Comparative genomics provides insights into the aquatic adaptations of mammals.

The ancestors of marine mammals once roamed the land and independently committed to an aquatic lifestyle. These macroevolutionary transitions have intrigued scientists for centuries. Here, we generated high-quality genome assemblies of 17 marine mammals (11 cetaceans and six pinnipeds), including eight assemblies at the chromosome level. Incorporating previously published data, we reconstructed the marine mammal phylogeny and population histories and identified numerous idiosyncratic and convergent genomic variations that possibly contributed to the transition from land to water in marine mammal lineages. Genes associated with the formation of blubber (NFIA), vascular development (SEMA3E), and heat production by brown adipose tissue (UCP1) had unique changes that may contribute to marine mammal thermoregulation. We also observed many lineage-specific changes in the marine mammals, including genes associated with deep diving and navigation. Our study advances understanding of the timing, pattern, and molecular changes associated with the evolution of mammalian lineages adapting to aquatic life.

Echolocation clicks of free-ranging Indo-Pacific finless porpoises (Neophocaena phocaenoides) in Hainan waters.

The echolocation clicks of free-ranging Indo-Pacific finless porpoises (IPFPs, Neophocaena phocaenoides) have been rarely studied in the wild. This paper aims at describing the echolocation-click characteristics of IPFPs and examining whether IPFPs adapt their sonar system to the habitats in Hainan waters, China. The echolocation clicks were recorded using a 13 elements star-shaped array of hydrophones. A total of 65 on-axis clicks were identified and analyzed. IPFPs use echolocation clicks with a source level (SL) of 158 ± 9 dB re: 1 µPa peak-peak, mean peak, and centroid frequency of 134 ± 3 kHz, -3 dB bandwidth of 14 ± 2 kHz and produce at inter-click intervals of 104 ± 51 ms. The results relative to other porpoises show that finless porpoises in Hainan waters produce clicks with moderate SLs and high peak frequency. These results could be useful in detecting the presence and estimating the density of IPFPs during passive acoustic monitoring in the study area and serve to shed light on the interpopulation variation of click characteristics of finless porpoises as well.

Ranging pattern development of a declining delphinid population: A potential cascade effect of vessel activities.

It is generally accepted that vessel activity causes various behavioral responses of cetaceans and undermines individual fitness. Whether or how it can lead to a demographic response of populations remains rarely examined. In the northern Beibu Gulf, China, vessel activities have sharply increased in the past two decades, while abnormal demographic dynamics was recently noted for the resident Indo-Pacific humpback dolphins. The present study first examined the humpback dolphins' utilization distribution (UD) from 2003 to 2019. Habitat suitability was then modeled with the sighting data collected before the most recent population reduction. Finally, we tried to disentangle the anthropogenic driver of dolphin demography by cross-referring the spatiotemporal development of dolphins' UD, vessel activities, and habitat suitability. Our results showed that the dolphins' UD shrank substantially during the port expansion in the early 2010s, and we suggest that the consequential increase in vessel activities might impose extra marine stressors on the resident humpback dolphins. To reduce the boat interaction, the dolphins steadily shifted their core area to a less suitable area in the east during 2015-2017, when unnaturally low survivals were recorded. Afterward, the dolphin core area partially shifted back to the more suitable area in the west, which corresponded to the improving dolphin survival in 2018. Our finding suggested that the vessel activity may be responsible for the dolphin displacement, while staying in the less suitable area may further lead to a more severe and acute demographic consequence on the population. The underlying and indirect impact of vessel activities as disclosed by the present study is particularly important for port management, marine planning, and conservation practice regarding coastal cetaceans, especially for those resident and endangered populations inhabiting the urbanized coastal areas.

Influence of acoustic habitat variation on Indo-Pacific humpback dolphin (Sousa chinensis) in shallow waters of Hainan Island, China.

The Indo-Pacific humpback dolphin (IPHD, Sousa chinensis) is a coastal species inhabiting tropical and warm-temperate waters. The presence of this vulnerable dolphin was recently discovered in shallow waters southwest of Hainan Island, China. The influence of the acoustic habitat on the distribution and behavior of IPHD was investigated using an array of passive acoustic platforms (n = 6) that spanned more than 100 km of coastline during a 75-day monitoring period. Its presence was assessed within 19 215 five-min recordings by classifying echolocation clicks using machine learning techniques. Spectrogram analysis was applied to further investigate the acoustic behavior of IPHD and to identify other prominent sound sources. The variation in the ambient noise levels was also measured to describe the spatiotemporal patterns of the acoustic habitat among the different sampling sites. Social and feeding sounds of IPHD (whistles and click-series of pulsed sounds) were identified together with other biological sources (finless porpoise, soniferous fishes, and snapping shrimps) and anthropogenic activities (ship noise, explosions, and sonars). Distribution, acoustic behavior, and habitat use of this nearshore dolphin species were strongly influenced by the abundance of soniferous fishes, and under similar conditions, the species was more acoustically active in locations with lower noise levels.

In vitro and in vivo evaluation of chitosan scaffolds combined with simvastatin-loaded nanoparticles for guided bone regeneration.

The objective of this study was to fabricate and characterize chitosan combined with different amounts of simvastatin-loaded nanoparticles and to investigate their potential for guided bone regeneration in vitro and in vivo. Different SIM-CSN formulations were combined into a chitosan scaffold (SIM-CSNs-S), and the morphology, simvastatin release profile, and effect on cell proliferation and differentiation were investigated. For in vivo experiments, ectopic osteogenesis and the critical-size cranial defect model in SD rats were chosen to evaluate bone regeneration potential. All three SIM-CSNs-S formulations had a porous structure and exhibited sustained simvastatin release. CSNs-S showed excellent degradation and biocompatibility characteristics. The 4 mg SIM-CSNs-S formulation stimulated higher BMSC ALP activity levels, demonstrated significantly earlier collagen enhancement, and led to faster bone regeneration than the other formulations. SIM-CSNs-S should have a significant effect on bone regeneration.

Echolocation signals of free-ranging pantropical spotted dolphins (Stenella attenuata) in the South China Sea.

Echolocation signals of free-ranging pantropical spotted dolphins (Stenella attenuata) in the western Pacific Ocean have not been studied much. This paper aims to describe the characteristics of echolocation signals of S. attenuata in the northern South China Sea. A six-arm star array with 13 hydrophones was used and a total of 131 on-axis clicks were identified to analyze the acoustic features of the echolocation signals of dolphins. The mean center frequency was 89 ± 13 kHz, with mean peak-to-peak sound source levels of 190 ± 6 dB re: 1 µPa @ 1 m. The mean -3 dB bandwidth and root-mean-square bandwidth were 62 ± 15 kHz and 26 ± 3 kHz, respectively, with mean -10 dB duration of 18 ± 4 µs and root-mean-square duration of 6 ± 2 µs. The results showed that click parameters of S. attenuata in the northern South China Sea are different from those of clicks of the species in Hawaii waters. The differences in click parameters may be due to both behavioral context and/or environmental adaptation of S. attenuata in different habitats.

Whistles emitted by Indo-Pacific humpback dolphins (Sousa chinensis) in Zhanjiang waters, China.

Whistles emitted by Indo-Pacific humpback dolphins in Zhanjiang waters, China, were collected by using autonomous acoustic recorders. A total of 529 whistles with clear contours and signal-to-noise ratio higher than 10 dB were extracted for analysis. The fundamental frequencies and durations of analyzed whistles were in ranges of 1785-21 675 Hz and 30-1973 ms, respectively. Six tonal types were identified: constant, downsweep, upsweep, concave, convex, and sine whistles. Constant type was the most dominant tonal type, accounting for 32.51% of all whistles, followed by sine type, accounting for 19.66% of all whistles. This paper examined 17 whistle parameters, which showed significant differences among the six tonal types. Whistles without inflections, gaps, and stairs accounted for 62.6%, 80.6%, and 68.6% of all whistles, respectively. Significant intraspecific differences in all duration and frequency parameters of dolphin whistles were found between this study and the study in Malaysia. Except for start frequency, maximum frequency and the number of harmonics, all whistle parameters showed significant differences between this study and the study conducted in Sanniang Bay, China. The intraspecific differences in vocalizations for this species may be related to macro-geographic and/or environmental variations among waters, suggesting a potential geographic isolation among populations of Indo-Pacific humpback dolphins.

Nanogels of carboxymethyl chitosan and lysozyme encapsulated amorphous calcium phosphate to occlude dentinal tubules.

This study aimed to develop of a rapid and effective method to occlude dentinal tubules using carboxymethyl chitosan and lysozyme (CMC/LYZ) nanogels with encapsulated amorphous calcium phosphate (ACP) based on the transformation of ACP to HAP. In this work, CMC/LYZ was used to stabilize ACP and form CMC/LYZ-ACP nanogels, and then the nanogel-encapsulated ACP was applied to exposed dentinal tubule surfaces. The morphology of the nanogels was examined by transmission electron microscopy (TEM). Distribution and quantity of elements in CMC/LYZ-ACP nanogels were determined by element mapping and energy dispersive X-Ray spectroscopy (EDX). Scanning electron microscopy (SEM) images, XRD measurements and nanoindentation were applied to check the efficacy of tubular occlusion. TEM revealed that CMC/LYZ-ACP nanogels were spherical dense gel particles with size approximately 50-500 nm. Element mapping and EDX indicated that C, N, O, Ca, P, and S in the microspheres are thoroughly represented. SEM images shows that the thickness of the coating layer was approximately 1-2 µm and the depth to which the mineralized substance enters the dentinal tubule was approximately 4-8 µm. XRD measurements and nanoindentation indicated that the occluding mineralized substance observed were similar to nature dentin. CMC can form spherical dense nanogels loaded with ACP under the participation of lysozyme. The CMC/LYZ-ACP nanogels could increase the dentinal tubule occluding effectiveness. These results indicated that finding and developing novel nanomaterials of CMC/LYZ-ACP would be an effective strategy for the treatment of dentin hypersensitivity.

Broadband ship noise and its potential impacts on Indo-Pacific humpback dolphins: Implications for conservation and management.

Ship noise pollution has raised considerable concerns among regulatory agencies and cetacean researchers worldwide. There is an urgent need to quantify ship noise in coastal areas and assess its potential biological impacts. In this study, underwater broadband noise from commercial ships in a critical habitat of Indo-Pacific humpback dolphins was recorded and analyzed. Data analysis indicated that the ship noise caused by the investigated commercial ships with an average length of 134 ± 81 m, traveling at 18.8 ± 2.5 km/h [mean ± standard deviation (SD), n = 21] comprises mid-to-high components with frequencies approaching and exceeding 100 kHz, and the ship noise could be sensed auditorily by Indo-Pacific humpback dolphins within most of their sensitive frequency range. The contributions of ship noise to ambient noise were highest in two third-octave bands with center frequencies of 8 and 50 kHz, which are within the sensitive hearing range of Indo-Pacific humpback dolphins and overlap the frequency of sounds that are biologically significant to the dolphins. It is estimated that ship noise in these third-octave bands can be auditorily sensed by and potentially affect the dolphins within 2290 ± 1172 m and 848 ± 358 m (mean ± SD, n = 21), respectively.

Mid- to high-frequency noise from high-speed boats and its potential impacts on humpback dolphins.

The impact of noise made by vessels on marine animals has come under increased concern. However, most measurements on noise from vessels have only taken into account the low-frequency components. For cetaceans operating in the mid- and high-frequencies, such as the Indo-Pacific humpback dolphin (Sousa chinensis), mid- to high-frequency noise components may be of more concern, in terms of their potential impacts. In this study, noise made by a small high-speed boat was recorded using a broadband recording system in a dolphin watching area focusing on the effects on humpback dolphins in Sanniang Bay, China. The high-speed boat produced substantial mid- to high-frequency noise components with frequencies to >100 kHz, measured at three speeds: ∼40, 30, and 15 km/h. The noise from the boat raised the ambient noise levels from ∼5 to 47 decibels (dB) root-mean-square (rms) across frequency bands ranging from 1 to 125 kHz at a distance of 20 to 85 m, with louder levels recorded at higher speeds and at closer distances. To conclude, the noise produced by the small high-speed boat could be heard by Sousa chinensis and therefore potentially had adverse effects on the dolphins.

Floating macro-litter pollution in the northern South China Sea.

Marine litter pollution, particularly plastics pollution, is an increasing global concern. While various studies have contributed useful information on this topic, there has been a scarcity of data on floating marine macro-litter (FMML) in poorly monitored areas such as the South China Sea (SCS). This paper describes a large-scale FMML assessment research in the northern SCS. Our data indicated the ubiquitous presence, abundant quantity, spatiotemporal variability, complex composition, and potential sources of FMML in the investigated region during boreal spring-summer periods over multiple years. According to observer-based records, the average FMML density was estimated to be 131.0 ± 91.8 items/km2 (mean ± SD), with anthropogenic FMML density of 118.7 ± 86.2 items/km2. Anthropogenic and natural items accounted for 90.6% and 5.5% of the total, respectively. Plastics (72.0%) and styrofoam (9.3%) dominated the recorded items. The great majority of items (92.1%) were characterized by small size of ≤20 cm. Labels of plastic bottle/packaging litter indicated that identifiable sources included surrounding countries of the SCS. Fishing activities were recognized as key sources of FMML, with 15.3% of FMML items likely being fishing-related. Globally, known estimates of FMML densities could vary from 0.002 to 578 items/km2, with plastics accounting for 34.8-99.0%. Therefore, marine pollution from anthropogenic FMML in our investigated area ranked at a medium-to-high level around the globe. To conclude, this study demonstrated that the SCS is one of the world's hotspot areas with FMML pollution and sheds light on marine litter pollution, especially plastics pollution, in this intensively human-exploited but poorly monitored region. In future research, FMML pollution in other sections of SCS and possible negative impacts of FMML on marine ecosystems and megafauna should be further examined.

A genome and single-nucleus cerebral cortex transcriptome atlas of the short-finned pilot whale Globicephala macrorhynchus.

Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short-finned pilot whale (Globicephala macrorhynchus) single-nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome-scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short-finned pilot whale by single-nucleus RNA-sequencing (snRNA-seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA-seq data from the short-finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution.

Species diversity and spatiotemporal patterns based on cetacean stranding records in China, 1950-2018.

Stranding data can provide conservation-valuable information on cetaceans over long time and large space, representing a low-cost but useful approach to monitor these indicator species and their inhabiting environments. Here, we established a national dataset by collating all available records of cetacean strandings (CSs) along >30,000-km coastline of China over seven decades. Between 1950 and 2018, a total of 1763 CSs were recorded across 36 cetacean species from eight families. Importantly, 30.5% of the recorded species are currently recognized as threatened levels on the IUCN Red List. In quantity, Odontocete species accounted for 89.9% of total CSs. In 1763 CSs, 91.8% were events of single individual. Furthermore, 31.9% and 42.4% were events of alive and dead animals, respectively. The number of CSs increased gradually from 1950 to 2018, and more rapidly between 1990 and 2018. CSs occurred in all months, while a seasonal pattern could be observed with 38.5% reports between March and June. The most commonly recorded species were finless porpoises (Neophocaena spp., n = 492) and Indo-Pacific humpback dolphin (Sousa chinensis, n = 291). The highest number of CSs (n = 478) was documented in Hong Kong, while the greatest species richness (n = 28) and the highest stranding density (24.6 CSs per 100-km coastline) were observed in Taiwan. Several CS hotspots were identified in the southern and eastern China, while hotspots differed among taxonomic categories. To conclude, these findings provided a comprehensive understanding of cetacean communities in the coastal waters of China, which are beneficial for improving further research, conservation, and management on cetaceans.

Tailoring S-vacancy concentration changes the type of the defect and photocatalytic activity in ZFS.

Defect engineering is crucial in the development of semiconductor catalyst activity. However, the influence of defect/vacancy density and states on catalysis remains vague. Thus, the optimized sulfur vacancy (SV) state is achieved among Fe-ZnS models (ZFS) via a chemical etching strategy for photocatalytic degradation (PD). As the SV concentration (ρSV) increases, the predominant state of vacancies changes from isolated defects－a state to a combination of a state and vacancy clusters－e state, as verified by positron annihilation and X-ray absorption fine structure spectra. However, the two types of defect states activated the intrinsic activity of the crystal via radically different mechanisms and exerted different degrees of influence on PD activity, as revealed by first-principles calculations and quantitative structure-activity relationship. Our results suggest that the SV activity is strongly influenced by its concentration in the ZFS crystal, while the vacancy concentration is not a control parameter for the PD activity, but a defect form. The underlying essence of atomic defects behavior affecting crystal catalytic activity at the atomic level is also revealed in this paper. Uncovering these structural relationships provide a theoretical basis for designing effective catalysts.

Functional extinction of dugongs in China.

Dugongs (Dugong dugon) experienced a serious population decline in China during the twentieth century, and their regional status is poorly understood. To determine their current distribution and status, we conducted a large-scale interview survey of marine resource users across four Chinese provinces and reviewed all available historical data covering the past distribution of dugongs in Chinese waters. Only 5% of 788 respondents reported past dugong sightings, with a mean last-sighting date of 23 years earlier, and only three respondents reported sightings from within the past 5 years. Historical records of dugongs peak around 1960 and then decrease rapidly from 1975 onwards; no records are documented after 2008, with no verified field observations after 2000. Based on these findings, we are forced to conclude that dugongs have experienced rapid population collapse during recent decades and are now functionally extinct in China. Our study provides evidence of a new regional loss of a charismatic marine megafaunal species, and the first reported functional extinction of a large vertebrate in Chinese marine waters. This rapid documented population collapse also serves as a sobering reminder that extinctions can occur before effective conservation actions are developed.

The biogeography of group sizes in humpback dolphins (Sousa spp.).

Humpback dolphins (Sousa spp.) are obligate shallow-water and resident species, and they typically live in fission-fusion societies composed of small-sized groups with changeable membership. However, we have scant knowledge of their behavioral ecology, starting with potential factors influencing inter-population variability of their group sizes. Here, we compiled a new global dataset of humpback dolphin group sizes based on 150 published records. Our data indicated an inter-specific consistency of group-living strategy among the 4 species in the Sousa genus, as these species preferred living in small-sized groups with a mean size of mostly no more than 10, a minimum size of single individual or small pairs, and a maximum size of several tens or ≈100. In addition, we clearly showed the geographic variations in group sizes of humpback dolphins at a global scale. We found that the geographic variations in humpback dolphin group sizes were primarily associated with the latitude, sea surface temperature, and abundance. To conclude, our findings provide insights into social dynamics and socioecological trade-offs of humpback dolphins, and help better understand how these resident animals adapted to their shallow-water habitats from the perspectives of biogeography and socioecology.

Microbial diversity and structure in the gastrointestinal tracts of two stranded short-finned pilot whales (Globicephala macrorhynchus) and a pygmy sperm whale (Kogia breviceps).

Information on the gut microbiome composition of different mammals could provide novel insights into the evolution of mammals and succession of microbial communities in different hosts. However, there is limited information on the gut microbiome composition of marine mammals, especially cetaceans because of sampling constraints. In this study, we investigated the diversity and composition of microbial communities in the stomach, midgut, and hindgut of 2 stranded short-finned pilot whales (Globicephala macrorhynchus) and hindgut of a stranded pygmy sperm whale (Kogia breviceps) by using 16S rRNA gene amplicon sequencing technology. On the basis of the 50 most abundant operational taxonomic units, principal coordinate analysis, and non-metric multidimensional scaling analysis, we confirmed that the gut microbial communities of the 3 whales were different. Our results revealed that the gut microbiome of 1 stranded short-finned pilot whale GM16 was dominated by Firmicutes (mainly Clostridium) and Fusobacteria; whereas that of the other pilot whale GM19 was composed of Gammaproteobacteria and Bacteroidetes (mainly Vibrio and Bacteroides, respectively), probably caused by intestinal disease and antibiotic treatment. The gut microbiome of the pygmy sperm whale was dominated by Firmicutes and Bacteroidetes. Moreover, different gastrointestinal tract regions harbored different microbial community structures. To our knowledge, this is the first report of the gut microbiome of short-finned pilot whales, and our findings will expand our current knowledge on microbial diversity and composition in the gastrointestinal tract of cetaceans.

Expression of miR-192-5p in colon cancer serum and its relationship with clinicopathologic features.

Colon cancer has a poor prognosis due to a lack of biomarkers for early diagnosis and prognosis. The present study analyzed serum miR-192-5p expression levels in colon cancer patients and their correlations with clinicopathologic features. Relative mRNA expression was assessed by real-time fluorescence-based quantitative PCR in the serum of 164 colon cancer patients and 60 healthy controls. Patients were enrolled in a high or low miR-192-5p group according to the cutoff value determined by ROC curve analysis. The Kaplan-Meier method and univariate and multivariate Cox regression models were applied to analyze the risk factors influencing the postoperative survival of colon cancer patients. miR-192-5p mRNA expression in the colon cancer group was significantly reduced compared with the control group (P<0.01). Low miR-192-5p expression was significantly associated with a poor differentiation degree, lymphatic metastasis, vascular invasion, and high TNM stage (P=0.027, 0.001, 0.010, and <0.001, respectively). Colon cancer patients in the low miR-192-5p group exhibited a low survival rate (P<0.001). The independent risk factors for postoperative survival included lymphatic metastasis, a high TNM stage, and miR-192-5p<1.16 (P=0.017, 0.025, and 0.008, respectively). miR-192-5p may represent a promising biomarker for early diagnosis and prognosis in colon cancer patients.

Cetacean occurrence and diversity in whale-watching waters off Mirissa, Southern Sri Lanka.

Scientific information is vital to the conservation of cetaceans and the management of whale-watching activities. The southern coastal waters of Sri Lanka are near a narrow continental shelf and biologically abundant in cetacean species. Although the occurrence of cetaceans has been investigated in certain waters of Sri Lanka, few surveys have been conducted along the southern coast. To fill this gap, we conducted boat-based surveys from January to May 2017 to investigate the occurrence, diversity, and behavior of cetaceans in the waters off Mirissa, covering a survey area of 788.9 km2 . During 55 survey days, we recorded a total of 242 cetacean sightings and identified at least 9 species (3 mysticetes and 6 odontocetes). The blue whale was the most common mysticete species (167 of 174 mysticete encounters), followed by the Omura's whale (4 of 174) and Bryde's whale (3 of 174). The spinner dolphin was the most common odontocete species (28 of 68 odontocete encounters), followed by the sperm whale (18 of 68), common bottlenose dolphin (13 of 68), short-finned pilot whale (5 of 68), melon-headed whale (2 of 68), and killer whale. Blue whales and sperm whales exhibited a clear preference for outer shelf and high slope areas, and blue whales were observed feeding along these waters. The present study provides near-baseline information on cetacean occurrence and diversity in whale-watching waters off southern Sri Lanka, and highlights the urgent need for proper management strategies for whale-watching activities.

Photo-identification comparison of four Indo-Pacific humpback dolphin populations off southeast China.

Indo-Pacific humpback dolphins (Sousa chinensis) inhabit shallow coastal waters of the Indo-Pacific region including southeast China, with at least 6 putative populations identified to date in Chinese waters. However, the connectivity among these populations has not yet been fully investigated. In the present study, we compared and cross-matched photographic catalogs of individual dolphins collected to date in the Pearl River Delta region, Leizhou Bay, Sanniang Bay, and waters southwest of Hainan Island, a total of 3158 individuals, and found no re-sighting of individual dolphins among the 4 study areas. Furthermore, there was a notable difference in the pigmentation pattern displayed by individuals from these 4 regions. We suggest that this may be a phenotypical expression of fine-scale regional differentiation among humpback dolphin groups, possibly distinct populations. Given the considerable conservation management implications it may carry (e.g. definition of management units), further research is much needed.