Home / Evolution & Extinction / The Molecular Clock and/or/versus the Fossil Record

! E.M. Armstrong et al. (2023): One hundred important questions facing plant science: an international perspective. Open access, New Phytologist, 238: 470–481.
"... we present the outcome of a global collaboration to identify emerging plant research themes.
[...] Over 600 questions were collected from anyone interested in plants, which were reduced to a final list of 100 ..."

Y. Asar et al. (2022): Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution. In PDF, bioRxiv.
See also here.
! Note figure 1 (on PDF-page 9): A flowchart of simulation study. About molecular and morphological phylograms, morphological characters and sequence alignments.

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. ..."

J. Barba-Montoya et al. (2023): Molecular timetrees using relaxed clocks and uncertain phylogenies. Free access, Frontiers in Bioinformatics, 3: 1225807. doi: 10.3389/fbinf.2023.1225807.
"... A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals ..."

! J. Bechteler et al. (2023): Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. Free access, American Journal of Botany, https://doi.org/10.1002/ajb2.16249.
"... The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more, and propose ten new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later ..."

! 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.

! R.B.J. Benson et al. (2021): Biodiversity across space and time in the fossil record. Free access, Current Biology, 31: R1225-R1236.
Note figure 3: Distribution of geographic and environmental sampling in the marine and terrestrial fossil records.
"... it will be impossible to directly estimate total global biodiversity from fossil data, principally because the fossil record is not complete enough
[...] the fossil record provides the only dataset that might allow us to put constraints on this important question, using information from exceptional, well-sampled but spatially and temporally restricted windows. These windows provide the best information on local, regional and environmental diversity levels, and how they vary in space ..."

! 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. Open access, Palaeontology, 50: 23-40.
Note text figure 1: Patterns of diversification of: A, families of marine invertebrates; B, species of vascular land plants; C, families of non-marine tetrapods; and D, families of insects.

! 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).
Still available through the Internet Archive´s Wayback Machine.

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.

! A.M.C. Bowles et al. (2023): The origin and early evolution of plants. Open access, Trends in Plant Science, 28.
Note figure 2: Phylogeny of early plant evolution with a selection of available genomic resources.
Figure 3: Fossils of possible and probable early archaeplastids.
! Figure 4: Summary of molecular estimates for the timescale of archaeplastid evolution.
"... Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic ..."

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.

! J.J. Brocks et al. (2023): Lost world of complex life and the late rise of the eukaryotic crown. In PDF, Nature, https://doi.org/10.1038/s41586-023-06170-w. See also here.
Note figure 1: Geological time chart comparing the molecular fossil, microfossil and phylogenetic records of early eukaryote evolution.

! 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 (2024): Embracing uncertainty: The way forward in plant fossil phylogenetics. Open access, American Journal of Botany. https://doi.org/10.1002/ajb2.16282.
"... Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics
[...] Given the nature of plant fossil and morphological data, embracing uncertainty by exploring support within the data represents a more productive and heuristic research program than trying to achieve the same support and resolution given by molecular data ..."

! M. Coiro et al. (2023): Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity. Open access, New Phytologist, doi: 10.1111/nph.19010.
Note figure 1: Global distribution of Cycadales.
! Figure 2: Bayesian total-evidence dated phylogeny of Cycadales.
! Figure 3: Ages of extant genera and fossil placements. Phylogenetic relationships for extant and extinct cycads.
! Figure 4: Historical biogeography of cycads.
"... Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses.
[...] Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic.
[...] We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups ..."

! 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.
See also here.
! Note figure 2: Concordance of palaeontological data, phylogenetic hypotheses, macroevolutionary events and molecular clock.

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. ..."

I.H. Escapa and S. Catalano (2013): Phylogenetic Analysis of Araucariaceae: Integrating Molecules, Morphology, and Fossils. In PDF, International Journal of Plant Sciences. See also here.
"... Monophyletic Araucariaceae is the sister group of Podocarpaceae, forming the order Araucariales. Monophyly of Araucaria and Agathis is also strongly supported by the data. The results of both molecular and combined analyses indicate that Wollemia and Agathis form a clade (=agathioid clade) sister to Araucaria ..."

J.R. Flores et al. (2023): Dating the evolution of the complex thalloid liverworts (Marchantiopsida): total-evidence dating analysis supports a Late Silurian-Early Devonian origin and post-Mesozoic morphological stasis. In PDF, New Phytologist, doi: 10.1111/nph.19254.
See also here.
"... Phylogenetic analyses were performed on a combined dataset of 130 discrete characters and 11 molecular markers
[...] Total-evidence dating analyses support the radiation of Marchantiopsida during Late Silurian-Early Devonian (or Middle Ordovician when the outgroup is excluded) and that of Ricciaceae in the Middle Jurassic ..."

! 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. ..."

T. Fujiwara et al. (2023): Evolution of genome space occupation in ferns: linking genome diversity and species richness. Open access, Annals of Botany, 131: 59–70.

! 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. ..."

! D.E. Greenwalt (2023); Paleobiology Department at the Smithsonian’s National Museum of Natural History: Remnants of Ancient Life: The New Science of Old Fossils. Google books.
See also here.
"... We used to think of fossils as being composed of nothing but rock and minerals, all molecular traces of life having vanished long ago. We were wrong. Remnants of Ancient Life reveals how the new science of ancient biomolecules — pigments, proteins, and DNA that once functioned in living organisms tens of millions of years ago — is opening a new window onto the evolution of life on Earth. ..."

! R. Grønfeldt Winther and E. Willerslev (2023): Wilson and Sarich (1969): The birth of a molecular evolution research paradigm. Open access, PNAS, 20: e222047312.

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.

S.Y.W. Ho (2020): The molecular clock and evolutionary rates across the tree of life. Abstract. In: S.Y.W. Ho (ed.): The molecular evolutionary clock. Springer International Publishing, 3–23.

! S.Y.W. Ho and S. Duchêne (2014): Molecular-clock methods for estimating evolutionary rates and timescales. Free access, Molecular ecology, 23: 5947–5965.
"... The molecular clock presents a means of estimating evolutionary rates and timescales using genetic data.
[...] We provide an outline of the various clock methods and models that are available, including the strict clock, local clocks, discrete clocks and relaxed clocks. Techniques for calibration and clock-model selection are also described, along with methods for handling multilocus data sets.

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.

! S. Kumar&xnbsp;(2005): Molecular clocks: four decades of evolution. Open access, Nature Reviews Genetics, 6: 654–662.
Don't miss the Timeline: Four decades of molecular clocks.

B.B. Lamont et al. (2022): Gondwanan origin of the Dipterocarpaceae-Cistaceae-Bixaceae is supported by fossils, areocladograms, ecomorphological traits and tectonic-plate dynamics. Free access, Frontiers of Biogeography, 14.

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

M.S.Y. Lee and S.Y.W. Ho (2016): Molecular clocks. Current biology, 26: R399-R402.
See also here.
Note figure 3: Divergence dates derived from molecular clocks are often older than those suggested by the fossil record.

A.B. Leslie and R.B.J. Benson (2022): Neontological and paleontological congruence in the evolution of Podocarpaceae (coniferales) reproductive morphology. Free access, Front. Ecol. Evol., 10: 1058746. doi: 10.3389/fevo.2022.1058746
"... Although molecular and fossil data regarding the deep evolution of Podocarpaceae reproductive structures are sparse, they are complementary. Both suggest that cones, seeds, and leaves evolved as a suite of traits in a stepwise manner in response to changing ecological conditions from the Early Cretaceous through the early Cenozoic ..."

! 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 ..."

C.C. Loron et al. (2023): Molecular fingerprints resolve affinities of Rhynie chert organic fossils. Open access, Nature Communications, 4.
"... we demonstrate that the famously exquisite preservation of cells, tissues and organisms in the Rhynie chert accompanies similarly impressive preservation of molecular information. These results provide a compelling positive control that validates the use of infrared spectroscopy to investigate the affinity of organic fossils in chert. ..."

! MAdLand — Molecular Adaptation to Land: Plant Evolution to Change.
The MAdLand community has made contributions to publicly available data resources for plant (evolutionary) biology and expanded the list of organismal systems accessible for research. Note the statement of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) for the established Priority Programme SPP 2237. Worth checking out:
MAdLand Publications.
The interactive and downloadable Plant Evolution Poster.
Exhibition posters "Grün, Steine, Erde. Unsere Welt im Wandel" (in German, by M. Schreiber and S. Gould).

! 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.

N. Mongiardino Koch et al. (2021): Fossils improve phylogenetic analyses of morphological characters. Open access, Proc. R. Soc. B, 288: 20210044.
"... Fossils provide our only direct window into evolutionary events in the distant past.
[...] Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary.
[...] Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history ..."

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.

F. Naggs (2022): The tragedy of the Natural History Museum, London. Free access, Megataxa, 007: 085–112.

! 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). ..."

K.J. Niklas and B.H. Tiffney (2022): Viridiplantae Body Plans Viewed Through the Lens of the Fossil Record and Molecular Biology. Open access, Integrative and Comparative Biology,
"... A review of the fossil record coupled with insights gained from molecular and developmental biology reveal a series of body plan transformations that gave rise to the first land plants. Across diverse algal clades, including the green algae and their descendants, the plant body plan underwent a unicellular -- colonial -- simple multicellular -- complex multicellular transformation series. ..."
Note figure 4: Scenarios for the evolution of the first land plant sporophyte resulting from delayed zygotic meiosis.

J.H. Nitta et al. (2022): An open and continuously updated fern tree of life. Free access, Front. Plant Sci., 13: 909768. doi: 10.3389/fpls.2022.909768.

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

! K. Padian et al. (1994): Cladistics and the fossil record: the uses of history. In PDF, Annual Review of Earth and Planetary Sciences, 22: 63-89.
See also here.

! 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.

! K.J. Peterson et al. (2007): Molecular palaeobiology. Free access, Palaeontology, 50: 775-809.

Plantcode
(Stefan A. Rensing University of Freiburg, Faculty of Chemistry and Pharmacy).
Plantcode scientists are are interested in the evolution of plants sensu lato - i.e., the photosynthetic eukaryotes. Go to:
List of publications.

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.

K.M. Pryer et al. (2004): Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. Open access, American Journal of Botany, 91: 1582-1598.

! 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. ..."

P.K. Raval et al. (2023): A molecular atlas of plastid and mitochondrial adaptations across the evolution from chlorophyte algae to angiosperms. Free access, bioRxiv, doi: https://doi.org/10.1101/2023.09.01.555919.
"... Algae and plants carry two organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages ..."

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

S.S. Renner (2005): Relaxed molecular clocks for dating historical plant dispersal events. In PDF, Trends in plant science, 10: 550-558.
See also here.

! Mark Ridley (2004): Evolution (Third edition). In PDF. 786 pages, Blackwell Publishing company. See likewise here (Google books), or there.
Note especially:
Chapter 1.3, "A short history of evolutionary biology", Start at PDF-page 33.
! Part 5, Macroevolution. Chapter 18, "The History of Life", Start at PDF-page 558.
About plant evolution note:
Chapter 3, "The Evidence for Evolution", Start at PDF-page 43.
Chapter 14, "Speciation", Start at PDF-page 416.
Chapter 19, "Evolutionary Genomics", Start at PDF-page 591.

! 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. ..."

M.A. Romanova et al. (2023): All together now: Cellular and molecular aspects of leaf development in lycophytes, ferns, and seed plants. In PDF, Front. Ecol. Evol., 11: 1097115. doi: 10.3389/fevo.2023.1097115. See also here.
"... To understand leaf origin in sporophytes of land plants, we have combined the available molecular and structural data on development of leaves with different morphologies in different plant lineages ..."
Note figure 10: Phylogenetic tree for land plants and their structural and regulatory innovations.
Figure 11: Hypothesized scenario for the evolutionary emergence of leaves in lycophytes.

! H. Sauquet et al. (2017): The ancestral flower of angiosperms and its early diversification. Free acces, Nature Communications, 8.
Note figure 1: Three-dimensional model of the ancestral flower reconstructed.
"... We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels ..."
Also worth checking out:
! Was war die erste Blüte der Erdgeschichte? In German, by Ulf von Rauchhaupt, 2023, Frankfurter Allgemeine Zeitung.

! H. Schneider et al. (2004): Ferns diversified in the shadow of angiosperms. In PDF, Nature, 428: 553–557. See also here (abstract).
! Note figure 1: Phylogenetic chronograms of ferns (a) and angiosperms (b), and proportional lineages-through-time (LTT) plots for angiosperms and polypods (c).
"... we report divergence time estimates for ferns and angiosperms based on molecular data, with constraints from a reassessment of the fossil record. We show that polypod ferns (>80% of living fern species) diversified in the Cretaceous, after angiosperms ..."

! M.H. Schweitzer (2023): Paleontology in the 21st Century. Free access, Biology, 12, 487. https:// doi.org/10.3390/biology12030487.

M.H. Schweitzer (2004): Molecular paleontology: some current advances and problems. In PDF, Annales de paléontologie, 90: 81-102.
See also here.

! 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.

! 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.

! C.H. Wellmann et al. (2023). Terrestrialization in the Ordovician. Open access, Geological Society, London, Special Publications, 532.
"... This contribution reviews the evidence for terrestrial organisms during the Ordovician (microbial, land plant, fungal, animal)
[...] We conclude that the Ordovician was a critical period during the terrestrialization of planet Earth that witnessed the transition from a microbial terrestrial biota to one dominated by a vegetation of the most basal land plants. ..."

! J.J. Wiens (2003): Missing data, incomplete taxa, and phylogenetic accuracy. Free access, Systematic Biology, 52: 528–538.
"... The problem of missing data is widely considered to be the most significant obstacle in reconstructing phylogenetic relationships of fossil taxa
[...] The goal of this study has been identify the general mechanisms by which missing data may affect phylogenetic accuracy ..."

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

Wikipedia, the free encyclopedia:
Category:Evolution of plants
! Timeline of plant evolution.
Evolutionary history of plants.

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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