The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Dating divergences in the Fungal Tree of Life: review and new analyses
Abstract
The collection of papers in this issue of Mycologia documents considerable improvements in taxon sampling and phylogenetic resolution regarding the Fungal Tree of Life. The new data will stimulate new attempts to date divergences and correlate events in fungal evolution with those of other organisms. Here, we review the history of dating fungal divergences by nucleic acid variation and then use a dataset of 50 genes for 25 selected fungi, plants and animals to investigate divergence times in kingdom Fungi. In particular, we test the choice of fossil calibration points on dating divergences in fungi. At the scale of our analysis, substitution rates varied without showing significant within-lineage correlation, so we used the Langley-Fitch method in the R8S package of computer programs to estimate node ages. Different calibration points had a dramatic effect on estimated divergence dates. The estimate for the age of the Ascomycota/Basidiomycota split was 1808000000 y ago when calibrated assuming that mammals and birds diverged 300000000 y ago, 1489000000 y ago when calibrated assuming that the 400000000 y old fungal fossil Paleopyrenomycites devonicus represents Sordariomycetes and approximately 400000000 y ago when calibrated assuming 206000000 y ago for the plant eudicot/monocot divergence. An advantage of a date of approximately 400000000 y ago for the Ascomycota/Basidiomycota divergence is that the radiation of fungi associated with land plants would not greatly precede the earliest land plant fossils. Acceptance of approximately 400000000 y ago for the Ascomycota/Basidiomycota split would require that P. devonicus be considered a deeply branching Ascomycota. To improve on current estimates of divergence times, mycologists will require calibration points from within groups of fungi that share similar substitution rates. The most useful calibration is likely to depend on the discovery and description of continuous records of fossil fungi, or their spores, that show recognizable shifts in morphology.
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Citations
Cites
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750
Divergence time and evolutionary rate estimation with multilocus data.
Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962
Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision
Graur, D., & Martin, W. (2004) · Trends in Genetics · doi:10.1016/j.tig.2003.12.003 · Cited by 669
The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
Douzery, E. J. P., Snell, E. A., Bapteste, E., Delsuc, F., & Philippe, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403984101 · Cited by 638 · cited 4×
“…(Blagoderov et al 2002, Peterson et al 2004) and a maximum of 417 000 000 y, the age of the first primitive hexapod fossils (Gaunt and Miles 2002, Douzery et al 2004); and the divergence of eudicots within the angiosperms, with a minimum age of 144 000 000 and maximum of 206 000 000 y (Sanderson…”
BackgroundMethodInfluentialDetermining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock
Doolittle, R. F., Feng, D.-F., Tsang, S., Cho, G., & Little, E. (1996) · Science · doi:10.1126/science.271.5248.470 · Cited by 581
Wang, D. Y.-C., Kumar, S., & Hedges, S. B. (1999) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.1999.0617 · Cited by 493 · cited 6×
“As a geologic calibration they used Paleopyrenomycites at 400 000 000 y as a minimum date for Sordariomycetes, and they compared results when the animal-fungal divergence was specified as either 1 576 000 000 y ago (Wang et al 1999) or 965 000 000 y ago (Doolittle et al 1996).”
BackgroundMethodResultInfluentialEstimating metazoan divergence times with a molecular clock
Peterson, K. J., Lyons, J. B., Nowak, K. S., Takacs, C. M., Wargo, M. J., & McPeek, M. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401670101 · Cited by 461
A methodological bias toward overestimation of molecular evolutionary time scales
Rodríguez-Trelles, F., Tarrío, R., & Ayala, F. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.122231299 · Cited by 116 · cited 1×
“— Rodriguez-Trelles et al (2002) noted that frequency distributions of divergence times calculated for multiple genes showed a skew toward older times because recent times are constrained by the present, whereas older times have no such constraint.”
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Cited by
The Colletotrichum gloeosporioides species complex
Weir, B. S., Johnston, P. R., & Damm, U. (2012) · Studies in Mycology · doi:10.3114/sim0011 · Cited by 1,646
Martinez, D., Berka, R. M., Henrissat, B., Saloheimo, M., Arvas, M., Baker, S. E., Chapman, J., Chertkov, O., Coutinho, P. M., Cullen, D., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1403 · Cited by 1,240
Dimensions of biodiversity in the Earth mycobiome
Peay, K. G., Kennedy, P. G., & Talbot, J. M. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.59 · Cited by 721
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
Fedorova, N. D., Khaldi, N., Joardar, V. S., Maiti, R., Amedeo, P., Anderson, M. J., Crabtree, J., Silva, J. C., Badger, J. H., Albarraq, A., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000046 · Cited by 508
Zheng, P., Xia, Y., Xiao, G., Xiong, C., Hu, X., Zhang, S., Zheng, H., Huang, Y., Zhou, Y., Wang, S., et al. (2011) · Genome Biology · doi:10.1186/gb-2011-12-11-r116 · Cited by 454
Metadata
- Authors
- Taylor, J. W., & Berbee, M. L.
- Venue
- Mycologia
- Publisher
- Informa UK Limited
- Published
- 2006-11
- Volume
- 98
- Issue
- 6
- Pages
- 838-849
- ISSN
- 0027-5514 (ISSN-L)
- 1557-2536
- OpenAlex
- W2170817105
- Cited by
- 424
- References
- 9
- FWCI
- 4.79
- Type
- journal article
- Language
- en
- Open access
- closed
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