PONE-D-21-19346

Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific

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Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: This manuscript examines the phylogeography of the mangrove crabs Perisesarma in the West Pacific. The result is clear and straightforward and should be published after some minor revision.

The MS is well written and the only aspects for improvement is it lacks references that are concerning on the phylogeography of mangrove organisms in the West Pacific for comparative purposes in the discussion. The authors consider phylogeography of intertidal species as a whole example. In fact, mangroves and rocky shores species may have different phylogeography patterns, because the local environment and currents in mangroves are much slower that rocky shore species. There are several major examples of phylogeography pattern of mangrove organisms which should be take into account for comparisons in the discussion. This includes:

1)Introduction: Lines 48, authors stated to state some factors to affect phylogeography of intertidal species. The formation of Isthmus of Panama have affect the genetic differentiation of Pacific and Caribbean crab populations (land mass mechanisms). The authors should cite some references concerning this mechanisms on mangrove crabs, including fiddler crabs:

Thurman CL, Alber RE, Hopkins MJ, Shih HT. 2021. Morphological and genetic variation among populations of the fiddler crab Minuca burgersi (Holthuis, 1967) (Crustacea: Brachyura: Ocypodidae) from shores of the Caribbean Basin and western South Atlantic Ocean. Zool Stud 60:19. doi:10.6620/ZS.2021.60-19.

2)In addition to land mass mechanisms, some species can perform trans-Pacific dispersal mechanisms and resulted in some degree of genetic differentiation. This should also be stated in the introduction.

Trans-Pacific mechanisms

Hongjamrassilp W, Murase A, Miki R, Hastings PA. 2020. Journey to the west: trans-Pacific historical biogeography of fringehead blennies in the genus Neoclinus (Teleostei: Blenniiformes). Zool Stud 59:9. doi:10.6620/ZS.2020.59-09

3)Below are some phylogeography of mangrove organisms in the West Pacific and I would suggest the authors to cite and use their results to compare with the pattern in Perisesarma, as these organisms almost share similar habitats.

Mangrove mudskippers:

Chen, W., Hong, W. S., Chen, S. X., Wang, Q., & Zhang, Q. Y. (2015).

Population genetic structure and demographic history of the mudskipper

Boleophthalmus pectinirostris on the northwestern pacific coast.

Environmental Biology of Fishes, 98(3), 845–856.

Mangrove snails:

Kojima, S., Hayashi, I., Kim, D., Iijima, A., & Furota, T. (2004). Phylogeography

of an intertidal direct-developing gastropod Batillaria cumingi around

the Japanese Islands. Marine Ecology Progress Series, 276, 161–172.

Kojima, S., Kamimura, S., Iijima, A., Kimura, T., Mori, K., Hayashi, I., & Furota,

T. (2005). Phylogeography of the endangered tideland snail Batillaria

zonalis in the Japanese and Ryukyu Islands. Ecological Research, 20(6),

686–694.

Kojima, S., Kamimura, S., Kimura, T., Hayashi, I., Iijima, A., & Furota, T. (2003).

Phylogenetic relationships between the tideland snails Batillaria flectosiphonata

in the Ryukyu Islands and B. multiformis in the Japanese

Islands. Zoological Science, 20(11), 1423–1433.

Mangrove barnacles:

Chang, Y. W., J. S. M. Chan, R. Hayashi, T. Shuto, L. M. Tsang, K. H. Chu and B. K. K. Chan* (2017). Genetic differentiation of the soft shore barnacle Fistulobalanus albicostatus (Cirripedia: Thoracica: Balanomorpha) in the West Pacific. Marine Ecology-An Evolutionary Perspective, 38(2): e12422.

Mangrove crabs:

Wong, K. J. H., Chan, B. K. K., & Shih, H. T. (2010). Taxonomy of the sand bubbler crabs Scopimera globosa De Haan, 1835, and S. tuberculate Stimpson, 1858 (Crustacea: Decapoda: Dotillidae) in East Asia, with description of a new species from the Ryukyus, Japan. Zootaxa, 2345, 43–59.

4)In the discussion, lines 438, the authors consider Philippines may be the origin of the clades that disperse northward in the West Pacific (sharing of genotype between Taiwan and the Philippines). Similar observation and conclusion was also addressed in the intertidal barnacle Hexechamaesipho and, Bresidium and Sesarmop crabs.

Please cite and refer to this example:

Tsang, L. M., B. K. K. Chan, G. A Williams and K. H. Chu (2013). Who is moving where? Molecular evidence reveals patterns of range shift in the acorn barnacle Hexechamaesipho pilsbryi in Asia. Marine Ecology Progress Series, 488: 187-200.

Li JJ, Shih HT, Ng PKL. 2020. The Taiwanese and Philippine species of the terrestrial crabs Bresedium Serène and Soh, 1970 and Sesarmops Serène and Soh, 1970 (Crustacea: Decapoda: Brachyura), with descriptions of two new species. Zool Stud 59:16. doi:10.6620/

ZS.2020.59-16.

Ng PKL, Li JJ, Shih HT. 2020. What is Sesarmops impressus (H. Milne Edwards, 1837) (Crustacea: Brachyura: Sesarmidae)? Zool Stud 59:27. doi:10.6620/ZS.2020.59-27.

5)Part of the above reference already show some of the glacial refugia. For more details on the glacial refugia in the West Pacific, the authors should refer:

Wu, T. H., Tsang, L. M., Chan, B. K. K., & Chu, K. H. (2015). Cryptic diversity

and phylogeography of the island-associated barnacle Chthamalus

moro in Asia. Marine Ecology, 36(3), 368–378.

Tsang, L. M., Chan, B. K. K., Wu, T. H., Ng, W. C., Chatterjee, T., Williams,

G. A., & Chu, K. H. (2008). Population differentiation in the barnacle

Chthamalus malayensis: Postglacial colonization and recent connectivity

across the Pacific and Indian Oceans. Marine Ecology Progress Series,

364, 107–118.

Chan, B. K. K., Tsang, L. M., & Chu, K. H. (2007). Morphological and genetic

differentiation of the acorn barnacle Tetraclita squamosa (Crustacea, Cirripedia) in East Asia and description of a new species of Tetraclita. Zoologica Scripta, 36(1), 79–91.

Reviewer #2: This is a study focusing on the phylogeography of the Parasesarma bidens species complex from West Pacific. While the methods of analyses were adequate, some biogeographical explanations based on the limited sample size should be more conservative.

Major comments:

* The included clades of this complex might be problematic. According to the trees in Shahdadi & Schubart (2017), Li et al. (2019), and Shahdadi et al. (2020), 3 spp. (bengalense, capensis, guttatum) in the Indian Ocean probably belong to the major clade of the bidens complex and at least closely related with the complex. The authors should include sequences of the above 3 spp. and might need to rewrite the part of "Phylogeny, phylogeography and evolutionary history" in Discussion.

* L391, L399, L438-440: As the authors also mentioned that large sample size from Taiwan and Philippines are needed (L440-441), it is apparently too early to say one area could be considered as the origin. Otherwise, it will be more convincing by citing related references that Philippines is the origin of some marine species.

* L428-430: There might be barriers between Taiwan and China for some crab species, however populations in both areas of some species might show identical. For example, Austruca lactea (Shih, H.-T., Kamrani, E., Davie, P. J. F. & Liu, M.-Y., 2009. Genetic evidence for the recognition of two fiddler crabs, Uca iranica and U. albimana (Crustacea: Brachyura: Ocypodidae), from the northwestern Indian Ocean, with notes on the U. lactea species-complex. Hydrobiologia 635: 373-382) and some Metaplax spp. (Shih, H.-T., Hsu, J.-W., Wong, K. J. H. & Ng, N. K. 2019. Review of the mudflat varunid crab genus Metaplax (Crustacea, Brachyura, Varunidae) from East Asia and northern Vietnam. ZooKeys 877: 1-29). It might be necessary to discuss the larval behavior/ecology of related organisms and the ocean currents in this region (e.g. Taiwan Strait).

Other comments:

* L30, L103: COX1 and 16S ?

* L95: "The latter species": It's clear to use the species name here.

* L149: [51] is a study of freshwater crabs with only 16S and H3. I will suggest the authors check all the references and see if they are really relevant.

* L15-156: It is better to use species from the sister clades as outgroup. See "major comments #1".

* L160: Will suggest to use the newest version of MEGA.

* L173-174: Try to use formal citation and reference for "Microsoft Excel (2013)".

* L175: ARLEQUIN => ARLEQUIN 3.5; and delete "3.5" in L182.

* L184 and others: Japan is composed by several large and small islands, but could not be considered as "mainland"! Will suggest to use "main islands of Japan" instead.

* L194-196: It is confused that ".... (COX1) 16 sequences (including those from GenBank) with a length of 610 basepairs.....". Just say how many sequences you have from this study and how many sequences from GenBank. Rewrite this sentence.

* L229: It should be confused whether it is necessary to provide 2 haplotype networks of COX1? One single tree of COX1 should be enough to provide strong evidence of the 5 clades and their relationship.

* L325: If the authors did not run the test of rate constancy or similar tests, it is not adequate to say that the substitute rate is "a relatively precise time estimate", compared with the relaxed method (fossil data and other geological evidences" (L322-323).

* L346: "major East Asian island" => "major islands in eastern Asia", because the Philippines is not a part of "East Asia".

* L440: samples size => sample size

* L393: Provide citation for "melting pot".

* L425-428: For freshwater discharge in eastern Americas, I might suggest cite two relevant papers: (1) Thurman, C. L. , Hopkins, M. J., Brase, A. L. & Shih, H.-T. 2018. The unusual case of the widely distributed fiddler crab Minuca rapax (Smith, 1870) from the western Atlantic: an exemplary polytypic species. Invertebrate Systematics 32(6): 1465-1490. (2) Thurman, C. L, Alber, R. E., Hopkins, M. J. & Shih, H.-T. 2021. Morphological and genetic variation among populations of the fiddler crab Minuca burgersi (Holthuis, 1967) (Crustacea: Brachyura: Ocypodidae) from shores of the Caribbean Basin and western South Atlantic Ocean. Zoological Studies 60: 19.

* Fig. 1: It will be clear for readers to mark the names for the major localities on the map.

* Fig. 2: A separated BI tree with all the haplotype names is suggested to be included in supporting information (similar to S3 Figure for ML tree). "P. Sanguimanus" => "P. sanguimanus".

* S1 Table: Full names of museums for the abbreviation should be provided. In "size", all values in CW should be round to one decimal place. "14,47"=>"14.5". "Honlong" => "Houlong". BTW I found several haplotypes in S1 Table were not appeared in S3 figure! Need to check them carefully.

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Reviewer #2: No

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PONE-D-21-19346R1Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West PacificPLOS ONE

Dear Dr. Shahdadi,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Dear authors,

Most of the comments were addressed. But I noticed that in the references list of your MS, most of the author name Chan, BKK was mis-spelled as Chan BK. Please correct all the Chan BK into Chan BKK in the reference list.

Best wishes,

Benny

Please submit your revised manuscript by Dec 11 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Benny K.K. Chan, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

Dear authors,

Most of the comments were addressed. But I noticed that in the references list of your MS, most of the author name Chan, BKK was mis-spelled as Chan BK. Please correct all the Chan BK into Chan BKK in the reference list.

Best wishes,

Benny

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Reviewers' comments:

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Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific

PONE-D-21-19346R2

Dear Dr. Shahdadi,

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Benny K.K. Chan, Ph.D

Academic Editor

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