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The common non-contact, automatic body size measurement methods based on the whole livestock point cloud are complex and prone to errors. Therefore, a cattle body measuring system is proposed. The system includes a new algorithm called dynamic unbalanced octree grouping (DUOS), based on PointNet++, and an efficient method of body size measurement based on segmentation results. This system is suitable for livestock body feature sampling. The network divides the cow into seven parts, including the body and legs. Moreover, the key points of body size are located in the different parts. It combines density measurement, point cloud slicing, contour extraction, point cloud repair, etc. A total of 137 items of cattle data are collected. Compared with some of the other models, the DUOS algorithm improves the accuracy of the segmentation task and mean intersection by 0.53% and 1.21%, respectively. Moreover, compared with the manual measurement results, the relative errors of the experimental measurement results are as follows: withers height, 1.18%; hip height, 1.34%; body length, 2.52%; thoracic circumference, 2.12%; abdominal circumference, 2.26%; and cannon circumference, 2.78%. In summary, the model is proven to have a good segmentation effect on cattle bodies and is suitable for cattle body size measurement.

Beibu Gulf’s (BBG) Indo-Pacific humpback dolphins present both a genetic differentiation and phenotypical differences from conspecifics from other areas of the South China Sea. Given the recent urbanization and industrialization in southern China, humpback dolphins from the BBG warrant conservation attention. However, this population’s demographic trend is unclear, making it hard to take conservation measures. To assess the population status of humpback dolphins in the BBG, photo-identification surveys were conducted between 2015 and 2019 in the inshore region surrounding the Dafeng River Estuary, which represents the most urbanized and industrialized coastal area of the BBG region. Robust design modeling suggested a constant survival for the female adults (0.89, 95% CI: 0.83–0.94). In comparison, the survival of the juvenile and sex-undetermined adults dropped from 0.92 (95% CI: 0.75–0.98) in 2015 to 0.86 (95% CI: 0.71–0.94) in 2016 and bounced back to 0.89 (95% CI: 0.80–0.94) in 2018. The low level of survival may justify the rapid decline in the annual population size from 156 (95% CI: 133–184) in 2015 to 102 (95% CI: 98–107) in 2019. We found little impact of emigration on the dolphin demographic process. Instead, the low and fluctuating survivals, although with overlapping confidence intervals, seemingly suggested a presence of strong marine stressor(s). Our study highlighted that obtaining high-resolution data is essential to improving our understanding of the demographic dynamics. Moreover, the anthropogenic stress in the BBG region should be quantitatively studied in both temporal and spatial perspectives, to help depict the ecological response of the dolphins to anthropogenic activities.

Small-and-coastal-form Bryde’s whales (Balaenoptera edeni edeni) are known to inhabit coastal and continental shelf waters. However, little is known on their ethological activities, especially underwater behaviours. Here, we deployed a suction cup tag on a small-and-coastal-form Bryde’s whale to study its ethological activities in Dapeng Bay, a coastal water of Shenzhen off the east Pearl River Estuary, China. The whale was tagged for 6 hours in total and displayed a head-lifting feeding behaviour 77 times during two tag deployments. The swim speed, dive duration and depth and bottom duration were collected by the tag to describe detailed information on dive profiles. The rate of feeding behaviours was observed decreasing with the presence of anthropogenic whale-approaching (AWA) boat activities occurring close (within 300 m) to the animal. Our study, for the first time, investigated behaviours of Bryde’s whales using suction cup tagging in Chinese waters. The results reveal the dive and feeding patterns of a small-and-coastal-form Bryde’s whale with short-term monitoring and provide a fundamental advancement in the knowledge of both the diving behaviour and the behavioural response of this subspecies to human activities. The findings are valuable for possible rescue of the investigated whale and for policy and management regarding conservation of this subspecies as well.

The Pearl River Delta (PRD) region on the southeast coast of China is among the largest and most populated metropolitan regions of the world, subjecting the Indo-Pacific humpback dolphins ( Sousa chinensis ) inhabiting coastal waters of this region – apparently the largest population of this species – to intense anthropogenic pressure. In this 5-year study (2011-2015), we applied mark-recapture techniques to quantify population parameters of humpback dolphins in the main body of the extensive estuarine system of the Pearl River, the Lingding Bay (LB), the most urbanized and industrialized part of PRD. The super-population size was estimated at 928 individuals (95% CI=823-1046), which however over-represents the latest number of extant animals. Annual estimates fluctuated between 708 and 750 dolphins, and likely reflect most accurately the latest/current number of humpback dolphins in waters of LB. Both the overall and annual estimates generated by our study are considerably lower than previously published abundance estimates. Apparent survival rates were generally low, estimated at 0.943 (SE = 0.008, 95% CI = 0.929-0.958) and 0.815 (SE = 0.025, 95% CI = 0.766-0.866) for adults and juveniles, respectively. In conjunction with limited recruitment, they may have led to a substantial decline in population numbers over the past two decades. Notably, dolphins exhibited heterogeneous apparent survival rates across the complex anthropogenic seascape of LB. Adult individuals that use Hong Kong waters as their primary habitat exhibited 6.2% higher survival rates than those in other parts of LB. This difference tripled (19.2%) for juveniles, a likely expression of their susceptibility to environmental and/or anthropogenic stresses. We suggest that the difference in survival is largely due to heterogeneous anthropogenic stressors that vary spatially across the estuary, among which habitat loss, pollution, and declining prey resources appear to be the primary threats. Based on our latest findings, we call for a strategic conservation planning with the highest priority given to preserve the remaining key dolphin habitats in Hong Kong waters, and to quantify and mitigate the impacts of major stressor(s) in Guangdong (mainland China) waters. Given the encroachment of ever-more-intense human activities on the coastal habitats of humpback dolphins, understanding their demographic response and the underlying mechanisms of the population processes may prove instrumental in the formulation of a conservation management strategy that can secure their continuous survival.

Compounds with incommensurate structural modulations have been extensively studied in last several decades. However, the relationship between structurally incommensurate/commensurate phases and associated electronic states remains enigmatic. Here we report the coexisting of complex incommensurate structures and highly unusual electronic roughness on the surface of in situ cleaved IrTe 2 by using scanning tunnelling microscopy/spectroscopy, corroborated with extensive density-functional theory calculations. This behaviour is traced to structural instability, which induces a structural transition from a trigonal to a triclinic lattice below transition temperature, giving rise to the formation of unidirectional structural modulations with distinct wavelengths, accompanied by the opening of a ‘pseudo’-gap in the surface layer. With further cooling the surface adopts a structure that reflects an ~6 × periodicity that is different from the bulk 5 × periodicity. Calculations show that the structure distortion is not associated with a charge density wave, but is rather associated with Te p-electron bonding. Understanding the structural relationship and electronic states between incommensurate/commensurate phases remains an ongoing challenge. Here, the authors report incommensurate structures and electronic roughness on the surface of cleaved IrTe 2 .

Understanding the population history of wide-ranging species, especially those ranging over varying landscapes, helps in deciphering the evolutionary force (s) that shaped the present genetic diversity/structure of regional fauna. In the shelf region, evolution of coastal morphology through glacial oscillations played an important role in shaping the contemporary genetic structure of coastal marine organisms, although the type and extent of such influence may differ between ecologically dissimilar species, such as marine mammals vs. other marine vertebrates. We reconstructed the demographic trajectories of four populations of the finless porpoise (Neophocaena spp.), covering a wide latitudinal range in the western Pacific and using coalescent-based techniques. Subsequently, we compare the findings with the evolution of suitable ecological niche by reconstructing historic sea level fluctuations with a maximum entropy method. Our results indicate that the finless porpoise was distributed along the continental slope during the low stand of sea level, while the post-glacial marine transgression enabled the porpoise to re-colonize a vast region of the shelf, leading to the most recent expansion of the genus in east Asia. We underscore that inferences of past demographic events are sensitive to the evolutionary model of microsatellite loci and the proportion of multi-step mutation. For coastal cetaceans inhabiting complex coastal habitats, caution has to be exercised when examining demographic parameters to prevent biased inferences due to historic gene flow during marine transgression. Systematic sampling scheme should be encouraged for rigorous quantification of demographic parameters, which may be further applied to more adaptable methods such as approximate Bayesian computation.

Chinese white dolphin (Sousa chinensis), also known as the Indo-Pacific humpback dolphin, has been classified as “Vulnerable” on the IUCN Red List of Threatened Species. It is a special cetacean species that lives in tropical and subtropical nearshore waters, with significant differences from other cetaceans. Here, we sequenced and assembled a draft genome of the Chinese white dolphin with a total length of 2.3 Gb and annotation of 18,387 protein-coding genes. Genes from certain expanded families are potentially involved in DNA replication and repairing, suggesting that they may be related to adaptation of this marine mammal to nearshore environments. We also discovered that its historical population had undergone a remarkable bottleneck incident before the Mindel glaciation. In addition, a comparative genomic survey on antihypertensive peptides (AHTPs) among five representative mammals with various residential habitats (such as remarkable differences in exogenous ion concentrations and sea depth) revealed that these small bioactive peptides were highly conserved among these examined mammals, and they had the most abundant hits in collagen subunit proteins, especially for two putative AHTP peptides Gly-Leu-Pro (GLP) and Leu-Gly-Pro (LGP). Our genome assembly will be a valuable resource for further genetic researches on adaptive ecology and conservation biology of cetaceans, and for in-depth investigations into bioactive peptides in aquatic and terrestrial mammals for development of peptide-based drugs to treat various human cardiovascular diseases.

Satellite-tagging is increasingly becoming a powerful biotelemetry approach to obtain remote measurement through tracking free-living cetaceans, which can fill knowledge gaps on cetaceans and facilitate conservation management. Here, we made a first biologging attempt on baleen whales in Chinese waters. An adult Bryde’s whale in the Beibu Gulf was tagged to investigate potential occurrence areas and migration routes of this poorly studied species. The whale was satellite-tracked for ~6 days with 71 filtered Argos satellite locations, resulting in a linear movement distance of 464 km. At each satellite-tracking location, the water depth was measured as 42.1 ± 24.8 m on average. During the satellite-tracking period, the whale’s moving speed was estimated at 5.33 ± 4.01 km/h. These findings expanded the known distribution areas of Bryde’s whales in the Beibu Gulf and provided an important scientific basis for the regional protection of this species. We suggest that fine-scale movements, habitat use, and migratory behavior of Bryde’s whales in the Beibu Gulf need more biotelemetry research, using long-term satellite-tracking tags and involving enough individuals. Furthermore, the genetic relationship and possible connectivity of Bryde’s whales in the Beibu Gulf and adjacent waters should be examined.

The rough-toothed dolphin (Steno bredanensis), the single extant species of the genus Steno, inhabits tropical and subtropical oceans. It is an attractive species for studying aquatic adaptation and evolution. The latest advances in high-throughput sequencing are transforming the study of marine mammals and contributing to understanding various phenomena at the species and population level by determining high-quality genomes. Here, to comprehensively understand the genetic features and explore the molecular basis of aquatic adaption, the chromosome-level genome assembly and comparative genomics analyses of S. bredanensis were performed. The 2.30 Gb final genome assembly of S. bredanensis (scaffold N50 length of 105.53 Mb) was obtained using single-tube long fragment read (stLFR) and Hi-C technologies. The genome assembly clearly revealed the preservation of large chromosomal fragments between S. bredanensis and the melon-headed whale (Peponocephala electra). The S. bredanensis genome contained 19,451 predicted protein-coding genes, of which about 92.33% have functional annotations. The genome assembly and gene sets showed high completeness, with a BUSCO score of 90.6% and 97.3%, respectively. We also identified several positively selected genes specific to S. bredanensis, which may be related to fat cell differentiation, tooth morphogenesis, and immunoregulatory activity. Finally, the demographic dynamics of S. bredanensis were estimated by the pairwise sequentially Markovian coalescent (PSMC) model and found that the population was affected by the climate at the time. We demonstrated that improved continuity and accuracy of the assembled sequence warranted the adoption of this chromosome-level genome as the reference genome and advanced the understanding of genetic features of the rough-toothed dolphin, which will be essential for future evolutionary studies and the protection of this species.

Physical and electrochemical phenomena at the surfaces of transition metal oxides and their coupling to local functionality remains one of the enigmas of condensed matter physics. Understanding the emergent physical phenomena at surfaces requires the capability to probe the local composition, map order parameter fields and establish their coupling to electronic properties. Here we demonstrate that measuring the sub-30-pm displacements of atoms from high-symmetry positions in the atomically resolved scanning tunnelling microscopy allows the physical order parameter fields to be visualized in real space on the single-atom level. Here, this local crystallographic analysis is applied to the in-situ -grown manganite surfaces. In particular, using direct bond-angle mapping we report direct observation of structural domains on manganite surfaces, and trace their origin to surface-chemistry-induced stabilization of ordered Jahn–Teller displacements. Density functional calculations provide insight into the intriguing interplay between the various degrees of freedom now resolved on the atomic level. The surface of complex oxides can show properties very different to the bulk. Here, the authors observe unexpected surface Jahn–Teller ordering on the surface of La 5/8 Ca 3/8 MnO 3 thin films that can be traced to the pattern of oxygen adatoms.