He-Qun Liu

Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins

Since their divergence from the terrestrial artiodactyls, cetaceans have fully adapted to an aquatic lifestyle, which represents one of the most dramatic transformations in mammalian evolutionary history. Numerous morphological and physiological characters of cetaceans have been acquired in response to this drastic habitat transition, such as thickened blubber, echolocation, and ability to hold their breath for a long period of time. However, knowledge about the molecular basis underlying these adaptations is still limited. The sequence of the genome of Tursiops truncates provides an opportunity for a comparative genomic analyses to examine the molecular adaptation of this species. Here, we constructed 11,838 high-quality orthologous gene alignments culled from the dolphin and four other terrestrial mammalian genomes and screened for positive selection occurring in the dolphin lineage. In total, 368 (3.1%) of the genes were identified as having undergone positive selection by the branch-site model. Functional characterization of these genes showed that they are significantly enriched in the categories of lipid transport and localization, ATPase activity, sense perception of sound, and muscle contraction, areas that are potentially related to cetacean adaptations. In contrast, we did not find a similar pattern in the cow, a closely related species. We resequenced some of the positively selected sites (PSSs), within the positively selected genes, and showed that most of our identified PSSs (50/52) could be replicated. The results from this study should have important implications for our understanding of cetacean evolution and their adaptations to the aquatic environment.

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.

Integrative analysis of young genes, positively selected genes and lncRNAs in the development of Drosophila melanogaster

BackgroundYoung genes and genes under positive selection commonly contribute to adaptive phenotypic evolution. Early developmental stages are very important for establishing phenotypes, which might be helpful for studying the evolutionary patterns of these rapidly evolving genes.ResultsHere, we performed a weighted gene co-expression network analysis to identify modules of co-expressed genes at different stages of Drosophila melanogaster development. We found that young genes, including duplicated, orphan, and young lncRNA genes, are significantly enriched among modules associated with specific developmental stages. In addition, genes undergoing rapid amino acid sequence evolution driven by positive selection showed a similar proportion of essentiality with other genes, and enrichment in modules for specific developmental stages.ConclusionsOur integrative analysis revealed important roles for the origin of new genes and rapid amino acid sequence evolution in development that may account for specific phenotype evolution in Drosophila melanogaster.

Multiple Episodes of Convergence in Genes of the Dim Light Vision Pathway in Bats

The molecular basis of the evolution of phenotypic characters is very complex and is poorly understood with few examples documenting the roles of multiple genes. Considering that a single gene cannot fully explain the convergence of phenotypic characters, we choose to study the convergent evolution of rod vision in two divergent bats from a network perspective. The Old World fruit bats (Pteropodidae) are non-echolocating and have binocular vision, whereas the sheath-tailed bats (Emballonuridae) are echolocating and have monocular vision; however, they both have relatively large eyes and rely more on rod vision to find food and navigate in the night. We found that the genes CRX, which plays an essential role in the differentiation of photoreceptor cells, SAG, which is involved in the desensitization of the photoactivated transduction cascade, and the photoreceptor gene RH, which is directly responsible for the perception of dim light, have undergone parallel sequence evolution in two divergent lineages of bats with larger eyes (Pteropodidae and Emballonuroidea). The multiple convergent events in the network of genes essential for rod vision is a rare phenomenon that illustrates the importance of investigating pathways and networks in the evolution of the molecular basis of phenotypic convergence.

The first test experiment performed at the electron cooler of storage rings in Lanzhou

The cooler storage ring (CSR) project was launched in 2000 at the Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou. In 2007, the installation was completed and the commissioning of CSRs gained great success, a new highly precise generation of collision experiments will become accessible even for the heaviest ion species. A commissioning RR experiment was performed at the electron cooler with Ar18+ ions, the results are reported. And the further development of the experiments at cooler will be discussed.

Mitochondrial genomes uncover the maternal history of the Pamir populations

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 Pamirs and the surrounding lowlands in Central Asia. We construct the Central Asian (including both highlanders and lowlanders) mtDNA haplogroup tree at the highest resolution. All the matrilineal components are assigned into the defined mtDNA haplogroups in East and West Eurasians. No basal lineages that directly emanate from the Eurasian founder macrohaplogroups M, N, and R are found. Our data support the origin of Central Asian being the result of East–West Eurasian admixture. The coalescence ages for more than 93% mtDNA lineages in Central Asians are dated after the last glacial maximum (LGM). The post-LGM and/or later dispersals/admixtures play dominant roles in shaping the maternal gene pool of Central Asians. More importantly, our analyses reveal the mtDNA heterogeneity in the Pamir highlanders, not only between the Turkic Kyrgyz and the Indo-European Tajik groups, but also among three highland Tajiks. No evidence supports positive selection or relaxation of selective constraints in the mtDNAs of highlanders as compared to that of lowlanders. Our results suggest a complex history for the peopling of Pamirs by multiple waves of migrations from various genetic resources during different time scales.

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.

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.

Divergence of dim-light vision among bats (order: Chiroptera) as estimated by molecular and electrophysiological methods.

Dim-light vision is present in all bats, but is divergent among species. Old-World fruit bats (Pteropodidae) have fully developed eyes; the eyes of insectivorous bats are generally degraded, and these bats rely on well-developed echolocation. An exception is the Emballonuridae, which are capable of laryngeal echolocation but prefer to use vision for navigation and have normal eyes. In this study, integrated methods, comprising manganese-enhanced magnetic resonance imaging (MEMRI), f-VEP and RNA-seq, were utilized to verify the divergence. The results of MEMRI showed that Pteropodidae bats have a much larger superior colliculus (SC)/ inferior colliculus (IC) volume ratio (3:1) than insectivorous bats (1:7). Furthermore, the absolute visual thresholds (log cd/m2•s) of Pteropodidae (−6.30 and −6.37) and Emballonuridae (−3.71) bats were lower than those of other insectivorous bats (−1.90). Finally, genes related to the visual pathway showed signs of positive selection, convergent evolution, upregulation and similar gene expression patterns in Pteropodidae and Emballonuridae bats. Different results imply that Pteropodidae and Emballonuridae bats have more developed vision than the insectivorous bats and suggest that further research on bat behavior is warranted.

The uncertainty of population relationship and divergence time inferred by the multiple sequentially Markovian coalescent model

The human colonization and adaptation of Tibetan Plateau attract wide concerns in recent years. To date, the permanent human occupation of Tibetan Plateau is a topic of hot dispute in archaeology [1, 2]. Massive genetic studies have been conducted to address this issue by estimating the divergence time between highland Tibetans and lowland populations (e.g., Han; Table S1). The comprehensive analyses of mitochondrial DNA and Y chromosome markers revealed at least two distinct migratory waves into the Tibetan Plateau. The early Upper Paleolithic migration was dated ~30 kilo years ago (kya); in addition, the later Neolithic colonization was traced back to 10–7 kya [3, 4]. By analyzing data of exome and genome-wide single-nucleotide polymorphisms, Tibetan and Han populations were proposed to diverge 2750 [5] and 4725 years ago [6], respectively. The two recent studies based on wholegenome re-sequencing dated this divergence to 15–9 kya [7] and 58–44 kya [8], respectively. Thus, the time for divergence between Tibetan and other populations is still in chaos. To address the issue, we employ the multiple sequential Markovian coalescent (MSMC) [9] approach to infer the demographic history of Tibetan and other lowland populations in East Asia. The high-depth (>30×) genomic sequencing data (Table S2) include Tibetan (n= 8, newly generated in this study), Han (n= 3), Tu (n= 2), Mongolian (n= 2), and Japanese (n= 3) [10]. We perform calculation for eight (i.e., four diploid genomes; Fig. 1c) and four (i.e., two diploid genomes; Fig. 1b) haplotypes, respectively. These computations are repeated with another independent sampling and the results are largely consistent (Figure S1,S2). We find that MSMC based on eight haplotypes presents more coalescent events than that based on four haplotypes. When considering four haplotypes, our MSMC results show two kinds of splits: the early one is 23–15 kya indicated by Han-Japanese and Tibetan-Han; the later one is 19–11 kya represented by Tibetan-Japanese, Tibetan-Mongolian, and Tibetan-Tu (Fig. 1b). It is unable to further discern the divergence differences within the two major splits (e.g., Han-Japanese and Tibetan-Han). As compared the MSMC results of four haplotypes, each pair of population divergence can be identified based on eight haplotypes (Fig. 1c), suggesting that genomic data of eight haplotypes are more informative to increase the molecular resolution. Confusingly, the inferred divergence patterns of eight haplotypes were different from those of four haplotypes. As for the Tibetan population, the early split inferred by using eight and four haplotypes is from Japanese at 25–20 kya and from Han at 23–15 kya, respectively. Both calculations suggest the Tibetan having closest relationship with the Mongolian population. The Tibetan-Mongolian divergence is dated as 19–11 and 16–10 kya by using eight and four haplotypes, respectively. When did Tibetan split from other populations? We cannot give a clear answer to this question based on current analyses of genomic data. Indeed, our results can provide some caveats here. Because of the relative high computation These authors contributed equally: Xing-Yan Yang, and Shan-Shan Dai.