the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 20 Jan 2025
Global Acritarch Database (>110 000 occurrences)
Abstract. Acritarchs, microfossils with an algal affinity, are of great significance for studying the origin and evolution of early life on Earth. Acritarch data are currently dispersed across various research institutions and databases worldwide, lacking unified integration and standardization. Palynodata was the largest database of acritarchs, containing 15 fields, 111 382 entries, 812 238 metadata items, and 7385 references. However, it lacked references post-2007 and excluded geographic data. Here, we collected and organized previous data, adding 24 fields, 4531 entries, 1 882 081 metadata points, and 424 references, to build a new global acritarch database. The expanded database now contains a total of 39 fields, covering genera, species, and related geological information (geological timescale, location, modern latitude and longitude, paleolatitude and paleolongitude, stratum, and others), amounting to 115 947 entries, 2 694 671 metadata, and 7816 references. Each entry is associated with fields that facilitate a better understanding of the geographical distribution and changes over geological timescales of acritarchs, thereby revealing their temporal and spatial distribution patterns and evolution throughout the history of the Earth. This article describes GAD version 1.0, which is available at https://doi.org/10.5281/zenodo.13828633 (Shu et al., 2024).
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RC1: 'Comment on essd-2024-577', Jan Hennissen, 10 Mar 2025
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Overall Comments
In this paper, Shu and co-authors present the compilation of a database, the Global Acritarch Database (GAD), comprising acritarch taxa from the literature and their associated metadata. They build on the database from Palynodata.ru adding data from publications post 2007. In total, the GDA contains 115,947 entries with, where possible, data on palaeolatitude and palaeolongitude. The authors perform basic exploratory data analysis that reveal that the majority of studies originate from the current Northern Hemisphere with a focus on the Palaeozoic Eon.
The manuscript is well-structured and is easy to follow. To improve readability even more, I encourage the authors to avoid the past tense, which is unnecessary in most places where it was used (e.g., P.4 L. 97 and 122).
I find the presentation of the exploratory data analysis in Figure 5–10 effective and I believe it will help researchers identifying knowledge gaps spatially (e.g., Southern Hemisphere) and temporally (e.g., Late Cambrian and Permian).
The GAD is presented as a csv and I imported it into R to interrogate the dataset. Below are a number of comments that I found during this exercise. These should be addressed before ethe manuscript is formally published.
In addition, I added an annotated pdf of the paper with a non-exhaustive list of mostly editorial comments.
Specific comments
P. 1, L. 14: “Acritarchs, microfossils with an algal affinity” Rephrase. Acritarchs are an artificial polyphyletic group of microfossils of unknown biological affinity (Downie et al., 1963; Evitt, 1963; Kroeck et al., 2022; Strother, 1996). It is true that many acritarchs likely have an algal affinity and only a small number are non-algal which the authors state themselves in lines 27–31. This should be reflected in the opening line of the abstract rather than the definitive statement that is there now.
P. 1, L. 24: the link to the Zenodo page for the GAD works but note the spelling mistake in the title of the page “Gobal” instead of “Global”. This spelling mistake is also perpetuated in the filename of the csv file upon downloading the GAD.
In the GAD CSV:
- check spelling of column title AL which should be “Reference”. Unfortunately, many of the references which contain special symbols have had those replaced with “?”. This is not a critical issue, but it could impede linking to the original publications.
- To increase ease of use, it would be nice to have doi’s for the references included as a separate column.
- Genus and Species name are in a separate column which makes it easy to interrogate the database. However, the original name is in a single column (genus and species name together). It would be easier to use if those were separated into two columns as well.
- Each entry has an associated Doc number. Is there a separate list with all documents and their numbers?
- The column “Species name” should be replaced with “Species epithet”.
P. 5, L. 129: “Time Field”. I think “Age” may be more appropriate. Note that it is not a single field that is assigned to the definition of the age of an entry (I count 12 separate columns that are used to define the age).
P. 5, L. 142: Same as above: Location Field. There is more than 1 field that describes the location.
P. 5, L. 146: Check the correct reference for “Google Satellite Electronic Maps”.
P. 5, L. 153: Should there not be a paragraph break after addition. The next paragraph should then start with (6) The reference field.
P. 5., L. 156: as mentioned above, special characters seem to have caused issues with frequent “?” etc.
P.8, Table 3: “Species name” should be replaced with “Species epithet”. For example in the case of Pterospermopsis australiensis. The genus name Pterospermopsis the species name is Pterospermopsis australiensis while the species epithet is australiensis. Note that this should also be changed in the GAD proper as the column now entitled “Species name” contains in fact species epithets.
Figure 2: “Too old” is not a reason for not being able to find literature.
Figure 3: the commas in the “Time” field come out looking like accents.
P. 10, L. 178: on importing the database and filtering for references I arrive at 7799 unique entries (not 7816) and only 1170 unique sample locations (not 2993).
Figure 5: “Number of literature” should be replaced with “Number of published studies”
P. 17, L. 263: “The large volume and consistent structure of data in GAD allow for a comprehensive analysis of acritarch evolution over geological timescales”. I disagree with this statement. At best, it shows the patterns of research interest for acritarchs in the global research community throughout the geological timescale. As pointed out by the authors in Figures 7 and 8, the number of studies is highly biased, with the majority of studies conducted in areas currently in the Northern Hemisphere. I am not sure if this is in response to acritarch evolution. This is especially hard to prove when dealing with a polyphyletic group like acritarchs where the inclusion of species within this group may be tenuous, especially in the Palaeozoic. I think Figure 10 provides an interesting analysis of the available data in the GAD, but I think there is more to its observed distribution than explained by the authors in Paragraph 3.7.
P. 18, L. 285: GAD and PBDB: write out abbreviations in full again in the conclusions.
References
Downie, C., et al., 1963. Dinoflagellates, hystrichospheres and the classification of the acritarchs. Stanford University Publications Geological Sciences 7, 1-16
Evitt, W.R., 1963. A discussion and proposals concerning fossil dinoflagellates, hystrichospheres and acritarchs. Proceedings of the National Academy of Sciences 49, 298-302 doi:10.1073/pnas.49.3.298.
Kroeck, D.M., et al., 2022. A review of Paleozoic phytoplankton biodiversity: Driver for major evolutionary events? Earth Sci. Rev. 232, 104113 https://doi.org/10.1016/j.earscirev.2022.104113.
Strother, P.K., 1996. Acritarchs, in: Jansonius, J., McGregor, D.C. (Eds.), Palynology: Principles and Applications. American Association of Stratigraphic Palynologists Foundation, Salt Lake City, USA, pp. 81-106
Data sets
Gobal Acritarch Database Xiang Shu et al. https://doi.org/10.5281/zenodo.13828507
Model code and software
Code encountered during the drawing process Xiang Shu https://doi.org/10.5281/zenodo.13829040
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