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Old Saturday 3rd November 2012, 13:46   #1
Ian Lewis
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Stejneger's Stonechat

BOU TSC 2011 8/9/11
Mitochondrial DNA sequences of the eastern
Siberian stejnegeri are highly divergent from those
of western Siberian maurus and are sister to the
Saxicola torquatus complex (Zink et al. 2009). At
this stage, however, we are unable to support
specific rank for stejnegeri because the position of
the Chinese subspecies przewalskii has not yet been
determined. The name przewalskii would have
nomenclatural priority over stejnegeri if the two are
conspecific. Therefore, stejnegeri is tentatively
included in Saxicola maurus. Pending further analysis,
variegatus, armenicus and indicus are provisionally
retained as conspecific with S. maurus:

In view of the recent Siberian Stonechat at Portland, Dorset being confirmed as stejnegeri by DNA analysis, does anyone know if any studies are in progress on przewalskii or any other stonechat taxa?
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Old Sunday 4th November 2012, 13:02   #2
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Everything surrounding this complex remains a mess to my eye. (Far too many unanswered questions...)
  • przewalskii (Pleske, 1889): no genetic data, indeed. But it's not only this taxon that is a problem.
  • indicus (Blyth, 1847): the only available data is a cytochrome b sequence from Illera et al. 2008. Clustered with a leucurus (Blyth, 1847) sequence (as well as, more oddly, one and a half rubicola sequences from Spain), falling outside an Africa-WP-Central Asia clade, a position compatible with that of the the stejnegeri haplogroup. The sequences cannot be compared directly to anything from the Far East, though, because only nd2 and cox1 have been sequenced from bird from this area. There is another leucurus cytb in GenBank that is similar.
  • armenicus Stegmann, 1935: no genetic data.
  • variegatus (Gmelin, 1774): Zink et al. 2009 sequenced 8 birds that they identified as this taxon: 4 from Astrakhan, and 4 from the Rostov area (further W, an area from where they also had 3 birds they ID'd as rubicola; note that this is clearly outside the range of variegatus given by Cramp, and that they did not explain how they ID'd the birds). Two of the Astrakhan birds and two of the Rostov birds clustered together as the sister group of the Central-asian maurus haplogroup, the other two Rostov variegatus had perfectly typical maurus haplotypes. The other two Astrakhan variegatus had perfectly typical stejnegeri haplotypes.
Effective, direct gene flow between stejnegeri itself and variegatus seems geographically improbable... But the idea that stejnegeri haplotypes might be present in all the intervening populations between these two taxa (south of maurus, that is) doesn't seem far-fetched to me at all...

Last edited by l_raty : Sunday 4th November 2012 at 13:25. Reason: sorry, mistake about Rostov variegatus
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Old Sunday 4th November 2012, 13:54   #3
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Quote:
Originally Posted by l_raty View Post
Effective, direct gene flow between stejnegeri itself and variegatus seems geographically improbable... But the idea that stejnegeri haplotypes might be present in all the intervening populations between these two taxa (south of maurus, that is) doesn't seem far-fetched to me at all...
So that could give S (m) maurus (monotypic) and S (m) variegatus (incl armenicus, indicus, przewalskii, stejnegeri).
[The type locality of variegatus is Şamaxı, Azerbaijan (~640km S of Astrakhan).]

Last edited by Richard Klim : Sunday 4th November 2012 at 14:17.
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Old Sunday 4th November 2012, 18:25   #4
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Originally Posted by Richard Klim View Post
So that could give S (m) maurus (monotypic) and S (m) variegatus (incl armenicus, indicus, przewalskii, stejnegeri).
[The type locality of variegatus is Şamaxı, Azerbaijan (~640km S of Astrakhan).]
'Could... But variegatus as far as can be told from the data seems to be an admixture of two(/three) "divergent" mtDNA clades, hence what you should do with it is unclear. If excluded, this could also result in S. indicus.
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Old Sunday 4th November 2012, 18:44   #5
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'Could... But variegatus as far as can be told from the data seems to be an admixture of two(/three) "divergent" mtDNA clades, hence what you should do with it is unclear.
Indeed, Laurent. I was just musing that the population further south, in the area of the type locality (ie, indisputably variegatus), might be purer examples of your putative southern/eastern clade.

Last edited by Richard Klim : Monday 5th November 2012 at 13:57. Reason: clarity.
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Old Monday 5th November 2012, 13:00   #6
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Originally Posted by Ian Lewis View Post
In view of the recent Siberian Stonechat at Portland, Dorset being confirmed as stejnegeri by DNA analysis...
Birding Frontiers: Stejneger's Stonechat in the Netherlands?

PS. For completeness, link to earlier BF thread: Stonechats.

Last edited by Richard Klim : Monday 5th November 2012 at 13:02. Reason: PS.
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Old Tuesday 6th November 2012, 11:15   #7
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Quote:
Originally Posted by Richard Klim View Post
So that could give S (m) maurus (monotypic) and S (m) variegatus (incl armenicus, indicus, przewalskii, stejnegeri).
[The type locality of variegatus is Şamaxı, Azerbaijan (~640km S of Astrakhan).]
The type locality of variegatus is not Şamaxı, Azerbaijan but Bandar-e Anzali, Iran:
http://www.nm.cz/admin/files/PM/down...sky-gmelin.pdf
This is in armenicus range, so armenicus should be called variegatus, and the population now known as variegatus shloud be called amaliae according the link above.
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Old Tuesday 6th November 2012, 11:18   #8
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Originally Posted by l_raty View Post
Everything surrounding this complex remains a mess to my eye. (Far too many unanswered questions...)
  • przewalskii (Pleske, 1889): no genetic data, indeed. But it's not only this taxon that is a problem.
  • indicus (Blyth, 1847): the only available data is a cytochrome b sequence from Illera et al. 2008. Clustered with a leucurus (Blyth, 1847) sequence (as well as, more oddly, one and a half rubicola sequences from Spain), falling outside an Africa-WP-Central Asia clade, a position compatible with that of the the stejnegeri haplogroup. The sequences cannot be compared directly to anything from the Far East, though, because only nd2 and cox1 have been sequenced from bird from this area. There is another leucurus cytb in GenBank that is similar.
  • armenicus Stegmann, 1935: no genetic data.
  • variegatus (Gmelin, 1774): Zink et al. 2009 sequenced 8 birds that they identified as this taxon: 4 from Astrakhan, and 4 from the Rostov area (further W, an area from where they also had 3 birds they ID'd as rubicola; note that this is clearly outside the range of variegatus given by Cramp, and that they did not explain how they ID'd the birds). Two of the Astrakhan birds and two of the Rostov birds clustered together as the sister group of the Central-asian maurus haplogroup, the other two Rostov variegatus had perfectly typical maurus haplotypes. The other two Astrakhan variegatus had perfectly typical stejnegeri haplotypes.
Effective, direct gene flow between stejnegeri itself and variegatus seems geographically improbable... But the idea that stejnegeri haplotypes might be present in all the intervening populations between these two taxa (south of maurus, that is) doesn't seem far-fetched to me at all...

Although a lot is still undiscovered in the saxicola genus (you could call that a mess) the split between maurus and stejnegeri is very claer as reported in Zink et al. 2009. For both (sub)species they used >50 individuals.
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Old Tuesday 6th November 2012, 12:16   #9
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Quote:
Originally Posted by sanderbot View Post
The type locality of variegatus is not Şamaxı, Azerbaijan but Bandar-e Anzali, Iran:
http://www.nm.cz/admin/files/PM/down...sky-gmelin.pdf
This is in armenicus range, so armenicus should be called variegatus, and the population now known as variegatus shloud be called amaliae according the link above.
Mlíkovský 2011:
"TYPE SERIES: S.G. Gmelin (1774b: 104) described a single specimen, which is thus the holotype.
TYPE LOCALITY: S.G. Gmelin (1774b: 105-107) described this bird among those he encountered in the Bandar-e Anzali region (see S.G. Gmelin 1774b: 97), but added (p. 107): “Dieser Vogel ist mir von Schamachie aus überall vorgekommen” (“I encountered this bird everywhere starting in Schamachie [= Şamaxı]”), i.e. everywhere between Şamaxı and Bandar-e Anzali (see also Hartert 1910: 707). This means that the described specimen (holotype) originated from Bandar-e Anzali, Iran, to which I restrict here the type locality. The acceptance of Şamaxı as the type locality (e.g. Štegman 1935: 46; Gladkov 1954b: 530; Ripley 1964b: 107) is incorrect.""

ICZN:
"72.1.1. type series: all the specimens on which the author established a nominal species-group taxon (with the exception of those excluded [Art. 72.4.1]); in the absence of holotype designation, or the designation of syntypes, or the subsequent designation of a lectotype, all are syntypes and collectively they constitute the name-bearing type;"

The fact that Gmelin actually described in detail only one specimen doesn't make it a holotype. If he did not designate a holotype explicitly, and based his taxonomic concept on more than one bird (or can be assumed to have done so, see Rec.73F), then there is no holotype: all these birds (ie, all the birds he encountered everywhere between Şamaxı and Bandar-e Anzali) are syntypes.

Last edited by l_raty : Tuesday 6th November 2012 at 13:00.
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Old Tuesday 6th November 2012, 12:20   #10
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Originally Posted by sanderbot View Post
Although a lot is still undiscovered in the saxicola genus (you could call that a mess) the split between maurus and stejnegeri is very claer as reported in Zink et al. 2009. For both (sub)species they used >50 individuals.
It is as clear as something based exclusively on mtDNA, extracted from individuals from only a part of the range of a taxon, can be...

(Tree in attachment mainly based on the data from Zink et al. 2009. (Sub)specific IDs are (hopefully...) exactly as published in the corrigendum to Zink et al. 2009; which criteria were used for identification was not explained in the paper.)
Attached Files
File Type: pdf Saxicola-nd2.pdf (12.5 KB, 248 views)

Last edited by l_raty : Tuesday 6th November 2012 at 12:54.
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Old Tuesday 6th November 2012, 12:48   #11
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I think Laurent's words are well chosen.
Quote:
Originally Posted by l_raty View Post
Everything surrounding this complex remains a mess to my eye...
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Old Tuesday 6th November 2012, 13:18   #12
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Armenicus

Just curious – whereabouts is the type locality of armenicus ('Adshafana, Kurdistan')?

PS. I must learn to avoid terms like 'indisputably'.

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Old Tuesday 6th November 2012, 19:07   #13
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Richard said "whereabouts is the type locality of armenicus ('Adshafana, Kurdistan')?"
Such a simple question, but google has no answer. Must be a German, Russian approximation of the Kurdish place name. I have seen it as Dorf Adshafana?? I have seen Vaurie called it next door to Armenia??
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Old Tuesday 6th November 2012, 19:19   #14
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Am I right in thinking that Laurent's tree would support the separation of maurus from stejnegeri IF just two "stejnegeri" were misidentified (and were in fact maurus) AND eight "maurus" were misidentified (and were in fact stejnegeri)? Not impossible perhaps? The fact that variegatus appears in both sides of the relevant parts of the tree is really unhelpful though as this taxon at least should be easy to identify..

cheers, alan
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Old Tuesday 6th November 2012, 19:22   #15
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Originally Posted by Richard Klim View Post
Just curious – whereabouts is the type locality of armenicus ('Adshafana, Kurdistan')?
The online "fuzzy gazetteers", such as http://dma.jrc.it/services/fuzzyg/ or http://isodp.hof-university.de/fuzzyg/query/, didn't give any meaningful answer either.
It'd be interesting to know how Stegmann wrote it. "Adshafana" is how it was written in Peter's Check-list; but they also transcribed "Şamaxı" as "Shemakha"...
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Old Tuesday 6th November 2012, 19:40   #16
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I would guess the Mongolian maurus are all stejnegeri.
The variegatus specimens are odd, especially since Rostov should not be variegatus territory I believe.
From combining two articles, it is clear that the basal clades (closely linked to leucurus) are the East/South Asian ones (which you would exect for a Saxicola). It is unclear how far west these come (no samples for armenicus and variegatus is not entirely trustworthy), or how stejnegeri is related to indicus (especially as przewalskii wasn't sampled).

Basal DNA turning up in Spain could hint at "relict" mtDNA in some western populations... something I would not find entirely odd (there are relict taxa in Spain/Morocco, so why wouldn't a "basal clade" Stonechat have occurred there before it got swamped by Out-of-Africa rubicola?)
I can also see birds with maurus mtDNA hybridise with "basal" birds on their migration route, causing a mixed population.

However, I would guess only large samples (and preferably some back up by other genetic markers) will give a clearer picture.
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Old Tuesday 6th November 2012, 19:43   #17
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Am I right in thinking that Laurent's tree would support the separation of maurus from stejnegeri IF just two "stejnegeri" were misidentified (and were in fact maurus) AND eight "maurus" were misidentified (and were in fact stejnegeri)? Not impossible perhaps? The fact that variegatus appears in both sides of the relevant parts of the tree is really unhelpful though as this taxon at least should be easy to identify..
Again, this is how they ID'd the birds in the paper's corrigendum, and I don't know how they reached these ID's.
- Both haplogroups co-occurred in the Chitinska Oblast (labelled "Rus: Chita" in my tree), but all the birds from this Oblast were nevertheless called stejenegeri: this is how you get some stejnegeri in the maurus clade.
- The geographical haplotype divide passes across the middle of Mongolia, but all the birds from this country were nevertheless called maurus: this is how you get some maurus in the stejnegeri clade. There was no co-occurrence of the haplogroups at any individual site there.
- Additionally, I also have absolutely no idea why the Rostov birds called variegatus are not plain rubicola with a wrong haplotype. As far as I can tell from the literature, rubicola is the only taxon that should occur at this place.
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Old Tuesday 6th November 2012, 19:55   #18
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Again, this is how they ID'd the birds in the paper's corrigendum, and I don't know how they reached these ID's.
- Both haplogroups co-occurred in the Chitinska Oblast (labelled "Rus: Chita" in my tree), but all the birds from this Oblast were nevertheless called stejenegeri: this is how you get some stejnegeri in the maurus clade.
- The geographical haplotype divide passes across the middle of Mongolia, but all the birds from this country were nevertheless called maurus: this is how you get some maurus in the stejnegeri clade. There was no co-occurrence of the haplogroups at any individual site there.
- Additionally, I also have absolutely no idea why the Rostov birds called variegatus are not plain rubicola with a wrong haplotype. As far as I can tell from the literature, rubicola is the only taxon that should occur at this place.
Laurent

Very many thanks, that all makes sense. The alleged "variegatus" the only really (very) odd anomaly without obvious explanation, given its distinctiveness.

cheers, alan
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Old Tuesday 6th November 2012, 20:06   #19
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Originally Posted by Xenospiza View Post
Basal DNA turning up in Spain could hint at "relict" mtDNA in some western populations... something I would not find entirely odd (there are relict taxa in Spain/Morocco, so why wouldn't a "basal clade" Stonechat have occurred there before it got swamped by Out-of-Africa rubicola?)
In BOLD, the stejnegeri BIN also apparently includes one "Saxicola torquata" from Sweden and one "Saxicola rubicola" from Rogaland, Norway, albeit the details of these birds are not publicly accessible.

OTOH (and I don't really know what to do with this): one of the two "basal" Spanish cytb sequences in Illera et al. is clearly a chimera. EU421091: this seq is indicus-like (100% identical to their EU421081), up to a 'N' in position 744 of the entire cytb; the rest is a perfectly standard rubicola sequence (100% identical to their EU421090). (This seq also ends up at the end of an oddly long branch in their tree.)

Quote:
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Basal DNA turning up in Spain could hint at "relict" mtDNA in some western populations... something I would not find entirely odd (there are relict taxa in Spain/Morocco, so why wouldn't a "basal clade" Stonechat have occurred there before it got swamped by Out-of-Africa rubicola?)
But under such a scenario, surely you wouldn't expect the western basal haplotypes to be identical to eastern basal haplotypes...?
(Logically they should be more distinct from eastern haplotypes than the haplotypes of these Out-of-African rubicola are from African birds.)

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Old Tuesday 6th November 2012, 20:08   #20
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Richard said "whereabouts is the type locality of armenicus ('Adshafana, Kurdistan')?"
Such a simple question, but google has no answer. Must be a German, Russian approximation of the Kurdish place name. I have seen it as Dorf Adshafana?? I have seen Vaurie called it next door to Armenia??
Unfortunately Dorf is just German for village. So it's presumably a village in Kurdistan - and therefore could theoretically be in Turkey, Iraq, Iran or Armenia (all partly within the range of armenicus), but perhaps now officially known by an alternative name used/mandated by the modern nation...?

PS. Urquhart & Bowley 2002 (Stonechats):
Quote:
S. m. armenica
Breeds as far north as the 42nd parallel [= eg, Dagestan]..., primarily breeding south and east of the range of variegata, possibly intergrading with variegata where their ranges overlap in Transcaucasia. ...with breeding specimens obtained from Shemakha [= Şamaxı] and around Tbilisi [Georgia!] in Azerbaijan, and others collected from Zakataly in Georgia [= Zaqatala - in Azerbaijan!]...

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Old Tuesday 6th November 2012, 21:03   #21
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But under such a scenario, surely you wouldn't expect the western basal haplotypes to be identical to eastern basal haplotypes...?
No, indeed.
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Old Tuesday 6th November 2012, 21:39   #22
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Unfortunately Dorf is just German for village. So it's presumably a village in Kurdistan - and therefore could theoretically be in Turkey, Iraq, Iran or Armenia (all partly within the range of armenicus), but perhaps now officially known by an alternative name used by the modern nation...?
With no evidence or justification whatever I'm going to drop an Arabic-sounding prefix, change some pronunciation a bit, and end up with Şirvan, a town in the Kurdish part of south-eastern Turkey.
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Old Wednesday 7th November 2012, 08:16   #23
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Armenicus

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With no evidence or justification whatever I'm going to drop an Arabic-sounding prefix, change some pronunciation a bit, and end up with Şirvan, a town in the Kurdish part of south-eastern Turkey.
Sounds plausible, Paul. But Şirvan/Şêrwan (in Siirt Province) is probably near the westernmost limit for armenicus. And I've belatedly noticed the account in Roselaar 1995 (Songbirds of Turkey)...
Quote:
S. t. armenica Stegmann, 1935, 'Adshafana, Kurdistan' (near the border of Iran, Iraq, and Turkey). ...

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Old Wednesday 7th November 2012, 20:22   #24
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l_raty wrote "It'd be interesting to know how Stegmann wrote it." I have seen Аджарана, Курдистан. Not 100 percent sure this is Adshafana, Kurdistan, as I only dabbled with Ukrainian twenty years ago!
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Old Thursday 8th November 2012, 02:28   #25
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That would be "Adzharana" rather than "Adshafana". It wouldn't be hard to mistake an "r" for an "f" in handwriting in a Latin script, harder at any rate than the same mistake in a Cyrillic script ("р" mistaken for "ф").
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