Tip dating supports novel resolutions of controversial relationships among early mammals

The estimation of the timing of major divergences in early mammal evolution is challenging owing to conflicting interpretations of key fossil taxa. One contentious group is Haramiyida, the earliest members of which are from the Late Triassic. Many phylogenetic analyses have placed haramiyidans in a clade with multituberculates within crown Mammalia, thus extending the minimum divergence date for the crown group deep into the Triassic. A second taxon of interest is the eutherian Juramaia from the Middle–Late Jurassic Yanliao Biota, which is morphologically very similar to eutherians from the Early Cretaceous Jehol Biota and implies a very early origin for therian mammals. Here, we apply Bayesian tip-dated phylogenetic methods to investigate these issues. Tip dating firmly rejects a monophyletic Allotheria (multituberculates and haramiyidans), which are split into three separate clades, a result not found in any previous analysis. Most notably, the Late Triassic Haramiyavia and Thomasia are separate from the Middle Jurassic euharamiyidans. We also test whether the Middle–Late Jurassic age of Juramaia is ‘expected’ given its known morphology by assigning an age prior without hard bounds. Strikingly, this analysis supports an Early Cretaceous age for Juramaia, but similar analyses on 12 other mammaliaforms from the Yanliao Biota return the correct, Jurassic age. Our results show that analyses incorporating stratigraphic data can produce results very different from other methods. Early mammal evolution may have involved multiple instances of convergent morphological evolution (e.g. in the dentition), and tip dating may be a method uniquely suitable to recognizing this owing to the incorporation of stratigraphic data. Our results also confirm that Juramaia is anomalous in exhibiting a much more derived morphology than expected given its age, which in turn implies very high rates of evolution at the base of therian mammals.

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Reviewer(s)' Comments to Author:
Referee: 1 Comments to the Author(s) King and Beck use up-to-date tip-dating analyses to investigate the relationships among Mesozoic mammals, particularly early eutherians and haramiyids. They conclude that tip-dating alters evolutionary interpretations from other phylogenetic methods by explicitly including stratigraphic data, and note that Juramaia is more similar to later forms than would be expected given its age. The paper is to my mind strong; my comments below are mostly to do with the presentation of the Juramaia issue and a missing piece of the methodological puzzle.
'UNEXPECTED' MORPHOLOGY OF JURAMAIA The word "unexpected" comes across as potentially problematic from a philosophical perspective. The basic argument in favour of it would be "Juramaia looks like Cretaceous mammals, but is actually Jurassic. That's unexpected". But what you can and do quantify are branch lengths and evolutionary rate, and you can test for expectation only really on those parameters. In both of the citations given for Juramaia being "unexpectedly advanced", that phrase is only used exactly for Durlstotherium etc. rather than the Juramaia -Eutheria sister relationship by Bi et al., although the sentiments are certainly similar. However, both the Bi et al. and Meng papers discuss two possible explanations for the similarity between Juramaia and Eomaia. These are (a) an incorrect age estimate for Juramaia or (b) early appearance of eutherian-type dentition and then exceptionally slow rates of evolution. This is the justification for qualitatively noting that something is "unexpected". They also both caution that the fact that Juramaia is represented by a single specimen makes identification of a pattern practically impossible. I think it's worth noting that the age of the Yanliao Biota is now pretty solidly fixed in the Middle-Late Jurassic -a single adjective when bringing up the biota for the first time would suffice -and you already show what the implications are of a Jurassic Juramaia in terms of rate shifts. The final conclusion on this can, I think, be improved. In lines 290-293 you say "The Middle Jurassic age of Juramaia suggests unusually rapid rates of evolution at the base of therians and eutherians, followed by a period of exceptionally slow rates of eutherian evolution during the Early Cretaceous". That's all well and good, but I think it can be strengthened by reemphasising the 50-fold shift in rates (lines 197-199) but also actually telling us about what constitutes a statistically significant deviation from the null hypothesis -ie expectation -of equal rates across the phylogeny. This would be a simple matter of taking the internal branch lengths and comparing them with expected branch lengths with a chi-squared test. This would bring the manuscript back to its title and the lede and justifies the use of the word "unexpected".
I also think it's worth addressing in the discussion the fact that Juramaia is a single specimen of a single species that then leads to Eomaia being a single specimen of a single species, so we don't really know much about what eutherians are doing in that time at all besides the similarity of these two individuals. The implication of a huge slowdown is interesting, but that kind of long branch is potentially subject to radical change on the introduction of new specimens. MISSING METHODOLOGY I've looked through the paper and the supplementary data in detail and cannot find the details of the fossilised birth-death model. This needs to be added to the supplementary information, or, if it is already there, better signposted, because I cannot find it at all. Did, for instance, you use diversified sampling, and if not, why not, given that most phylogenetic datasets are built on the understanding that this is the case? What, actually, were the priors on taxon age for each of the standard analyses? All we know is that the priors for the Yanliao mammaliaforms when letting their position be a bit more anatomically-driven is a Laplace distribution with 90% within the Jurassic. By implication there are bounds on these mammaliaforms' date priors in the other analyses, but how were they defined? A uniform distribution across the uncertainty in date of the first appearance? If not, what, and why? If the choice of prior matters so much for Juramaia, then we need to know what the prior we are asked to compare the result from a Laplace prior with was.

SECTIONS
The paragraph beginning on Line 118 as far as 121 should not really be in the methods section as it strays into results and discussions. I understand why it ended up there from the point of view of explaining the need for further analysis, but all that's needed is something more like "To further investigate the relative effects of morphological data and topological priors on haramiyid phylogeny…". Otherwise you are revealing some of the results early and end up repeating yourself. CONSISTENCY I'd use the same headings for subsections across Methods, Results, and Discussion, for clarity and ease of switching back and forward. SMALL THINGS, TYPOS, GRAMMAR Line 45 -double space between 'Patagonia' and 'the'. Line 47 -double space between 'discussion' and 'is'. Line 48 -Juramaia sinensis, not sinsensis. Line 49 -The word should be composing (or another synonym), not comprising. The parts compose the whole; the whole comprises the parts. Line 50 -double space between 'morphology,' and 'Juramaia'. Line 57 and elsewhere -'Tip dating' when referring to the method as a noun. 'Tip-dating' is correct as a compound adjective, e.g. 'a recent tip-dating study' on line 60. Line 57 -double space between 'investigate' and 'these' Lines 79-80 -Square brackets seem like an odd choice here. Why not take the reference out of the brackets? On lines 262-263 you have square brackets for the reference within curved brackets. This could be avoided anyway by saying 'Markov model for variable characters (hereafter Mkv model)' which also avoids the issue of an unknown abbreviation. Line 138 -This is the first time BPP has appeared. Some will not recognise the acronym, so expand it. This may also be the case for Line 109 -MYA, although that might be a journal style anyway. See also Line 85 -'RWTY'; maybe worth noting that it's an R package as I at least assumed it was a method I was unfamiliar with. Line 141 -'well resolved', not 'well-resolved' Referee: 2 Comments to the Author(s) See attached file.

Is the length of the paper justified? Yes
Should the paper be seen by a specialist statistical reviewer? No Do you have any concerns about statistical analyses in this paper? If so, please specify them explicitly in your report. No It is a condition of publication that authors make their supporting data, code and materials available -either as supplementary material or hosted in an external repository. Please rate, if applicable, the supporting data on the following criteria.

Do you have any ethical concerns with this paper? No
Comments to the Author See attached file.

11-May-2020
Dear Mr King I am pleased to inform you that your manuscript RSPB-2020-0943 entitled "Tip dating supports novel resolutions of controversial relationships among early mammals" has been accepted for publication in Proceedings B. Congratulations!! The referee(s) have recommended publication, but also suggest some minor revisions to your manuscript. Therefore, I invite you to respond to the referee(s)' comments and revise your manuscript. Because the schedule for publication is very tight, it is a condition of publication that you submit the revised version of your manuscript within 7 days. If you do not think you will be able to meet this date please let us know.
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13-May-2020
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General comments
There's ongoing, contentious debate on allotherian relationships. Because allotherians likely evolved near the crown mammalian node, resolving this issue is especially important for understanding the origins and early evolution of mammals. Thus, the study by King and Beck is very relevant and should be of interest to a broad readership. I have no major concerns with the tip-dating methods or results. And the primary result (i.e. haramiyids are diphyletic) makes intuitive sense and offers somewhat of a compromise for the competing hypotheses. The second major conclusion of the paper is that Juramaia is morphologically very similar to much younger taxa, suggesting that therians evolved very rapidly early in their history and then experienced a long period of stasis (or Juramaia's age is incorrect). The analyses offer interesting insights on this topic. I don't have any critical concerns with the paper. However, I believe it would benefit greatly from two major additions, which I outline here.
To make the paper easier to follow for non-specialists, I recommend adding an introductory figure with simplified phylogenies that summarizes the competing allotherian hypotheses. I envision something like Figure  To truly account for both sides of the allotherian debate, it would be best to include a recent matrix from Meng. I recommend Wang et al. 2019 (Nature) because the described taxon is an allotherian (Jeholbaatar, a multituberculate). Meng's scoring of euharamiyid dental characters will likely unite multituberculates and euharamiyids in your analyses (as seen in the Krause-matrix results), but if you continue to see evidence of haramiyid diphyly then it will provide even stronger support for your results.
Personally, I agree with Luo's scorings of haramiyid dental characters -I think he's made a more compelling case for haramiyid occlusion (following Jenkins 1997 and Butler 2000) using CT scans and occlusal reconstructions (e.g. see Your results offer somewhat of a compromise on the debate over haramiyids, and you could consider re-framing some of the text to focus on this. Recovering euharamiyids as crown mammals supports Meng's view, and recovering Haramiyavia+Thomasia as stem mammals is consistent with Luo's view. You could consider putting greater emphasis on the current debate (e.g. by adding more text and citations to the first paragraph of the Introduction) and providing more discussion on how the results may serve as a compromise between the two sides.

Comments on Juramaia results
I'm concerned that the Juramaia results are influenced by sampling issues. The other Yanliao taxa are members of clades that are well-represented in the Jurassic, whereas Juramaia is the only therian in the Jurassic. If more Jurassic therians were discovered, would it drastically change the results of this study by introducing new morphological variation and altering branch lengths? One potential way to test this idea is to simulate Juramaia-like scenarios in other clades. For instance, you could remove Kuehneodon and set the age of the plagiaulacid multituberculates to ca. 126 Ma (to match the Jehol), and then predict the age of Rugosodon (the earliest multituberculate in the study) based on morphology. This could serve as somewhat of a sensitivity analysis to examine the influence of sampling on the Juramaia results.
Some authors (e.g. Sweetman et al. 2017 Acta Palaeo Polon) have posited that Juramaia is a stem therian rather than a eutherian. If this is the case, I doubt it'd alter your conclusions because there'd still be a very slow rate of morphological between Juramaia and other early therians. But it'd significantly alter some branch lengths, and thus likely change some results. For example, this topological change would likely lengthen the branch leading to eutherians, and thus in Figure 3a I'd expect Branch 2 to have much slower rates of evolution. I think this topic should be addressed at some point (even if it's in the supplement) because many readers may wonder what influence the phylogenetic position of Juramaia has on results.
Sinodelphys from the Jehol Biota (previously thought to be the oldest metatherian) is now believed to be a eutherian (Bi et al. 2018 Nature). Incorporating this change into analyses is probably beyond the scope of this study, but it's another variable that could influence the Juramaia/therian results. The authors could note whether they think that moving Sinodelphys to Eutheria would alter branch lengths and evolutionary rates.
Although the Huttenlocker (i.e. Luo) and Krause matrices include therians, the characters are primarily designed to investigate relationships in earlier groups such as docodonts, allotherians, and eutriconodonts. I wonder if this results in artificially slow evolutionary rates along early therian branches because there are few characters that help to distinguish these lineages.

Specific comments
Lines 9, 12, and 179: I don't think that "problematic" is the best term for describing the taxa. It's problematic that there are different interpretations of the fossils, but I'd be hesitant to state that haramiyids and Juramaia themselves are problematic. Juramaia has unexpected morphology given its age, but I think this makes it especially interesting (or simply raises questions about its provenance). For Line 12, maybe instead state "A second taxon of special interest is …". Lines 18-19: You state that Haramiyavia and Thomasia form a clade with tritylodontids, but you later devote a paragraph (Lines 270-285) to explaining why this relationship is unlikely. I agree with your skepticism on this relationship and recommend you remove the mention of it here, or rephrase the statement so that it's less assertive.
Lines 57-60: This section does not clearly introduce tip-dating approaches. Just stating "Tipdating" alone (Line 57) seems vague. Consider expanding the phrase (e.g. to "Tip-dating phylogenetic methods" or "Tip-dating Bayesian approaches for phylogenetic inference") and briefly mentioning how tip-dating approaches differ from more traditional phylogenetic methods. Similarly, "method" on Line 59 is vague. Maybe expand it to "phylogenetic method" or re-phrase the sentence. there is still support for a monophyletic allotheria when taxa are scored following Meng's interpretation) should be recognized. I predict you will get a similar (if not stronger) result if you use the Wang et al. (2019) matrix. I think it's fine to emphasize your Huttenlocker matrix result, especially because it presents a compelling alternative hypothesis for allotherian relationships, but it's important to also address the fact that differential scoring of key taxa and characters is still having a major effect on the results.
Lines 235-238: This could be a good point in the manuscript to incorporate my previous comment.
Lines 246-249: You should note that this result is based only on the Huttenlocker-matrix results, because the Krause-matrix results suggest monophyly or diphyly of Allotheria. Although there is compelling evidence for diphyly of haramiyids, you should be quick to acknowledge (here and throughout the manuscript) that there's considerable variation and uncertainty in the tree topologies.
Lines 246-252: The argument that placentals and marsupials have occasionally converged (in a broad sense) on allotherian-like dental traits has been frequently brought up in the literature (e.g., Simpson 1933, J Mamm; Lazzari et al. 2010, J Mamm Evol), so pointing this out is justified. However, I wouldn't call this "unsurprising". The dental convergence with placentals (e.g., muroid rodent molars), marsupials (e.g., blade-like cheek teeth), and even tritylodontids are only similar at a very superficial level (i.e., there has never been a strong case made for these characteristics being homologous). In contrast, it has been argued that the dentitions of haramiyidans and multituberculates are homologous, not homoplastic (Butler 2000, Acta Palaeo Polon; Butler & Hooker 2005, Acta Palaeo Polon; Meng papers). I think it's fine to touch on the fact that these dental traits are possibly convergent. However, I recommend also acknowledging the studies that argue a contrary point.
And although it's briefly mentioned in the Introduction, I'd give an example or two of how the dentitions are similar among allotherian groups (and rodents and polydolopimorphians). More broadly, I think that the paper would benefit from more discussion on the morphological traits of the early mammal groups being discussed in the paper. I know that Proc B has a short word limit, but if there's space I recommend an expanded discussion on topics such as dental characters and ear-jaw evolution, especially in allotherians.
Lines 270-285: I agree with this discussion and highly doubt that Haramiyavia+Thomasia are sister to tritylodontids. As you note, there are many traits that differentiate Haramiyavia+Thomasia from tritylodontids. But this highlights an underlying concern -the Huttenlocker/Luo and Krause matrix characters were generated to investigate relationships of mammaliaforms, not cynodonts. (This is analogous to my above comments on therians.) There are relatively few cynodont-specific characters in those matrices. And the scarcity of sampled cynodont taxa in the matrices may help to generate the long branches and 'attract' Haramiyavia+Thomasia. A cynodont-focused matrix might be more likely to separate tritylodontids from Haramiyavia+Thomasia. I recommend acknowledging this concern in the text.
Line 275: Although the chewing stroke was likely predominantly orthal in Haramiyavia, Butler (2000) suggested a significant palinal component in the chewing stroke of Thomasia.
Lines 288-293: This result might also suggest that Juramaia might not be Jurassic in age, and instead is Early Cretaceous, but you seem hesitant to bring it up (maybe previous commenters/reviewers on this manuscript have dismissed that possibility?). Personally, I think it's worth mentioning as a possibility, even if you doubt it's the case. I've also seen Juramaia's age questioned in Meng 2014 (Nat Sci Rev), and there might be other references that raise similar concerns.

Reviewer 1
Comments to the Author(s) King and Beck use up-to-date tip-dating analyses to investigate the relationships among Mesozoic mammals, particularly early eutherians and haramiyids. They conclude that tip dating alters evolutionary interpretations from other phylogenetic methods by explicitly including stratigraphic data, and note that Juramaia is more similar to later forms than would be expected given its age.
The paper is to my mind strong; my comments below are mostly to do with the presentation of the Juramaia issue and a missing piece of the methodological puzzle.
'UNEXPECTED' MORPHOLOGY OF JURAMAIA The word "unexpected" comes across as potentially problematic from a philosophical perspective. The basic argument in favour of it would be "Juramaia looks like Cretaceous mammals, but is actually Jurassic. That's unexpected". But what you can and do quantify are branch lengths and evolutionary rate, and you can test for expectation only really on those parameters. In both of the citations given for Juramaia being "unexpectedly advanced", that phrase is only used exactly for Durlstotherium etc. rather than the Juramaia -Eutheria sister relationship by Bi et al., although the sentiments are certainly similar. However, both the Bi et al. and Meng papers discuss two possible explanations for the similarity between Juramaia and Eomaia. These are (a) an incorrect age estimate for Juramaia or (b) early appearance of eutherian-type dentition and then exceptionally slow rates of evolution. This is the justification for qualitatively noting that something is "unexpected". They also both caution that the fact that Juramaia is represented by a single specimen makes identification of a pattern practically impossible.
Authors' response: We realise that the reported age of Juramaia has been questioned in several papers, but none of these paper shave presented evidence to support this conclusion besides qualitative remarks on its close morphological resemblance to the Jehol eutherians. We have quantified this resemblance for the first time by showing that, when the age of Juramaia is allowed to vary, our morphological clock analysis estimates the age of Juramaia to be similar to the Jehol eutherians. However, we emphasise that this does not show that the age of Juramaia is incorrect - Luo et al. (2011) clearly state that Juramaia is from the Daxishan/Daxigou site of Jianchang County of Liaoning Province, China, and the age of this locality is tightly constrained as ~160 MYA. In our opinion, the only way to show that the age of Juramaia is incorrect is by showing that the fossil does not come from that locality, and this is not something that our paper addresses. We therefore must assume that the reported age of Juramaia is correct. Our analysis simply shows that the known morphology of Juramaia is not what we would expect given its reported age and the assumptions of our analysis (model priors etc.). For this reason, we consider "unexpected" to be the most appropriate, neutral term for the situation regarding Juramaia. However, we have now taken care to put the word 'unexpected' in quotation marks throughout the paper.
I think it's worth noting that the age of the Yanliao Biota is now pretty solidly fixed in the Middle-Late Jurassic -a single adjective when bringing up the biota for the first time would suffice -and you already show what the implications are of a Jurassic Juramaia in terms of rate shifts. The final conclusion on this can, I think, be improved. In lines 290-293 you say "The Middle Jurassic age of Juramaia suggests unusually rapid rates of evolution at the base of therians and eutherians, followed by a period of exceptionally slow rates of eutherian evolution during the Early Cretaceous". That's all well and good, but I think it can be strengthened by re-emphasising the 50-fold shift in rates (lines 197-199) but also actually telling us about what constitutes a statistically significant deviation from the null hypothesis -ie expectation -of equal rates across the phylogeny. This would be a simple matter of taking the internal branch lengths and comparing them with expected branch lengths with a chi-squared test. This would bring the manuscript back to its title and the lede and justifies the use of the word "unexpected".
Authors' response: We have reiterated the 50-fold decrease: "…followed by a 50-fold rate decrease and a period of exceptionally slow eutherian morphological evolution during the Early Cretaceous" Our test of the age of Juramaia using relaxed priors ( figure 3, formerly figure 2) is the most intuitive and accurate way to test this 'expectation' and we also show the effect on branch rates in figure S13 (formerly figure 3). The reviewer states that the null hypothesis is equal rates across the phylogeny, but this is incorrect. We have used a relaxed clock model (the uncorrelated lognormal clock model) that specifically allows rates to vary between branches according to an underlying lognormal distribution. Indeed, this is exactly what we see -even when the age of Juramaia is allowed to vary, we still see considerable rate heterogeneity, between <0.01 and 0.08 transitions/character/million years (figure S10). As a result, a chi-squared test with a null expectation of equal rates is not appropriate here.
I also think it's worth addressing in the discussion the fact that Juramaia is a single specimen of a single species that then leads to Eomaia being a single specimen of a single species, so we don't really know much about what eutherians are doing in that time at all besides the similarity of these two individuals. The implication of a huge slowdown is interesting, but that kind of long branch is potentially subject to radical change on the introduction of new specimens.
Authors' response: We fully agree that there is a limit to how much we can conclude based on single specimens. However, even single specimens provide robust minimum age constraints on the evolution of particular features in specific lineages (assuming they can be correctly placed in the phylogeny). So, even though it's a single specimen, Juramaia shows that the morphology typical of known Early Cretaceous eutherians had originated by the Middle-Late Jurassic. Even if we find lots of eutherian fossils that fall on the long branch leading from Juramaia to other eutherians, it would not alter the fact that Eomaia, Ambolestes and other currently known Early Cretaceous eutherians have experienced a particularly low rate of morphological evolution.
To address the reviewer's point, we have added the following sentences to the end of the discussion: "However, this result requires further scrutiny, as it largely driven by two taxa, both of which are known from single specimens: Juramaia and Eomaia. The highly incomplete record of early eutherians makes it difficult to reach robust conclusions regarding the macroevolution of the group, and these may change with future discoveries." MISSING METHODOLOGY I've looked through the paper and the supplementary data in detail and cannot find the details of the fossilised birth-death model. This needs to be added to the supplementary information, or, if it is already there, better signposted, because I cannot find it at all. Did, for instance, you use diversified sampling, and if not, why not, given that most phylogenetic datasets are built on the understanding that this is the case? What, actually, were the priors on taxon age for each of the standard analyses? All we know is that the priors for the Yanliao mammaliaforms when letting their position be a bit more anatomically-driven is a Laplace distribution with 90% within the Jurassic. By implication there are bounds on these mammaliaforms' date priors in the other analyses, but how were they defined? A uniform distribution across the uncertainty in date of the first appearance? If not, what, and why? If the choice of prior matters so much for Juramaia, then we need to know what the prior we are asked to compare the result from a Laplace prior with was.
Authors' response: Diversified sampling is only relevant when there is a sample of extant taxa. We now state explicitly how taxon age priors were specified by adding the following sentence to our methods: "Tip dates were assigned uniform priors across the range of uncertainty for each taxon".
The supplementary information now includes the age ranges for every taxon including references. We also include a section in the supplementary information with the full details of the analysis.

SECTIONS
The paragraph beginning on Line 118 as far as 121 should not really be in the methods section as it strays into results and discussions. I understand why it ended up there from the point of view of explaining the need for further analysis, but all that's needed is something more like "To further investigate the relative effects of morphological data and topological priors on haramiyid phylogeny…". Otherwise you are revealing some of the results early and end up repeating yourself.
Authors' response: We have changed this to: "To test the effect of taxon age on the phylogenetic position of haramiyidans, we ran an analysis…" CONSISTENCY I'd use the same headings for subsections across Methods, Results, and Discussion, for clarity and ease of switching back and forward. Authors' response: changed as requested SMALL THINGS, TYPOS, GRAMMAR Line 45 -double space between 'Patagonia' and 'the'. Authors' response: changed as requested Line 47 -double space between 'discussion' and 'is'. Authors' response: changed as requested Line 48 -Juramaia sinensis, not sinsensis. Authors' response: changed as requested Line 49 -The word should be composing (or another synonym), not comprising. The parts compose the whole; the whole comprises the parts. Authors' response: changed as requested Line 50 -double space between 'morphology,' and 'Juramaia'. Authors' response: changed as requested Line 57 and elsewhere -'Tip dating' when referring to the method as a noun. 'Tip-dating' is correct as a compound adjective, e.g. 'a recent tip-dating study' on line 60. Authors' response: changed throughout as requested Line 57 -double space between 'investigate' and 'these' Authors' response: changed as requested Lines 79-80 -Square brackets seem like an odd choice here. Why not take the reference out of the brackets? On lines 262-263 you have square brackets for the reference within curved brackets. This could be avoided anyway by saying 'Markov model for variable characters (hereafter Mkv model)' which also avoids the issue of an unknown abbreviation. Authors' response: Changed to: "The Markov model for variable characters (hereafter Mkv) was used" Line 138 -This is the first time BPP has appeared. Some will not recognise the acronym, so expand it. Authors' response: changed as requested This may also be the case for Line 109 -MYA, although that might be a journal style anyway. Authors' response: We have changed MYA to Ma throughout to follow journal style See also Line 85 -'RWTY'; maybe worth noting that it's an R package as I at least assumed it was a method I was unfamiliar with. Authors' response:Changed to "was confirmed using the R package RWTY" Line 141 -'well resolved', not 'well-resolved' Authors' response:changed as requested

Reviewer 2 General comments
There's ongoing, contentious debate on allotherian relationships. Because allotherians likely evolved near the crown mammalian node, resolving this issue is especially important for understanding the origins and early evolution of mammals. Thus, the study by King and Beck is very relevant and should be of interest to a broad readership. I have no major concerns with the tip-dating methods or results. And the primary result (i.e. haramiyids are diphyletic) makes intuitive sense and offers somewhat of a compromise for the competing hypotheses. The second major conclusion of the paper is that Juramaia is morphologically very similar to much younger taxa, suggesting that therians evolved very rapidly early in their history and then experienced a long period of stasis (or Juramaia's age is incorrect). The analyses offer interesting insights on this topic. I don't have any critical concerns with the paper. However, I believe it would benefit greatly from two major additions, which I outline here.
To make the paper easier to follow for non-specialists, I recommend adding an introductory figure with simplified phylogenies that summarizes the competing allotherian hypotheses. I envision something like Figure 1  You could also consider adding a panel to the figure that highlights the considerable age difference between Juramaia and Jehol Biota therians.
Authors' response: Figure 2 (previously figure 1) highlights this difference, so we have referenced that. We feel that adding another panel to figure 1 would be redundant, and would take up unnecessary space.
My second major suggestion is to perform supplemental analyses using a character matrix from a recent Jin Meng paper. The two sides of the allotherian debate are driven by Jin Meng and Zhe-Xi Luo, and you have analyses that use a matrix from Luo (Huttenlocker et al. 2018), but you don't have equivalent analyses based on a Meng matrix. (Meng's matrices are derived from earlier Luo matrices, but scoring of many characters varies considerably, especially for allotherians.) Analyses using the Krause et al. 2014 matrix are fine, especially because it includes more multituberculates than the Meng and Luo matrices. Krause et al. followed Meng's scorings of haramiyid dental characters for their primary analysis, so their matrix indirectly represents Meng's interpretation of allotherians. However, many new allotherians have been published since 2014, and the only euharamiyidan in Krause et al. is Arboroharamiya. To truly account for both sides of the allotherian debate, it would be best to include a recent matrix from Meng. I recommend Wang et al. 2019 (Nature) because the described taxon is an allotherian (Jeholbaatar, a multituberculate). Meng's scoring of euharamiyid dental characters will likely unite multituberculates and euharamiyids in your analyses (as seen in the Krause-matrix results), but if you continue to see evidence of haramiyid diphyly then it will provide even stronger support for your results. Personally, I agree with Luo's scorings of haramiyid dental characters -I think he's made a more compelling case for haramiyid occlusion (following Jenkins 1997 and Butler 2000) using CT scans and occlusal reconstructions (e.g. see Your results offer somewhat of a compromise on the debate over haramiyids, and you could consider re-framing some of the text to focus on this. Recovering euharamiyids as crown mammals supports Meng's view, and recovering Haramiyavia+Thomasia as stem mammals is consistent with Luo's view. You could consider putting greater emphasis on the current debate (e.g. by adding more text and citations to the first paragraph of the Introduction) and providing more discussion on how the results may serve as a compromise between the two sides.
Authors' response:We thank the reviewer for this perceptive point. We have added the following text to our discussion "In some ways, our results represent a compromise between differing views on whether haramiyidans are crown-or stem-mammals: euharamiyidans fall within the crown-clade, whereas Haramiyavia+Thomasia fall outside."

Comments on Juramaia results
I'm concerned that the Juramaia results are influenced by sampling issues. The other Yanliao taxa are members of clades that are well-represented in the Jurassic, whereas Juramaia is the only therian in the Jurassic. If more Jurassic therians were discovered, would it drastically change the results of this study by introducing new morphological variation and altering branch lengths? One potential way to test this idea is to simulate Juramaia-like scenarios in other clades. For instance, you could remove Kuehneodon and set the age of the plagiaulacid multituberculates to ca. 126 Ma (to match the Jehol), and then predict the age of Rugosodon (the earliest multituberculate in the study) based on morphology. This could serve as somewhat of a sensitivity analysis to examine the influence of sampling on the Juramaia results. Authors' response:We have tested this by removing Kuehneodon and plagiaulacids, and predicting the age of Rugosodon. This is included as figure S11. This analysis does suggest that the Juramaia result could be partially (but not entirely) driven by sampling, and we now discuss this. Some authors (e.g. Sweetman et al. 2017 Acta Palaeo Polon) have posited that Juramaia is a stem therian rather than a eutherian. If this is the case, I doubt it'd alter your conclusions because there'd still be a very slow rate of morphological between Juramaia and other early therians. But it'd significantly alter some branch lengths, and thus likely change some results. For example, this topological change would likely lengthen the branch leading to eutherians, and thus in Figure 3a I'd expect Branch 2 to have much slower rates of evolution. I think this topic should be addressed at some point (even if it's in the supplement) because many readers may wonder what influence the phylogenetic position of Juramaia has on results. Sinodelphys from the Jehol Biota (previously thought to be the oldest metatherian) is now believed to be a eutherian (Bi et al. 2018 Nature). Incorporating this change into analyses is probably beyond the scope of this study, but it's another variable that could influence the Juramaia/therian results. The authors could note whether they think that moving Sinodelphys to Eutheria would alter branch lengths and evolutionary rates. Although the Huttenlocker (i.e. Luo) and Krause matrices include therians, the characters are primarily designed to investigate relationships in earlier groups such as docodonts, allotherians, and eutriconodonts. I wonder if this results in artificially slow evolutionary rates along early therian branches because there are few characters that help to distinguish these lineages.