Disentangling the Genetic Relationships of Three Closely Related Bandicoot Species across Southern and Western Australia
, Esther Levy 1, You Li 2, Steven J. B. Cooper 3,4, Margaret Byrne 1 and Kym Ottewell 1,*Round 1
Reviewer 1 Report
Thavornkanlapachai et al. show with a comprehensive genetic data set the genetic relationshiops of three related bandicoot species.
They add samples from Western Australia to existing samples and data sets and give new insights in the genetic relationship among the bandicoot species together with suggestions of conservation units. Analysis, results and discussion are clearly presented.
I do have only very few minor comments.
line 312: Add that also Victorian samples need to be removed to resolve structuring within WA.
line 364/365: Possible reasons for the high Fis values should be mentioned somewhere. Either shortly in the results part or in the discussion. Maybe samples within a site are coming likely from different populations and therefore the high Fis values are a consequence from the Wahlund-effect or non-random mating is a common behaviour in bandicoots?
Author Response
Reviewer #1:
Thavornkanlapachai et al. show with a comprehensive genetic data set the genetic relationships of three related bandicoot species.
They add samples from Western Australia to existing samples and data sets and give new insights in the genetic relationship among the bandicoot species together with suggestions of conservation units. Analysis, results and discussion are clearly presented.
I do have only very few minor comments.
line 312: Add that also Victorian samples need to be removed to resolve structuring within WA.
Response – The notation that Victorian samples were removed in hierarchical Structure analysis was mentioned in the previous paragraph. To avoid confusion, we moved the paragraph containing line 312 up so both paragraphs are adjacent to each other (see line 314).
line 364/365: Possible reasons for the high Fis values should be mentioned somewhere. Either shortly in the results part or in the discussion. Maybe samples within a site are coming likely from different populations and therefore the high Fis values are a consequence from the Wahlund-effect or non-random mating is a common behaviour in bandicoots?
Response – We agree that a Wahlund effect may explain the high FIS values. The suggestion of Wahlund effect has been added to the result section (line 380). Isoodon bandicoots have polygynandrous mating system, both male and female mate with multiple partners. If high FIS value is a result of non-random mating, it is less likely to be the result of their mating behaviours.
Reviewer 2 Report
The manuscript “Disentangling the genetic relationships of three closely-related bandicoot species across southern and western Australia” by Thavornkanlapachai et al. examines the phylotaxonomy of Australian Isoodon bandicoots. The main purpose of the work described in the article is to study the source of the discordance of phylogeographic units with current 18 taxonomic boundaries and is an attempt to generate data that better explains what is being observed there. The authors hope to use this data for to aid in future conservation management activities.
The paper in general addresses an essential issue for an interesting and important fauna species. It is well written in clear, concise English, and I found few problems with the paper itself in terms of style and clarity. The data was presented in a clear manner that is standard for phylotaxonomic analyses and the methodology employed is pretty standard as well. Although well written, I had a few issues with the paper which are listed below:
-(35-110) Because not all readers of Diversity will be familiar with bandicoots, I do not believe that the Introduction goes far enough in justifying the importance of the bandicoot species in terms of Australian ecology and ecology in general.
-(112-127) How did you sample the individuals for DNA extraction. You never state that explicitly. Tail clips? Ear clips? Buccal swabs?
-(113-154) I was very confused by the markers that were used and how they were generated. It was clear that the D-Loop sequences were amplified and then sequenced, compared, and analyzed. It was not clear how the data from the microsatellites was generated. Were they sequenced also? Please clarify specifically how each type of marker was dealt with.
-(156-213) Generally microsatellite data is analyzed by employing the number of repeats observed between different between phylogenetic groups. For genetic analysis did you use the sequence data itself or the length of repeat polymorphisms? Again, please clarify.
-(156-213) If you used the mixed data of repeat length vs. DNA sequence, then explain how these two types of data were combined to generate results.
Author Response
Reviewer #2:
The manuscript “Disentangling the genetic relationships of three closely-related bandicoot species across southern and western Australia” by Thavornkanlapachai et al. examines the phylotaxonomy of Australian Isoodon bandicoots. The main purpose of the work described in the article is to study the source of the discordance of phylogeographic units with current 18 taxonomic boundaries and is an attempt to generate data that better explains what is being observed there. The authors hope to use this data for to aid in future conservation management activities.
The paper in general addresses an essential issue for an interesting and important fauna species. It is well written in clear, concise English, and I found few problems with the paper itself in terms of style and clarity. The data was presented in a clear manner that is standard for phylotaxonomic analyses and the methodology employed is pretty standard as well. Although well written, I had a few issues with the paper which are listed below:
(35-110) Because not all readers of Diversity will be familiar with bandicoots, I do not believe that the Introduction goes far enough in justifying the importance of the bandicoot species in terms of Australian ecology and ecology in general.
Response – We have added an extra paragraph stating species’ biology, ecology and its importance to Australian ecology to the introduction section (line 64-73).
(112-127) How did you sample the individuals for DNA extraction. You never state that explicitly. Tail clips? Ear clips? Buccal swabs?
Response – We have included ear biopsies collection in line 130.
(113-154) I was very confused by the markers that were used and how they were generated. It was clear that the D-Loop sequences were amplified and then sequenced, compared, and analyzed. It was not clear how the data from the microsatellites was generated. Were they sequenced also? Please clarify specifically how each type of marker was dealt with.
Response – DNA extraction and microsatellite genotyping were conducted as described in Ottewell et al. [26]. However, we added a short description on how microsatellites were amplified and genotyped as suggested (line 132-136).
(156-213) Generally microsatellite data is analyzed by employing the number of repeats observed between different between phylogenetic groups. For genetic analysis did you use the sequence data itself or the length of repeat polymorphisms? Again, please clarify.
Response – We did indeed use the length of repeat polymorphisms. This information on how this data was generated has been included in line 132-136.
(156-213) If you used the mixed data of repeat length vs. DNA sequence, then explain how these two types of data were combined to generate results.
Response – For microsatellite data, we used repeat length polymorphisms of 10 loci. For mtDNA, we sequenced the D-loop region. We analysed microsatellites and mtDNA sequences separately. We added which data type/s were used in which analyses throughout the method section for additional clarification.
