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The Molecular Clock and/or/versus the Fossil Record


F.J.Ayala (1999): Molecular clock mirages. Abstract, BioEssays, 21: 71–75.
"... The hypothesis of the molecular clock proposes that molecular evolution occurs at rates that persist through time and across lineages, for a given gene.
[...] Four recent papers show that none of the predictive hypotheses that have been proposed can be generally maintained. The conclusion is that molecular evolution is dependent on the fickle process of natural selection. But it is a time-dependent process, so that accumulation of empirical data often yields an approximate clock, as a consequence of the expected convergence of large numbers. ..."

F.J.Ayala (1997): Vagaries of the molecular clock. Free access, Proc. Natl. Acad. Sci. USA, 94: 7776-7783.
"... The hypothesis of the molecular evolutionary clock asserts that informational macromolecules (i.e., proteins and nucleic acids) evolve at rates that are constant through time and for different lineages. The clock hypothesis has been extremely powerful for determining evolutionary events of the remote past for which the fossil and other evidence is lacking or insufficient. ..."

! C. Beimforde et al. (2014): Estimating the Phanerozoic history of the Ascomycota lineages: combining fossil and molecular data. In PDF, Molecular Phylogenetics and Evolution, 78: 386-398. See also here.

! M.J. Benton et al. (2009): Calibrating and constraining the molecular clock. PDF file, In: S.B. Hedges and S. Kumar (eds.): The Timetree of Life (see here).

M.J. Benton and B.C. Emerson (2007): How did life become so diverse? The dynamics of diversification according to the fossil record and molecular phylogenetics. PDF file, Palaeontology, 50: 23-40.
Website outdated, download a version archived by the Internet Archive´s Wayback Machine.

! M.J. Benton and P.C.J. Donoghue (2007): Paleontological Evidence to Date the Tree of Life. In PDF. See also here. Molecular biology and evolution.

Michael Benton, Department of Earth Sciences, University of Bristol, UK: Accuracy of Fossils and Dating Methods (an ActionBioscience.org original interview, American Institute of Biological Sciences).

M.J. Benton and P.N. Pearson (2001): Speciation in the fossil record. PDF file, Trends in Ecology and Evolution, 16.

M.J. Benton et al. 2000): Quality of the fossil record through time. Nature, 403: 534-537.
See also here.
"... new assessment methods, in which the order of fossils in the rocks (stratigraphy) is compared with the order inherent in evolutionary trees (phylogeny), provide a more convincing analytical tool: stratigraphy and phylogeny offer independent data on history. ..."

S. Bonneville et al. (2020): Molecular identification of fungi microfossils in a Neoproterozoic shale rock. In PDF, Science Advances, 6: eaax7599.

Brent H. Breithaupt (1992): The use of fossils in interpreting past environments. PDF file, Pages 147–158, in: Tested studies for laboratory teaching, Volume 13 (C. A. Goldman, Editor). Proceedings of the 13th Workshop/Conference of the Association for Biology Laboratory Education.
This expired link is now available through the Internet Archive´s Wayback Machine.

! L. Bromham and D. Penny (2003):&xnbsp; The modern molecular clock. Nature Reviews Genetics, 4: 216–224.
See also here.
"... The evolutionary dates measured by molecular clocks have been controversial, particularly if they clash with estimates taken from more traditional sources such as the fossil record.
[...] The molecular clock — a relatively constant rate of accumulation of molecular differences between species — was an unexpected discovery that has provided a window on the mechanisms that drive molecular evolution. ..."

G.E. Budd and S. Jensen (2020): A critical reappraisal of the fossil record of the bilaterian phyla. Abstract, Biological Reviews, 75_253-295.
"... Indeed, the combination of the body and trace fossil record demonstrates a progressive diversification through the end of the Proterozoic well into the Cambrian and beyond, a picture consistent with body plans being assembled during this time. ..."

G.E. Budd (2008): The earliest fossil record of the animals and its significance. Phil. Trans. R. Soc. B, 363: 1425–1434. See here.

R.J. Burnham (2008): Hide and Go Seek: What Does Presence Mean in the Fossil Record. Abstract, Annals of the Missouri Botanical Garden, 95: 51-71. See also here (in PDF).

! C. Cai et al. (2022): Integrated phylogenomics and fossil data illuminate the evolution of beetles. Open access, R. Soc. Open Sci. 9: 211771.
Note figure 2: Timescale of beetle evolution displayed as a family-level tree.
! "... Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic–Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution ..."

E. Callaway (2015): Computers read the fossil record. Palaeontologists hope that software can construct fossil databases directly from research papers. In PDF, Nature Toolbox. See also here.

! J.T. Clarke et al. (2011): Establishing a time-scale for plant evolution. PDF file, New Phytologist. See also here.
! Note figure 2: A representative tree of relationships between model representatives of the major land plant lineages whose plastid or nuclear genomes have been fully sequenced.
Figure 7: Chronogram for land plant evolution.
Figure 8: Chronograms for the six molecular clock analyses conducted.
"... We reject both a post-Jurassic origin of angiosperms and a post-Cambrian origin of land plants. Our analyses also suggest that the establishment of the major embryophyte lineages occurred at a much slower tempo than suggested in most previous studies. ..."

! M. Coiro et al. (2019): How deep is the conflict between molecular and fossil evidence on the age of angiosperms? Free access, New Phytologist, doi: 10.1111/nph.15708.
"... Critical scrutiny shows that supposed pre-Cretaceous angiosperms either represent other plant groups or lack features that might confidently assign them to the angiosperms. ..."

! F.L. Condamine et al. (2013): Macroevolutionary perspectives to environmental change. In PDF, Ecology letters.

! J.A. Cunningham et al. (2016): The origin of animals: can molecular clocks and the fossil record be reconciled? Open access, Bioessays, 39. See also here (in PDF).
Note figure 1: Summary of major Ediacaran and early Cambrian fossil assemblages.
! Figure 2. The mismatch between the fossil and molecular clock records of early animal evolution.
"... Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed.
[...] A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identification in the fossil record.

! M. Dohrmann and G. Wörheide (2017): Dating early animal evolution using phylogenomic data. Open access, Scientific reports, 7.
! Note Figure 4: Time-calibrated phylogeny of animals.

! P.C.J. Donoghue and Z. Yang (2016): The evolution of methods for establishing evolutionary timescales. In PDF, Phil. Trans. R. Soc., B 371.See also here (abstract).

P.C.J. Donoghue and M.J. Benton (2007): Rocks and clocks: calibrating the Tree of Life using fossils and molecules. In PDF, Trends in Ecology and Evolution.

A. Dornburg et al. (2011): Integrating Fossil Preservation Biases in the Selection of Calibrations for Molecular Divergence Time Estimation. PDF file, Syst. Biol., 60: 519-527.
Website saved by the Internet Archive´s Wayback Machine.

M. dos Reis et al. (2015): Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Free access, Current Biology, 25: 2939–2950.

E.J.P. Douzery et al. (2004): The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?. Free access, Proceedings of the National Academy of Sciences, USA, 101: 15386–15391.
Note figure 1: Divergence time estimates (Mya) among eukaryotes. White rectangles delimit95%credibility intervals on node ages. Stars indicate the six nodes under prior paleontological calibration.
! "... We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950–1,259 million years ago (Mya), animals diverged from choanoflagellates 761–957 Mya,
[...] Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be ~100 million years more ancient than the Cambrian boundary. ..."

! A.J. Drummond et al. (2006): Relaxed phylogenetics and dating with confidence. Open access, PLoS Biol 4: e88. DOI: 10.1371/journal.pbio.0040088.
"... In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. ..."

! F. Forrest (2009): Calibrating the Tree of Life: fossils, molecules and evolutionary timescales. Free access, Annals of Botany, 104: 789–794.
"... New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record.
[...] ! "...the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account. ..."

! P.G. Gensel (2021): When did terrestrial plants arise? Abstract, Science, 373: : 736-737.
"... There has been a discrepancy in the time of land plant origination between molecular clock estimations (based on genes and RNA) and fossil record estimates (based on morphology). On page 792 of this issue, Strother and Foster (6) describe fossilized spores whose characteristics raise the possibility that land plants arose by co-opting algal genes, along with acquiring de novo genes, and that the former would account for the molecular clock predating the fossil record. ..."

S. Guindon (2020): Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods. Open access, Frontiers in Genetics, 11.
"... molecular dating will undoubtedly keep playing a crucial role in biology in the future. Our understanding of important phenomena such as species diversification or dispersal, population migration and demography, or the molecular signature resulting from environmental changes, depends on our ability to date past evolutionary events. The wealth of available techniques to perform this task provides a powerful set of tools to make progress in this direction. ..."

! S.B. Hedges (2009): Life. PDF file, In: S.B. Hedges and S. Kumar (eds.): The Timetree of Life.
! See here.
These expired links are now available through the Internet Archive´s Wayback Machine.

! J.B. Hedges (2004): A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC evolutionary biology.

M.J. Hopkins et al. (2018): The inseparability of sampling and time and its influence on attempts to unify the molecular and fossil records. Free access, Paleobiology, 44: 561–574.
"... Although neither the molecular record nor the fossil record are perfect, the two records bear independent limitations, and what is missing from one is often available in the other. We must deal with the different and sometimes complex relationships between time and sampling to take full advantage of the complementary nature of the two records. ..."

M. Kearney (2002): Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. PDF file, Systematic biology, 51: 369-381.

! S.M. Kidwell and S.M. Holland (2002): The Quality of the Fossil Record: Implications for Evolutionary Analyses. PDF file, Annual Review of Ecology and Systematics, 33: 561-588. See also here.

Susan M. Kidwell and Karl W. Flessa: THE QUALITY OF THE FOSSIL RECORD: Populations, Species, and Communities.- Annu. Rev. Earth Planet. Sci. 1996 24: 433-464. Full Online Access via Annual Reviews, Go to Annual Reviews Search Page (Biomedical Sciences), Search for "Kidwell" (Field Author, Last Name).

M. Kowalewski and R.K. Bambach (2008): The limits of paleontological resolution. In PDF, High-resolution approaches in stratigraphic paleontology. This expired link is available through the Internet Archive´s Wayback Machine.

! Michel Laurin (2012): Recent progress in paleontological methods for dating the Tree of Life. In PDF, Frontiers in Genetics, 3.

! R. López-Antoñanzas et al. (2022): Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life. Open access, Biology, 11: 1185. https://doi.org/10.3390/ biology11081185.
"... The statistical techniques mentioned above have only begun to be applied to questions in palaeontology over the past decade but have found extensive applications in phylogenetic comparative analysis, quantitative genetics, and ecology. Complementary methodologies that combine morphological and molecular approaches can provide novel answers to broad evolutionary and deep-time questions ..."

! S Magallón et al. (2013): Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. Free access, American Journal of Botany, 100: 556-573.

G.J. Morgan (1998): Emile Zuckerkandl, Linus Pauling, and the molecular evolutionary clock, 1959-1965. In PDF, Journal of the History of Biology, 31: 155-178.
See also here.

H. Morlon et al. (2011): Reconciling molecular phylogenies with the fossil record. In PDF, PNAS, 108: 16327-16332.

! J.L. Morris et al. (2018): The timescale of early land plant evolution. In PDF, PNAS, 115. See also here.

! NATURE, Nature Debates: Andrew Smith, Department of Palaeontology, the Natural History Museum, London: Is the fossil record adequate? This debate introduces the topic and the conflicting viewpoints that surround it.

! Y. Nie et al. (2020): Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies. In PDF, Syst. Biol., 69: 1–16. See also here.
! Note figure 5: Time-tree of green plants.
! "... By taking into account various sources of uncertainty, we estimate that crown-group green plants originated in the Paleoproterozoic–Mesoproterozoic (1679.7–1025.6 Ma), crown-group Chlorophyta and Streptophyta originated in the Mesoproterozoic–Neoproterozoic (1480.0–902.9 Ma and 1571.8–940.9 Ma), and crown-group land plants originated in the Ediacaran to middle Ordovician (559.3– 459.9 Ma). ..."

Geobiology, Department of Earth Sciences, Oxford University: Questioning the evidence for Earth's oldest fossils.
Now provided by the Internet Archive´s Wayback Machine.

! Palaeontologia Electronica: Fossil Calibration Database. The Fossil Calibration Database is a curated collection of well-justified calibrations. They also promote best practices for justifying fossil calibrations and citing calibrations properly. Raising the Standard in Fossil Calibration! See also:
D.T. Ksepka et al. (2015): The Fossil Calibration Database, A New Resource for Divergence Dating. Abstract, Systematic Biology.

J.F. Parham et al. (2012): Best Practices for Justifying Fossil Calibrations. In PDF, Syst Biol., 61: 346-359. See also here (abstract). Darwin's theory of evolution; evolution as a mechanism for change; the nature of species; the nature of theory; paleontology, geology, and evolution; and determining the age of fossils and rocks. The Online booklet contains straightforward definitions as well as discussions of complex ideas. Navigate using the left-hand toolbar. There is also a PDF printable version available.

S.M. Porter (2004): The fossil record of early eukaryotic diversification. In PDF, Paleontological Society Papers, 10: 35-50.
Still available via Internet Archive Wayback Machine.
See also here.
Note figure 1: A current view of eukaryote phylogeny, based on a consensus of molecular and ultrastructural data.

! T.B. Quental and C.R. Marshall (2010): Diversity dynamics: molecular phylogenies need the fossil record. In PDF, Trends in ecology & evolution, 25: 434-441.
See also here.
"... It appears that molecular phylogenies can tell us only when there have been changes in diversification rates, but are blind to the true diversity trajectories and rates of origination and extinction that have led to the species that are alive today. ..."

R.R. Reisz and J. Müller (2004): Molecular timescales and the fossil record: a paleontological perspective. In PDF, Trends in Genetics.

D.L. Rabosky (2014): Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees. PLoS ONE, 9: e89543. doi:10.1371/journal.pone.0089543

! A. Rojas et al: (2021): A multiscale view of the Phanerozoic fossil record reveals the three major biotic transitions. Open access, Communications Biology, 4.
"... we demonstrate that Phanerozoic oceans sequentially harbored four global benthic mega-assemblages. Shifts in dominance patterns among these global marine mega-assemblages were abrupt (end-Cambrian 494 Ma; end- Permian 252 Ma) or protracted (mid-Cretaceous 129 Ma), and represent the three major biotic transitions in Earth’s history. ..."

! D. Silvestro et al. (2015): Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record. In PDF, New Phytologist, 207: 425-436.

! C. Strullu-Derrien et al. (2018): The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. Free access, New Phytologist, 220: 1012–1030.
! Note figure 1: Geological timescale with oldest known fossils. Left: Antiquity of genomic traits related to mycorrhizal evolution based on molecular clock estimates. Right: Oldest known fossils.
Figure 5: Simplified phylogenetic tree showing the minimum stratigraphic ranges of selected groups based on fossils (thick bars) and their minimum implied range extensions (thin lines).

D. Su et al. (2022): Large-scale phylogenomic analyses reveal the monophyly of bryophytes and neoproterozoic origin of land plants Open access, Molecular Biology and Evolution, 38: 3332–3344.
! Note figure 1: The concatenation species tree of land plants and their algal relatives.
! Figure 2: The coalescent species tree of land plants and their algal relatives.
"... We found that studies favoring a Neoproterozoic origin of land plants (980–682 Ma) are informed more by molecular data whereas those favoring a Phanerozoic origin (518–500 Ma) are informed more by fossil constraints. Our divergence time analyses highlighted the important contribution of the molecular data (time-dependent molecular change) when faced with contentious fossil evidence.
[..] A careful integration of fossil and molecular evidence will revolutionize our understanding of how land plants evolved.

Teaching Biology, Random Posts on Biological Topics (by Marc Srour, Enalia Physis Environmental Research Center, Cyprus): Taxonomic Bias in the Fossil Record: Is it really an issue?

! A.M.F. Tomescu (2021): Mysteries of the bryophyte–tracheophyte transition revealed: enter the eophytes. Free access, New Phytologist, Note fig. 1: Timeline and evolutionary hypothesis for early land plants. Worth checking out:
! D. Edwards et al. 2022a): Piecing together the eophytes–a new group of ancient plants containing cryptospores. Free access, New Phytologist, 233: 1440–1455.
! D. Edwards et al. 2022b): Earliest record of transfer cells in Lower Devonian plants. Free access, New Phytologist, 233: 1456–1465.

M.J. Watson and D.M. Watson (2020): Post-Anthropocene Conservation. Open access, Trends in Ecology & Evolution.

Wikipedia, the free encyclopedia:
Timeline of the evolutionary history of life.
! Molecular clock.
! Molekulare Uhr (in German).
DNA sequencing.
DNA-Sequenzierung (in German).

N. Wikström et al. (2022): No phylogenomic support for a Cenozoic origin of the “living fossil” Isoetes. OPen access, American Journal of Botany.

A.C. Wilson et al. (1987): Molecular time scale for evolution. Abstract, Trends in Genetics, Trends in Genetics Volume 3: 241-247.

! A.C. Wilson (1985): The molecular basis of evolution. In PDF, Scientific American, 253: 164-175.
See also here.

! H.S. Yoon et al. (2004): A molecular timeline for the origin of photosynthetic eukaryotes. PDF file, Mol. Biol. Evol., 21: 809-818. See also here.










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Last updated November 19, 2022