Zoological Research

476-487

Authors: Bao Wang, Lei Chen, Wen Wang

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.

506-521

Authors: 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

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.

532-540

Authors: Mei-Ling Zhang, Ming-Li Li, Adeola Oluwakemi Ayoola, Robert W. Murphy, Dong-Dong Wu, Yong Shao

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.

552-557

Authors: Wan-Sheng Jiang, Jie Li, Xiao-Zhong Lei, Zhou-Rui Wen, Yu-Zhang Han, Jun-Xing Yang, Jian-Bo Chang

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.

564-574

Authors: Yun-He Wu, Chatmongkon Suwannapoom, Nikolay A. Poyarkov, Jr., Parinya Paawangkhanant, Kai Xu, Jie-Qiong Jin, Robert W. Murphy, Jing Che

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.

580-582

Authors: Fei Wu, De-Jun Kong, Peng-Fei Shan, Jie Wang, Gladys Nyakeru Kungu, Guang-Yi Lu, Xiao-Jun Yang

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.

587-594

Authors: Wendy Li, Zhan-Shan(Sam) Ma

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.