Genetic Variation among Rare Florida Endemic Hymenocallis henryae Populations and the Implication for Conservation and Management
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe manuscript, “Genetic variation among rare Florida endemic Hymenocallis henryae populations and the implications for conservation and management,” is well written. Overall, this study has important implications for the conservation of Hymenocallis henryae. However, the following points need to be addressed before publication:
1. This study employs a robust methodology using genomic techniques (SNP analysis) to assess the genetic diversity and population structure of Hymenocallis henryae. The sampling approach, which covers multiple populations across the species' range, is commendable. However, some clarification is needed on the rationale for selecting certain sampling sites and sample sizes.
2. The authors have conducted appropriate population genetic analyses, including heterozygosity estimates, FST calculations, PCA, and ancestry analysis. The use of multiple analytical approaches strengthens the findings. However, it would be beneficial to include more details on the parameters used for some analyses (e.g., sNMF).
3. The results are well described with clear tables and figures. Table 1 provides a comprehensive overview of population statistics. However, Figure 3 (PCA plot) is mentioned but not included in the provided text, which makes it difficult to evaluate the results fully.
4. The manuscript is generally well-written, but some areas could benefit from improved clarity and organization. For example, the methods section jumps between field sampling, lab work, and data analysis in a way that can be confusing to follow.
5. Technical issues: There are some minor formatting issues, such as inconsistent spacing and numbering. Additionally, some acronyms (e.g., ANF, THSF) are used before being defined.
6. The authors mention that they are in the process of uploading data to Dryad. To ensure data accessibility, it would be beneficial to complete this before final publication.
Author Response
July 29, 2024
Dear Reviewer, Thank you very much for taking the time to review this manuscript. Please find the detailed responses below.
Comment 1. This study employs a robust methodology using genomic techniques (SNP analysis) to assess the genetic diversity and population structure of Hymenocallis henryae. The sampling approach, which covers multiple populations across the species' range, is commendable. However, some clarification is needed on the rationale for selecting certain sampling sites and sample sizes.
Response: The rationale for site selection was based on permit and site accessibility. We added clarification in line 118-119: 'Populations visited were chosen based on accessibility and permit availability and represented the extent of the known species distribution.'
Comment 2. The authors have conducted appropriate population genetic analyses, including heterozygosity estimates, FST calculations, PCA, and ancestry analysis. The use of multiple analytical approaches strengthens the findings. However, it would be beneficial to include more details on the parameters used for some analyses (e.g., sNMF).
Response 2: Additional information about parameters is added to line 260. 'The optimal number of ancestral populations (K) was chosen as the lowest cross-entropy value out of 10 K values tested.'
Comment 3. The results are well described with clear tables and figures. Table 1 provides a comprehensive overview of population statistics. However, Figure 3 (PCA plot) is mentioned but not included in the provided text, which makes it difficult to evaluate the results fully.
Response: Figure 3 is included in the results and submitted manuscript. It is possible the formatting was causing visibility issues. We have resolved this problem.
Comment 4. The manuscript is generally well-written, but some areas could benefit from improved clarity and organization. For example, the methods section jumps between field sampling, lab work, and data analysis in a way that can be confusing to follow.
Response: The flow of the methods section is parallel to the results section. We added section headers to indicate transitions between methods.
Comment 5. Technical issues: There are some minor formatting issues, such as inconsistent spacing and numbering. Additionally, some acronyms (e.g., ANF, THSF) are used before being defined.
Response : Some of the inconsistency in spacing may be due to the full justification of the text (i.e. flush borders) that is part of the template. This formatting can sometimes introduce inconsistent spacing. That being said, we did our best to address spacing and numbering. Location acronyms are presented in the Methods section when first mentioned; see lines 93-96. [This area included publicly managed lands (Apalachicola National Forest [ANF], Tate's Hell State Forest [THSF], Tyndall Air Force Base [Tyndall], and Eglin Air Force Base [EAFB]), privately managed land (Nokuse Plantation [NP], Apalachicola River Wildlife Environmental Area [ARWEA], St. Joseph's State Buffer Preserve [SJSBP]), and public unmanaged land (Panama City [PC], and Walton; Table 1)]
Comment 6. The authors mention that they are in the process of uploading data to Dryad. To ensure data accessibility, it would be beneficial to complete this before final publication.
Response: Files are currently being uploaded to Dryad. This will be complete before final publication. Dryad link: https://doi.org/10.5061/dryad.m63xsj4bb
Reviewer 2 Report
Comments and Suggestions for AuthorsHymenocallis henryae is a rare, charismatic spider-lily endemic to the Florida panhandle. The authors provide new information on its genetic diversity from studies of 19 extant populations, important for its conservation and registration as endangered species. Low genetic diversity limits its adaptive response to threats (habitat change, residential development, fire suppression) and several coastal populations were identified as threatened by sea level rise. This interesting paper is worthy of publication. A few comments are listed below:
L. 83 historical collections: were the type localities of the species included in the surveys? Or were they extirpated?
L.113 FNAI: acronym not listed in full for its first mention in text
Introduction: Mention the number of Hymenocallis species in the Florida panhandle, if there are closely related species and the number which are formally considered threatened.
Map: in the circles inset ARWEA includes ARWEA1 and ARWEA2? Can the Apalachiola river be shown on map? TYNDALL AFB includes 1, 2 and 3?
Table 1 at NP1 n.a.1 change for n.a.2 as stated at bottom of table.
Author Response
July 29, 2024
Dear Reviewer, Thank you very much for taking the time to review this manuscript. Please find the detailed responses below:
Comment 1. L. 83 historical collections: were the type localities of the species included in the surveys? Or were they extirpated?
Response 1: We determined that the populations in Walton Co. correspond to the historical area from which the regional type specimen was collected by Mary G. Henry. Unfortunately, we cannot determine if our sites correspond specifically to the site of the type specimen because no GPS coordinates are available for the type specimen (which was collected in 1962; https://www.tropicos.org/specimen/1784859). We added a sentence in the Methods line 97-98. 'Walton sites represent the location where the type specimens were collected in 1962 [10, 25]'
Comment 2. L.113 FNAI: acronym not listed in full for its first mention in text
Response 2: We added this acronym., line 116.
Comment 3. Introduction: Mention the number of Hymenocallis species in the Florida panhandle, if there are closely related species and the number which are formally considered threatened.
Response 3: These 2 sentences were added to the introduction, lines 68-71.
“The New World genus Hymenocallis includes about 50 species, of which 13 are found in Florida and four of them are endemic to the Florida panhandle [15], one of the five richest biodiversity hotspots in North America [16- 18]. Two of the endemic species, H. godfreyi and H. henryae, are state listed as endangered .
Comment 4. Map: in the circles inset ARWEA includes ARWEA1 and ARWEA2? Can the Apalachiola river be shown on map? TYNDALL AFB includes 1, 2 and 3?
Response 4: I added the Apalachicola river to the map (blue) and changed the names of the insets to be more specific.
Comment 5. Table 1 at NP1 n.a.1 change for n.a.2 as stated at bottom of table.
Response 5: Edit accepted.
