Ming-Shan Wang

Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens

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 resequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups. Further analyses revealed that several candidate genes in the calcium-signaling pathway are possibly involved in adaptation to the hypoxia experienced by these chickens, as these genes appear to have experienced directional selection in the two Tibetan chicken populations, suggesting a potential genetic mechanism underlying high altitude adaptation in Tibetan chickens. The candidate selected genes identified in this study, and their variants, may be useful targets for clarifying our understanding of the domestication of chickens in Tibet, and might be useful in current breeding efforts to develop improved breeds for the highlands.

AMOEBA-I: a shape-shifting modular robot for urban search and rescue

This work intends to enhance the mobility and flexibility of a tracked mobile robot through changing its shape in unstructured environments. A shape-shifting mobile robot, AMOEBA-I, has been developed. With three tracked modules, AMOEBA-I has nine locomotion configurations and three of them are symmetrical configurations. The key advantage of this design over other mobile robots is its adaptability and flexibility because of its various configurations. It can change its configuration fluently and automatically to adapt to different environments or missions. A modularized structure of the control system is proposed and designed for AMOEBA-I to improve the fault tolerance and substitutability of the system. The strategies of cooperative control, including cooperative shape shifting, cooperative turning and cooperative obstacle negotiation, have been proposed to improve the capability of shape shifting, locomotion and obstacle negotiation for AMOEBA-I. A series of experiments have been carried out, and demonstrated that such a structure possesses excellent mobility and high flexibility under various urban environments including stairs, a narrow space, an obstacle, uneven debris and an underground garage. Being small, portable, and remotely controlled, AMOEBA-I has potential applications in areas such as urban search and rescue and environment reconnaissance.

Domestication of the Dog from the Wolf Was Promoted by Enhanced Excitatory Synaptic Plasticity: A Hypothesis

Dogs shared a much closer relationship with humans than any other domesticated animals, probably due to their unique social cognitive capabilities, which were hypothesized to be a by-product of selection for tameness toward humans. Here, we demonstrate that genes involved in glutamate metabolism, which account partially for fear response, indeed show the greatest population differentiation by whole-genome comparison of dogs and wolves. However, the changing direction of their expression supports a role in increasing excitatory synaptic plasticity in dogs rather than reducing fear response. Because synaptic plasticity are widely believed to be cellular correlates of learning and memory, this change may alter the learning and memory abilities of ancient scavenging wolves, weaken the fear reaction toward humans, and prompt the initial interspecific contact.

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

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 relaxation of functional constraints on vision, but the evidence identifying the underlying genetic mechanisms responsible for this change has not been definitively characterized. Here, a genome-wide analysis of the domestic chicken and Red Junglefowl genomes showed significant enrichment for positively selected genes involved in the development of vision. There were significant differences between domestic chickens and their wild ancestors regarding the level of mRNA expression for these genes in the retina. Numerous additional genes involved in the development of vision also showed significant differences in mRNA expression between domestic chickens and their wild ancestors, particularly for genes associated with phototransduction and photoreceptor development, such as RHO (rhodopsin), GUCA1A, PDE6B and NR2E3. Finally, we characterized the potential role of the VIT gene in vision, which experienced positive selection and downregulated expression in the retina of the village chicken. Overall, our results suggest that positive selection, rather than relaxation of purifying selection, contributed to the evolution of vision in domestic chickens. The progenitors of domestic chickens harboring weaker vision may have showed a reduced fear response and vigilance, making them easier to be unconsciously selected and/or domesticated.

Pervasive introgression facilitated domestication and adaptation in the Bos species complex

Species of the Bos genus, including taurine cattle, zebu, gayal, gaur, banteng, yak, wisent and bison, have been domesticated at least four times and have been an important source of meat, milk and power for many human cultures. We sequence the genomes of gayal, gaur, banteng, wisent and bison, and provide population genomic sequencing of an additional 98 individuals. We use these data to determine the phylogeny and evolutionary history of these species and show that the threatened gayal is an independent species or subspecies. We show that there has been pronounced introgression among different members of this genus, and that it in many cases has involved genes of considerable adaptive importance. For example, genes under domestication selection in cattle (for example, MITF) were introgressed from domestic cattle to yak. Also, genes in the response-to-hypoxia pathway (for example, EGLN1, EGLN2 and HIF3a) have been introgressed from yak to Tibetan cattle, probably facilitating their adaptation to high altitude. We also validate that there is an association between the introgressed EGLN1 allele and haemoglobin and red blood cell concentration. Our results illustrate the importance of introgression as a source of adaptive variation and during domestication, and suggest that the Bos genus evolves as a complex of genetically interconnected species with shared evolutionary trajectories.Genome sequences of Bos species are sequenced and compared to determine their phylogeny and evolutionary history. Introgression pathways for genes under domestication selection are identified.

Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing

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 East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.

Olfactory genes in Tibetan wild boar

were assembled in Li et al.1 (total of 216 Gb) to the Duroc pig reference genome (Ssc10.2) and evaluated read depth for the 1,301 reported olfactory receptor genes7. We found that all these genes were supported by Tibetan wild boar sequencing reads, with an average depth of 100.4×, and more than 59% of these genes had sequencing depth greater than the average depth for the genome (~65.8×) (Fig. 1a,b). All these analyses imply that most olfactory receptor genes in Tibetan wild boar. We identified only 581 of these genes (longer than 900 bp), 30 of which were pseudogenes (Table 1). Olfactory receptor genes comprise the largest gene family, and members in each subfamily exhibit high levels of similarity, mainly emanating from segmental duplications7 whose complete assembly via WGSA is problematic. In our analysis, we unsurprisingly found a remarkably smaller number of segmental duplications in Tibetan wild boar than in Duroc pig (Table 1 and Supplementary Table 1). The Duroc pig genome was assembled by combining both BAC and WGSA approaches8, hence representing a more comprehensive strategy. This analysis therefore demonstrates the possibility that the contraction in olfactory receptor genes observed in Tibetan wild boar may be a property of methodological difference. To verify this, we further studied olfactory receptor genes in the genome of Wuzhishan pig, a non-high-altitude pig9. Its genome was assembled by WGSA, similarly to the Tibetan wild boar genome. We interestingly observed a contraction of both olfactory receptor genes and segmental duplications in Wuzhishan pig, as was also observed in Tibetan wild boar (Table 1 and Supplementary Table 1). In addition, we mapped the paired-end sequencing reads from Tibetan wild boar that To the Editor: In a previous study, Li et al.1 performed a genome sequencing and comparative analysis for Tibetan wild boars, which provided new insight into the genetic landscape for the high-altitude adaptation of this species. In their study, they performed de novo assembly with 131× coverage of the genome from a female Tibetan wild boar employing a whole-genome shotgun sequencing and assembly (WGSA) strategy with the SOAPdenovo program2. They reported an interesting finding of contraction of olfactory receptor genes in Tibetan wild boar and inferred that it was an adaptation attributable to the high-altitude environment with limited food variety. They also cited lower barometric pressure and lower humidity, which tend to decrease the capacity of air to carry odorants bound to vapor molecules, as well as lower temperature, which slows the diffusion of odorous molecules, as contributing factors. Their contextualization and explanation of this finding gives their conclusion quite some plausibility. However, in stark contrast, Qiu et al.3 demonstrated an expansion of olfactory receptor genes in yak (native to and the symbol of Tibet) in comparison to cattle. Two additional studies on the ground tit genome assembly via WGSA4,5 reported contradictory findings about the evolution of olfactory receptor genes in high altitude. Thus far, this discrepancy remains unresolved and unexplained. It is known that de novo genome assembly approaches based on WGSA perform poorly in assembling homogenous regions, such as segmental duplications and repeats6. We therefore postulated that the apparent contraction of olfactory receptor genes in Tibetan wild boar may be an illusion caused by limitations of WGSA and not an actual adaptation to high altitude. To test our speculation, we used 1,301 olfactory receptor genes (longer than 900 bp) reported by Nguyen et al.7 in Duroc pig8 (the reference genome of Sus scrofa, Ssc10.2) as queries to search olfactory receptor genes against the genome assembly of Tibetan wild boar (Supplementary Note). Consistent with the result of Li et al.1, we observed a contraction in Olfactory genes in Tibetan wild boar

Rapid Evolution of Genes Involved in Learning and Energy Metabolism for Domestication of the Laboratory Rat

The laboratory rat, widely used in biomedical research, is domesticated from wild brown rat. The origin and genetic mechanism underlying domestication of the laboratory rat remain largely elusive. In the present study, large scale genomes supported a single origin for the laboratory rat, possibly from a sister group to wild rats from Europe/Africa/Middle East. Genomic and transcriptomic analyses uncovered many artificially selected genes (e.g., FOXP2, B3GAT1, and CLOCK) involved in the nervous system. These genes associate with learning ability and regulation of circadian rhythm, which likely enabled the successful domestication of the laboratory rat. Particularly, many genes, including mitochondrial genes responsible for energy metabolism, displayed a substantially increased expression in the brain of laboratory rats compared with wild rats. Our findings demystify the origin and evolution of this model animal, and provide insight into the process of its domestication.

An Evolutionary Genomic Perspective on the Breeding of Dwarf Chickens

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 POU1F1 and IGF1, are under strong positive selection. Three allopatric dwarf bantams (Serama, Yuanbao, and Daweishan) with different breeding-histories, form distinct clusters and exhibit unique population structures. Parallel genetic mechanisms underlay their variation in body size. These findings provide insights into the multiple and complex pathways, depending on genomic variation, that chicken can take in response to aviculture selection for dwarfism.

Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication

BackgroundNumerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process.ResultsWe analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome. Our population genomic analysis indicates that 419 lincRNAs potentially evolved during artificial selection related to the domestication of chicken, while a comparative transcriptomic analysis identified 68 lincRNAs that were differentially expressed under different conditions. We also found 47 lincRNAs linked to special phenotypes.ConclusionsOur study provides a comprehensive view of the genome-wide landscape of lincRNAs in chicken. This will promote a better understanding of the roles of lincRNAs in domestication, and the genetic mechanisms associated with the artificial selection of domestic animals.