infanticidal attacks in howler monkeys involve assumed unrelated assailant and victim, therefore these instances align with the sexual selection hypothesis (Hrdy, 1979).
 
 

Frequency of enteroparasites in Cebidae and Callitrichidae primates at the Zoológico de Cali, Colombia: zoonotic implications

ResumenIntroducción. Los enteroparásitos pueden generar problemas en animales bajo cuidado humano en zoológicos y centros de acogida. Los animales silvestres presentan bajas cargas parasitarias, pero estas pueden ser mayores y llevar a manifestaciones clínicas cuando se trata de animales resguardados en recintos, lo que aumenta los gastos en tratamientos y cuidados médicos. Por otro lado, algunos enteroparásitos pueden causar infecciones zoonóticas en los cuidadores, los visitantes y otros animales del zoológico, así como afectar los programas de recuperación de especies amenazadas de extinción. Objetivos. Determinar la presencia y prevalencia de enteroparásitos con potencial de transmisión zoonótica en primates de las familias Cebidae y Callitrichidae del Zoológico de Cali, entre septiembre y noviembre de 2017.Materiales y métodos. Se hizo un estudio transversal prospectivo, para lo cual se recolectaron muestras seriadas de 50 individuos pertenecientes a siete especies de dos familias de primates y se analizaron mediante examen coprológico, flotación y coloración Kinyoun, entre septiembre y noviembre de 2017.Resultados. Según su prevalencia, los géneros de parásitos hallados en las siete especies de primates evaluadas, fueron Blastocystis spp., Trichomonas spp., Giardia spp., Entamoeba spp., Strongyloides spp., Cyclospora sp. y Trichuris sp. Conclusiones. Por lo menos, seis de los géneros de parásitos identificados tienen implicaciones zoonóticas, lo cual hace necesario establecer las posibles vías de infección de los primates del Zoológico de Cali e implementar protocolos de manejo que reduzcan el riesgo de transmisión a los humanos y a otros animales de la colección. Además, se presenta la información relevante sobre el potencial zoonótico de los enteroparásitos hallados.

Myological variation in the forearm anatomy of Callitrichidae and Lemuridae.

The anatomy of the primate forearm is frequently investigated in terms of locomotor mode, substrate use, and manual dexterity. Such studies typically rely upon broad, interspecific samples for which one or two representative taxa are used to characterize the anatomy of their genus or family. To interpret variation between distantly related taxa, however, it is necessary to contextualize these differences by quantifying variation at lower hierarchical levels, that is, more fine-grained representation within specific genera or families. In this study, we present a focused evaluation of the variation in muscle organization, integration, and architecture within two speciose primate families: the Callitrichidae and Lemuridae. We demonstrate that, within each lineage, several muscle functional groups exhibit substantial variation in muscle organization. Most notably, the digital extensors appear highly variable (particularly among callitrichids), with many unique configurations represented. In terms of architectural variables, both families are more conservative, with the exception of the genus Callimico-for which an increase is observed in forearm muscle mass and strength. We suggest this reflects the increased use of vertical climbing and trunk-to-trunk leaping within this genus relative to the more typically fine-branch substrate use of the other callitrichids. Overall, these data emphasize the underappreciated variation in forearm myology and suggest that overly generalized typification of a taxon's anatomy may conceal significant intraspecific and intrageneric variation therein. Thus, considerations of adaptation within the forearm musculature should endeavor to consider the full range of anatomical variation when making comparisons between multiple taxa within an evolutionary context.

Examining the molecular basis of coat color in a nocturnal primate family (Lorisidae).

Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage.

Working out the bipedal walking expenditure of energy based on foot morphology of different hominid genera: Implications for foot evolution

Among the Hominidae family of primates, Homo is characterized by more economical bipedal walking. Over the course of evolution towards bipedalism, the foot becomes the only organ directly interacting with substrate and likely influence the bipedal walking economy. However, working out the energy expenditure in bipedal walking from the specific aspect of foot morphology is still challenging, which hinders the understanding of the evolution of both hominid feet and economical bipedal walking. Here we present a functional model to quantitatively assess bipedal walking expenditure of energy from hominid foot morphology. According to our results, the feet of Homo are most suited to economical bipedal walking among hominids. However, the genus whose feet possess second best ability for economical bipedal walking is not our closest relative Pan, but is Gorilla. Using phylogenetically informed morphometric analyses, we further infer the evolutionary changes of hominid foot morphology and investigate the corresponding variation of bipedal walking expenditure. Our results reveal the economical bipedal walking benefits from the morphological changes of human foot after descending from the last common ancestor of hominids. Conversely, the foot morphologies of great apes reflect selections for other locomotor modes, at cost of larger energy expenditure in bipedal walking.

Diversification of CD1 Molecules Shapes Lipid Antigen Selectivity.

Molecular studies of host–pathogen evolution have largely focused on the consequences of variation at protein–protein interaction surfaces. The potential for other microbe-associated macromolecules to promote arms race dynamics with host factors remains unclear. The cluster of differentiation 1 (CD1) family of vertebrate cell surface receptors plays a crucial role in adaptive immunity through binding and presentation of lipid antigens to T-cells. Although CD1 proteins present a variety of endogenous and microbial lipids to various T-cell types, they are less diverse within vertebrate populations than the related major histocompatibility complex (MHC) molecules. We discovered that CD1 genes exhibit a high level of divergence between simian primate species, altering predicted lipid-binding properties and T-cell receptor interactions. These findings suggest that lipid–protein conflicts have shaped CD1 genetic variation during primate evolution. Consistent with this hypothesis, multiple primate CD1 family proteins exhibit signatures of repeated positive selection at surfaces impacting antigen presentation, binding pocket morphology, and T-cell receptor accessibility. Using a molecular modeling approach, we observe that interspecies variation as well as single mutations at rapidly-evolving sites in CD1a drastically alter predicted lipid binding and structural features of the T-cell recognition surface. We further show that alterations in both endogenous and microbial lipid-binding affinities influence the ability of CD1a to undergo antigen swapping required for T-cell activation. Together these findings establish lipid–protein interactions as a critical force of host–pathogen conflict and inform potential strategies for lipid-based vaccine development.