Charadriiformes (1 Viewer)

[Peter Kovalik]

Pacific Golden Plover

Jingjing Ding, Wei Liu, Yi Zhang, Qing Chang, and Chaochao Hu. The complete mitochondrial genome of Pacific golden plover Pluvialis fulva (Charadriiformes, charadriidae). Mitochondrial DNA Part B Vol. 1 , Iss. 1,2016.

[full article]

 

[Peter Kovalik]

Spotted Redshank

Yuanyuan Cheng, Lizhi Zhou, and Yuanqiu Dong. Complete mitochondrial genome of Tringa erythropus (Charadriiformes: Scolopacidae). Mitochondrial DNA Part B Vol. 1 , Iss. 1,2016.

[pdf]

 

[Peter Kovalik]

Terek Sandpiper

Wei Liu, Yi Zhang, Dongfang Hu, Xiaohui Ge, Peng Chen & Qing Chang (2016) The complete mitochondrial genome of Terek sandpiper, Xenus cinereus (Charadriiformes: Scolopacidae), Mitochondrial DNA Part B, 1:1, 732-733, DOI: 10.1080/23802359.2016.1233467

[pdf]

 

[Peter Kovalik]

Green sandpiper

Wan Chen, Chaochao Hu, and Qing Chang. The complete mitochondrial genome of Tringa ochropus (Charadriiformes, Scolopacidae). Mitochondrial DNA Part B Vol. 1 , Iss. 1,2016.

[pdf]

 

[Peter Kovalik]

Charadrius placidus

Mu-Yeong Lee, Hey Sook Jeon, Sang-Hwa Lee, and Junghwa An. The mitochondrial genome of the long-billed plover, Charadrius placidus (Charadriiformes: Charadriidae). Mitochondrial DNA Part B Vol. 2 , Iss. 1, 2017.

[pdf]

 

[Peter Kovalik]

Haematopus ostralegus

Mu-Yeong Lee, Hey Sook Jeon, Yu-Seong Choi, Sungbae Joo, and Junghwa An. Complete mitochondrial genome of Haematopus ostralegus (Charadriiformes: Haematopodidae). Mitochondrial DNA Part B Vol. 2 , Iss. 1, 2017.

[pdf]

 

[Dimitris]

Mu-Yeong Lee, Hey Sook Jeon, Yu-Seong Choi, Sungbae Joo, and Junghwa An. Complete mitochondrial genome of Haematopus ostralegus (Charadriiformes: Haematopodidae). Mitochondrial DNA Part B Vol. 2 , Iss. 1, 2017.

[pdf]

Is this from east Asian populations which are arguably a separate species from western ones?

 

[Nutcracker]

Is this from east Asian populations which are arguably a separate species from western ones?

Yes, H. o. osculans, it says so. They acknowledge its taxonomic uncertainty, but then fail to compare it with H. o. ostralegus , only with H. ater - which as far as I can see makes it a rather low value paper. But read it and see what you think yourself!

 

[Dimitris]

Yes, H. o. osculans, it says so. They acknowledge its taxonomic uncertainty, but then fail to compare it with H. o. ostralegus , only with H. ater - which as far as I can see makes it a rather low value paper. But read it and see what you think yourself!

Well they missed a great opportunity then. Or maybe they are working on another paper. Either way perfectly easy to download the sequences and do a bootstrap analysis at home

 

[SzimiStyle]

Is this from east Asian populations which are arguably a separate species from western ones?

Well the H. o. osculans has different winter plumage traits compared to H. o. longipes or the even more westerly H. o. ostralegus. Need proper study for clarifying its status (I know I said nothing new here :-O).

 

[Mysticete]

Yes, H. o. osculans, it says so. They acknowledge its taxonomic uncertainty, but then fail to compare it with H. o. ostralegus , only with H. ater - which as far as I can see makes it a rather low value paper. But read it and see what you think yourself!

That's been what I have noticed for most (all?) bird papers submitted to this journal. It's seems to be a rapid publication mill for papers that otherwise would probably not be published in mainstream bird/genetics journals. We have certainly moved past the point in science when just publishing a basic mitochondrial genome is particularly interesting or noteworthy, by itself and not part of a much larger study.

 

[SzimiStyle]

This is what I have got from one of the authors:

"we do not have any on-going study for phylogenetics of Oystercatcher. And also we have only one genetic samples for Mitochondrial genome study.
Best
Junghwa An"

 

[Dimitris]

This is what I have got from one of the authors:

"we do not have any on-going study for phylogenetics of Oystercatcher. And also we have only one genetic samples for Mitochondrial genome study.
Best
Junghwa An"

Well that's underwhelming. :-C

 

[Mysticete]

Personally I am not even sure all of these "we are publishing the mitochondrial genome of this one species" papers are even really worth posting in these threads. It's not like this is done as part of a greater systematic research program, but seems to be more about cranking out lots of papers really quickly.

 

[McMadd]

Personally I am not even sure all of these "we are publishing the mitochondrial genome of this one species" papers are even really worth posting in these threads. It's not like this is done as part of a greater systematic research program, but seems to be more about cranking out lots of papers really quickly.

http://www.birdforum.net/showthread.php?t=333936

 

[l_raty]

Charadrius

D'Urban Jackson, dos Remedios, Maher, Zefania, Haig, Oyler-McCance, Blomqvist, Burke, Bruford, Székely, Küpper. [in press.] Polygamy slows down population divergence in shorebirds. Evolution.
[abstract & supp info]

 

[l_raty]

Mu-Yeong Lee, Hey Sook Jeon, Sang-Hwa Lee, and Junghwa An. The mitochondrial genome of the long-billed plover, Charadrius placidus (Charadriiformes: Charadriidae). Mitochondrial DNA Part B Vol. 2 , Iss. 1, 2017.

[pdf]

I was hoping that this sequence might help to clarify the position of placidus, which remains unclear.
But the sequence is now available in GenBank ([KY419888]), and unfortunately all the loci I have checked (nd2, nd3, nd6, atp8-6, cyt-b, cox1, a part of the control region) appear to match C. alexandrinus...

Maybe more luck with the oystercatcher? (This sequence -- [KY419886] -- is not released yet.)

 

[l_raty]

Maybe more luck with the oystercatcher? (This sequence -- [KY419886] -- is not released yet.)

There is a suggestive, albeit unreleased, barcode in BOLD: go [here] (this is the page covering a barcode cluster [BIN] that includes all the non-American Haematopus spp), download the 'PDF tree' and find the Korean sequence...

 

[l_raty]

Maybe more luck with the oystercatcher? (This sequence -- [KY419886] -- is not released yet.)

There is a suggestive, albeit unreleased, barcode in BOLD: go [here] (this is the page covering a barcode cluster [BIN] that includes all the non-American Haematopus spp), download the 'PDF tree' and find the Korean sequence...

That one is good.

The cox1 sequence is identical to the unreleased BOLD sequence. Besides, GenBank has two sequences that match closely parts of the mitogenome, and are presumably osculans as well:

• a cyt-b [AF440782] (Ref: Chen X F, Wang X, Yuan XD, Tang MQ, Li YX, Guo YM, Li QW. 2003. [Sequence variation of mitochondrial cytochrome b gene and phylogenetic relationships among twelve species of Charadriiformes.] Yi Chuan Xue Bao 30 (5), 419-424.);
• a partial d-loop [AY524811] (Ref: "Wang X, Sun Y, Li Q-W. Structure and Evolution of the Mitochondrial DNA Control Region in shorebirds (Ave: Scolopacidae). Unpublished.").

The cyt-b is from Liaoning Province in China according to the associated reference ([pdf here]: "本研究所用的实验材料均采自辽宁省盘锦市双台子河口自然保护区"), which makes the bird an osculans based on range; I couldn't trace the ref associated to the d-loop as having been published and no geographical origin is specified in GenBank, but as two of the authors are also authors of the cyt-b paper, I suspect the source was the same.

Unfortunately, Old World oystercatchers appear to be generally very poorly differentiated in terms of mtDNA, and more material than is available for several of the forms (in particular fuliginosus, longirostris, moquini) would be needed to establish the relationships in this group with real confidence. However, osculans certainly seems 'distinct from' ostralegus, and in fact might well be closer to the other Pacific taxa than to the species it is supposed to be part of.

 

[Peter Kovalik]

Gallinago stenura

Hu C, Zhang C, Sun L, et al. The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes. Yue B-S, ed. PLoS ONE. 2017;12(4):e0175244. doi:10.1371/journal.pone.0175244.

[pdf]