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Phylogenetic species

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Old Saturday 28th June 2008, 08:27   #1
Daniel Philippe
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Phylogenetic species

Some authors recently published articles proposing alternative classification using PSC, such as:

http://www.specifysoftware.org/Infor...NP_BN_2004.pdf
for Mexico

http://www.oikos.ekol.lu.se/appendixdown/E4344.pdf
for Africa

http://zoo.bio.ufpr.br/diptera/bz023...priorities.pdf
for northeastern Brazil

http://www.specifysoftware.org/Infor...P_BCI_2006.pdf
for the Philippines

Are there other publications ?

Daniel
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Old Sunday 29th June 2008, 06:21   #2
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http://www.springerlink.com/content/...MOESM1_ESM.xls
for Palearctic (3 036 phylogenetic species of Palearctic songbirds)
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Old Wednesday 2nd July 2008, 08:59   #3
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Thank you Marek,

Hmm !! very long list … and as I wanted to know why, I found the article available here : http://www.springerlink.com/content/eu53t1726525u760/ .

On the whole, criteria to define a phylogenetic species seem to significantly differ from one author to another …

Daniel
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Old Wednesday 2nd July 2008, 16:58   #4
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Quote:
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Thank you Marek,

Hmm !! very long list … and as I wanted to know why, I found the article available here : http://www.springerlink.com/content/eu53t1726525u760/ .

On the whole, criteria to define a phylogenetic species seem to significantly differ from one author to another …

Daniel
It seems that there is no limit to the amount of splitting that could happen under the Phylogenetic species concept. Basically, if two birds look physically different in any way, under the PSC they're different species.

What would cause two birds who were distinguishable on appearance NOT to be split?
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Old Wednesday 2nd July 2008, 17:08   #5
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What would cause two birds who were distinguishable on appearance NOT to be split?
Perhaps the fact that there is no "parental pattern of ancestry and descent" in two individual birds...?

But I agree - Cracraft's PSC can be pushed extremely far, and does not contain any clear lower limit below which splitting should not be done.
That said, individual interpretations of the BSC can also vary widely from an author to another one. After all, Helbig did split the wagtails under (a variant of) the BSC...

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Old Wednesday 2nd July 2008, 17:19   #6
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Quote:
Originally Posted by Marek12 View Post
(3 036 phylogenetic species of Palearctic songbirds)
I went through the first lines to get a better idea, but I am not happy with everything. For instance :

Pitta (nympha) bertae
How can one decide it is (was ?) a phylogenetic species ?
The only info I found are in "Systematic notes on Asian birds. 5.1 - Types of the Pittidae":
"# 37. The type of P. bertae, a holotype by monotypy, once in the MNSG, has been reported lost (Arbocco et al., 1978; Passerin d’Entrèves et al., 1987). Six years after it was described the type figured in Salvadori (1874). This later picture does not qualify as type material. There is no doubt that this plate depicted the specimen in question and the identity of the bird is not in dispute so there is no need to designate a neotype."

Pachycephala (grisola) grisola
I thought P. cinerea was the correct name.

Pteruthius (xanthochlorus) obscurus
I haven’t found anything about this one.

Lanius (phoenicuroides) isabellinus
Isn’t it the contrary (isabellinus is senior) ?

Lanius (tephronotus) lahulensis
which seems to be a hybrid L. tephronotus x L. schach erythronotus (Rasmussen & Anderton 2005: Birds of South Asia, McCarthy 2006: Handbook of Avian Hybrids of the World)

Further comments ?

Daniel
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Old Thursday 3rd July 2008, 00:56   #7
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I think the most important part of the PSC is not diagnosability, but monophyletism, or 'separate evolutionary pathways'... this assures that, for example, a mutant will not be classified as a separate species. Surely, there still is a certain degree of subjectivity in the delimitation of species limits, but I believe it's smaller than with the BSC.
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Old Thursday 3rd July 2008, 15:11   #8
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I think the most important part of the PSC is not diagnosability, but monophyletism, or 'separate evolutionary pathways'... this assures that, for example, a mutant will not be classified as a separate species. Surely, there still is a certain degree of subjectivity in the delimitation of species limits, but I believe it's smaller than with the BSC.
So PSC is chiefly based not on whether two species CAN interbreed, rather on whether they DO interbreed?

Because if there is any, even occasional, hybridisation then the separate evolutionary pathways become very muddy.
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Old Thursday 3rd July 2008, 15:24   #9
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So PSC is chiefly based not on whether two species CAN interbreed, rather on whether they DO interbreed?

Because if there is any, even occasional, hybridisation then the separate evolutionary pathways become very muddy.
Not being an expert, why should the handling of hybrids differ between BSC and PSC? in both, the question is whether the hybridization happens often enough to allow genes from one lineage to significantly influence the other lineage and vice versa.

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Old Thursday 3rd July 2008, 16:45   #10
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Not being an expert, why should the handling of hybrids differ between BSC and PSC? in both, the question is whether the hybridization happens often enough to allow genes from one lineage to significantly influence the other lineage and vice versa.

Niels
I'm most certainly not an expert myself either
However I would have thought that even occasional hybridization (if that hybridization produces robust, fertile offpring) would transfer genes between populations on an ongoing basis, enough to blur the evolutionary lineages.
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Old Thursday 3rd July 2008, 17:23   #11
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I'm most certainly not an expert myself either
However I would have thought that even occasional hybridization (if that hybridization produces robust, fertile offpring) would transfer genes between populations on an ongoing basis, enough to blur the evolutionary lineages.
I'm also no expert but re hybridization I believe the argument runs that as long as the hybrids are at enough of a selective disadvantage to keep the hybrid zone from expanding out-of-control, species boundaries (however defined) can be maintained for very long periods, maybe indefinitely.
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Old Thursday 3rd July 2008, 20:28   #12
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I'm most certainly not an expert myself either
However I would have thought that even occasional hybridization (if that hybridization produces robust, fertile offpring) would transfer genes between populations on an ongoing basis, enough to blur the evolutionary lineages.
As I understand it, transfer yes, but the extent is the cause of discussion. How many copies need to be transferred before it makes a significant change to the pool of recipients? and isn't the definition of significant change about the same for the two species concepts?

Niels
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Old Friday 4th July 2008, 01:52   #13
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The amount of hybridiation allowed between two species is much bigger under the PSC than under the BSC. That is because if individuals of two populations only rarely interbreed, it’s not enough to blur the two populations’ evolutionary lineages. In fact, the PSC and the BSC each focus on different moments in the speciation process. I’ll use an imaginary example to explain:

1. There is one population of bird. All its individuals interbreed freely and there is no variation between them. Under any species concept, they’re all part of the same species.

2. A geographical bareer appears and divides the population. There are now two separate poplations, and they start evolving separetely.

3. The geographical bareer disappears after some time. And the two populations come in contact again. As a result of the time they were evolving separetely, they’re now slightly different morphologically from each other (are diagnosable) and hybridization between them is very difficult (but not impossible, and it still happens somettimes). At this point, there is still only one species under the BSC, but there are already two species under the PSC.

4. Because of selection against the hybrid, after some time in contct the populations become totally reproductively isolated, there’s zero hybridization. There are now two species under any species concept you use.


Note that in stage 3, there is nybridization between the populations, but not enough to 'blur the evolutionary lineages.)
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Old Friday 4th July 2008, 03:29   #14
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I would tend to disagree with the gist of the above. If it takes absolutely 100% lack of hybridization before two species are different in the BSC, then there would be only a single species of duck in the world. I have not seen anyone in favor of BSC ever say that there is only one species of duck.

Niels

Edit: I have not heard anyone in favor of any other species concept claim we only have one species of duck either
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Old Friday 4th July 2008, 23:08   #15
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I don't think it takes 100% lack of hybridization before two species are different in the BSC.... I said 'zero' in my example just to make things more clear hehehe.... The important thing is that the BSC allows much less hybrization than the PSC (even though 'much less' is of course very vague, and I wouldn't be able to precise quantitatively exactly how much hybridization each concept allows)
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Old Sunday 6th July 2008, 09:47   #16
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Hmm !! very long list … and as I wanted to know why, I found the article available here: http://www.springerlink.com/content/eu53t1726525u760/.
So, this is Kees Roselaar's work. The paper states that distribution maps and diagnoses for these 3,036 proposed phylogenetic species will be published by Roselaar & Shirihai (presumably in the passerine volume of their forthcoming Handbook of Geographical Variation and Distribution of Palearctic Birds). Wow!!

Does anyone know anything about the state of progress and expected publication date of this incredibly ambitious (and radical) work?

Richard
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Old Monday 11th August 2008, 09:35   #17
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So, this is Kees Roselaar's work.
In the list http://www.springerlink.com/content/...MOESM1_ESM.xls (l. 431-445), the Horned Lark is split into 4 "traditional" species:
Eremophila alpestris, E. penicillata, E. longirostris & E. elwesi.

Is there a ref for this ?

Last edited by Daniel Philippe : Monday 11th August 2008 at 09:46.
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Old Tuesday 12th August 2008, 10:47   #18
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Re: Pteruthius (xanthochlorus) obscurus
I haven’t found anything about this one.


“Pteruthius xanthochlorus, p. 95. Upper surface yellowish green; top of the head pale slate; throat white; under surface yellow; quills black, edged with white; tail black, with middle feathers and edges of the other yellowish green, the tips and outer web of exterior feathers, white. Length 41/4 in., bill from front 3 lin., from gape 31/2 lin., wings 2 in. 2 lin., tarsi 8 lin.”

Page 155, Catalogue of the Specimens and Drawings of Mammalia and Birds of Nepal of Nepal and Thibet presented by B. H. Hodgson to the British Museum.
(January 1847 J. E. & George Gray from Hodgson MS)

From some webpage: Nominate race recorded in SE Xizang; pallidus in Yunnan, Sichuan, S Gansu (Baishuijiang) and S Shaanxi (Qinling); race obscurus in Wuyishan NW Fujian.

The Birds of the Palearctic Fauna by Charles Vaurie says that Pteruthius xanthochlorus [sic] Gray, 1846, Cat. Mammal Birds Nepal and Tibet, p. 95 (name) and 155 (description) Nepal. Darker than occidentalis and with the crown in males blackish instead of ashy. Range Himalyas from Nepal eastward to Assam and neighboring southeastern Tibet and (southwestern?) Sikkim.

(About obscurus)
Pteruthius xanthochloris pallidus
Allotrius xanthochloris, Hodgs., var. pallidus David 1872 Nouv. Arch. Mus. Hist. Nat. Paris, 7 (1871), bull. Pp. 8, 14, Kokonoor {=northeastern Sikang} on the frontiers du Kokonoor according to David and Oustalet 1877 Oiseaux de la Chine p. 216 Pteruthius xanthochloris obscurus Stresemann 1925 Ornith. Monatsber., 33 p. 59 Fukien.
…ring not present in those and by being less yellowish above and greyer on the back and crown. Range: Northeastern Burma east to Northwestern Yunnan and Sikang to western Szechwan north apparently to the border of Tsinghai (Koko Nor), also Fukien, according to Yen (1934, L'Oiseau, p. 50), who states that obscurus is not separable in series from pallidus,

Les Oiseaux du Kwangsi (Chine), Yen Kwok Yung,, , L'Oiseau , Volume N. S. 4, p.24-51, (1934) page 50.

Ornithologische Monatsberichte
Herausgegeben von Dr. Ant. Reichenow.
Jarhg. 1 -> 1893 8vo Berlin

Green Shrike Babbler

Evidently someone disagrees with Yen and thinks that obscurus is different enough to be a species?
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Old Tuesday 12th August 2008, 10:57   #19
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Pachycephala (grisola) grisola
I thought P. cinerea was the correct name.

Systematic notes on Asian birds. 39.
The correct name for the Mangrove Whistler
Pachycephala cinerea (Blyth)
M.P. Walters

Disagrees with Mukherjee, A.K., 1970. Is the correct name of the Mangrove Whistler, Pachycephala cinerea (Blyth) or
Pachycephala grisola (Blyth)?— J. Bombay Nat. Hist. Soc. 67: 112-3.

The 2004 STANDARDISED COMMON AND SCIENTIFIC NAMES OF THE BIRDS OF THE INDIAN SUBCONTINENT – Ranjit Manakadan & Aasheesh Pittie agrees with Walters:

“Pachycephala grisola (Blyth, 1843) is now Pachycephala cinerea (Blyth, 1847), vide Walters 2003. Zool. Verh. Lieden. 344: 107-109”
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Old Tuesday 12th August 2008, 12:19   #20
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Re: Lanius lahulensis

Lanius tephronotus lahulensis Koelz 1950 Am.Mus.Novit. no.1452 p.7

http://digitallibrary.amnh.org/dspac...37/1/N1452.pdf

Remarks: Whistler and Kinnear (1933, Jour. Bombay Nat. Hist. Soc. Vol. 36, pp. 336-337) recognized this form but transferred Vigors’ tephronotus, to it, leaving Hodgson’s nipalensis for the real tephronotus, but this transfer of names is not justified. (see Mayr, 1947 Jour. Bombay Nat. Hist. Soc. Vol. 47, p. 126).

From a Catalogue of the Birds in the Museum of the Hon. East India Co.:
Lanius Tephronotus, Vigors
Collurio tephronotus Vigors, Proc. Zool. Soc. 1831 p. 43
Lanius nipalensis, Hodgs., Ind. Rev. I. p. 445 1837
Collurio obscurior, Hodgs., Gray Zool. Misc. (1844) . 84

Another source; Collurio nipalensis var. tephronotus Hodgson MS. The Bagaha Shrike



“This Shrike is common in the open country in Nepal,” says Mr. Hodgson, “in groves and gardens during winter, but resorts to the woods in summer. It feeds on all sorts of hard and soft (both flying and creeping) insects and their larvae and pupae; also small lizerds, feeble birds, mice, and almost any living thing the bird can master; perches on the upper and barer branches of trees and bushes, whence it descends to sseize its prey on the ground; sometimes picks it from foliage, but seldom seizes on the wing. Has a harsh voice, very like the kestril’s and is perpetually vociferating from its perch. It is bold and daring in its manners, and easily caught by any insect bait.” (Ind. Rev. I. p. 445)


Gray’s Zool. Miscellany is available on the internet but not the pages of Hodgson 1844.

Gould’s work was intended to illustrate new birds described in a
series of six papers by Nicholas Vigors in the “Proceedings of the Committee of Science and Correspondence
of the Zoological Society of London” (1831-1832) Collurio tephronotus was not illustrated in the “Century”. Systematic notes on Asian birds. 27. On the dates of publication of John Gould’s
“A Century of Birds from the Himalaya Mountains”
I.A.W. McAllan & M.D. Bruce

Catalogue of Indian Birds J.A.S.Bengal 1832, quoting Vigors, PZS 1831

“This bird was also observed to be closely allied to the last (Collurio erythronotus) and to differ from it only to sex and age. Until such points however could be ascertained, it was considered advisable to regard it as specifically distinct.”

Taxonomic status of eight Asian shrike species (Lanius): phylogenetic analysis based on Cyt b and CoI gene sequences
Authors: Zhang, Wei; Lei, Fu-Min; Liang, Gang; Yin, Zuo-Hua; Zhao, Hong-Feng; Wang, Hong-Jian; Krištín, Anton
Source: Acta Ornithologica, Volume 42, Number 2, December 2007 , pp. 173-180(8)
Publisher: Museum and Institute of Zoology, Polish Academy of Sciences

Abstract:
Complete Cyt b gene sequences (1143bp), partial CoI gene sequences (1176bp) and Cyt b gene sequences combined with CoI gene sequences (2319bp) from 22 samples of 8 Lanius species were analysed using the phylogenetic method. Molecular phylogenetic trees were reconstructed using the Maximum Parsimony (MP), Maximum Likelihood (ML), Neighbour-joining (NJ) and MrBayesV3.1 (BI) methods. 228 and 216 nucleotide sites were found to be substituted in the Cyt b gene and CoI gene sequences respectively, accounting for 19.5% and 18.4% of the total nucleotide sites in the Cyt b gene and CoI gene sequences. In the phylogenetic trees, L. minor and L. tigrinus were the first to diverge. Then, a parallel clade diverged: one was clustered with L. isabellinus and L. collurio, which formed a sister group; the other was clustered with L. schach and L. cristatus, which was parallel to the cluster of L. tephronotus and L. bucephalus. Shrikes L. isabellinus, L. collurio, L. schach and L. tephronotus were independent species. The melanistic form of L. schach is a variation group of L. schach.
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Old Tuesday 12th August 2008, 19:23   #21
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Re:Lanius (phoenicuroides) isabellinus
Isn’t it the contrary (isabellinus is senior) ?

Blanford in the Eastern Persia an account of the journeys of the Persian Boundry Commision (1876) says that isabellinus (Hemp. & Ehr. 1828) is different from L. cristatus (of which L. phaenicurus Pallas is a synonym) In Zoonomen it states:
Lanius isabellinus phoenicuroides Citation

* Peters Checkist 9:346 (= Mayr & Greenway 1960) cite this to Schalow in J.Orn. 23 1875. This is found in no.130, the "April" number of the J.Orn. which according to the pattern that is slowly emerging was probably delayed for a minimum of 3-8 months before it actually appeared.
* In Schalow's J.Orn. use of the name he attributes it to Severtzov in 1873, also in the J.Orn. where Severtzov uses the name Lanio phoenicuroides p.347 in a list, where it appears to be a nomen nudum.
* Severtzov also published the name L[anius] phaeicuroides in the Nov. 1875 number of Stray Feathers III no.5 p.429. My interpretation of the Richmond Index card in this case is that Severtzov was using L. phaenicuroides for L. phaenicuris (described in that work at p.144). So the Schalow use of the name may very will be the first valid instance of use. If not, the date could be a problem as the Nov. Stray Feathers volume could quite possibly have preceeded the "April" J.Orn. number for that year.
Shrikes are messed up!
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Old Wednesday 13th August 2008, 12:22   #22
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Thanks for the info mb.

I went a bit further and found many little things. For instance I wonder about the nuthatches (l. 1852-1880):

S. europaea is split in 3 “traditional” species: europaea, asiatica and arctica (based on Zink & al. 2006 ?)

S. castanea is split in 2 “traditional” species: castanea and cinnamoventris (based on Y. Red’kin & M. Konovalova 2006 and/or Dickinson 2006 ?)

Sinensis, 1871 is included in S. nagaensis, 1874 (???)
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Old Monday 10th November 2008, 23:49   #23
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Quote:
Originally Posted by mb1848 View Post
Taxonomic status of eight Asian shrike species (Lanius): phylogenetic analysis based on Cyt b and CoI gene sequences
Authors: Zhang, Wei; Lei, Fu-Min; Liang, Gang; Yin, Zuo-Hua; Zhao, Hong-Feng; Wang, Hong-Jian; Krištín, Anton
Source: Acta Ornithologica, Volume 42, Number 2, December 2007 , pp. 173-180(8)
Publisher: Museum and Institute of Zoology, Polish Academy of Sciences

Abstract:
Complete Cyt b gene sequences (1143bp), partial CoI gene sequences (1176bp) and Cyt b gene sequences combined with CoI gene sequences (2319bp) from 22 samples of 8 Lanius species were analysed using the phylogenetic method. Molecular phylogenetic trees were reconstructed using the Maximum Parsimony (MP), Maximum Likelihood (ML), Neighbour-joining (NJ) and MrBayesV3.1 (BI) methods. 228 and 216 nucleotide sites were found to be substituted in the Cyt b gene and CoI gene sequences respectively, accounting for 19.5% and 18.4% of the total nucleotide sites in the Cyt b gene and CoI gene sequences. In the phylogenetic trees, L. minor and L. tigrinus were the first to diverge. Then, a parallel clade diverged: one was clustered with L. isabellinus and L. collurio, which formed a sister group; the other was clustered with L. schach and L. cristatus, which was parallel to the cluster of L. tephronotus and L. bucephalus. Shrikes L. isabellinus, L. collurio, L. schach and L. tephronotus were independent species. The melanistic form of L. schach is a variation group of L. schach.
Sorry, possibly not directly related to the rest of the thread - I was just wondering if anybody would have seen this paper in its entirety.
(I have tried to write to the authors, but with no luck up to now.)

(I'd be particularly interested in the geographical origin/subspecific identity of the Isabelline and Bull-headed Shrikes they used in this study. As stated in the abstract, their Isabelline Shrike sequences are well distinct from those of collurio - but this is in sharp contrast with sequences of L. i. phoenicuroides (of course, isabellinus is senior...) from Kazakhstan published by other authors, that fall well among collurio sequences. For Bull-headed Shrike, their sequences indeed form a single cluster with those of L. tephronotus - but those of L. b. bucephalus from Korea and Japan published by other authors are very much distinct, appearing basal to cristatus + tephronotus...)

L -
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Old Tuesday 11th November 2008, 14:39   #24
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I found this link http://www.ingentaconnect.com/conten...00002/art00007 to where you can purchase the paper, but you probably knew that already. No open access

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Old Wednesday 12th November 2008, 00:20   #25
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Anton Kristin, Institute of Forest Ecology of the Slovak Academy of Sciences, Sturova 2, 960 53 Zvolen, Slovakia
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