Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf.

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation

Intrauterine Growth Restriction Induces Adulthood Chronic Metabolic Disorder in Cardiac and Skeletal Muscles

ObjectiveAlthough population-based studies of intrauterine growth restriction (IUGR) demonstrated a series of postnatal complications, several studies identified that IUGR could definitely cause dysfunction of metabolism of cardiac and skeletal muscles in the perinatal period and early life. However, it is still unknown if such metabolic alternation would remain for long term or not, and whether normal protein diet administration postnatally would protect the IUGR offsprings from a “catch-up growth” and be able to reverse the premature metabolic remodeling.Materials and MethodsWe established an IUGR rat model with pregnant rats and a low-protein diet, and the developmental phenotypes had been carefully recorded. The cardiac and skeletal muscles had been collected to undergo RNA-seq.ResultsAccording to a series of comparisons of transcriptomes among various developmental processes, programmed metabolic dysfunction and chronic inflammation activity had been identified by transcriptome sequencing in IUGR offsprings, even such rats presented a normal developmental curve or body weight after normal postnatal diet feeding.ConclusionThe data revealed that IUGR had a significant adverse impact on long-term cardiovascular function in rats, even they exhibit good nutritional status. So that, the fetal stage adverse events would encode the lifelong disease risk, which could hide in young age. This study remaindered that the research on long-term molecular changes is important, and only nutrition improvement would not totally reverse the damage of IUGR

Virome and metagenomic analysis reveal the distinct distribution of microbiota in human fetal gut during gestation

Studies have shown that fetal immune cell activation may result from potential exposure to microbes, although the presence of microbes in fetus has been a controversial topic. Here, we combined metagenomic and virome techniques to investigate the presence of bacteria and viruses in fetal tissues (small intestine, cecum, and rectum). We found that the fetal gut is not a sterile environment and has a low abundance but metabolically rich microbiome. Specifically, Proteobacteria and Actinobacteria were the dominant bacteria phyla of fetal gut. In total, 700 species viruses were detected, and Human betaherpesvirus 5 was the most abundant eukaryotic viruses. Especially, we first identified Methanobrevibacter smithii in fetal gut. Through the comparison with adults’ gut microbiota we found that Firmicutes and Bacteroidetes gradually became the main force of gut microbiota during the process of growth and development. Interestingly, 6 antibiotic resistance genes were shared by the fetus and adults. Our results indicate the presence of microbes in the fetal gut and demonstrate the diversity of bacteria, archaea and viruses, which provide support for the studies related to early fetal immunity. This study further explores the specific composition of viruses in the fetal gut and the similarities between fetal and adults’ gut microbiota, which is valuable for understanding human fetal immunity development during gestation

Genome sequencing highlights the dynamic early history of dogs

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11-16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary

Phylogeography of the South China Field Mouse (Apodemus draco) on the Southeastern Tibetan Plateau Reveals High Genetic Diversity and Glacial Refugia

The southeastern margin of the Tibetan Plateau (SEMTP) is a particularly interesting region due to its topographic complexity and unique geologic history, but phylogeographic studies that focus on this region are rare. In this study, we investigated the phylogeography of the South China field mouse, Apodemus draco, in order to assess the role of geologic and climatic events on the Tibetan Plateau in shaping its genetic structure. We sequenced mitochondrial cytochrome b (cyt b) sequences in 103 individuals from 47 sampling sites. In addition, 23 cyt b sequences were collected from GenBank for analyses. Phylogenetic, demographic and landscape genetic methods were conducted. Seventy-six cyt b haplotypes were found and the genetic diversity was extremely high (π = 0.0368; h = 0.989). Five major evolutionary clades, based on geographic locations, were identified. Demographic analyses implied subclade 1A and subclade 1B experienced population expansions at about 0.052-0.013 Mya and 0.014-0.004 Mya, respectively. The divergence time analysis showed that the split between clade 1 and clade 2 occurred 0.26 Mya, which fell into the extensive glacial period (EGP, 0.5-0.17 Mya). The divergence times of other main clades (2.20-0.55 Mya) were congruent with the periods of the Qingzang Movement (3.6-1.7 Mya) and the Kun-Huang Movement (1.2-0.6 Mya), which were known as the most intense uplift events in the Tibetan Plateau. Our study supported the hypothesis that the SEMTP was a large late Pleistocene refugium, and further inferred that the Gongga Mountain Region and Hongya County were glacial refugia for A. draco in clade 1. We hypothesize that the evolutionary history of A. draco in the SEMTP primarily occurred in two stages. First, an initial divergence would have been shaped by uplift events of the Tibetan Plateau. Then, major glaciations in the Pleistocene added complexity to its demographic history and genetic structure

Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs

Abstract To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication, two ancient dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. We find dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow, which confounds previous inferences of dog origins. In dogs, the domestication bottleneck was severe involving a 17 to 49-fold reduction in population size, a much stronger bottleneck than estimated previously from less intensive sequencing efforts. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was far larger than represented by modern wolf populations. Conditional on mutation rate, we narrow the plausible range for the date of initial dog domestication to an interval from 11 to 16 thousand years ago. This period predates the rise of agriculture and, along with new evidence from variation in amylase copy number, implies that the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that surprisingly, none of the extant wolf lineages from putative domestication centers are more closely related to dogs, and the sampled wolves instead form a sister monophyletic clade. This result, in combination with our finding of dogwolf admixture during the process of domestication, suggests a re-evaluation of past hypotheses of dog origin is necessary. Finally, we also detect signatures of selection, including evidence for selection on genes implicated in morphology, metabolism, and neural development. Uniquely, we find support for selective sweeps at regulatory sites suggesting gene regulatory changes played a critical role in dog domestication

MC-UNet: Martian Crater Segmentation at Semantic and Instance Levels Using U-Net-Based Convolutional Neural Network

Crater recognition on Mars is of paramount importance for many space science applications, such as accurate planetary surface age dating and geological mapping. Such recognition is achieved by means of various image-processing techniques employing traditional CNNs (convolutional neural networks), which typically suffer from slow convergence and relatively low accuracy. In this paper, we propose a novel CNN, referred to as MC-UNet (Martian Crater U-Net), wherein classical U-Net is employed as the backbone for accurate identification of Martian craters at semantic and instance levels from thermal-emission-imaging-system (THEMIS) daytime infrared images. Compared with classical U-Net, the depth of the layers of MC-UNet is expanded to six, while the maximum number of channels is decreased to one-fourth, thereby making the proposed CNN-based architecture computationally efficient while maintaining a high recognition rate of impact craters on Mars. For enhancing the operation of MC-UNet, we adopt average pooling and embed channel attention into the skip-connection process between the encoder and decoder layers at the same network depth so that large-sized Martian craters can be more accurately recognized. The proposed MC-UNet is adequately trained using 2∼32 km radii Martian craters from THEMIS daytime infrared annotated images. For the predicted Martian crater rim pixels, template matching is subsequently used to recognize Martian craters at the instance level. The experimental results indicate that MC-UNet has the potential to recognize Martian craters with a maximum radius of 31.28 km (136 pixels) with a recall of 0.7916 and F1-score of 0.8355. The promising performance shows that the proposed MC-UNet is on par with or even better than other classical CNN architectures, such as U-Net and Crater U-Net

3D LiDAR and multi-technology collaboration for preservation of built heritage in China: A review

In recent years, the technical application of 3D LiDAR has gradually expanded to the field of built heritage. 3D scanning, high-precision measurement, and reconstruction have enriched the methods of built heritage preservation and significantly improved the quality of heritage preservation in China. 3D LiDAR has broken through the limitations of a single technology application and played a greater role in the field of heritage preservation on different scales. Through the collaboration of multi-technology, such as 3D printing, digital mapping, internet of things, machine learning, intelligent sensors, close-range photogrammetry, infrared detection, stress wave tomography, material analysis, XR technology, reverse engineering, etc., 3D LiDAR shows its technological advantages on exploring the remote real-time monitoring and digitization of the built heritage, geological and environmental data collection, prediction of sedimentation, deformation monitoring, weather monitoring,system life cycle health detection, digital reproduction of built heritage for developing scientific problems and engineering practices such as building contour recognition, information feature matching, structural reinforcement and damaged component replacement. In addition, through the docking with GIS, HBIM, XR, and CIM, it provides fine digital models and high-precision data benchmarks which contribute to the heritage visual reproduction; and through the docking with 3Ds Max, SketchUp, and other modeling software, it has contributed to the renewal design of the built heritage, space optimization, and the scientificity and rationality of the heritage value evaluation. However, past technology applications also highlighted many problems such as limited recorded information, a large amount of data, high difficulty in collaboration, non-standardized and fragmented data, and difficulty in data mining and comprehensive utilization. There are still deficiencies in building a built heritage data backplane, and the development of a dynamic, three-dimensional, intelligent and refined heritage monitoring system, and further research is needed on these issues. This study reviews the previous academic progress and application of 3D LiDAR in the reconstruction of built heritage and multi-technology collaboration in the process of preservation, clarifies the current research hotspots and methods, the frontier issues of concern, and also clarifies the specific problems and challenges in the future