Genomic insights into ruminant evolution: from past to future prospects
Bao Wang, Lei Chen, Wen Wang
2019 Vol. 40 (6): 476-487
Chromosomal level assembly and population sequencing of the Chinese tree shrew genome
Yu Fan, Mao-Sen Ye, Jin-Yan Zhang, Ling Xu, Dan-Dan Yu, Tian-Le Gu, Yu-Lin Yao, Jia-Qi Chen, Long-Bao Lv, Ping Zheng, Dong-Dong Wu, Guo-Jie Zhang, Yong-Gang Yao
2019 Vol. 40 (6): 506-521
      18 November 2019, Volume 40 Issue 6 Previous Issue   
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    Contents
    Zoological Research. 2019, 40 (6): 471-587.  
    Abstract ( 33 )   RICH HTML PDF (68182KB) ( 44 )   Save
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    Editorial
    From our roots, we grow
    Yong-Gang Yao, Hua Shen
    Zoological Research. 2019, 40 (6): 471-475.   DOI: 10.24272/j.issn.2095-8137.2019.060
    Abstract ( 161 )   RICH HTML ( 18 )   PDF (633KB) ( 197 )   Save
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    Review
    Genomic insights into ruminant evolution: from past to future prospects
    Bao Wang, Lei Chen, Wen Wang
    Zoological Research. 2019, 40 (6): 476-487.   DOI: 10.24272/j.issn.2095-8137.2019.061
    Abstract ( 222 )   RICH HTML ( 18 )   PDF (971KB) ( 201 )   Save

    Ruminants (Ruminantia) are among the most successful herbivorous mammals, exhibiting wide-ranging morphological and ecological characteristics (such as headgear and multichambered stomach) and including various key livestock species (e.g., cattle, buffalo, yak, sheep, and goat). Understanding their evolution is of great significance not only in scientific research but also in applications potential for human society. The rapid growth of genomic resources provides unprecedented opportunities to dissect the evolutionary histories and molecular mechanisms underlying the distinct characteristics of ruminants. Here we summarize our current understanding of the genetic, morphological, and ecological diversity of ruminants and provide prospects for future studies.

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    Antimicrobial peptides: new hope in the war against multidrug resistance
    James Mwangi, Xue Hao, Ren Lai, Zhi-Ye Zhang
    Zoological Research. 2019, 40 (6): 488-505.   DOI: 10.24272/j.issn.2095-8137.2019.062
    Abstract ( 402 )   RICH HTML ( 27 )   PDF (844KB) ( 542 )   Save

    The discovery of antibiotics marked a golden age in the revolution of human medicine. However, decades later, bacterial infections remain a global healthcare threat, and a return to the pre-antibiotic era seems inevitable if stringent measures are not adopted to curb the rapid emergence and spread of multidrug resistance and the indiscriminate use of antibiotics. In hospital settings, multidrug resistant (MDR) pathogens, including carbapenem-resistant Pseudomonas aeruginosa, vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), and extended-spectrum β-lactamases (ESBL) bearing Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae are amongst the most problematic due to the paucity of treatment options, increased hospital stay, and exorbitant medical costs. Antimicrobial peptides (AMPs) provide an excellent potential strategy for combating these threats. Compared to empirical antibiotics, they show low tendency to select for resistance, rapid killing action, broad-spectrum activity, and extraordinary clinical efficacy against several MDR strains. Therefore, this review highlights multidrug resistance among nosocomial bacterial pathogens and its implications and reiterates the importance of AMPs as next-generation antibiotics for combating MDR superbugs.

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    Articles
    Chromosomal level assembly and population sequencing of the Chinese tree shrew genome
    Yu Fan, Mao-Sen Ye, Jin-Yan Zhang, Ling Xu, Dan-Dan Yu, Tian-Le Gu, Yu-Lin Yao, Jia-Qi Chen, Long-Bao Lv, Ping Zheng, Dong-Dong Wu, Guo-Jie Zhang, Yong-Gang Yao
    Zoological Research. 2019, 40 (6): 506-521.   DOI: 10.24272/j.issn.2095-8137.2019.063
    Abstract ( 546 )   RICH HTML ( 12 )   PDF (4103KB) ( 299 )   Save

    Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://www.treeshrewdb.org) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research.

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    Superior intestinal integrity and limited microbial translocation are associated with lower immune activation in SIVmac239-infected northern pig-tailed macaques (Macaca leonina)
    Ming-Xu Zhang, Tian-Zhang Song, Hong-Yi Zheng, Xue-Hui Wang, Ying Lu, Han-Dan Zhang, Ting Li, Wei Pang, Yong-Tang Zheng
    Zoological Research. 2019, 40 (6): 522-531.   DOI: 10.24272/j.issn.2095-8137.2019.047
    Abstract ( 194 )   RICH HTML ( 7 )   PDF (1383KB) ( 117 )   Save

    Microbial translocation is a cause of systemic immune activation in HIV/SIV infection. In the present study, we found a lower CD8+ T cell activation level in Macaca leonina (northern pig-tailed macaques, NPMs) than in Macaca mulatta (Chinese rhesus macaques, ChRMs) during SIVmac239 infection. Furthermore, the levels of plasma LPS-binding protein and soluble CD14 in NPMs were lower than those in ChRMs. Compared with ChRMs, SIV-infected NPMs had lower Chiu scores, representing relatively normal intestinal mucosa. In addition, no obvious damage to the ileum or colon epithelial barrier was observed in either infected or uninfected NPMs, which differed to that found in ChRMs. Furthermore, no significant microbial translocation (Escherichia coli) was detected in the colon or ileum of infected or uninfected NPMs, which again differed to that observed in ChRMs. In conclusion, NPMs retained superior intestinal integrity and limited microbial translocation during SIV infection, which may contribute to their lower immune activation compared with ChRMs.

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    Reports
    Conserved sequences identify the closest living relatives of primates
    Mei-Ling Zhang, Ming-Li Li, Adeola Oluwakemi Ayoola, Robert W. Murphy, Dong-Dong Wu, Yong Shao
    Zoological Research. 2019, 40 (6): 532-540.   DOI: 10.24272/j.issn.2095-8137.2019.057
    Abstract ( 150 )   RICH HTML ( 9 )   PDF (2885KB) ( 104 )   Save

    Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.

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    Systematic relationships of Chinese freshwater semisulcospirids (Gastropoda, Cerithioidea) revealed by mitochondrial sequences
    Li-Na Du, Jun Chen, Guo-Hua Yu, Jun-Xing Yang
    Zoological Research. 2019, 40 (6): 541-551.   DOI: 10.24272/j.issn.2095-8137.2019.033
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    The systematics of Semisulcospiridae in China is revised here based on morphological characters and mitochondrial phylogenetics. Phylogenetic relationships within the Chinese semisulcospirids were assessed via DNA sequences from mitochondrial analysis (cytochrome c oxidase I and 16S rRNA). This research contains most morphospecies of semisulcospirids previously recorded in China. Based on these results, the family of Chinese Semisulcospiridae is represented by three genera: i.e., viviparous Semisulcospira B?ttger, 1886, oviparous Hua Chen, 1943 and Koreoleptoxis Burch and Jung, 1988. These genera can be distinguished from each other by reproductive anatomy, reproductive mode, and radula features. Species of Hua are mainly distributed in southwest China and Guangxi, whereas Koreoleptoxis and Semisulcospira are mainly distributed in south and northeast China.

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    Letters to the editor
    Sinocyclocheilus sanxiaensis, a new blind fish from the Three Gorges of Yangtze River provides insights into speciation of Chinese cavefish
    Wan-Sheng Jiang, Jie Li, Xiao-Zhong Lei, Zhou-Rui Wen, Yu-Zhang Han, Jun-Xing Yang, Jian-Bo Chang
    Zoological Research. 2019, 40 (6): 552-557.   DOI: 10.24272/j.issn.2095-8137.2019.065
    Abstract ( 349 )   RICH HTML ( 16 )   PDF (1516KB) ( 471 )   Save

    A blind fish of Sinocyclocheilus (Cypriniformes: Cyprinidae)was caught in open water in the Three Gorges (Sanxia)reservoir, at a depth of 20 m in the mainstream of YangtzeRiver in Zigui County, Hubei Province, China. This fish can beeasily distinguished from all other congeners by externalmorphological characteristics, and is estimated to havediverged from its sister group about 0.55 million years ago(Ma). The geologically well separated locality of this specieshas expanded the distribution of Sinocyclocheilus cavefishfrom around N25° (latitude) to above N30° . Herein, wedescribe this new species as Sinocyclocheilus sanxiaensis sp.nov., and discuss the possible reasons why the speciesappears, surprisingly, in the Three Gorges reservoir.

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    A new species of the genus Raorchestes (Anura: Rhacophoridae) from Yunnan Province, China
    Yun-He Wu, Chatmongkon Suwannapoom, Kai Xu, Jin-Min Chen, Jie-Qiong Jin, Hong-Man Chen, Robert W. Murphy, Jing Che
    Zoological Research. 2019, 40 (6): 558-563.   DOI: 10.24272/j.issn.2095-8137.2019.066
    Abstract ( 140 )   RICH HTML ( 14 )   PDF (1254KB) ( 189 )   Save

    A new bush frog species, Raorchestes cangyuanensis sp. nov., from Cangyuan, Yunnan Province, China, is described based on morphological and molecular analyses. It differs from all known congeners by a combination of the following characters: body size small, adult snout-vent length (SVL) 16.1–20.0 mm in males (n=3); tympanum indistinct; tips of all fingers and toes expanded into discs with circummarginal grooves; rudimentary webbing between toes; fingers and toes with lateral dermal fringes; inner and outer metacarpal tubercles present; heels meeting when limbs held at right angles to body; crotch with a distinct black patch; discs of fingers and toes orange; male with external single subgular vocal sac and reddish nuptial pad at the base of first finger.

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    A new species of the genus Xenophrys (Anura:Megophryidae) from northern Thailand
    Yun-He Wu, Chatmongkon Suwannapoom, Nikolay A. Poyarkov, Jr., Parinya Paawangkhanant, Kai Xu, Jie-Qiong Jin, Robert W. Murphy, Jing Che
    Zoological Research. 2019, 40 (6): 564-574.   DOI: 10.24272/j.issn.2095-8137.2019.032
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    Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other known congeners, and therefore we describe a new species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.

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    First record of the ferret-badger Melogale cucphuongensis Nadler et al., 2011 (Carnivora: Mustelidae), with description of a new subspecies, in southeastern China
    Song Li, Guo-Hua Yu, Shuo Liu, Chang-Shan Jin
    Zoological Research. 2019, 40 (6): 575-579.   DOI: 10.24272/j.issn.2095-8137.2019.067
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    The ferret-badger Melogale cucphuongensis was first described from Cuc Phuong National Park in Vietnam, with no subsequent reports in later years. During our surveys of the Wuyishan Mountains of Fujian Province in southeastern China during May 2018, a Melogale specimen was identified. Analysis based on pelage and skull characteristics as well as molecular data indicated it to be a new subspecies, which we nominated as Melogale cucphuongensis guadunensis subsp. nov. This is the first record of the species in China. Therefore, this research not only expands the distribution range of the species beyond Vietnam, but also indicates that geographic variation of the species should have been proceeding in southeastern China.

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    Ongoing green peafowl protection in China
    Fei Wu, De-Jun Kong, Peng-Fei Shan, Jie Wang, Gladys Nyakeru Kungu, Guang-Yi Lu, Xiao-Jun Yang
    Zoological Research. 2019, 40 (6): 580-582.   DOI: 10.24272/j.issn.2095-8137.2019.069
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    The green peafowl (Pavo muticus) is one of the most threatened pheasants in the world. In China, it is widely appreciated for its beauty as well as historical and cultural value, but current populations number less than 500 individuals. Recently, Tang and colleagues reported in Science that the green peafowl is likely to become extinct due to the construction of the Jiasajiang Level 1 Hydropower Station within the Red River Upstream District (RRUD) and thus called for a stop to this project (Tang et al., 2019). According to our recent surveys, however, this species is still extant in 22 counties of Yunnan Province, China, among which, only two within the RRUD have been predicted to be affected by floods from the hydropower station. Therefore, the conclusion that the species will likely go extinct in China upon completion of the dam is unwarranted. In fact, construction of the Jiasajiang Level 1 Hydropower Station was stopped in August 2017. The main challenge for green peafowl conservation is that over 65% of the population occurs outside of protected reserves in China. Fortunately, the Chinese government has adopted an Ecological Redline (ERL) strategy to achieve ecological civilization plans, thus bringing new hope to the conservation of green peafowls both inside and outside of protected reserves. As a top conservation priority for China, the government is fully committed to conserving this peafowl.

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    Direct sunlight exposure reduces hair cortisol levels in rhesus monkeys (Macaca mulatta)
    Xiao-Li Feng, He-Long Che, Xi Ning, Xue-Ying Ba, Juan-Li, Jing-Fang Zhang, Yun Wang, Zheng-Fei Hu, Xin-Tian Hu, Xiao-Feng Ren
    Zoological Research. 2019, 40 (6): 583-586.   DOI: 10.24272/j.issn.2095-8137.2019.064
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    Major depressive disorder (MDD), commonly known as depression, is a mental disease characterized by a core symptom of low mood. It lasts at least two weeks (Badamasi et al., 2019; Wang et al., 2019) and is frequently accompanied by low self-esteem, loss of interest in routinely enjoyable activities, low energy, and unexplained pain (Huey et al., 2018; Park et al., 2012; Post & Warden, 2018; Rice et al., 2019; Xiao et al., 2018). Approximately 2%–8% of adults with MDD commit suicide (Richards & O'Hara, 2014; Strakowski & Nelson, 2015), and around half of suicidal individuals suffer depression or other mood disorders (Bachmann, 2018).

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    Diversity scaling of human vaginal microbial communities
    Wendy Li, Zhan-Shan(Sam) Ma
    Zoological Research. 2019, 40 (6): 587-594.   DOI: 10.24272/j.issn.2095-8137.2019.068
    Abstract ( 114 )   RICH HTML ( 4 )   PDF (618KB) ( 118 )   Save

    The composition and diversity of the human vaginal microbial community have been investigated intensively due to the diversity-stability relationship (DSR)-based hypothesis for bacterial vaginosis (BV) etiology, which was first proposed in the 1990s and has received renewed interest in recent years. Nevertheless, diversity changes (scaling) across individuals in a cohort or population have not yet been addressed, which is significant both theoretically and practically. Theoretically, biodiversity scaling is the core of biogeography, and practically, inter-subject heterogeneity is critical for understanding the etiology and epidemiology of human microbiome-associated diseases such as BV. Here we applied the diversity-area relationship (DAR), a recent extension to the classic species-area relationship (SAR), to study diversity scaling of the vaginal microbiome by reanalyzing reported data collected from 1 107 postpartum women. The model used here characterized the power-law (or its extension) relationships between accrued diversity and areas (numbers of individuals), upon which four biogeographic profiles were thus defined. Specifically, we established the DAR profile (relationship between diversity scaling parameter and so-termed diversity order (q)), similarly pair-wise diversity overlap (PDO) profile, maximal accrual diversity (MAD) profile, and ratio of individual-level to population-level diversity (RIP) profile. These four profiles offer valuable tools to assess and predict diversity scaling (changes) in the human vaginal microbiome across individuals, as well as to understand the dynamics of vaginal microbiomes in healthy women.

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Vol 40, No 6  (18 November 2019)

Indexed by SCI-E
2018 Impact Factor 1.556
52/170 Zoology (Q2)
2019 Journal Citation Reports®

Bimonthly, Since 1980
Editor-in-Chief: Yong-Gang Yao
ISSN: 2095-8137
CN: 53-1229/Q

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