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

Asadobay, Pacarina; Urquía, Diego O.; Künzel, Sven; Espinoza-Ulloa, Sebastian A.; Vences, Miguel; Páez-Rosas, Diego

doi:10.7717/peerj.16047

Cited by 3 publications

(1 citation statement)

References 41 publications

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“…This observation held true regardless of whether the genetic distances were estimated using autosomal SNVs or mtDNA (Additional file 2: Data S6). Our and previously reported [18] intrageneric Zalophus phylogeny aligns with f4-statistic that showed higher genetic affinity between Z. wollebaeki and Z. californianus compared to the affinity each of them had with Z. japonicus. The genetic distances between Z. japonicus and its extant genetic donors, C. ursinus and E. jubatus, showed significant disparities between estimates based on mtDNA and autosomal SNVs (Fig.…”

Section: Complex Introgressive Speciation Of Zalophus Species Explain...supporting

confidence: 82%

Dokdo sea lionZalophus japonicusgenome reveals its evolutionary trajectory before extinction

Kim,

Blazyte,

Choi

et al. 2024

Preprint

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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.

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Section: Complex Introgressive Speciation Of Zalophus Species Explain...supporting

confidence: 82%

Dokdo sea lionZalophus japonicusgenome reveals its evolutionary trajectory before extinction

Kim,

Blazyte,

Choi

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction

Kim,

Blazyte,

Choi

et al. 2024

Preprint

View full text Add to dashboard Cite

Background The Dokdo sea lion (Zalophus japonicus), commonly referred to as Gangchi in Korea also 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 and speciation compared to other Otariidae species or how the rapid decline affected the species’ genetic diversity. Results To raise the Dokdo sea lion from this relative obscurity, we sequenced DNA from 16 Z. japonicus’ bone fragments, obtained from Dokdo and Ulleungdo islands in Korea. Our genome-wide SNP-based analyses establish Z. japonicus as the earliest diverged species within its genus, significantly redefining its evolutionary relationship with the California (Z. californianus) and Galapagos (Z. wollebaeki) sea lions. Our research further elucidates the phylogeny of Z. japonicus, shedding light on the complexity of the genetic isolation process within its genus that was prompted by the geographic isolation of the three populations of Zalophus ancestral stock. Conversely, the genetic signature of Dokdo sea lion genome can be modeled as an evolutionary pathway involving gene flow from Otariidae species with shared range. In addition, we discovered, population decline of the Z. japonicus started already over 1,000 years ago, however, Z. japonicus genome maintained a relatively high heterozygosity despite nearing extinction. Conclusions Our genome-scale analysis has eliminated ambiguity in the phylogeny of Z. japonicus and shed light on the evolutionary pathways underlying its speciation and the genetic diversity before its extinction. Broadly, this study highlights the importance of genome-scale analysis for the extinct marine megafauna to elucidate the complexity of their gene flow and subsequent genetic diversities among extant species. Furthermore, this study offers retrospective genomic insights into the extinction process of a carnivorous marine mammal, information that could aid conservation efforts towards extant Otariidae species.

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Colonization record of the Galápagos’ vertebrate clades: Biogeographical issues plus a conservation insight

Ali,

Fritz

2024

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Our focus is the colonization history of the Galápagos’ vertebrate clades: 11 land-bound groups (eight reptiles, three rodents) and 13 taxa of flyers and swimmers (ten winged birds, two pinnipeds, one penguin). Using ‘colonization intervals’ and ‘colonization profiles’, it is clear that the two sets of taxa assembled very differently. The former includes older clades with between one, and potentially eight, predating the emergence of the oldest island (4 Mya). For the origin of some lineages, now-sunken landmasses associated with the Galápagos mantle-plume hotspot must have been involved, but for others it could reflect taxonomic uncertainties. In contrast, the taxa of flyers and swimmers are markedly younger, indicating either higher rates of colonization and extirpation for these sorts of animal, or continued genetic influx from mainland populations, or some combination of both factors. Concerning the first, possible drivers are the environmental stressors associated with the El Niño–La Niña climate system; the recent clades may be vulnerable to extreme events within the oscillation sequence, perhaps on ≥104-year timescales. Therefore, loose temporal thresholds might exist for the archipelago’s vertebrate groups beyond which selection fortifies them from the most challenging of seasonal states. Moreover, in a world of climate uncertainty, the findings appear relevant to conservation initiatives suggesting a focusing on the younger elements within the Galápagos’ biota.

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

Cited by 3 publications

References 41 publications

Dokdo sea lionZalophus japonicusgenome reveals its evolutionary trajectory before extinction

Dokdo sea lionZalophus japonicusgenome reveals its evolutionary trajectory before extinction

Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction

Colonization record of the Galápagos’ vertebrate clades: Biogeographical issues plus a conservation insight

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