Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences

Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in domestication.However,domestication histories of these two lineages remain enigmatic.We therefore compared several population characteristics between these two lineages based on global sampling,which included 171 sequences obtained in this study(including Middle Asian,East Asian,and African samples)plus 536 published sequences(including European,Asian,and African samples).The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop(D-loop)sequences,respectively.The Clade I lineage experienced an increase in population size more than 8000 years ago and shows a complex haplotype network.In contrast,the population size of the Clade II lineage has remained relatively constant,with a simpler haplotype network.Although the distribution of the two lineages was almost equal across the Eurasian mainland,they still presented discernible but complex geographic bias in most parts of Africa,which are known as their domestication sites.Donkeys from sub-Saharan Africa tended to descend from the Clade I lineage,whereas the Clade II lineage was dominant along the East and North coasts of Africa.Furthermore,the migration routes inferred from diversity decay suggested different expansion across China between the two lineages.Altogether,these differences indicated non-simultaneous domestication of the two lineages,which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa,respectively.

The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks

Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses(SC2r-CoVs).Here,we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species,and detected positive signals in muscles of four Manis javanica and,for the first time,one M.pentadactyla.Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia.Using in-solution hybridization capture sequencing,we assembled a partial pangolin SC2r-CoV(pangolin-CoV)genome sequence of 22895 bp(MP20)from the M.pentadactyla sample.Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M.javanica seized by Guangxi Customs.A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated.Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated.Given the potential infectivity of pangolin-CoVs,the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.

Re-evaluating data quality of dog mitochondrial,Y chromosomal,and autosomal SNPs genotyped by SNP array

Quality deficiencies in single nucleotide polymorphism （SNP） analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was -43.8%, with 980 （18.1%）individuals completely missing mitochondrial SNP genotyping （missingness rate=l）. In males, the genotype missingness rate was -28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping （locus missingness rate=0）, whereas 5.9% of autosomal SNPs had a locus missingness rate=l. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.

A human-specific insertion promotes cell proliferation and migration by enhancing TBC1D8B expression

Human-specific insertions play important roles in human phenotypes and diseases.Here we reported a 446-bp insertion(Insert-446)in intron 11 of the TBC1D8B gene,located on chromosome X,and traced its origin to a portion of intron 6 of the EBF1 gene on chromosome 5.Interestingly,Insert-446 was present in the human Neanderthal and Denisovans genomes,and was fixed in humans after human-chimpanzee divergence.We have demonstrated that Insert-446 acts as an enhancer through binding transcript factors that promotes a higher expression of human TBC1D8B gene as compared with orthologs in macaques.In addition,over-expression TBC1D8B promoted cell proliferation and migration through“a dual finger”catalytic mechanism(Arg538 and Gln573)in the TBC domain in vitro and knockdown of TBC1D8B attenuated tumorigenesis in vivo.Knockout of Insert-446 prevented cell proliferation and migration in cancer and normal cells.Our results reveal that the human-specific Insert-446 promotes cell proliferation and migration by upregulating the expression of TBC1D8B gene.These findings provide a significant insight into the effects of human-specific insertions on evolution.

Sex-biased adaptation shapes uniparental gene pools in Tibetans

During the past two decades, a series of archaeological and genetic investigations substantially improve our perception of the hominin settlement of the Tibetan Plateau(Zhang et al., 2022). In addition to the identification of Tibetan selectionnominated genes contributing to the high-altitude adaptation(Zheng et al.,2023).

Comparative population genomics reveals genetic basis underlying body size of domestic chickens

Body size is the most important economic trait for animal production and breeding.Several hundreds of loci have been reported to be associated with growth trait and body weight in chickens.The loci are mapped to large genomic regions due to the low density and limited number of genetic markers in previous studies.Herein,we employed comparative population genomics to identify genetic basis underlying the small body size of Yuanbao chicken(a famous ornamental chicken)based on 89 whole genomes.The most significant signal was mapped to the BMP10 gene,whose expression was upregulated in the Yuanbao chicken.Overexpression of BMP10 induced a significant decrease in body length by inhibiting angiogenic vessel development in zebrafish.In addition,three other loci on chromosomes 1,2,and 24 were also identified to be potentially involved in the development of body size.Our results provide a paradigm shift in identification of novel loci controlling body size variation,availing a fast and efficient strategy.These loci,particularly BMP10,add insights into ongoing research of the evolution of body size under artificial selection and have important implications for future chicken breeding.

A Matrilineal Genetic Legacy from the Last Glacial Maximum Confers Susceptibility to Schizophrenia in Han Chinese

Mitochondrial dysfunction has been widely reported in schizophrenia patients. To dissect the matrilineal structure of Han Chinese with or without schizophrenia and to decipher the maternal influence and evolutionary history of schizophrenia, a total of 1212 schizophrenia patients and 1005 matched healthy controls, all of Han Chinese origin, were recruited in Hunan Province, China. We classified haplogroup for each individual based on mitochondrial DNA （mtDNA） sequence variations and compared the haplogroup distribution pattern between cases and controls. Haplogroup B5a presented a higher frequency in cases than in controls （P = 0.02, OR = 1.67, 95% CI = [1.09, 2.56]）, and this result could be confirmed by permutation analysis. Age estimation of haplogroup B5a in cases revealed a much younger age than that of controls, which was coincident with the Northern Hemisphere deglaciation at the end of the Last Glacial Maximum. Analysis of complete mtDNA in five patients belonging to haplogroup B5a showed that this background effect might be caused by haplogroup- defining variants m.8584G〉A and m.10398A〉G. Our results showed that matrilineal risk factor for schizophrenia had an ancient origin and might acquire a predisposing effect on schizophrenia due to the environment change and/or orchestration with other nuclear genetic factors appeared recently in human evolutionary history.

Was chicken domesticated in northern China?New evidence from mitochondrial genomes

The timing and location of chicken(Gallus gallus domesticus)domestication have remained controversial for over a century[1].Several researchers have proposed China as one of the early centers for chicken domestication[2].This is based on a few archaeological‘‘chicken"remains discovered in China(Table S1).Recently,one investigation detected mitochondrial DNA(mt DNA)haplotypes

A cryptic mitochondrial DNA link between North European and West African dogs

Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA（mt DNA） D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups（matrilines; clades）： A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf（Canis lupus lupaster）. The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1（but not the entire haplogroup D） coalescing around 12,000 years ago. Incorporating molecular anthropological evidence,we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.

Genetic variation and cryptic lineage diversity of the Nigerian red-headed rock agama Agama agama associate with eco-geographic zones

Nigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism.Among its vertebrate fauna,reptiles have broad distributions,thus,they constitute a compelling system for assessing the impact of ecological variation and geographic isolation on species diversification.The red-headed rock agama,Agama agama,lives in a wide range of habitats and,thus,it may show genetic structuring and diversification.Herein,we tested the hypothesis that ecology affects its genetic structure and population divergence.Bayesian inference phylogenetic analysis of a mitochondrial DNA(mtDNA)gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic regions.Genetic differences among populations based on the mtDNA also correlated with geographic distance. The ecologicalniche model for the matrilines had a good fit and robust performance. Population divergence alongthe environmental axes was associated with climatic conditions, and temperature ranked highestamong all environmental variables for forest specialists, while precipitation ranked highest for theforest/derived savanna, and savanna specialists. Our results cannot reject the hypothesis that nicheconservatism promotes geographic isolation of the western populations of Nigerian A. agama.Thus, ecological gradients and geographic isolation impact the genetic structure and population divergenceof the lizards. This species might be facing threats due to recent habitat fragmentation,especially in western Nigeria. Conservation actions appear necessary.

A paratlei mechanism underlying frizzle in domestic chickens

Dear Editor,The feather,a highly keratinized tissue with variations in the shape,distribution,pigmentation,and structure,is an attractive topic in developmental and evolutionary biology (Boer et al.,2017).