Re: [dinosaur] Would non-avian dinosaur survive through the whole Cenozoic?

Outcrop area is not necessarily a good proxy for predicting 
(terrestrial) diversity, see e.g. Dunhill (2012), Dunhill et al. (2014), 
Walker et al. (2017), and getting outcrop area/exposure area on a global 
scale is a non-trivial task (even less so the density of fossils per 
formation). So far, we are still waiting for a good proxy that reflects 
sampling/research effort, etc.

The authors tried to account for various sampling biases with the data 
that was available at the time. If you try to implement the modelling 
approach they took you will see that it is a very neat framework 
(especially its flexibility is quite nice, as pointed out by Mitchell et 
al., 2019), but it required hell a lot of work to carry out. They went 
way beyond of what similar studies did in the past, which also tried to 
correct for sampling bias (e.g., Benson & Mannion, 2012; Benson & 
Upchurch, 2013; Tennant et al., 2016).
Obviously, there will always be room for improvements. Chiarenza et al. 
(2019) is a very neat approach to the topic, and definitely needs 
further consideration. I would argue that (at least the way it is 
implemented at the moment) the results of Chiarenza et al. (2019) can 
also be interpreted in a different way and do not necessarily show what 
they are claiming they show (see also the reviewers' comments in the 
supplement). Nonetheless, it is definitely an exciting contribution to 
the issue.

I am not so sure what you mean with "actually known fossils". The 
results are obviously based on what is known at the moment - but that is 
trivial and also holds true for the opposite interpretation of the 
fossil record. So, I think I misunderstand you here: What do you mean by 
this?

The shape of the curves is determined by the mathematical properties of 
the involved models. For a model with constant speciation/cladogenetic 
rates (I will stick to speciation since that is the commonly used term) 
and extinction rates (with spec. rates > ext. rates) you expect a linear 
increase in the number of speciation events in log space through time. 
If speciation rate decreases through time and is ultimately surpassed by 
extinction rate, you expect a quadratic relationship (also holds true 
for the opposite case, where speciation rate increases through time + 
extinction rate remains constant).
You then fit your models to the data and assess which model performs 
best. That will tell you whether non-avian dinosaurs as a whole were in 
decline or not (in terms of speciational capability). You can add 
various covariates to account for other effects involved (e.g., sampling 
bias, extrinsic controls on speciation dynamics, etc.), but it is not 
necessary for the model per se.
Note also, that for some ornithischian subclades, no decline is recovered.


I did not want to start a discussion (not enough time, I am afraid), but 
merely point out, that the following statement does not necessarily 
reflect current consensus:
"The idea that few new species _did_ evolve in the last few million 
years of the Cretaceous has long been abandoned: it was based simply on 
the fact that the Campanian record of North America is better than the 
Maastrichtian record of North America."



Benson, R. B. J. & Mannion, P. D.
Multi-variate models are essential for understanding vertebrate 
diversification in deep time
/Biology Letters, /*2012*/, 8/, 127-130

Benson, R. B. & Upchurch, P.
Diversity trends in the establishment of terrestrial vertebrate 
ecosystems: interactions between spatial and temporal sampling biases
/Geology, /*2013*/, 41/, 43-46

Chiarenza, A. A.; Mannion, P. D.; Lunt, D. J.; Farnsworth, A.; Jones, L. 
A.; Kelland, S.-J. & Allison, P. A.
Ecological niche modelling does not support climatically-driven dinosaur 
diversity decline before the Cretaceous/Paleogene mass extinction
/Nature Communications, /*2019*/, 10/, 1091

Dunhill, A. M.
Problems with using rock outcrop area as a paleontological sampling 
proxy: rock outcrop and exposure area compared with coastal proximity, 
topography, land use, and lithology
/Paleobiology, /*2012*/, 38/, 126-143

Dunhill, A. M.; Hannisdal, B. & Benton, M. J.
Disentangling rock record bias and common-cause from redundancy in the 
British fossil record
/Nature Communications, /*2014*/, 5/, 4818

Mitchell, J. S.; Etienne, R. S. & Rabosky, D. L.
Inferring diversification rate variation from phylogenies with fossils
/Systematic Biology, /*2019*/, 68/, 1-18

Tennant, J. P.; Mannion, P. D. & Upchurch, P.
Sea level regulated tetrapod diversity dynamics through the 
Jurassic/Cretaceous interval
/Nature Communications, /*2016*/, 7/, 12737

Walker, F. M.; Dunhill, A. M.; Woods, M. A.; Newell, A. J. & Benton, M. J.
Assessing sampling of the fossil record in a geographically and 
stratigraphically constrained dataset: the Chalk Group of Hampshire, 
southern UK
/Journal of the Geological Society, /*2017*/, 174/, 509-521



On 05/12/2019 18:10, David Marjanovic wrote:
> See the "early" in the URL? If you have access, go to the non-early 
> site https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=JMxjjbIZXCWilersPs1bzRx-3mUwTiQUzlyzWk7v7k4&m=mFS9ot0ORoNynzhR7CeMr7Fvnqm1pwfj47kvY_fqFV0&s=TntQrRm3CXGTjULl-vBfaLsOJCjROep-r9zlYUXTntY&e=  
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=ESPn79XeGs9KxsU0zwcoQW6oJv2zWyTWECmdPrr8KsI&e=> 
> and scroll down to the "Materials and Methods" section. There it says 
> at the end:
>
>
>       *Extrinsic Factors.*
>
> Because the fossil record has long been known to be incomplete (50 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D50&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=ib7w64KELV_Iu9iG0d8n5pd6f28slJp1DWM_wJv9Zec&e=>, 
> 51 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D51&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=JpZwHV_EFCAMe0L4HQS9cnpsnCuPqkBBHJCHDkYN-pA&e=>), 
> it is possible that the observed slowdown and downturn are byproducts 
> of undersampling. This assumption would imply that there is a 
> systematic downward bias in the phylogeny toward recent times, which 
> would be counter to the usual expectation for poor sampling (50 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D50&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=ib7w64KELV_Iu9iG0d8n5pd6f28slJp1DWM_wJv9Zec&e=>, 
> 51 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D51&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=JpZwHV_EFCAMe0L4HQS9cnpsnCuPqkBBHJCHDkYN-pA&e=>). 
> Here, to test the effect of such biases, we fitted additional models 
> with appropriate covariates, including stage-level formation counts 
> (because formation count is widely reported to be associated with 
> sampling bias) (9 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D9&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=7taLPIxRx7ZX4uH9od5OOmpvakVzMnScG9yZEkx74kU&e=>, 
> 10 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D10&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=1bnAjs6kvTy01QprSXQ7HN60cQ3ne2P-8oN6HG7a0H0&e=>, 
> 12 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D12&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=kK5sOpRDKX9HbpPJRpHk-0lrGSQ2nKFHMnPYU9UueQM&e=>, 
> 35 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D35&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=6UZozPOEZ5qEmQRzBAe_OCeZSApFu4DBu6HMFeHusfI&e=>, 
> 44 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D44&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=LBpiCOdjJ952--fF4WC2yTvN3LDedRRPb8NLMHHwrF4&e=>, 
> 52 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D52&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=GOfjZw8FnRZa45Gy4UWxzq2N_RJ2qfDEoJNyQ4_x4Mo&e=>, 
> 53 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D53&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=9cYYg0ipbBjJjp8KiRj9qDSox8QDATQlTDNua_UmVXo&e=>), 
> taxon-specific formation counts (the number of formations in which a 
> taxon is found), taxon-specific collection count (the number of fossil 
> collections in which a taxon is represented), cladewise valid taxa 
> counts (the known underrepresentation in the phylogeny) (54 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D54&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=w6VIVQxQ0GVjbEWUoIlw_xlXLk4c1xQrGmDV-YhwEFE&e=>), 
> fossil quality scores (state of preservation) (55 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D55&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=KXuhGNN5kdtvHQB3iXn3b2k5z8BeALKQKM2amxkCtg0&e=>), 
> and body size (smaller taxa are less likely to be preserved) (56 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D56&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=-BAHdcj7AAHcdqTpcPv6Dag0c7MuQq6QAar54fAE9DA&e=>).
>
> As an indirect measure of the influence of geography on speciation 
> dynamics, such as segregation by geographic barriers (30 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D30&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=VeYfcdh6KAX6AfFDMw8DJQicMPdFkLlT9AfVBKlQNlE&e=>), 
> we used Mesozoic eustatic sea-level reconstructions (34 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D34&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=MMkxnIbd63gjFzwZa_mVOBFDel9gGNwDCdeTvnFe6Ds&e=>) 
> as an additional covariate in our models (mean sea-level value along 
> each terminal branch). We also tested the ecological limit on clade 
> diversification or the possible effects of niche saturation by adding 
> a measure of intraclade diversity taken as the number of contemporary 
> branches (including internal branches) for each taxon (the number of 
> tips in time-sliced trees) (48 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_113_18_5036-23ref-2D48&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=rZ8CFQMgRRufHIeFR1dURapBWr_tcplXyA_OOTBLSeU&e=>). 
> All data files are available in Datasets S1–S13 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.pnas.org_lookup_suppl_doi-3A10.1073_pnas.1521478113_-2D_DCSupplemental&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=mLVmZGIWvOAtegO17_Q4QkN0hdzj0y7X7qvZKevuGlo&s=ETE-1pVqs4j4siSbkZqjAEj1ION_zc35G0xk0Qm5Wqw&e=>.
>
> As far as I can tell, all this assumes that if the quality of 
> preservation is the same in two formations, then they will produce the 
> same number of specimens if all else is equal; not all else is equal, 
> and the corrections for this are listed. What is not listed, as far as 
> I understand, are the area on which each formation is exposed now (as 
> opposed to the area over which it was deposited; that's what the sea 
> level correction is for), and the density of fossils in each formation 
> (apparently higher in the Dinosaur Park than in the Hell Creek, AFAIK).
> On top of all that, the emphasis on actually known fossils (spelled 
> out at the start of the "Materials and Methods" section) means that 
> all conclusions are heavily biased toward North America. If there was 
> a decline there but an increase in Africa, we're simply not going to 
> find out anytime soon.
> Finally, the curves in the figures are awfully smooth for spanning so 
> much time. Why would they be? How would that work?
> (...Also, may I request that people stop saying "speciation" when they 
> mean cladogenesis? There's only one of 150 species concepts under 
> which those are reliably the same thing, and it's never used.)
> *Gesendet:* Mittwoch, 04. Dezember 2019 um 20:59 Uhr
> *Von:* "Mailing" <[email protected]>
> *An:* [email protected]
> *Betreff:* Re: [dinosaur] Would non-avian dinosaur survive through the 
> whole Cenozoic?
>
> There was a slow-down in speciation rates prior to the K-Pg, see:
>
> Sakamoto, M.; Benton, M. J. & Venditti, C.
> Dinosaurs in decline tens of millions of years before their final 
> extinction
> /Proceedings of the National Academy of Sciences, /*2016*/, 113/, 
> 5036-5040
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.pnas.org_content_early_2016_04_13_1521478113.abstract&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=JMxjjbIZXCWilersPs1bzRx-3mUwTiQUzlyzWk7v7k4&m=mFS9ot0ORoNynzhR7CeMr7Fvnqm1pwfj47kvY_fqFV0&s=hIgkYcz2_1fe-tcuOXY99gUOdQ7ZJ3XRASmGy_Mca2c&e= 
>