What do we know about the fossil record of pinnipeds? A historiographical investigation

The fossil record of pinnipeds (seals, fur seals and walruses) is globally distributed, spanning from the late Oligocene to the Holocene. This record shows a complex evolutionary history that could not otherwise be inferred from their extant relatives, including multiple radiations and iterative ecomorphological specializations among different lineages, many of which are extinct. The fossil record of pinnipeds is not uniformly represented in space and time, however, leaving some gaps in our knowledge. We performed a historiographical investigation of the published fossil record of pinnipeds based on the information available in the Paleobiology Database, with the aim to broadly characterize and evaluate it from a taxonomic, geographical and temporal perspective. We identified major trends, strengths and weaknesses of the pinniped fossil record, including potential biases that may affect our interpretations. We found that 39% of the record corresponds to extant taxa, which are essentially from the Pleistocene and Holocene. There is a larger record from the Northern Hemisphere, suggesting biases in sampling and collection effort. The record is not strongly biased by sedimentary outcrop bias. Specifically, for extinct species, nearly half of them are represented by a single occurrence and a large proportion have type specimens consisting of single isolated postcranial elements. While the pinniped fossil record may have adequate temporal and taxonomic coverage, it has a strong geographical bias and its comparability is hindered by the incompleteness of type specimens. These results should be taken into account when addressing patterns of their past diversity, evolutionary history and paleoecology.

2) Is there some way to visualize geographic bias? E.g. some sort of a map or graph showing the proclivity for particular authors to work on fossils from their own continent v. material from other continents.
3) Uhen and Pyenson also investigated lineage duration/taxon longevity; such an approach here should be easily done. 4) I share similar concerns about the quality of pinniped holotypes; why not reproduce a version of Uhen and Pyenson's figure 4, but breaking down skull v. cranium v. skeleton v. postcrania. 5) I'm also curious about reevaluation of certain taxa and declaration of nomina dubia, junior synonyms, etc.; is there anyway to quantify the number of changes in taxonomic opinion per taxon (which should be countable in the PBDB) and track this perhaps A) by decade or B) by author?
And lastly 6) Uhen and Pyenson ultimately used the dataset to assemble a graph showing richness, origination, and extinction rates for Pinnipedia. Is there a reason this was not attempted here?
I would very much like to see a different version of supp figure 1 where the # of occurrences is plotted by stage rather than by epoch, and perhaps leave out the Holocene. This would hopefully reflect some finer resolution; for example, based on the Pacific record, I would predict a dip in the number of occurrences during the early Pleistocene.
Is it possible to investigate/plot (perhaps with a subset of the data) inferred depositional environment or rock type v. number of occurrences or time? E.g. sandstone, siltstone, mudstone/shale, carbonate, nonmarine, etc. I am seriously concerned by the number of Holocene "fossil" occurrences (n=459; 1/3 of the entire dataset). Most of these appear to be modern sightings of live animals or modern skeletons rather than actual fossil (or, rather, subfossil), although some do appear to be zooarchaeological. The distribution and publishing record of modern occurrences of live animals has no bearing on the publication/research history of fossilized examples. This part of the dataset really needs to be thoroughly vetted. Matter of fact, this exact point was brought up by Mark Uhen at the 2018 SVP meeting: most of these Holocene occurrences are not fossil/subfossil/zooarchaeological occurrences, and he pointed out in the Q&A session that these records do not belong in the dataset. I concur, and a cursory glance at article titles in the dataset for these records suggest they are studies of extant marine mammals and not fossil occurrences.

Minor Comments
Supplementary Figure 1 should absolutely be moved into the main text.
What do the authors mean by 'taxonomic validity'? This has a very specific meaning in taxonomy and refers only to whether or not a name is available, and confers zero information about the quality of a holotype specimen and therefore whether or not the taxon is even diagnosable (which is what we really care about). Please correct this.
The paper discusses extinct/extant species, but many extinct species are "neospecies" (in the sense that it is used in paleornithology) within extant genera. Perhaps there is some utility in investigating fossils that represent extant genera, but not extant species? 373: Probably very important to note that pinnipeds had a northern hemisphere origin, which will strongly influence the biogeographic distribution -this is overprinted by research and field effort bias. 378: correct to "Because of the" 395: What are the oldest remains in Peru and Chile? The Peruvian cetacean record goes back to the middle Miocene. On the PBDB most seem to be Serravallian/Langhian with one purported Aquitanian record from the Gaiman Formation from a conference abstract. This may not reflect publication bias against the southern hemisphere and might actually reflect a later arrival of phocids to the southern hemisphere. For example, pinnipeds of any sort are not present within the quite densely sampled record of marine vertebrates from the Oligocene and earliest Miocene Canterbury Basin sequence of NZ, and the earliest known pinnipeds from Australasia date to about the Miocene/Pliocene boundary in both Australia and NZ. If I recall correctly, South Africa shows a similar pattern. 400-404: Could you propose some discrete tests/ways to evaluate these hypotheses? 411-412: If this is the "Cape Kidnappers fur seal", then this is a Holocene specimen that washed out of a Maori midden and is less than 700 years old. Citation: Weston, R. J., Repenning, C. A., and Fleming, C. A., 1973, Modern age of supposed Pliocene seal, Arctocephalus caninus Berry (=Phocarctos hookeri Gray), from New Zealand: New Zealand Jour. Sci.,v. 16,no. 3, It is worth noting that in many places Pleistocene pinniped assemblages (especially in the North Pacific and Europe) are quite similar, if not identical, to the modern local fauna. 417: relative paucity 419-422: I think it would be fair to cite Boessenecker (2013: Geodiversitas) here as that paper includes such a discussion of Pleistocene pinniped faunas from the eastern North Pacific, as it regards Pliocene-Holocene faunal change.
458: perhaps change to "non-associated elements" 465: non-associated rather than associating 466: Rahmat et al. did not use the phrase 'holotypic series' and list most of the specimens as referred specimens, and this should be corrected -or perhaps correct to 'hypodigm'. Further, Dewaele et al. (2018: Royal Society Open Science) considered Terranectes to be a nomen dubium; this absolutely should be explained here and cited. 467: Please provide an example of artificially increasing taxonomic diversity by the naming of non-comparable parts (e.g. Leptophoca is probably a good example). Furthermore, what about taxonomic oversplitting, such as is the case with Allodesmus, where one species has been given a new species name each time a *slightly* different complete skeleton has been unearthed? (e.g. Allodesmus gracilis + kelloggi = A. kernensis). 475: "widely acknowledged standards" -please provide a citation to a review paper on the topic; I believe several have just been published this year in Geological Curator.

24-Apr-2019
Dear Dr Valenzuela-Toro: Manuscript ID RSOS-190234 entitled "What do we know about the fossil record of pinnipeds? A historiographic investigation" which you submitted to Royal Society Open Science, has been reviewed. The comments from reviewers are included at the bottom of this letter.
In view of the criticisms of the reviewers, the manuscript has been rejected in its current form. However, a new manuscript may be submitted which takes into consideration these comments.
Please note that resubmitting your manuscript does not guarantee eventual acceptance, and that your resubmission will be subject to peer review before a decision is made.
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We look forward to receiving your resubmission. One review was a one-sentence recommendation to reject, but the grounds were not valid. Reviewer 2's review is extensive and thoughtful, and the authors should respond to all his points with equal care. In many ways the paper is as much a review as an analysis, but I think it is valuable because the data are thoughtfully considered in their various contexts, and the manuscript is very well written. The title as it stands implies "review," and if it could be changed to reflect the "analysis" part I suspect it would resonate better. I would recommend a "reject/resub" decision mainly because our "major revision" timeline is three weeks and you will want to take the time to run the zooarchaeological analyses separately, as Reviewer 2 suggests (I don't think the data should be eliminated, only analyzed separately).
One caveat, and please clarify: The "Pull of the Recent," as Raup defined it, does not have the meaning you use here (but I can't think of the correct term at the moment). As he defined it, the best example is Sphenodon: the clade is unknown in the fossil record since the Cretaceous, but the presence of living Sphenodon "pulls" the range all through the Tertiary without a single fossil. I recognize that people sometimes misuse his original meaning, but even so ... and anyway might you actually have a true POTR example in the pinniped record?
Reviewers' Comments to Author: Reviewer: 1 Comments to the Author(s) In my opinion, this is a review of the fossil record based on a database, not a research article.

Reviewer: 2
Comments to the Author(s) Major Comments This study is a critical advance in the study of fossil pinnipeds, and a 'sequel' in a way to the seminal study by Uhen and Pyenson (2007). I applaud the authors' efforts, and think this is a nice dataset that can be explored in some 'fun' and enlightening ways -and I have suggested numerous additional avenues of investigation that I would like to see either fulfilled or concretely addressed.
I am curious about a few other questions/patterns that could be addressed from this dataset: 1) Aside from the two most prolific units; some sort of a scatterplot showing the relationship of the number of fossil occurrences X the # of taxa per unit might be interesting. This would be helpful for those of us wanting to learn more about some of the other units aside from the Calvert/Yorktown.
2) Is there some way to visualize geographic bias? E.g. some sort of a map or graph showing the proclivity for particular authors to work on fossils from their own continent v. material from other continents.
3) Uhen and Pyenson also investigated lineage duration/taxon longevity; such an approach here should be easily done. 4) I share similar concerns about the quality of pinniped holotypes; why not reproduce a version of Uhen and Pyenson's figure 4, but breaking down skull v. cranium v. skeleton v. postcrania. 5) I'm also curious about reevaluation of certain taxa and declaration of nomina dubia, junior synonyms, etc.; is there anyway to quantify the number of changes in taxonomic opinion per taxon (which should be countable in the PBDB) and track this perhaps A) by decade or B) by author?
And lastly 6) Uhen and Pyenson ultimately used the dataset to assemble a graph showing richness, origination, and extinction rates for Pinnipedia. Is there a reason this was not attempted here?
I would very much like to see a different version of supp figure 1 where the # of occurrences is plotted by stage rather than by epoch, and perhaps leave out the Holocene. This would hopefully reflect some finer resolution; for example, based on the Pacific record, I would predict a dip in the number of occurrences during the early Pleistocene.
Is it possible to investigate/plot (perhaps with a subset of the data) inferred depositional environment or rock type v. number of occurrences or time? E.g. sandstone, siltstone, mudstone/shale, carbonate, nonmarine, etc. I am seriously concerned by the number of Holocene "fossil" occurrences (n=459; 1/3 of the entire dataset). Most of these appear to be modern sightings of live animals or modern skeletons rather than actual fossil (or, rather, subfossil), although some do appear to be zooarchaeological. The distribution and publishing record of modern occurrences of live animals has no bearing on the publication/research history of fossilized examples. This part of the dataset really needs to be thoroughly vetted. Matter of fact, this exact point was brought up by Mark Uhen at the 2018 SVP meeting: most of these Holocene occurrences are not fossil/subfossil/zooarchaeological occurrences, and he pointed out in the Q&A session that these records do not belong in the dataset. I concur, and a cursory glance at article titles in the dataset for these records suggest they are studies of extant marine mammals and not fossil occurrences.

Minor Comments
Supplementary Figure 1 should absolutely be moved into the main text.
What do the authors mean by 'taxonomic validity'? This has a very specific meaning in taxonomy and refers only to whether or not a name is available, and confers zero information about the quality of a holotype specimen and therefore whether or not the taxon is even diagnosable (which is what we really care about). Please correct this.
The paper discusses extinct/extant species, but many extinct species are "neospecies" (in the sense that it is used in paleornithology) within extant genera. Perhaps there is some utility in investigating fossils that represent extant genera, but not extant species?
Regarding the "Ecomorphotype hypothesis" -I think somewhat more commentary is warranted, and add at least one sentence explaining the "logic" behind Koretsky's principle (e.g. analogy with extant taxa; group I mandible must go with group I femur, etc.).
A cursory glance at the dataset (~10 minutes) found a number of errors: 1) A record of Allodesmus from the Oligocene Pysht Formation does not exist, and is not reported in Boessenecker and Churchill (2018). I suspect that this record stems from Hunt and Barnes (1994) and has been misattributed to our paper for some strange reason. If true, it was actually identified as "Otariidae indet." (=Otarioidea or Pinnipedimorpha of later authors) and no relation to Allodesmus or Desmatophocidae was implied by these authors.
2) The maximum age of Ontocetus emmonsi reported from South Carolina (Boessenecker et al., 2018) is far too old; the age range is about 1.8-1.1 Ma, which is squarely within the Calabrian stage; in the SOI it is shown with an incorrect maximum age of Piacenzian (3.6 Ma).
I understand that these are probably errors made during entry into the PBDB, and therefore constitute an extra level of data corruption between publication and database entry. However, since the present study is about historiography and as of yet not a study of the efficacy of the PBDB, some vetting should probably be done to extinguish bogus fossil occurrences that have been entered improperly or attributed to the wrong publication.
Minor corrections 279-282: Many of these holotypes mentioned (4 out of 10) are housed at small Japanese institutions, which in fairness deserves commentary or mention. Probably very important to note that pinnipeds had a northern hemisphere origin, which will strongly influence the biogeographic distribution -this is overprinted by research and field effort bias.
378: correct to "Because of the" 395: What are the oldest remains in Peru and Chile? The Peruvian cetacean record goes back to the middle Miocene. On the PBDB most seem to be Serravallian/Langhian with one purported Aquitanian record from the Gaiman Formation from a conference abstract. This may not reflect publication bias against the southern hemisphere and might actually reflect a later arrival of phocids to the southern hemisphere. For example, pinnipeds of any sort are not present within the quite densely sampled record of marine vertebrates from the Oligocene and earliest Miocene Canterbury Basin sequence of NZ, and the earliest known pinnipeds from Australasia date to about the Miocene/Pliocene boundary in both Australia and NZ. If I recall correctly, South Africa shows a similar pattern. 400-404: Could you propose some discrete tests/ways to evaluate these hypotheses? 411-412: If this is the "Cape Kidnappers fur seal", then this is a Holocene specimen that washed out of a Maori midden and is less than 700 years old. Citation: Weston, R. J., Repenning, C. A., and Fleming, C. A., 1973, Modern age of supposed Pliocene seal, Arctocephalus caninus Berry (=Phocarctos hookeri Gray), from New Zealand: New Zealand Jour. Sci.,v. 16,no. 3, 416-418: It is worth noting that in many places Pleistocene pinniped assemblages (especially in the North Pacific and Europe) are quite similar, if not identical, to the modern local fauna. 417: relative paucity 419-422: I think it would be fair to cite Boessenecker (2013: Geodiversitas) here as that paper includes such a discussion of Pleistocene pinniped faunas from the eastern North Pacific, as it regards Pliocene-Holocene faunal change.
458: perhaps change to "non-associated elements" 465: non-associated rather than associating 466: Rahmat et al. did not use the phrase 'holotypic series' and list most of the specimens as referred specimens, and this should be corrected -or perhaps correct to 'hypodigm'. Further, Dewaele et al. (2018: Royal Society Open Science) considered Terranectes to be a nomen dubium; this absolutely should be explained here and cited. 467: Please provide an example of artificially increasing taxonomic diversity by the naming of non-comparable parts (e.g. Leptophoca is probably a good example). Furthermore, what about taxonomic oversplitting, such as is the case with Allodesmus, where one species has been given a new species name each time a *slightly* different complete skeleton has been unearthed? (e.g. Allodesmus gracilis + kelloggi = A. kernensis).
475: "widely acknowledged standards" -please provide a citation to a review paper on the topic; I believe several have just been published this year in Geological Curator.
Author's Response to Decision Letter for (RSOS-190234

Are the interpretations and conclusions justified by the results? Yes
Is the language acceptable? Yes

Do you have any ethical concerns with this paper? No
Have you any concerns about statistical analyses in this paper? Yes

Recommendation? Accept with minor revision (please list in comments)
Comments to the Author(s) Sent to both Editor and Author (Appendix B).

Review form: Reviewer 4
Is the manuscript scientifically sound in its present form? No

Recommendation?
Major revision is needed (please make suggestions in comments)

Comments to the Author(s)
This manuscript represents a significant contribution to pinniped paleontology. The authors have provided quantitative data behind a statement very much thrown around by pinniped paleontologists: that the fossil record of pinnipeds is poor. The study does an excellent job outlining why this may be, with a highlight on future directions for the field. The authors have done this by taking advantage of an excellent resource: the Paleobiology Database (PBD). However, due to the nature of PBD, some extra vetting of the raw data (Supplemental Table 1) needs to be done to improve the accuracy of the analysis (please refer to specifics in review (see Appendix C)). I also recommend the authors take a second look at their results and discussion before the next submission, to check whether the conclusions they are making from the data provided by the PBD make sense in relation to the literature. Most of these issues may be rectified by taking care around the use of the term "occurrences" that appears frequently in text to refer to data in Supp. Table 1. This is only in regards to minor statements in the text, and none of the larger results/conclusions should be affected. There are a few major and minor corrections I have suggested, as well as corrections to the raw dataset.

28-Sep-2019
Dear Dr Valenzuela-Toro On behalf of the Editor, I am pleased to inform you that your Manuscript RSOS-191394 entitled "What do we know about the fossil record of pinnipeds? A historiographic investigation" has been accepted for publication in Royal Society Open Science subject to minor revision in accordance with the referee suggestions. Please find the referees' comments at the end of this email.
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Once again, thank you for submitting your manuscript to Royal Society Open Science and I look forward to receiving your revision. If you have any questions at all, please do not hesitate to get in touch. Comments to the Author(s) This manuscript represents a significant contribution to pinniped paleontology. The authors have provided quantitative data behind a statement very much thrown around by pinniped paleontologists: that the fossil record of pinnipeds is poor. The study does an excellent job outlining why this may be, with a highlight on future directions for the field. The authors have done this by taking advantage of an excellent resource: the Paleobiology Database (PBD). However, due to the nature of PBD, some extra vetting of the raw data (Supplemental Table 1) needs to be done to improve the accuracy of the analysis (please refer to specifics in review). I also recommend the authors take a second look at their results and discussion before the next submission, to check whether the conclusions they are making from the data provided by the PBD make sense in relation to the literature. Most of these issues may be rectified by taking care around the use of the term "occurrences" that appears frequently in text to refer to data in Supp. Table 1. This is only in regards to minor statements in the text, and none of the larger results/conclusions should be affected. There are a few major and minor corrections I have suggested, as well as corrections to the raw dataset.

22-Oct-2019
Dear Dr Valenzuela-Toro, I am pleased to inform you that your manuscript entitled "What do we know about the fossil record of pinnipeds? A historiographic investigation" is now accepted for publication in Royal Society Open Science.
You can expect to receive a proof of your article in the near future. Please contact the editorial office (openscience_proofs@royalsociety.org and openscience@royalsociety.org) to let us know if you are likely to be away from e-mail contact --if you are going to be away, please nominate a coauthor (if available) to manage the proofing process, and ensure they are copied into your email to the journal.
Due to rapid publication and an extremely tight schedule, if comments are not received, your paper may experience a delay in publication.
Royal Society Open Science operates under a continuous publication model (http://bit.ly/cpFAQ). Your article will be published straight into the next open issue and this will be the final version of the paper. As such, it can be cited immediately by other researchers. As the issue version of your paper will be the only version to be published I would advise you to check your proofs thoroughly as changes cannot be made once the paper is published. This study is a critical advance in the study of fossil pinnipeds, and a 'sequel' in a way to the seminal study by Uhen and Pyenson (2007). I applaud the authors' efforts, and think this is a nice dataset that can be explored in some 'fun' and enlightening ways -and I have suggested numerous additional avenues of investigation that I would like to see either fulfilled or concretely addressed.
I am curious about a few other questions/patterns that could be addressed from this dataset: 1) Aside from the two most prolific units; some sort of a scatterplot showing the relationship of the number of fossil occurrences X the # of taxa per unit might be interesting. This would be helpful for those of us wanting to learn more about some of the other units aside from the Calvert/Yorktown. Figure 3).

RESPONSE: We agree and we included accumulation (rarefaction) curves for Calvert, Astoria, Yorktown and Purisima formations (Supplementary
2) Is there some way to visualize geographic bias? E.g. some sort of a map or graph showing the proclivity for particular authors to work on fossils from their own continent v. material from other continents. Figure 2) showing in more detail the geographic inclination in the study of fossil taxa by the six most prolific authors describing extinct pinnipeds. This new graph shows more clearly the tendency of those authors to study fossil remains from areas closer to their permanent residency versus others from other regions or continents.

RESPONSE: Yes, we have included a new visual representation (Supplemental
3) Uhen and Pyenson also investigated lineage duration/taxon longevity; such an approach here should be easily done.

RESPONSE:
We disagree on both counts: first, should not have conducted a study of lineage duration because this analysis is outside the scope of this paper. Our study attempts to provide a general analysis of the quality and modes of the fossil record of pinnipeds rather than an exhaustive analysis of the duration/taxon longevity, which is more of a question of evolutionary patterns in the fossil record. Second, we do not think it could easily be done, as such investigations require a robust, time-calibrated phylogeny, and detailed assessment of the stratigraphic range of the fossil taxa in question. 4) I share similar concerns about the quality of pinniped holotypes; why not reproduce a version of Uhen and Pyenson's figure 4, but breaking down skull v. cranium v. skeleton v. postcrania. Figure  3A, B). However, we agree with the reviewer and changed the aesthetic of the figure to make it more clear (now Figure 5A). Additionally, we added a new figure (5B) addressing the completeness (articulated skeletons v. associated elements v. isolated elements) of the type specimens. 5) I'm also curious about reevaluation of certain taxa and declaration of nomina dubia, junior synonyms, etc.; is there any way to quantify the number of changes in taxonomic opinion per taxon (which should be countable in the PBDB) and track this perhaps A) by decade or B) by author?

RESPONSE:
We agree with this suggestion, although we did not include a more in-depth analysis of this matter in our revision because we consider this issue to be outside the scope of this study. However, in our revision, we speculate that taxa described longer ago are more prone to reevaluations over time, and as a result, we expect that they are more exposed to changes in their systematic and taxonomic identity. We addressed this issue in the main text.
And lastly 6) Uhen and Pyenson ultimately used the dataset to assemble a graph showing richness, origination, and extinction rates for Pinnipedia. Is there a reason this was not attempted here? RESPONSE: Again, as with the comment of lineage duration, evolutionary rates is a topic outside of the scope of the manuscript.
I would very much like to see a different version of supp figure 1 where the # of occurrences is plotted by stage rather than by epoch, and perhaps leave out the Holocene. This would hopefully reflect some finer resolution; for example, based on the Pacific record, I would predict a dip in the number of occurrences during the early Pleistocene.

RESPONSE:
Agree. We modified Supplemental Figure 1 with the aim to provide a finer resolution of the geologic time, but also a more complete representation of the record, including extant and extinct species. Part A of this figure shows the number of occurrences of extinct and extant species over geologic time (by stages) of both extant and extinct species of pinnipeds.
Is it possible to investigate/plot (perhaps with a subset of the data) inferred depositional environment or rock type v. number of occurrences or time? E.g. sandstone, siltstone, mudstone/shale, carbonate, nonmarine, etc.

RESPONSE:
We consider that this is outside the scope of this study. I am seriously concerned by the number of Holocene "fossil" occurrences (n=459; 1/3 of the entire dataset). Most of these appear to be modern sightings of live animals or modern skeletons rather than actual fossil (or, rather, subfossil), although some do appear to be zooarchaeological. The distribution and publishing record of modern occurrences of live animals has no bearing on the publication/research history of fossilized examples. This part of the dataset really needs to be thoroughly vetted. Matter of fact, this exact point was brought up by Mark Uhen at the 2018 SVP meeting: most of these Holocene occurrences are not fossil/subfossil/zooarchaeological occurrences, and he pointed out in the Q&A session that these records do not belong in the dataset. I concur, and a cursory glance at article titles in the dataset for these records suggest they are studies of extant marine mammals and not fossil occurrences.

RESPONSE:
We agree with this concern. We updated the dataset used in the analysis and we manually removed false fossil and subfossil pinniped occurrences from the dataset. After this revision, the record of fossil (and subfossil) occurrences from the Pleistocene and Holocene includes 495 records (compared with 459 only from the Holocene from the last version). Some of the results obtained after this correction changed (with regard to the original version of this manuscript); however, the major trends were maintained. We strongly think that it is not necessary to ban these occurrences after this amendment because the Quaternary record of pinnipeds is an important component of the record that constitutes one of the few available evidence for understanding several questions regarding the origin, biogeography, and conservation of living species of pinnipeds.

Minor Comments
Supplementary Figure 1 should absolutely be moved into the main text.

RESPONSE:
Agree. We moved Supplementary Figure 1 into the main text.
What do the authors mean by 'taxonomic validity'? This has a very specific meaning in taxonomy and refers only to whether or not a name is available, and confers zero information about the quality of a holotype specimen and therefore whether or not the taxon is even diagnosable (which is what we really care about). Please correct this.

RESPONSE: Corrected.
The paper discusses extinct/extant species, but many extinct species are "neospecies" (in the sense that it is used in paleornithology) within extant genera. Perhaps there is some utility in investigating fossils that represent extant genera, but not extant species?

RESPONSE:
We discussed only five extinct species belong to extant genera (Callorhinus gilmorei, Histriophoca alekseevi, Neophoca palatina, Otaria fisheri, and Phoca moori), representing ~5% of the total of extinct species. Furthermore, most of those species are also represented by a single occurrence (the only exception is C. gilmorei with 9 occurrences of referred material). Based on the low number of extinct species, we consider unnecessary to perform a different analysis based on the fossils that represent extant genera versus extant species. Nevertheless, we added a sentence in the main text about this issue.
Regarding the "Ecomorphotype hypothesis" -I think somewhat more commentary is warranted, and add at least one sentence explaining the "logic" behind Koretsky's principle (e.g. analogy with extant taxa; group I mandible must go with group I femur, etc.).

RESPONSE:
Agree. We added additional sentences explaining in more detail the fundamentals of the Ecomorphotype hypothesis.
A cursory glance at the dataset (~10 minutes) found a number of errors: 1) A record of Allodesmus from the Oligocene Pysht Formation does not exist, and is not reported in Boessenecker and Churchill (2018). I suspect that this record stems from Hunt and Barnes (1994) and has been misattributed to our paper for some strange reason. If true, it was actually identified as "Otariidae indet." (=Otarioidea or Pinnipedimorpha of later authors) and no relation to Allodesmus or Desmatophocidae was implied by these authors.
2) The maximum age of Ontocetus emmonsi reported from South Carolina (Boessenecker et al., 2018) is far too old; the age range is about 1.8-1.1 Ma, which is squarely within the Calabrian stage; in the SOI it is shown with an incorrect maximum age of Piacenzian (3.6 Ma).

RESPONSE: Corrected.
3) Paleobio database often lists the first, but incorrect, reference for a fossil assemblage. Boessenecker (2011) did not report any fossil pinnipeds; these were reported by Boessenecker (2013), a follow up to the 2011 study, which reported sharks/fish/birds etc.

RESPONSE:
Titanotaria orangensis was missing because this taxon was published in October 2018, 6 months later the data were downloaded from PBDB. The same holds for Nanodobenus (published in August 2018). We updated our analysis to April 29, 2019, so those taxa are now included.
I understand that these are probably errors made during entry into the PBDB, and therefore constitute an extra level of data corruption between publication and database entry. However, since the present study is about historiography and as of yet not a study of the efficacy of the PBDB, some vetting should probably be done to extinguish bogus fossil occurrences that have been entered improperly or attributed to the wrong publication.

RESPONSE:
We agree with this statement; however, an evaluation of the data entry for the PBDB is outside the scope of this manuscript. Nevertheless, we performed an exhaustive revision (to the best of our abilities) of the data used in this study to reduce imprecisions in the data.
Minor corrections 279-282: Many of these holotypes mentioned (4 out of 10) are housed at small Japanese institutions, which in fairness deserves commentary or mention. 373: Probably very important to note that pinnipeds had a northern hemisphere origin, which will strongly influence the biogeographic distribution -this is overprinted by research and field effort bias.

RESPONSE:
Agree. We added a sentence including this point.
378: correct to "Because of the" RESPONSE: Corrected. 395: What are the oldest remains in Peru and Chile? The Peruvian cetacean record goes back to the middle Miocene. On the PBDB most seem to be Serravallian/Langhian with one purported Aquitanian record from the Gaiman Formation from a conference abstract. This may not reflect publication bias against the southern hemisphere and might actually reflect a later arrival of phocids to the southern hemisphere. For example, pinnipeds of any sort are not present within the quite densely sampled record of marine vertebrates from the Oligocene and earliest Miocene Canterbury Basin sequence of NZ, and the earliest known pinnipeds from Australasia date to about the Miocene/Pliocene boundary in both Australia and NZ. If I recall correctly, South Africa shows a similar pattern.

RESPONSE:
Agree. The pinniped fossil record from South America from the Neogene is referred mostly to occurrences from units from the middle Miocene to the Pliocene (more recent than the fossil record of pinnipeds from the eastern coast of the North Pacific, for instance). Thus, a general comparison of the pinniped fossil record from the Neogene from the coast of California and the western coast of South America is potentially biased by this temporal difference. We have added a sentence in the main text clarifying that we are only comparing contemporaneous fossil occurrences from the middle Miocene to the Pliocene from both regions. 400-404: Could you propose some discrete tests/ways to evaluate these hypotheses?

RESPONSE:
At the moment, we see these hypotheses as good subjects for minor, future studies, beyond the scope of this paper. 411-412: If this is the "Cape Kidnappers fur seal", then this is a Holocene specimen that washed out of a Maori midden and is less than 700 years old. Citation: Weston, R. J., Repenning, C. A., and Fleming, C. A., 1973 467: Please provide an example of artificially increasing taxonomic diversity by the naming of non-comparable parts (e.g. Leptophoca is probably a good example). Furthermore, what about taxonomic oversplitting, such as is the case with Allodesmus, where one species has been given a new species name each time a *slightly* different complete skeleton has been unearthed? (e.g. Allodesmus gracilis + kelloggi = A. kernensis).

RESPONSE:
We agree and have added an example of a case of artificially increased taxonomic diversity by the assignation of fragmentary elements. Also, we added a brief discussion about the potential taxonomic oversplit in Allodesmus from the Sharktooth Hill bonebed (Round Mountain Silt). 475: "widely acknowledged standards" -please provide a citation to a review paper on the topic; I believe several have just been published this year in Geological Curator.

RESPONSE:
We have revised the text to mention best practices, as we think those words best fit the meaning implied by the suggestion. Geological Curator's Group merely advocates guidelines for standards in UK collections, and we see little traction (or widespread knowledge) of these guidelines outside of this community. Instead, our manuscript focuses on examples of bad practices in specimen-based research, which may ameliorate some of the problems we have observed. This ms. reviews the taxonmic, temporal and geographic record of pinnipeds and uses the PBDB to explore the record and its potential biases including diversity estimations. The ms is a nice complement to an earlier historiographic study of the cetacean and sirenian fossil record (Uhen and Pyenson, 2007). It is also a good critique of taxonomic problems that ensue when using non-associated elements and the untested "ecomorphological approach" as a basic for taxonomic identity of fossil pinnipeds (especially phocids) resulting in questionable (at best) phylogenetic relationships.
In this resubmission. the authors appear to have addressed reviewers' concerns that have considerably improved the ms. I suggest only a few additional minor revisions.
Valenzuela and Koch 2019 is an abstract---given the ephemeral nature of abstracts it would be better to cite a paper.
Graphs employ different Geologic time scale (stages vs ages--epoch names)-for the benefit of the general reader and consistency I suggest using both stage as well as ages --epoch names for all.
This manuscript represents a significant contribution to pinniped paleontology. The authors have provided quantitative data behind a statement very much thrown around by pinniped paleontologists: that the fossil record of pinnipeds is poor. The study does an excellent job outlining why this may be, with a highlight on future directions for the field.
The authors have done this by taking advantage of an excellent resource: the Paleobiology Database (PBD). However, due to the nature of PBD, some extra vetting of the raw data (Supplemental Table  1) needs to be done to improve the accuracy of the analysis (please refer to specifics in review). I also recommend the authors take a second look at their results and discussion before the next submission, to check whether the conclusions they are making from the data provided by the PBD make sense in relation to the literature. Most of these issues may be rectified by taking care around the use of the term "occurrences" that appears frequently in text to refer to data in Supp. Table 1. This is only in regards to minor statements in the text, and none of the larger results/conclusions should be affected.
There are a few major and minor corrections I have suggested, as well as corrections to the raw dataset.

Major manuscript edits
 The use of the term "occurrence" seems to occasionally be conflated with the fossil record.
The definition provided in the Methods section refers to geographical collections, but some of the time this is not what is being discussed in the text. Occasionally the use of "occurrences" in text is in reference to the literature, published specimens, or fossil sites. This has resulted in a lot of confusion while reviewing this manuscript, especially when several statements are made about the "occurrences" of specific species of fossil pinnipeds. Throughout the manuscript, it is occasionally unclear whether the actual published fossil record of pinnipeds is being discussed, or collection effort by museums (which is what the current definition could refer to). This issue is enhanced when assessing the raw data in Supplemental Table 1. For example: existing confusion about the age of particular sites in the literature means many listed "occurrences" are actually double-ups of records from the same site (just split into two time Periods). This artificially inflates the number of "occurrences" being discussed. I advise the authors revise the use of "occurrences" in the text, to avoid this confusion. Alternatively, make it clear that occasionally, "occurrences" will be used as a proxy term for what is being discussed in text (e.g. the fossil record). If the authors go with the latter, there is at least one instance where this will be problematic (Page 13, the discussion of the most represented extinct species, see minor comments for this section).
 I would like to see the Methods section split up into the sub-heading format that the Results and Discussion sections are in, for clarity.
 Most critically, there are some major and minor problems with the occurrences listed in Supp. Table 1. These errors, while minor in most instances, affect the accuracy of the results. This is especially pertinent when it comes to conclusions drawn from occurrences from the Southern Hemisphere. I have made some specific suggestions for fixes below in the Dataset corrections section. But I recommend the authors take another look at the dataset beyond these suggestions to ensure the accuracy of the raw data.