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Scolopaci

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Old Monday 17th May 2010, 18:04   #1
Peter Kovalik
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Scolopaci

Gibson 2010. Phylogenetic relationships among the Scolopaci (Aves: Charadriiformes): Implications for the study of behavioural evolution.
Here
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Old Wednesday 19th May 2010, 19:56   #2
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Anyone has the contact details of Rosemary?

Cheers, Szimi
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Old Wednesday 19th May 2010, 20:10   #3
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Anyone has the contact details of Rosemary?
http://labs.eeb.utoronto.ca/abaker/rosemary.html
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Old Thursday 20th May 2010, 07:27   #4
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Gracias :)
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Old Friday 11th June 2010, 10:44   #5
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Incl. Scolopaci:

Anders Ödeen, Olle Håstad, and Per Alström
Evolution of ultraviolet vision in shorebirds (Charadriiformes)
Biol. Lett. June 23, 2010 6:370-374
Abstract
Electronic supplementary material
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Old Thursday 17th June 2010, 09:50   #6
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Pluvialis

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Incl. Scolopaci:

Anders Ödeen, Olle Håstad, and Per Alström
Evolution of ultraviolet vision in shorebirds (Charadriiformes)
Biol. Lett. June 23, 2010 6:370-374
Abstract
Electronic supplementary material
Non-monophyletic origin of Charadriidae

By Ödeen et al Charadriidae is polyphyletic (or paraphyletic) if Pluvialis is considered to be a member of Charadriidae

Similar results:
- Ericson, Envall, Irestedt & Norman, 2003. Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data. BMC Evolutionary Biology 2003, 3:16.
Full paper

- Baker, Pereira & Paton, 2007. Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds. Biol. Lett. (2007) 3, 205–209.
Full paper

- Fain & Houde, 2007. Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves). BMC Evolutionary Biology 2007, 7:35.
Full paper
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Old Monday 2nd April 2012, 19:28   #7
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Gibson & Baker

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Gibson 2010. Phylogenetic relationships among the Scolopaci (Aves: Charadriiformes): Implications for the study of behavioural evolution. Here
Gibson & Baker (in press). Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes). Mol Phylogenet Evol. [abstract]
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Old Wednesday 25th July 2012, 09:30   #8
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Polynesian sandpipers

Cibois, Dekker, Pasquet & Thibault (in press). New insights into the systematics of the enigmatic Polynesian sandpipers Aechmorhynchus parvirostris and Prosobonia leucoptera. Ibis. [abstract]
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Old Friday 10th August 2012, 18:37   #9
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Polynesian sandpipers

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Cibois, Dekker, Pasquet & Thibault (in press). New insights into the systematics of the enigmatic Polynesian sandpipers Aechmorhynchus parvirostris and Prosobonia leucoptera. Ibis. [abstract]
John Boyd (TiF):
www.jboyd.net/Taxo/changes.html [10 Aug 2012]
www.jboyd.net/Taxo/List8.html#scolopacidae
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Old Thursday 13th September 2012, 21:39   #10
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Chubbia

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Gibson & Baker (in press). Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes). Mol Phylogenet Evol. [abstract]
AOU-SACC Proposal #546 (Remsen, Sep 2012): Resurrect Chubbia.

[As John Boyd (TiF): www.jboyd.net/Taxo/List8.html#scolopacidae]

Last edited by Richard Klim : Thursday 13th September 2012 at 21:48.
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Old Friday 14th September 2012, 07:53   #11
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Originally Posted by Richard Klim View Post
AOU-SACC Proposal #546 (Remsen, Sep 2012): Resurrect Chubbia.

[As John Boyd (TiF): www.jboyd.net/Taxo/List8.html#scolopacidae]
Cox1 sequences suggest that G. undulata is still closer to Coenocorypha than G. (Chubbia) imperialis, thus resurrecting Chubbia seems unlikely to solve the problem...
(With the exception of these two, "large southern" Gallinago are basically unsampled in phylogenetic studies. Lymnocryptes, however, is clearly not embedded in Gallinago, as sampled up to now.)

(I have significant problems with the data in Gibson & Baker 2012.)

I've attached a cox1 ML consensus tree (all Charadriiformes), if anyone is interested.
Attached Files
File Type: pdf cox1-Charadriif-consensus.pdf (20.3 KB, 232 views)
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Old Friday 14th September 2012, 08:19   #12
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Chubbia

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Cox1 sequences suggest that G. undulata is still closer to Coenocorypha than G. (Chubbia) imperialis, thus resurrecting Chubbia seems unlikely to solve the problem...
Perhaps Xylocota Bonaparte,1839 should be resurrected for G undulata: World Bird Info.
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Old Friday 14th September 2012, 10:37   #13
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Chubbia

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Perhaps Xylocota Bonaparte,1839 should be resurrected for G undulata: World Bird Info.
Yes, this seems possible.
But then again no data is available for stricklandii or jamesoni, hence we can't be sure that Chubbia is monophyletic. And what about nobilis? Or, in the Old World, nemoricola, solitaria...?
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Old Sunday 16th September 2012, 19:17   #14
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Has G. p. magellanica (Magellanic Snipe) been sampled relative to the rest of South American Snipe?

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Old Monday 17th September 2012, 06:45   #15
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South American Snipe

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Has G. p. magellanica (Magellanic Snipe) been sampled relative to the rest of South American Snipe?
There are 5 birds labelled Gallinago paraguaiae in BOLD, 3 from Corrientes, N Argentina, 1 from Rio Grande do Sul, S Brasil, and 1 from Guyana.
These have all very similar barcodes.

But this record in BOLD (not included in the tree I posted the other day; record not ID'd, but it is the only record in its BIN, and the BIN is labelled "Gallinago gallinago"; from Neuquen, C Argentina, in May) is most likely a magellanica.
The sequence is basal in the Common Snipe group, like those of paraguaiae, but it differs from the latters by a bit more than 2% (see attachment).


(There are also two divergent (~3% divergence) cyt-b sequences of Gallinago paraguaiae in GenBank (FJ603655 and JQ963047), a situation that normally should suggest divergence exists within this taxon. But these two were apparently obtained from the same voucher specimen ("L50137", Brazil), which is, well, kind of a problem...)

L -
Attached Files
File Type: pdf cox1-Scolopacid-all-consensus.pdf (10.5 KB, 189 views)

Last edited by l_raty : Monday 17th September 2012 at 07:46. Reason: added title
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Old Monday 17th September 2012, 06:57   #16
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South American Snipe

Jaramillo 2003 (Birds of Chile) comments:
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Preliminary analysis of sounds produced by southern magellanica compared to more northern paraguaiae demonstrate that the two have significantly different winnowing displays. The level of difference is as great as in other species pairs of Gallinago. Puna Snipe is also different, corroborating more recent recognition of this as a species. Further analyses and vocal data will likely confirm species-level differences between magellanica and paraguaiae. The Falklands population has yet to be subjected to vocal analysis.
AOU-SACC: "proposal badly needed."
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Old Monday 17th September 2012, 12:54   #17
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Thanks!

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Old Tuesday 18th September 2012, 15:13   #18
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"And what about nobilis?"

My experience of this bird is a morphologically pretty typical, diurnal (not nocturnal), wetland inhabiting Gallinago sort of Snipe. But you never know what mtDNA will turn up.
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Old Tuesday 18th September 2012, 20:17   #19
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In the SACC proposal to resurrect Chubbia it states there is no reason why some snipe would not converge on “woodcockness”, and in fact there may be a continuum between the two groups in ecology and morphology. And, I favor resurrecting Chubbia because I think that the limited data so far puts the burden-of-proof on the position that merges it into Chubbia, especially because no explicit rationale was published for its merger into Gallinago. De Schauensee did not give a rational for the merger but in 1968 Jehl gave a good rational, I think. And it revolves around convergence.

R E L AT I O N S H I PS IN THE CHARADRII (SHOREBIRDS):

A TAXONOMIC STUDY BASED ON COLOR PATTERNS OF THE DOWNY YOUNG

Joseph Jehl Jr. SAN DIEGO SOCIETY OF NATURAL HISTORY MEMOIRS

Memoir 3, pages 1-54, figures 1-31,

Issued September 30, 1968

I follow De Schauensee (1966) in merging Chubbia with Gallinago. The idea of close affinity between Gallingo and Scolopax is of long standing. Adults of these genera are morphologically similar and several South American species of Gallinago (stricklandii.janies- oni, imperialis) that were formerly placed in Chubbia (Peters, 1934) seem to bridge the gap neatly between the longer-legged, slender snipe and the squat, robust woodcocks. Yet, chicks of
Scolopax and GalUnago are dissimilar. The close relationship of these genera is so widely accepted that the lack of similarity in their chicks may
indicate little more than the danger of relying on too few characters in determining relationships. Since snipe tend to nest in marshy areas and
woodcocks in forested regions, some differences in chick patterns might be predicted. However, in view of the similarity of downy patterns within
other wader subfamilies, it is somewhat disturbing to find that nowhere among the snipe and their allies are there downy patterns that even vaguely
approximate that of Scolopax. and, furthermore, that the variation in snipe and woodcock downy plumage is insufficient to give any clues to how one
plumage pattern could have been evolved from the other. This transformation is far more difficult to achieve than reference to the pattern diagrams
might suggest, for it requires extensive changes in color and feather structure as well as in pattern icf. Figs. 2 M, N; 16, 17). On the other hand, it requires little imagination to visualize the evolution of a
Scolopax pattern from that of a tringine sandpiper.

Although Scolopax and Gallinago can be pre- sumed to have arisen from a common ancestor, which may have been tringine, the great differences between their chicks suggest that these genera are more distantly related than is currently recognized. Pending a re-examination of these rela- tionships I suggest that a separate subfamily, Gallinagoninae, be established for the snipe and their allies. This separation has also been suggested by Verheyen (1958a) on the basis of osteological characters as well as chick plumages.
The chicks of species formerly assigned to Chubbia are typically snipelike. I interpret the similarities between the adults and Scolopax as convergent. These woodcock-like snipe occur only in South America, where the most extensive snipe radiation has taken place; woodcocks, in spite of their otherwise widespread distribution, are ab- sent from that continent.
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Old Wednesday 10th October 2012, 07:09   #20
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Arenariinae

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Gibson & Baker (in press). Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes). Mol Phylogenet Evol. [abstract]
Banks 2012. Classification and Nomenclature of the Sandpipers (Aves: Arenariinae). Zootaxa 3513: 86–88. [preview]
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Old Saturday 13th October 2012, 07:04   #21
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SACC proposal

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Originally Posted by Richard Klim View Post
Gibson & Baker (in press). Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes). Mol Phylogenet Evol. [abstract]
Quote:
Originally Posted by Richard Klim View Post
Banks 2012. Classification and Nomenclature of the Sandpipers (Aves: Arenariinae). Zootaxa 3513: 86–88. [preview]
AOU-SACC Proposal #555 (Remsen, Oct 2012): Reclassification of the Scolopacidae.
Quote:
The above does not deal with the problems of generic limits in the Calididrinae, e.g., sister relationship of Aphriza to C. canutus; see Banks (2012). Dick Banks is submitting a proposal to NACC on this, and I suggest we do not meddle until dust settled.

Last edited by Richard Klim : Saturday 13th October 2012 at 07:37. Reason: NACC proposal.
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Old Sunday 21st October 2012, 07:28   #22
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TiF

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AOU-SACC Proposal #555 (Remsen, Oct 2012): Reclassification of the Scolopacidae.
John Boyd (TiF):
www.jboyd.net/Taxo/changes.html [20 Oct 2012]
www.jboyd.net/Taxo/List8.html#scolopacidae
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Old Monday 22nd October 2012, 19:44   #23
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Thanks for sharing this. Interesting changes! Buttonquails are well inside the group of shorebirds.

Best, Szimi
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Old Tuesday 23rd October 2012, 20:26   #24
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(I have significant problems with the data in Gibson & Baker 2012.)
Trying to crawl my way through this... (Sorry: quite long!) Gibson (2010) and Gibson & Baker (2012) offered only a purely Bayesian analysis, which is not something a trust a lot, so I was interested to see how the results would look if analysed with Maximum Likelihood.

The analysis was based on 5 genes: 12S-rRNA (12s, mitochondrial), cytochrome oxidase subunit-1 (cox1/coi/barcode, mitochondrial), cytochrome b (cytb, mitochondrial), NADH dehydrogenase subunit-2 (nd2, mitochondrial), and Recombination Activating Gene 1 (rag1, nuclear, exon). Reconstructing exactly their dataset is not really possible, however, because (1) their cox1 sequences were taken from a "concurrent DNA barcoding study in [thei]r lab" (presumably Rebecca Elbourne's MSc thesis), and (2) for the other genes, they clearly took many of their sequences from earlier datasets; in both cases, they did not detail which sequences they used. Sequences specifically associated to this work appear in GenBank under accession numbers JQ962980-JQ963056: although these were presumably all used in the analysis, they undoubtedly only represent a small subset of the analysed matrix (77 sequences in total; the full data matrix has 86 taxa * 5 genes = 430 cells).

Cox1 sequences, for all the taxa in the tree except Hydrophasianus chirurgus and Microparra capensis (both also lacking in Rebecca Elbourne's thesis), can easily be retrieved from BOLD. Except in a few rare cases, several sequences are available for each taxon, and their congruence can readily be checked. These data look entirely problem-free to me. As to the other 4 genes and included taxa, a list of what can be retrieved from GenBank appears in the attached .txt file (mostly interesting to buid your own idea about possible gaps in the sampling).

I presumed that, where sequences are not available either in GenBank or in BOLD, the gene must have been coded as missing data for the given taxon in the analysis (ie., a part of the data was not kept away from the public). On the other hand, it is certain that a part of what can be accessed in GenBank, in particular sequences published by entirely different research groups, was not used in the analysis, even though it existed.

================

I first started with some exploratory analysis of the non-cox1 data, building trees for each gene (in some cases for specific parts of the genes), trying to compare sequences derived from the same taxon, looking at alignments, etc. The data, unfortunately (and as I already wrote above), does not appear completely problem-free. What follows is a list of issues involving sequences that were prossibly/presumably included in the analysis.
  • - Phalaropus tricolor, cytb: AY894240 (voucher: RCA87-192, 870 bp, Pereira & Baker 2005)
    - Gallinago gallinago, cytb: FJ603652-54 (voucher: multiple, 702 bp, Baker et al. 2009)
    - Gallinago gallinago, cytb: FJ787309-10 (voucher: 5984/5312, 943 bp, Hering & Päckert 2010)
    - Gallinago gallinago, cytb: AF194445-6 (voucher: /, 277 bp, Austin unpubl.)
    - Gallinago delicata, cytb: FJ603651 (voucher: 1B-2986, 702 bp, Baker et al. 2009)

    These are all near-identical; in trees, they appear embedded in Gallinago.
    Conclusion: AY894240 (Pereira & Baker 2005) is presumably misidentified, and is G. gallinago/delicata.
  • - Limnodromus scolopaceus, 12s: EF373090 (voucher: MKP-1523, 552 bp, Baker et al. 2007)
    - Limnodromus scolopaceus, 12s: AF285806 (voucher: /, 462 bp, Spellman & Winker 2001)
    - Phalaropus tricolor, 12s: DQ674581 (voucher: /, 1042 bp, Fain & Houde 2007)

    EF373090 is near-identical to DQ674581, but highly divergent from DQ674581; in trees, EF373090 and DQ674581 cluster with Phalaropus tricolor AY894155, then with tringines, not with scolopacines.
    Conclusion: EF373090 (Baker et al. 2007) is presumably misidentified, and is Phalaropus tricolor.
  • - Limnodromus scolopaceus, cytb: EF373140 (voucher: MKP-1523, 925 bp, Baker et al. 2007)
    - Limnodromus scolopaceus, cytb: AF285819 (voucher: /, 1019 bp, Spellman & Winker 2001)

    EF373140 is highly divergent from AF285819; in trees, it appears as the sister group of (Phalaropus fulicarius JQ963055 + Phalaropus lobatus AY894239), and associated to tringines, not to scolopacines; for AF285819, see below.
    Conclusion: EF373140 (Baker et al. 2007) is problematic/misidentified; considering that Baker et al.'s 12s "Limnodromus scolopaceus" appears to be a misidentified Phalaropus tricolor, it seems reasonable to me to assume that the same applies to their cytb.
  • - Gallinago gallinago, 12s: EF373082 (voucher: MKP-1590, 554 bp, Baker et al. 2007)
    - Gallinago gallinago, 12s: DQ674576 (voucher: /, 1044 bp, Fain & Houde 2007)
    - Gallinago gallinago, 12s: FJ603664-66 (voucher: multiple, 675 bp, Baker et al. 2009)
    - Limnodromus scolopaceus, 12s: AF285806 (voucher: /, 462 bp, Spellman & Winker 2001)

    EF373082 is near-identical to AF285806, but highly divergent from DQ674576 and FJ603664-66 (which are all near-identical to one another); in trees, EF373082 and AF285806 appear as the sister group of (Limnodromus griseus JQ962988 + Limnodromus sp. DQ674578).
    Conclusion: EF373082 (Baker et al. 2007) is presumably misidentified, and is Limnodromus scolopaceus.
  • - Gallinago gallinago, cytb: EF373132 (voucher: MKP-1590, 943 bp, Baker et al. 2007)
    - Gallinago gallinago, cytb: FJ603652-54 (voucher: multiple, 702 bp, Baker et al. 2009)
    - Gallinago gallinago, cytb: FJ787309-10 (voucher: 5984/5312, 943 bp, Hering & Päckert 2010)
    - Gallinago gallinago, cytb: AF194445-6 (voucher: /, 277 bp, Austin unpubl.)
    - Gallinago delicata, cytb: FJ603651 (voucher: 1B-2986, 702 bp, Baker et al. 2009)
    - Limnodromus scolopaceus, cytb: AF285819 (voucher: /, 1019 bp, Spellman & Winker 2001)

    EF373132 is highly divergent from FJ603652-54, FJ787309-10, AF194445-6, and FJ603651 (which are all near-identical to one another); in trees, it clusters first with AF285819, then with Limnodromus griseus JQ963049. However, EF373132 and AF285819 are not near-identical; they start the same, remain so over the first 345 bp of EF373132, then start diverging more and more until the end of the sequence (suggesting a sequencing problem in one of them); the overal distance between them is about 5%; in trees, this divergence is reconstructed as fully autapomorphic for AF285819; looking at the distances between the two sequences and their nearest BLAST matches also shows that AF285819 is globally more distant from all closely-related shorebird sequences than EF373132.
    Conclusion: This one is a though call. EF373132 is clearly not G. gallinago, and is at least mostly L. scolopaceus; as Baker et al.'s 12s "G. gallinago" appears to be, in its entirety, a misidentified L. scolopaceus, it seems reasonable to consider that the same could apply to their cytb. But this doesn't solve everything: besides this consideration, either EF373132 or AF285819 still appears to be incorrect due to a sequencing problem; the apparent autapomorphic character of the divergence of AF285819 leads me to think that a sequencing problem occurred there. IOW: I think the most likely explanations to what I see, is that (1) EF373132 (Baker et al. 2007) is misidentified, and is Limnodromus scolopaceus (but I see no strong suggestion that it suffers other problems); and (2) AF285819 (Spellman & Winker 2001), although correctly identified, suffers from a sequencing problem.
  • - Gallinago delicata, cytb: JQ963043 (voucher: JGS-1783, 852 bp, Gibson & Baker 2012)
    - Gallinago gallinago, cytb: FJ603652-54 (voucher: multiple, 702 bp, Baker et al. 2009)
    - Gallinago gallinago, cytb: FJ787309-10 (voucher: 5984/5312, 943 bp, Hering & Päckert 2010)
    - Gallinago gallinago, cytb: AF194445-6 (voucher: /, 277 bp, Austin unpubl.)
    - Gallinago delicata, cytb: FJ603651 (voucher: 1B-2986, 702 bp, Baker et al. 2009)

    JQ963043 is made of two sequenced fragments (353 and 411 bp respectively), separated by an 88 bp non-sequenced gap (a "poly-N" in the sequence). This sequence is congruent with the other sequences of G. gallinago/delicata listed above, except for the 213 last bp of the first sequenced fragment: this part differs by 15 substitutions (and has an additional 13 unidentified positions, which suggests a problem as well).
    Conclusion: there was apparently a problem with the sequencing of this part of JQ963043 (Gibson & Baker 2012).
  • - Numenius minutus, cytb: EF373145 (voucher: S-072-78498, 963 bp, Baker et al. 2007)
    - Numenius arquata, cytb: AF417929 (voucher: /, 1143 bp, Chen et al. 2003)

    These two sequences are near-identical; in trees, they appear embedded in the "large curlew" group (clading with N. madagascariensis AF417925, as the sister group of N. americanus JQ963052) which is the position of N. arquata (both based on traditional morphology/biogeography, and on all other available mt genes).
    Conclusion: EF373145 is presumably misdentified, and is Numenius arquata.
  • - Numenius tahitiensis, 12s: JQ962997 (voucher: BTCU-113, 550 bp, Gibson & Baker 2012)
    - Limosa limosa islandica, 12s: JQ962990 (voucher: MKP-1596, 555 bp, Gibson & Baker 2012)

    These two sequences are near-identical; in trees, they appear embedded in Limosa.
    Conclusion: JQ962997 (Gibson & Baker 2012) is presumably misdentified, and is a western L. limosa, probably L. l. islandica.
  • - Phalaropus lobatus, rag1: AY894222 (voucher: JMP-2057, 885 bp, Pereira & Baker 2005)
    - Microparra capensis, rag1: EF373194 (voucher: MKP-1479, 2611 bp, Baker et al. 2007)
    - Tringa stagnatilis, rag1: AY894219 (voucher: MKP-1353, 885 bp, Pereira & Baker 2005)

    AY894222 and EF373194 are near-identical (where EF373194 overlaps with the others = first 854 bp of EF373194, last 854 bp of the other two); in trees based on this fragment, these three sequences cluster together with high support, outside both Scolopacidae and Jacanidae. BLAST searches based on these sequences produce odd results, with Haematopus ater AY228794 appearing systematically among the closest matches.
    Conclusion: where they overlap, these three sequences are presumably wrong, but I can't identify the problem precisely. Note that the rest of EF373194, as far as can be judged, behaves "normally" (ie., Microparra clusters with Irediparra and Actophilornis in Jacanidae) and may perfectly be correct.
Of course it can be difficult to be sure that an apparently wrong sequence in GenBank was actually used in a published analysis. This is particularly true for simple misidentifications, as sequences may as well have been interverted at the time of deposition, and the analysis might be fully correct. Here, however, some aspects of the published tree also suggest that the dataset was not "fully clean". The relationships within Numenius in this tree, in particular, are clearly wrong as far as I'm concerned, but not unexpected given the problems described above (tahitiensis "most divergent", attracted towards godwits due to its 12s Limosa sequence; minutus probably closer to "large curlews" than it really is, due to its arquata cytb). The long branches leading to Gallinago gallinago and G. delicata, as well as the "less-than-1" PP associated to this node, might also be linked to the inclusion of wrong sequences (these taxa are not supposed to differ at all genetically). Similarly, the long branch leading to, and the weakness of the tree reconstruction (low PPs) around Tringa stagnatilis might easily be due to the rag1 sequence AY894219.

================

Taking the above into consideration, I reconstructed a dataset, using cox1 sequences from BOLD, and sequences of the other 4 genes, as available in GenBank. I omitted the sequences that looked problematic to me, or used them as being what I believed they are, as explained above. I divided this dataset into 9 partition as in Gibson & Baker 2012: one for the 12s, one for 1st and 2nd positions of each of the 4 coding genes, one for 3rd positions of each of the 4 coding genes; I selected models for these partitions based on the AICc criterion in TreeFinder; then I reconstructed a "best" ML tree, and ran a 100-replicate bootstrap analysis. The unbootstrapped tree and the consensus tree from the bootstrap analysis are attached.

The results are rather similar to Gibson & Baker's, with the main exception of the curlews (I omitted the two problematic sequences, which resulted in a tree consistent with single-gene analyses - minutus most divergent, tahitiensis sister to whimbrels. The support for internal nodes, in ML, is rather weak. The Calidris radiation, in particular, also appears basically unresolved (which is rather unsurprising, given that many of the taxa actually stand in the matrix based on a cox1 sequence only).

(My take at high PP/low BS, is that this indicates that a "best" tree is clearly identified given the dataset, but that this tree should probably be expected to be highly sensitive to the addition of new data.)

OK, I'll stop with this for now (but I'd welcome thoughts on the above).

Cheers, L -

Last edited by l_raty : Wednesday 24th October 2012 at 06:42. Reason: added 2 missing sequence authorships
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Old Wednesday 24th October 2012, 01:51   #25
alytothrix
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Excellent work, Laurent. It seems that quite a few of these issues could have been caught if the authors of the various papers had BLASTed all of their sequences before using them in their analyses. At least the results are not affected too badly.
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