Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data

徐奎鹏; 唐祥海; 王璐; 于欣孜; 孙佩佩; 茅云翔

doi:10.1007/s00343-018-7054-4

Your Location：

Home >

Browse articles >

Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data

Biology | Updated：2023-05-19

- Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data
- Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data
- 海洋湖沼学报（英文） 2018年36卷第3期页码：870-881
- Affiliations：
  
  1.Key Laboratory of Marine Genetics and Breeding(Ocean University of China), Ministry of Education, Qingdao 266000, China
  2.Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Author bio：
  
  TANG Xianghai, txianghai@ouc.edu.cn
  MAO Yunxiang, yxmao@ouc.edu.cn
- Funds：
  
  the National Natural Science Foundation of China(31372517);the Aoshan Technology Innovation Program of Qingdao National Laboratory for Marine Science and Technology(2015ASKJ02);the National Infrastructure of Fishery Germplasm Resources(2016DKA30470)
- DOI：10.1007/s00343-018-7054-4
  中图分类号：
- 收稿：2017-02-24，
  
  录用：2017-4-11，
  
  网络首发：2017-05-27，
  
  纸质出版：2018-05
- Accepted：
Scan QR Code
徐奎鹏, 唐祥海, 王璐, 等. Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data[J]. 海洋湖沼学报（英文）, 2018,36(3):870-881.

Kuipeng XU, Xianghai TANG, Lu WANG, et al. Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data[J]. Chinese Journal of Oceanology and Limnology, 2018, 36(3): 870-881.
徐奎鹏, 唐祥海, 王璐, 等. Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data[J]. 海洋湖沼学报（英文）, 2018,36(3):870-881. DOI： 10.1007/s00343-018-7054-4.

Kuipeng XU, Xianghai TANG, Lu WANG, et al. Divergence time, historical biogeography and evolutionary rate estimation of the order Bangiales (Rhodophyta) inferred from multilocus data[J]. Chinese Journal of Oceanology and Limnology, 2018, 36(3): 870-881. DOI： 10.1007/s00343-018-7054-4.

摘要

Abstract

Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust phylogenies among the red algae

but the divergence times

historical biogeography and evolutionary rates of Bangiales have rarely been studied. Phylogenetic relationships within the Bangiales were examined using the concatenated gene sets from all available organellar genomes. This analysis has revealed the topology (((

Bangia

Porphyra

)

Pyropia

)

Wildemania

). Molecular dating indicates that Bangiales diversified approximately 246.40 million years ago (95% highest posterior density (HPD)=194.78-318.24 Ma

posterior probability (PP)=0.99) in the Late Permian and Early Triassic

and that the ancestral species most likely originated from eastern Gondwanaland (currently New Zealand and Australia) and subsequently began to spread and evolve worldwide. Based on pairwise comparisons

we found a slower rate of nucleotide substitutions and lower rates of diversification in Bangiales relative to Florideophyceae. Compared with Viridiplantae (green algae and land plants)

the evolutionary rates of Bangiales and other Rhodophyte groups were found to be dramatically faster

by more than 3-fold for plastid genome (ptDNA) and 15-fold for mitochondrial genome (mtDNA). In addition

an average 2.5-fold lower dN/dS was found for the algae than for the land plants

which indicates purifying selection of the algae.

关键词

Keywords

references

Abascal F, Zardoya R, Posada D. 2005. ProtTest:selection of best-fit models of protein evolution. Bioinformatics, 21(9):2 104-2 105.

Barraclough T G, Savolainen V. 2001. Evolutionary rates and species diversity in flowering plants. Evolution, 55(4):677-683.

Bell C D, Soltis D E, Soltis P S. 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany, 97(8):1 296-1 303.

Bengtson S, Sallstedt T, Belivanova V, Whitehouse M. 2017.Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae. PLoS Biology, 15(3):e2000735.

Berger B A, Kriebel R, Spalink D, Sytsma K J. 2016.Divergence times, historical biogeography, and shifts in speciation rates of Myrtales. Molecular Phylogenetics and Evolution, 95:116-136.

Blouin N A, Brodie J A, Grossman A C, Xu P, Brawley S H. 2011. Porphyra:a marine crop shaped by stress. Trends in Plant Science, 16(1):29-37.

Broom J E S, Farr T J, Nelson W A. 2004. Phylogeny of the Bangia flora of New Zealand suggests a southern origin for Porphyra and Bangia (Bangiales, Rhodophyta).Molecular Phylogenetics and Evolution, 31(3):1 197-1 207.

Buschiazzo E, Ritland C, Bohlmann J, Ritland K. 2012. Slow but not low:genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evolutionary Biology, 12:8.

Butterfield N J. 2000. Bangiomorpha pubescens n. gen., n. sp.:implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology, 26(3):386-404.

Campbell M A, Presting G, Bennett M S, Sherwood A R. 2014.Highly conserved organellar genomes in the Gracilariales as inferred using new data from the Hawaiian invasive alga Gracilaria salicornia (Rhodophyta). Phycologia, 53(2):109-116.

Capella-Gutiérrez S, Silla-Martínez J M, Gabaldón T. 2009.trimAl:a tool for automated alignment trimming in largescale phylogenetic analyses. Bioinformatics, 25(15):1 972-1 973.

Casey R. 1964. The cretaceous period. Geological Society, London, Special Publications, 1(1):193-202.

Christenhusz M J M, Byng J W. 2016. The number of known plants species in the world and its annual increase.Phytotaxa, 261(3):201-217.

Chumakov N M, Zharkov M A. 2002. Climate during PermianTriassic biosphere reorganizations, Article 1:climate of the early Permian. Stratigraphy and Geological Correlation, 10(6):586-602.

Contreras-Moreira B, Vinuesa P. 2013. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis.AppliedandEnvironmental Microbiology, 79(24):7 696-7 701.

Conway E, Mumford Jr T F, Scagel R F. 1975. The genus Porphyra in British Columbia and Washington. Syesis, 8:185-244.

Davies T J, Savolainen V, Chase M W, Moat J, Barraclough T G. 2004. Environmental energy and evolutionary rates in flowering plants. Proceedings of the Royal Society B:Biological Sciences, 271(1553):2 195-2 200.

Deng J B, Drew B T, Mavrodiev E V, Gitzendanner M A, Soltis P S, Soltis D E. 2015. Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae. Molecular Phylogenetics and Evolution, 83:86-98.

Drouin G, Daoud H, Xia J N. 2008. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Molecular Phylogenetics and Evolution, 49(3):827-831.

Drummond A J, Suchard M A, Xie D, Rambaut A. 2012.Bayesian phylogenetics with BEAUti and the BEAST 1.7.Molecular Biology and Evolution, 29(8):1 969-1 973.

Dumont H J, Vanfleteren J R, De Jonckheere J F, Weekers P H H. 2005. Phylogenetic relationships, divergence time estimation, and global biogeographic patterns of calopterygoid damselflies (Odonata, Zygoptera) inferred from ribosomal DNA sequences. Systematic Biology, 54(3):347-362.

Guiry M D, Guiry G M. 2017. AlgaeBase. World-Wide Electronic Publication, National University of Ireland, Galway, http://www.marinespecies.org/aphia.php?p=sourcedetails&id=37 http://www.marinespecies.org/aphia.php?p=sourcedetails&id=37 .

Hagopian J C, Reis M, Kitajima J P, Bhattacharya D, de Oliveira M C. 2004. Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids.Journal of Molecular Evolution, 59(4):464-477.

Herron M D, Hackett J D, Aylward F O, Michod R E. 2009.Triassic origin and early radiation of multicellular volvocine algae. Proceedings of the National Academy of Sciences of the United States of America, 106(9):3 254-3 258.

Hua J M, Smith D R, Borza T, Lee R W. 2012. Similar relative mutation rates in the three genetic compartments of Mesostigma and Chlamydomonas . Protist, 163(1):105-115.

Huelsenbeck J P, Ronquist F. 2001. MRBAYES:Bayesian inference of phylogenetic trees. Bioinformatics, 17(8):754-755.

Hughey J R. 2016. Genomic and phylogenetic analysis of the complete plastid Genome of the California endemic seaweed Wildemania schizophylla (Bangiaceae).Madroño, 63(1):34-38.

Janouškovec J, Liu S L, Martone P T, Carré W, Leblanc C, Collén J, Keeling P J. 2013. Evolution of red algal plastid genomes:ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS One, 8(3):e59001.

Katoh K, Kuma K I, Toh H, Miyata T. 2005. MAFFT version 5:improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33(2):511-518.

Kim K J, Lee H L. 2004. Complete chloroplast genome sequences from Korean ginseng ( Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Research, 11(4):247-261.

Kimura M. 1984. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.

Lanfear R, Ho S Y W, Love D, Bromham L. 2010. Mutation rate is linked to diversification in birds. Proceedings of the National Academy of Sciences of the United States of America, 107(47):20 423-20 428.

Lee J, Cho C H, Park S I, Choi J W, Song H S, West J A, Bhattacharya D, Yoon H S. 2016. Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants. BMC Biology, 14:75.

Leliaert F, Smith D R, Moreau H, Herron M D, Verbruggen H, Delwiche C F, De Clerck O. 2012. Phylogeny and molecular evolution of the green algae. Critical Reviews in Plant Sciences, 31(1):1-46.

Levin D A, Wilson A C. 1976. Rates of evolution in seed plants:net increase in diversity of chromosome numbers and species numbers through time. Proceedings of the National Academy of Sciences of the United States of America, 73(6):2 086-2 090.

Lu Y, Ran J H, Guo D M, Yang Z Y, Wang X Q. 2014.Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes. PLoS One, 9(9):e107679.

Milstein D, Oliveira M C, Martins F M, Matioli S R. 2008.Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the eastern coast of South America. BMC Evolutionary Biology, 8:308.

Müller K M, Oliveira M C, Sheath R G, Bhattacharya D. 2001. Ribosomal DNA phylogeny of the Bangiophycidae(Rhodophyta) and the origin of secondary plastids. American Journal of Botany, 88(8):1 390-1 400.

Ogg J G, Agterberg F, Gradstein F. 2004. A geologic time scale 2004. In : Abstracts with Programs-Geological Society of America, 36: 74.

Ohta N, Matsuzaki M, Misumi O, Miyagishima S Y, Nozaki H, Tanaka K, Shin-I T, Kohara Y, Kuroiwa T. 2003. Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA Research, 10(2):67-77.

Posada D, Crandall K A. 1998. MODELTEST:testing the model of DNA substitution. Bioinformatics, 14(9):817-818.

Reith M, Munholland J. 1995. Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Molecular Biology Reporter, 13(4):333-335.

Robba L, Russell S J, Barker G L, Brodie J. 2006. Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta). American Journal of Botany, 93(8):1 101-1 108.

Ronquist F, Cannatella D. 1997. Dispersal-vicariance analysis:a new approach to the quantification of historical biogeography. Systematic Biology, 46(1):195-203.

Saunders G W, Hommersand M H. 2004. Assessing red algal supraordinal diversity and taxonomy in the context of contemporary systematic data. American Journal of Botany, 91(10):1 494-1 507.

Smith D R, Arrigo K R, Alderkamp A C, Allen A E. 2014. Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae. Molecular Phylogenetics and Evolution, 71:36-40.

Smith D R, Hua J M, Lee R W, Keeling P J. 2012. Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture. Molecular Phylogenetics and Evolution, 65(1):339-344.

Smith D R. 2015. Mutation rates in plastid genomes:they are lower than you might think. Genome Biology and Evolution, 7(5):1 227-1 234.

Stamatakis A. 2014. RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9):1 312-1 313.

Stanley S M. 1988. Paleozoic mass extinctions; shared patterns suggest global cooling as a common cause. American Journal of Science, 288(4):334-352.

Sutherland J E, Lindstrom S C, Nelson W A, Brodie J, Lynch M D J, Hwang M S, Choi H G, Miyata M, Kikuchi N, Oliveira M C, Farr T, Neefus C, Mols-Mortensen A, Milstein D, Müller K M. 2011. A new look at an ancient order:generic revision of the Bangiales (Rhodophyta).Journal of Phycology, 47(5):1 131-1 151.

Swofford D L. 2003. PAUP * : Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.

Venditti C, Pagel M. 2010. Speciation as an active force in promoting genetic evolution. Trends in Ecology & Evolution, 25(1):14-20.

Verbruggen H, Maggs C A, Saunders G W, Le Gall L, Yoon H S, De Clerck O. 2010. Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life. BMC Evolutionary Biology, 10:16.

Wang L, Mao Y X, Kong F N, Li G Y, Ma F, Zhang B L, Sun P P, Bi G Q, Zhang F F, Xue H F, Cao M. 2013. Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis . PLoS One, 8(5):e65902.

Webster A J, Payne R J H, Pagel M. 2003. Molecular phylogenies link rates of evolution and speciation. Science, 301(5632):478.

Wolfe K H, Li W H, Sharp P M. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences of the United States of America, 84(24):9 054-9 058.

Xiao S H, Knoll A H, Yuan X L, Pueschel C M. 2004. Phosphatized multicellular algae in the Neoproterozoic Doushantuo Formation, China, and the early evolution of florideophyte red algae. American Journal of Botany, 91(2):214-227.

Xiao S H, Zhang Y, Knoll A H. 1998. Three-dimensional preservation of algae and animal embryos in a Neoproterozoic phosphorite. Nature, 391(6667):553-558.

Yang E C, Boo S M, Bhattacharya D, Saunders G W, Knoll A H, Fredericq S, Graf L, Yoon H S. 2016. Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Scientific Reports, 6:21361.

Yang E C, Kim K M, Kim S Y, Lee J, Boo G H, Lee J H, Nelson W A, Yi G M, Schmidt W E, Fredericq S, Boo S M, Bhattacharya D, Yoon H S. 2015. Highly conserved mitochondrial genomes among multicellular red algae of the Florideophyceae. Genome Biology and Evolution, 7(8):2 394-2 406.

Yang Z H. 2007. PAML 4:phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8):1 586-1 591.

Yoon H S, Hackett J D, Ciniglia C, Pinto G, Bhattacharya D. 2004. A molecular timeline for the origin of photosynthetic eukaryotes. Molecular Biology and Evolution, 21(5):809-818.

Yoon H S, Müller K M, Sheath R G, Ott F D, Bhattacharya D. 2006. Defining the major lineages of red algae(Rhodophyta). Journal of Phycology, 42(2):482-492.

Yu Y, Harris A, He X J. 2010. S-DIVA (Statistical DispersalVicariance Analysis):a tool for inferring biogeographic histories. Molecular Phylogenetics and Evolution, 56(2):848-850.

Zhao L, Li X, Zhang N, Zhang S D, Yi T S, Ma H, Guo Z H, Li D Z. 2016. Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids. Molecular Phylogenetics and Evolution, 105:166-176.

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

Morphological and molecular analyses of a Philine kinglipini outbreak in summer of 2022 in Jiaozhou Bay, China

Phylogenetic, evolutionary, and biogeographic origin of the genus Sheathia (Batrachospermales, Rhodophyta)

Morphological characters and DNA barcoding of Syngnathus schlegeli in the coastal waters of China

Phylogeny of Saccharina and Laminaria (Laminariaceae, Laminariales, Phaeophyta) in sequence-tagged-site markers

基于最大似然估计的点火概率曲线计算模型取点方法