The angiosperm radiation played a dual role in the diversification of insects and insect pollinators

Domain: earth_science
Published: 2024-01-22
Editorial outcome: accept

Abstract
Interactions with angiosperms have been hypothesised to play a crucial role in driving diversification among insects, with a particular emphasis on pollinator insects. However, support for coevolutionary diversification in insect–plant interactions is weak. Macroevolutionary studies of insect and plant diversities support the hypothesis that angiosperms diversified after a peak in insect diversity in the Early Cretaceous. Here, we used the family-level fossil record of insects as a whole, and insect pollinator families in particular, to estimate diversification rates and the role of angiosperms on insect macroevolutionary history using a Bayesian process-based approach. We found that angiosperms played a dual role that changed through time, mitigating insect extinction in the Cretaceous and promoting insect origination in the Cenozoic, which is also recovered for insect pollinator families only. Although insects pollinated gymnosperms before the angiosperm radiation, a radiation of new pollinator lineages began as angiosperm lineages increased, particularly significant after 50 Ma. We also found that global temperature, increases in insect diversity, and spore plants were strongly correlated with origination and extinction rates, suggesting that multiple drivers influenced insect diversification and arguing for the investigation of different explanatory variables in further studies.

Introduction
Today, flowering plants (angiosperms) dominate most terrestrial ecosystems and provide an important part of the food chain and niche requirements for many other organisms. It is estimated that angiosperms account for about 90% of all land plants (embryophytes), or about 300,000 living species1. Their origin was one of the most transformative events in Earth’s history. However, the age of crown angiosperms remains highly uncertain2. There is almost universal molecular support for a pre-Cretaceous origin of stem angiosperms3, ranging from 310 to 380 million years ago (Ma) depending on the study4–7. In contrast, the earliest fossil remains that can be assigned with high confidence to crown angiosperms are tricolpate pollen grains from the Barremian–Aptian transition (121 Ma8). The fossil record still provides fundamental evidence for the origin of crown angiosperms, except for the lineages of some flies, bees, and long-proboscid butterflies25.

It was thought that the first seed plants were wind-pollinated until some insects diversified and began to feed on gymnosperm ovule secretions in a surface-fluid-feeding manner or on gymnosperm pollen26,27. However, we now know that Cretaceous plants were pollinated by a different spectrum of pollinator agents28, predating that of nectar- and pollen-feeding insects on angiosperms29 (Fig. 1). The complex interactions between potential pollinators and gymnosperms appear to have persisted at least since the early Permian (283–273 Ma), predating the first flowering plants by more than 100 Ma30,31. Since then, there is a diverse, well-documented Cretaceous pollinator community found in sediments and ambers, supporting gymnosperm–insect pollination modes and host associations with ginkgoaleans, cycads, conifers, and bennettitalean gymnosperms during the Early Cretaceous and the early Late Cretaceous27,28,32–36 (Fig. 1). In contrast, evidence for angiosperm-pollen consumers or flower visitors does not appear in the fossil record until the Late Cretaceous, around 99 Ma28,36,37. Insects continued pollinating flowering plants since then38,39. The ensuing question is: what effect did the radiation of angiosperms since the Cretaceous have on the diversification of insects, and in particular pollinating insects, given that insects have been diversifying with and pollinating gymnosperms since the Permian?

Elucidating when, how and why the ecological transformation of ecosystems began with the coevolution between insects and angiosperms has become a topic of recent interest10,25,39,40. Relying on qualitative comparisons has limitations, and there are few quantitative tests to assess whether coevolution has driven diversification between plants and insects. In this study we tested the widely held hypothesis of the impact of angiosperm radiation on insect diversification in general, and on insect pollinators in particular, using the fossil record. To complement our results, we also analysed the role that five additional variables (diversity dependence, gymnosperms, spore plants, continental fragmentation, and temperature) may have had on insect diversification rates. We hypothesise that the radiation of angiosperms had a positive effect on insect diversification rates, mainly by increasing origination rates, but may also have reduced extinction rates by facilitating the shift of gymnosperm pollinators to angiosperms as angiosperms diversified and gymnosperms entered a phase of diversity decline from the Late Cretaceous onwards.

Results
To estimate whether insect origination and/or extinction rates varied through time and whether they could be correlated to the angiosperm radiation, we retrieved the family-level fossil dataset of ref. 19. We used the Bayesian process-based approach implemented in PyRate 341, which models simultaneously the rates of preservation and their variation across taxa, the times of origination and extinction of each taxon, and then the rates of origination and extinction through time. By estimating the preservation rates, PyRate corrects the ages of origination and extinction of each taxon that can alleviate known issues of the fossil record such as the temporal incompleteness of the fossil record42. As expected, we recovered a dynamic accumulation of family diversity with major increases in family richness during the Cretaceous and the Cenozoic (Fig. 2a), in line with previous studies20. We also repeated the analysis, including only the families from this same fossil dataset that were cited as extant or extinct pollinator28, including also the possible pollinators to be as inclusive as possible (Fig. 2a). To clearly differentiate a fossil pollinator and a fossil possible pollinator, we relied on a recent review of insect pollination through deep time28.

We then relied on the Bayesian multivariate birth-death (MBD) model implemented in PyRate to simultaneously estimate correlations between diversification dynamics and multiple environmental variables, with the statistical support being estimated with a shrinkage weight (\omega) for each correlation parameter (G) for origination (G\lambda) and extinction (G\mu) depending on each environmental variable43. We focused on the role of angiosperms but are aware that several other drivers may have also complementary impacted the diversification of insects (see Methods for details). In addition to the relative diversity of angiosperms, we thus incorporated five additional variables: the number of insect families through time (diversity dependence), diversity of gymnosperms, and spore plants6, the continental fragmentation44, and global temperature45.

We first estimated origination and extinction rates over the entire evolutionary history of insects (i.e. from the mid-Carboniferous to the present), for which angiosperms were absent from the fossil record until the Early Cretaceous. Our modelling results show that, of the six tested variables, angiosperms could have promoted a faster diversification of insects once they co-diversified since the Cretaceous (Supplementary Data 1a). Specifically, we found that the rise of flowering plants not only could have driven the origination of insect families (\omega\lambda=0.576 and G\lambda=0.823), but they could have also strongly buffered them against extinction (\omega\mu=0.802 and G\mu=-1.799; Supplementary Data 1a). We then performed the same diversification analyses but with rates only estimated for the time interval covering the ATR (sensu ref. 10, from 100 to 50 Ma) and another set of analyses with rates only estimated in the aftermath of the ATR (from 50 Ma to present). The ATR-centred analyses indicated that this period is strongly correlated with a reduced insect extinction rates (\omega\mu=0.95 and G\mu = -4.555) but did not affect insect origination rates (Fig. 3, Supplementary Data 1b). The post-ATR analyses indicated that this period is strongly correlated with an increased insect origination rates (\omega\lambda=0.645 and G\lambda=1.052) and decreased insect extinction rates (\omega\mu=0.797 and G\mu = -1.791), but lesser than during the ATR (Fig. 3, Supplementary Data 1c). Therefore, angiosperms seem to have a dual role that has changed through time with an attenuation of the extinction in the Cretaceous and the beginning of the Cenozoic and a driver of origination in the Cenozoic, from 50 Ma onwards.

Second, we tested whether there was also a relationship between angiosperm radiation and the pollinating insect families by repeating the MBD analysis to estimate origination and extinction rates across pollinator groups only (including the possible pollinators, according to ref. 28). Our Bayesian modelling results shows that, among the six tested variables, angiosperms may have promoted diversification of pollinator insects once they had co-diversified since the Cretaceous not only due to a strong and positive correlation with origination rates (\omega\lambda=0.943 and G\lambda=3.663) but also to a strong and negative correlation with extinction rates (\omega\mu=0.967 and G\mu=-5.487) (Supplementary Data 2a). Thus, the global rise of flowering plants may not only have driven the emergence of insect pollinator families but may also have buffered them against extinction, as similarly found for the whole insect record. Performing the same diversification analyses with rates estimated only for the time interval covering the ATR (from 100 to 50 Ma) and another set of analyses with rates estimated only in the post-ATR period (from 50 Ma to the present), we found that the ATR-centred analyses indicated that the rise of angiosperms was strongly correlated with a decrease in pollinator extinction rates (\omega\mu=0.978 and G\mu = -7.239) and also with an increase in pollinator origination rates (\omega\lambda=0.799 and G\lambda = 1.558; Fig. 3, Supplementary Data 2b). This evolutionary pattern is maintained in the Cenozoic, with the post-ATR analyses showing that this period is strongly correlated with both an increase in insect origination rates and a decrease in insect extinction rates. Compared to rates during the ATR, the correlation with origination rates is stronger (G\lambda = 1.558 vs. G\lambda = 3.638), while the correlation with extinction rates is weaker (G\mu = -7.239 vs. G\mu = -5.535; Fig. 3, Supplementary Data 2c).

With the aim of accounting for any bias in our results due to heterogeneity in preservation rates for specific groups in the fossil record46,47, we repeated the MBD analyses to test whether the relationship between angiosperm radiation and the five most diverse insect orders (i.e. Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera) held. We collected specific families by orders and found idiosyncratic family-level accumulation curves, suggesting different diversification dynamics (Fig. 2b), which is expected given their differences in life history, key innovations and ages (e.g. 19,46–49). By dividing the timeframe into the ATR (100–50 Ma) and the post-ATR period (50 Ma–Present), our Bayesian modelling results show that there is still a common factor with the angiosperms promoting diversification in the post-ATR period, although we also found clade-specific responses (Fig. 4, Supplementary Data 3). The angiosperm effect appears to operate either through a positive correlation with divergence rates (for Diptera and Lepidoptera,) or through a negative correlation with extinction rates (Diptera, Hemiptera, and Hymenoptera). For Coleoptera, we found no significant correlation, but we are very close to inferring a negative correlation with extinction rates during the ATR.

It is also important to highlight that the rise of angiosperms is not the only driver with a significant identified effect on insect evolution. As expected, we also found other factors at play. Notably, a negative diversity-dependent effect of origination rates as a major driver for insects as a whole (Fig. 3, Supplementary Data 1), for pollinator insects only (Fig. 3, Supplementary Data 2), and for the five analysed orders in the post-ATR period, but also during the ATR for Coleoptera and Hemiptera (Fig. 3, Supplementary Data 3). The third important factor recovered in the analyses is the effect of past global temperature. It resulted negatively correlated with origination and positively correlated with extinction, such that warmer climates led to lower origination and higher extinction for insects as a whole (Fig. 3, Supplementary Data 1). Global temperature is also found to have a strong negative correlation for the origination rates with pollinator insects in all analyses, indicating lower origination during warmer climates (Fig. 3, Supplementary Data 2). We found that it also influences origination rates through a negative correlation during the ATR (for Coleoptera, Hemiptera, and Hymenoptera) and through a negative correlation with origination rates during the post-ATR period (for all orders except Lepidoptera) (Fig. 4, Supplementary Data 3). Relative spore plant diversity is also found to have a strong positive correlation with both general insect origination and extinction rates, suggesting that higher spore plant diversity spurred insect turnover (Fig. 3, Supplementary Data 1). For pollinator insects, spore plants were only correlated, but strongly, with origination rates (Fig. 3, Supplementary Data 2). Relative gymnosperm diversity is never recovered as a significant driver in the analyses of all insect families, but is found to be an important driver in the analyses of pollinating insect families. Specifically, gymnosperms correlate positively with both origination rates and negatively with extinction rates (Fig. 3, Supplementary Data 2). Relative gymnosperm diversity is also a primer with effect on the origination rates of Hymenoptera during the post-ATR period (Fig. 4, Supplementary Data 3).

Methods
Fossil data and multivariate birth-death analyses
We retrieved the times of origination and times of extinction for 1527 families, including 671 extant and 856 extinct families, which have been estimated from more than 38,000 fossil occurrences at the family level19. From this entire insect fossil dataset, we extracted only the pollinator families (including possible pollinator families) based on the most recent work28, representing 174 families. From the original database, we extracted also the families of the five most diverse insect orders, which correspond to 165 families in Coleoptera, 219 in Hemiptera, 176 in Diptera, 116 in Hymenoptera, and 43 in Lepidoptera. To examine changes in insect family diversity, changes in pollinator family diversity and changes in the family diversity divided by orders through time, we reconstructed the lineages-through-time using PyRate 342 using the origination and extinction times of all insect families as input file (-ltt1 option; R scripts available in the FigShare repository).

A birth-death model (MBD) has been developed and implemented in PyRate to test for a correlation between speciation and extinction rates and changes in environmental variables43. We used the MBD model to assess the extent to which biotic and abiotic factors can explain temporal variation in speciation and extinction rates. In the MBD model, speciation and extinction rates can vary through time, but equally across all lineages, through correlations with multiple time-continuous variables, and the strengths and signs (positive or negative) of the correlations are jointly estimated for each variable43. The MBD model incorporates temporal fluctuations of environmental variables, so that the speciation and extinction rates can depend on variations in each factor. The correlation parameters can take negative values indicating negative correlation, or positive values for positive correlations. If their value is estimated to be close to zero, no correlation is estimated. A Markov chain Monte Carlo (MCMC) algorithm jointly estimates the baseline speciation (\lambda0) and extinction (\mu0) rates and all correlation parameters (G\lambda and G\mu) using a horseshoe prior to control for over-parameterisation and for the potential effects of multiple testing. The horseshoe prior provides an efficient approach to distinguishing correlation parameters that should be treated as noise (and therefore shrunk around 0) from those that are significantly different from 0 and represent true signal. For all insects, pollinator insects only, and the five insect orders, we ran the MBD model with 50 million MCMC iterations and sampling every 50,000 to approximate the posterior distribution of all parameters (\lambda0, \mu0, ten G\lambda, ten G\mu, and the shrinkage weights of each correlation parameter, \omegaG). We summarised the results of the MBD analyses by calculating the posterior median and 95% credible interval of all correlation parameters and the mean of the respective shrinkage weights (over ten replicates), as well as the median and 95% credible interval of the baseline speciation and extinction rates.

The MBD model assumes that diversification rates vary continuously over time with a given variable. However, it is possible for rates to vary positively in one-time interval and negatively in another time interval89. In other words, the drivers of diversification may vary over time. We therefore tested whether the impact of angiosperm diversity was similar over time, during the ATR (100–50 Ma, sensu 10) and after the ATR (50–0 Ma). The MBD analyses were thus performed with time constraints to estimate rates within this time interval by setting up the -maxT 100 minT 50 or -maxT 50 minT 0 option to represent the ATR and post-ATR periods, respectively. The Python and R scripts are available in the FigShare repository.

Palaeoenvironmental variables
To identify putative mechanisms of insect diversification, we examined the correlation between a series of past environmental variables and origination/extinction rates over their entire history. We focused on the role of six palaeoenvironmental variables, also called proxies, which have been linked to biodiversity change. These proxies were classified as either abiotic or biotic controls as follows: (i) Biotic controls: Ecological interactions with rapidly expanding clades are increasingly recognised as important macroevolutionary drivers14,86. Insects experienced drastic floristic changes throughout their evolutionary history with the origin and rapid radiation of angiosperms at the expense of a decline in diversity of gymnosperms and ferns. The rise and dominance of angiosperms may have contributed to altering the dietary regimes of herbivorous insects, which could in turn have affected insects that depend on herbivores by a cascading effect. We used the relative generic diversity trajectories of angiosperms, gymnosperms, and spore plants (mostly composed of ferns) based on previous estimates of plant diversity that estimated genus-level diversification dynamics of these groups and estimated the times of origination and extinction of all plant genera6, which allows computing the temporal dynamic of diversity changes and converted into relative generic diversity14,43. Note that the relative plant group diversities do not sum to 1. The angiosperm and gymnosperm diversities come from ref. 6, and the spore plant diversity comes from ref. 43. In the latter study, the authors derived the relative diversities of all plant groups. Their diversities do not add up to 1, probably because they are not all from the same study. Biotic interactions within insects could also have influenced their diversification. For instance, we could draw hypotheses of diversity dependence such that insects could either impact or be impacted by their own diversity. In other words, the change in their diversity can affect their diversification as proposed in diversity-dependent hypotheses. We thus included the palaeodiversity of all insect families to account for diversity dependence within insects as an independent variable. Note that the MBD model does a data scaling (-r 0 option) with all variables so that the trends in diversity fluctuations are used but not the change in absolute diversity values, which homogenises the fact that insect diversity and relative plant diversity are for different taxonomic levels. (ii) Abiotic controls: Climate change (variations from warming to cooling periods) is one of the most probable drivers of diversification changes throughout the history of life14,90. Major trends in global climate change through time are typically estimated from relative proportions of different oxygen isotopes (\delta18O) in samples of benthic foraminifer shells. We merged \delta18O global temperature data from different sources (91 for the Cenozoic 92; for the rest of the Phanerozoic) to provide \delta18O data spanning the full time-range over which insect families originated. Second, global continental fragmentation, as approximated by plate tectonic change over time, has also been proposed as a driver of diversity dynamics44,87. We retrieved the index of continental fragmentation developed by ref. 44 using palaeogeographic reconstructions for 1-million-year time intervals. This index approaches 1 when all plates are not connected (complete plate fragmentation) and approaches 0 when there is maximum aggregation. All these variables were used as input data for the MBD model. The files for the environmental data are available in the FigShare repository.

Figures
Figures were created using CorelDRAW Graphics Suite software, version 19.0. (www.coreldraw.com). Fig. 2 was designed based on the results obtained after the data analysis with the software R.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "In this interesting manuscript, the authors test the impact of multiple historical variables, including diversity of angiosperms, on diversification of insects through the Mesozoic and Cenozoic. They find evidence for a significant impact of past angiosperm diversity on insect speciation and extinction, and for distinct variations of this impact in two time periods (100-50 Ma, 50-0 Ma). While these results are certainly important and worthy of publication, I have some reservations on the manuscript itself as well as the scope of the analyses, which I will attempt to outline below. I hope the authors find these comments helpful.\n1. General presentation and discussion: while generally well written, the text would benefit from extra care throughout, with quite a few problematic sentences and typographical errors, and the logic not always clear. Arguably, this is a difficult, very broad topic to write on, and the authors did a great job of taking into account a considerable body of recent (and older) literature on the diversification of both angiosperms (but see below) and insects, making parts of the text read more like a review article. However, one key issue in my opinion is the attempt to tackle a much more ambitious question than that asked by the title and analyses: it is clear throughout the text that the authors also want to discuss the role of insects (and other variables including key traits) on angiosperm diversification. This is particularly clear throughout the discussion, which focusses much more on angiosperm diversification than insect diversification. Clearly, the two are intricately linked (at least for part of their history), as this study contributes to show, but the shift in focus left me rather confused. Hence, given the analyses presented and the primary expertise of both authors, I would recommend to rewrite much of the discussion to focus on insect diversification.\n2. Angiosperm questions: despite the remarkable effort to synthesize the complex, and sometimes contradictory literature on the origin and diversification of angiosperms, there are a few important mixups and misrepresentations in various places that call for great caution in revising the text (noted further below under Minor comments).\n3. Data and analyses: the entire study is based on three variations of a single analysis using previously published data. I do not think this precludes publication, and the analysis itself is a clever macroevolutionary approach modelling the multivariate impacts of various variables on speciation and extinction rates of the fossil record. Yet I believe incomplete discussion of the merits and limitations of this approach is provided in this manuscript, particularly compared to alternative methods and sources of data:\n(a) The entire focus for insects is on family origination and extinction, presumably due to the limitation of the data used. Do we expect the same results as those of a hypothetical (but desirable) analysis that would focus on insect species origination and extinction? And is there a potential inconsistency with using genus-level past diversity curves for plants as explanatory variables? (Note the latter only becomes clear while inspecting the paper by Silvestro et al. 2015, which provided the source data for plants. I think this should be made clear in this new study.)\n(b) Curiously, for reasons I do not fully understand, the authors have opted to use relative rather than absolute past (generic) diversity of various plant groups as variables of the model of insect origination and extinction. This requires some justification. Furthermore, because the three relative diversity variables of angiosperms, gymnosperms, and spore plants were concurrently used in the same model, there is a potential risk of interdependence. I do not know whether this is a problem with the model used, but would expect to see this aspect discussed as well.\n(c) As the authors are well aware, alternative macroevolutionary methods based on dated phylogenies of extant taxa also exist to address similar questions (including some methods developed by the second author). These have recently become the topic of a heated debate related to model identifiability, and their ability to accurately estimate extinction rates have also long been questioned. Yet, given their prevalence in the literature, and given the inherent biases and limitations of the fossil record used here, it would seem critical to briefly discuss the merits and limitations of both approaches in this study.\nMinor comments\nL15: insert “an” before “important” (note there are may other similar minor typos spread across the text, which I won’t attempt to list exhaustively here)\nL17-18: given that we still have no idea when angiosperms evolved (as in their crown age), I would disagree with this statement\nL36-37: many issues with this sentence; first, as ref. 2 showed, support for a pre-Cretaceous crown age of angiosperm has little to do with molecular data themselves; second, crown angiosperms have not been dated as 310-380 Ma in the studies cited (you must be referring to the crown age of seed plants / the stem age of angiosperms here, as in your original preprint)\nL39-41: not if we accept a pre-Cretaceous origin of crown angiosperms; ref. 10 definitely did not assert a Cretaceous crown ancestor; suggest updating plausible range to 270-140 Ma as in ref. 2\nL47: decline in what?\nL52-53: which early-diverging groups are you referring to here? (not clear if insects or plants)\nL63: which first plants?; note the first land plants could certainly not be wind-pollinated as they had no pollen (which is a synapomorphy of seed plants)\nL65: reword “ancient plants” (too vague)\nL72: replace “ginkogaleans” with “ginkgoaleans”?\nL76-77: rephrase (not clear)\nL82-83: in general, I am not entirely comfortable with the attempt to capture and follow three distinct key periods that previous authors have defined to refer to important aspects of angiosperm diversification (Angiosperm Radiation, Cretaceous Terrestrial Revolution, Angiosperm Terrestrial Revolution), as they might be perceived by some readers as different views on the same process, which I don’t think they are. This risk of confusion becomes very apparent in the legend of this (and other figures), which refers to “The period of angiosperm evolution”. I find these terms confusing because they could be read as “the period during which crown angiosperms originated” (which we do not know and is definitely older than any of these three intervals) or “the period during which angiosperms have continuously evolved” (which would be the period since their origin to the Present).\nL84-85: is the time scale the same for A and B? if so, why is B restricted to the interval from ca. 145-55 Ma?\nL98: Condamine et al. (fossil insect dataset) is ref. 19\nL112-113: same comment as above (L82-83)\nL115-116: only in the fossil record (as the authors know, numerous colleagues believe angiosperms were actually present before the Cretaceous)\nL119: Table 1 was not included in the manuscript file provided to me for review\nL129: not sure what is meant by “the rise of angiosperms” after the ATR (by the end of the ATR, angiosperms would have long risen by all possible measures)\nL140-141: I understand this is the result of the multivariate analysis, but it read strangely to me as relative angiosperm and gymnosperm diversity would be strongly correlated to one another (see my main comment above in point 3c)\nL160: replace “superiority” with “advantage”?\nL164-167: not sure where this statement comes from; I see that ref. 53 wrote something similar in describing the findings of one earlier study, but the reality is we do not really know and still lack any robust macroevolutionary statistical approaches to measure the impact of singular traits (i.e., those originating only once) on diversification rates\nL179-183: hard to follow here (particularly L182, the logic of which is unclear to me)\nL183-185: I agree, which is why this whole discussion read very strangely to me (as an attempt to synthesize current knowledge on drivers of diversification in angiosperms, which remains highly incomplete, has now been reviewed more than once in recent literature, and is portrayed rather confusingly in the text here)\nL189: there are definitely more key studies to consider here, in addition to ref. 6, in particular the paper by Magallon et al. in Annals of Botany 123: 491–503, 2019\nL211-212: strange statement\nL226-227: I don’t think we really know this, given that data still lack on pollination of most species of angiosperms\nL235: that peak is not clear to me in Fig. 2 (which shows instead that insect family richness has never been so high than in the last 40 Ma)\nL245: ref. 10 drafted the angiosperm spindle as hypothetical and largely unknown (see legend of their Fig. 1), which I think should be noted here as well if reproduced; on the other hand, ref. 10 did certainly not depict detailed spindles of the various gymnosperm lineages, so the legend and citation here must be corrected\nL247-248: I am not familiar with ref. 99, but find it very odd and confusing to still recognise here the possibility of Gnetales being closely related to angiosperms (as denoted by the hyphenated branch), an old idea now dismissed by most phylogenetic analyses published over the last two decades\nL248: I have reservations on the use of TimeTree (which averages over all studies in their database, regardless of quality and assumptions), but I suppose accurate divergence times (and their uncertainty) are not critical to either this figure or this study\nL260: strange sentence, needs rewording\nL270-273: I don’t disagree, but this is a rather underwhelming closing statement in that various authors have already suggested the same and it remains somewhat disconnected from this study (perhaps some rewriting needed)\nL279: wrong Condamine et al. paper cited here? Shouldn’t this be ref. 19 instead?\nL510: first author should be Lagomarsino\nHervé Sauquet", "reviewer_2": "This manuscript addresses drivers of insect diversification during the Cretaceous and Cenozoic at the family level using fossil data. It uses a Bayesian approach applied to fossil origination and extinction data to develop and assess birth-death models and parameterize correlations between those births and deaths and other continuously varying ecological parameters. These include the richness of different taxa, including insect families and the richness of different plant groups, plus sea surface temperature estimates and the fragmentation of continents. Models are developed for two 50Myr time periods to assess to what extent the associations have varied over time, and these time periods are chosen to match periods described as the Angiosperm Terrestrial revolution (angiosperms replacing other plants, notably Gymnosperms), and the later period of Angiosperm dominance. The authors report that insect origination and extinction are explained by a number of variables, but not gymnosperm diversity. Origination rates are enhanced by spore plant diversity, angiosperm diversity (but only in the later time period) and reduced by insect diversity (implying diversity-dependence). Extinction rates are also enhanced by spore plant diversity, continental fragmentation in the first time period, and reduced by angiosperm diversity. The authors conclude a changing role for angiosperms affecting insect diversity in association with several other variables.\nThe questions addressed by this work are of wide appeal: angiosperms and insects collectively comprise about three quarters of extant macroscopic species described on Earth, and because insects and plants interact, there has long been speculation on how they could have affected each other’s macroevolution. Fossil data provide some advantages over purely phylogenetic data based on extant taxa as they are probably better sources for estimating extinction rates. The analytical methods used are current and appropriate for the data. The results of the paper are interesting as they are the first to my knowledge which explicitly test several potential environmental drivers of insect diversity at a global scale, and test how those change over time. The findings should contribute to the developing story of how the global taxonomic composition and richness changes of the last 100Myr came about.\nWhilst I think there is the backbone of an interesting paper here, I also feel that there are some significant issues for the authors to consider to make it more interesting and robust. These relate to the way the story is developed in the introduction and discussion, the scope of the analyses performed and how those relate to the story, and the sensitively of the results to potential biases and variations in the data. There are also some textual/content issues. I list these below. I hope they are useful to the authors in developing this work further.\n1. Table 1 is mentioned several times in the main text but seemed to be absent from the manuscript. Since this seems to contain important results, it’s difficult to make a full decision on the manuscript.\n2. The introduction and discussion seem to mismatch the results and methods quite significantly. This makes a confusing story for the reader. Specifically, large parts of the introduction and discussion are spent developing a story about plant pollinator interactions. For example, Figure 1 is all about pollinators and their interactions with angiosperms or gymnosperms. This is fair enough and interesting. However, it is then a bit surprising to find that the data and results cover all insects, not just pollinators. If I were testing an hypothesis about plant pollinator interactions, I would design my data around those groups. The discussion is extensively about pollinator interactions too, but of course a vast number of the species included in the families covered by the data are not pollinators at all. Plenty of the species and families do not directly interact with plants: granted most probably do indirectly, which is relevant to a general insect-angiosperm story, but this is hardly mentioned. In addition there are a great number of ways insects interact with plants that do not include pollination, herbivory being the most obvious and probably important. There is almost nothing on herbivory here! Maybe the focus needs also to consider larval as well as adult interactions. This seems like a rather large oversight, or at least it is confusing for the reader. I think that the authors should decide if they want to test ideas about pollination or a much more general set of ideas about how plants affect insects, but whatever they choose the story should match the data and analyses.\n3. Similar to the above there is a focus to some extent in the introduction and especially in the discussion on angiosperm diversification, but the results and analyses focus exclusively on how angiosperms affect insect macroevolution. It’s almost as if the results were written by someone with interests in insects but discussion by someone with interests in angiosperms. Now, given that the term co-diversification or co-evolution is used liberally, I was expecting analyses on how insects affect angiosperms as well as vis-versa. The data imply that this could be done, so I was wondering why not. The results are better suited to a narrative exclusively focussed on insects and not focusing on angiosperm macroevolution.\n4. Insect fossils come from a variety of sources but two main sources are impression fossils such as from lake sediments, and specimens preserved in amber. These are two very different types of preservation, with the latter being much more sparse and episodic but giving much better sampling (and higher implied richness). The PyRate method models preservation changes but it would seem a bit risky to base all conclusions on a mixed dataset that combines these two sources of evidence because the preservation characteristics are so different. It would be sensible I think to conduct a sensitively analysis by doing additional analyses on a single (e.g. non-amber) subset or if possible both subsets (amber and non-amber) to see how robust the results are to this variation in data sources: this has been done for example in ref 20, and it should be straightforward to extract the data from PBDB. Similarly, some exploration of taxonomic subsets would be very sensible given that different trophic groups would be expected to have more direct or indirect associations with angiosperms.\n5. The discussion hardly discusses your actual findings at all. Why should higher angiosperm diversity reduce extinction rates in insects? Has any literature proposed this before? There is a vast literature on density-dependent diversification in insects but not much has been cited: for example see the papers discussed in the reviews by Mayhew in 2007 (Biol. Rev.) and 2018 (Ent Exp et Appl). Are you surprised that it seems to work via reductions in origination rather than rises in extinction? Would you expect continental fragmentation to have the observed effect on extinction and why? Given your hypotheses are you surprised by the non-effect of gymnosperm diversity on extinction? Could a subset of older families show different results as in figure 1? Could you test that? The temperature effects conform to some previous results on invertebrates but not all. The contrary papers are not mentioned. Why might they exist?\n6. The whole issue of working at the family level is not discussed anywhere but I think the reasons and caveats need to be mentioned somewhere, at least in the discussion. For example, extinction of a family implies very different species level rates for some families than others. Very species rich families will be almost impossible to send extinct, whilst species poor ones might go extinct easily. Is it likely that species richness across families has shown systematic trends over time? Are family level data in plants and insect comparable and the most relevant data in which to make these comparisons? In reality, we are simply using this level in order to reduce gaps in the record. Why would one expect family level diversity in plants to have any effect on family level diversity in insects: what assumptions are built into that?\n7. Another caveat is that the PyRate models assume that rates are the same at any moment in time in all lineages. Of course we know that taxon-specific rates exist in insects. What are the consequences of this breakage of assumptions for accurately estimating rates? I know the methods are what we have, but the reader needs to be alerted to caveats.\n8. If you keep the existing text and figures, I have minor suggested edits:\ni) Line 15 drivers\nii) Line 47 delete and\niii) Line 77 using angiosperm resources extensively until the\niv) Line 131: dual influence?\nv) Line 134: Nevertheless, the rise of\nvi) Line 136: correlated with reduced origination rates\nvii) Lien 145: focussed on the\nviii) Figure 3 legend and axis labels: No units or title on the x-axis scale: from the main text one would naively assume this to be a correlation coefficient but it cannot be. Why not have the confidence intervals on the bars?\nix) Line 172: cell sizes; herbaceousness,\nx) Line 185: approach that\nxi) I felt Figure 4 was not needed; it’s not results and this is not a review paper.\nxii) Line 260: found that flowering plant diversity correlates with a faster\nxiii) Line 266-7. Other hand, a link seems to exist between\nxiv) Line 335: need to say what taxonomic level these data exist at.\nxv) Line 367. I didn’t have access to the data, but they certainly weren’t in the main text: supplementary materials?", "reviewer_3": "This manuscript investigates the potential effects of flowering plants on insect diversification. The link between angiosperms and insects has been hypothesized and studied for quite some time, prompted by the many ecological relationships through pollination and other interactions. Given the high diversity of insects, it is natural that this is a topic of widespread interest.\nThe methods calculate origination, extinction, and diversity from the fossil record, but the techniques do not appear to account for sampling biases or methodological shortcomings of range-through diversity methods. Most notable is the “pull of the recent,” which is visible in the family accumulation plot in figure 2. When information from the extant insect fauna is combined with fossil data, this has the effect of inflating diversity and reducing origination and extinction in more recent time periods. (Technically, it is older time periods that have artificially-low diversity because they do not benefit from the range extensions caused by including extant data.)\nBecause the analysis didn’t account for specific challenges of the fossil record, many of the conclusions about the role of angiosperms could instead be spurious correlations between the angiosperm dominance time series and the pull of the recent. Likewise, reduced origination during times of high diversity (lines 135-137) could be diversity dependence, but also could reflect the pull of the recent bias. It is possible that there are true effects, but I don’t think the argument is convincing now because the methods are not appropriate for dealing with fossil data, and do not attempt to discuss or address widely-known biases.\nA lot of the discussion section seemed to be on topics that are tangential to the results, rather than making the case that the results are true biological patterns, or explaining why the drivers had an effect on insect diversification. For example, why might spore plants also have influenced insect diversification? A lot of the discussion reads like background information about angiosperm evolution, which is interesting, but I didn’t think it was strongly connected to your specific goal in this manuscript.\nIn general, I think it is extremely difficult to work with origination and extinction in the insect fossil record (even harder than trying to reconstruct diversity, which itself is very challenging). Shifts in the dominant preservation mode (amber vs. compression fossils) from one time period to the next cause apparent origination/extinction spikes because the two modes tend to record different types of families. There are huge variations in the number of insects recorded in different time periods, including very few large localities between about 100 Ma and 50 Ma. Because of that, a lot of extinctions that actually occurred later in the Cretaceous will all cluster earlier. Originations will also be artificially clustered at some of the “super-Lagerstatte” (the extraordinarily well-sampled Baltic amber is one example; likely a number of those families evolved earlier but have not yet been discovered because of the limited Late Cretaceous and Paleocene record). It may be possible to extract some real signal, but I’m fairly skeptical, and it would require careful analysis that deals with the complexity of the insect fossil record.\nIt was also difficult to evaluate the results because I couldn’t find table 1 and there didn’t appear to be a dataset containing the potential drivers (spore plant, gymnosperm, angiosperm dominance, temperature, continental fragmentation). Perhaps I missed those on the website, but it would have been very helpful to see a graph of angiosperm dominance through time so that I could visually compare it to insect diversification.\nSincerely,\nMatthew Clapham"}, "author_response": "RESPONSE TO REVIEWERS´ COMMENTS\nReviewer #1 (Remarks to the Author):\nIn this interes(cid:415)ng manuscript, the authors test the impact of mul(cid:415)ple historical variables, including\ndiversity of angiosperms, on diversifica(cid:415)on of insects through the Mesozoic and Cenozoic. They find\nevidence for a significant impact of past angiosperm diversity on insect specia(cid:415)on and ex(cid:415)nc(cid:415)on, and\nfor dis(cid:415)nct varia(cid:415)ons of this impact in two (cid:415)me periods (100-50 Ma, 50-0 Ma). While these results are\ncertainly important and worthy of publica(cid:415)on, I have some reserva(cid:415)ons on the manuscript itself as well\nas the scope of the analyses, which I will a(cid:425)empt to outline below. I hope the authors find these\ncomments helpful.\nThank you for your thorough review and overall posi(cid:415)ve insights. We appreciate all the comments and\nhave addressed all of them below.\n1. General presenta(cid:415)on and discussion: while generally well wri(cid:425)en, the text would benefit from extra\ncare throughout, with quite a few problema(cid:415)c sentences and typographical errors, and the logic not\nalways clear. Arguably, this is a difficult, very broad topic to write on, and the authors did a great job of\ntaking into account a considerable body of recent (and older) literature on the diversifica(cid:415)on of both\nangiosperms (but see below) and insects, making parts of the text read more like a review ar(cid:415)cle.\nHowever, one key issue in my opinion is the a(cid:425)empt to tackle a much more ambi(cid:415)ous ques(cid:415)on than\nthat asked by the (cid:415)tle and analyses: it is clear throughout the text that the authors also want to discuss\nthe role of insects (and other variables including key traits) on angiosperm diversifica(cid:415)on. This is\npar(cid:415)cularly clear throughout the discussion, which focusses much more on angiosperm diversifica(cid:415)on\nthan insect diversifica(cid:415)on. Clearly, the two are intricately linked (at least for part of their history), as\nthis study contributes to show, but the shi(cid:332) in focus le(cid:332) me rather confused. Hence, given the analyses\npresented and the primary exper(cid:415)se of both authors, I would recommend to rewrite much of the\ndiscussion to focus on insect diversifica(cid:415)on.\nWe understand this point. Perhaps the issue comes from the fact that our first a(cid:425)empt to submit a\nmanuscript to Nature Communica(cid:415)ons included a review of both plant and insect life history and\nevolu(cid:415)on. However, following the indica(cid:415)ons from the editorial office, we had to delete the review\nsec(cid:415)on and focus on the analyses and their results. During the revision, we have tried to create a fresh\nthread in the manuscript.\n2. Angiosperm ques(cid:415)ons: despite the remarkable effort to synthesize the complex, and some(cid:415)mes\ncontradictory literature on the origin and diversifica(cid:415)on of angiosperms, there are a few important\nmixups and misrepresenta(cid:415)ons in various places that call for great cau(cid:415)on in revising the text (noted\nfurther below under Minor comments).\nThank you for this note. We have considered the cited comment in the revised manuscript if more\ndetailed data is provided below.\n3. Data and analyses: the en(cid:415)re study is based on three varia(cid:415)ons of a single analysis using previously\npublished data. I do not think this precludes publica(cid:415)on, and the analysis itself is a clever\nmacroevolu(cid:415)onary approach modelling the mul(cid:415)variate impacts of various variables on specia(cid:415)on and\nex(cid:415)nc(cid:415)on rates of the fossil record. Yet I believe incomplete discussion of the merits and limita(cid:415)ons of\nthis approach is provided in this manuscript, par(cid:415)cularly compared to alterna(cid:415)ve methods and sources\nof data:\n(a) The en(cid:415)re focus for insects is on family origina(cid:415)on and ex(cid:415)nc(cid:415)on, presumably due to the limita(cid:415)on\nof the data used. Do we expect the same results as those of a hypothe(cid:415)cal (but desirable) analysis that\nwould focus on insect species origina(cid:415)on and ex(cid:415)nc(cid:415)on? And is there a poten(cid:415)al inconsistency with\nusing genus-level past diversity curves for plants as explanatory variables? (Note the la(cid:425)er only\nbecomes clear while inspec(cid:415)ng the paper by Silvestro et al. 2015, which provided the source data for\nplants. I think this should be made clear in this new study.)\nAn analysis focusing on insect species (or even genera) from the fossil record would take several years\nto complete. We have considered using families as a representa(cid:415)on of origina(cid:415)on and ex(cid:415)nc(cid:415)on rates\nin insect evolu(cid:415)on. Of course, we agree that finest analyses (at lower taxonomic levels) would provide\na more robust signal, but the results are highly unlikely to reach the reviewer’s whish at this point.\nGenus-level fossil-based analyses are only star(cid:415)ng to be published, but for a limited (cid:415)meframe, as it is\nincredibly complicated to compile all the data with cau(cid:415)on (Jouault et al. 2022 – Nat. Comm.).\n(b) Curiously, for reasons I do not fully understand, the authors have opted to use rela(cid:415)ve rather than\nabsolute past (generic) diversity of various plant groups as variables of the model of insect origina(cid:415)on\nand ex(cid:415)nc(cid:415)on. This requires some jus(cid:415)fica(cid:415)on. Furthermore, because the three rela(cid:415)ve diversity\nvariables of angiosperms, gymnosperms, and spore plants were concurrently used in the same model,\nthere is a poten(cid:415)al risk of interdependence. I do not know whether this is a problem with the model\nused, but would expect to see this aspect discussed as well.\nThank you for this point. It would be ideal to rely on the ‘absolute past diversity’ for each plant group,\nbut it’s currently impossible to get descent es(cid:415)mates for each of these clades. To our knowledge, the\nmost recent and updated es(cid:415)mates of past diversity for these three groups is Silvestro et al. (2015 –\nNew Phytol.). This study s(cid:415)ll provides rough es(cid:415)mates of the past diversity of plants, and as such we\nprefer to rely on rela(cid:415)ve diversity rather than absolute diversity. That being said, note that the curves\nof both diversity es(cid:415)mates will be very similar, but one is standardized from 0 to 1 (rela(cid:415)ve), while the\nother represents number of genera (absolute). We have now be(cid:425)er explained the ra(cid:415)onale behind the\nuse of rela(cid:415)ve diversity in our analyses in the Methods sec(cid:415)on.\n(c) As the authors are well aware, alterna(cid:415)ve macroevolu(cid:415)onary methods based on dated phylogenies\nof extant taxa also exist to address similar ques(cid:415)ons (including some methods developed by the second\nauthor). These have recently become the topic of a heated debate related to model iden(cid:415)fiability, and\ntheir ability to accurately es(cid:415)mate ex(cid:415)nc(cid:415)on rates have also long been ques(cid:415)oned. Yet, given their\nprevalence in the literature, and given the inherent biases and limita(cid:415)ons of the fossil record used here,\nit would seem cri(cid:415)cal to briefly discuss the merits and limita(cid:415)ons of both approaches in this study.\nThank you for this other good point. It’s not a simple one to address here but we agree with the referee\nthat alterna(cid:415)ve modelling approaches do exist to es(cid:415)mate rates of diversifica(cid:415)on. The fossil record is\none way, but molecular dated phylogenies is another one. It is true that phylogene(cid:415)c birth-death\nmodels are now widespread to test macroevolu(cid:415)onary hypotheses and that there is major debate in\nthe reliability of rate es(cid:415)mates from them that stem from Kubo & Iwasa (1995 – Evolu(cid:415)on) and\nreanimated by Louca & Pennell (2020 – Nature), including many studies in between. We would have\nloved to es(cid:415)mate diversifica(cid:415)on rates from the latest family-level insect dated phylogeny (certainly\nRainford et al. 2014 – PloS One) if a similar phylogene(cid:415)c birth-death model would have existed to test\nmul(cid:415)ple variables simultaneously. However, we agree that it is cri(cid:415)cal to discuss the merits and\nlimita(cid:415)ons of both approaches in this study, which we have done in the revised version.\nMinor comments\nL15: insert “an” before “important” (note there are may other similar minor typos spread across the\ntext, which I won’t a(cid:425)empt to list exhaus(cid:415)vely here)\nAdded. We have paid a(cid:425)en(cid:415)on to remove typos and gramma(cid:415)cal errors from the text during the\nrevision.\nL17-18: given that we s(cid:415)ll have no idea when angiosperms evolved (as in their crown age), I would\ndisagree with this statement\nWe agree that angiosperm age is difficult to circumscribe. However, the corresponding sentence is\nbased on the ar(cid:415)cle by Benton et al. (2022 – New Phytol.), where the reviewer signs as an author, and\nwhere it is established that the terrestrial revolu(cid:415)on produced by angiosperms begins 100 million years\nago (called the Angiosperm Terrestrial Revolu(cid:415)on). In the text we cite the controversy regarding the\npaleontological and molecular data for the evolu(cid:415)on of angiosperms, but this is just the abstract.\nNonetheless, we have substan(cid:415)ally rephrased the abstract.\nL36-37: many issues with this sentence; first, as ref. 2 showed, support for a pre-Cretaceous crown age\nof angiosperm has li(cid:425)le to do with molecular data themselves; second, crown angiosperms have not\nbeen dated as 310-380 Ma in the studies cited (you must be referring to the crown age of seed plants\n/ the stem age of angiosperms here, as in your original preprint)\nWe agree. “This age is almost en(cid:415)rely condi(cid:415)oned by its own prior distribu(cid:415)on” (Sauquet et al. 2022 –\nJ. Exp. Bot., ref. 2 in the text). Because of that we included ref. 2 first. But there are different results\nthat we must cite (even that condi(cid:415)oned), and in all of them they use molecular support and get similar\npre-Cretaceous origin for the STEM angiosperms (these last words changed accordingly, thanks). We\nshowed again the contrast with fossils including the ref. 8, showing first evidence of tricolpate pollen\nL39-41: not if we accept a pre-Cretaceous origin of crown angiosperms; ref. 10 definitely did not assert\na Cretaceous crown ancestor; suggest upda(cid:415)ng plausible range to 270-140 Ma as in ref. 2\nThe sentence “The age of crown Angiospermae, variously dated from 250–140 Ma, remains\ncontroversial and a ma(cid:425)er of intense research from both palaeobotanical and fossil-calibrated\nmolecular da(cid:415)ng approaches” has been extracted from ref. 10. (Benton et al., 2022). As we indicated\nin our manuscript. However, we slightly changed our word to be clearer in the new text.\nL47: decline in what?\nSorry for the confusion. It was a decline in conifers. It was accidentally missing a(cid:332)er the edi(cid:415)on\nfollowing the editor instruc(cid:415)ons. Now solved.\nL52-53: which early-diverging groups are you referring to here? (not clear if insects or plants)\nIt is referring to the insect peak cited in the previous sentence: “Insect family-richness peaked during\nthe Early Cretaceous around 125 Ma, when angiosperms were s(cid:415)ll rare [20–21]. This peak occurred…”\nWe tried to be more specific now to avoid confusion.\nL63: which first plants?; note the first land plants could certainly not be wind-pollinated as they had no\npollen (which is a synapomorphy of seed plants)\nCorrect, thank you for the nuance. We included “first seed plants”.\nL65: reword “ancient plants” (too vague)\nWe changed it by “Cretaceous plants”.\nL72: replace “ginkogaleans” with “ginkgoaleans”?\nThank you. Changed.\nL76-77: rephrase (not clear)\nDone: “But insects not only pollinated gymnosperms un(cid:415)l, at least, the Late Cretaceous [32, 35–36],\nthey con(cid:415)nue pollina(cid:415)ng flowering plants since their emergence [32, 35, 38–39].”\nL82-83: in general, I am not en(cid:415)rely comfortable with the a(cid:425)empt to capture and follow three dis(cid:415)nct\nkey periods that previous authors have defined to refer to important aspects of angiosperm\ndiversifica(cid:415)on (Angiosperm Radia(cid:415)on, Cretaceous Terrestrial Revolu(cid:415)on, Angiosperm Terrestrial\nRevolu(cid:415)on), as they might be perceived by some readers as different views on the same process, which\nI don’t think they are. This risk of confusion becomes very apparent in the legend of this (and other\nfigures), which refers to “The period of angiosperm evolu(cid:415)on”. I find these terms confusing because\nthey could be read as “the period during which crown angiosperms originated” (which we do not know\nand is definitely older than any of these three intervals) or “the period during which angiosperms have\ncon(cid:415)nuously evolved” (which would be the period since their origin to the Present).\nWe agree with the reviewer about the possible confusion and have therefore changed “the period of\nangiosperm evolu(cid:415)on” to “the period of increase in terrestrial biodiversity” for clarity. However, we\nhave kept the three periods in the figure, as they show different concepts depending on the reference.\nL84-85: is the (cid:415)me scale the same for A and B? if so, why is B restricted to the interval from ca. 145-55\nMa?\nYes, it is the same scale. It is like that because were original data extracted from Peris et al. (2017) ref.\n35. We clarified that: “Data extracted from [35].”\nL98: Condamine et al. (fossil insect dataset) is ref. 19\nCorrected. Thank you.\nL112-113: same comment as above (L82-83)\nAlso changed following the same answer.\nL115-116: only in the fossil record (as the authors know, numerous colleagues believe angiosperms\nwere actually present before the Cretaceous)\nCorrect. We included this comment: “for which angiosperms were absent in the fossil record un(cid:415)l the\nEarly Cretaceous”.\nL119: Table 1 was not included in the manuscript file provided to me for review\nWe are sorry for this issue. Because we made different a(cid:425)empts to submit the manuscript to the journal\nperhaps the table was misplaced at some point of the process. We have now fixed this in the revised\nversion.\nL129: not sure what is meant by “the rise of angiosperms” a(cid:332)er the ATR (by the end of the ATR,\nangiosperms would have long risen by all possible measures).\nWe meant the (cid:415)me of the ATR itself. We changed it to be clearer.\nL140-141: I understand this is the result of the mul(cid:415)variate analysis, but it read strangely to me as\nrela(cid:415)ve angiosperm and gymnosperm diversity would be strongly correlated to one another (see my\nmain comment above in point 3c)\nSorry for the confusion. We have indeed performed mul(cid:415)variate analyses with 6 variables, of which\nthe rela(cid:415)ve diversi(cid:415)es of angiosperms, gymnosperms, and spore plants were included as explanatory\nvariables in the model. Our analyses do not find evidence for correla(cid:415)on between the insect\ndiversifica(cid:415)on and gymnosperm rela(cid:415)ve diversity. We could not assess the correla(cid:415)on between\nangiosperms and gymnosperms in this study with the data in hand.\nL160: replace “superiority” with “advantage”?\nDone.\nL164-167: not sure where this statement comes from; I see that ref. 53 wrote something similar in\ndescribing the findings of one earlier study, but the reality is we do not really know and s(cid:415)ll lack any\nrobust macroevolu(cid:415)onary sta(cid:415)s(cid:415)cal approaches to measure the impact of singular traits (i.e., those\norigina(cid:415)ng only once) on diversifica(cid:415)on rates\nExactly, and instead of these singular traits, “intrinsic key innova(cid:415)ons, extrinsic factors such as\ngeography and environment, or trait–environment combina(cid:415)ons are important drivers of\ndiversifica(cid:415)on rates” (refs. 59 and 60).\nL179-183: hard to follow here (par(cid:415)cularly L182, the logic of which is unclear to me)\nThe sentence has been rephrased in the reviewed version.\nL183-185: I agree, which is why this whole discussion read very strangely to me (as an a(cid:425)empt to\nsynthesize current knowledge on drivers of diversifica(cid:415)on in angiosperms, which remains highly\nincomplete, has now been reviewed more than once in recent literature, and is portrayed rather\nconfusingly in the text here).\nWe hope the discussion was clearer a(cid:332)er including the suggested modifica(cid:415)ons along the text.\nL189: there are definitely more key studies to consider here, in addi(cid:415)on to ref. 6, in par(cid:415)cular the paper\nby Magallon et al. in Annals of Botany 123: 491–503, 2019\nWe agree. The literature on this topic is dense. We have included the proposed reference.\nL211-212: strange statement\nWe referred to the fact that what we are analyzing is what originated the modern ecosystems on Earth.\nL226-227: I don’t think we really know this, given that data s(cid:415)ll lack on pollina(cid:415)on of most species of\nangiosperms\nWe changed it including “known”.\nL235: that peak is not clear to me in Fig. 2 (which shows instead that insect family richness has never\nbeen so high than in the last 40 Ma)\nThe apprecia(cid:415)on that insect family richness is greater in last 40 Ma is correct, but there is a peak\nundoubtedly 125 Ma to which we referred along the text in different sec(cid:415)ons.\nL245: ref. 10 dra(cid:332)ed the angiosperm spindle as hypothe(cid:415)cal and largely unknown (see legend of their\nFig. 1), which I think should be noted here as well if reproduced; on the other hand, ref. 10 did certainly\nnot depict detailed spindles of the various gymnosperm lineages, so the legend and cita(cid:415)on here must\nbe corrected\nInforma(cid:415)on updated.\nL247-248: I am not familiar with ref. 99, but find it very odd and confusing to s(cid:415)ll recognise here the\npossibility of Gnetales being closely related to angiosperms (as denoted by the hyphenated branch),\nan old idea now dismissed by most phylogene(cid:415)c analyses published over the last two decades.\nThe figure has been deleted in the new version, following recommenda(cid:415)ons from another reviewer.\nL248: I have reserva(cid:415)ons on the use of TimeTree (which averages over all studies in their database,\nregardless of quality and assump(cid:415)ons), but I suppose accurate divergence (cid:415)mes (and their uncertainty)\nare not cri(cid:415)cal to either this figure or this study.\nWe personally agree with the reviewer in all this content.\nL260: strange sentence, needs rewording\nWe have reworded the sentence, thank you for the sugges(cid:415)on.\nL270-273: I don’t disagree, but this is a rather underwhelming closing statement in that various authors\nhave already suggested the same and it remains somewhat disconnected from this study (perhaps\nsome rewri(cid:415)ng needed)\nWe deleted this last sentence.\nL279: wrong Condamine et al. paper cited here? Shouldn’t this be ref. 19 instead?\nYes, thank you.\nL510: first author should be Lagomarsino\nChanged.\nHervé Sauquet\nReviewer #2 (Remarks to the Author):\nThis manuscript addresses drivers of insect diversifica(cid:415)on during the Cretaceous and Cenozoic at the\nfamily level using fossil data. It uses a Bayesian approach applied to fossil origina(cid:415)on and ex(cid:415)nc(cid:415)on\ndata to develop and assess birth-death models and parameterize correla(cid:415)ons between those births\nand deaths and other con(cid:415)nuously varying ecological parameters. These include the richness of\ndifferent taxa, including insect families and the richness of different plant groups, plus sea surface\ntemperature es(cid:415)mates and the fragmenta(cid:415)on of con(cid:415)nents. Models are developed for two 50Myr (cid:415)me\nperiods to assess to what extent the associa(cid:415)ons have varied over (cid:415)me, and these (cid:415)me periods are\nchosen to match periods described as the Angiosperm Terrestrial revolu(cid:415)on (angiosperms replacing\nother plants, notably Gymnosperms), and the later period of Angiosperm dominance. The authors\nreport that insect origina(cid:415)on and ex(cid:415)nc(cid:415)on are explained by a number of variables, but not\ngymnosperm diversity. Origina(cid:415)on rates are enhanced by spore plant diversity, angiosperm diversity\n(but only in the later (cid:415)me period) and reduced by insect diversity (implying diversity-dependence).\nEx(cid:415)nc(cid:415)on rates are also enhanced by spore plant diversity, con(cid:415)nental fragmenta(cid:415)on in the first (cid:415)me\nperiod, and reduced by angiosperm diversity. The authors conclude a changing role for angiosperms\naffec(cid:415)ng insect diversity in associa(cid:415)on with several other variables.\nThe ques(cid:415)ons addressed by this work are of wide appeal: angiosperms and insects collec(cid:415)vely\ncomprise about three quarters of extant macroscopic species described on Earth, and because insects\nand plants interact, there has long been specula(cid:415)on on how they could have affected each other’s\nmacroevolu(cid:415)on. Fossil data provide some advantages over purely phylogene(cid:415)c data based on extant\ntaxa as they are probably be(cid:425)er sources for es(cid:415)ma(cid:415)ng ex(cid:415)nc(cid:415)on rates. The analy(cid:415)cal methods used\nare current and appropriate for the data. The results of the paper are interes(cid:415)ng as they are the first\nto my knowledge which explicitly test several poten(cid:415)al environmental drivers of insect diversity at a\nglobal scale, and test how those change over (cid:415)me. The findings should contribute to the developing\nstory of how the global taxonomic composi(cid:415)on and richness changes of the last 100Myr came about.\nThank you for your review and the posi(cid:415)ve assessment. Everything is clear up to this point.\nWhilst I think there is the backbone of an interes(cid:415)ng paper here, I also feel that there are some\nsignificant issues for the authors to consider to make it more interes(cid:415)ng and robust. These relate to\nthe way the story is developed in the introduc(cid:415)on and discussion, the scope of the analyses performed\nand how those relate to the story, and the sensi(cid:415)vely of the results to poten(cid:415)al biases and varia(cid:415)ons\nin the data. There are also some textual/content issues. I list these below. I hope they are useful to the\nauthors in developing this work further.\n1. Table 1 is men(cid:415)oned several (cid:415)mes in the main text but seemed to be absent from the manuscript.\nSince this seems to contain important results, it’s difficult to make a full decision on the manuscript.\nThis is correct, we are sorry for this error. It was misplaced at some point of the submi(cid:425)ed process,\nwhich we did different (cid:415)mes for some reasons.\n2. The introduc(cid:415)on and discussion seem to mismatch the results and methods quite significantly. This\nmakes a confusing story for the reader. Specifically, large parts of the introduc(cid:415)on and discussion are\nspent developing a story about plant pollinator interac(cid:415)ons. For example, Figure 1 is all about\npollinators and their interac(cid:415)ons with angiosperms or gymnosperms. This is fair enough and\ninteres(cid:415)ng. However, it is then a bit surprising to find that the data and results cover all insects, not\njust pollinators. If I were tes(cid:415)ng an hypothesis about plant pollinator interac(cid:415)ons, I would design my\ndata around those groups. The discussion is extensively about pollinator interac(cid:415)ons too, but of course\na vast number of the species included in the families covered by the data are not pollinators at all.\nPlenty of the species and families do not directly interact with plants: granted most probably do\nindirectly, which is relevant to a general insect-angiosperm story, but this is hardly men(cid:415)oned. In\naddi(cid:415)on there are a great number of ways insects interact with plants that do not include pollina(cid:415)on,\nherbivory being the most obvious and probably important. There is almost nothing on herbivory here!\nMaybe the focus needs also to consider larval as well as adult interac(cid:415)ons. This seems like a rather\nlarge oversight, or at least it is confusing for the reader. I think that the authors should decide if they\nwant to test ideas about pollina(cid:415)on or a much more general set of ideas about how plants affect\ninsects, but whatever they choose the story should match the data and analyses.\nWe agree with these comments, it’s fair. It was our original inten(cid:415)on to focus on insect pollinator but\nwe struggled to test our hypotheses using only pollinator groups because of the lack of defini(cid:415)on for\ninsect pollinator groups focused in the fossil record. This was the reason why we used all insect data\navailable as a proxy for insect pollina(cid:415)on. However, in the mean(cid:415)me, a publica(cid:415)on arose reviewing the\npollinator habits from insect groups (Peña-Kairath et al. 2023 – Trends Ecol. Evol.), co-authored by the\nfirst author of this current study. During the revision, we have used data from this study to categorize\ninsect families as pollinators and we have then performed new diversifica(cid:415)on analyses to present a\nmore focused analysis in the new version of the manuscript to fit be(cid:425)er with our introduc(cid:415)on,\ndiscussion, and figures about pollinators. Nonetheless, we think it’s important to keep the results for\ninsect families as a whole because, as you men(cid:415)oned, this is relevant to the study of insect-plant\ninterac(cid:415)ons and for comparison with the pollinators themselves.\n3. Similar to the above there is a focus to some extent in the introduc(cid:415)on and especially in the\ndiscussion on angiosperm diversifica(cid:415)on, but the results and analyses focus exclusively on how\nangiosperms affect insect macroevolu(cid:415)on. It’s almost as if the results were wri(cid:425)en by someone with\ninterests in insects but discussion by someone with interests in angiosperms. Now, given that the term\nco-diversifica(cid:415)on or co-evolu(cid:415)on is used liberally, I was expec(cid:415)ng analyses on how insects affect\nangiosperms as well as vis-versa. The data imply that this could be done, so I was wondering why not.\nThe results are be(cid:425)er suited to a narra(cid:415)ve exclusively focussed on insects and not focusing on\nangiosperm macroevolu(cid:415)on.\nWe do agree that our results are be(cid:425)er suited to a narra(cid:415)ve exclusively focused on insect\nmacroevolu(cid:415)on and not on angiosperm macroevolu(cid:415)on. The text was structured differently. We hope\nthis version will be liked by the reviewer.\nWe do not use co-diversifica(cid:415)on and co-evolu(cid:415)on liberally, but on the contrary. We followed strictly\nthe original descrip(cid:415)on of the idea of co-evolu(cid:415)on, but addressing this issue from co-diversifica(cid:415)on,\nwhich it is the unique results that we can offer. We try to use the correct term at all (cid:415)mes, co-evolu(cid:415)on\nfor the concept, co-diversifica(cid:415)on for our results.\n4. Insect fossils come from a variety of sources but two main sources are impression fossils such as\nfrom lake sediments, and specimens preserved in amber. These are two very different types of\npreserva(cid:415)on, with the la(cid:425)er being much more sparse and episodic but giving much be(cid:425)er sampling\n(and higher implied richness). The PyRate method models preserva(cid:415)on changes but it would seem a\nbit risky to base all conclusions on a mixed dataset that combines these two sources of evidence\nbecause the preserva(cid:415)on characteris(cid:415)cs are so different. It would be sensible I think to conduct a\nsensi(cid:415)vely analysis by doing addi(cid:415)onal analyses on a single (e.g. non-amber) subset or if possible both\nsubsets (amber and non-amber) to see how robust the results are to this varia(cid:415)on in data sources: this\nhas been done for example in ref 20, and it should be straigh(cid:414)orward to extract the data from PBDB.\nSimilarly, some explora(cid:415)on of taxonomic subsets would be very sensible given that different trophic\ngroups would be expected to have more direct or indirect associa(cid:415)ons with angiosperms.\nIn order to make the results more in line with our original idea, as the reviewer suggested earlier, we\nhave selected the families that are pollinators (or were pollinators at some point in their evolu(cid:415)on).\nHowever, although the proposed complementary analyses suggested by the reviewer will certainly be\nvery frui(cid:414)ul, we feel that it goes beyond the aim of our work. We do not intend to analyse taphonomic\nissues, which have been addressed in ref. 20 and others, but the rela(cid:415)onship between plants and\npollinator insects. However, even if we were to follow the reviewer’s sugges(cid:415)ons, it would mean that\nwe would have to completely rebuild the database used for the study in order to be able to include the\ntype of fossil from which each record was obtained, since some are in amber, some in compression,\nand some in both. This work and the combina(cid:415)ons it would involve would be the subject of a new study\nby itself, as was done ref. 20 cited in the text.\n5. The discussion hardly discusses your actual findings at all. Why should higher angiosperm diversity\nreduce ex(cid:415)nc(cid:415)on rates in insects? Has any literature proposed this before? There is a vast literature on\ndensity-dependent diversifica(cid:415)on in insects but not much has been cited: for example see the papers\ndiscussed in the reviews by Mayhew in 2007 (Biol. Rev.) and 2018 (Ent Exp et Appl). Are you surprised\nthat it seems to work via reduc(cid:415)ons in origina(cid:415)on rather than rises in ex(cid:415)nc(cid:415)on? Would you expect\ncon(cid:415)nental fragmenta(cid:415)on to have the observed effect on ex(cid:415)nc(cid:415)on and why? Given your hypotheses\nare you surprised by the non-effect of gymnosperm diversity on ex(cid:415)nc(cid:415)on? Could a subset of older\nfamilies show different results as in figure 1? Could you test that? The temperature effects conform to\nsome previous results on invertebrates but not all. The contrary papers are not men(cid:415)oned. Why might\nthey exist?\nWe think that the reviewer has very high expecta(cid:415)ons of the results that we can discuss in this paper.\nThe discussion we offer was intended to be focused on the rela(cid:415)onship of pollinators with plants. We\ndo not analyze the rest of the factors, but we simply show that the one we are interested in have an\neffect, but we also want to men(cid:415)on that there are other factors that should be considered in the future,\nas we commented in the conclusion. Because the journals such as NC are subject to very strict content\nrules (such as the number of words, references, etc.), it is difficult to sa(cid:415)sfy all the indica(cid:415)ons at the\nsame (cid:415)me when some of them are contrary to each other. The reference Mayhew in 2007 (Biol. Rev.)\nhas been included in the list and properly cited along the text.\n6. The whole issue of working at the family level is not discussed anywhere but I think the reasons and\ncaveats need to be men(cid:415)oned somewhere, at least in the discussion. For example, ex(cid:415)nc(cid:415)on of a family\nimplies very different species level rates for some families than others. Very species rich families will\nbe almost impossible to send ex(cid:415)nct, whilst species poor ones might go ex(cid:415)nct easily. Is it likely that\nspecies richness across families has shown systema(cid:415)c trends over (cid:415)me? Are family level data in plants\nand insect comparable and the most relevant data in which to make these comparisons? In reality,\nwe are simply using this level in order to reduce gaps in the record. Why would one expect family level\ndiversity in plants to have any effect on family level diversity in insects: what assump(cid:415)ons are built into\nthat?\nThe first reason to work with families and not with genera or species is prac(cid:415)cal. It results highly difficult\nto manage data from around 1500 insect species. But if we referred to the about 1 million named insect\nspecies (Stork, 2018, Annual Review of Entomology) it will be impossible to manage.\nIn addi(cid:415)on, errors derived from synonymy or name changes between species and genera, and even\nmore so when we refer to the fossil record, are reduced if we deal with families than in lower taxonomic\nlevels.\nA(cid:332)er these two considera(cid:415)ons, it will result very interes(cid:415)ng to discuss about if rich families would be\nmore probably to become ex(cid:415)nct than poor ones. But we would answer that it does not depend on\nthe number but on the distribu(cid:415)on and their habitat, as well as the degree of specificity in the resources\nused by their species. We have not considered whether the families of plants and families of insects\ncorrespond to a comparable degree or not, because it is not the aim of our work to discuss these types\nof ques(cid:415)ons. Without minimizing this ques(cid:415)on, the ques(cid:415)on we are trying to answer is another: to\nwhat extent did insects and angiosperms evolve at the same (cid:415)me?\nThe last ques(cid:415)on: “Why would one expect family level diversity in plants to have any effect on family\nlevel diversity in insects: what assump(cid:415)ons are built into that?” is more like the ones revealed in this\nmanuscript. We do not analyze why this rela(cid:415)onship occurs or does not occur, but rather we try to\ndemonstrate if it really occurs, as it has been stated in different works over (cid:415)me without having offered\nany empirical proof that this is really the case.\n7. Another caveat is that the PyRate models assume that rates are the same at any moment in (cid:415)me in\nall lineages. Of course we know that taxon-specific rates exist in insects. What are the consequences of\nthis breakage of assump(cid:415)ons for accurately es(cid:415)ma(cid:415)ng rates? I know the methods are what we have,\nbut the reader needs to be alerted to caveats.\nWe agree with this comment. Indeed, the PyRate birth-death models assume that rates are\nhomogeneous across clades but heterogeneous over (cid:415)me. We are also aware that rates are likely to\nhave varied across the phylogeny of insects (e.g. Condamine et al. 2016 – Sci. Rep.; Blaimer et al. 2023\n– Nat. Comm.; Kawahara et al. 2023 – Nat. Ecol. Evol.). During the revision, we have performed analyses\nwith insect pollinator families only to study their specific diversifica(cid:415)on. All these results are presented\nin the revised version of the manuscript. Nonetheless, we have also added a sec(cid:415)on with a few\nsentences to present the limits of the methods used in this study.\n8. If you keep the exis(cid:415)ng text and figures, I have minor suggested edits:\ni) Line 15 drivers\nii) Line 47 delete and\niii) Line 77 using angiosperm resources extensively un(cid:415)l the\niv) Line 131: dual influence?\nv) Line 134: Nevertheless, the rise of\nvi) Line 136: correlated with reduced origina(cid:415)on rates\nvii) Lien 145: focussed on the\nviii) Figure 3 legend and axis labels: No units or (cid:415)tle on the x-axis scale: from the main text one would\nnaively assume this to be a correla(cid:415)on coefficient but it cannot be. Why not have the confidence\nintervals on the bars?\nix) Line 172: cell sizes; herbaceousness,\nx) Line 185: approach that\nxi) I felt Figure 4 was not needed; it’s not results and this is not a review paper.\nxii) Line 260: found that flowering plant diversity correlates with a faster\nxiii) Line 266-7. Other hand, a link seems to exist between\nxiv) Line 335: need to say what taxonomic level these data exist at.\nxv) Line 367. I didn’t have access to the data, but they certainly weren’t in the main text: supplementary\nmaterials?\nThank you for all these sugges(cid:415)ons. All these minor mistakes were considered and many of them were\nmodified accordingly.\nFigure 4 was ini(cid:415)ally included because the mo(cid:415)va(cid:415)on of the paper was to be a review. However, a(cid:332)er\nthe comments from the editor, the paper is more and more a new-results manuscript. With that, we\nagree with the reviewer and because we need more space for the new figures from the analysis, we\ndecided to delete Figure 4.\nReviewer #3 (Remarks to the Author):\nThis manuscript inves(cid:415)gates the poten(cid:415)al effects of flowering plants on insect diversifica(cid:415)on. The link\nbetween angiosperms and insects has been hypothesized and studied for quite some (cid:415)me, prompted\nby the many ecological rela(cid:415)onships through pollina(cid:415)on and other interac(cid:415)ons. Given the high\ndiversity of insects, it is natural that this is a topic of widespread interest.\nWe thank you for your review and comments mostly associated to the methodological aspects of our\nstudy. We have tried to address all of them.\nThe methods calculate origina(cid:415)on, ex(cid:415)nc(cid:415)on, and diversity from the fossil record, but the techniques\ndo not appear to account for sampling biases or methodological shortcomings of range-through\ndiversity methods. Most notable is the “pull of the recent,” which is visible in the family accumula(cid:415)on\nplot in figure 2. When informa(cid:415)on from the extant insect fauna is combined with fossil data, this has\nthe effect of infla(cid:415)ng diversity and reducing origina(cid:415)on and ex(cid:415)nc(cid:415)on in more recent (cid:415)me periods.\n(Technically, it is older (cid:415)me periods that have ar(cid:415)ficially-low diversity because they do not benefit from\nthe range extensions caused by including extant data.)\nWe respec(cid:414)ully disagree that the method cannot accounted for the known biases of the fossil record.\nPyRate is a Bayesian process-based model that is specifically designed to simultaneously model the\nrates of preserva(cid:415)on and their varia(cid:415)on through (cid:415)me and across taxa, the (cid:415)mes of origin and ex(cid:415)nc(cid:415)on\nof each taxon, and then the rates of origina(cid:415)on and ex(cid:415)nc(cid:415)on through (cid:415)me. By es(cid:415)ma(cid:415)ng the rates of\npreserva(cid:415)on, PyRate “corrects” the ages of origin and ex(cid:415)nc(cid:415)on of each taxon instead of directly\ncoun(cid:415)ng the taxa as they appear in the fossil record. In this way, we move from observed ages to\nes(cid:415)mated ages, which can alleviate some of the problems of the fossil record, such as ar(cid:415)ficial peaks\nin ex(cid:415)nc(cid:415)on and specia(cid:415)on due to lack of sampling or the reservoir effect. It is important to men(cid:415)on\nthat PyRate has been thoroughly tested under a wide range of condi(cid:415)ons, such as low levels of\npreserva(cid:415)on (down to 1–3 fossil occurrences per species on average), severely incomplete taxon\nsampling (up to 80% missing), and high propor(cid:415)on of singletons (exceeding 30% of the taxa in some\ncases)(Silvestro et al. 2014 – Syst. Biol., 2015 - PNAS, 2019 – Paleobiol.). As opposed to other methods\n(including boundary- crossers and three-(cid:415)mers), which are prone to edge effects and tend to fla(cid:425)en\nthe ex(cid:415)nc(cid:415)on es(cid:415)mates, especially during mass ex(cid:415)nc(cid:415)ons, PyRate recovers the dynamics of\nspecia(cid:415)on and ex(cid:415)nc(cid:415)on rates, including sudden rate changes and mass ex(cid:415)nc(cid:415)ons (Silvestro et al.\n2019 – Paleobiol.).\nBecause the analysis didn’t account for specific challenges of the fossil record, many of the conclusions\nabout the role of angiosperms could instead be spurious correla(cid:415)ons between the angiosperm\ndominance (cid:415)me series and the pull of the recent. Likewise, reduced origina(cid:415)on during (cid:415)mes of high\ndiversity (lines 135-137) could be diversity dependence, but also could reflect the pull of the recent\nbias. It is possible that there are true effects, but I don’t think the argument is convincing now because\nthe methods are not appropriate for dealing with fossil data, and do not a(cid:425)empt to discuss or address\nwidely-known biases.\nWe also respec(cid:414)ully disagree that the method is inappropriate for dealing with fossil data, and that we\nhave not accounted for the known biases of the fossil record. We have responded to the la(cid:425)er point\nabove. We have added a dedicated sec(cid:415)on to discuss widely known biases and to show the limita(cid:415)ons\nof our study. Regarding spurious correla(cid:415)ons, the Bayesian framework of PyRate also allows mul(cid:415)ple\nhypotheses about the drivers of diversifica(cid:415)on to be tested simultaneously (Lehtonen et al. 2017 - Sci.\nRep.). The mul(cid:415)variate birth-death model we use has been shown to be robust to several biases.\nSilvestro et al. (2017 - Evol. Ecol. Res.) show that the model, and in par(cid:415)cular its new implementa(cid:415)on\nbased on the horseshoe prior (which we used), can robustly infer diversity dependence within clades\nfrom fossil data in a wide range of diversifica(cid:415)on scenarios. However, in the limita(cid:415)ons of the study, we\nexplained that our work did not explore many variables and that further studies are needed. We also\nrecognize that our study provides testable hypotheses for future studies that may challenge and/or\ncomplement our results as new data and models become available.\nA lot of the discussion sec(cid:415)on seemed to be on topics that are tangen(cid:415)al to the results, rather than\nmaking the case that the results are true biological pa(cid:425)erns, or explaining why the drivers had an effect\non insect diversifica(cid:415)on. For example, why might spore plants also have influenced insect\ndiversifica(cid:415)on? A lot of the discussion reads like background informa(cid:415)on about angiosperm evolu(cid:415)on,\nwhich is interes(cid:415)ng, but I didn’t think it was strongly connected to your specific goal in this manuscript.\nWe agree with the reviewer. Because of that we performed new analyses and changed the focus of the\ndiscussion, dele(cid:415)ng informa(cid:415)on about evolu(cid:415)on of angiosperms and including new references, also\nfollowing the instruc(cid:415)ons from the reviewer 2. We hope the new version sa(cid:415)sfies the reviewer now.\nIn general, I think it is extremely difficult to work with origina(cid:415)on and ex(cid:415)nc(cid:415)on in the insect fossil\nrecord (even harder than trying to reconstruct diversity, which itself is very challenging). Shi(cid:332)s in the\ndominant preserva(cid:415)on mode (amber vs. compression fossils) from one (cid:415)me period to the next cause\napparent origina(cid:415)on/ex(cid:415)nc(cid:415)on spikes because the two modes tend to record different types of\nfamilies. There are huge varia(cid:415)ons in the number of insects recorded in different (cid:415)me periods,\nincluding very few large locali(cid:415)es between about 100 Ma and 50 Ma. Because of that, a lot of\nex(cid:415)nc(cid:415)ons that actually occurred later in the Cretaceous will all cluster earlier. Origina(cid:415)ons will also be\nar(cid:415)ficially clustered at some of the “super-Lagersta(cid:425)e” (the extraordinarily well-sampled Bal(cid:415)c amber\nis one example; likely a number of those families evolved earlier but have not yet been discovered\nbecause of the limited Late Cretaceous and Paleocene record). It may be possible to extract some real\nsignal, but I’m fairly skep(cid:415)cal, and it would require careful analysis that deals with the complexity of\nthe insect fossil record.\nWe do agree with this general comment about the difficulty of es(cid:415)ma(cid:415)ng reliable diversifica(cid:415)on rates\nfrom the fossil record. The fossil record is inherently incomplete and heterogeneous across clades and\nthrough (cid:415)me, making any es(cid:415)mates of diversifica(cid:415)on processes tenta(cid:415)ve. Accordingly, we must take\nthese sampling biases into account. This is precisely the aim of PyRate models, which a(cid:425)empt to model\nsimultaneously the rates of preserva(cid:415)on and their varia(cid:415)on across taxa, the (cid:415)mes of origina(cid:415)on and\nex(cid:415)nc(cid:415)on of each taxon, and then the rates of origina(cid:415)on and ex(cid:415)nc(cid:415)on through (cid:415)me. By es(cid:415)ma(cid:415)ng\nthe preserva(cid:415)on rates, PyRate corrects the ages of origina(cid:415)on and ex(cid:415)nc(cid:415)on of each taxon. We thus\nmove from observed ages to es(cid:415)mated ages, which can alleviate some issues of the fossil record, such\nas the ar(cid:415)ficial peaks of ex(cid:415)nc(cid:415)on and specia(cid:415)on due to no sampling or Lagerstä(cid:425)e effect, respec(cid:415)vely.\nPyRate is not the final solu(cid:415)on to the problems found when studying the fossil record, but it’s a step\nforward. In the revised version, we have added a sec(cid:415)on that presents and discusses the limita(cid:415)ons of\nour study, including the problems with the fossil record that you men(cid:415)on here.\nIt was also difficult to evaluate the results because I couldn’t find table 1 and there didn’t appear to be\na dataset containing the potential drivers (spore plant, gymnosperm, angiosperm dominance,\ntemperature, con(cid:415)nental fragmenta(cid:415)on). Perhaps I missed those on the website, but it would have\nbeen very helpful to see a graph of angiosperm dominance through (cid:415)me so that I could visually\ncompare it to insect diversifica(cid:415)on.\nWe are sorry about the missing Table 1. It resulted from a misplaced issue at some point of the\nsubmission process, which we did different (cid:415)mes for some reasons. It should be fixed now. Note that\nwe have now added Table 2 that reports the results obtained for insect pollinator families only.\nThe angiosperm rela(cid:415)ve diversity has now been added to Figure 2.\nSincerely,\nMa(cid:425)hew Clapham"}]

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