Charadriiformes (1 Viewer)

gusasp said:

Surprising stuff! Especially the placement of tricollaris & forbesi. They've been previously considered conspecific, now they are presumably in different genera! To my eye this seems very strange.

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Seconded. (But note that support for the position of both, besides the fact that they are both in "CRD I(a)", and not embedded in the hyalicula/melodus/semipalmatus/vociferus subgroup, is very low.)
And look at Fig. 2 (an earlier version is in the thesis, p. 131): this shows 6 trees, obtained with the 6 genes they used (cox1, nd3, adh5, bfib7, myo, rag1); tricollaris and forbesi there are both in "CRD I" in trees a, b, c and e; but tricollaris ends up in "CRD II" in tree d, and in tree f it is forbesi that ends up there. This discrepancy is somewhat surprising, particularly given that, for most species, the six genes recover similar relationships.
Direct access to the data referenced in the thesis (KM001088-KM001594) appears to be open in GenBank (although the sequences are not retrieved by searches). However, they clearly added data for some species since (in the thesis, they lacked bicinctus cox1, placidus nd3/rag1, melodus myo/nd3, ruficapillus adh5, morinellus nd3/adh5/bfib7/myo; but these species are now present in all 6 trees in Fig.2), and I have no idea where these are. (Nor, actually, if they have been deposited anywhere.)

l_raty said:

However, they clearly added data for some species since (in the thesis, they lacked bicinctus cox1, placidus nd3/rag1, melodus myo/nd3, ruficapillus adh5, morinellus nd3/adh5/bfib7/myo; but these species are now present in all 6 trees in Fig.2)

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Mmh, no, that doesn't seem to be correct inference. (? NB - I don't have any actual experience with BEAST.) In fact, the 6 gene trees all include all the taxa in the thesis as well, despite an explicit statement that, for several of them, data were entirely lacking for some of the loci. Thus these 6 trees would appear to be the individual gene trees that were co-estimated during the joint analysis of the 6 loci, not trees estimated independently based on the sequence data from a single locus. (I'm quite uncertain of the actual meaning of such trees, though. If species represented by no data at all for a given locus find a place in the gene tree inferred for this locus, and this place seems coherent with the rest, this means that the inference of this tree is significantly constrained by the information contained in the other loci...)

For six species (Charadrius alticola, asiaticus, forbesi, obscurus, peronii, placidus), the data were obtained from toe pads of museum specimens. For these, the sequences that were amplified were shorter (different pairs of primers delimiting shorter amplicons). ...In a number of cases, presumably shorter than 200bp, which is the lower limit for sequences that GenBank will proceed. The following sequences which, as far as I understand, they did amplify, are lacking in the deposited data set:
About these, I cannot say anything. Regarding the sequences that are available in the deposited data set:

1. cox1:
   • KM001331-2 Charadrius veredus: both are identified by the BOLD ID engine as Stiltia isabella. I think these may have been replaced with correct sequences at some point between the production of the thesis and that of the paper, however (the species was basal in the "cox1" tree (a) shown in the thesis; it is sister to asiaticus as expected in the equivalent tree in the paper).
   • KM001298-300 Charadrius peronii: KM001299 may be correct; the other two are very similar to one another but differ from the first one; most of the substitutions are grouped in the central part of the sequence (bp1-110: 4; bp111-290: 32; bp291-385: 0); this central part (bp111-290) is 100% identical to a Gallinago paraguaiae sequence in BOLD, nested within Gallinago in ID trees, and unlike any Charadrius.
   • KM001301-3 Charadrius placidus: BOLD finds no match to the entire sequence; bp1-130: no match in BOLD, nearest matches in BLAST are Calidris melanotos sequences, no Charadrius in the nearest 100 matches; bp131-300: fully identical to 10 congruent sequences of Charadrius alticola (7 from BOLD, and the 3 sequences of the present study); bp300-429: BOLD again finds no match, nearest matches in BLAST are Charadrius dubius sequences. In the "cox1" trees, this species ended up basal in CRD II (both in the thesis and paper), while it was within CRD I in the species tree.
   • (KM001333-5 Vanellus miles: the three sequences are congruent and fall within Vanellus, but they differ a lot from the 4 sequences that are in BOLD; divergence seems stronger towards the end of the sequences (BOLD finds V. miles as nearest match when run on the first 200bp only [albeit distance still around 3%], but finds no match at all when run on the whole sequence), which I do not expect in a coding gene. These sequences were not used in the paper.)
2. nd3: I see no problem.
   (KM001266-7 Charadrius collaris: these sequences are not congruent with two older sequences, but the problem here is clearly with these two older sequences (FR823281: first part = alexandrinus, second part = ruficapillus; FR823282: first part congruent with the new sequences; second part = alexandrinus; these are associated to Rheindt et al. 2011 in GenBank, but I see no evidence in the work that they were used there).)
3. adh5: I see no problem in the data that were used for the paper.
   (KM001163 Vanellus miles: this sequence differs from the other two (KM001161-2), which are congruent; all substitutions are in the central part of the sequence (bp1-210: 0; bp211-340: 9; bp241-599: 0); the divergence is reconstructed as wholly autapomorphic. This part of this sequence may be not be fully correct; if given the choice, I would rather not use this sequence. These sequences were not used in the paper.)
4. myo: I see no problem.
5. bfib7: KM001489-90 Charadrius tricollaris: these three sequences are fully identical to the three sequences of C. thoracicus (KM001482-4), and fall in a position consistent with the latter. C. tricollaris ends up in CRD II, sister to thoracicus in the "bfib7" (d) tree, both in the thesis and in the paper. (But note that, in these trees, it is not apparent that the divergence is zero.) This may be what caused this species to end up in an unexpectedly basal position within CRD I(a) in the species trees.
   (KM001470-2 Pluvialis squatarola: presumably not a problem, but there is an interesting, obvious 86bp inversion in the three sequences; not present in P. dominica; I had to replace these 86bp by their reverse complement to restore base homology in the alignment.)
6. rag1: KM001514-5 Charadrius bicinctus: these two sequences are only one substitution away from the three sequences of Vanellus miles (KM001586-8), and nested within Vanellus...? In the "rag1" tree (f) of the thesis, this species also clusters with Vanellus; in the equivalent tree of the paper (no Vanellus included), the species is highly divergent and falls between CRD I and CRD II.

I've joined 6 single gene trees, and a combined ML tree including all the Charadriidae species with available data, constructed with a data set from which I removed the sequences that I view as problematic (based on the above). (I tried several other, more restricted data set compositions [less taxa, but less gappy matrix]--I can post these as well if there is interest, but the topology didn't change significantly. Keep in mind that for the six "museum toe pad species", only the available part of the data was included. C. placidus was excluded entirely, as the only publicly available sequences for this species currently are the cox1 sequences discussed above, and these I think are incorrect.)

(For what it's worth, my own current preference would be to use Charadrius for the clade sister to Eudromias [ie., all the species with bright eye ring and/or bill base], and Anarhynchus for the clade sister to Peltohyas [which groups species with invariably dull/dark eye ring and bill].)

sequel

l_raty said:

(I'm quite uncertain of the actual meaning of such trees, though. If species represented by no data at all for a given locus find a place in the gene tree inferred for this locus, and this place seems coherent with the rest, this means that the inference of this tree is constrained by the information contained in the other loci...)

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That's correct. This is a *BEAST analysis, which reconstructs a species tree based on sequence data from multiple loci, in a Markov chain process. The algorithm simultaneously reconstructs individual gene trees for each locus, and a species tree. The topology of the individual gene trees provides information as to which species tree topologies are more likely, and simultaneously, the topology of the reconstructed species tree provides information to each gene tree reconstruction as to which gene trees are most likely. So, even if there are no data available for a species at a particular taxon, the individuals from that species won't be placed randomly in that gene tree, but rather at the nodes that are most likely based on the species tree topology.

For this reason, though, you don't usually see the individual gene trees from *BEAST analyses in publications. In fact, since *BEAST assumes that any incongruence between gene trees is due to incomplete lineage sorting, it's important to reconstruct each gene tree individually, in a non-species tree context (to do a standard maximum likelihood or Bayesian analysis), since a severe topological mismatch between individual gene trees and the species tree could be a sign of introgression or some other process which the *BEAST algorithm can't take into account.

Ukridge said:

The topology of the individual gene trees provides information as to which species tree topologies are more likely, and simultaneously, the topology of the reconstructed species tree provides information to each gene tree reconstruction as to which gene trees are most likely. So, even if there are no data available for a species at a particular taxon, the individuals from that species won't be placed randomly in that gene tree, but rather at the nodes that are most likely based on the species tree topology.

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Thank you for the answer. I am in fact somewhat more concerned at the idea that species for which there are data at a particular gene might have their position on that very gene tree determined by the species tree. Eg., the algorithm here apparently "invented" a reciprocal monophyly and a deep divergence in the "bfib7" tree between C. thoracicus (n=3) and C. tricollaris (n=3), despite the actual sequences are perfectly identical for the six specimens. IOW, what the algorithm came up with as "most likely gene tree", given the information provided by the other genes, seems plainly impossible.

For this reason, though, you don't usually see the individual gene trees from *BEAST analyses in publications. In fact, since *BEAST assumes that any incongruence between gene trees is due to incomplete lineage sorting, it's important to reconstruct each gene tree individually, in a non-species tree context (to do a standard maximum likelihood or Bayesian analysis), since a severe topological mismatch between individual gene trees and the species tree could be a sign of introgression or some other process which the *BEAST algorithm can't take into account.

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Given that the five other genes place tricollaris in CRD I, finding it in CRD II based on bfib7, with these two groups estimated to have diverged some 60 MYA (cf. also Baker et al. 2007 [here]: node "C4"), is indeed a serious mismatch. The tricollaris in this study are actually Madagascan Ch. [t.] bifrontatus (recently split by HBW/BL; cox1 here 1.6-1.7% away from South African tricollaris sequences in BOLD). Of course thoracicus is Madagascan as well, hence geography at least would not prevent introgression. However, there is certainly no suggestion of hybridization between these two species in the literature. And are there really documented cases of introgression at this level of divergence...? In terms of genetic distance, CRD I vs. CRD II is more than Haematopodidae vs. Recurvirostridae.
(In fact, McCarthy 2006 [pdf] lists a grand total of two hybrid combinations involving Charadrius: (1) hiaticula x semipalmatus, and (2) "Charadrius novaeseelandiae [Shore Plover] × Vanellus miles [Masked Lapwing] NHR. Braithwaite and van Tets 1975." The latter however seems to originate in a misquote, and I suspect it never existed: the cited work [p.180-181 in this pdf] only addresses hybridization between "Lobibyx miles" and "Lobibyx novaehollandiae" [now both usually lumped as Vanellus miles], and doesn't say a word about Shore Plover.)

Laurent, I can assure you that Thinornis novaeseelandiae [Shore Plover] × Vanellus miles [Masked Lapwing have never been documented hybridising in the primary literature. The mind boggles as to how this could even work - as an aside I would love to know what the largest size dimorphism in hybridising species has lead to offspring!

HOWEVER Thinornis novaeseelandiae has hybridised with Charadrius obscurus New Zealand Plover. http://notornis.osnz.org.nz/system/files/SoBird23_Sep2005.pdf Page 8

Paul

McCarthy's mind must have been miles away when he wrote that . . . o

PScofield said:

HOWEVER Thinornis novaeseelandiae has hybridised with Charadrius obscurus New Zealand Plover. http://notornis.osnz.org.nz/system/files/SoBird23_Sep2005.pdf Page 8

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Thanks, Paul, interesting--this is the same distance as tricollaris-thoracicus, then.

Nutcracker said:

McCarthy's mind must have been miles away when he wrote that . . . o

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This is not his wildest theory, though... o

l_raty said:

This is not his wildest theory, though... o

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For those as yet unenlightened...
www.birdforum.net/showpost.php?p=2934411&postcount=2

Glareolidae

TiF Update June 3
The pratincoles and coursers have been rearranged based on Cohen (2011). The monotypic genus Stiltia has been merged into Glareola.

See [this thread] for Cohen 2011.

Cohen's thesis uses a single gene (ND2) harvested from the 5 used in Baker et al 2007's "Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds" (Biol. Lett. 2007 3 205-210; DOI: 10.1098/rsbl.2006.0606.). Baker et al 2007 found using 5 nucleic and mitochondrial genes in a Bayesian chronogram (Fig 2) that Stiltia and Glareola probably diverged in the mid-Oligocene. Lumping these two genera based on an unpublished PhD thesis that uses one gene seems a little premature to me.

PScofield said:

Cohen's thesis uses a single gene (ND2) harvested from the 5 used in Baker et al 2007's "Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds" (Biol. Lett. 2007 3 205-210; DOI: 10.1098/rsbl.2006.0606.). Baker et al 2007 found using 5 nucleic and mitochondrial genes in a Bayesian chronogram (Fig 2) that Stiltia and Glareola probably diverged in the mid-Oligocene. Lumping these two genera based on an unpublished PhD thesis that uses one gene seems a little premature to me.

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TiF Update June 9
More on Pratincoles and Coursers

Supraorbital ossification

Hughes 2015. Evolution of supraorbital ossification in Charadriiformes. Auk 132(3): 685-696. [abstract]

TiF Update June 9
More on Pratincoles and Coursers

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Hmm
Table 4.1 in Cohen's thesis shows he only used a single gene of Stiltia hence the absence of Stiltia from Figs 4.5-4.8. It is not unusual to use just a single gene from one or two species in such Mixed-model Bayesian analysis but it is far from ideal and one might speculate that this might be a reason for the unorthodox position of Stiltia in this study. The gene used was was ND2 it was the very same sequence Baker used (EF373268). I note that Livezey (2010) using more than 1000 morphological characters, including many of the 47 that Cohen used, resolved Stiltia as sister to all other Glareola. I think that keeping Stiltia in a separate genus until a robust study is published in a peer-reviewed journal is prudent.

Glareolidae

John Boyd (TiF):
www.jboyd.net/Taxo/changes.html (11 Jun 2015)
www.jboyd.net/Taxo/List7a.html#glareolidae
www.jboyd.net/Taxo/Glareolidae.pdf

Xiaohui Ge, Dongfang Hu, Fangzheng Zhao, Tingting Yu, Baowei Zhang, Qing Chang. The complete mitochondrial genome of Eurynorhynchus pygmeus (Charadriiformes: Scolopacidae). Mitochondrial DNA. Early online. Posted online on June 11, 2015.

Abstract:
The complete mitochondrial DNA genome of spoon-billed sandpiper Eurynorhynchus pygmeus was determined by using the polymerase chain reaction method and the phylogenetic tree including 15 species of Charadriiformes were reconstructed to validate our samples in this study. The circular mitogenome (16,707 bp in length) contains 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes and a control region. The content of four kinds of bases of the complete mitochondrial DNA is 31.29% for A, 24.85% for T, 13.84% for G and 30.02% for C, respectively.

*

Dongfang Hu, Xiaohui Ge, Fangzheng Zhao, Wenli Xie, and Qing Chang. The complete mitochondrial genome of Recurvirostra avosetta (Charadriiformes: Recurvirostridea). Mitochondrial DNA. Early online. Posted online on June 11, 2015.

Abstract:
The complete mitochondrial genome of Recurvirostra avosetta (Charadriiformes: Recurvirostridea) is a circular DNA with 16,897 bp in length, which contained 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The overall base compositions of the complete mtDNA are A (31.72%), T (23.59%), G (13.56%), and C (31.13%). The non-coding regions include a control region (1333 bp) and a few intergenic spacers (range from 17 to 90). The phylogentic trees were also reconstructed to validate the samples.

Saunders's Gull

Yoon, Cho & Park (in press). The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes). Gene. [abstract]

Could someone interpret this highly tech material? :eek!:

Richard Klim said:

Dos Remedios, Lee, Burke, Székely & Küpper (in press). North or South? Phylogenetic and biogeographic origins of a globally distributed avian clade. Mol Phylogenet Evol. [abstract] [Fig 1]

[See also: New Zealand Plover (Barth et al 2013, TiF).]

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pdf - accepted version here

Scolopacidae

Nurul Ashikeen Ab Razak, Mustafa Abdul Rahman & Andrew Alek Tuen. Phylogenetic Relationships of Waders (Charadriiformes: Scolopacidae) in Sarawak Inferred from Cytochrome Oxidase I and Recombinant Activating Gene 1. Sains Malaysiana 45(7)(2016): 1089–1095.

[pdf]