Next Article in Journal
Asexual Reproduction and Strobilation of Sanderia malayensis (Scyphozoa, Pelagiidae) in Relation to Temperature: Experimental Evidence and Implications
Next Article in Special Issue
On the Systematics and Biodiversity of the Palaeoannelida
Previous Article in Journal
Occupancy of the American Three-Toed Woodpecker in a Heavily-Managed Boreal Forest of Eastern Canada
Previous Article in Special Issue
The Early Branching Group of Orbiniida Sensu Struck et al., 2015: Parergodrilidae and Orbiniidae
Review
Peer-Review Record

Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview

Diversity 2021, 13(2), 36; https://doi.org/10.3390/d13020036
Reviewer 1: Anonymous
Reviewer 2: Anonymous
Diversity 2021, 13(2), 36; https://doi.org/10.3390/d13020036
Received: 17 December 2020 / Revised: 14 January 2021 / Accepted: 18 January 2021 / Published: 20 January 2021
(This article belongs to the Special Issue Systematics and Diversity of Annelids)

Round 1

Reviewer 1 Report

In the last decade, there was an increase in the number of papers on molecular systematics of clitellates. To my opinion, the authors did a great job of summarizing the available data on species delimitation using molecular methods in this group. Of course, there are many more studies where cryptic diversity was found but systematic implications were not stated explicitly, but presumed. I think this paper deserves to be published its present form, and can only make a few minor remarks.

L43 "borrowing and interstitial habitats of most clitellates" - burrowing, I guess.
L108, 196, 197 - the names of genera and species should be in italics
L226 - delete "3.1. Subsection"

Author Response

Thank you for your comment and suggestions. We have implemented all the changes suggested be the reviewer.

Reviewer 2 Report

Overall this manuscript has been well written although for a review paper it's actually quite short; reads more like a mini-review than an actual review. To make the article more informative and detail I think the authors should provide a table showing every study where cryptic speciation among clitellates have been resolved by molecular methods from the earliest publication date to the latest. It doesn't have to be a complex table but rather it will give readers and those interested in pursuing this line of research a visual what's been done.

I have a few other comments and suggestions for this manuscript:

Line 34: Sedentaria is a subclass of the polychaetes and should be referred to as such. The term taxon as it is used here is  awkward

Line 88: The authors discuss older methods such as protein gel electrophoresis and non-sequencing DNA methods but do not provide the success rate of these methods. Were they successful at species delimitation of clitellates? Were there any limitations that caused clitellate research to explore other molecular avenues?

Line 134 – A distinct monophyletic group cannot be interpreted as a species; it can be called a novel operational taxonomic unit (OTU) or an evolutionary significant unit (ESU) but a species is an evolutionarily dynamic lineage that has to have taxonomical information that lines up with the genetic data.

Line 144 – The authors should discuss the ‘barcode gap’ before delving into ABGD as it is an important issue in DNA barcoding.

Line 183 – Has there been any whole genome phylogenomic work on clitellates yet? Not reduced representation like rad-seq but full genomic studies?

Line 194 – There are different types of RAD-Seq analyses that can be utilized for DNA barcoding for e.g. 'regular' RAD-seq which I believe is what the authors are referring to here but there is also ddRAD, and a number of others. The authors should expand on those other types of RAD-Seq techniques here, and which ones have been used for which studies on clitellates.

Line 223 – The term ‘good’ to describe morphological description is very vague here and I’m not exactly sure what the authors mean. Once a cryptic complex has been untangled, the various species must possess certain taxonomically informative traits that allows for proper diagnosis (see comment above) before they can be separated and given an official name. 

Line 227 – DNA barcoding is largely dependent on the reliability of the reference databases such as GenBank and BoLD. Ideally a voucher linked sequence is the best type of sequence to use in delimitation analysis. However there are many studies where a voucher cannot be linked to a sequence or the species was inaccurately identified by a non-specialist and the sequence deposited under the species’ nominal name. This occurs quite a lot with polychaetes so I wonder, - is this an issue for Clitellates also?

 

Author Response

Overall this manuscript has been well written although for a review paper it's actually quite short; reads more like a mini-review than an actual review. To make the article more informative and detail I think the authors should provide a table showing every study where cryptic speciation among clitellates have been resolved by molecular methods from the earliest publication date to the latest. It doesn't have to be a complex table but rather it will give readers and those interested in pursuing this line of research a visual what's been done.

We have added such a table as a supplementary table-

 

I have a few other comments and suggestions for this manuscript:

Line 34: Sedentaria is a subclass of the polychaetes and should be referred to as such. The term taxon as it is used here is  awkward

We have changed taxon to “subclass”, to indicate that this is also awkward, considering that Clitellata (or Oligochaeta) traditionally have been given class (or subclass) rank.

 

Line 88: The authors discuss older methods such as protein gel electrophoresis and non-sequencing DNA methods but do not provide the success rate of these methods. Were they successful at species delimitation of clitellates? Were there any limitations that caused clitellate research to explore other molecular avenues?

It is hard to give a success rate, but in general these methods seem to work quite well, and in the cases where the same groups have been studied with other methods the result has been similar. We have added this to the end of the section about protein gel electrophoresis

Line 134 – A distinct monophyletic group cannot be interpreted as a species; it can be called a novel operational taxonomic unit (OTU) or an evolutionary significant unit (ESU) but a species is an evolutionarily dynamic lineage that has to have taxonomical information that lines up with the genetic data.

In many cases that is what is done. I see what you are saying, but in practice distinct lineages are often being interpreted as separate species, or as potential species or OUT etc. depending on the authors. We have changed it to “potential species”

 

Line 144 – The authors should discuss the ‘barcode gap’ before delving into ABGD as it is an important issue in DNA barcoding.

We have added a short section about barcoding gap on L 134-136

 

Line 183 – Has there been any whole genome phylogenomic work on clitellates yet? Not reduced representation like rad-seq but full genomic studies?

No, the closest is trancriptomes, we have added a short short section about whole genome sequencing.

 

Line 194 – There are different types of RAD-Seq analyses that can be utilized for DNA barcoding for e.g. 'regular' RAD-seq which I believe is what the authors are referring to here but there is also ddRAD, and a number of others. The authors should expand on those other types of RAD-Seq techniques here, and which ones have been used for which studies on clitellates.

Good point, there are actually two different RAD-seq variants used (standard and ddRAD), and we have re-written the section to reflect this.

 

Line 223 – The term ‘good’ to describe morphological description is very vague here and I’m not exactly sure what the authors mean. Once a cryptic complex has been untangled, the various species must possess certain taxonomically informative traits that allows for proper diagnosis (see comment above) before they can be separated and given an official name.

We have added a short explanation in the text, with “good” we mean following the standard within the specific group and including all the characters used for separating species. Even if there are no distinguishing morphological characters found, we still think that species can by given official names, if genetic evidence strongly supports speciation, but it is still important to show in detail to what extent there is morphological variation within and between the species.

 

Line 227 – DNA barcoding is largely dependent on the reliability of the reference databases such as GenBank and BoLD. Ideally a voucher linked sequence is the best type of sequence to use in delimitation analysis. However there are many studies where a voucher cannot be linked to a sequence or the species was inaccurately identified by a non-specialist and the sequence deposited under the species’ nominal name. This occurs quite a lot with polychaetes so I wonder, - is this an issue for Clitellates also?

It is a problem when using publicly available data. Misidentifications are common, and we agree that it is important to store vouchers from the specimens studied so that it is possible to check the identifications in the future. We have added a few lines about this in the text.

 

Back to TopTop