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Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution., (© 2023. Science China Press.)

Effects of climate warming on trophic cascades are increasingly reported for large herbivores occupying northern latitudes. During the last 40 years, moose (Alces alces) in northeast China have lost nearly half of their historical distribution through their habitat shifting northwards. There are many possible causes of bottom-up and top-down effects of temperature and for moose in northeast China they are poorly understood. Of particular relevance are the effects of extrinsic environmental factors on gene flow, nutritional adaptions, and gut microbiota that occur as moose populations retreat northwards. We combined molecular biology, nutritional ecology and metagenomics to gain deeper mechanistic insights into the effects of temperature on moose populations. In this study, we revealed that the direction and intensity of gene flow is consistent with global warming driving retreats of moose populations. We interpret this as evidence for the northward movement of moose populations, with cooler northern populations receiving more immigrants and warmer southern populations supplying emigrants. Comparison across latitudes showed that warmer late spring temperatures were associated with plant community composition and facilitated related changes in moose protein and carbohydrate intake through altering forage availability, forage quality and diet composition. Furthermore, these nutrient shifts were accompanied by changes in gut microbial composition and functional pathways related to nutrient metabolism. This study provided insights into mechanisms driving effects of spatial heterogeneous warming on genetic, nutritional and physiological adaptions related to key demographic rates and patterns of survival of heat-sensitive ungulates along a latitude gradient. Understanding such changes helps to identify key habitat areas and plant species to ensure accurate assessment of population status and targeted management of moose populations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Background: Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and alpaca., Results: Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the alpaca from the vicuña. Introgression was much higher in the alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α., Conclusions: The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.

Flea beetles (Coleoptera, Chrysomelidae, Galerucinae, Alticini) are a hyperdiverse group of organisms with approximately 9900 species worldwide. In addition to walking as most insects do, nearly all the species of flea beetles have an ability to jump and this ability is commonly understood as one of the key adaptations responsible for its diversity. Our investigation of flea beetle jumping is based on high-speed filming, micro-CT scans and 3D reconstructions, and provides a mechanical description of the jump. We reveal that the flea beetle jumping mechanism is a catapult in nature and is enabled by a small structure in the hind femur called an 'elastic plate' which powers the explosive jump and protects other structures from potential injury. The explosive catapult jump of flea beetles involves a unique 'high-efficiency mechanism' and 'positive feedback mechanism'. As this catapult mechanism could inspire the design of bionic jumping limbs, we provide a preliminary design for a robotic jumping leg, which could be a resource for the bionics industry.

The distribution area of moose in China has been shrinking back toward the north and northeast because of climate change and human disturbance, and the population number has been declining. Between 2011 and 2015, we studied moose at six sites in the northeast of China during the snowy seasons. We collected fecal samples and plant samples that were used to estimate population densities for moose, as well as their macro-nutrient selection. Out of a total of 257 fecal samples collected at six sites, we identified a total of 120 individual moose (57 females and 63 males). The population density (moose/km 2 ± SE) was highest at Hanma with 0.305 ± 0.064 moose/km 2 and lowest at Meitian with only 0.028 ± 0.013 moose/km 2 . Forage availability was different among sites, with the lowest availability at Mohe (58.17 number/20 m 2 ) and highest was Zhanhe (250.44 number/20 m 2 ). Moose at Zhanhe, Hanma, and Nanwenghe had a balanced diet with higher N:C (1:7), while at Meitian, Shuanghe and Mohe the N:C was 1:8. Our results indicate that the southern areas had low forage quality and quantity and this may be the reason for the distribution of the population of moose shrinking northward.

Surveying the activity rhythms of sympatric herbivorous mammals is essential for understanding their niche ecology, especially for how they partition resources and their mechanisms of coexistence. Over a five-year period, we conducted infrared camera-trapping to monitor the activity rhythms of coexisting red serow ( Capricornis ) and Chinese serow ( rubidus ) in the remote mountainous region of Pianma, Mt. Gaoligong, Yunnan, China. Cameras captured images of red serow and Chinese serow on 157 and 179 occasions, respectively. We used circular kernel density models to analyze daily activity rhythms and how temporal variations in activity ensure their co-existence. Although their overall activity levels and patterns were similar, temporal activity and behavior partitioning among the two species occurred during the wet season. Compared with Chinese serows, red serows exhibited less variable daily activity levels, patterns, as well as feeding and vigilance behaviors between seasons. When the two species occasionally ranged together, red serows tended to alter their activity pattern while Chinese serows significantly increased their activity level. Red serow and Chinese serow are exploitative competitors but coexist by altering their daily activity rhythms when in contact and changing activity patterns during the wet season, enabling their coexistence.C. milneedwardsii milneedwardsii ) in the remote mountainous region of Pianma, Mt. Gaoligong, Yunnan, China. Cameras captured images of red serow and Chinese serow on 157 and 179 occasions, respectively. We used circular kernel density models to analyze daily activity rhythms and how temporal variations in activity ensure their co-existence. Although their overall activity levels and patterns were similar, temporal activity and behavior partitioning among the two species occurred during the wet season. Compared with Chinese serows, red serows exhibited less variable daily activity levels, patterns, as well as feeding and vigilance behaviors between seasons. When the two species occasionally ranged together, red serows tended to alter their activity pattern while Chinese serows significantly increased their activity level. Red serow and Chinese serow are exploitative competitors but coexist by altering their daily activity rhythms when in contact and changing activity patterns during the wet season, enabling their coexistence., Competing Interests: The authors declare no conflict of interest.

The existence of cooperation is problematic for those who view the world through an evolutionary lens. Although natural selection disfavors unconditional cooperation, cooperators who can distinguish cooperators from defectors and discontinue their interactions with the latter can be favored. Economic experiments have indicated that human beings indeed adopt such strategies when they detect defectors. Experiments have also shown that human beings also use those strategies in interactions involving more than two individuals as both cooperators and defectors may be present among opponent players. In such cases, it is not obvious whether it is better to continue or stop the interaction. In this study, I analyzed three-player prisoner's dilemma games. My findings algebraically reveal that both tolerant cooperators, who want to continue interacting with their current partners comprising one cooperator and one defector, and intolerant cooperators, who choose to discontinue such interactions, can survive when the cost of cooperation is small. In addition, my numerical analysis indicates that the coexistence of tolerant and intolerant cooperators cannot be an evolutionary outcome., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

An upsurge in anthropogenic impacts has hastened the decline of the red panda ( Ailurus fulgens ). The red panda is a global conservation icon, but holistic conservation management has been hampered by research being restricted to certain locations and population clusters. Building a comprehensive potential habitat map for the red panda is imperative to advance the conservation effort and ensure coordinated management across international boundaries. Here, we use occurrence records of both subspecies of red pandas from across their entire range to build a habitat model using the maximum entropy algorithm (MaxEnt 3.3.3k) and the least correlated bioclimatic variables. We found that the subspecies have separate climatic spaces dominated by temperature-associated variables in the eastern geographic distribution limit and precipitation-associated variables in the western distribution limit. Annual precipitation (BIO12) and maximum temperature in the warmest months (BIO5) were major predictors of habitat suitability for A. f. fulgens and A. f. styani , respectively. Our model predicted 134,975 km 2 of red panda habitat based on 10 percentile thresholds in China (62% of total predicted habitat), Nepal (15%), Myanmar (9%), Bhutan (9%), and India (5%). Existing protected areas (PAs) encompass 28% of red panda habitat, meaning the PA network is currently insufficient and alternative conservation mechanisms are needed to protect the habitat. Bhutan's PAs provide good coverage for the red panda habitat. Furthermore, large areas of habitat were predicted in cross-broader areas, and transboundary conservation will be necessary.

Ecosystem services (the benefits to humans from ecosystems) are estimated globally at $125 trillion/year [1, 2]. Similar assessments at national and regional scales show how these services support our lives [3]. All valuations recognize the role of biodiversity, which continues to decrease around the world in maintaining these services [4, 5]. The giant panda epitomizes the flagship species [6]. Its unrivalled public appeal translates into support for conservation funding and policy, including a tax on foreign visitors to support its conservation [7]. The Chinese government has established a panda reserve system, which today numbers 67 reserves [8, 9]. The biodiversity of these reserves is among the highest in the temperate world [10], covering many of China's endemic species [11]. The panda is thus also an umbrella species [12]-protecting panda habitat also protects other species. Despite the benefits derived from pandas, some journalists have suggested that it would be best to let the panda go extinct. With the recent downlisting of the panda from Endangered to Vulnerable, it is clear that society's investment has started to pay off in terms of panda population recovery [13, 14]. Here, we estimate the value of ecosystem services of the panda and its reserves at between US$2.6 and US$6.9 billion/year in 2010. Protecting the panda as an umbrella species and the habitat that supports it yields roughly 10-27 times the cost of maintaining the current reserves, potentially further motivating expansion of the reserves and other investments in natural capital in China., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The adaptive evolution of influenza virus is an important question, but predicting its evolutionary future will be more challenging. Here, we investigated the mutation characteristic of influenza virus based on the complete genome data of 2009 (H1N1) influenza A virus. By assuming that evolution proceeds via the accumulation of mutations, we analyzed the mutation networks at four different time stages and found that the network structure follows the characteristics of a scale-free network. These results will be important for epidemiology and the future control of influenza viruses. Furthermore, we predicted the predominant mutation virus strain by using the early mutation network of influenza viruses, and this result was consistent with the WHO recommendation for the candidate vaccine of influenza virus. The key contribution of this study is that we explained the biological significance of this scale-free network for influenza pandemic and provided a potential method for predicting the candidate vaccine by using the early-stage network.

Skin pigmentation and coat pigmentation are two of the best-studied examples of traits under natural selection given their quantifiable fitness interactions with the environment (e.g., camouflage) and signalling with other organisms (e.g., warning coloration). Previous morphological studies have found that skin pigmentation variation in the Virginia opossum (Didelphis virginiana) is associated with variation in precipitation and temperatures across its distribution range following Gloger's rule (lighter pigmentation in temperate environments). To investigate the molecular mechanism associated with skin pigmentation variation, we used RNA-Seq and quantified gene expression of wild opossums from tropical and temperate populations. Using differential expression analysis and a co-expression network approach, we found that expression variation in genes with melanocytic and immune functions is significantly associated with the degree of skin pigmentation variation and may be underlying this phenotypic difference. We also found evidence suggesting that the Wnt/β-catenin signalling pathway might be regulating the depigmentation observed in temperate populations. Based on our study results, we present several alternative hypotheses that may explain Gloger's rule pattern of skin pigmentation variation in opossum, including changes in pathogen diversity supporting a pathogen-resistant hypothesis, thermal stress associated with temperate environments, and pleiotropic and epistatic interactions between melanocytic and immune genes., (© 2018 John Wiley & Sons Ltd.)

The existence of cooperation is a mysterious phenomenon and demands explanation, and direct reciprocity is one key potential explanation for the evolution of cooperation. Direct reciprocity allows cooperation to evolve for cooperators who switch their behavior on the basis of information about the opponent's behavior. Here, relevant to direct reciprocity is information deficiency. When the opponent's last move is unknown, how should players behave? One possibility is to choose cooperation with some default probability without using any further information. In fact, our previous paper (Kurokawa, 2016a) examined this strategy. However, there might be beneficial information other than the opponent's last move. A subsequent study of ours (Kurokawa, 2017) examined the strategy which uses the own last move when the opponent's last move is unknown, and revealed that referring to the own move and trying to imitate it when information is absent is beneficial. Is there any other beneficial information else? How about strong belief (i.e., have infinite memory and believe that the opponent's behavior is unchanged)? Here, we examine the evolution of strategies with strong belief. Analyzing the repeated prisoner's dilemma game and using evolutionarily stable strategy (ESS) analysis against an invasion by unconditional defectors, we find the strategy with strong belief is more likely to evolve than the strategy which does not use information other than the opponent player's last move and more likely to evolve than the strategy which uses not only the opponent player's last move but also the own last move. Strong belief produces the extended reciprocity and facilitates the evolution of cooperation. Additionally, we consider the two strategies game between strategies with strong belief and any strategy, and we consider the four strategies game in which unconditional cooperators, unconditional defectors, pessimistic reciprocators with strong belief, and optimistic reciprocators with strong belief are present., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Based on the classic imitation dynamics (Hofbauer and Sigmund, 1998, Evolutionary Games and Population Dynamics, Cambridge University Press), the imitation dynamics with time delay is investigated, where the probability that an individual will imitate its opponent's own strategy is assumed to depend on the comparison between the past expected payoff of this individual's own strategy and the past expected payoff of its opponent's own strategy, i.e. there is a time delay effect. For the two-phenotype model, we show that if the system has an interior equilibrium and this interior equilibrium is stable when there is no time delay, then there must be a critical value of time delay such that the system tends to a stable periodic solution when the time delay is larger than the critical value. On the other hand, for three-phenotype (rock-scissors-paper) model, the numerical analysis shows that for the stable periodic solution induced by the time delay, the amplitude and the period will increase with the increase of the time delay. These results should help to understand the evolution of behavior based on the imitation dynamics with time delay., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

One key potential explanation for the evolution of cooperation is conditional cooperation. This allows cooperation to evolve for cooperators who switch their behavior on the basis of information about the opponent's behavior or reputation. However, information about the opponent's behavior or reputation is sometimes unavailable, and previous studies have assumed that a player cooperates with some default probability when no information about the opponent's previous behavior or reputation is available. This default probability has been interpreted as the player's "optimism". Here, we make use of the fact that even if a player cannot observe the opponent's previous behavior or reputation, he may still condition his future behavior based on his own past behavior and in such a case, he can behave persistently. In this paper, we especially consider the case where information about the opponent's "behavior" is sometimes absent and the iterated prisoner's dilemma game between the same two individuals is played. Here, we examine the evolution of strategies that can refer to the own behavior in the previous round. Using evolutionarily stable strategy (ESS) analysis and analyzing replicator dynamics, we find that conditioning his future behavior based on his own past behavior is beneficial for the evolution. Persistence facilitates the evolution of cooperation., (Copyright © 2017 Elsevier Inc. All rights reserved.)

To understand control interventions, the molecular epidemiology of acute hemorrhagic conjunctivitis (AHC) was investigated from 2004 to 2014.A total of 613,485 AHC cases (annualized cases 55,771) with two deaths were included. Our findings showed that AHC was reported in all provinces, predominantly in Southern and Eastern China. The incidence rates were highest in 2007 (5.65/100,000) and 2010 (21.78/100,000) respectively. A clear seasonal pattern was identified with a peak from August to October. AHC cases occurred in all age groups; however, five to 14 years was the predominant group [23.06%, 133, 510/578,909]. The median age was 24 years (one month~97 years). The median duration from onset to diagnosis was 1.5 days, and there was no difference between the <15, 15~60 and >60-year-old patients [p = 0.0653]. The phylogenetic analysis of 100 nonstructural proteins (3C) and 84 structural proteins (VP1) revealed that AHC outbreaks were caused by Coxsackievirus A24 variant. Genotypes G4-c5a, G4-c5b, and G4-c3 co-circulated with both temporal and geographical overlaps. In conclusion, despite the overall steady decline in the number of AHC cases since the peak in 2010, it still remains a serious public health problem in Southern and Eastern China that targets on the school aged children under 15 years old.

Several post-translational modifications in host cells are hijacked by pathogens to facilitate their propagation. A number of components of the influenza virus have been reported to be modified by small ubiquitin-like modifier (SUMO) proteins during infection. We hypothesized that the MAPK/ERK pathway could be modified by SUMO1 because the SUMOylation of MEK1 was quickly eliminated after influenza A virus infection. We identified host cell MEK1 as a target of SUMO1 through LC/MS/MS, and enhanced MEK1 SUMOylation inhibited the infection of the virus, while inhibition of host cell MEK1 SUMOylation facilitated virus propagation. Further investigation demonstrated that the MAPK/ERK pathway is downregulated by MEK1 SUMOylation, which is inhibited by influenza virus infection. Furthermore, membrane accumulation of hemagglutinin promoted MEK1 phosphorylation and gradually abrogated the MEK1 SUMOylation. Taken together, we report a possible mechanism in which HA may trigger the ERK pathway in influenza A virus-infected cells as the switch from MEK1 SUMOylation to phosphorylation, facilitating virus infection.

Many species of primates are considered seasonal breeders, but the set of factors, such as food availability, day length and temperature, that influence the timing of reproductive events for both wild and captive individuals remains unclear. Here, we examine the role of factors in shaping breeding patterns in Rhinopithecus roxellana , a temperate colobine primate. We used circular statistics to describe and compare the patterns of reproductive seasonality among individuals in 13 captive groups and two free ranging but provisioned groups at various locations throughout China. Almost 90% of births occurred in March, April and May in adult females residing in both free ranging ( n  = 131) and captive groups ( n  = 407). Births occurred principally in 2-4 months prior to the peak of food availability, while conceptions occurred in 1-2 months after the peak of food availability in free ranging but provisioned groups. Day length (latitude) had a significant effect on the timing of reproduction. However, females that experienced a wide variation of temperature between the lowest and highest monthly average temperature had a later conception date. These results support that day length and temperature might be factor influencing the timing of reproductive activity., Competing Interests: The authors declare there are no competing interests.

Cooperation coexisting with defection is a common phenomenon in nature and human society. Previous studies for promoting cooperation based on kin selection, direct and indirect reciprocity, graph selection and group selection have provided conditions that cooperators outcompete defectors. However, a simple mechanism of the long-term stable coexistence of cooperation and defection is still lacking. To reveal the effect of direct reciprocity on the coexistence of cooperation and defection, we conducted a simple experiment based on the Prisoner's Dilemma (PD) game, where the basic idea behind our experiment is that all players in a PD game should prefer a cooperator as an opponent. Our experimental and theoretical results show clearly that the strategies allowing opting out against defection are able to maintain this stable coexistence.

The difference between childhood infections with avian influenza viruses A(H5N1) and A(H7N9) remains an unresolved but critically important question. We compared the epidemiological characteristics of 244 H5N1 and 41 H7N9 childhood cases (<15 years old), as well as the childhood cluster cases of the two viruses. Our findings revealed a higher proportion of H5N1 than H7N9 childhood infections (31.1% vs. 6.4%, p = 0.000). However, the two groups did not differ significantly in age (median age: 5.0 vs. 5.5 y, p = 0.0651). The proportion of clustered cases was significantly greater among children infected with H5N1 than among children infected with H7N9 [46.7% (71/152) vs. 23.6% (13/55), p = 0.005], and most of the childhood cases were identified as secondary cases [46.4% (45/97) vs. 33.3% (10/30), p = 0.000]. Mild status accounted for 79.49% and 22.66%, severe status for 17.95% and 2.34%, and fatal cases for 2.56% and 75.00% of the H7N9 and H5N1 childhood infection cases (all p<0.05), respectively. The fatality rates for the total, index and secondary childhood cluster cases were 52.86% (37/70), 88.5% (23/26) and 33.33% (15/45), respectively, in the H5N1 group, whereas no fatal H7N9 childhood cluster cases were identified. In conclusion, lower severity and greater transmission were found in the H7N9 childhood cases than in the H5N1 childhood cases., Competing Interests: The authors have declared that no competing interests exist.

Porcine reproductive and respiratory syndrome virus (PRRSV) is known to cause reproductive disorders, such as abortion, in pregnant sows as well as immunosuppressive respiratory complications, leading to severe respiratory tract infections in young pigs. In this study, an in-depth analysis of the miRNomes in mock- and virus-infected pig lungs was carried out. We found that highly expressed ssc-miR-30d-R&#95;1 was decreased in infected lungs, and reduced levels were significantly correlated with infection by PRRSV. Moreover, ssc-miR-30d-R&#95;1 was shown to target Toll-like receptor 4 (TLR4) and to suppress the production of immune cytokines through inhibition of the TLR4/MyD88/NF-κB pathway. ssc-miR-30d-R&#95;1 significantly reduced viral infections and pathological changes in pig lungs in vivo. Our current study reveals the miRNomes of PRRSV-infected pig lungs and indicates that ssc-miR-30d-R&#95;1 is potential therapeutic agent for controlling PRRSV infection.

The largest nosocomial outbreak of Middle East respiratory syndrome (MERS) occurred in South Korea in 2015. Health Care Personnel (HCP) are at high risk of acquiring MERS-Coronavirus (MERS-CoV) infections, similar to the severe acute respiratory syndrome (SARS)-Coronavirus (SARS-CoV) infections first identified in 2003. This study described the similarities and differences in epidemiological and clinical characteristics of 183 confirmed global MERS cases and 98 SARS cases in Taiwan associated with HCP. The epidemiological findings showed that the mean age of MERS-HCP and total MERS cases were 40 (24~74) and 49 (2~90) years, respectively, much older than those in SARS [SARS-HCP: 35 (21~68) years, p = 0.006; total SARS: 42 (0~94) years, p = 0.0002]. The case fatality rates (CFR) was much lower in MERS-HCP [7.03% (9/128)] or SARS-HCP [12.24% (12/98)] than the MERS-non-HCP [36.96% (34/92), p<0.001] or SARS-non-HCP [24.50% (61/249), p<0.001], however, no difference was found between MERS-HCP and SARS-HCP [p = 0.181]. In terms of clinical period, the days from onset to death [13 (4~17) vs 14.5 (0~52), p = 0.045] and to discharge [11 (5~24) vs 24 (0~74), p = 0.010] and be hospitalized days [9.5 (3~22) vs 22 (0~69), p = 0.040] were much shorter in MERS-HCP than SARS-HCP. Similarly, days from onset to confirmation were shorter in MERS-HCP than MERS-non-HCP [6 (1~14) vs 10 (1~21), p = 0.044]. In conclusion, the severity of MERS-HCP and SARS-HCP was lower than that of MERS-non-HCP and SARS-non-HCP due to younger age and early confirmation in HCP groups. However, no statistical difference was found in MERS-HCP and SARS-HCP. Thus, prevention of nosocomial infections involving both novel Coronavirus is crucially important to protect HCP.

High-quality and complete gene models are the basis of whole genome analyses. The giant panda (Ailuropoda melanoleuca) genome was the first genome sequenced on the basis of solely short reads, but the genome annotation had lacked the support of transcriptomic evidence. In this study, we applied RNA-seq to globally improve the genome assembly completeness and to detect novel expressed transcripts in 12 tissues from giant pandas, by using a transcriptome reconstruction strategy that combined reference-based and de novo methods. Several aspects of genome assembly completeness in the transcribed regions were effectively improved by the de novo assembled transcripts, including genome scaffolding, the detection of small-size assembly errors, the extension of scaffold/contig boundaries, and gap closure. Through expression and homology validation, we detected three groups of novel full-length protein-coding genes. A total of 12.62% of the novel protein-coding genes were validated by proteomic data. GO annotation analysis showed that some of the novel protein-coding genes were involved in pigmentation, anatomical structure formation and reproduction, which might be related to the development and evolution of the black-white pelage, pseudo-thumb and delayed embryonic implantation of giant pandas. The updated genome annotation will help further giant panda studies from both structural and functional perspectives.

Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species.

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits., (Copyright © 2014, American Association for the Advancement of Science.)

The highly polymorphic genes within the major histocompatibility complex (MHC) not only play a major role in immunity resistance, but also seem to provide hints for mate choice in some animal populations. In the present study we investigated MHC-related mate choice in a small natural population (group size 40-55 individuals) of a polygynous primate, the Sichuan snub-nosed monkey (Rhinopithecus roxellana). We found that there was no evidence either for MHC-disassortative mating, or for females to mate with males based on MHC heterozygosity or specific alleles. Nevertheless, of the 11 alleles identified, we found that the frequencies of 2 alleles, Rhro-DRB2 (P < 0.01) and Rhro-DRB5 (P < 0.05) were higher in offspring than in their parents. These findings suggest that MHC-DRB in this population of R. roxellana is unlikely to be associated with mating preferences. Limited female opportunities for mate choice are likely due, in part, to the harem breeding structure present in R. roxellana, and the relatively small number of resident adult males in our study band (N = 4-6). In addition, we suggest that differences in the frequency of particular alleles across generations may be linked to parasite resistance in a fluctuating environment; however, confirmation of this finding requires further study., (© 2013 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.)

Steroid hormones affect sex determination in a variety of vertebrates. The feminizing effects of exposure to estradiol and the masculinizing effects of aromatase inhibition during development are well established in a broad range of vertebrate taxa, but paradoxical findings are occasionally reported. Four independent experiments were conducted on two turtle species with temperature-dependent sex determination (Chrysemys picta and Chelydra serpentina) to quantify the effects of egg incubation temperature, estradiol, and an aromatase inhibitor on offspring sex ratios. As expected, the warmer incubation temperatures induced female development and the cooler temperatures produced primarily males. However, application of an aromatase inhibitor had no effect on offspring sex ratios, and exogenous applications of estradiol to eggs produced male offspring across all incubation temperatures. These unexpected results were remarkably consistent across all four experiments and both study species. Elevated concentrations of estradiol could interact with androgen receptors or inhibit aromatase expression, which might result in relatively high testosterone concentrations that lead to testis development. These findings add to a short list of studies that report paradoxical effects of steroid hormones, which addresses the need for a more comprehensive understanding of the role of sex steroids in sexual development., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Geographic variation in life-history traits among populations of wide-ranging species is influenced by both spatial and temporal aspects of the environment. Rarely, however, are the effects of both aspects examined concurrently. We collected gravid female lizards (Sceloporus undulatus) from northern (Indiana), central (Mississippi) and southern (Florida) populations, spanning nearly the full latitudinal range of the species, to examine among population differences in strategies of reproductive energy allocation. Adult females from the southern population were smaller, and produced fewer and smaller eggs in their first clutches than did females from the more northern populations. Southern females were more likely to produce a second clutch, and second clutches were smaller than first clutches for females from the 2 northern populations. Together these trends eliminated population differences in overall reproductive output after accounting for body size. The trend for greater reproductive energy to be allocated to first clutches at higher latitudes, and to later clutches at lower latitudes is corroborated by published data from field studies on multiple populations. Distributing reproductive effort by producing more clutches of smaller eggs may be an adaptive response to the long season available for egg incubation and lizard activity in sub-tropical southern environments. In contrast, allocating greater resources to early reproduction may enhance maternal fitness in the relatively short activity seasons that characterize more northern sites., (© 2013 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.)

One of the main topics in population genetics is identification of adaptive selection among populations. For this purpose, population history should be correctly inferred to evaluate the effect of random drift and exclude it in selection identification. With the rapid progress in genomics in the past decade, vast genome-scale variations are available for population genetic analysis, which however requires more sophisticated models to infer species' demographic history and robust methods to detect local adaptation. Here we aim to review what have been achieved in the fields of demographic modeling and selection detection. We summarize their rationales, implementations, and some classical applications. We also propose that some widely-used methods can be improved in both theoretical and practical aspects in near future.

Although sex-biased dispersal has profound effects on the viability of small and isolated populations resulting from habitat change and anthropogenic disturbance, the direction and strength of sex-biased dispersal in the endangered Sichuan snub-nosed monkey (Rhinopithexus roxellana) remains poorly understood. Here, we investigated dispersal patterns of R. roxellana using 15 polymorphic microsatellite loci. Using noninvasive methods we obtained 337 fecal samples from individuals residing in four multilevel troops that inhabit the Shennongjia Nature Reserve (SNR). Our study site contains an isolated population of approximately 1,000 Sichuan snub-nosed monkeys located in the easternmost distribution of the species' range. Our results indicated that the mean coefficient of relatedness among troop members was low (mean relatedness ± SE = 0.038 ± 0.025). However, the mean relatedness of monkeys residing in the same troop was significantly higher than the mean relatedness of monkeys belonging to different troops, suggesting that some members of the same troop were closely relatived. Sex-biased dispersal tests revealed that dispersal in R. roxellana was male-biased. Moreover, analysis of isolation-by-distance indicated that the correlation between pairwise genetic distance and geographical distance was positive for females, while it was negative for males. These data suggest that males tended to disperse further than females, although these values were not statistically significant. Considering previous field data collected on Sichuan snub-nosed monkeys from other sites, we suggest that mating competition among males and female mate choice represent the major causes of male-biased dispersal in R. roxellana., (© 2013 Wiley Periodicals, Inc.)

Extractive foraging (EF) involves the exploitation of hidden or embedded foods, generally any food that is not visible to the naked eye. Therefore, EF is particularly important for survival in marginal habitats as it provides seasonal fallback foods in low food availability seasons. Although many studies consider primates' EF behavior and category, colobine species are usually categorized as non-extractive foragers and few studies quantitatively examine their EF behavior. In this study, we examined the EF behavior of one colobine species, the gray snub-nosed monkey (Rhinopithecus brelichi), at Yangaoping in Fanjingshan National Nature Reserve, Guizhou. We recorded 6 categories of EF behaviors. The most frequently sought-out foods were seeds, young bamboo and invertebrates. Extracted foods accounted for an average of 26.02% of feeding records. As the monkey engages in little EF behavior in the winter when the food availability is low, these results seem to do not support the hypothesis that EF serves to secure additional resources during lean times in marginal or seasonal habitats. According to these findings, we suggest R. brelich should be considered as an extractive forager. Our study also highlights the need for increased representation of colobines in the EF literature to better inform the discussion concerning its link to primate brain evolution., (© 2013 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.)

The giant panda (Ailuropoda melanoleuca) was taken to the brink of extinction in the 1980s through a combination of deforestation, large-scale loss of bamboo in the core of its range, poaching, and zoo collection, causing over 1000 deaths from the 1950s. It was thought that the drastic population decline was likely to impose a severe impact on population viability. Here, based on temporal genotyping of individuals, we show that this rapid decline did not significantly reduce the overall effective population size and genetic variation of this species, or of the two focal populations (Minshan and Qionglai) that declined the most. These results are contrary to previously assumptions, probably because the population decline has not produced the expected negative impact due to the short time scale involved (at most 10 generations), or because previous surveys underestimated the population size at the time of decline. However, if present-day habitat fragmentation and limited migration of giant pandas remains, we predict a loss of genetic diversity across the giant pandas' range in the near future. Thus, our findings highlight the substantial resilience of this species when facing demographic and environmental stochasticity, but key conservation strategies, such as enhancing habitat connectivity and habitat restoration should be immediately implemented to retain the extant genetic variation and maintain long-term evolutionary potential of this endangered species.

Few species attract much more attention from the public and scientists than the giant panda (Ailuropoda melanoleuca), a popular, enigmatic but highly endangered species. The application of molecular genetics to its biology and conservation has facilitated surprising insights into the biology of giant pandas as well as the effectiveness of conservation efforts during the past decades. Here, we review the history of genetic advances in this species, from phylogeny, demographical history, genetic variation, population structure, noninvasive population census and adaptive evolution to reveal to what extent the current status of the giant panda is a reflection of its evolutionary legacy, as opposed to the influence of anthropogenic factors that have negatively impacted this species. In addition, we summarize the conservation implications of these genetic findings applied for the management of this high-profile species. Finally, on the basis of these advances and predictable future changes in genetic technology, we discuss future research directions that seem promising for giant panda biology and conservation., (© 2012 Blackwell Publishing Ltd.)

Human activities have caused worldwide loss and fragmentation of natural habitats, resulting in the decline and isolation of wild populations, consequently increasing their risks of extinctions. We investigated the genetic consequences of anthropogenic effects on the Sichuan snub-nosed monkeys (Rhinopithecus roxellana) in the Shennongjia Nature Reserve (SNR), which is a small and isolated distribution of R. roxellana in China and would continue to be threatened by habitat degradation and loss, using extensive sampling and 16 microsatellite loci. High level of genetic variation was observed from 202 individuals collected from three R. roxellana populations (SNR population, Sichuan-Gansu population and Shaanxi population). However, R. roxellana in SNR showed the lowest genetic diversity. The likelihood analysis of migration/drift equilibrium indicated that the SNR population suffered much stronger effect of drift than the other two populations, indicating that small populations are prone to be affected by drift. The STRUCTURE analysis identified two clusters, separating the SNR population from the other two populations, suggesting an increasing drift-induced differentiation between SNR and the other two populations. Bottleneck tests revealed that R. roxellana in SNR experienced a severe population decline (37-fold) during the past 500 years as a consequence of human population expansion. The current effective population size (Ne) in SNR is less than 100 and the ratio of Ne to the census population size is approximately 0.08. Based on our findings, we suggest that the SNR population should be monitored systematically and considered as an important conservation and management unit.

The role of the Quaternary ice ages in forming the contemporary genetic structure of populations has been well studied in a number of global regions. However, due to the different nature of glaciations and complex topography, their role in shaping eastern Eurasian genetic diversity, particular in areas surrounding the Tibetan Plateau have remained largely unstudied. We aimed to address this question by examining the genetic structure of an alpine forest-associated taxon, the blood pheasant (Ithaginis cruentus) to infer its phylogeographic history. We detected three phylogenetic lineages and four current population groups. By comparing molecular and palaeovegetation data, we found that major glaciations during the Pleistocene have had a major impact upon the current genetic diversity of this species. Coalescent simulations indicate that the populations retreated to different refugia during some glacial periods in the Pleistocene, but persisted through the last glacial maximum (LGM). The most significant recent population expansion was found to have occurred before the LGM, during which palaeoclimatic data indicate that the climate was both warmer and wetter than today. In contrast, during the LGM populations may have adopted an altitudinal shift strategy in order to track changes in alpine glaciers, exemplifying a general response for montane species in the region where alpine glaciations were not large enough to cause qualitative changes in vegetation. Although analysis based on a plumage related gene showed that divergent selection may have contributed to current patterns of intra-specific diversity, demographic isolation is inferred to have played a more dominant role., (© 2011 Blackwell Publishing Ltd.)

The Tibetan Plateau is one of the top 10 biodiversity hotspots in the world and acts as a modern harbour for many rare species because of its relatively pristine state. In this article, we report a landscape genetic study on the Yunnan snub-nosed monkey (Rhinopithecus bieti), a primate endemic to the Tibetan Plateau. DNA was extracted from blood, tissue and fecal samples of 135 wild individuals representing 11 out of 15 extant monkey groups. Ten microsatellite loci were used to characterize patterns of genetic diversity. The most striking feature of the population structure is the presence of five subpopulations with distinct genetic backgrounds and unique spatial regions. The population structure of R. bieti appears to be shaped by anthropogenic landscape features as gene flow between subpopulations is strongly impeded by arable land, highways and human habitation. A partial Mantel test showed that 36.23% (r = 0.51, P = 0.01) of the genetic distance was explained by habitat gaps after controlling for the effect of geographical distance. Only 4.92% of the genetic distance was explained by geographical distance in the partial Mantel test, and no significant correlation was found. Estimation of population structure history indicates that environmental change during the last glacial maximum and human impacts since the Holocene, or a combination of both, have shaped the observed population structure of R. bieti. Increasing human activity on the Plateau, especially that resulting in habitat fragmentation, is becoming an important factor in shaping the genetic structure and evolutionary potential of species inhabiting this key ecosystem.

The golden monkey (Rhinopithecus roxellana) is one of the most endangered primate species due to its dramatically shrinking distribution during the past 400 years. Its populations are restricted to three isolated regions, Qinglin (QL), Sichuan/Gansu (SG), and Shennongjia (SNJ) in China. As with other snub-nosed monkeys in China and Vietnam, the biology and evolution of this species is still poorly known. To assess genetic differentiation and explore the relationships among populations of golden monkeys from different geographic locations, 379 bp of mitochondrial DNA control region (CR) hypervariable segment I (HVI) was studied from 60 individuals. Twelve haplotypes were identified from seven populations within the three regions. Haplotype diversity was high (0.845), whereas nucleotide diversity among all haplotypes was low (0.0331). The most recent common ancestor (TMRCA) among mtDNA haplotypes was estimated to have lived approximately 0.48-0.32 million years ago. None of the haplotypes is shared among any of the three regions. Phylogenetic analysis and AMOVA revealed clear and significant phylogeographic structure between the three regions. However, only SG contained haplotypes of the two main clades, indicating either incomplete random sorting of haplotypes or a complex history with phases of population subdivisions and merging of populations. The phylogeographic structure implies that R. roxellana should be regarded as separate management units (MUs) for each of the three regions. It is likely that recent phylogeographic history has shaped the pattern of genetic differentiation observed in the golden monkey and that its populations have suffered significant demographic fluctuation.