The complete mitochondrial genome of Japanese sea lion, <i>Zalophus japonicus</i> (Carnivora: Otariidae) analyzed using the excavated skeletal remains from Ulleungdo, South Korea

Kim, Eun-Bi; Kim, Myung Joon; Hwang, In-Seo; Park, Hyemin; Lee, Sang‐Heon; Kim, Hyun Woo

doi:10.1080/23802359.2021.1945503

Cited by 4 publications

(7 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The general features of Zalophus wollebaeki mitogenome—such as length, GC content, and PCGs, rRNAs, and tRNAs found—were consistent to those of the other two Zalophus mitogenomes: Z. japonicus (16,698 bp; Kim et al, 2021 ) and Z. californianus (16,677 bp; Arnason et al, 2006 ). It must be noted that Z. wollebaeki was sequenced with the Illumina method, while Z. japonicus and Z. californianus were sequenced through Sanger ( Arnason et al, 2006 ; Kim et al, 2021 ). All three sequences presented a high similitude regardless of the sequencing method used.…”

Section: Discussionsupporting

confidence: 70%

“…In animals, due to its high copy numbers compared to nuclear DNA, it is a particularly suited marker to be obtained from low-quality DNA samples ( DeSalle & Hadrys, 2017 ). For the genus Zalophus , complete mitogenome sequences have been published both for the California sea lion, Z. californianus , and the extinct Japanese sea lion, Z. japonicus ( Arnason et al, 2006 ; Kim et al, 2021 ). Here, we complement the mitogenomic resources for Zalophus genus, by a complete mitogenome, sequenced from DNA extracted from a scat sample of Z. wollebaeki .…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion (Zalophus wollebaeki) from scat DNA

Asadobay,

Urquía,

Künzel

et al. 2023

PeerJ

View full text Add to dashboard Cite

Background The Galapagos sea lion, Zalophus wollebaeki, is an endemic and endangered otariid, which is considered as a sentinel species of ecosystem dynamics in the Galapagos archipelago. Mitochondrial DNA is an important tool in phylogenetic and population genetic inference. In this work we use Illumina sequencing to complement the mitogenomic resources for Zalophus genus—the other two species employed Sanger sequencing—by a complete mitochondrial genome and a molecular clock of this species, which is not present in any case. Materials and Methods We used DNA obtained from a fresh scat sample of a Galapagos sea lion and shotgun-sequenced it on the Illumina NextSeq platform. The obtained raw reads were processed using the GetOrganelle software to filter the mitochondrial Zalophus DNA reads (∼16% survive the filtration), assemble them, and set up a molecular clock. Results From the obtained 3,511,116 raw reads, we were able to assemble a full mitogenome of a length of 16,676 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), and two ribosomal RNAs (rRNA). A time-calibrated phylogeny confirmed the phylogenetic position of Z. wollebaeki in a clade with Z. californianus, and Z. japonicus, and sister to Z. californianus; as well as establishing the divergence time for Z. wollebaeki 0.65 million years ago. Our study illustrates the possibility of seamlessly sequencing full mitochondrial genomes from fresh scat samples of marine mammals.

show abstract

Section: Discussionsupporting

confidence: 70%

Section: Introductionmentioning

confidence: 99%

Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion (Zalophus wollebaeki) from scat DNA

Asadobay,

Urquía,

Künzel

et al. 2023

PeerJ

View full text Add to dashboard Cite

show abstract

“…Based on the results from ancient DNA analysis extracted from skeletal remains of Japanese sea lions, Sakahira and Niimi [3] reported that Z. japonicus diverged from Z. californianus approximately 2.2 million years ago in the late Pliocene epoch. Recently, Kim et al [4] found that Z. japonicus was closely related to Z. californianus with 98.61% sequence identity based on the first completed mitochondrial genome sequence of Z. japonicus recently excavated from an archaeological site on Ulleungdo, Korea (Figure 1). [5] (grey color) and archaeological sites of the Zalophus japonicus in the East/Japan Sea from [3,4,[6][7][8].…”

Section: Introductionmentioning

confidence: 99%

“…Recently, Kim et al [4] found that Z. japonicus was closely related to Z. californianus with 98.61% sequence identity based on the first completed mitochondrial genome sequence of Z. japonicus recently excavated from an archaeological site on Ulleungdo, Korea (Figure 1). [5] (grey color) and archaeological sites of the Zalophus japonicus in the East/Japan Sea from [3,4,[6][7][8].…”

Section: Introductionmentioning

confidence: 99%

“…Not much information on the ecology and specific population of Z. japonicus is currently available, since they had been extinct before various scientific research works were conducted. Based on the fragmented historical and official records from Korea and Japan, we reconstructed the population of Z. japonicus on Dokdo (hereafter the Dokdo sea lion) using population models with ecological parameters of the California sea lion (Z. californianus) which is genetically closely related to the Dokdo sea lion [3,4]. The main objectives of this study was to reconstruct the population size of the Dokdo sea lion from a simple fitting curve with the existing historical records and to explore the effect of human hunting pressure on the population.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The First Population Simulation for the Zalophus japonicus (Otariidae: Sea Lions) on Dokdo, Korea

Lee

Cho

Kim

et al. 2022

JMSE

Self Cite

View full text Add to dashboard Cite

The Japanese sea lion (Z. japonicus) has been regarded as an extinct species since the last report on Dokdo in 1951. Not much ecological information on the Z. japonicus on Dokdo (hereafter Dokdo sea lion) is currently available. Using a discrete time stage-structured population model, we reconstructed the Dokdo sea lion population to explore the effect of human hunting pressure on them. This study provides the first estimate for the Dokdo sea lion population from 1900 to 1951. The reconstructed capture numbers of the Dokdo sea lion and the parameters estimated in this study were well matched with the recorded numbers and ecological parameters reported previously for the Californian sea lion. Based on the reconstructed population, their number rapidly declined after hunting started and it took less than 10 years for a 70% decline of the initial population, which would be considered to be an extinction risk. Since some caveats exist in this study, some caution about our results is necessary. However, this study demonstrates how rapidly human over-hunting can cause the extermination of a large local population. This study will be helpful to raise people’s awareness about endangered marine animals such as local finless porpoises in Korea.

show abstract

Dokdo sea lionZalophus japonicusgenome reveals its evolutionary trajectory before extinction

Kim,

Blazyte,

Choi

et al. 2024

Preprint

View full text Add to dashboard Cite

BackgroundThe Dokdo sea lion (Zalophus japonicus), commonly referred to as Gangchi in Korea and known as the Japanese sea lion, was endemic to the Northwest Pacific coast before becoming extinct in the 1950s. Little is known about its origins, speciation compared to otherOtariidaespecies or how the rapid decline affected the species’ genetic diversity.ResultsTo raise the Dokdo sea lion from this relative obscurity, we sequenced DNA from 16Z. japonicus’ bone fragments, obtained from Dokdo and Ulleungdo islands in Korea. Our analysis establishesZ. japonicusas the earliest diverged species within its genus, significantly redefining its evolutionary relationship with the California (Z. californianus) and Galapagos (Z. wollebaeki) sea lions. This genome-scale analysis clarifies the phylogeny ofZ. japonicus, shedding light on its speciation and the evolutionary pathways that shaped its genetic diversity before its extinction. In addition, we discovered, population decline of theZ. japonicusstarted already 1,000 years ago, however,Z. japonicusgenome maintained a relatively high heterozygosity despite, nearing extinction.ConclusionsOur genome-scale analysis eliminated ambiguity inZ. japonicusphylogeny, and shed light on the evolutionary pathways underlying its speciation. This study highlights the importance of the genome-scale analysis for extinct species to understand their complex evolutionary histories and conservation status.

show abstract

The complete mitochondrial genome of Japanese sea lion, Zalophus japonicus (Carnivora: Otariidae) analyzed using the excavated skeletal remains from Ulleungdo, South Korea

Cited by 4 publications

References 6 publications

Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion (Zalophus wollebaeki) from scat DNA

Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion (Zalophus wollebaeki) from scat DNA

The First Population Simulation for the Zalophus japonicus (Otariidae: Sea Lions) on Dokdo, Korea

Dokdo sea lionZalophus japonicusgenome reveals its evolutionary trajectory before extinction

Contact Info

Product

Resources

About