Journal of Marine Science and Engineering

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21 pages, 2401 KiB

Open AccessArticle

Different Microsatellite Mutation Models May Lead to Contrasting Demographic Inferences through Genealogy-Based Approaches: A Case Study of the Finless Porpoise off the East Asian Coast

by Wenzhi Lin, Leszek Karczmarski, Chen Zeng, Dingyu Luo and Songhai Li

J. Mar. Sci. Eng. 2023, 11(3), 524; https://doi.org/10.3390/jmse11030524 - 28 Feb 2023

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Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Recent Advances in Marine Mammal Research in Indo-Pacific Area)

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11 pages, 3882 KiB

Open AccessArticle

Chromosome-Level Genome Assembly of the Rough-Toothed Dolphin (Steno bredanensis)

by Haiyu Gao, Hui Kang, Yaolei Zhang, Jiahao Wang, Wenzhi Lin, Peijun Zhang, Mingli Lin, Mingming Liu, Guangyi Fan and Songhai Li

J. Mar. Sci. Eng. 2023, 11(2), 418; https://doi.org/10.3390/jmse11020418 - 15 Feb 2023

Cited by 2 | Viewed by 2124

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Recent Advances in Marine Mammal Research in Indo-Pacific Area)

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11 pages, 1311 KiB

Open AccessArticle

Distribution and Abundance of the Blue Whale (Balaenoptera musculus indica) off Sri Lanka during the Southwest Monsoon 2018

by Liyanage U. S. P. Kirumbara, Jayasinghe R. P. P. Krishantha, Krakstad Jens-Otto and Arulananthan Kanapathipillai

J. Mar. Sci. Eng. 2022, 10(11), 1626; https://doi.org/10.3390/jmse10111626 - 02 Nov 2022

Cited by 4 | Viewed by 1984

Abstract

Blue whales Balaenoptera musculus are the most abundant and widely distributed cetacean species in Sri Lankan waters. A vessel-based opportunistic line transect survey focusing on marine mammals was conducted in Sri Lankan waters between 24 June to 12 July 2018, while an ecosystem [...] Read more.

Blue whales Balaenoptera musculus are the most abundant and widely distributed cetacean species in Sri Lankan waters. A vessel-based opportunistic line transect survey focusing on marine mammals was conducted in Sri Lankan waters between 24 June to 12 July 2018, while an ecosystem survey was performed by the R/V Dr. Fridtjof Nansen. The entire transect length was 2090 km within an area of 3895 km². Overall, 72% (n = 57) of blue whale observations were group assemblages ranging between 1 and 5 individuals out of a total of 79 sightings. The largest aggregations of blue whales were recorded at the intersection of the submarine canyon off the coastline of Mirissa and busy shipping lanes between Dondra Head and Galle, where previous ship strikes were recorded. Overall, the average observed group size was 2.64 (CV, 12.34%; 95% CI, 2.07–3.38), the average group density was 0.0029 km⁻² (CV, 35.96%; 95% CI, 0.00145–0.00610), and the total blue whale abundance within the survey area was 513 individuals (CV, 38.02%; 95% CI, 243–1083). These survey results fill vital knowledge gaps regarding the abundance and distribution of blue whales in Sri Lanka, which is essential for the establishment of management and conservation strategies. Full article

(This article belongs to the Special Issue Recent Advances in Marine Mammal Research in Indo-Pacific Area)

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16 pages, 2215 KiB

Open AccessArticle

First Suction Cup Tagging on a Small and Coastal Form Bryde’s Whale (Balaenoptera edeni edeni) in China to Investigate Its Dive Profiles and Foraging Behaviours

by Lijun Dong, Mingming Liu, Wenzhi Lin and Songhai Li

J. Mar. Sci. Eng. 2022, 10(10), 1422; https://doi.org/10.3390/jmse10101422 - 03 Oct 2022

Cited by 3 | Viewed by 1716

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Recent Advances in Marine Mammal Research in Indo-Pacific Area)

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20 pages, 2808 KiB

Open AccessArticle

Pygmy Blue Whale Diving Behaviour Reflects Song Structure

by Andrew M. Davenport, Christine Erbe, Micheline-Nicole M. Jenner, K. Curt S. Jenner, Benjamin J. Saunders and Robert D. McCauley

J. Mar. Sci. Eng. 2022, 10(9), 1227; https://doi.org/10.3390/jmse10091227 - 02 Sep 2022

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Abstract

Passive acoustic monitoring is increasingly employed to monitor whales, their population size, habitat usage, and behaviour. However, in the case of the eastern Indian Ocean pygmy blue whale (EIOPB whale), its applicability is limited by our lack of understanding of the behavioural context [...] Read more.

Passive acoustic monitoring is increasingly employed to monitor whales, their population size, habitat usage, and behaviour. However, in the case of the eastern Indian Ocean pygmy blue whale (EIOPB whale), its applicability is limited by our lack of understanding of the behavioural context of sound production. This study explored the context of singing behaviour using a 7.6-day biotelemetry dataset from a single EIOPB whale moving north from 31.5° S to 28.5° S along the Western Australian coast and a simultaneously collected, but separate, acoustic recording. Diving behaviour was classified using an automated classification schema. Singing was identified in the depth, pitch, and fluking time series of the dive profile. The EIOPB whale sang profusely as it migrated, spending more time singing during the day (76.8%) than at night (64.9%), and most during twilight periods (83.3%). The EIOPB whale almost exclusively produced the three-unit (P3) song while milling. It sang the two-unit (P2) song in similar proportions to the P3 song while travelling, except at night when P3 was sung 2.7 times more than P2. A correlation between singing depth, migration duration, and water temperature provides a biological basis to explain depth preferences for sound production, which may contribute to the cause of intra- and inter-annual sound frequency trends. Full article

(This article belongs to the Special Issue Recent Advances in Marine Mammal Research in Indo-Pacific Area)

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12 pages, 646 KiB

Open AccessArticle

The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation

by Yao Ming, Xueying Yu, Wei Liu, Jingzhen Wang and Wenhua Liu

J. Mar. Sci. Eng. 2022, 10(6), 834; https://doi.org/10.3390/jmse10060834 - 20 Jun 2022

Cited by 2 | Viewed by 1638

Abstract

Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback [...] Read more.

Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management. Full article

(This article belongs to the Special Issue Recent Advances in Marine Mammal Research in Indo-Pacific Area)

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18 pages, 3467 KiB

Open AccessArticle

Seasonal Trends and Diel Patterns of Downsweep and SEP Calls in Chilean Blue Whales

by Laura Redaelli, Sari Mangia Woods, Rafaela Landea and Laela Sayigh

J. Mar. Sci. Eng. 2022, 10(3), 316; https://doi.org/10.3390/jmse10030316 - 23 Feb 2022

Cited by 2 | Viewed by 2541

Abstract

To learn more about the occurrence and behaviour of a recently discovered population of blue whales, passive acoustic data were collected between January 2012 and April 2013 in the Chiloense ecoregion of southern Chile. Automatic detectors and manual auditing were used to detect [...] Read more.

To learn more about the occurrence and behaviour of a recently discovered population of blue whales, passive acoustic data were collected between January 2012 and April 2013 in the Chiloense ecoregion of southern Chile. Automatic detectors and manual auditing were used to detect blue whale songs (SEP calls) and D calls, which were then analysed to gain insights into temporal calling patterns. We found that D call rates were extremely low during winter (June–August) but gradually increased in spring and summer, decreasing again later during fall. SEP calls were absent for most winter and spring months (July–November) but increased in summer and fall, peaking between March and April. Thus, our results support previous studies documenting the austral summer residency of blue whales in this region, while suggesting that some individuals stay longer, highlighting the importance of this area as a blue whale habitat. We also investigated the daily occurrence of each call type and found that D calls occurred more frequently during dusk and night hours compared to dawn and day periods, whereas SEP calls did not show any significant diel patterns. Overall, these findings help to understand the occurrence and behaviour of endangered Chilean blue whales, enhancing our ability to develop conservation strategies in this important Southern Hemisphere habitat. Full article

(This article belongs to the Special Issue Recent Advances in Marine Mammal Research in Indo-Pacific Area)

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8 pages, 5285 KiB

Open AccessCase Report

Anomalous Coloration of Indo-Pacific Humpback Dolphins off Southern China

by Wenzhi Lin, Shenglan Chen, Ruiqiang Zheng, Agathe Serres, Binshuai Liu, Mingli Lin, Mingming Liu and Songhai Li

J. Mar. Sci. Eng. 2023, 11(2), 348; https://doi.org/10.3390/jmse11020348 - 04 Feb 2023

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Abstract

The Indo-Pacific humpback dolphin is characterized by a particular ontogenic change in body color from dark gray at birth to pure white (or with a few dark-gray spots) after reaching adulthood. Here, we report a spectrum of anomalous body color patterns observed on [...] Read more.

The Indo-Pacific humpback dolphin is characterized by a particular ontogenic change in body color from dark gray at birth to pure white (or with a few dark-gray spots) after reaching adulthood. Here, we report a spectrum of anomalous body color patterns observed on Indo-Pacific humpback dolphins off southern China. The occurrence of hypopigmentation and hyperpigmentation was described and compared among six putative dolphin populations. Low rates of anomalies in body color patterns were observed (<1%), except for hypopigmentation, which was prevalent in dolphins residing in the mid-Pearl-River-Delta region (3.3%). Full article

(This article belongs to the Special Issue Recent Advances in Marine Mammal Research in Indo-Pacific Area)

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