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Two species of Southeast Asian cats in the genus
Catopuma with diverging histories: an island endemic forest
specialist and a widespread habitat generalist
Riddhi P. Patel, Daniel W. Förster, Andrew C. Kitchener, Mark D. Rayan, Shariff W.
Mohamed, Laura Werner, Dorina Lenz, Hans Pfestorf, Stephanie Kramer-Schadt, Viktoriia
Radchuk, Jörns Fickel and Andreas Wilting
Article citation details
R. Soc. open sci. 3: 160350.
http://dx.doi.org/10.1098/rsos.160350
Review timeline
Original submission:
Revised submission:
Final acceptance:
24 May 2016
12 September 2016
13 September 2016
Note: Reports are unedited and appear as
submitted by the referee. The review history
appears in chronological order.
Review History
RSOS-160350.R0 (Original submission)
Review form: Reviewer 1
Is the manuscript scientifically sound in its present form?
Yes
Are the interpretations and conclusions justified by the results?
Yes
Is the language acceptable?
Yes
Is it clear how to access all supporting data?
Accession numbers for some mtDNA genome sequences are still required (Bay cat).
© 2016 The Authors. Published by the Royal Society under the terms of the Creative Commons
Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use,
provided the original author and source are credited
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2
Do you have any ethical concerns with this paper?
No
Have you any concerns about statistical analyses in this paper?
No
Recommendation?
Accept with minor revision (please list in comments)
Comments to the Author(s)
Review:
This paper combines extensive molecular and morphological datasets for the Asian golden cat
with smaller but comparative datasets for the Bornean bay cat in order to review the evolutionary
history of these taxa at both inter- and intra-specific levels.
The analyses conducted are appropriate and comprehensive, resulting in a convincing pattern of
molecular and morphological variation throughout the Asian golden cat distribution, as well as
insights into the variation of bay cats.
The molecular data in particular represents a significant amount of work in the generation and
analysis of whole mtDNA genomes form multiple archived samples.
The paper is very well constructed, easy to understand and the standard of English is high
throughout, although some grammatical/usage errors are present.
The paper will be of interest to a broad range of scientists working on felids, Southeast Asian
biogeography and evolutionary reconstruction. It is also a potentially important contribution to
the conservation management of the focal species. I would therefore be happy to recommend the
paper for submission once the authors have had the opportunity to consider and address my
remarks below.
Major comment
The pelage results for the bay cat are interesting as, following the authors’ argument for the Asian
golden cat, the results do seem to suggest that the bay cat was exposed to / adapted to multiple
environmental conditions. However the authors’ state throughout that the bay cat is an evergreen
forest specialist and hence was less able to adapt to environmental change. If pelage variation
does imply selection for different habitat types, then the implication is that the bay cat may not
have been restricted to the tropical evergreen habitat postulated in the distribution analysis.
Which in turn has implications for the hypothesized speciation event and the overall narrative
regarding restricted bay cat distribution during the LGM.
Can the authors please provide some comment or explanation to this point as there appears to be
some contradiction between the data and its interpretation in the two species.
Minors comments
Abstract
Line 23 ‘…between the two species of ~3.16 M…’
Introduction
It would be useful to define what constitutes the ‘Sunda Shelf’
Downloaded from http://rsos.royalsocietypublishing.org/ on June 17, 2017
3
P3L15
delete ‘Here,’
P4 L24
Is there a reference for the size difference observations?
P4 L37
‘In the current study…’
P6 L44
P6 L46
P6 L51
haplotype (singular)
patterns (plural)
‘…as these are poorly…’
P8 L33
multi-co-linearity
P9 L31 What percentage of bases were replaced with N’s due to depth < 5X?
P9 L47 The results of a haplotype network are discussed but the method is not described in the
earlier section. Please add a brief description to the Methods.
Figure 3 Please explain branch colouration in legend.
P12 L46 ‘…likely took…’
P13 L2 …these ‘potential early arriving’ Asian…
P13 L51 …’colonizations’…
P14 L4 …’relative to their Sundaic…’
P14 L1-6
The statement regarding selection as the definite reason for less pelage variation
in the southern range is probably a little strong. Founder effects could also account for some of
this pattern. I would suggest “…may be the result of selection…”, particularly given the results
for the bay cat pelage (many morphs, one habitat type – see above)
P15 L56 ‘habitats were confined…’
Review form: Reviewer 2 (Thomas von Rintelen)
Is the manuscript scientifically sound in its present form?
Yes
Are the interpretations and conclusions justified by the results?
Yes
Is the language acceptable?
Yes
Is it clear how to access all supporting data?
Supplementary material adequate and clear.
Do you have any ethical concerns with this paper?
No
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4
Have you any concerns about statistical analyses in this paper?
No
Recommendation?
Accept with minor revision (please list in comments)
Comments to the Author(s)
The conclusions of the paper seem generally well justified. I cannot follow the argumentation of
the authors regarding "multiple colonization events on Sumatra". There are two clear-cut clades,
one containing all Sumatran samples plus the one from Peninsular Malaysia, and I fail to see how
this can provide evidence for multiple colonization events of Sumatra since the Toba eruption.
The evidence of the "tree-like pattern of Sumatran samples in the haplotype network" is at best
circumstantial. In a similar vein, "the sample from Peninsular Malaysia, which is genetically
positioned between samples from Mainland Indochina and those from Sumatra", is the basalmost branch in the Sumatra clade, which is consistent with a colonization of Sumatra from the
North, but in the absence of more samples from Malaysia this is all that can be said about this, I
believe. I would urge the authors to rephrase these two section of the discussion and back down a
bit on the "multiple colonization" scenario. One minor issue here: I do not see the point of midpoint rooting - please root the tree in Fig 3 using the bay cat as outgroup. And how can a single
tree be reconstructed using both ML and BI, as the caption implies? Finally, one last minor point:
when referring to museum samples (Fig. S2), please cite them using the full museum accession
numbers including the institutional acronym, not just part of the number calling it "specimen ID"
- this should read, e.g., ZMB Mam. 91060...
Decision letter (RSOS-160350)
02-Sep-2016
Dear Mrs Patel
On behalf of the Editors, I am pleased to inform you that your Manuscript RSOS-160350 entitled
"Two species of the genus Catopuma with diverging histories: An island endemic forest
specialist and a wide-spread habitat generalist." has been accepted for publication in Royal
Society Open Science subject to minor revision in accordance with the referee suggestions. Please
find the referees' comments at the end of this email.
The reviewers and handling editors have recommended publication, but also suggest some minor
revisions to your manuscript. Therefore, I invite you to respond to the comments and revise your
manuscript.
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• Data accessibility
It is a condition of publication that all supporting data are made available either as
supplementary information or preferably in a suitable permanent repository. The data
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5
accessibility section should state where the article's supporting data can be accessed. This section
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critically for important intellectual content; and 3) final approval of the version to be published.
All contributors who do not meet all of these criteria should be included in the
acknowledgements.
We suggest the following format:
AB carried out the molecular lab work, participated in data analysis, carried out sequence
alignments, participated in the design of the study and drafted the manuscript; CD carried out
the statistical analyses; EF collected field data; GH conceived of the study, designed the study,
coordinated the study and helped draft the manuscript. All authors gave final approval for
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6
processing of the revised manuscript, please be as specific as possible in your response to the
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Kind regards,
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[email protected]
on behalf of Kevin Padian
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[email protected]
Associate Editor Comments to Author:
Associate Editor: 1
Comments to the Author:
Two reviewers have examined your paper and although they find it interesting and the
conclusions are generally justified there are some fairly substantial 'minors' that you will need to
address in your revision for it to be accepted. Please outline your responses in detail.
Reviewer comments to Author:
Reviewer: 1
Comments to the Author(s)
Review:
This paper combines extensive molecular and morphological datasets for the Asian golden cat
with smaller but comparative datasets for the Bornean bay cat in order to review the evolutionary
history of these taxa at both inter- and intra-specific levels.
Downloaded from http://rsos.royalsocietypublishing.org/ on June 17, 2017
7
The analyses conducted are appropriate and comprehensive, resulting in a convincing pattern of
molecular and morphological variation throughout the Asian golden cat distribution, as well as
insights into the variation of bay cats.
The molecular data in particular represents a significant amount of work in the generation and
analysis of whole mtDNA genomes form multiple archived samples.
The paper is very well constructed, easy to understand and the standard of English is high
throughout, although some grammatical/usage errors are present.
The paper will be of interest to a broad range of scientists working on felids, Southeast Asian
biogeography and evolutionary reconstruction. It is also a potentially important contribution to
the conservation management of the focal species. I would therefore be happy to recommend the
paper for submission once the authors have had the opportunity to consider and address my
remarks below.
Major comment
The pelage results for the bay cat are interesting as, following the authors’ argument for the Asian
golden cat, the results do seem to suggest that the bay cat was exposed to / adapted to multiple
environmental conditions. However the authors’ state throughout that the bay cat is an evergreen
forest specialist and hence was less able to adapt to environmental change. If pelage variation
does imply selection for different habitat types, then the implication is that the bay cat may not
have been restricted to the tropical evergreen habitat postulated in the distribution analysis.
Which in turn has implications for the hypothesized speciation event and the overall narrative
regarding restricted bay cat distribution during the LGM.
Can the authors please provide some comment or explanation to this point as there appears to be
some contradiction between the data and its interpretation in the two species.
Minors comments
Abstract
Line 23 ‘…between the two species of ~3.16 M…’
Introduction
It would be useful to define what constitutes the ‘Sunda Shelf’
P3L15
delete ‘Here,’
P4 L24
Is there a reference for the size difference observations?
P4 L37
‘In the current study…’
P6 L44
P6 L46
P6 L51
haplotype (singular)
patterns (plural)
‘…as these are poorly…’
P8 L33
multi-co-linearity
P9 L31 What percentage of bases were replaced with N’s due to depth < 5X?
Downloaded from http://rsos.royalsocietypublishing.org/ on June 17, 2017
8
P9 L47 The results of a haplotype network are discussed but the method is not described in the
earlier section. Please add a brief description to the Methods.
Figure 3 Please explain branch colouration in legend.
P12 L46 ‘…likely took…’
P13 L2 …these ‘potential early arriving’ Asian…
P13 L51 …’colonizations’…
P14 L4 …’relative to their Sundaic…’
P14 L1-6
The statement regarding selection as the definite reason for less pelage variation
in the southern range is probably a little strong. Founder effects could also account for some of
this pattern. I would suggest “…may be the result of selection…”, particularly given the results
for the bay cat pelage (many morphs, one habitat type – see above)
P15 L56 ‘habitats were confined…’
Reviewer: 2
Comments to the Author(s)
The conclusions of the paper seem generally well justified. I cannot follow the argumentation of
the authors regarding "multiple colonization events on Sumatra". There are two clear-cut clades,
one containing all Sumatran samples plus the one from Peninsular Malaysia, and I fail to see how
this can provide evidence for multiple colonization events of Sumatra since the Toba eruption.
The evidence of the "tree-like pattern of Sumatran samples in the haplotype network" is at best
circumstantial. In a similar vein, "the sample from Peninsular Malaysia, which is genetically
positioned between samples from Mainland Indochina and those from Sumatra", is the basalmost branch in the Sumatra clade, which is consistent with a colonization of Sumatra from the
North, but in the absence of more samples from Malaysia this is all that can be said about this, I
believe. I would urge the authors to rephrase these two section of the discussion and back down a
bit on the "multiple colonization" scenario. One minor issue here: I do not see the point of midpoint rooting - please root the tree in Fig 3 using the bay cat as outgroup. And how can a single
tree be reconstructed using both ML and BI, as the caption implies? Finally, one last minor point:
when referring to museum samples (Fig. S2), please cite them using the full museum accession
numbers including the institutional acronym, not just part of the number calling it "specimen ID"
- this should read, e.g., ZMB Mam. 91060...
Author's Response to Decision Letter for (RSOS-160350)
See Appendix A.
AppendixDownloaded
A
from http://rsos.royalsocietypublishing.org/ on June 17, 2017
Responses to reviewer’s comments:
Reviewer: 1
Major comment
The pelage results for the bay cat are interesting as, following the authors’ argument for the
Asian golden cat, the results do seem to suggest that the bay cat was exposed to / adapted to
multiple environmental conditions. However the authors’ state throughout that the bay cat is
an evergreen forest specialist and hence was less able to adapt to environmental change. If
pelage variation does imply selection for different habitat types, then the implication is that
the bay cat may not have been restricted to the tropical evergreen habitat postulated in the
distribution analysis. Which in turn has implications for the hypothesized speciation event
and the overall narrative regarding restricted bay cat distribution during the LGM.
*** We agree that our phrasing has been misleading. In contrast to the Asiatic golden cat the
colour morphs of the Bay cat are less distinctive and represent more a gradient from reddish
to greyish. We also think that all three colour variants of the bay cat are actually associated
with closed evergreen forests and red, brown and greyish black are all colourations which
provide in a darker shaded environment a better camouflage. In contrast the much brighter
reddish and spotted Asiatic golden cat morph are clearly adaptations to more open forest
conditions. We have therefore rephrased the discussion about the bay cat to avoid and
confusion here. This section reads now:
L384-391: “For the bay cat, three different coat colours (red, brown and greyish black) have
been recorded intermixed from different regions of Borneo. In contrast to the Asiatic golden
cat’s coat colour morphs, which are highly contrasting and distinctive, the bay cat’s
polymorphism is tonally neutral. Close examination of the pelage of the greyish black morphs
show an underlying reddish coloration (e.g., FMNH 8378) and we suspect that some
individuals may change coloration during their lives as has been recorded for the
polymorphic African golden cat, Caracal aurata (Pocock, 1907). Given that most of the bay
cat’s likely mammalian predators and prey have dichromatic vision, this means that these
colour variants are not visually distinct from each other, especially in the low light levels of
closed-canopy forests. Therefore, this observation supports the species distribution
projections, which suggested that the bay cat has likely been restricted to more homogenous
evergreen rainforests during the Plio- and Pleistocene. In contrast the brighter Asiatic golden
cat morphs could be seen as an adaptation to open deciduous forests.”
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FMNH 8378 – photos above show full colour and mixture of red and greyish black
coloration. Photos below show same imags with colour removed so that red and greyish
black appear tonally similar.
Minor comments
Abstract
Line 40
‘…between the two species of ~3.16 M…’
*** L40 we added ‘the’ in Abstract
Introduction
It would be useful to define what constitutes the ‘Sunda Shelf’
***L 59-62 we added this information and the sentence reads now:
In particular the Sunda Shelf which comprises Peninsular, Sumatra, Borneo, Java, Bali and
other smaller islands is of great interest to evolutionary biologists [1], as alternating glacial
and interglacial periods resulted in the emergence and submergence of land bridges between
the larger landmasses [2–4].
L58
delete ‘Here,’
*** L58 we deleted ‘Here,’
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L91
Is there a reference for the size difference observations?
The size differences were observed by JH Mazák and AC Kitchener (see graph below). The
data used for this graph will be used for another study and are so far not fully analysed.
Therefore these data cannot be integrated in this manuscript. We added however the reference
to the unpublished data in the manuscript (JH Mazák and ACK unpublished data).
L99
‘In the current study…’
*** L99, we change the phrase to ‘In the current study…’
L165
haplotype (singular)
*** L165, We change it to haplotype
L166
patterns (plural)
*** L166, We change it to patterns
L169
‘…as these are poorly…’
*** L169, we changed it to ‘these’
L217
multi-co-linearity
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*** L217 We did not change this, because we think the term multicollinearity is a common
term in regression analysis.
L243 what percentages of bases were replaced with N’s due to depth < 5X?
*** L243 now we added this number, each sample has 1-2% of N’s due to a sequencing
depth < 5x
The results of a haplotype network are discussed but the method is not described in
the earlier section. Please add a brief description to the Methods.
*** L162-163 we added NETWORK method description in method section.
Figure 3
Please explain branch colouration in legend.
***We have explained branch colouration in figure legend.
L334 ‘…likely took…’
*** L334 we changed the order of the words to ‘…likely took…’
L341 …these ‘potential early arriving’ Asian…
*** L341 we changed the phrase to ‘potential early arriving’
L363 …’colonizations’…
*** L363 we corrected the word to ’colonizations’
L373 …’relative to their Sundaic…’
*** L373 we changed the phrase to ’relative to their Sundaic’ in
L372-374
The statement regarding selection as the definite reason for less pelage
variation in the southern range is probably a little strong. Founder effects could also account
for some of this pattern. I would suggest “…may be the result of selection…”, particularly
given the results for the bay cat pelage (many morphs, one habitat type – see above)
*** L372-374 we edited the sentence as suggested. It reads now:
“The pronounced morphological diversity of Asian golden cats on the mainland relative to
their Sundaic conspecifics may be the result of selection over a long time and can be
interpreted as local adaptation to the more diverse habitats [53]”
L435 ‘habitats were confined…’
*** L435 we corrected the word to ‘were’
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Reviewer: 2
Major comment
The conclusions of the paper seem generally well justified. I cannot follow the argumentation
of the authors regarding "multiple colonization events on Sumatra". There are two clear-cut
clades, one containing all Sumatran samples plus the one from Peninsular Malaysia, and I fail
to see how this can provide evidence for multiple colonization events of Sumatra since the
Toba eruption. The evidence of the "tree-like pattern of Sumatran samples in the haplotype
network" is at best circumstantial. In a similar vein, "the sample from Peninsular Malaysia,
which is genetically positioned between samples from Mainland Indochina and those from
Sumatra", is the basal-most branch in the Sumatra clade, which is consistent with a
colonization of Sumatra from the North, but in the absence of more samples from Malaysia
this is all that can be said about this, I believe. I would urge the authors to rephrase these two
section of the discussion and back down a bit on the "multiple colonization" scenario.
***The position of the Malaysian sample changed, depending on the rooting and the
network. The new tree rooted with the bay cat show that this sample is positioned between
samples from Mainland Indochina and Sumatra. This does not contradict that it is the basalmost branch to all Sumatran samples. We have clarified this by referring to the network and
figure 3. This sentence reads now:
L349-353 “A probable post-Toba expansion of Asian golden cats from southern China and
northern Indochina, areas which were less or not affected by Toba, is also supported by the
sample from Peninsular Malaysia, which is the basal-most branch of the Sundaic clade and
based on the network (Figure S1) and phylogenetic tree (Figure 3) genetically positioned
between samples from Mainland Indochina and those from Sumatra.”
We also agree that in the absence of additional samples from Peninsular Malaysia it is
difficult to conclude the “multiple colonizations”. We still think that a single colonisation
event would likely have resulted in a much more star-like pattern of the Sumatran samples,
however we agree that the found pattern could have also been explained by a directional e.g.
north-to-south expansion of golden cats in Sumatra. Therefore we have rephrased this section
and it reads now:
L361-367 “The tree-like pattern of the Sumatran samples in the haplotype network (Fig. S1)
indicated either a directional north-to-south expansion of golden cats after a single
colonization. However, multiple colonizations events on Sumatra from the Peninsular
Malaysia cannot be excluded. To test these scenarios additional samples from Peninsular
Malaysia and from Sumatra with precise locality information would be needed. A haplotype
radiation from a few founders in Central Sumatra would have resulted in a star-like pattern
[51] and is thus rather unlikely.”
Minor comment
I do not see the point of mid-point rooting - please root the tree in Fig 3 using the bay cat as
outgroup. Downloaded from http://rsos.royalsocietypublishing.org/ on June 17, 2017
***We changed the rooting of the phylogenetic tree in Figure 3 and used the Bay cat as an
outgroup
How can a single tree be reconstructed using both ML and BI, as the caption implies?
*** L638 RaXML and MrBayes had identical topologies. The shown phylogenetic tree is
based on RaXML. We have edited the Figure 3 caption and it reads now:
“Maximum Likelihood phylogenetic tree derived from Asian golden cat mitogenomes using
the Bay cat (Catopuma badia) as outgroup. The Bayesian phylogenetic tree provided
identical topologies. Support values for nodes were obtained from ML analysis (RaXML) and
Bayesian inference (MrBayes). Only values > 80% (RaXML) and > 0.9 (posterior probability
values for Bayesian trees) are shown. Smaller values are denoted with *. Haplotypes and their
origins is listed separately (additional file 1).”
Finally, one last minor point: when referring to museum samples (Fig. S2), please cite them
using the full museum accession numbers including the institutional acronym, not just part of
the number calling it "specimen ID" - this should read, e.g., ZMB Mam. 91060...
***L 670 Figure S2, We added full museum accession numbers including the institutional
acronyms. It now reads as
“Different coat colour morph of Asian golden cat; four different coat colours with two
different geographic locations each: spotted morph a) Sikkim-India, specimen ID: ZMB
Mam. 91060 b) Tibet, specimen ID: ZMB Mam. 57913; black morph c) Yunnan- China,
specimen ID: ZMB Mam. 43467 d) Sikkim- India, specimen ID: ZMB Mam. 91059; red
morph e) Sumatra, specimen ID: NMNL Mam. 1732 f) Siam-Indochina, specimen ID: ZRC
Mam. .4.1067; brown morph g) Tibet, specimen ID: AMNH Mam. 28250 h) Fujian-China,
specimen ID: AMNH Mam. 84393”