The Taxonomic Status of Genera within the Fabeae (Vicieae), with a Special Focus on Pisum

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The reviewed paper is a substantial contribution to the ongoing discussion on the taxonomy of the Fabeae. The problem (which is probably worth  emphasizing in the text even more) is that this group includes numerous species of exceptional value both as crops and model objects. Many of this tribe's genera have their names dating back to antiquity. Whereas numerous genera are being renamed, merged or split every year, any changes in this particular tribe would be exceptionally sensitive, not only for taxonomists but also for specialists in genetics, developmental biology and alike. This reasoning might probably be even more convincing when suggesting to retain as many generic names as possible.
I have no major concerns about this paper. Some minor corrections can be found in the manuscript file (see attached) and mostly refer to typos. This work is an interesting point to the lasting discussion in taxonomy.
I would recommend the authors to decide whether this paper needs traditional sections like 'Discussion'. It has no results and the part of the text preceding discussion contains a lot of discussion making it hardly separable from the subsequent part. Of course, it is a matter of taste.
This paper can be recommended for publication provided all necessary corrections are made. I wish the authors good luck.

Comments for author File: Comments.pdf

Author Response

1, Re: The reviewed paper is a substantial contribution to the ongoing discussion on the taxonomy of the Fabeae. The problem (which is probably worth emphasizing in the text even more) is that this group includes numerous species of exceptional value both as crops and model objects. Many of this tribe's genera have their names dating back to antiquity. Whereas numerous genera are being renamed, merged or split every year, any changes in this particular tribe would be exceptionally sensitive, not only for taxonomists but also for specialists in genetics, developmental biology and alike. This reasoning might probably be even more convincing when suggesting to retain as many generic names as possible.

We thank the reviewer for these comments. It is indeed the case that many species within this tribe have ancient names, and that there are several important crop species within this tribe. We want to keep the article focussed on the single issue of name changes which have been made and for which we provide evidence that these changes are, at least currently, unjustified.

For valid names in the current binomial system, it is names post dating Linnaeus that are relevant (1753); it is perhaps relevant that the proposed Lathyrus oleraceus in fact predates this constraint.

2, Re: I have no major concerns about this paper. Some minor corrections can be found in the manuscript file (see attached) and mostly refer to typos. This work is an interesting point to the lasting discussion in taxonomy.

These are helpful edits and we have made corrections and comments as detailed below.

3, Re: I would recommend the authors to decide whether this paper needs traditional sections like 'Discussion'. It has no results and the part of the text preceding discussion contains a lot of discussion making it hardly separable from the subsequent part. Of course, it is a matter of taste.

On balance we decided to leave this as it is, reflecting the change from the comments mainly on the phylogenetic data to a more general discussion.

4, Re: This paper can be recommended for publication provided all necessary corrections are made. I wish the authors good luck.

Again we thank the reviewer for their care and efforts to improve the manuscript.

5, Comments made on the text

Minor typographical errors are not discussed here, but are edited in the revised manuscript using track changes. We thank the reviewer for these corrections and apologise for the errors. Other issues are commented upon line by line. The revision of Figure 1, (replacing Ervilla with Ervilia) has been made without track changes.

Line 20 ‘but without any additional relevant information’ the reviewer reasonably asks ‘what sort of information is expected?’. Clearly some additional data on the distribution of sequence variants or character differences could change the basis on which taxa are grouped. Our point here is that there is no additional data whatsoever, there is no basis on which to make any conclusion which could not have been made in the Schaefer et al. (2012) publication. Schaefer et al. gave due consideration to their data and made a series of suggestions as to what implications this may have for the naming of these taxa. This was entirely reasonable and a sensible way to proceed. The jump to one of these possibilities in the absence of additional evidence has not been justified.

Line 37 ‘this structural rearrangement affects the evolutionary rate of plastid genes’ has been changed to ‘this structural rearrangement affects the rate of evolution of plastid genes’

Line 54 ‘three-genus scheme’ vs ‘three-genera scheme’. We think ‘three-genus scheme’ is correct, by analogy with ‘a two-horse race’ rather than ‘a two-horses race’. It is perplexing and clearly ‘a scheme with three genera’ would be correct.

Line 67 We agree that V. monantha is correct, and have changed the name accordingly; however Schaefer et al. used V. monanthos.

Line 95 The original reference for Pisum formosum from 1861, and this information is available in reference [9] so that citation has been added rather than the original name.

Lines 103 to 106 We agree that the sentence construction in the subjunctive is a little problematic. We have replaced:

‘On the other hand, were there two monophyletic lineages Lathyrus, as implied by the chronogram of Figure 1B, then, in that case, the choice would be whether to elevate one subgroup of Lathyrus to a new genus, or to combine Lathyrus with Pisum plus Vavilovia.’

 with:

‘On the other hand, if we accept that there are two monophyletic lineages, designated Lathyrus-1 and Lathyrus-1&2 in the chronogram of Figure 1B, then it would be possible either to elevate the smaller subgroup of Lathyrus to a new genus, or to combine Lathyrus with Pisum plus Vavilovia. The former option has four genera, and the latter has only one.’

 

In addition to these edits, we have added a paragraph concerning other relevant phylogenetic analyses which have appeared since Schaefer et al. (2012). These studies include fewer taxa than Schaefer et al., so are not really decisive concerning the main point of the manuscript, but they should be relevant to a reader. This also required the addition of several references.

We have focused attention on Schaefer et al. [8] because this is the most complete in terms of species sampling. Nevertheless additional studies have been published which are relevant to the issue of the taxonomic position of Pisum with respect to Lathyrus. Robledillo et al. [18] present a phylogeny, based on centromeric repeated sequences (which are unusual within Pisum and Lathyrus), which positions Pisum as basal to a monophyletic group which includes Lathyrus, but distinct from a monophyletic Vicia. Zhao et al. [19], based an analysis of 15,000 nuclear genes in the Fabaceae shows the same relationship. However, two plastid gene-based phylogenies [20, 21] place Pisum within a monophyletic Lathyrus clade. In these analyses the position of L. clymenum (and L. ochrus in [20]) is critical to the interpretation of the relationship of Pisum (and Vavilovia) to the remainder of Lathyrus but the support for a particular branching structure is low. The branching pattern of these phylogenies may depend on the species included or excluded from the analysis and also on whether the plastid or nuclear genome is being analyzed. Similarly, the nature of the nuclear DNA sequences may again have an impact reflecting patterns of gene duplication [19] or perhaps their function [18].

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

It is clear that molecular biology does not solve all the problems of systematics, we have seen this over the years, however, these methodologies have been refined. A good example is the LPWG, which has been gradually advancing in the search for the best classification of legumes and today shows us that in plant systematics nothing is set in stone, there have been drastic changes at the level of subfamilies, tribes, and genera. And there is no need to fear these changes, all in the interest of being able to better understand and classify living entities. This study of systematically repeats the advances and problems faced by the Fabeae tribe (Vicieae), non-monophyletic genera, to discern whether to group several genera into one or segregate genera even for taxonomic convenience (same case of the Mimosoideae Clade, today the Mimoseae tribe within the Caesalpinioideae subfamily). The authors provide an overview of the intricate relationships of genera and species within this tribe Fabeae, and consider that with current knowledge in phylogenetic analysis, there is no real evidence to warrant renaming some genera within this tribe such as Lens, Vavilovia and Pisum, perhaps in the future and when a new and deeper knowledge of this group of genera is available, this can be done. And this makes sense, we cannot unfoundedly segregate or unite genera into one without adequate scientific bases, although if we do so, we must take into account that these changes are synonymized in a short period of time or are not accepted by taxonomists. An excellent review by the authors, congratulations on your contribution.

Comments for author File: Comments.pdf

Author Response

1, Re: It is clear that molecular biology does not solve all the problems of systematics, we have seen this over the years, however, these methodologies have been refined. A good example is the LPWG, which has been gradually advancing in the search for the best classification of legumes and today shows us that in plant systematics nothing is set in stone, there have been drastic changes at the level of subfamilies, tribes, and genera.

We fully agree. Molecular analyses are very informative.

2, Re: And there is no need to fear these changes, all in the interest of being able to better understand and classify living entities. This study of systematically repeats the advances and problems faced by the Fabeae tribe (Vicieae), non-monophyletic genera, to discern whether to group several genera into one or segregate genera even for taxonomic convenience (same case of the Mimosoideae Clade, today the Mimoseae tribe within the Caesalpinioideae subfamily).

Indeed. Given the best information concerning a phylogeny there are two issues to be decided. The first is how to group organisms; at what level to divide organisms into different taxonomic levels; where divisions should be considered to separate different species vs subspecies or genera vs species. These are operational decisions that should both reflect the phylogenetic structure and also have utility to people interested in these relationships. The second issue is, given the groupings, what names are appropriate. To a large degree the second issue follows directly from the first, in conjunction with historical precedent. All that needs to be feared is inconsistency or confusion.

The point of the manuscript is that the grouping of taxonomic entities relevant to Pisum vs Lathyrus and Lens vs Vicia is not clear. It is not clear what decisions need to be made because the support for different groupings is not decisive. Given the data we have, there are different possible ways that the groupings could be made. A secondary issue is that, if indeed the taxonomic groupings that are consistent with the renaming of Pisum, Vavilovia and Lens are eventually established as being well supported, then there are several good alternative systems of nomenclature that should be considered.

The authors provide an overview of the intricate relationships of genera and species within this tribe Fabeae, and consider that with current knowledge in phylogenetic analysis, there is no real evidence to warrant renaming some genera within this tribe such as Lens, Vavilovia and Pisum, perhaps in the future and when a new and deeper knowledge of this group of genera is available, this can be done.

Precisely.

And this makes sense, we cannot unfoundedly segregate or unite genera into one without adequate scientific bases, although if we do so, we must take into account that these changes are synonymized in a short period of time or are not accepted by taxonomists. An excellent review by the authors, congratulations on your contribution.

We thank the reviewer for these comments.

Author Response File: Author Response.pdf