Quotes Links Genetics don't line up with Fossil record.

[ScrappyMarcus]

Broad “rocks vs. clocks” / reconciliation papers
1. Morlon et al., 2011 (PNAS) – shows that diversification patterns inferred from molecular phylogenies often contradict patterns seen directly in the fossil record, and discusses why and how to reconcile them.
https://www.pnas.org/doi/10.1073/pnas.1102543108
2. Yang, 2016 (Phil. Trans. B) – reviews dating conflicts and how priors/calibrations can clash with tree constraints (“rocks vs. clocks”).
https://royalsocietypublishing.org/doi/ ... .2015.0126
3. Guindon, 2020 (Frontiers in Genetics, open-access review) – details strengths/weaknesses of molecular dating and why clock models + calibrations can yield inaccurate ages versus fossils.
https://pmc.ncbi.nlm.nih.gov/articles/PMC7267027/
4. Ronquist et al., 2016 (Phil. Trans. B) – “Closing the gap between rocks and clocks” (total-evidence dating) explicitly addresses the systematic conflicts and methods to narrow them.
https://royalsocietypublishing.org/doi/ ... .2015.0136
5. Quental & Marshall, 2010 (Trends Ecol Evol) – explains why molecular phylogenies and the fossil record can disagree on diversity dynamics and why fossils are still necessary.
https://www.sciencedirect.com/science/a ... 4710001011
Specific clade/time disagreements
6. Cambrian animal origins: The Cambrian Conundrum (Erwin et al., 2011, Science) – argues molecular clocks place animal divergences far earlier than their first fossil appearances (classic timing mismatch).
PubMed → https://pubmed.ncbi.nlm.nih.gov/22116879/
Historical Geobiology Research Group (open PDF) → https://historical-geobiology.stanford. ... undrum.pdf
7. Angiosperms (flowering plants): Coiro et al., 2019 (New Phytologist) – assesses how molecular dates for angiosperm origins conflict with paleobotanical evidence and what fossils imply.
https://nph.onlinelibrary.wiley.com/doi ... /nph.15708
Placental mammals:
8. O’Leary et al., 2013 (Science) – morphology+fossils suggest crown placentals arise after the K–Pg, clashing with many older molecular estimates placing them deep in the Cretaceous.
https://pubmed.ncbi.nlm.nih.gov/23393258/
9. Phillips, 2016 (Syst. Biol.) – reviews why large conflicts with younger fossil records persist despite improved molecular models.
https://academic.oup.com/sysbio/article ... 46/2468935
10. Springer et al., 2017 (Mol. Phylogenet. Evol.) – debates Cretaceous vs. Paleogene timing of the placental radiation; highlights ongoing discrepancies.
https://www.sciencedirect.com/science/a ... 0316302421
Methodology showing why conflicts happen
11. Carruthers et al., 2020 (Mol. Biol. Evol.) – empirical/simulation work showing that adding many fossil calibrations with relaxed clocks can still fail to improve accuracy, explaining persistent fossil–molecular mismatches.
https://academic.oup.com/mbe/article/37/5/1508/5695717
12. Benton/Donoghue line of work (classic reviews on rate variation & calibration that drive clock–fossil discrepancies).
“Rocks and clocks: calibrating the Tree of Life using fossils and molecules” (Trends Ecol Evol, 2007) → https://www.sciencedirect.com/science/a ... 4707001553
“Paleontological Evidence to Date the Tree of Life” (Mol. Biol. Evol., 2007, open PDF) → https://academic.oup.com/mbe/article-pd ... msl150.pdf
13. (maybe) Note: you’ll also find topology conflicts (molecules vs. morphology/fossils) in groups like turtles, early mammals, early birds, etc.; some recent phylogenomics papers claim resolution after long periods of disagreement—which itself documents that earlier conflicts existed.
Example (birds overview): https://pmc.ncbi.nlm.nih.gov/articles/PMC4083789/
Quotes with sources
13. Cambrian timing
“[T]he major animal clades diverged many tens of millions of years before their first appearance in the fossil record.”
Source: Erwin et al., Science (2011) → https://repository.si.edu/bitstream/han ... m_2011.pdf
14. Phylogenies vs fossils (general)
“Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record.”
Source: Morlon et al., PNAS (2011) → https://www.phyloeco.bio.ens.psl.eu/pdf ... withSM.pdf
15. Why fossils still matter for diversification
“Molecular phylogenies… are blind to the true diversity trajectories and rates of origination and extinction…”
Source: Quental & Marshall, Trends Ecol Evol (2010) → https://pubmed.ncbi.nlm.nih.gov/20646780/
16. Placental mammals: post-K–Pg (fossil-calibrated)
“[Tree]… when calibrated with fossils, shows that crown clade Placentalia and placental orders originated after the K–Pg boundary.”
Source: O’Leary et al., Science (2013) → https://pubmed.ncbi.nlm.nih.gov/23393258/
17. Systematic dating bias across big radiations
“There is a wider pattern of conflict between molecular dates and fossil evidence for the timing of major diversifications.”
Source: Phillips, BMC Evol Biol (2018) → https://bmcecolevol.biomedcentral.com/a ... 018-1218-x
(and noted the correction inline).
18. “...the most recent inference techniques, including tip-dating and all approaches based on the fossilized-birth-death model, ignore this information, thereby enabling node age estimates that potentially contradict what is known from the fossil record.” — Stéphane Guindon, Frontiers in Genetics (2020). FrontiersPMC
19. “Molecular dating analyses that consistently retrieve pre-Cretaceous ages for crown-group angiosperms have eroded confidence in the fossil record, which indicates a radiation and possibly also origin in the Early Cretaceous.” — Coiro, Doyle & Hilton, New Phytologist (2019). PubMed
20. (same paper; concrete example) “The earliest unambiguous fossil evidence of angiosperms is from the Early Cretaceous; the pollen record conflicts strongly with Triassic and Early Jurassic molecular ages…” — Coiro, Doyle & Hilton, New Phytologist (2019). PubMed
21. “Cetaceans provide a striking example: standard phylogenetic inferences are strikingly inconsistent with fossil data… Rate variation across clades can reconcile them.” — Morlon et al., PNAS (2011).
22. Big-picture Cambrian timing tension (short synthesis): “The major animal clades diverged many tens of millions of years before their first appearance in the fossil record.” — Erwin et al., “The Cambrian Conundrum,” Science (2011).