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Charadriiformes

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Old Sunday 5th March 2017, 12:50   #76
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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]

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Old Tuesday 7th March 2017, 11:16   #77
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Originally Posted by Peter Kovalik View Post
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.)
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Old Tuesday 7th March 2017, 12:05   #78
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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...
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Old Friday 17th March 2017, 11:10   #79
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Originally Posted by l_raty View Post
Quote:
Originally Posted by l_raty View Post
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.
Attached Files
File Type: pdf H.x.osculans.pdf (819.5 KB, 128 views)

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Old Friday 26th May 2017, 07:50   #80
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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.

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Old Friday 26th May 2017, 07:57   #81
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Ashari, H., & Astuti, D. (2017). Study on Phylogenetic Status of Javan Plover Bird (Charadrius, Charadriidae, Charadriiformes) through DNA Barcoding Analysis. Biosaintifika: Journal of Biology & Biology Education, 9(1), 49-57.

abstract anf pdf here
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Old Saturday 27th May 2017, 22:56   #82
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Quote:
Originally Posted by Peter Kovalik View Post
Ashari, H., & Astuti, D. (2017). Study on Phylogenetic Status of Javan Plover Bird (Charadrius, Charadriidae, Charadriiformes) through DNA Barcoding Analysis. Biosaintifika: Journal of Biology & Biology Education, 9(1), 49-57.

abstract anf pdf here
Considering the similarities in plumage characteristics between Kentish and Malaysian Plover, I'm a bit surprised the latter was not included in this study.
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Old Wednesday 23rd August 2017, 09:11   #83
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Charadrius pallidus

dos Remedios, N., Küpper, C., Székely, T., Baker, N., Versfeld, W. and Lee, P. L. M. (), Genetic isolation in an endemic African habitat specialist. Ibis. Accepted Author Manuscript. doi:10.1111/ibi.12520

Abstract:

The Chestnut-banded Plover Charadrius pallidus is a near-threatened shorebird species endemic to mainland Africa. We examined levels of genetic differentiation between its two morphologically and geographically distinct subspecies, C. p. pallidus in southern Africa (population size 11 000-16 000) and C. p. venustus in eastern Africa (population size 6 500). In contrast to other plover species that maintain genetic connectivity over thousands of kilometres across continental Africa, we found profound genetic differences between remote sampling sites. Phylogenetic network analysis based on four nuclear and two mitochondrial gene regions, and population genetic structure analyses based on 11 microsatellite loci, indicated strong genetic divergence, with 2.36% mitochondrial sequence divergence between individuals sampled in Namibia (southern Africa) and those of Kenya and Tanzania (eastern Africa). This distinction between southern and eastern African populations was also supported by highly distinct genetic clusters based on microsatellite markers (global FST: 0.309, G’ST = 0.510, D = 0.182). Behavioural factors that may promote genetic differentiation in this species include habitat specialisation, monogamous mating behaviour and sedentariness. Reliance on an extremely small number of saline lakes for breeding and limited dispersal between populations are likely to promote reproductive and genetic isolation between eastern and southern Africa. We suggest that the two Chestnut-banded Plover subspecies may warrant elevation to full species status. To fully assess this distinction, additional sample collection will be needed, with analysis of genetic and phenotypic traits from across the species’ entire breeding range.
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Old Friday 8th September 2017, 23:11   #84
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Natalie has just posted this resume for the wider public in our blog.
CHESTNUT-BANDED PLOVERS – SPECIALISTS ISOLATED AND AT RISK
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Old Tuesday 30th October 2018, 05:38   #85
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Charadrius hiaticula

Thies L., Tomkovich P., dos Remedios N., Lislevand T., Pinchuk P., Wallander J., Dänhardt J., Ţórisson B., Blomqvist D. & Küpper C. (2018) Population and subspecies differentiation in a high latitude breeding wader, the Common Ringed Plover Charadrius hiaticula. ARDEA 106 (2): 163-176.

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Exploring the patterns of genetic structure in the context of geographical and phenotypic variation is important to understand the evolutionary processes involved in speciation. We investigated population and subspecies differentiation in the Common Ringed Plover Charadrius hiaticula, a high latitude wader that breeds in arctic and temperate zones from northeast Canada across Eurasia to the Russian Far East. Three subspecies, hiaticula, tundrae and psammodromus, are currently widely recognised, whereas a fourth subspecies, kolymensis, has been proposed based on geographic isolation and phenotypic differences. We genotyped 173 samples from eleven Common Ringed Plover breeding sites, representing all four putative subspecies, at eight polymorphic microsatellite loci to examine the patterns of population and subspecies differentiation. Bayesian clustering identified three genetic clusters among samples, corresponding to the breeding sites of the three currently recognised subspecies. The existence of the subspecies kolymensis was not supported. We also detected the presence of a previously unknown hybridisation zone extending from Northern Scandinavia to Belarus. Differentiation of the subspecies tundrae and hiaticula most likely occurred in allopatry on the Eurasian continent during past glaciation events, followed by population expansion leading to colonisation of Iceland and Greenland. The lack of genetic differentiation within the tundrae subspecies is consistent with ongoing range expansion and high gene flow maintained through migratory behaviour. We discuss the importance of historic climate changes, migratory behaviour and mating system on shaping the observed pattern of genetic differentiation.
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Old Thursday 15th November 2018, 09:32   #86
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Madagascar & St Helena

Dos Remedios N., Küpper C., Székely T., Zefania S., Burns F., Bolton M. & Lee P.L.M., 2018. Genetic structure among Charadrius plovers on the African mainland and islands of Madagascar and St Helena. Ibis

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Old Wednesday 21st November 2018, 18:30   #87
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Canary Islands Oystercatcher

The Canary Islands Oystercatcher is usually treated as a separate species (Haematopus meadewaldoi). However, new data shared yesterday "on" the ‘BOU 2018 Twitter Conference’ showed that the specific status is not justified.

See this twitter thread (tree in tweet 5, and the study authors in 6). No need to log-in to read.

Quote:

“A maximum-likelihood tree places the previously unsequenced African Black Oystercatcher as sister species to Eurasian Oystercatcher. Canary Islands Oystercatchers fall, with high confidence, within the range of genetic variation in Eurasian Oystercatchers”.
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Old Thursday 22nd November 2018, 10:57   #88
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Melanistic subspecies? Fascinating.
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Old Thursday 22nd November 2018, 12:46   #89
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worth noting Gary Nunn's comments though:
'It is quite possible a small population of Canary Islands Oystercatcher is prone to introgression from nearby regional forms, that doesn’t detract from their potential genome wide uniqueness, I would wait on whole genome characterization.'

and


'All this shows is that the “traditional” Eurasian Oystercatcher is paraphyletic, it’s no big surprise frankly given the conservative species concept popular in ornithology, I think there is a lot more detail to pan out here with genome sequencing...'
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Old Thursday 22nd November 2018, 12:53   #90
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So lump African Black Oystercatcher?
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Old Thursday 22nd November 2018, 13:40   #91
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So lump African Black Oystercatcher?
On this evidence, yes. Further sequencing may end up proving otherwise, of course. But that could be a while coming yet.


EDIT: Sorry, forget this reply!! I somehow mis-read it as Canary Islands Oyk, the subject of the discussion . . . African stays separate. Apologies!

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Old Thursday 22nd November 2018, 14:06   #92
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On this evidence, yes. Further sequencing may end up proving otherwise, of course. But that could be a while coming yet.
Oh Dear, John won't be happy, if he's been there that is?

I do hope the authors credentials stand up to his scrutiny........
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Old Thursday 22nd November 2018, 14:32   #93
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What would be the basis for lumping African Black from this dataset? Surely it forms a distinct lineage separate from other forms, and thus could be treated as a distinct species, sister to Eurasian. The argument being presented is that Canary Islands Oystercatcher should be lumped with Eurasian.
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Old Thursday 22nd November 2018, 16:20   #94
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Not very scientific I know but Wiki has this re Canary.....

'Hockey (1982) showed that the Canary Islands oystercatcher was a full species distinct from the African oystercatcher Haematopus moquini, of which it was formerly considered a subspecies; these two were occasionally lumped as subspecies of the Eurasian oystercatcher. Though this bird was long known to naturalists, it was considered a mere local population of the African black oystercatcher until 1913 (Bannerman 1913). '
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Old Thursday 22nd November 2018, 23:11   #95
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Not very scientific I know but Wiki has this re Canary.....

'Hockey (1982) showed that the Canary Islands oystercatcher was a full species distinct from the African oystercatcher Haematopus moquini, of which it was formerly considered a subspecies; these two were occasionally lumped as subspecies of the Eurasian oystercatcher. Though this bird was long known to naturalists, it was considered a mere local population of the African black oystercatcher until 1913 (Bannerman 1913). '
The recent research is addressing this question to resolve the taxonomy of Canary Islands Oystercatcher. The conclusion is that Canary Islands is genetically distinct from African, but is genetically not separable from Eurasian (at least in terms of mitochondrial DNA, as mentioned above a genome-wide study may show more). African is closely related to Eurasian genetically, but is distinct from it.
Thus, based on the evidence presented here, African and Eurasian remain as two distinct species, but Canary Islands should be lumped into Eurasian.
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Old Friday 23rd November 2018, 09:18   #96
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Forgive me my lack o access to the recent literature - why oystercatchers so easily switch between pied and all-black plumage?
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Old Friday 23rd November 2018, 19:38   #97
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The recent research is addressing this question to resolve the taxonomy of Canary Islands Oystercatcher. The conclusion is that Canary Islands is genetically distinct from African, but is genetically not separable from Eurasian (at least in terms of mitochondrial DNA, as mentioned above a genome-wide study may show more). African is closely related to Eurasian genetically, but is distinct from it.
Thus, based on the evidence presented here, African and Eurasian remain as two distinct species, but Canary Islands should be lumped into Eurasian.
I'll be completely honest, this is the first time that I've seen that people consider the Canary's form a full species.
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Old Friday 23rd November 2018, 20:33   #98
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I'll be completely honest, this is the first time that I've seen that people consider the Canary's form a full species.
I'm not certain but I think my first copy of Heinzel, Fitter & Parslow had it as a separate species, but that was several decades ago.
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Old Friday 23rd November 2018, 21:21   #99
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Forgive me my lack o access to the recent literature - why oystercatchers so easily switch between pied and all-black plumage?
And why are the pied forms more attached to sandy beaches and the black ones to rocky shores?
There must be very few genes regulating the pied plumage.
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Old Friday 23rd November 2018, 21:28   #100
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Vaurie 1965, Bds. Palearctic Fauna, Non-Passeriformes, p. 370, and, by inference, Voous 1977, List Recent Holarctic Bd. Sp., p. 16, both considered meadewaldoi as a subsp. of Haematopus moquini, as did Cramp et al. 1983, BWP, III, p. 35. Johnsgard 1981, Plovers Sandpipers Snipes Wld., p. 56, treated it as a subsp. of H. ostralegus. Beaman 1994, Palearctic Bds., p. 29, listed Haematopus meadewaldoi Canary Islands Oystercatcher as a distinct species, as did Hayman et al. 1986, Shorebirds, p. 46, pl. 5.

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