The Journal of the Acoustical Society of America, 2012
ABSTRACT Transmitting biosonar clicks and auditory evoked potential (AEP) responses triggered by ... more ABSTRACT Transmitting biosonar clicks and auditory evoked potential (AEP) responses triggered by the clicks were synchronously recorded during echolocation in an Atlantic bottlenose dolphin (Tursiops truncatus) trained to wear suction-cup EEG electrodes and to detect targets by echolocation. Three targets with target strengths of 34, 28 and 22 dB were used at a target distance of 2 to 6.5 m for each target. The results demonstrated that the AEP appeared to both transmitting echolocation clicks and echoes during echolocation, with AEP complexes consisting of alternative positive and negative waves. The echo-related AEP amplitudes were obviously lower than the transmitting click-related AEP amplitudes for all the targets at the investigated target distances. However, for targets with target strengths of 22 and 28 dB, the echo-related AEP response amplitudes increased at further target distances, demonstrating an overcompensation of echo attenuation with target distance in the echo-perception system of the dolphin biosonar. Measurement and analysis of transmitting click intensities showed that the click levels increased with target distance (R). The results demonstrated that a dual-component biosonar control system formed by intensity compensation behavior in both the transmission and receiving phases of a biosonar cycle exists synchronously in the dolphin biosonar system.
Dugongs ( Dugong dugon ) experienced a serious population decline in China during the twentieth c... more 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 o...
Immunization with peptides derived from apolipoprotein B-100 (ApoB-100) has been shown to amelior... more Immunization with peptides derived from apolipoprotein B-100 (ApoB-100) has been shown to ameliorate atherosclerosis in apolipoprotein E knockout (ApoE-/-) mice. However, the exact mechanism underlying the therapeutic effects remains elusive. To shed light on this mechanism, we immunized ApoE-/- mice that were fed a Western diet with either malondialdehyde-modified ApoB-100 peptide 210 (P210) emulsified in Freund's adjuvant or anti-malondialdehyde-modified P210 antibody (P210-Ab). Mice immunized with Freund's adjuvant or bovine serum albumin served as controls. Macrophages were incubated in vitro with oxidized low-density lipoprotein (ox-LDL) or ox-LDL plus P210-Ab. Our results show that P210-Ab promoted cholesterol efflux, inhibited lipid accumulation in vitro, and reduced plasma levels of high-sensitivity C-reactive protein (hsCRP), monocyte chemoattractant protein-1 (MCP-1), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6). Furthermore, dramatically increased...
2020 IEEE 11th Sensor Array and Multichannel Signal Processing Workshop (SAM), 2020
In this paper, we propose a block sparsity-based method to reconstruct marine mammal whistle call... more In this paper, we propose a block sparsity-based method to reconstruct marine mammal whistle calls. Considering the block structure of harmonic chirp, we form an overcomplete group chirp dictionary to enhance the estimating resolution under iterative greedy approach. The resulting sparse estimator, also named Block Orthogonal Matching Pursuit based Discrete Chirp Fourier Transform (Block-OMP based DCFT), is able to achieve an acceptable estimating result in a noisy environment. We illustrate the performance of the resulting estimator using both simulated and collected dolphin whistles.
The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallo... more The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallow waters from the South China Sea to the Asian coast of the Indian Ocean. However, a recent study suggested that the humpback dolphin from the Bay of Bengal may represent a distinct phylogenetic species. In this study, we sequenced 915-bp mtDNA segments from five geographic populations in both Chinese and Thai waters; together with previously published sequences, these data revealed that the ancestral Indo-Pacific humpback dolphin might have split during the transition from the Oligocene to Miocene (23.45 Mya, 95% HPD: 16.65 - 26.55 Mya), and then dispersed along the Pacific and Indian Ocean coasts of Asia. Genetic differentiation was detected between most of the examined populations, except for only a few pairwise populations in the northern South China Sea. Genetic differentiation/distance between the humpback dolphins from the northern and southern South China Sea met the sub-species threshold value proposed for marine mammals, whereas that between the humpback dolphins in the Pacific and the Indian Ocean was above the species threshold. Bayesian inference of historic gene flow indicated low but constant northward gene flow along the Indian Ocean coast; however, there was a recent abrupt increase in gene flow in the Pacific region, likely due to the shortening coastline at the low stand of sea level. Our results revealed that the current taxonomic classification of Indo-Pacific humpback dolphins may not reflect their phylogeography. This article is protected by copyright. All rights reserved.
Beaked whales represent around 25% of known extant cetacean species, yet they are the least known... more Beaked whales represent around 25% of known extant cetacean species, yet they are the least known of all marine mammals. Identification of many Mesoplodon species has relied on examination of a few stranded individuals. Particularly, the ginkgo-toothed beaked whale (Mesoplodon ginkgodens) and Deraniyagala's beaked whale (Mesoplodon hotaula) are among the least-known of beaked whale species, without confirmed sightings of living individuals to date. We present a sighting of three free-ranging individuals of M. ginkgodens / hotaula whale from a dedicated marine mammal vessel survey carried out in the South China Sea in April and May 2019. Photographic data (301 photographs) from the sighting were compared to photos of fresh stranded ginkgo-toothed beaked whale and Deraniyagala's beaked whale from both historical and unpublished records. We found that free-ranging M. gingkodens and M. hotaula individuals can be easily distinguished from other Mesoplodon species due to differences in melon and gape shapes and coloration patterns. However, accurate at-sea differentiation of M. ginkgodens and M. hotaula may not be possible due to high similarity in both coloration and scarring patterns. In addition to our photo-identification data, we collected what we believe to be the first preliminary descriptions of surfacing behavior and diving patterns of one of these species. Finally, the presence of scars possibly caused by fishing gear or marine litter raises concerns about anthropogenic impacts and conservation of these poorly-known species. This article is protected by copyright. All rights reserved.
The underwater soundscape is an important ecological element affecting numerous aquatic animals, ... more The underwater soundscape is an important ecological element affecting numerous aquatic animals, in particular dolphins, which must identify salient cues from ambient ocean noise. In this study, temporal variations in the soundscape of Jiaotou Bay were monitored from February 2016 to January 2017, where a population of Indo-Pacific humpback dolphins (Sousa chinensis) has recently been a regular sighting. An autonomous acoustic recorder was deployed in shallow waters, and 1/3-octave band sound pressure levels (SPLs) were calculated with central frequencies ranging from 25 Hz to 40 kHz, then were grouped into 3 subdivided bands via cluster analysis. SPLs at each major band showed significant differences on a diel, fishing-related period, seasonal, and tidal phase scale. Anthropogenic noise generated by passing ships and underwater explosions were recorded in the study area. The fish and dolphin acoustic activities both exhibited diel and seasonal variations, but no tidal cycle patterns. A negative significant relationship between anthropogenic sound detection rates and dolphin detection rates were observed, and fish detection rates showed no effect on dolphin detection rates, indicating anthropogenic activity avoidance and no forced foraging in dolphins in the study area. The results provide fundamental insight into the acoustic dynamics of an important Indo-Pacific humpback dolphin habitat within a coastal area affected by a rapid increase in human activity, and demonstrate the need to protect animal habitat from anthropogenic noises.
Despite an increasing appreciation in the importance of host–microbe interactions in ecological a... more Despite an increasing appreciation in the importance of host–microbe interactions in ecological and evolutionary processes, information on the gut microbial communities of some marine mammals is still lacking. Moreover, whether diet, environment, or host phylogeny has the greatest impact on microbial community structure is still unknown. To fill part of this knowledge gap, we exploited a natural experiment provided by an aquarium with belugas (Delphinapterus leucas) affiliated with family Monodontidae, Pacific white-sided dolphins (Lagenorhynchus obliquidens) and common bottlenose dolphin (Tursiops truncatus) affiliated with family Delphinidae, and Cape fur seals (Arctocephalus pusillus pusillus) affiliated with family Otariidae. Results show significant differences in microbial community composition of whales, dolphins, and fur seals and indicate that host phylogeny (family level) plays the most important role in shaping the microbial communities, rather than food and environment. ...
Information on the gut microbiome composition of different mammals could provide novel insights i... more 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 two 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 three whales were different. Our results revealed that the gut microbiome of one 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. This article is protected by copyright. All rights reserved.
Observer-based counts and photo-identification are two well-established methods with an extensive... more Observer-based counts and photo-identification are two well-established methods with an extensive use in cetacean studies. Using these two methods, group size has been widely reported, especially for small dolphins. Both methods may come with potential errors in estimating the group size, yet there is still a lack of comparison between both methods over a broad range of group size. Particularly, biogeographical variances in group size estimates were often mixed with methodological variances, making it difficult to compare estimates from different geographic regions. Here, group size estimates of a small, shallow-water, and near-shore delphinid species, Indo-Pacific humpback dolphins (Sousa chinensis), were simultaneously sampled using observer-based counts and photo-identification at three regions in the northern South China Sea. Data showed that dolphin group size from two methods were highly variable and associated with sampling regions. Generalized linear mixed models (GLMMs) ind...
Abstract The release of piscivorous fishes is considered crucial to alleviate eutrophication and ... more Abstract The release of piscivorous fishes is considered crucial to alleviate eutrophication and fish miniaturization, as well as to develop sustainable fisheries management strategy for Yangtze lakes. In order to promote the stock enhancement programme of a new released piscivorous fish species Culter mongolicus, growth, recapture rates, reproduction and impact of size-at-release for hatchery-reared juveniles were evaluated in three Yangtze shallow lakes during a five-year period. C. mongolicus displayed important growth capability with a body weight reaching commercial size (> 500 g) during the second released year and about 1500 g in the third year. However, a sharp decline of growth appeared quickly after several years of releasing, indicating possible issue of density-dependent growth caused by over-stocking. The recapture rates for one-month-old juveniles were less than 5%, but increased to more than 20 % when one-year-old fingerlings were selected as release size. Gonad examination and catch analysis showed that released juveniles could not succeed in building the recruitment stock due to over-fishing. Thus hatchery-reared juveniles should be released annually. Management actions that prioritize the release of fewer but larger fingerlings will improve the recapture rate and subsequent economic benefit. A new stock enhancement strategy that changes the present release-catch cycle from two years to one was proposed accordingly.
Reproductive hormones in serum concentrations of progesterone, estradiol and testosterone in fema... more Reproductive hormones in serum concentrations of progesterone, estradiol and testosterone in female Indo-Pacific bottlenose dolphins (Tursiops aduncus, n = 12) housed in Ocean Park Hong Kong were investigated in the present study. Results showed that, onset of puberty of captive Indo-Pacific bottlenose dolphins was at 5 y while sexual maturity is at six. Average serum progesterone concentrations in non-pregnant sexually mature individuals was 0.33(0.25-0.97) ng/mL (interquartile), significantly higher than in immature ones 0.26(0.25-0.38) ng/mL. This study found significant difference in serum estradiol concentrations between individuals at the onset of puberty (9.5±1.7 pg/mL, ±SD) and not (below detection limit 9 pg/mL). A slightly seasonal breeding pattern, with progesterone values tend to be higher from February to October (0.38[0.25-1.07] ng/mL) was inferred. During pregnancy, serum progesterone concentrations range from 10.54±8.74 ng/mL (indexed month post-conception [IMPC] 0) to 25.49±12.06 ng/mL (IMPC 2), and display a bimodal pattern with two peaks in early- (25.49±12.06 ng/mL, IMPC 2) and late-pregnancy (21.71±10.25 ng/mL, IMPC 12) respectively. Serum estradiol concentrations can seldom be detected in early-pregnancy and increase constantly in mid- (9.45±1.83 pg/mL) and late-pregnancy (11.88±3.81 pg/mL), with a spike (15.45±6.78 pg/mL) one month prior to delivery. Serum testosterone concentrations elevate significantly in IMPC 7 (0.36±0.10 ng/mL) compared to other months (0.16±0.10 ng/mL) of the year. The present study provides normal concentration profiles for some reproductive hormones in female Indo-Pacific bottlenose dolphins; and can contribute to the breeding monitoring of this species. Also, our study would shed further light on the reproductive physiology of small cetaceans. This article is protected by copyright. All rights reserved.
China was home to the world’s secondhighest diversity of gibbons in the 20th century, but these s... more China was home to the world’s secondhighest diversity of gibbons in the 20th century, but these species have all suffered extensive population declines, and regional species losses continue (1, 2). The Hainan gibbon (Nomascus hainanus), formerly widespread across Hainan Island (3), is now the rarest primate and among the rarest mammals (4). It represents one of the oldest gibbon lineages (5) but has received limited conservation attention compared with many other species in China. Hunting and habitat loss have reduced the species to a single high-elevation population in Bawangling National Nature Reserve (4, 6). Restricted to 15 km of fragmented rain forest within this reserve, the Hainan gibbon has persisted with fewer than 30 individuals for several decades (3, 6, 7). With China’s plan to establish a national park on Hainan, the species has a renewed chance at recovery, but challenges remain. Although the Hainan gibbon population received inconsistent financial support for protective measures in the 1980s and 1990s (6), conservation efforts since then have yielded promising signs. Two newly formed social groups were discovered in 2015 and 2019, and based on these positive trends, the total population size now likely exceeds 30 individuals (8). However, the species has extremely low genetic diversity (9), and forest degradation and conversion present barriers to the range expansion necessary Edited by Jennifer Sills for recovery (7). Increased enforcement has eliminated hunting as a threat (6, 7), but the tiny population is inherently vulnerable to stochastic events such as emerging zoonotic disease outbreaks and extreme climatic events. In 2015, the National Park system was established as China’s new protected area framework (10). Hainan Tropical Rainforest National Park will be established in 2020 (11) and will cover almost one-seventh of Hainan’s land area. The Hainan gibbon, as Hainan’s endemic primate (2), has been designated the national park’s flagship species (12). Raising the species’ profile is an important step, but crucial data gaps remain, and National Park management must be evidence-based and guided by new research. In addition to increasing funding, it is essential to improve monitoring with innovative technologies, to understand habitat structure and resource distribution, and to implement science-led forest restoration. In situ conservation remains the priority, but feasibility of intensive recovery strategies under potential emergency scenarios must be appraised (7). Assessment of future climate change impacts is also urgently needed. Effective Hainan gibbon conservation and long-term protection of China’s tropical biodiversity require robust scientific understanding, including insights from the recovery of other highly threatened species. Hui Liu*, Heidi Ma, Susan M. Cheyne, Samuel T. Turvey Wuzhishan National Long Term Forest Ecosystem Research Station, College of Forestry, Hainan University, Haikou 570228, China. Institute of Zoology, Zoological Society of London, London NW1 4RY, UK. Faculty of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK. *Corresponding author. Email: [email protected]
The Journal of the Acoustical Society of America, 2017
In 2014, Indo-Pacific humpback dolphins were recorded for the first time in waters southwest of H... more In 2014, Indo-Pacific humpback dolphins were recorded for the first time in waters southwest of Hainan Island, China. In this paper, the temporal occurrence of Indo-Pacific humpback dolphins in this region was detected by stationary passive acoustic monitoring. During the 130-day observation period (from January to July 2016), 1969 click trains produced by Indo-Pacific humpback dolphins were identified, and 262 ten-minute recording bins contained echolocation click trains of dolphins, of which 70.9% were at night and 29.1% were during the day. A diurnal rhythm with a nighttime peak in acoustic detections was found. Passive acoustic detections indicated that the Indo-Pacific humpback dolphins frequently occurred in this area and were detected mainly at night. This information may be relevant to conservation efforts for these dolphins in the near future.
The Journal of the Acoustical Society of America, 2019
Whistles emitted by Indo-Pacific humpback dolphins in Zhanjiang waters, China, were collected by ... more 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-tonoise 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.
Marine mammals are important models for studying convergent evolution and aquatic adaption, thus ... more Marine mammals are important models for studying convergent evolution and aquatic adaption, thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of sperm whale including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparison with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements (LINEs) and expanded gene families, and contraction of MHC region genes which were specific to sperm whale. By comparing to sheep and cattle, we conducted analysis of positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publically available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.
TheChinesegovernmentimplementedtheambitioussouth-northwatertransferproject(SNWTP),whichaimstotran... more TheChinesegovernmentimplementedtheambitioussouth-northwatertransferproject(SNWTP),whichaimstotransportwaterfromtheYangtzetothenorthofChina where water shortages are severe. Although the ecological impacts of this project havebeenaddressedpublically,thereremainsapoorunderstandingoftheeffectsof suchlarge-scalewatertransfersonthepopulationsofaquaticspecies.Thepotential ecologicalimpactsofsuchwatertransfersontheHongzeLakefishassemblagesare assessed here using Self-Organizing Map (SOM) and Random Forest (RF) modeling. Using SOM, twenty-three fish species in 15 sampling sites were classified into two assemblagesandfoursub-assemblagescorrespondingtofourdistincthabitats(deep watermacrophytes,deepwaterbaresilt,shallowwaterbaresilt,andshallowwater macrophytes).TheRFmodelfurthershowedthatwaterdepthandtransparencywere theabioticdriversunderpinningfishassemblagesinHongzeLake.AstheSNWTPis forecastedtomodifythedistributionofwaterdepthandwaterclarity,majorknock-on effectsareexpectedondownstreamlakefishassemblages.
The Journal of the Acoustical Society of America, 2012
ABSTRACT Transmitting biosonar clicks and auditory evoked potential (AEP) responses triggered by ... more ABSTRACT Transmitting biosonar clicks and auditory evoked potential (AEP) responses triggered by the clicks were synchronously recorded during echolocation in an Atlantic bottlenose dolphin (Tursiops truncatus) trained to wear suction-cup EEG electrodes and to detect targets by echolocation. Three targets with target strengths of 34, 28 and 22 dB were used at a target distance of 2 to 6.5 m for each target. The results demonstrated that the AEP appeared to both transmitting echolocation clicks and echoes during echolocation, with AEP complexes consisting of alternative positive and negative waves. The echo-related AEP amplitudes were obviously lower than the transmitting click-related AEP amplitudes for all the targets at the investigated target distances. However, for targets with target strengths of 22 and 28 dB, the echo-related AEP response amplitudes increased at further target distances, demonstrating an overcompensation of echo attenuation with target distance in the echo-perception system of the dolphin biosonar. Measurement and analysis of transmitting click intensities showed that the click levels increased with target distance (R). The results demonstrated that a dual-component biosonar control system formed by intensity compensation behavior in both the transmission and receiving phases of a biosonar cycle exists synchronously in the dolphin biosonar system.
Dugongs ( Dugong dugon ) experienced a serious population decline in China during the twentieth c... more 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 o...
Immunization with peptides derived from apolipoprotein B-100 (ApoB-100) has been shown to amelior... more Immunization with peptides derived from apolipoprotein B-100 (ApoB-100) has been shown to ameliorate atherosclerosis in apolipoprotein E knockout (ApoE-/-) mice. However, the exact mechanism underlying the therapeutic effects remains elusive. To shed light on this mechanism, we immunized ApoE-/- mice that were fed a Western diet with either malondialdehyde-modified ApoB-100 peptide 210 (P210) emulsified in Freund's adjuvant or anti-malondialdehyde-modified P210 antibody (P210-Ab). Mice immunized with Freund's adjuvant or bovine serum albumin served as controls. Macrophages were incubated in vitro with oxidized low-density lipoprotein (ox-LDL) or ox-LDL plus P210-Ab. Our results show that P210-Ab promoted cholesterol efflux, inhibited lipid accumulation in vitro, and reduced plasma levels of high-sensitivity C-reactive protein (hsCRP), monocyte chemoattractant protein-1 (MCP-1), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6). Furthermore, dramatically increased...
2020 IEEE 11th Sensor Array and Multichannel Signal Processing Workshop (SAM), 2020
In this paper, we propose a block sparsity-based method to reconstruct marine mammal whistle call... more In this paper, we propose a block sparsity-based method to reconstruct marine mammal whistle calls. Considering the block structure of harmonic chirp, we form an overcomplete group chirp dictionary to enhance the estimating resolution under iterative greedy approach. The resulting sparse estimator, also named Block Orthogonal Matching Pursuit based Discrete Chirp Fourier Transform (Block-OMP based DCFT), is able to achieve an acceptable estimating result in a noisy environment. We illustrate the performance of the resulting estimator using both simulated and collected dolphin whistles.
The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallo... more The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallow waters from the South China Sea to the Asian coast of the Indian Ocean. However, a recent study suggested that the humpback dolphin from the Bay of Bengal may represent a distinct phylogenetic species. In this study, we sequenced 915-bp mtDNA segments from five geographic populations in both Chinese and Thai waters; together with previously published sequences, these data revealed that the ancestral Indo-Pacific humpback dolphin might have split during the transition from the Oligocene to Miocene (23.45 Mya, 95% HPD: 16.65 - 26.55 Mya), and then dispersed along the Pacific and Indian Ocean coasts of Asia. Genetic differentiation was detected between most of the examined populations, except for only a few pairwise populations in the northern South China Sea. Genetic differentiation/distance between the humpback dolphins from the northern and southern South China Sea met the sub-species threshold value proposed for marine mammals, whereas that between the humpback dolphins in the Pacific and the Indian Ocean was above the species threshold. Bayesian inference of historic gene flow indicated low but constant northward gene flow along the Indian Ocean coast; however, there was a recent abrupt increase in gene flow in the Pacific region, likely due to the shortening coastline at the low stand of sea level. Our results revealed that the current taxonomic classification of Indo-Pacific humpback dolphins may not reflect their phylogeography. This article is protected by copyright. All rights reserved.
Beaked whales represent around 25% of known extant cetacean species, yet they are the least known... more Beaked whales represent around 25% of known extant cetacean species, yet they are the least known of all marine mammals. Identification of many Mesoplodon species has relied on examination of a few stranded individuals. Particularly, the ginkgo-toothed beaked whale (Mesoplodon ginkgodens) and Deraniyagala's beaked whale (Mesoplodon hotaula) are among the least-known of beaked whale species, without confirmed sightings of living individuals to date. We present a sighting of three free-ranging individuals of M. ginkgodens / hotaula whale from a dedicated marine mammal vessel survey carried out in the South China Sea in April and May 2019. Photographic data (301 photographs) from the sighting were compared to photos of fresh stranded ginkgo-toothed beaked whale and Deraniyagala's beaked whale from both historical and unpublished records. We found that free-ranging M. gingkodens and M. hotaula individuals can be easily distinguished from other Mesoplodon species due to differences in melon and gape shapes and coloration patterns. However, accurate at-sea differentiation of M. ginkgodens and M. hotaula may not be possible due to high similarity in both coloration and scarring patterns. In addition to our photo-identification data, we collected what we believe to be the first preliminary descriptions of surfacing behavior and diving patterns of one of these species. Finally, the presence of scars possibly caused by fishing gear or marine litter raises concerns about anthropogenic impacts and conservation of these poorly-known species. This article is protected by copyright. All rights reserved.
The underwater soundscape is an important ecological element affecting numerous aquatic animals, ... more The underwater soundscape is an important ecological element affecting numerous aquatic animals, in particular dolphins, which must identify salient cues from ambient ocean noise. In this study, temporal variations in the soundscape of Jiaotou Bay were monitored from February 2016 to January 2017, where a population of Indo-Pacific humpback dolphins (Sousa chinensis) has recently been a regular sighting. An autonomous acoustic recorder was deployed in shallow waters, and 1/3-octave band sound pressure levels (SPLs) were calculated with central frequencies ranging from 25 Hz to 40 kHz, then were grouped into 3 subdivided bands via cluster analysis. SPLs at each major band showed significant differences on a diel, fishing-related period, seasonal, and tidal phase scale. Anthropogenic noise generated by passing ships and underwater explosions were recorded in the study area. The fish and dolphin acoustic activities both exhibited diel and seasonal variations, but no tidal cycle patterns. A negative significant relationship between anthropogenic sound detection rates and dolphin detection rates were observed, and fish detection rates showed no effect on dolphin detection rates, indicating anthropogenic activity avoidance and no forced foraging in dolphins in the study area. The results provide fundamental insight into the acoustic dynamics of an important Indo-Pacific humpback dolphin habitat within a coastal area affected by a rapid increase in human activity, and demonstrate the need to protect animal habitat from anthropogenic noises.
Despite an increasing appreciation in the importance of host–microbe interactions in ecological a... more Despite an increasing appreciation in the importance of host–microbe interactions in ecological and evolutionary processes, information on the gut microbial communities of some marine mammals is still lacking. Moreover, whether diet, environment, or host phylogeny has the greatest impact on microbial community structure is still unknown. To fill part of this knowledge gap, we exploited a natural experiment provided by an aquarium with belugas (Delphinapterus leucas) affiliated with family Monodontidae, Pacific white-sided dolphins (Lagenorhynchus obliquidens) and common bottlenose dolphin (Tursiops truncatus) affiliated with family Delphinidae, and Cape fur seals (Arctocephalus pusillus pusillus) affiliated with family Otariidae. Results show significant differences in microbial community composition of whales, dolphins, and fur seals and indicate that host phylogeny (family level) plays the most important role in shaping the microbial communities, rather than food and environment. ...
Information on the gut microbiome composition of different mammals could provide novel insights i... more 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 two 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 three whales were different. Our results revealed that the gut microbiome of one 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. This article is protected by copyright. All rights reserved.
Observer-based counts and photo-identification are two well-established methods with an extensive... more Observer-based counts and photo-identification are two well-established methods with an extensive use in cetacean studies. Using these two methods, group size has been widely reported, especially for small dolphins. Both methods may come with potential errors in estimating the group size, yet there is still a lack of comparison between both methods over a broad range of group size. Particularly, biogeographical variances in group size estimates were often mixed with methodological variances, making it difficult to compare estimates from different geographic regions. Here, group size estimates of a small, shallow-water, and near-shore delphinid species, Indo-Pacific humpback dolphins (Sousa chinensis), were simultaneously sampled using observer-based counts and photo-identification at three regions in the northern South China Sea. Data showed that dolphin group size from two methods were highly variable and associated with sampling regions. Generalized linear mixed models (GLMMs) ind...
Abstract The release of piscivorous fishes is considered crucial to alleviate eutrophication and ... more Abstract The release of piscivorous fishes is considered crucial to alleviate eutrophication and fish miniaturization, as well as to develop sustainable fisheries management strategy for Yangtze lakes. In order to promote the stock enhancement programme of a new released piscivorous fish species Culter mongolicus, growth, recapture rates, reproduction and impact of size-at-release for hatchery-reared juveniles were evaluated in three Yangtze shallow lakes during a five-year period. C. mongolicus displayed important growth capability with a body weight reaching commercial size (> 500 g) during the second released year and about 1500 g in the third year. However, a sharp decline of growth appeared quickly after several years of releasing, indicating possible issue of density-dependent growth caused by over-stocking. The recapture rates for one-month-old juveniles were less than 5%, but increased to more than 20 % when one-year-old fingerlings were selected as release size. Gonad examination and catch analysis showed that released juveniles could not succeed in building the recruitment stock due to over-fishing. Thus hatchery-reared juveniles should be released annually. Management actions that prioritize the release of fewer but larger fingerlings will improve the recapture rate and subsequent economic benefit. A new stock enhancement strategy that changes the present release-catch cycle from two years to one was proposed accordingly.
Reproductive hormones in serum concentrations of progesterone, estradiol and testosterone in fema... more Reproductive hormones in serum concentrations of progesterone, estradiol and testosterone in female Indo-Pacific bottlenose dolphins (Tursiops aduncus, n = 12) housed in Ocean Park Hong Kong were investigated in the present study. Results showed that, onset of puberty of captive Indo-Pacific bottlenose dolphins was at 5 y while sexual maturity is at six. Average serum progesterone concentrations in non-pregnant sexually mature individuals was 0.33(0.25-0.97) ng/mL (interquartile), significantly higher than in immature ones 0.26(0.25-0.38) ng/mL. This study found significant difference in serum estradiol concentrations between individuals at the onset of puberty (9.5±1.7 pg/mL, ±SD) and not (below detection limit 9 pg/mL). A slightly seasonal breeding pattern, with progesterone values tend to be higher from February to October (0.38[0.25-1.07] ng/mL) was inferred. During pregnancy, serum progesterone concentrations range from 10.54±8.74 ng/mL (indexed month post-conception [IMPC] 0) to 25.49±12.06 ng/mL (IMPC 2), and display a bimodal pattern with two peaks in early- (25.49±12.06 ng/mL, IMPC 2) and late-pregnancy (21.71±10.25 ng/mL, IMPC 12) respectively. Serum estradiol concentrations can seldom be detected in early-pregnancy and increase constantly in mid- (9.45±1.83 pg/mL) and late-pregnancy (11.88±3.81 pg/mL), with a spike (15.45±6.78 pg/mL) one month prior to delivery. Serum testosterone concentrations elevate significantly in IMPC 7 (0.36±0.10 ng/mL) compared to other months (0.16±0.10 ng/mL) of the year. The present study provides normal concentration profiles for some reproductive hormones in female Indo-Pacific bottlenose dolphins; and can contribute to the breeding monitoring of this species. Also, our study would shed further light on the reproductive physiology of small cetaceans. This article is protected by copyright. All rights reserved.
China was home to the world’s secondhighest diversity of gibbons in the 20th century, but these s... more China was home to the world’s secondhighest diversity of gibbons in the 20th century, but these species have all suffered extensive population declines, and regional species losses continue (1, 2). The Hainan gibbon (Nomascus hainanus), formerly widespread across Hainan Island (3), is now the rarest primate and among the rarest mammals (4). It represents one of the oldest gibbon lineages (5) but has received limited conservation attention compared with many other species in China. Hunting and habitat loss have reduced the species to a single high-elevation population in Bawangling National Nature Reserve (4, 6). Restricted to 15 km of fragmented rain forest within this reserve, the Hainan gibbon has persisted with fewer than 30 individuals for several decades (3, 6, 7). With China’s plan to establish a national park on Hainan, the species has a renewed chance at recovery, but challenges remain. Although the Hainan gibbon population received inconsistent financial support for protective measures in the 1980s and 1990s (6), conservation efforts since then have yielded promising signs. Two newly formed social groups were discovered in 2015 and 2019, and based on these positive trends, the total population size now likely exceeds 30 individuals (8). However, the species has extremely low genetic diversity (9), and forest degradation and conversion present barriers to the range expansion necessary Edited by Jennifer Sills for recovery (7). Increased enforcement has eliminated hunting as a threat (6, 7), but the tiny population is inherently vulnerable to stochastic events such as emerging zoonotic disease outbreaks and extreme climatic events. In 2015, the National Park system was established as China’s new protected area framework (10). Hainan Tropical Rainforest National Park will be established in 2020 (11) and will cover almost one-seventh of Hainan’s land area. The Hainan gibbon, as Hainan’s endemic primate (2), has been designated the national park’s flagship species (12). Raising the species’ profile is an important step, but crucial data gaps remain, and National Park management must be evidence-based and guided by new research. In addition to increasing funding, it is essential to improve monitoring with innovative technologies, to understand habitat structure and resource distribution, and to implement science-led forest restoration. In situ conservation remains the priority, but feasibility of intensive recovery strategies under potential emergency scenarios must be appraised (7). Assessment of future climate change impacts is also urgently needed. Effective Hainan gibbon conservation and long-term protection of China’s tropical biodiversity require robust scientific understanding, including insights from the recovery of other highly threatened species. Hui Liu*, Heidi Ma, Susan M. Cheyne, Samuel T. Turvey Wuzhishan National Long Term Forest Ecosystem Research Station, College of Forestry, Hainan University, Haikou 570228, China. Institute of Zoology, Zoological Society of London, London NW1 4RY, UK. Faculty of Social Sciences, Oxford Brookes University, Oxford OX3 0BP, UK. *Corresponding author. Email: [email protected]
The Journal of the Acoustical Society of America, 2017
In 2014, Indo-Pacific humpback dolphins were recorded for the first time in waters southwest of H... more In 2014, Indo-Pacific humpback dolphins were recorded for the first time in waters southwest of Hainan Island, China. In this paper, the temporal occurrence of Indo-Pacific humpback dolphins in this region was detected by stationary passive acoustic monitoring. During the 130-day observation period (from January to July 2016), 1969 click trains produced by Indo-Pacific humpback dolphins were identified, and 262 ten-minute recording bins contained echolocation click trains of dolphins, of which 70.9% were at night and 29.1% were during the day. A diurnal rhythm with a nighttime peak in acoustic detections was found. Passive acoustic detections indicated that the Indo-Pacific humpback dolphins frequently occurred in this area and were detected mainly at night. This information may be relevant to conservation efforts for these dolphins in the near future.
The Journal of the Acoustical Society of America, 2019
Whistles emitted by Indo-Pacific humpback dolphins in Zhanjiang waters, China, were collected by ... more 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-tonoise 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.
Marine mammals are important models for studying convergent evolution and aquatic adaption, thus ... more Marine mammals are important models for studying convergent evolution and aquatic adaption, thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of sperm whale including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparison with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements (LINEs) and expanded gene families, and contraction of MHC region genes which were specific to sperm whale. By comparing to sheep and cattle, we conducted analysis of positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publically available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.
TheChinesegovernmentimplementedtheambitioussouth-northwatertransferproject(SNWTP),whichaimstotran... more TheChinesegovernmentimplementedtheambitioussouth-northwatertransferproject(SNWTP),whichaimstotransportwaterfromtheYangtzetothenorthofChina where water shortages are severe. Although the ecological impacts of this project havebeenaddressedpublically,thereremainsapoorunderstandingoftheeffectsof suchlarge-scalewatertransfersonthepopulationsofaquaticspecies.Thepotential ecologicalimpactsofsuchwatertransfersontheHongzeLakefishassemblagesare assessed here using Self-Organizing Map (SOM) and Random Forest (RF) modeling. Using SOM, twenty-three fish species in 15 sampling sites were classified into two assemblagesandfoursub-assemblagescorrespondingtofourdistincthabitats(deep watermacrophytes,deepwaterbaresilt,shallowwaterbaresilt,andshallowwater macrophytes).TheRFmodelfurthershowedthatwaterdepthandtransparencywere theabioticdriversunderpinningfishassemblagesinHongzeLake.AstheSNWTPis forecastedtomodifythedistributionofwaterdepthandwaterclarity,majorknock-on effectsareexpectedondownstreamlakefishassemblages.
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