Min-Sheng Peng

• PhD
• Research Associate at State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology

As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cham people remain a welter of con...

Milk consumption is prevalent in daily diets of Tibetans. To digest the milk sugar lactose, lactase persistence (LP) should be required. However, little is known about the genetic basis of LP in Tibetans. We screened 495 Tibetan individuals for five previously reported single-nucleotide polymorphisms (SNPs): -13907C/G (rs41525747), -13910C/T (rs498...

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domesti...

More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (i.e. cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives. Nevertheless, few efforts have been performed to evaluate the sequence data quality, which heavily imp...

Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200~4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome of a Tibetan chicken, and re-seq...

Mitochondrial function relies on the coordinated interactions between genes in the mitochondrial (mtDNA) and nuclear genomes. Imperfect interactions following mitonuclear incompatibility may lead to reduced fitness. MtDNA introgressions across species and populations are common and well documented. Various strategies may be expected to reconcile mi...

The feralization of domestic chicken makes the conservation and management of red jungle fowl (Gallus gallus) more complicated and challenging. We collected two Sulawesi feral chickens, located east of the Wallace Line, for whole‐genome sequencing and de novo genome assembly. Phylogenetic and f4‐statistics analyses indicated that the Sulawesi feral...

Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified a complex structural variant causi...

Background Structural variations (SVs) are widespread across genome and have a great impact on evolution, disease, and phenotypic diversity. Despite the development of numerous bioinformatic tools, commonly referred to as SV callers, tailored for detecting SVs using whole genome sequence (WGS) data and employing diverse algorithms, their performanc...

Recombination serves as a central force driving the evolution of genomic diversity in sexually reproducing organisms. Despite its fundamental role, the evolutionary dynamics of recombination rates remain largely elusive. The domestication of animals, characterized by dynamic selective pressures, provides a unique lens through which to investigate t...

Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in...

Background Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products. Results We integrated archeological evidence and genetic analysis to sh...

The wild African harlequin quails (Coturnix delegorguei delegorguei) of Western Kenya suffer from incessant hunting, habitat fragmentation, and the effects of climate change. These challenges, among others, have forced them to breed under intensive pressure, disrupting normal evolutionary processes. Here, we provide the first overview of the select...

African swine fever (ASF) is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally. After the first Nigerian outbreak in 1997, there have been frequent reports of ASF in pig-producing regions in the country. To facilitate control, it is important to understand the genotype and phylogeneti...

Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia and four breeds and 12 village dogs from the Middle East. We gath...

Long-read sequencing technology is a powerful approach with application in various genetic and genomic researches. Herein, we developed the pipeline for long amplicon high-fidelity (HiFi) sequencing and then applied it for sequencing mitochondrial DNA (mtDNA) genomes from pools of 79 Tibetan Mastiffs. We amplified the mtDNA genome with long-range P...

African wild suids consist of several endemic species that represent ancient members of the family Suidae and have colonized diverse habitats on the African continent. However, limited genomic resources for African wild suids hinder our understanding of their evolution and genetic diversity. In this study, we assembled high-quality genomes of a com...

The Muscovy duck (Cairina moschata) is an economically important poultry species, which is susceptible to fatty liver. Thus, the Muscovy duck may serve as an excellent candidate animal model of non-alcoholic fatty liver disease. However, the mechanisms underlying fatty liver development in this species are poorly understood. In this study, we repor...

Objectives: Domestic pigeons (Columba livia domestica) have diverse plumage pigmentations. Melanocortin 1 receptor (MC1R) gene variation has been correlated with color traits. The associa¬tion between MC1R and plumage coloration in African domestic pigeons is yet to be investigated. Materials and Methods: Herein, we report the relationships betwee...

Background: Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nig...

Hunting wild African harlequin quails (Coturnix delegorguei delegorguei) using traditional methods in Western Kenya has been ongoing for generations, yet their genetic diversity and evolutionary history are largely unknown. In this study, the genetic variation and demographic history of wild African harlequin quails were assessed using a 347bp mito...

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 fo...

Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nigerian cattle...

Background Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and i...

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for n...

The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and...

The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Bal...

Despite recent anthropogenic interference, south‐eastern (SE) Nigeria historically hosts a myriad of pristine forest habitats that could sustain diverse amphibian assemblages. Currently, land conversion of primary forests through human activities has led to modified habitats, such as agricultural fields and secondary forest. This calls for biodiver...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspe...

Background: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which cover...

Background: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers...

Background: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers...

Background Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers...

Background: During Early Indian Ocean trade, many species of animals were transported along the routes and destinations especially in eastern Africa. The influence of this historical trade on genetic relationships of historically popular pets such as domestic cats, in East African Coast and Persian Gulf has never been evaluated. Herein, we analyzed...

Historically Panaspis wahlbergi (Smith, 1849) has been the only assignable species present in Kenya. Recent studies have shown that it comprises multiple cryptic species and the nominal species is now restricted to southern Africa. Newly collected mitochondrial data (16S rRNA) helped to resolve the status of the Kenyan populations, which revealed t...

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 obtaine...

Background Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers...

Abstract In the original publication of this article [1], the colors of the Fig. 1 are wrong, and are revised in the updated figure below:

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 ag...

Background The ability to digest dietary lactose is associated with lactase persistence (LP) in the intestinal lumen in human. The genetic basis of LP has been investigated in many populations in the world. Iran has a long history of pastoralism and the daily consumption of dairy products; thus, we aim to assess how LP has evolved in the Iranian po...

In conclusion, our analyses of sub-haplogroup C1 and haplogroups A reveal the recent expansion of domestic chicken in northern China at least from a maternal perspective. The molecular dating does not support the scenario of early Holocene chicken domestication in northern China, although the time estimates with a huge 95% HPD should be treated wit...

The genus Agama is diverse and found commonly in Africa. The dearth of herpetological studies in Nigeria has limited knowledge on the genetic diversity and distribution of Agama and the matrilineal affinities within the West African (WA) radiation. This limits an understanding of the biogeography of West Africa. Thus, we collected 112 specimens of...

The complete mitochondrial genomes of two Sri Lankan junglefowl (Gallus lafayetti: CJF) individuals were sequenced by using next-generation sequencing technique. Samples were collected from Rathnapura and Pelmadulla areas in Sri Lanka. The complete mitochondrial DNA is 16,839 bp in length, with a typical mitogenome structure composed of a non-codin...

2018) Complete mitochondrial genome of Sri Lankan Junglefowl (Galluslafayetti) and phylogenetic study, Mitochondrial DNA Part B, 3:1, 83-84, ABSTRACT The complete mitochondrial genomes of two Sri Lankan junglefowl (Gallus lafayetti: CJF) individuals were sequenced by using next-generation sequencing technique. Samples were collected from Rathnapura...

The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle Eas...

The Pamirs, among the world’s highest mountains in Central Asia, are one of homelands with the most extreme high altitude for several ethnic groups. The settlement history of modern humans on the Pamirs remains still opaque. Herein, we have sequenced the mitochondrial DNA (mtDNA) genomes of 382 individuals belonging to eight populations from the Pa...

Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 Af...

The evolutionary history for dwarfism in chickens remains an enigma. Herein, we explore the evolution of the Serama, the smallest breed of chicken. Leveraging comparative population genomics, analyses identify several genes that are potentially associated with the growth and development of bones and muscles. These genes, and in particular both POU1...

Preaxial polydactyly (PPD) is congenital hand malformation characterized by the duplication of digit. Herein, we scan the genome-wide SNPs for a large Chinese family with PPD-II/III. We employ the refined IBD algorithm to identify the identity-by-decent (IBD) segments and compare the frequency among the patients and normal relatives. A total of 72...

The present study was undertaken to investigate mitochondrial DNA (mtDNA) control region sequences of Hazaras from Pakistan, so as to generate mtDNA reference database for forensic casework in Pakistan and to analyze phylogenetic relationship of this particular ethnic group with geographically proximal populations. Complete mtDNA control region (nt...

Background: The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by...

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 (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe a...

The dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (n = 305) in comparison with published European (n =...

Online accessibility and continuous updating of software packages is important for their application and resource-sharing. We evaluated the accessibility and update status of 214 software packages published in Molecular Ecology Resources in the past 15 years (2001–2015) and reported the associated benefits and missed opportunities. Original publica...

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 mitochondrial, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall,...

Backyard poultry production in Africa suffers major setbacks due to factors such as disease and parasite infestation. This has resulted to dwindling quantities of meat and eggs produced and also increased mortality rate observed in poultry birds. We carried out a study on 90 helmeted guinea fowls from Bungoma South, Teso North, Bungoma West, Mt. El...

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 mitochondrial, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall,...

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...

The mitochondrial DNA (mtDNA) control region (nucleotide position 16024-576) sequences were generated through Sanger sequencing method for 317 self-identified Kashmiris from all districts of Azad Jammu & Kashmir Pakistan. The population sample set showed a total of 251 haplotypes, with a relatively high haplotype diversity (0.9977) and a low random...

A recent study by Shannon et al. (1) proposes a Central Asian domestication origin of dogs, based upon the finding that Central Asia had the lowest short-range linkage disequilibrium (LD) among village dogs across the globe. A reanalysis of their data, however, suggests that these conclusions may require revision.

As noted by Darwin, chickens have the greatest phenotypic diversity of all birds, but an interesting evolutionary difference between domestic chickens and their wild ancestor, the Red Junglefowl, is their comparatively weaker vision. Existing theories suggest that diminished visual prowess among domestic chickens reflect changes driven by the relax...

We analyzed genetic diversity of 215 mitochondrial DNA (mtDNA) D-loop sequences from seven populations of domesticated helmeted guinea fowl (Numida meleagris) in Nigeria and compared that with results of samples collected in Kenya (n = 4) and China (n = 22). In total, 241 sequences were assigned to 22 distinct haplotypes. Haplotype diversity in Nig...

In a recent study, Xiang et al. (1) analyze ancient chicken mtDNA from northern China, together with published modern chicken data, and they proposed that the chicken was domesticated in northern China as early as 10,000 y ago. However, a reanalysis of their data suggested that the data are overinterpreted.

Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system fo...