Reconstructing the population history of the sandy beach amphipod Haustorioides japonicus using the calibration of demographic transition (CDT) approach


Autoři: Kay Sakuma aff001;  Risa Ishida aff001;  Taketoshi Kodama aff001;  Yoshitake Takada aff001
Působiště autorů: Japan Sea National Fisheries Research Institute, Fisheries Research and Education Agency, Niigata, Japan aff001
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223624

Souhrn

Calibration of the molecular rate is one of the major challenges in marine population genetics. Although the use of an appropriate evolutionary rate is crucial in exploring population histories, calibration of the rate is always difficult because fossil records and geological events are rarely applicable for rate calibration. The acceleration of the evolutionary rate for recent coalescent events (or more simply, the time dependency of the molecular clock) is also a problem that can lead to overestimation of population parameters. Calibration of demographic transition (CDT) is a rate calibration technique that assumes a post-glacial demographic expansion, representing one of the most promising approaches for dealing with these potential problems in the rate calibration. Here, we demonstrate the importance of using an appropriate evolutionary rate, and the power of CDT, by using populations of the sandy beach amphipod Haustorioides japonicus along the Japanese coast of the northwestern Pacific Ocean. Analysis of mitochondrial sequences found that the most peripheral population in the Pacific coast of northeastern Honshu Island (Tohoku region) is genetically distinct from the other northwestern Pacific populations. By using the two-epoch demographic model and rate of temperature change, the evolutionary rate was modeled as a log-normal distribution with a median rate of 2.2%/My. The split-time of the Tohoku population was subsequently estimated to be during the previous interglacial period by using the rate distribution, which enables us to infer potential causes of the divergence between local populations along the continuous Pacific coast of Japan.

Klíčová slova:

Evolutionary rate – Haplotypes – Phylogenetic analysis – Phylogenetics – Population genetics – Beaches – Fossil calibration – Marine geology


Zdroje

1. Ho SYW, Duchêne S. Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol. 2014;23: 5947–5965. doi: 10.1111/mec.12953 25290107

2. Grant WS. Problems and cautions with sequence mismatch analysis and Bayesian skyline plots to infer historical demography. J Hered. 2015;106: 333–346. doi: 10.1093/jhered/esv020 25926628

3. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. Time-dependent rates of molecular evolution. Mol Ecol. 2011;20: 3087–3101. doi: 10.1111/j.1365-294X.2011.05178.x 21740474

4. Palumbi SR. Genetic divergence, reproductive isolation, and marine speciation. Annu Rev Ecol Syst. 1994;25: 547–572. doi: 10.1146/annurev.es.25.110194.002555

5. Kumar S. Molecular clocks: four decades of evolution. Nat Rev Genet. 2005;6: 654–662. doi: 10.1038/nrg1659 16136655

6. Bromham L. The genome as a life-history character: Why rate of molecular evolution varies between mammal species. Phil Trans R Soc Lond B Biol Sci. 2011;366: 2503–2513.

7. Ho SYW, Phillips MJ, Cooper A, Drummond AJ. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 2005;22: 1561–1568. doi: 10.1093/molbev/msi145 15814826

8. Burridge CP, Craw D, Fletcher D, Waters JM. Geological dates and molecular rates: Fish DNA sheds light on time dependency. Mol Biol Evol. 2008;25: 624–633. doi: 10.1093/molbev/msm271 18281273

9. Crandall ED, Sbrocco EJ, DeBoer TS, Barber PH, Carpenter KE. Expansion dating: Calibrating molecular clocks in marine species from expansions onto the Sunda Shelf following the last glacial maximum. Mol Biol Evol. 2012;29: 707–719. doi: 10.1093/molbev/msr227 21926069

10. Grant WS, Liu M, Gao T, Yanagimoto T. Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species). Mol Phylogenet Evol. Elsevier Inc.; 2012;65: 203–212. doi: 10.1016/j.ympev.2012.06.006 22750109

11. Hoareau TB. Late glacial demographic expansion motivates a clock overhaul for population genetics. Syst Biol. 2016;65: 449–464. doi: 10.1093/sysbio/syv120 26683588

12. Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher A V, et al. Rise and fall of the Beringian steppe bison. Science. 2004;306: 1561–1565. doi: 10.1126/science.1101074 15567864

13. Takada Y, Sakuma K, Fujii T, Kojima S. Phylogeography of the sandy beach amphipod Haustorioides japonicus along the Sea of Japan: Paleogeographical signatures of cryptic regional divergences. Estuar Coast Shelf Sci. 2018; 200: 19–30. doi: 10.1016/j.ecss.2017.10.012

14. Kamihira Y. Ecological studies of sand-burrowing amphipod Haustorioides japonicus (Dogielinotidae), on the south-western Hokkaido, Japan. Rev Hakodate Univ. 1992;1: 1–106 (in Japanese).

15. Takada Y, Kajihara N, Mochizuki S, Murakami T. Effects of environmental factors on the density of three species of peracarid crustaceans in micro-tidal sandy shores in Japan. Ecol Res. 2015; 30: 101–109. doi: 10.1007/s11284-014-1215-5

16. Kamihira Y. Geographic distribution of Dogielinotidae amphipods in the Northwest Pacific. The Rev Hakodate Univ. 2000; 31: 91–99 (in Japanese).

17. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005;22: 1185–1192. doi: 10.1093/molbev/msi103 15703244

18. Asahida T, Kobayashi T, Saitoh K, Nakayama I. Tissue preservation and total DNA extraction form fish stored at ambient temperature using buffers containing high concentration of urea. Fish Sci. 1996;62: 727–730. doi: 10.2331/fishsci.62.727

19. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Hansson B, editor. Mol Mar Biol Biotechnol. 1994;3: 294–9. 7881515

20. Maddison DR, Maddison WP. MacClade 4: Analysis of phylogeny and character evolution. Version 4.0. 2000. Sinauer Associates, Sunderland, Massachusetts.

21. Katoh K, Standley DM. MAFFT Multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30: 772–780. doi: 10.1093/molbev/mst010 23329690

22. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for Bigger Datasets. Mol Biol Evol. 2016;33: 1870–1874. doi: 10.1093/molbev/msw054 27004904

23. Excoffier L, Lischer HEL. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010;10: 564–567. doi: 10.1111/j.1755-0998.2010.02847.x 21565059

24. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23: 254–267. doi: 10.1093/molbev/msj030 16221896

25. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123: 585–595. 2513255

26. Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 1997;147: 915–925. 9335623

27. Ramos-Onsins SE, Rozas J. Statistical properties of new neutrality tests against population growth. Mol Biol Evol. 2002;19: 2092–2100. doi: 10.1093/oxfordjournals.molbev.a004034 12446801

28. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 2017;34: 3299–3302. doi: 10.1093/molbev/msx248 29029172

29. Drummond AJ, Suchard M a., Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29: 1969–1973. doi: 10.1093/molbev/mss075 22367748

30. Rambaut A, Suchard MA, Drummond AJ. Tracer v1.6. 2013. Available from http://tree.bio.ed.uk/software/tracer/

31. Jouzel J, Masson-Delmotte V, Cattani O, Dreyfus G, Falourd S, Hoffmann G, et al. Orbital and millennial Antarctic climate variability over the past 800,000 years. Science. 2007;317: 793–796. doi: 10.1126/science.1141038 17615306

32. Venables WN, Ripley BD. Modern Applied Statistics with S. Fourth Edition. 2002. Springer, New York.

33. R Core Team. R: A language and environment for statistical computing. R foundation for statistical computing. 2018. Vienna, Austria. URL https://www.R-project.org/.

34. Knowlton N, Weigt LA. New dates and new rates for divergence across the Isthmus of Panama. Proc R Soc London Ser B Biol Sci. 1998;265: 2257–2263. doi: 10.1098/rspb.1998.0568

35. Hasegawa M, Kishino H, Yano TA. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22: 160–174. doi: 10.1007/bf02101694 3934395

36. Yang Z. Estimating the pattern of nucleotide substitution. J Mol Evol. 1994;39: 105–111. doi: 10.1007/bf00178256 8064867

37. Suzuki Y, Yamahira K, Kajihara N, Takada Y. Spatial variation in population dynamics of the sand-burrowing amphipod Haustorioides japonicus. Popul Ecol. 2013;55: 107–119. doi: 10.1007/s10144-012-0358-x

38. Harada N, Sato M, Seki O, Timmermann A, Moossen H, Bendle J, et al. Sea surface temperature changes in the Okhotsk Sea and adjacent North Pacific during the last glacial maximum and deglaciation. Deep Res Part II. 2012;61–64: 93–105. doi: 10.1016/j.dsr2.2011.12.007

39. Kojima S, Segawa R, Hayashi I, Okiyama M. Phylogeography of a deep-sea demersal fish, Bothrocara hollandi, in the Japan Sea. Mar Ecol Prog Ser. 2001;217: 135–143. doi: 10.3354/meps217135

40. Kokita T, Nohara K. Phylogeography and historical demography of the anadromous fish Leucopsarion petersii in relation to geological history and oceanography around the Japanese Archipelago. Mol Ecol. 2011;20: 143–164. doi: 10.1111/j.1365-294X.2010.04920.x 21062386

41. Sakuma K, Ueda Y, Hamatsu T, Kojima S. Contrasting population histories of the deep-Sea demersal fish, Lycodes matsubarai, in the Sea of Japan and the Sea of Okhotsk. Zoolog Sci. 2014;31: 375–82. doi: 10.2108/zs130271 24882098

42. Sakuma K, Ueda Y, Ito M, Kojima S. Demographic histories of two deep-sea eelpouts, Lycodes japonicus and Lycodes ocellatus: paleoenvironmental implications of the western North Pacific deep waters. Ichthyol Res. 2015;62: 363–367. doi: 10.1007/s10228-014-0441-8

43. Hirase S, Takeshima H, Nishida M, Iwasaki W. Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography. Genome Biol Evol. 2016;8: 1267–1278. doi: 10.1093/gbe/evw063 27016485

44. Koizumi I, Tada R, Narita H, Irino T, Aramaki T, Oba T, et al. Paleoceanographic history around the Tsugaru Strait between the Japan Sea and the Northwest Pacific Ocean since 30 cal kyr BP. Palaeogeogr Palaeoclimatol Palaeoecol. 2006;232: 36–52. doi: 10.1016/j.palaeo.2005.09.003

45. Sawai Y, Namegaya Y, Okamura Y, Satake K, Shishikura M. Challenges of anticipating the 2011 Tohoku earthquake and tsunami using coastal geology. Geophys Res Lett. 2012;39: n/a–n/a. doi: 10.1029/2012GL053692

46. Seike K, Shirai K, Kogure Y. Disturbance of shallow marine soft-bottom environments and megabenthos assemblages by a huge Tsunami induced by the 2011 M9.0 Tohoku-Oki Earthquake. PLoS One. 2013;8: e65417. doi: 10.1371/journal.pone.0065417 23762365

47. Seike K, Kitahashi T, Noguchi T. Sedimentary features of Onagawa Bay, northeastern Japan after the 2011 off the Pacific coast of Tohoku Earthquake: sediment mixing by recolonized benthic animals decreases the preservation potential of tsunami deposits. J Oceanogr. 2016;72: 141–149. doi: 10.1007/s10872-015-0297-1

48. Goto R, Sakamoto S, Hayakawa J, Seike K. Underwater observations of the giant spoon worm Ikeda taenioides (Annelida: Echiura: Ikedidae) in a subtidal soft-bottom environment in northeastern Japan, which survived tsunamis of the 2011 off the Pacific Coast of Tohoku Earthquake. J Oceanogr. 2017;73: 103–113. doi: 10.1007/s10872-016-0380-2

49. Sakanishi Y, Kurashima A, Dazai A, Abe T, Aoki M, Tanaka J. Long-term changes in a kelp bed of Eisenia bicyclis (Kjellman) Setchell due to subsidence caused by the 2011 Great East Japan Earthquake in Shizugawa Bay, Japan. Phycol Res. 2018;66: 253–261. doi: 10.1111/pre.12331

50. Audzijonyte A, Vainola R. Phylogeographic analyses of a circumarctic coastal and a boreal lacustrine mysid crustacean, and evidence of fast postglacial mtDNA rates. Mol Ecol. 2006;15: 3287–3301. doi: 10.1111/j.1365-294X.2006.02998.x 16968271

51. Copilaş-Ciocianu D, Sidorov D, Gontcharov A. Adrift across tectonic plates: molecular phylogenetics supports the ancient Laurasian origin of old limnic crangonyctid amphipods. Org Divers Evol. 2019;19: 191–207. doi: 10.1007/s13127-019-00401-7


Článek vyšel v časopise

PLOS One


2019 Číslo 10

Nejčtenější v tomto čísle

Tomuto tématu se dále věnují…


Kurzy

Zvyšte si kvalifikaci online z pohodlí domova

Léčba bolesti v ordinaci praktického lékaře
nový kurz
Autoři: MUDr. PhDr. Zdeňka Nováková, Ph.D.

Revmatoidní artritida: včas a k cíli
Autoři: MUDr. Heřman Mann

Jistoty a nástrahy antikoagulační léčby aneb kardiolog - neurolog - farmakolog - nefrolog - právník diskutují
Autoři: doc. MUDr. Štěpán Havránek, Ph.D., prof. MUDr. Roman Herzig, Ph.D., doc. MUDr. Karel Urbánek, Ph.D., prim. MUDr. Jan Vachek, MUDr. et Mgr. Jolana Těšínová, Ph.D.

Léčba akutní pooperační bolesti
Autoři: doc. MUDr. Jiří Málek, CSc.

Nové antipsychotikum kariprazin v léčbě schizofrenie
Autoři: prof. MUDr. Cyril Höschl, DrSc., FRCPsych.

Všechny kurzy
Kurzy Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se