The phylogenetic relationship and demographic history of rhesus macaques (Macaca mulatta) in subtropical and temperate regions, China.

Pleistocene climatic oscillations exerted significant influences on the genetic structure and demography of rhesus macaque (Macaca mulatta) in eastern China. However, the evolutionary history of rhesus macaques in subtropical and temperate China remained unclear and/or controversial. Herein, we analyzed the autosomes, mitochondrial genomes, and Y-chromosomes from 84 individuals of Chinese rhesus macaque. The results revealed that (1) all individuals were clustered into pan-west and pan-east genetic groups, which exhibited Shaanxi Province as the northernmost region of western dispersal route of rhesus macaques in China; (2) in subtropical and temperate China, rhesus macaques were divided into four lineages (TH, DB, HS, and QL), and their divergence times corresponded to the Penultimate Glaciation (300-130 kya) and Last Glaciation (70-10 kya), respectively; (3) the individuals from Mt. Taihangshan (TH) are closely related to individuals from Mt. Dabashan (DB) in the autosomal tree, rather than individuals from Mt. Huangshan (HS) as indicated by the mitogenome tree, which supports the hypothesis that the ancestral rhesus macaques radiated into Mt. Taihangshan from Mt. Huangshan via Mt. Dabashan; and (4) the demographic scenario of the four lineages showed the ancestral rhesus macaques bottleneck and expansion corresponding to the suitable habitat reduction and expansion, which confirmed they had experienced northward recolonization and southward retreat events from Mt. Huangshan area via Northern China Plain to Northernmost China along with Pleistocene glacial cycles. This study provides a new insight into understanding how Pleistocene glaciation has influenced faunal diversity in subtropical and temperate China, especially for those exhibiting differential patterns of sex dispersal.

DNA metabarcoding reveals the seasonal variation of dietary composition of Taihangshan macaque (Macaca mulatta tcheliensis), Jiyuan, north China.

Dietary analysis in wildlife is fundamental for understanding their flexible response to seasonal changes and developing effective conservation management measures. Taihangshan macaque (Macaca mulatta tcheliensis) is the northernmost population of rhesus macaque, currently only distributed in the southern Mt. Taihangshan area. This area belongs to a semi-arid region resulting in limited plant food availability for Taihangshan macaques, with seasonal variation. Herein, we used a chloroplast trnL DNA metabarcoding approach to identify the plant diet diversity and composition from 100 fecal samples of Taihangshan macaque in four seasons (spring, summer, autumn, and winter) from 2020 to 2021. The results revealed that (1) a total of 48 distinct families, 88 genera, and 52 species within the 105 food items that were consumed by Taihangshan macaques throughout the year; (2) the diversity of food items exhibited significant differences across the four seasons; (3) Rosaceae, Rhamnaceae, Fagaceae, and Poaceae are the preferential food items for Taihangshan macaques and have different relative abundances, fluctuating with seasonal variation. DNA metabarcoding can expand our understanding of the repertoire of food items consumed by Taihangshan macaques by detecting some consumed food items in this population that were not yet discovered using traditional methods. Therefore, the integrative results from traditional methods and DNA metabarcoding can provide a fundamental understanding of dietary composition to guide the conservation management of Taihangshan macaques.

Phylogeography and demographic history of macaques, fascicularis species group, in East Asia: Inferred from multiple genomic markers.

Climate changes at larger scales have influenced dispersal and range shifts of many taxa in East Asia. The fascicularis species group of macaques is composed of four species and is widely distributed in Southeast and East Asia. However, its phylogeography and demographic histories are currently poorly understood. Herein, we assembled autosomal, mitogenome, and Y-chromosome data for 106 individuals, and combined them with 174 mtDNA dloop haplotypes of this species group, with particular focus on the demographic histories and dispersal routes of Macaca fuscata, M. cyclopis, and M. mulatta. The results showed: (1) three monophyletic clades for M. fuscata, M. cyclopis, and M. mulatta based on the multiple genomics analyses; (2) the disparate demographic trajectories of the three species after their split ∼1.0 Ma revealed that M. cyclopis and M. fuscata were derived from an ancestral M. mulatta population; (3) the speciation time of M. cyclopis was later than that of M. fuscata, and their divergence time occurred at the beginning of "Ryukyu Coral Sea Stage" (1.0-0.2 Ma) when the East China Sea land bridge was completely submerged by the sea level rose; and (4) the three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) of Southwestern China divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. These results shed light on understanding not only the evolutionary history of the fascicularis species group but also the formation mechanism of faunal diversity in East Asia during the Pleistocene.

Chromosome-level genome provides insight into the evolution and conservation of the threatened goral (Naemorhedus goral).

BACKGROUND: Gorals Naemorhedus resemble both goats and antelopes, which prompts much debate about the intragenus species delimitation and phylogenetic status of the genus Naemorhedus within the subfamily Caprinae. Their evolution is believed to be linked to the uplift of the Qinghai-Tibet Plateau (QTP). To better understand its phylogenetics, the genetic information is worth being resolved. RESULTS: Based on a sample from the eastern margin of QTP, we constructed the first reference genome for Himalayan goral Naemorhedus goral, using PacBio long-read sequencing and Hi-C technology. The 2.59 Gb assembled genome had a contig N50 of 3.70 Mb and scaffold N50 of 106.66 Mb, which anchored onto 28 pseudo chromosomes. A total of 20,145 protein-coding genes were predicted in the assembled genome, of which 99.93% were functionally annotated. Phylogenetically, the goral was closely related to muskox on the mitochondrial genome level and nested into the takin-muskox clade on the genome tree, rather than other so-called goat-antelopes. The cladogenetic event among muskox, takin and goral occurred sequentially during the late Miocene (~ 11 - 5 Mya), when the QTP experienced a third dramatic uplift with consequent profound changes in climate and environment. Several chromosome fusions and translocations were observed between goral and takin/muskox. The expanded gene families in the goral genome were mainly related to the metabolism of drugs and diseases, so as the positive selected genes. The Ne of goral continued to decrease since ~ 1 Mya during the Pleistocene with active glaciations. CONCLUSION: The high-quality goral genome provides insights into the evolution and valuable information for the conservation of this threatened group.

Toxicity of leachate from smoked cigarette butts to terrestrial animals: A case study on the earthworm Eisenia fetida.

Cigarette butts, as easily overlooked littered wastes, have been evaluated for toxicity in various researches. In this study, we investigated the toxic effects of smoked cigarette butt leachate (SCBL) on the earthworm Eisenia fetida. The results showed the following: 1) E. fetida avoided SCBL in artificial soil, and the avoidance rate was positively correlated with the concentration of SCBL but negatively correlated with the exposure time; 2) the LD50 of SCBL on earthworms at 36 and 48 h of exposure were 3.71 × 10-4 and 2.67 × 10-4 butts/cm2, respectively. Moreover, both the body surface and intestinal tissues of E. fetida were damaged after exposure to SCBL; 3) the survival rates of E. fetida exposed to artificial soil with an SCBL of 3.6 butts/kg for 7 and 14 days were 80.00 ± 7.07 % and 68.00 ± 4.47 %, respectively; and 4) the mean biomass of the surviving E. fetida in all treated groups decreased with increasing SCBL concentration and exposure time. We concluded that SCBL exerted significant negative effects on soil animals, and suggested that SCBs should be collected, detoxified, and reused before entering the natural environment.

Genetic structure and recent population demographic history of Taihangshan macaque (Macaca mulatta tcheliensis), North China.

Massive actions have been and are being taken into protecting the world's primates from extinction, while the study of the properties of genetic diversity, demographic history, and ecological relationships will benefit the understanding of the long-term survival of a species. The Taihangshan macaque (Macaca mulatta tcheliensis), a subspecies of rhesus macaque (Macaca mulatta), is endemic to China and currently restricted to southern Mt. Taihangshan area. Herein, we evaluated the genetic diversity, population structure, and demographic history of this subspecies using mitochondrial (Cytb and high variable region I: HVR I) and nuclear markers (microsatellite loci) of 131 individuals collected from 9 localities covering the distribution range of this subspecies. Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades, THS-east and THS-west. Low genetic diversity (π: 0.00266 ± 0.00016) but high haplotype diversity (Hd : 0.80352 ± 0.015) were detected in the Taihangshan macaques, particularly in THS-east. Analyses of demographic history suggested that the Taihangshan macaques experienced first a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years. We suggest that bridging the neighbor populations (i.e. setting corridors) would facilitate the male-mediated gene flow and subsequently increase the genetic diversity of the Taihangshan macaque populations.

Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice.

BACKGROUND: The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domestication remains unknown due to lack of adequate genomic sequences of wild mice. RESULTS: We analyze the genetic relationships by whole-genome resequencing of 36 wild mice and 36 inbred strains. All classical inbred mice cluster together distinctly from wild and wild-derived inbred mice. Using nucleotide diversity analysis, Fst, and XP-CLR, we identify 339 positively selected genes that are closely associated with nervous system function. Approximately one third of these positively selected genes are highly expressed in brain tissues, and genetic mouse models of 125 genes in the positively selected genes exhibit abnormal behavioral or nervous system phenotypes. These positively selected genes show a higher ratio of differential expression between wild and classical inbred mice compared with all genes, especially in the hippocampus and frontal lobe. Using a mutant mouse model, we find that the SNP rs27900929 (T>C) in gene Astn2 significantly reduces the tameness of mice and modifies the ratio of the two Astn2 (a/b) isoforms. CONCLUSION: Our study indicates that classical inbred mice experienced high selection pressure during domestication under laboratory conditions. The analysis shows the positively selected genes are closely associated with behavior and the nervous system in mice. Tameness may be related to the Astn2 mutation and regulated by the ratio of the two Astn2 (a/b) isoforms.

Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items.

Food supply is one of the major drivers of animal behavior, and the gut microbiome is an important mediator between food supply and its effects on physiology. However, predicting the outcome of diet change on microbiome and consequences for the animal has proven extremely challenging. We propose this reflects processes occurring at different scales. Inadequate accounting for the multi-level complexity of nutrition (nutrients, foods, diets) obscures the diet influence on microbiome and subsequently animal. Here, we present a detailed year-round, multi-level analysis of diet and microbiome changes in a wild population of a temperate primate, the rhesus macaque (Macaca mulatta). Total daily food and nutrient intake of 6 male and 6 female macaques was monitored in each of the 4 seasons (total 120 days observations). For each individual, we found significant variation in the microbiome between all 4 seasons. This response was more strongly correlated with changes in macronutrient intake than with food items and much of the response could be explained at the level of 6 ecological guilds-sets of taxa sharing similar responses to nutrient intake. We conclude that study of diet, microbiome, and animal performance in ecology will more effectively identify patterns if diet is recorded at the level of nutrient intake. Although microbiome response to diet does show variation in species-level taxa in response to food items, there is greater commonality in response at the level of guilds. A goal for microbiome researchers should be to identify genes encoding microbial attributes that can define such guilds.

Ultramorphological Comparison of Proboscis and Associated Sensilla of Scotogramma trifolii and Protoschinia scutosa (Lepidoptera: Noctuidae).

The proboscis is an important feeding organ for the glossatan moths, mainly adapted to the flower and non-flower visiting habits. The clover cutworm, Scotogramma trifolii Rottemberg, and the spotted clover moth, Protoschinia scutosa (Denis & Schiffermuller), are serious polyphagous pests, attacking numerous vegetables and crops, resulting in huge economic losses. However, the feeding behavior and mechanisms of the adult stage remain unsatisfactorily explored. In this study, the proboscis morphology of S. trifolii and P. scutosa are described in detail using scanning electron microscopy, with the aim of investigating the morphological differences and feeding behavior of these two species. The proboscises of S. trifolii and P. scutosa are similar in morphology and structure and are divided into three zones (Zone 1-3) based on the morphological changes of the dorsal legulae. Three sensillum types are located on the proboscises of both species, sensilla chaetica, sensilla basiconica, and sensilla styloconica. Significant differences were observed in the length of the proboscis and each zone between these two species, as well as in sensilla size and number. Based on the morphology of the proboscis and associated sensilla, S. trifolii and P. scutosa are potential flower visitors, which was also reinforced by the pollen observed at the proboscis tip. These results will strengthen our understanding of the structure of the proboscis related to the feeding behavior of Noctuidae.

Spondyloarthritis in Taihangshan Macaques (Macaca mulatta tcheliensis).

The rhesus macaque (Macaca mulatta) is the most widely distributed nonhuman primate species, and captive populations play an important role in biomedical research due to close phylogenetic and physiological similarity to human beings. However, to our best knowledge, the spondyloarthritis (SpA) in rhesus macaques has been exclusively reported in captive or semicaptive populations rather than wild counterparts. In the present study, we report 2 cases of SpA observed in Taihangshan macaques (Macaca mulatta tcheliensis) inhabiting the Taihangshan Macaque National Nature Reserve, Henan Province, China. Among these 2 cases, one can be diagnosed as ankylosing spondylitis (AS) following accepted medical criteria, and another case showed evident fusion at the pubic symphysis which could be specific to rhesus macaque AS. We discuss the potential causes leading directly or indirectly to the development of SpA.

Sensilla of the antenna and proboscis of Athetis lepigone (Möschler) (Lepidoptera: Noctuidae).

Sensory structures on the antennae and mouthparts of insects are associated with various activities, such as host location, feeding, attracting a mate, and identifying a suitable oviposition site. Athetis lepigone (Möschler) is an important polyphagous Eurasian pest with more than 30 species of host plants. The larvae target bud leaves, prop roots, and tender stems of many agricultural crops, but the feeding habits of the adults remain poorly known. Aiming to understand the feeding behavior of the species, we investigated the fine morphology of its antennae and proboscis using scanning electron microscopy. The antennae of both sexes are filiform, and bear eight types of sensilla: Böhm's bristles, sensilla squamiformia, trichodea, chaetica, basiconica, coeloconica, styloconica, and auricillica. Sensilla trichodea are the most abundant among these sensillum types. The proboscis consists of two elongated, interlocked maxillary galeae that enclose the food canal by dorsal and ventral legulae. The external galeal surface is covered with numerous triangular microtrichia on Zone 1 and abundant blunt microbumps on Zone 2. The surface of the food canal bears closely connected and smooth semicircular ridges, gradually tapering toward the proboscis tip. Three types of sensilla are noticeable on the proboscis: sensilla trichodea, basiconica, and styloconica. We briefly discuss the putative functional significance of the antennal and proboscis sensilla and, based on the specific structural modifications of the proboscis, predict a flower-visiting habit for A. lepigone.

Multivariate similarity clustering analysis: a new method regarding biogeography and its application in global insects.

A new method, multivariate similarity clustering analysis (MSCA) method, was established for biogeographical distribution analyzing. General similarity formula (GSF), the core of MSCA method, can be used to calculate the similarity coefficients between 2 and among any ≥ 3 geographical units. Taking the global insects as example, we introduced the steps to use of GSF and consequent clustering processes of this method in details. Firstly, geographical distributions of certain taxa (e.g. Insecta) were categorized into basic geographical units (BGUs); Secondly, similarity coefficients between 2 and among n BGUs were calculated using GSF. Thirdly, hierarchical clustering was conducted according to values of similarity coefficients (from high to low); then a clustering diagram was generated. Finally, a framework of biogeographical division map was established for the target taxa (e.g. Insecta). We concluded that the MSCA method was efficiently applied in analyzing the biogeographical distribution of given biological taxa; the geographical regions regarding global insects were categorized into 7 Realms with 20 sub-Realms based on the results of MSCA method.

Neonatal nipple preference and maternal cradling laterality in wild Taihangshan macaques (Macaca mulatta tcheliensis).

Lateralized behavior is considered an observable phenotype of cerebral functional asymmetry and has been documented in many mammalian species. In the present study, we examined evidence of lateralization in neonatal nipple contact, maternal cradling, and the relationship between these two behaviors during the first 12 weeks of life in wild Taihangshan macaques (Macaca mulatta tcheliensis). The results showed that across our sample of nine mother-infant dyads: (1) Seven of nine neonates exhibited a significant left-side nipple preference during the first 12 weeks of life, whereas eight of nine mothers displayed a significant right-side cradling preference; (2) at the population level, there was a significant preference for left nipple contact by neonatal Taihangshan macaques and a significant right-hand maternal cradling preference; (3) at the population level, there was a nonsignificant negative correlation between neonatal nipple preference and maternal cradling bias; and (4) the strength of individual neonatal nipple preference and maternal cradling laterality were not correlated. We conclude that asymmetry in nipple contact of Taihangshan macaques occurs early in behavioral development. Given that infant Taihangshan macaques are able to nurse and cling unassisted to their mothers within a few days after birth, it appears that the infant rather than its mother is responsible for determining a nipple-side preference. Our results indicating a left-side nipple bias in 78% of wild neonatal Taihangshan macaques are most consistent with the heartbeat hypothesis.

Living near the limits: Effects of interannual variation in food availability on diet and reproduction in a temperate primate, the Taihangshan macaque (Macaca mulatta tcheliensis).

Nutrient intake of animals is influenced by an interplay of external and internal factors, such as food availability and reproductive state, respectively. We used the nutritional geometry framework to analyze individual-based data on energy and nutrient intake in relation to reproductive state in a population of rhesus macaques (Macaca mulatta tcheliensis), which live in a harsh high-latitude habitat, the Taihangshan mountains of China, and exhibit strong reproductive seasonality. We combined data over a 3-year period on food availability, diets, reproductive output, and components of maternal investment to understand how Taihangshan macaques respond to variation in food availability and nutrition in reproduction. Our results show there was high interannual variation in availability of an important staple source of fat and carbohydrates (nonprotein energy), seeds of oak (Quercus spp). Despite this variability in seed availability skewing the dietary macronutrient ratios considerably (from 12.96% to 30.12% dietary energy from protein), total metabolizable energy intake was maintained across years during pregnancy. Lactating females had higher mean daily energy intakes than pregnant females. As in pregnant females, energy intake was maintained constant across years, but only when seed availability enabled the contribution of available protein to energy intake to be maintained between 15.32% (2013) and 17.97% (2015). In 2014, when seeds were scarce, lactating females had a shortfall in energy intake compared with 2013 and 2015. This corresponded with a reduction in the number of females giving birth (11 out of 23), but there was no interannual difference in survival rates. Compared to 2013 and 2015, in 2014 females had greater weight loss (drew on body reserves), moved less, and spent more time nursing their offspring. We discuss implications of these results for range limitation in Taihangshan macaques.

Occurrence of Selected Zoonotic Fecal Pathogens and First Molecular Identification of Hafnia paralvei in Wild Taihangshan Macaques (Macaca mulatta tcheliensis) in China.

Rhesus macaques (Macaca mulatta) are hosts to a range of zoonotic and potentially zoonotic pathogens. The present study firstly provides a broader investigation of the presence and prevalence of zoonotic fecal pathogens in wild Taihangshan macaques, a subspecies of rhesus macaque in China. A total of 458 fecal samples were collected between September 2015 and November 2016. Fourteen genera of intestinal parasites (four genera of protozoans and ten genera of helminths) and twelve genera of bacteria were tested for using PCR amplification. The overall samples prevalence of parasitic infection was 98.25%. Entamoeba spp. (89.96%), Balantidium coli (70.09%), and Isospora spp. (28.38%) were the most prevalent protozoa, whereas the predominant prevalent helminths were Trichuris sp. (93.23%), Strongyloides spp. (73.36%), and Oesophagostomum sp. (31.66%). Ten genera of intestinal bacteria were detected in samples of rhesus macaques, including Shigella (31.66%), Escherichia coli (29.91%), Klebsiella pneumoniae (28.38%), Leptospira (26.64%), Campylobacter jejuni (18.34%), Salmonella (13.32%), etc. Eight samples (1.75%) were tested Hafnia-positive based on sequences analysis of 16S rRNA and ampC gene. This is the first molecular characterization of Hafnia infection in NHPs. Our cross-sectional prevalence study provides important information for monitoring the potential transmission of zoonotic infections from wild rhesus macaques.

Dietary diversity of an ecological and macronutritional generalist primate in a harsh high-latitude habitat, the Taihangshan macaque (Macaca mulatta tcheliensis).

Recent advances in niche theory have stressed the importance of understanding dietary generalism at multiple levels, including the range of habitat and foods exploited by a species, foods exploited within populations, and patterns of nutrient intake. Here we apply this framework to examine the dietary strategy of the Macaca mulatta, a primate species that is second only to humans in their breadth of geographical distribution, and occupy diverse ecological habitats from cold temperate to tropical latitudes. A recent study showed that the Taihangshan subspecies ( M. mulatta tcheliensis) in China, which is found at the northern latitudinal limit of the species range, respond to ecologically constrained interannual variation in the macronutrient ratios of the spring diet in a way that theory predicts should be associated with ecological generalism. Here we further extend this study, examining the relationships between seasonal variation in food availability and the patterns of food selection across a full year. We found that, despite the ecological and macronutritional generalism of the species, Taihangshan macaques subsist on a relatively small range of foods (57 different foods, spread across 8 categories comprising seeds, fruits, buds, flowers, leaves, herbs, young bark, and twigs), but face considerable seasonal variation in the combinations available. In spring and summer, when seeds were scarce, leaves accounted for 60.3 ± 13.8% of their diet (dry matter [DM] %), and herbs contributed 31.7 ± 22.2%. However, in autumn and winter, when seeds were abundant, they contributed 68.5 ± 22.7% of the diet while herbs accounted for 18.9 ± 12.9% on a DM. Although young bark and twigs were available in all seasons, the macaques only fed on them in winter. We present comparative data from the literature on the diets of M. mulatta and other Macaca species, to interpret this pattern of resource use within the framework of multilevel niche theory.

Molecular Characterization of Entamoeba spp. in Wild Taihangshan Macaques (Macaca mulatta tcheliensis) in China.

BACKGROUND: Entamoeba spp. is one of the most common enteric parasites of humans and animals. PURPOSE: However, little information is available regarding prevalence and genotypes of Entamoeba spp. in wild Taihangshan macaques (Macaca mulatta tcheliensis). METHODS: In the present study, a total of 458 fecal samples from wild rhesus macaque in Taihangshan mountains area between September 2015 and November 2016, were collected and examined for the presence of six Entamoeba species by PCR amplification of the SSU rRNA gene. RESULTS: The overall prevalence of Entamoeba spp. infection was 89.96% (412/458). Four species of Entamoeba detected in our survey were E. chattoni (88.43%), E. hartmanni (79.91%), E. coil (69.87%) and E. dispar (58.30%), and among these, 398 (84.93%) were mixed infections. Phylogenetic analysis revealed that isolates were clustered into four known genotypes. CONCLUSION: The present study firstly provides important information about the prevalence and diversity of Entamoeba species infecting wild Taihangshan macaques in China. Enough attention should be paid to monitor the potential interspecies transmission in the region.