Larval Retention and Homing Behaviour Shape the Genetic Structure of the Bullet Tuna (Auxis rochei) in the Mediterranean Sea

Round 1

Reviewer 1 Report

Your research is very good and provides knowledge regarding current genetics. Some minor things may have to be added to your manuscript.

Comments for author File: Comments.pdf

Author Response

Dear Editor,

The majority of suggested changes were incorporated into the manuscript. Please see the attachment with the new version of the manuscript with the minor changes incorporated.

Specific responses to the reviewer's comments:

Comment [P1]: please see L24-26 in the new document

Comment [P2]: please see L39 in the new document

Comment [P3]: no changes made. Please note that information related to population structure in the Scombridae family is explained and referenced in the second paragraph of the present section. More information on this topic is explained and discussed in paragraphs 2 and 5 in the discussion section.

Comment[4]: Please see L129 in the new document

Comment[5]: Please see L113-115 in the new document

Comment [6]: please see L204 in the new document

Comment [7]: Please see L289-291 in the new document

Comment [8]: Please see L342-343 in the new document

Comment [9]: no changes made, please see L416 and below in the new document

Comment[10]: Please see L435-437 in the new document

Reviewer 2 Report

The manuscript titled “Larval retention and homing behaviour shape the genetic structure of the Bullet tuna (Auxis rochei) in the Mediterranean Sea” identified two genetically distinct populations of Bullet tuna (Auxis rochei) within the Mediterranean Sea using a mitochondrial and a set of nuclear markers. The manuscript is very well-written, the methodology is appropriate, and the discussion/conclusions are justified by the results. I recommend that the manuscript be published after editorial changes. Such as “Line 12 and others: scientific names should be italicized. “Bullet tuna (Auxis rochei) is an epipelagic fish with a worldwide distribution……”

Furthermore, in this study, authors used seven microsatellite loci as nuclear markers. The results showed an abundance of null alleles, which might affect some of the results in this study. However, the authors well discussed the point with appropriate justification. I would recommend the use of the Next Generation Sequencing (NGS) approach, such as RADseq or DArTseq (which uses complexity reduction methods) instead of microsatellite loci for future studies. This will reduce the speculation because of null alleles as well as might aid in the genetic differentiation hypothesis between Alger and Mahdia.

Author Response

Dear Editor,

All minor changes were incorporated into the manuscript.

Response to the reviewer:

Comment 1: all species names were italicized

Comment 2: A comment about the usage of the RadSeq methodology or similar was incorporated into the manuscript. Please see L449-452 in the new document.

Reviewer 3 Report

In this study, Judith and colleagues perform a classic population genetic investigation on Bullet tuna populations from 7 sites in the Mediterranean. The study investigated population structure, genetic diversity (pi, He, Ho etc.), population differentiation (Fst, AMOVA), IBD, HWD, etc. for the populations using mtDNA and seven nuclear microsatellite makers. The study resulted in a series of pop genetic matrices indicating that the bullet tuna within the western and central Mediterranean regions differentiated into two stocks: Peninsular-Strait of Gibraltar vs. North African. The study discussed these phylogeographic observations in a “biotic and abiotic factors” framework, concluding that, as entitled, larval retention and homing behavior shape the genetic structure (the observed genetic diversity distribution across the populations in 7 sites).

The population genomics approaches adopted are sound and well explained, and the interpretations are justified based on the results reported. A technical concern here is the low-density makers used (mtDNA + 7 microsatellite makers). However, large individual sample sizes (431 + 276) partially compensate for this flaw. The study did not involve highly complex analyses, such as selection scans, so high-density nuclear markers might not be critically needed.

Overall, this manuscript is of interest to researchers of Bullet tuna and conservation. The paper is well written and structured and worthy of contributing to Fishes.

There are nevertheless a major and a minor suggestions from my side:

1-   Tune down the confirmative statement about the reason behind the observed population structure in the title and abstract. The study did not directly provide ecological, e.g., life history, data and analyses, and just discussed the hypothesis in the final paragraph before the conclusion. So direct causal reasoning is hard to establish.

 Line 22: add “likely” before “caused by …”.

2-   Line: 148-149: expand the method to get the best fitting model. What program was used?

Author Response

Dear Editor,

The two comments were answered and modified int the new version of the manuscript.

Specific responses to the two commentaries:

Line 22: add “likely” before “caused by …” please see L22 in the new document

Line: 148-149: A clarification of the best-fitting model was incorporated. Please see L152 in the new document