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形態測量學,分子演化與生物資訊的結合 -- Studying the phylogeny of freshwater eels PowerPoint Presentation
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形態測量學,分子演化與生物資訊的結合 -- Studying the phylogeny of freshwater eels. 交通大學 生物資訊所 林 勇 欣. The genus Anguilla. Ege (1939) Dana Report. Ege (1939) Dana Report. Ege (1939) Dana Report. I. II. III. IV. Ege (1939) Dana Report. NJ tree. I. I. II. II. IV. IV. IV. II. I. I. II.

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形態測量學,分子演化與生物資訊的結合

-- Studying the phylogeny of freshwater eels

交通大學 生物資訊所

林 勇 欣

slide8

I

II

III

IV

Ege (1939) Dana Report

slide9

NJ tree

I

I

II

II

IV

IV

IV

II

I

I

II

ML tree

III

III

III

III

III

III

IV

IV

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25.9

30.1

30.2

27.3

25.8

29.0

28.2

29.7

26.9

30.3

28.2

27.0

29.0

27.0

27.0

27.0

27.2

Tree length = 17

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27.0

27.0

25.8

28.2

27.3

27.0

28.2

27.2

25.9

29.7

26.9

27.0

29.0

30.2

30.1

29.0

30.3

30.3

Tree length = 14.7

27.3

27.3

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Coding the original shape data as discrete values based on some criterion and treating them as input data for cladistic parsimony analyses (e.g. Fink & Zelditch, 1995) was questioned in several aspects (Rohlf, 1998; Adams & Rosenberg, 1998).

An alternative approach is to use phylogenetic methods that can utilize morphometric data in its original form rather than forcing them into integer codes (Rohlf, 2002).

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27.0

27.0

25.8

28.2

27.3

27.0

28.2

27.2

25.9

29.7

26.9

27.0

29.0

30.2

30.1

29.0

30.3

30.3

Tree length = 14.7

slide16

A: [0,3,0]

A

O: [?,?,?]

A

2.35

C: [4,0,0]

3.39

B: [0,0,0]

C

1.02

B

C

B

A: [0,3,0]

A

2

5

3

3

C

1

B

C: [4,0,0]

B: [0,0,0]

4

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I

I

II

II

IV

IV

IV

II

I

I

II

III

III

III

III

III

III

IV

IV

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Journal of Evolutionary Biology

Reviewer 1:

Most importantly, there are several serious issues with the quality of the data. The molecular phylogeny presented in Fig. 2 designates four groupings that are defined based on the molecular data (A-D). However the nodes supporting these grouping are not well supported by bootstrap support at all - three are below 50% and one is only 55%. I would have stoped the study right here, since all further conclusions and analyses are highly suspect since they are based on extremely weak initial support for the molecular phylogeny.

Moreover, the regression analyses of the Ege morphological traits does not take any phylogenetic history into consideration and ignores 10 years of work on the "comparative method".

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Journal of Evolutionary Biology

Editor:

Thank you very much for the clarification. I agree that reviewer could have been more clearer in his comments, and you are quite correct that his views can be contested. However, at this stage, the file of ms 000195 has been closed, and I am not in position of changing my earlier decision.

However, given the high level of expertise of the reviewer, the misunderstanding here is most likely stemming from the way you have presented your case. If you feel that you can improve the presentation and that the criticism of the reviewer ifs unjustified, I will allow you to resubmit your work to JEB. However, if you decide to do this, please make sure that you are crystal clear in the points where you think the referee has misunderstood you. You may suggest potential reviewers if you resubmit (the ms will be treated as a new submission.

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Journal of Evolutionary Biology – second submission

Reviewer 1:

This is a detail rich paper with no major flaws in the analysis or interpretation of the data. It is nice and re-assuring that the morphometric phylogeny of eels is now consistent with molecular data. However, this does not advance our knowledge on the phylogeny of eels substantially because a molecular phylogeny should always be preferred over morphological analyses if there is doubt. Therefore, I see the scope of the paper as too limited for a journal that covers important questions of general evolutionary biology such as JEB.

slide25

Journal of Evolutionary Biology – second submission

Reviewer 2:

There are major problems with the writing of the paper. Authors should first consult a native English speaker with a good background in phylogenetics. With his/her help, the entire manuscript should be rewritten so that in each sentence it is entirely clear what the authors intend to say. As it stands now, so much of the writing is either unclear or plainly wrong that I will not take the time to try and correct everything with reference to a pdf. Here are some examples:

p.2., l.14: "approach should be extremely useful" - for what purpose?

p.3,l.21-22: what do you mean by "p values less than 0.001"? - Does this mean topologies differed significantly? Why not say so?

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Journal of Evolutionary Biology – second submission

Reviewer 2:

p.4,l.1: do you mean "none of the 4 groups proposed by Ege is monophyletic" or do you mean " not all of the 4 groups are monophyletic?“

p.4,l.4/6: what are "two different groups species"? Two species belonging to different groups?

In general: if you use "significantly" as an adverb, place it directly after the verb!

p.10,l.9: replace "topology" by "position" (a single species can show no topology)

p.10, l.21: "loses very less information" - makes no sense. Same in line 7, p.11.

slide27

Journal of Evolutionary Biology – second submission

Reviewer 2:

p.12,l.14-22: paragraph is impossible to follow without a drawing to illustrate the character in question

p.13,l.4: "group b,e & f consist of ..." - delete "both" (you are listing three!)

p.14,l.12: replace "sequentially" by "consequently“

p.15, l.2: morphological characters were employed or used for phylogenetic reconstruction (not "applied")

p.15,l.14: "both have similar agreement" - replace by "show good agreement”

slide28

Journal of Evolutionary Biology – second submission

Editor:

Although I think your that you have clarified your presentation so as that the misunderstading that surfaced during the previous round of refereeing is not anymore present, both reviews were quite critical about your paper. Both of the referees meant that the language would require considerable attention beyond any editorial copy editing. Also, the other referee expressed a view that although interesting, the paper might be better suited for some more taxonomically orientated journal. Given the two negative referee reports, this means that I cannot accept this paper for publication in the Journal of Evolutionary Biology.

slide29

Zoologica Scripta

Reviewer 2:

1. This attempt to make phylogeny using morphological characters is new. However, I doubted that the characters of genus Anguilla can be used for this method, because there were two molecular phylogeny (Lin et al. 2001a; Aoyama et al. 2001) with different results. I think that you should apply other fish groups which were clearly estimated by molecular phylogeny trees to these method rather than genus Anguilla.

5. It is necessary to discuss evolution of morphological characters of

freshwater eel. Because this paper discussed only congruence between morphological and molecular phylogeny trees estimated by yourself.

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致謝

清華大學 曾晴賢

繁玉萍

鄧惠瑜

交通大學黃鎮剛

楊進木

臺灣師範大學林思民

中山大學顏聖紘