A study was conducted on the identifications of the degraded samples of sika deer （Cervus nippon） and red deer （Cervus elaphus） by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes s...A study was conducted on the identifications of the degraded samples of sika deer （Cervus nippon） and red deer （Cervus elaphus） by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes sequences. 402 bp Cytb genes were achieved by PCR-sequencing using DNA extracted from 8 case samples, and contrasted with 27 sequences of Cytb gene downloaded from GenBank database. The values of three nucleotide distance between three suspected samples and sika deer were identical （0.026±0.006）, which was smaller than the smallest nucleotide distance between eastern red deer and sika deer （0.036）. Furthermore, phylogenetic analysis of sika deer and red deer indicated that the evidences located within the same cluster as sika deer. The evidences were sika deer materials. As the same way, other three suspected samples were derived from red deer. The results were further confirmed by phylogenetic and nucleotide distance analysis of 387 bp 12s rRNA gene. The method was powerful and less time-consuming and helpful to reduce the related cases with wildlife.展开更多
Behaviors of sika deer in spring were studied by scan sampling, ad libitum sampling, and all-occurrence recording methods during 1998. The results showed that behaviors of sika deer in spring can be classified by seve...Behaviors of sika deer in spring were studied by scan sampling, ad libitum sampling, and all-occurrence recording methods during 1998. The results showed that behaviors of sika deer in spring can be classified by seven categories: grazing, ruminating, bedding, moving, standing, drinking, alert, agonistic and other behaviors. Various behavioral models were more regular. Grazing behavior was a kind of mainly behavioral model.展开更多
Cervus sichuanicus is a species of sika deer （Cervus nippon Group）. To date, research has mainly focused on quantity surveying and behavior studies, with genetic information on this species currently deficient. To p...Cervus sichuanicus is a species of sika deer （Cervus nippon Group）. To date, research has mainly focused on quantity surveying and behavior studies, with genetic information on this species currently deficient. To provide scientific evidence to assist in the protection of this species, we collected Sichuan sika deer fecal samples from the Sichuan Tiebu Nature Reserve （TNR） and extracted DNA from those samples. Microsatellite loci of bovine were used for PCR amplification. After GeneScan, the genotype data were used to analyze the genetic diversity and population structure of the Sichuan sika deer in TNR. Results showed that the average expected heterozygosity of the Sichuan sika deer population in TNR was 0.562, equivalent to the average expected heterozygosity of endangered animals, such as Procapra przewalsldi. Furthermore, 8 of 9 microsatellite loci significantly deviated from the Hardy-Weinberg equilibrium and two groups existed within the Sichuan sika deer TNR population. This genetic structure may be caused by a group of Manchurian sika deer （Cervus hortulorum） released in TNR.展开更多
The scale of deer breeding has gradually increased in recent years and better information management is necessary,which requires the identification of individual deer.In this paper,a deer face dataset is produced usin...The scale of deer breeding has gradually increased in recent years and better information management is necessary,which requires the identification of individual deer.In this paper,a deer face dataset is produced using face images obtained from different angles,and an improved residual neural network(ResNet)-based recognition model is proposed to extract the features of deer faces,which have high similarity.The model is based on ResNet-50,which reduces the depth of the model,and the network depth is only 29 layers;the model connects Squeeze-and-Excitation(SE)modules at each of the four layers where the channel changes to improve the quality of features by compressing the feature information extracted through the entire layer.A maximum pooling layer is used in the ResBlock shortcut connection to reduce the information loss caused by messages passing through the ResBlock.The Rectified Linear Unit(ReLU)activation function in the network is replaced by the Exponential Linear Unit(ELU)activation function to reduce information loss during forward propagation of the network.The preprocessed 6864 sika deer face dataset was used to train the recognition model based on SEResnet,which is demonstrated to identify individuals accurately.By setting up comparative experiments under different structures,the model reduces the amount of parameters,ensures the accuracy of the model,and improves the calculation speed of the model.Using the improved method in this paper to compare with the classical model and facial recognition models of different animals,the results show that the recognition effect of this research method is the best,with an average recognition accuracy of 97.48%.The sika deer face recognition model proposed in this study is effective.The results contribute to the practical application of animal facial recognition technology in the breeding of sika deer and other animals with few distinct facial features.展开更多
Collagen from tendon of Yezo sika deer was prepared by limited pepsin digestion. The yield of collagen was very high;35.7% on the basis of lyophilized dry weight. The secondary structure of this collagen was different...Collagen from tendon of Yezo sika deer was prepared by limited pepsin digestion. The yield of collagen was very high;35.7% on the basis of lyophilized dry weight. The secondary structure of this collagen was different from that of porcine skin by ATR-FTIR analysis, although it was the same characteristics, e.g. SDS-PAGE, subunit composition, ther-mal behavior, as porcine collagen. Since taking up a problem of bovine spongiform encephalopathy infection in land animals such as calf or bovine, collagen from aquatic materials has been used in various industries. However, the present study indicates that tendon of Yezo sika deer as by-product of meat industry will have potential as an important collagen source for use in the foods, cosmetics, and medical fields.展开更多
To determine the effects of sika deer (Cervus nippon) browsing on the physical defences of the Japanese pricklyash “Zanthoxylum ailanthoides Sieb. et Zucc.” (Rutaceae), we compared the length and density of prickles...To determine the effects of sika deer (Cervus nippon) browsing on the physical defences of the Japanese pricklyash “Zanthoxylum ailanthoides Sieb. et Zucc.” (Rutaceae), we compared the length and density of prickles on Japanese islands which were under different browsing pressures. We measured the length and density of prickles on the midribs, leaf rachis, and stems. We found that the prickles of Z. ailanthoides on Kashima island were not significantly longer or at higher densities than those in the neighbouring areas;the longest pickles at the highest densities were found on Akune island. The density of sika deer on Akune (ca. 520-600/km2) was higher than that on Kashima (ca. 38.5/km2), and consequently, Akune was under greater browsing pressure. Our results suggest that the increased length and density of prickles on Akune is a response by Z. ailanthoides to the high density of sika deer found on the island.展开更多
To clarify the modification of physical defences of Glochidion obovatum Sieb. et Zucc., we compared the length of spine-like branches and frequency of lateral branches of G. obovatum between Kashima Island, which supp...To clarify the modification of physical defences of Glochidion obovatum Sieb. et Zucc., we compared the length of spine-like branches and frequency of lateral branches of G. obovatum between Kashima Island, which supports a high density of sika deer (Cervus nippon), and its neighbouring areas. The length of spine-like branches of G. obovatum in Kashima Island was not significantly longer than that of the neighbouring areas, but the frequency of lateral branches on the island was higher than that of the neighbouring areas. Since the branches of G. obovatum are heavily foraged by the sika deer, the shrub form of the species has evolved into the bonsai form, suggesting increased frequency of occurrence of lateral branches, which could develop as shoot-like branches. Thus, the observed features are facultative defence mechanisms of G. obovatum against heavy browsing in a small-sized island with very high density of sika deer.展开更多
Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identif...Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.展开更多
Despite the scientific and medicinal importance of diploid sika deer(Cervus nippon),its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed.To explore mechanisms underlying...Despite the scientific and medicinal importance of diploid sika deer(Cervus nippon),its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed.To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae,we report,for the first time,a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies,which was anchored to 32 homologous groups with a pair of sex chromosomes(XY).Several expanded genes(RET,PPP2R1A,PPP2R1B,YWHAB,YWHAZ,and RPS6)and positively selected genes(eIF4E,Wnt8A,Wnt9B,BMP4,and TP53)were identified,which could contribute to rapid antler growth without carcinogenesis.A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis.Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer(Cervus elaphus),and the olfactory sensation of sika deer might be more powerful than that of red deer.Obvious inversion regions containing olfactory receptor genes were also identified,which arose since the divergence.In conclusion,the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler,chromosome evolution,and multi-omics research of cervid animals.展开更多
The prevention and control of invasive of alien species is an important work for nature reserves.This study analyzes the development trend of the alien species sika deer in Liancheng National Nature Reserve.From Octob...The prevention and control of invasive of alien species is an important work for nature reserves.This study analyzes the development trend of the alien species sika deer in Liancheng National Nature Reserve.From October 2019 to June 2020,3523 valid photos and videos of terrestrial animals were acquired from 130 camera traps,and sika deer were recorded in 21 photos from 13 traps.The survival of the sika deer population was investigated by means of morphological identification,population structure analysis,species relative abundance indices,and species spatial association analysis.A total of 13 sika deer individuals were identified by camera trapping,including two kids and three subadults representing the reproductive capacity of the population.Spatially,sika deer is not associated with any local species and was outside the spatial association network of terrestrial animals in Liancheng National Nature Reserve,indicating that the sika deer population has not been integrated into the local community and has failed to perform its ecological function.It is worth noting that the reserve provides habitat suitable for sika deer and that the population has adequate reproductive capacity.Due to the lack of large apex predators in the reserve,the population size of ungulates such as sika deer,red deer,and Siberian roe deer may expand and lead to population outbreaks and the associated problems for the ecosystem.To restore large-and medium-sized carnivores and avoid the population outbreak of the species,the present challenges require immediate attention in Liancheng National Nature Reserve.展开更多
Velvet antler is an important and precious traditional Chinese animal medicine,and was used for strengthening the kidney,anti-fatigue,improving sexual function and so on.But the evaluation methods of velvet antler and...Velvet antler is an important and precious traditional Chinese animal medicine,and was used for strengthening the kidney,anti-fatigue,improving sexual function and so on.But the evaluation methods of velvet antler and the scientific evidence for the use of antler is insufficient.Materials and Vacuum freeze drier was used for dehydration of the fresh antler at-60.,6 pa for 24 h.展开更多
文摘A study was conducted on the identifications of the degraded samples of sika deer （Cervus nippon） and red deer （Cervus elaphus） by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes sequences. 402 bp Cytb genes were achieved by PCR-sequencing using DNA extracted from 8 case samples, and contrasted with 27 sequences of Cytb gene downloaded from GenBank database. The values of three nucleotide distance between three suspected samples and sika deer were identical （0.026±0.006）, which was smaller than the smallest nucleotide distance between eastern red deer and sika deer （0.036）. Furthermore, phylogenetic analysis of sika deer and red deer indicated that the evidences located within the same cluster as sika deer. The evidences were sika deer materials. As the same way, other three suspected samples were derived from red deer. The results were further confirmed by phylogenetic and nucleotide distance analysis of 387 bp 12s rRNA gene. The method was powerful and less time-consuming and helpful to reduce the related cases with wildlife.
文摘Behaviors of sika deer in spring were studied by scan sampling, ad libitum sampling, and all-occurrence recording methods during 1998. The results showed that behaviors of sika deer in spring can be classified by seven categories: grazing, ruminating, bedding, moving, standing, drinking, alert, agonistic and other behaviors. Various behavioral models were more regular. Grazing behavior was a kind of mainly behavioral model.
基金supported by the National Natural Science Foundation of China(30870308 and 31071944)the Shanghai Rising-Star Program(10QA1402200)
文摘Cervus sichuanicus is a species of sika deer （Cervus nippon Group）. To date, research has mainly focused on quantity surveying and behavior studies, with genetic information on this species currently deficient. To provide scientific evidence to assist in the protection of this species, we collected Sichuan sika deer fecal samples from the Sichuan Tiebu Nature Reserve （TNR） and extracted DNA from those samples. Microsatellite loci of bovine were used for PCR amplification. After GeneScan, the genotype data were used to analyze the genetic diversity and population structure of the Sichuan sika deer in TNR. Results showed that the average expected heterozygosity of the Sichuan sika deer population in TNR was 0.562, equivalent to the average expected heterozygosity of endangered animals, such as Procapra przewalsldi. Furthermore, 8 of 9 microsatellite loci significantly deviated from the Hardy-Weinberg equilibrium and two groups existed within the Sichuan sika deer TNR population. This genetic structure may be caused by a group of Manchurian sika deer （Cervus hortulorum） released in TNR.
基金This research was supported by the Science and Technology Department of Jilin Province[20210202128NC http://kjt.jl.gov.cn]The People’s Republic of China Ministry of Science and Technology[2018YFF0213606-03 http://www.most.gov.cn]+1 种基金the Jilin Province Development and Reform Commission[2019C021 http://jldrc.jl.gov.cn]the Science and Technology Bureau of Changchun City[21ZGN27 http://kjj.changchun.gov.cn].
文摘The scale of deer breeding has gradually increased in recent years and better information management is necessary,which requires the identification of individual deer.In this paper,a deer face dataset is produced using face images obtained from different angles,and an improved residual neural network(ResNet)-based recognition model is proposed to extract the features of deer faces,which have high similarity.The model is based on ResNet-50,which reduces the depth of the model,and the network depth is only 29 layers;the model connects Squeeze-and-Excitation(SE)modules at each of the four layers where the channel changes to improve the quality of features by compressing the feature information extracted through the entire layer.A maximum pooling layer is used in the ResBlock shortcut connection to reduce the information loss caused by messages passing through the ResBlock.The Rectified Linear Unit(ReLU)activation function in the network is replaced by the Exponential Linear Unit(ELU)activation function to reduce information loss during forward propagation of the network.The preprocessed 6864 sika deer face dataset was used to train the recognition model based on SEResnet,which is demonstrated to identify individuals accurately.By setting up comparative experiments under different structures,the model reduces the amount of parameters,ensures the accuracy of the model,and improves the calculation speed of the model.Using the improved method in this paper to compare with the classical model and facial recognition models of different animals,the results show that the recognition effect of this research method is the best,with an average recognition accuracy of 97.48%.The sika deer face recognition model proposed in this study is effective.The results contribute to the practical application of animal facial recognition technology in the breeding of sika deer and other animals with few distinct facial features.
文摘Collagen from tendon of Yezo sika deer was prepared by limited pepsin digestion. The yield of collagen was very high;35.7% on the basis of lyophilized dry weight. The secondary structure of this collagen was different from that of porcine skin by ATR-FTIR analysis, although it was the same characteristics, e.g. SDS-PAGE, subunit composition, ther-mal behavior, as porcine collagen. Since taking up a problem of bovine spongiform encephalopathy infection in land animals such as calf or bovine, collagen from aquatic materials has been used in various industries. However, the present study indicates that tendon of Yezo sika deer as by-product of meat industry will have potential as an important collagen source for use in the foods, cosmetics, and medical fields.
文摘To determine the effects of sika deer (Cervus nippon) browsing on the physical defences of the Japanese pricklyash “Zanthoxylum ailanthoides Sieb. et Zucc.” (Rutaceae), we compared the length and density of prickles on Japanese islands which were under different browsing pressures. We measured the length and density of prickles on the midribs, leaf rachis, and stems. We found that the prickles of Z. ailanthoides on Kashima island were not significantly longer or at higher densities than those in the neighbouring areas;the longest pickles at the highest densities were found on Akune island. The density of sika deer on Akune (ca. 520-600/km2) was higher than that on Kashima (ca. 38.5/km2), and consequently, Akune was under greater browsing pressure. Our results suggest that the increased length and density of prickles on Akune is a response by Z. ailanthoides to the high density of sika deer found on the island.
文摘To clarify the modification of physical defences of Glochidion obovatum Sieb. et Zucc., we compared the length of spine-like branches and frequency of lateral branches of G. obovatum between Kashima Island, which supports a high density of sika deer (Cervus nippon), and its neighbouring areas. The length of spine-like branches of G. obovatum in Kashima Island was not significantly longer than that of the neighbouring areas, but the frequency of lateral branches on the island was higher than that of the neighbouring areas. Since the branches of G. obovatum are heavily foraged by the sika deer, the shrub form of the species has evolved into the bonsai form, suggesting increased frequency of occurrence of lateral branches, which could develop as shoot-like branches. Thus, the observed features are facultative defence mechanisms of G. obovatum against heavy browsing in a small-sized island with very high density of sika deer.
基金This work was supported by the National Key R&D Program of China(Grant No.2018YFD0502204)the Agricultural Science and Technology Innovation Program of China(Grant No.CAAS-ASTIP-2019-ISAPS)+1 种基金the Special Animal Genetic Resources Platform of National Scientific and Technical Infrastructure Center(Grant No.NSTIC TZDWZYK2019)the Sika deer Genome Project of China(Grant No.20140309016YY).
文摘Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.
基金the National Key R&D Program of China(Grant No.2018YFC1706601)the Natural Science Foundation of Heilongjiang Province of China(Grant No.C2017012)。
文摘Despite the scientific and medicinal importance of diploid sika deer(Cervus nippon),its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed.To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae,we report,for the first time,a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies,which was anchored to 32 homologous groups with a pair of sex chromosomes(XY).Several expanded genes(RET,PPP2R1A,PPP2R1B,YWHAB,YWHAZ,and RPS6)and positively selected genes(eIF4E,Wnt8A,Wnt9B,BMP4,and TP53)were identified,which could contribute to rapid antler growth without carcinogenesis.A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis.Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer(Cervus elaphus),and the olfactory sensation of sika deer might be more powerful than that of red deer.Obvious inversion regions containing olfactory receptor genes were also identified,which arose since the divergence.In conclusion,the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler,chromosome evolution,and multi-omics research of cervid animals.
基金supported by the National Natural Science Foundation of China(grants 32171545 and 41801220).
文摘The prevention and control of invasive of alien species is an important work for nature reserves.This study analyzes the development trend of the alien species sika deer in Liancheng National Nature Reserve.From October 2019 to June 2020,3523 valid photos and videos of terrestrial animals were acquired from 130 camera traps,and sika deer were recorded in 21 photos from 13 traps.The survival of the sika deer population was investigated by means of morphological identification,population structure analysis,species relative abundance indices,and species spatial association analysis.A total of 13 sika deer individuals were identified by camera trapping,including two kids and three subadults representing the reproductive capacity of the population.Spatially,sika deer is not associated with any local species and was outside the spatial association network of terrestrial animals in Liancheng National Nature Reserve,indicating that the sika deer population has not been integrated into the local community and has failed to perform its ecological function.It is worth noting that the reserve provides habitat suitable for sika deer and that the population has adequate reproductive capacity.Due to the lack of large apex predators in the reserve,the population size of ungulates such as sika deer,red deer,and Siberian roe deer may expand and lead to population outbreaks and the associated problems for the ecosystem.To restore large-and medium-sized carnivores and avoid the population outbreak of the species,the present challenges require immediate attention in Liancheng National Nature Reserve.
文摘Velvet antler is an important and precious traditional Chinese animal medicine,and was used for strengthening the kidney,anti-fatigue,improving sexual function and so on.But the evaluation methods of velvet antler and the scientific evidence for the use of antler is insufficient.Materials and Vacuum freeze drier was used for dehydration of the fresh antler at-60.,6 pa for 24 h.
