Data for: Hidden population turnover of small odontocetes in the northwestern North Pacific during the Holocene
Data files
Feb 25, 2025 version files 4.72 KB
-
DataS1.dat
1.29 KB
-
DataS2.dat
1.29 KB
-
README.md
2.14 KB
Abstract
Despite numerous studies on the rise and fall of terrestrial megafauna in the Late Quaternary, knowledge about marine megafauna from this period remains limited. In this study, we performed radiocarbon dating and partial mitochondrial DNA sequencing from the skeletal remains of three species of small odontocetes (Pacific white-sided dolphins, Dall’s porpoises, and harbour porpoises) excavated from prehistoric archaeological sites around the Japanese shore dating back to 8500 – 1000 years ago (ya). Pacific white-sided dolphins that habituated the eastern coast of Hokkaido around 2000 ya belonged to different maternal groups than those from over 5000 ya and today. Furthermore, the species composition excavated from eastern Hokkaido sites varies between 5000 and 2000 ya. These findings suggest two significant population turnovers of small odontocetes on the east coast of Hokkaido, a transitional zone between the coastal area of East Asia and the offshore North Pacific. Notably, the first turnover, occurring between 5000 and 2000 ya, represents the oldest evidence of local population turnovers of marine megafauna during the Late Quaternary.
https://doi.org/10.5061/dryad.j9kd51cnm
Description of the data and file structure
Files are stored in BaySICS (Sandoval-Castellanos et al. 2014) input file (.dat) format
dataS1.dat (an input file for Scenario 1)
A01 – A34: contemporary Hokkaido individuals sequenced in this study
A35 – A38: Higashi-Kushiro individuals
B01 – B24: contemporary offshore individuals reported by Hayano et al. (2004)
C01 – C12: Nusamai individuals
dataS2.dat (an input file for Scenario 2)
A01 – A34: contemporary Hokkaido individuals sequenced in this study
A35 – A38: Higashi-Kushiro individuals
B01 – B12: Nusamai individuals
C01 – C24: contemporary offshore individuals reported by Hayano et al. (2004)
common parameters
Mutation rate of the mtDNA D-loop region: 0.32 [/site/million years] (Sigurðardóttir et al. 2000)
Ne1: 1000 (Suzuki et al. 2023)
No. of simulations: 10000
Compared summary statistics: HapTypes, PrivHaps, SegSites, PairDiffs, NucDiver, GenDiver, TajmaD.
References
Sandoval-Castellanos, E., Palkopoulou, E., & Dalén, L. (2014). Back to BaySICS: a user-friendly program for Bayesian statistical inference from coalescent simulations. PLoS ONE 9, e98011. doi:10.1371/journal.pone.0098011
Sigurðardóttir, S., Helgason, A., Gulcher, J. R., Stefansson, K., & Donnelly, P. (2000). The mutation rate in the human mtDNA control region. Am. J. Hum. Genet. 66, 1599-1609. doi:10.1086/302902
Suzuki, M., Ohno, K., Sawayama, E., Morinaga, S., Kishida, T., Matsumoto, T., & Kato, H. (2023). Genomics reveals a genetically isolated population of the Pacific white-sided dolphin (Lagenorhynchus obliquidens) distributed in the Sea of Japan. Mol. Ecol. 32, 881-891. doi:10.1111/mec.16797
Files and variables
File: DataS1.dat
Description: BaySICS input file for Scenario 1
File: DataS2.dat
Description: BaySICS input file for Scenario 2
