Rob Hutchinson
Soft Lad
By "Talaud Islands Ninox sp" are you referring to Chocolate Boobook N. randi as described by King or are you doubting that the birds on Talaud are indeed this species?
Rob
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Owls 2 (König & Weick) (1 Viewer)
- Thread starter Richard Klim
- Start date
By "Talaud Islands Ninox sp" are you referring to Chocolate Boobook N. randi as described by King or are you doubting that the birds on Talaud are indeed this species?
Rob
Murray Lord
Well-known member
Sooty Owls - split or lump
Sooty Owls in Australia have traditionally in recent years been treated as two species - the Lesser Sooty Owl, T. multipunctata and the Sooty Owl T. tenebricosa, which is also found in New Guinea. In the 2002 paper "Unravelling a biogeographical knot: origin of the ‘leapfrog’ distribution pattern of Australo-Papuan sooty owls (Strigiformes)and logrunners (Passeriformes)", available at http://journals.royalsociety.org/content/kruq5eyymwwxy1nt/fulltext.pdf the authors concluded based on genetic grounds that they should be lumped. The relevant conclusions read as follows:
"Low levels of sequence divergence among sooty owls
raise doubts about the current circumscription of the
complex into two species. All three taxa were similarly
divergent from one another in both the mitochondrial
(0.60–0.80%) and nuclear (0.20–0.40%) DNA sequences
(table 1b). Comparison with cytochrome b or ND2
sequences of strigid owls indicates that these estimates are
an order of magnitude lower than typically observed
among owl species. Examples include: 9.0–12.0% in the
Strix aluco–butleri–woodfordii complex (Heidrich & Wink
1994); 6.3–8.8% in the Otus atricapillus complex
(Heidrich et al. 1995); and 5.4% in the Ninox rufa–strenua
complex (Norman et al. 1998). Levels observed among
sooty owls are comparable with subspecific differentiation
within the Boobook owl Ninox novaeseelandiae (1.5–2.3%)
(Norman et al. 1998) and in birds generally (Avise &
Walker 1998). Consequently, the complex is best treated
as a single species, T. tenebricosa, as was the case prior to
the revision of Schodde & Mason (1981)."
Yet now the paper by Wink et al (link earlier in this thread) cites genetic evidence to support them being two separate species.
I have looked at the tables in the Wink paper, but I do not understand from them whether the information published (basically the numbers on the diagram) allow you to compare Wink's results with those in the earlier paper.
Can anyone enlighten me as to how each paper can cite genetic material as supporting the opposite conclusions? Is it just that Wink is more of a splitter - does he just set the bar lower as to what degree of difference constitutes a separate species? As he has split the Boobook Owl into four species, he would presumably disagree with using the comparison between them to justify the Sooty Owls not being split.
Sooty Owls in Australia have traditionally in recent years been treated as two species - the Lesser Sooty Owl, T. multipunctata and the Sooty Owl T. tenebricosa, which is also found in New Guinea. In the 2002 paper "Unravelling a biogeographical knot: origin of the ‘leapfrog’ distribution pattern of Australo-Papuan sooty owls (Strigiformes)and logrunners (Passeriformes)", available at http://journals.royalsociety.org/content/kruq5eyymwwxy1nt/fulltext.pdf the authors concluded based on genetic grounds that they should be lumped. The relevant conclusions read as follows:
"Low levels of sequence divergence among sooty owls
raise doubts about the current circumscription of the
complex into two species. All three taxa were similarly
divergent from one another in both the mitochondrial
(0.60–0.80%) and nuclear (0.20–0.40%) DNA sequences
(table 1b). Comparison with cytochrome b or ND2
sequences of strigid owls indicates that these estimates are
an order of magnitude lower than typically observed
among owl species. Examples include: 9.0–12.0% in the
Strix aluco–butleri–woodfordii complex (Heidrich & Wink
1994); 6.3–8.8% in the Otus atricapillus complex
(Heidrich et al. 1995); and 5.4% in the Ninox rufa–strenua
complex (Norman et al. 1998). Levels observed among
sooty owls are comparable with subspecific differentiation
within the Boobook owl Ninox novaeseelandiae (1.5–2.3%)
(Norman et al. 1998) and in birds generally (Avise &
Walker 1998). Consequently, the complex is best treated
as a single species, T. tenebricosa, as was the case prior to
the revision of Schodde & Mason (1981)."
Yet now the paper by Wink et al (link earlier in this thread) cites genetic evidence to support them being two separate species.
I have looked at the tables in the Wink paper, but I do not understand from them whether the information published (basically the numbers on the diagram) allow you to compare Wink's results with those in the earlier paper.
Can anyone enlighten me as to how each paper can cite genetic material as supporting the opposite conclusions? Is it just that Wink is more of a splitter - does he just set the bar lower as to what degree of difference constitutes a separate species? As he has split the Boobook Owl into four species, he would presumably disagree with using the comparison between them to justify the Sooty Owls not being split.
l_raty
laurent raty
The numbers on the trees published by Wink are bootstrap supports - a measure of the solidity of the phylogenetic reconstruction, not a measure of the levels of divergence.
Branch lengths are proportional to the genetic distance in Wink's trees, thus you can (to some extent, at least) assess the levels of divergence by looking at them. You should measure the total horizontal distance that you have to go along the tree, from a sample to another one (thus, first leftwards, back to their closest common ancestor, then rightwards to the other sample; vertical distances do not count), then compare this to the scale bar below the tree, that represents a 10% devergence - if the phylogenetic reconstruction is solid, this should give you an approximation of the distance between the two samples.
This would still not allow more than a rough comparison of the two studies, though, because the genes sequenced differ between them, and different genes do not necessarily evolve at the same pace. The tree that has both Sooty Owls in Wink's paper is based on a bit more than 1000 base pairs of the cytochrome b. Norman et al. had 1215 base pairs of mtDNA, but only 300 of which them came from the cyt-b; the rest was from two other genes, ND2 and ATP8.
I'll try to have a closer look at the data and come back if I can find more. (But Wink's data set is only partly available in GenBank; i.a., only one of his tenebricosa, and none of his multipunctata are there...)
Of course, Wink is a splitter...
l_raty
laurent raty
At least two of the cyt-b sequences from the recent paper have problems.
- Tyto delicatula sumbaensis (GenBank EU349005): this sequence includes a gap of 48 base pairs, indicating that it was sequenced in two parts. The 245 base pairs that precede the gap are highly divergent from all other Tyto sequences; the rest is almost identical to other sequences ascribed to T. delicatula ssp.
- Tyto furcata furcata (GenBank EU349005): here, there is no gap to indicate two separately sequenced fragments, but the first 300 bp or so are very close to those of the sumbaensis sequence (thus also unlike any other Tyto); the remaining part of the sequence is close to other sequences ascribed to T. furcata ssp.
I tried a BLAST search on the first 250 base pairs of these two sequences, and the closest matches I got (in both cases) were Hydrobates pelagicus...
These two taxa both appear quite divergent from their close relatives in Wink's cyt-b tree, but they are only represented by the above two sequences, and this makes this result clearly problematic. When I remove the Hydrobates-like parts of the sequences, sumbaensis does not appear particularly divergent from other T. delicatula ssp. at all; furcata remains basal to other T. furcata ssp., but its divergence level is strongly reduced.
I've joined two trees based on the long cyt-b sequences that are in GenBank (almost all of them from the Wink lab), one with the complete sequences, the other with the first part of the sumbaensis and furcata sequences removed - so you can see the difference.
- Tyto delicatula sumbaensis (GenBank EU349005): this sequence includes a gap of 48 base pairs, indicating that it was sequenced in two parts. The 245 base pairs that precede the gap are highly divergent from all other Tyto sequences; the rest is almost identical to other sequences ascribed to T. delicatula ssp.
- Tyto furcata furcata (GenBank EU349005): here, there is no gap to indicate two separately sequenced fragments, but the first 300 bp or so are very close to those of the sumbaensis sequence (thus also unlike any other Tyto); the remaining part of the sequence is close to other sequences ascribed to T. furcata ssp.
I tried a BLAST search on the first 250 base pairs of these two sequences, and the closest matches I got (in both cases) were Hydrobates pelagicus...
These two taxa both appear quite divergent from their close relatives in Wink's cyt-b tree, but they are only represented by the above two sequences, and this makes this result clearly problematic. When I remove the Hydrobates-like parts of the sequences, sumbaensis does not appear particularly divergent from other T. delicatula ssp. at all; furcata remains basal to other T. furcata ssp., but its divergence level is strongly reduced.
I've joined two trees based on the long cyt-b sequences that are in GenBank (almost all of them from the Wink lab), one with the complete sequences, the other with the first part of the sumbaensis and furcata sequences removed - so you can see the difference.
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l_raty
laurent raty
Here is another tree, this one based only on the cyt-b fragment sequenced by Norman et al. This fragment corresponds to the first part of the long sequences of the Wink lab, as well as to shorter sequences that they produced for earlier publications (but I think are partly included in the last analysis).
(Here, I've left the "sumbaensis" and "furcata" sequences in place - when these sequences are shortened to match Norman et al.'s fragment, only the apparently "non-Tyto" part remains, thus they are unlikely to interfere badly with the rest of the analysis. I've also added a Hydrobates sequence to the pot, just to see what happened...)
The only tenebricosa sequence from the recent paper that is in GenBank (EU349010) appears consistent with the sequences deposited by Norman et al. in GenBank in 2002 (AY14803-). Over this 300 base pair fragment, Wink's sequence differs from each of the Norman et al's sequences by only one single mutation... A different one in each case.
(That said, the distance between T. capensis and T. longimembris - or even the distance between T. glaucops and the core of the T. furcata group - is not much larger.)
(Here, I've left the "sumbaensis" and "furcata" sequences in place - when these sequences are shortened to match Norman et al.'s fragment, only the apparently "non-Tyto" part remains, thus they are unlikely to interfere badly with the rest of the analysis. I've also added a Hydrobates sequence to the pot, just to see what happened...)
The only tenebricosa sequence from the recent paper that is in GenBank (EU349010) appears consistent with the sequences deposited by Norman et al. in GenBank in 2002 (AY14803-). Over this 300 base pair fragment, Wink's sequence differs from each of the Norman et al's sequences by only one single mutation... A different one in each case.
(That said, the distance between T. capensis and T. longimembris - or even the distance between T. glaucops and the core of the T. furcata group - is not much larger.)
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Murray Lord
Well-known member
Many thanks Laurent, that's very interesting. What might cause that result with Hydrobates - not cleaning your test tube properly? Out of curiosity are the comparisons you have done something that anyone could do, with information available online, or did you need access to particular computer programmes to do it?
The conclusions Wink reaches on Boobooks also seem to contract the conclusions of the following paper (which I haven't read): Norman, J.A., Olsen, P., Christidis, L. (1998) Molecular genetics confirms taxonomic affinities of the endangered Norfolk Island Boobook Owl Ninox novaeseelandiae undulata. Biological Conservation 86: 33-36
Just to see if I am understanding Wink's diagram's correctly, is it suggesting (based on the relative horizontal length of the lines) the genetic difference between the two samples of T. castanops is comparable in magnitude to that between T. castanops and T. novahollandiae? The Masked Owls are the third example of where the Koenig book recognises more Australian species than the Australian checklist does. Overall the Austalian checklist recognises eight non-vagrant owls (excluding Christmas and Norfolk Islands); Koenig recognises twelve.
Murray
The conclusions Wink reaches on Boobooks also seem to contract the conclusions of the following paper (which I haven't read): Norman, J.A., Olsen, P., Christidis, L. (1998) Molecular genetics confirms taxonomic affinities of the endangered Norfolk Island Boobook Owl Ninox novaeseelandiae undulata. Biological Conservation 86: 33-36
Just to see if I am understanding Wink's diagram's correctly, is it suggesting (based on the relative horizontal length of the lines) the genetic difference between the two samples of T. castanops is comparable in magnitude to that between T. castanops and T. novahollandiae? The Masked Owls are the third example of where the Koenig book recognises more Australian species than the Australian checklist does. Overall the Austalian checklist recognises eight non-vagrant owls (excluding Christmas and Norfolk Islands); Koenig recognises twelve.
Murray
l_raty
laurent raty
Maybe - hard to be sure. Test tubes could also have have been interchanged at some point, or a problem could even have happened later, when partial sequences were combined to get a single long sequence. (This type of thing is much less rare than we would like it to be - and I think it goes undetected quite easily, even through peer-review processes. [I've seen obvious hybrid sequences in data sets from studies published in high-profile journals, such as Mol. Phylogenet. Evol.] If you limit yourself to reading the paper presenting the analysis of a data set including such sequences, it can be perfectly impossible to detect them.)
GenBank is accessible from here: http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore
I copied the sequences from there into a text file and aligned them by hand. (With many genes, I'd use Clustal for the alignment [freely available from http://www.clustal.org] but the cyt-b very rarely has any insertions or deletions, thus aligning it is usually straightforward - you just have to move the sequences to the right or to the left until they match, adding or removing "-"s at the start, then check the end for security.)
I did the analyses with TreeFinder http://www.treefinder.de, which is freeware.
Nucleotide BLAST searches can be performed here: http://blast.ncbi.nlm.nih.gov/Blast...astSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome
I turned the trees into pdfs with GhostView, that you can get freely at http://pages.cs.wisc.edu/~ghost/gsview
(And, incidentally, my PC runs Ubuntu Linux - http://www.ubuntu.com - thus even my OS is free.
)Thus, no, you don't need any particular access - the data and the tools are both out there and accessible to anyone with a computer and an Internet connection.
Where is the contradiction?
I don't have this particular paper either but, based on what they deposited in GenBank, their analyses must have included single sequences of undulata, novaeseelandiae and leucopsis, plus single sequences of N. rufa and N. strenua that were presumably used to root the tree. From their abstract: "The resulting data clearly identified N. n. undulata as being more closely related to N. n. novaeseelandiae than to N. n. leucopsis (Tasmania) which it also resembles in outward appearance."
Wink et al.'s Figure 4B shows undulata and novaeseelandiae to be very close to each other, and leucopsis farther away - thus exactly the same thing.
No - you should always go from branch tip to branch tip, even when talking about taxa. The distance between castanops and novaehollandiae would be the average distance separating one of the castanops samples from one of the novaehollandiae samples - probably about twice the distance between the two castanops samples.
Cheers,
Laurent -
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Murray Lord
Well-known member
Let me rephrase - the tree they arrived at may have looked the same but their interpretation of what it indicates about how many species of Boobook there are is totally different. Have a look at this statement by Les Christidis, one of the authors of the 1998 paper, and compare it to the treatment of the same species in the Koenig book.
Thanks for all those links - most interesting. All I have to overcome now is the fact I would have no idea what I was doing if I tried to use any of them...
l_raty
laurent raty
Christidis & Boles (2008) repeated a similar statement - and, yes, there is indeed an obvious difference of interpretation. (In defense of Olsen 1999, though, it could be argued that there was no real "misquotation" in HBW, because the exaggeratedly poor referencing system enforced by the editors of this series simply makes this impossible - Olsen's text alludes to "molecular differences," but there is no way to know whether these were indeed derived or not from the two Norman et al. 1998 papers...)
I'm not sure on what, exactly, the split N. leucopsis is based, but I would agree that it has no strong molecular basis, and that the cyt-b and ND2 data in the two Norman et al. (1998) papers certainly do not make it necessary.
However, the split as implemented in HBW is another story. HBW retained leucopsis as conspecific with novaeseelandiae (as indeed recommended by Norman et al.), but split a N. boobook made only of taxa from the mainland of Australia. Even if, in Norman et al's papers, "the Tasmanian Boobook Owl samples were included to represent the Australian Boobook," these papers in practice did not include any mainland Australian specimen, thus they are actually completely irrelevant to this version of the split - they can neither support, nor refute it.
In their 1998 paper on the specific status of N. natalis (abstract here), Norman et al. argued in favor of a three-way split of the "N. squamipila complex" based on the finding that the genetic divergence levels between the three races they had tested were "comparable to the levels of divergence observed between obviously distinct species such as N. rufa and N. strenua (5.4%) and were consistently greater than observed among subspecies within the monophyletic N. novaeseelandiae complex (1.5% to 2.3% between novaeseelandiae, leucopsis and undulata)." Their phylogenetic reconstructions also placed N. s. squamipila basal to a clade grouping N. s. natalis, N. s. hypogramma, N. connivens, and the N. novaeseelandiae complex - the support given to this clade by sequence analysis alone was admittedly low, but all of these taxa also shared a 6 bp insertion in the ND2 gene, which squamipila and the other Ninox did not have. I've checked a few other published ND2 sequences from GenBank: this insertion is also clearly lacking in other owls, as well as in parrots. Insertions/deletions in the ND2 gene are very rare events, and it seems very unlikely that this particular insertion could have happened twice, or that it could have been exactly reversed in squamipila only, thus its presence adds a lot of support to the hypothesis that squamipila falls outside this group (in terms of mtDNA, at least). Within this group, ND2 united novaeseelandiae, leucopsis and undulata with some support, but the relationships between them, connivens, natalis and hypogramma were otherwise very poorly resolved. The distance between natalis and hypogramma (4%) was also the lowest in the "N. squamipila complex" - making a split of natalis (from hypogramma) actually much more poorly supported in molecular terms than that of squamipila from these two. (Yet, oddly, many subsequent authors - including König & Weick - accepted the former but not the latter... A consequence of the title of the paper...?)
If you now look at the trees in the recent Wink paper, I would argue that the case of N. boobook is quite similar to, and looks at least as good as, that of N. natalis. The cytochrome b is the only gene to have been sequenced for both N. boobook and N. novaeseelandiae as circumscribed in HBW. This gene entirely fails to resolve N. novaeseelandiae s.l. as a monophyletic group. The longer available cyt-b sequences (see also the attached file below) suggest the existence of a clade including four lineages - boobook, novaeseelandiae, rudolfi (a bit surprisingly omitted from Wink et al's Figure 4, while they did have a sequence; rudolfi does appear in their Figure 1, that is based on cyt-b+RAG-1), and connivens - that are all separated by quite comparable levels of divergence. This admittedly does not prove conclusively that N. novaeseelandiae s.l. is not monophyletic, but neither did Norman et al. (1998) prove conclusively that natalis and hypogramma are not sister taxa. The uncorrected distance between boobook and novaeseelandiae, based on these long cytochrome b sequences, is 4.36%. The distance between N. rufa and N. strenua is only 3.65%...
L -
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Peter Kovalik
Well-known member
I am not sure if you have seen this change of name for Gymnoglaux:
http://si-pddr.si.edu/dspace/bitstream/10088/7471/1/VZ_380_Margarobyas.pdf
http://si-pddr.si.edu/dspace/bitstream/10088/7471/1/VZ_380_Margarobyas.pdf
Peter Kovalik
Well-known member
Sorry, I overlooked...
SzimiStyle
The Shorebird Addict
Anyone can help to find the subspecies of Eastern Barn Owl (Tyto javanica)?
Thanks, Szimi
Thanks, Szimi
Richard Klim
-------------------------
Eastern Barn Owl
http://books.google.com/books?id=SF...istidis & boles&pg=PA167#v=onepage&q=&f=false
[IOC additionally splits T deroepstorffi 'Andaman Masked Owl' (monotypic).]
[König & Weick 2008 retains sspp stertens & javanica within T alba 'Common Barn Owl'; but recognises T deroepstorffi 'Andaman Barn Owl' (monotypic), T deliculata 'Australian Barn Owl' (including sspp sumbaensis, meeki, deliculata, interposita), and T crassirostris 'Boang Barn Owl' (monotypic).]
Richard
My understanding is that Tyto javanica 'Eastern Barn Owl' (as split by Christidis & Boles 2008) includes all populations from southern Asia through Australia and the Pacific, and therefore includes sspp stertens, javanica, deroepstorffi, sumbaensis, meeki, deliculata, 'interposita', crassirostris.
http://books.google.com/books?id=SF...istidis & boles&pg=PA167#v=onepage&q=&f=false
[IOC additionally splits T deroepstorffi 'Andaman Masked Owl' (monotypic).]
[König & Weick 2008 retains sspp stertens & javanica within T alba 'Common Barn Owl'; but recognises T deroepstorffi 'Andaman Barn Owl' (monotypic), T deliculata 'Australian Barn Owl' (including sspp sumbaensis, meeki, deliculata, interposita), and T crassirostris 'Boang Barn Owl' (monotypic).]
Richard
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SzimiStyle
The Shorebird Addict
Thanks a lot RIchard. I wonder what will happen with some of the 'American' subspecies. Will there be further splits?
Szimi
Szimi
Richard Klim
-------------------------
American barn owls
[And AOU recognised North American pratincola as a species until 1931...]
Richard
Well, König & Weick already separate New World barn owls as four species (furcata, bargei, insularis, punctatissima), and identify one further potential split (contempta), but there seems to be little support elsewhere. AOU-SACC suggests possible recognition of T punctatissima (citing Wink et al 2008).
[And AOU recognised North American pratincola as a species until 1931...]
Richard
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Richard Klim
-------------------------
Himalayan Owl
[Correct spelling: Strix nivicolum.]
Michiel de Boer on Oriental Birding today...The split is recognised by IOC and Cornell/Clements, except that (contra König & Weick) Cornell treats it as monotypic (excluding sspp ma and yamadae).
mb1848
Well-known member
"Third is probably the female call again completely different from Tawny Owl actually it reminded me strongly of the female of Strix rufipes which is a South American species."
"Syrnium nivicolum, The hooting is varied by a hoarse screeching note which the shikaris declare to be uttered by the female."
The Valley of Kashmir 1895 Sir Walter Roper Lawrence.
"Syrnium nivicolum, The hooting is varied by a hoarse screeching note which the shikaris declare to be uttered by the female."
The Valley of Kashmir 1895 Sir Walter Roper Lawrence.
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