Comparative analysis and phylogenetic and evolutionary implications of mitogenomes of Chinese Sinocyclocheilus cavefish(Cypriniformes:Cyprinidae)

DEAR EDITOR,Cavefish are of considerable interest due to the remarkable morphological changes that occurred during their adaptation to cave or subterranean river habitats.These changes are thought to involve trade-offs in metabolic requirements and energy utilization.Mitochondria play a vital role in oxygen use and energy metabolism;thus,mitochondrial genes are likely to have experienced specific selective pressures during cavefish evolution.In this study,we assembled and annotated the mitogenome of Sinocyclocheilus sanxiaensis,a typical cavefish species in China.Using this sequence and other available mitogenomes from the NCBI database,we reconstructed an updated phylogeny of Sinocyclocheilus based on 29 species.Five species groups were revealed,with the recently erected S.microphthalmus species group supported.To determine whether divergent selective pressures have acted on the protein-coding genes(PCGs)of the 29 Sinocyclocheilus species exhibiting different morphological features(including eye shape and body color),the fish were classified into three groups according to their cave-related traits.The branch model test revealed higher nonsynonymous/synonymous substitution ratios(ω)in the cave-dwelling groups,potentially resulting from a balance between adaptive selection and relaxed functional constraints.Sophisticated analysis using site and branch-site models identified 24 highly credible positive selection sites located on nine PCGs,with most sites also showing radical changes in amino acid properties.This study sheds light on the phylogeny and mitogenomic evolution of Sinocyclocheilus cavefish,highlighting their successful adaptation and survival in subterranean environments.

Phylogenetic Relationships of the Genus Paramesotriton(Caudata: Salamandridae) with the Description of a New Species from Qixiling Nature Reserve, Jiangxi, Southeastern China and a Key to the species

The matrilineal genealogy of the genus Paramesotriton is hypothesized based on DNA sequences from mitochondrial NADH subunit two （ND2） and its flanking tRNAs （tRN^Arp and a partial tRNA^Ala）. The genealogy identifies a highly divergent, unnamed lineage from Qixiling Nature Reserve, Jiangxi, China and places it as the sister taxon of P. chinensis. The newly discovered population differs from other congeners by several features of external morphology including having large clusters of dark brown conical warts on the dorsum of the head, lateral surface of the body and dorsolateral ridges. Its intermittent dorsal vertebral ridge is the same color as other parts of the dorsum and tail narrows gradually from the base to the tip. Further, the new population differs from all congeners by an uncorrected P-distance of more than 9.38% in ND2. Consequently, we describe the new species of Asian warty newt （Salamandridae） as Paramesotriton qixilingensis sp. nov.

On the origin and evolution of new genes——a genomic and experimental perspective

The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved young genes. Two indispensible steps are involved in this process： origin of new gene copies through various mutational mechanisms and evolution of novel functions, which fur- ther more leads to fixation of the new copies within populations. The theoretical framework for the former step formed in 1970s. Ohno proposed gene duplication as the most important mechanism producing new gene copies. He also believed that the most common fate for new gene copies is to become pseudogenes. This classical view was validated and was also challenged by the characterization of the first functional young gene jingwei in Drosophila. Recent genome-wide comparison on young genes of Drosophila has elucidated a compre- hensive picture addressing remarkable roles of various mechanisms besides gene duplication during origin of new genes. Case surveys revealed it is not rare that new genes would evolve novel structures and functions to contribute to the adaptive evolution of organisms. Here, we review recent advances in understanding how new genes originated and evolved on the basis of genome-wide results and ex- perimental efforts on cases. We would finally discuss the future directions of this fast-growing research field in the context of functional genomics era.

A transgenic monkey model for the study of human brain evolution

Why humans have large brains with higher cognitive abilities is a question long asked by scientjsts.However,much remains unknown,especially the underlying genetic mechanisms.With the use of a transgenic mon key model,we showed that human-specific sequenee changes of a key brain development gene(Primary microcephaly 1,MCPH7)could result in detectable molecularand cognitive changes resembling human neoteny,a no table characteristic developed during human evolution.This study was published in National Science Review(Shi et al.,2019).

Evolution of neurotransmitter gamma-aminobutyric acid,glutamate and their receptors

Gamma-aminobutyric acid(GABA)and glutamate are two important amino acid neurotransmitters widely present in the nervous systems of mammals,insects,round worm,and platyhelminths,while their receptors are quite diversified across different animal phyla.However,the evolutionary mechanisms between the two conserved neurotransmitters and their diversified receptors remain elusive,and antagonistic interactions between GABA and glutamate signal transduction systems,in particular,have begun to attract significant attention.In this review,we summarize the extant results on the origin and evolution of GABA and glutamate,as well as their receptors,and analyze possible evolutionary processes and phylogenetic relationships of various GABAs and glutamate receptors.We further discuss the evolutionary history of Excitatory/Neutral Amino Acid Transporter(EAAT),a transport protein,which plays an important role in the GABA-glutamate“yin and yang”balanced regulation.Finally,based on current advances,we propose several potential directions of future research.

EPAS1 prevents telomeric damage-induced senescence by enhancing transcription of TRF1,TRF2,and RAD50

Telomeres are nucleoprotein structures located at the end of each chromosome,which function in terminal protection and genomic stability.Telomeric damage is closely related to replicative senescence in vitro and physical aging in vivo.As relatively long-lived mammals based on body size,bats display unique telomeric patterns,including the upregulation of genes involved in alternative lengthening of telomeres(ALT),DNA repair,and DNA replication.At present,however,the relevant molecular mechanisms remain unclear.In this study,we performed cross-species comparison and identified EPAS1,a well-defined oxygen response gene,as a key telomeric protector in bat fibroblasts.Bat fibroblasts showed high expression of EPAS1,which enhanced the transcription of shelterin components TRF1 and TRF2,as well as DNA repair factor RAD50,conferring bat fibroblasts with resistance to senescence during long-term consecutive expansion.Based on a human single-cell transcriptome atlas,we found that EPAS1 was predominantly expressed in the human pulmonary endothelial cell subpopulation.Using in vitro-cultured human pulmonary endothelial cells,we confirmed the functional and mechanistic conservation of EPAS1 in telomeric protection between bats and humans.In addition,the EPAS1 agonist M1001 was shown to be a protective compound against bleomycin-induced pulmonary telomeric damage and senescence.In conclusion,we identified a potential mechanism for regulating telomere stability in human pulmonary diseases associated with aging,drawing insights from the longevity of bats.

Phylogenetic and morphological significance of an overlooked flying squirrel(Pteromyini,Rodentia)from the eastern Himalayas with the description of a new genus

The flying squirrels(Pteromyini,Rodentia)are the most diverse and widely distributed group of gliding mammals.Taxonomic boundaries and relationships within flying squirrels remain an area of active research in mammalogy.The discovery of new specimens of Pteromys(Hylopetes)leonardi Thomas,1921,previously considered a synonym of Hylopetes alboniger,in Yunnan Province,China allowed a morphological and genetic reassessment of the status of this taxon.Phylogenetic reconstruction was implemented using sequences of two mitochondrial(12S ribosomal RNA and 16S ribosomal RNA)and one nuclear(interphotoreceptor retinoid-binding protein)gene fragments.Morphological assessments involved examinations of features preserved on skins,skulls,and penises of museum specimens,supplemented with principal component analysis of craniometric data.Together these assessments revealed that this taxon should be recognized not only as a distinct species,but should also be placed within a new genus,described here as Priapomys gen.nov.

Vicariance and monsoon as drivers of diversification of nemacheilid loaches(Teleostei:Cypriniformes)around the Hengduan Mountains of China

DEAR EDITOR,High mountainous terrains facilitate the diversification of biota by providing a variety of opportunities for isolation(Favre et al.,2015).Within the Nemacheilidae family of loaches,the highly diverse Nemacheilini tribe is a polyphyletic group,with extensive distribution across the Indian and Eurasian plates(Chen et al.,2019;Sgouros et al.,2019).

Discovery of a wild,genetically pure Chinese giant salamander creates new conservation opportunities

Effective conservation of threatened biota relies on accurate assessments and scientific guidance.As an unfortunate example,Chinese giant salamanders(Andrias,CGS)remain critically endangered in nature.Misguided conservation efforts,e.g.,commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids,have further compromised conservation initiatives.Limited information on wild populations of CGS poses a significant conservation challenge.Following 18-month long field monitoring,we now report the discovery of a wild population of CGS in a closed nature reserve in Jiangxi Province,China.Genomic assessments reveal its genetic distinctiveness and do not detect genetic admixture with other species.Based on morphological and molecular evidences,we describe this CGS as a new species Andrias jiangxiensis sp.nov.This is the only known species of CGS today with a genetically pure,reproducing,in situ population.This discovery emphasizes the important role that closed nature reserves play in protecting species,and the necessity of integrating long-term field monitoring and genetic assessments.It sets a new pathway for discovering and conserving endangered species,especially for those biotas that are similarly being extirpated by anthropogenic translocations and overexploitation.

Huangshan population of Chinese Zacco platypus （Teleostei, Cyprinidae） harbors diverse matrilines and high genetic diversity

Six main mitochondrial DNA （mtDNA） lineages have been described in minnow （Zacco platypus） samples obtained from northern, western and southern China Perdices et al. （2004） predicted that further sampling of other tributaries might discover more lineages of this species. In this study, we collected 26 Zacco platypus individuals in the Huangshan area of eastern China and determined the cytochrome b （cytb） sequence variations. Combined with reported data in GenBank, we identified ten matrilines （Zacco A-J） in a total of 169 samples, with relatively high molecular divergence found among them. The Huangshan population had the greatest genetic variation among all sampled regions and hosted six of the ten matrilines. Our results highlight the significance of the Huangshan area for the conservation of Zacco platypus.

Dynamic evolution of transposable elements,demographic history,and gene content of paleognathous birds

Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.

Complete mitochondrial genome of the Thai Red Junglefowl (Gallus gallus) and phylogenetic analysis

DEAR EDITOR,In this study, we sequenced the complete mitochondrial genome （mitogenome） of the Thai Red Junglefowl （RJF; Gallus gallus） using the next-generation sequencing （NGS） platform of the Ion Torrent PGM. Samples were taken from Mae Wang District, Chiang Mai Province, northern Thailand Our data showed the complete mitogenome to be 16 785 bp in length, composed by 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The genome nucleotide composition was 30.3% A, 23.7% T, 32.5% C, and 13.5% G, resulting in a high percentage of A＋T （50.4%）. Phylogenetic analysis revealed that the mitogenome belonged to haplogroup X, whereas those of all domestic chickens belong to haplogroups A to G. This newly released mitogenome sequence will advance further evolutionary and population genetics study of the RJF and domestic chicken The availability of the G. gallus mitogenome will also contribute to further conservation genetics research of a unique species, listed as ＇data deficient＇ in Thailand.

The ubiquity and coexistence of two FBPases in chloroplasts of photosynthetic eukaryotes and its evolutionary and functional implications

In photosynthetic eukaryotes,there are two well-characterized fructose-1,6-bisphosphatases(FBPases):the redox-insensitive cytosolic FBPase(cyFBPase),which participates in gluconeogenesis,and the redoxsensitive chloroplastic FBPase(cpFBPasel),which is a critical enzyme in the Calvin cycle.Recent studies have identified a new chloroplastic FBPase,cpFBPase2;however,its phylogenetic distribution,evolutionary origin,and physiological function remain unclear.In this study,we identified and characterized these three FBPase isoforms in diverse,representative photosynthetic lineages and analyzed their phylogeny.In contrast to previous hypotheses,we found that cpFBPase2 is ubiquitous in photo synthetic eukaryotes.Additionally,all cpFBPase2 s from diverse lineages form a monophyly,suggesting cpFBPase2 is not a recently evolved enzyme restricted to land plants but rather evolved early in the evolution of photo synthetic organisms,and most likely,in the common ancestor of photosynthetic eukaryotes.cyFBPase was probably first duplicated to produce cpFBPase2,and then the latter duplicated to produce cpFBPase1.The ubiquitous coexistence of these two cpFBPases in chloroplasts is most likely the consequence of adaptation to different redox conditions of photosynthesis,especially those caused by recurrent changes in light conditions.

Multilocus phylogeny suggests a distinct species status for the Nepal population of Assam macaques(Macaca assamensis):implications for evolution and conservation

Phylogenetic relationships within the sinica-group of macaques based on morphological,behavioral,and molecular characteristics have remained controversial.The Nepal population of Assam macaques(Macaca assamensis)(NPAM),the westernmost population of the species,is morphologically distinct but has never been used in phylogenetic analyses.Here,the phylogenetic relationship of NPAM with other congeners was tested using multiple mitochondrial and Ychromosomal loci.The divergence times and evolutionary genetic distances among macaques were also estimated.Results revealed two major mitochondrial DNA clades of macaques under the sinica-group:the first clade included M.thibetana,M.sinica,and eastern subspecies of Assam macaque(M.assamensis assamensis);the second clade included M.radiata together with species from the eastern and central Himalaya,namely,M.leucogenys,M.munzala,and NPAM.Among the second-clade species,NPAM was the first to diverge from the other members of the clade around 1.9 million years ago.Our results revealed that NPAM is phylogenetically distinct from the eastern Assam macaques and closer to other species and hence may represent a separate species.Because of its phylogenetic distinctiveness,isolated distribution,and small population size,the Nepal population of sinica-group macaques warrants detailed taxonomic revision and high conservation priority.

Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics

The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.

Restocking of Anabarilius grahami in Lake Fuxian,Southwest China:morphological and genetic effects

DEAR EDITOR,The restocking of the endangered Kanglang white minnow(Anabarilius grahami)in Lake Fuxian,China,has been conducted for 13 years.However,few studies have reported on the effectiveness of the captive breeding and release of this species.

Chromosomal level assembly and population sequencing of the Chinese tree shrew genome

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.

Ecology and social system of northern gibbons living in cold seasonal forests

Gibbons in China represent the northernmost margin of present day gibbon species distribution （around N25°）. Compared to tropical habitats, northern gibbon habitats are characterized by low temperatures and remarkable seasonal variation in fruit abundance How gibbons adapt to their cold and seasonal habitats and what ecological factors affect their sociality are key questions for understanding their ecology and social system evolution, the elucidation of which will contribute to the conservation of these special populations/species. According to preliminary short-term studies, northern gibbons consume more leaves and use larger home ranges than tropical gibbons. Interestingly, some Nomascus groups consist of more than one adult female. However, these preliminary results are not well understood or incorporated into current socio-ecological theories regarding gibbon species. To better understand northern gibbons, our team has systematically studied three habituated groups of Nomascus concolor, three groups of N. nasutus, and two habituated groups of Hoolock tianxing since 2002. In this paper, we stress the challenges facing gibbons living in northern habitats and summarize their behavioral adaptations to their harsh environments. We also describe the northern gibbon social system and discuss the potential relationships between their ecology and sociality. Finally, we highlight future research questions related to northern gibbons in China.

Genomic and transcriptomic analyses reveal selection of genes for puberty in Bama Xiang pigs

The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.