Emberiza (1 Viewer)

[Daniel Philippe]

Oldish paper in Russian:

Koblik, A. E., 2007. Taxonomical revision of genus Emberiza sensu lato L. (Emberizidae, Aves). Comments to the checklist of the birds of Russian Federation. Ornitologiya 34 (2): 141-163.

Summary
The level of ecological and morphological diversity of the Old World Buntings Emberiza sensu lato suggests that this group has diverged beyond the genus scale. Variability of the bill structure shows that method of food processing in the bill is greatly dependent on the trophic preferences of each Bunting species. Both, the level and type of trophic specialization are reflected in habitat distribution and breeding range position, seasonal migrations and other ecological and morphological traits. Parallel and convergent evolution are both also common within the group of Buntings. Molecular data also show high level of isolation in philums of Old World Buntings. Thus, a taxonomical revision splits the Emberiza sensu lato genus into the following genera: Miliaria, Emberiza sensu stricto (with 5 subgenera), Granativora, Cristemberiza, Schoeniclus, and Ocyris (with 4 subgenera). Several of the defined genera of Old World Buntings may share a recent common ancestor with other genera of New World Sparrows rather than with other genera of Old World Buntings.

 

[Richard Klim]

John Boyd (TiF) indicates possible genera/subgenera: www.jboyd.net/Taxo/Emberizidae.pdf.

Also interesting is the treatment in Balatsky. Birds of Northern Eurasia. (spp 580–609)

 

[Peter Kovalik]

Oldish paper in Russian:

Koblik, A. E., 2007. Taxonomical revision of genus Emberiza sensu lato L. (Emberizidae, Aves). Comments to the checklist of the birds of Russian Federation. Ornitologiya 34 (2): 141-163.

:t: Thank you Daniel.
PDF here

 

[Melanie]

Zootaxa 3795 (4): 497–500 (14 May 2014)
The dating of the ornithological section of Middendorff's Reise in den äussersten Norden und Osten Sibiriens, with comments on the nomenclature of Pallas’s Bunting Emberiza pallasi Cabanis (Aves: Emberizidae)
JIŘÍ MLÍKOVSKÝ

http://mapress.com/zootaxa/2014/f/z03795p500f.pdf

 

[l_raty]

Zootaxa 3795 (4): 497–500 (14 May 2014)
The dating of the ornithological section of Middendorff's Reise in den äussersten Norden und Osten Sibiriens, with comments on the nomenclature of Pallas’s Bunting Emberiza pallasi Cabanis (Aves: Emberizidae)
JIŘÍ MLÍKOVSKÝ

This is presumably explained on p.498 (lacking in the preview pdf), but polaris taking precedence over pallasi is mainly a consequence of Mlíkovský 2012 [pdf] having re-dated Cabanis' Museum Heineanum: Singvögel [here] to 1853.

Edit - Just noticed that, although the header of the first page indeed says "Zootaxa 3795 (4): 497–500", the page numbers appear to be 597-600. It's p.598 that is lacking.

 

[Peter Kovalik]

Qiongqiong Ren, Jian Yuan, Liqian Ren, Liqin Zhang, Lei Zhang, Lan Jiang, Dongsheng Chen, Xianzhao Kan and Baowei Zhang, 2014. The complete mitochondrial genome of the yellow-browed bunting, Emberiza chrysophrys (Passeriformes: Emberizidae) and phylogenetic relationships within the genus Emberiza. Journal of Genetics, Accepted article.

[PDF]

 

[Richard Klim]

TiF

Qiongqiong Ren, Jian Yuan, Liqian Ren, Liqin Zhang, Lei Zhang, Lan Jiang, Dongsheng Chen, Xianzhao Kan and Baowei Zhang, 2014. The complete mitochondrial genome of the yellow-browed bunting, Emberiza chrysophrys (Passeriformes: Emberizidae) and phylogenetic relationships within the genus Emberiza. Journal of Genetics, Accepted article. [PDF]

John Boyd (TiF):
www.jboyd.net/Taxo/changes.html (4 Jul 2014)
www.jboyd.net/Taxo/List30.html#emberizidae
www.jboyd.net/Taxo/Emberizidae.pdf

 

[l_raty]

Qiongqiong Ren, Jian Yuan, Liqian Ren, Liqin Zhang, Lei Zhang, Lan Jiang, Dongsheng Chen, Xianzhao Kan and Baowei Zhang, 2014. The complete mitochondrial genome of the yellow-browed bunting, Emberiza chrysophrys (Passeriformes: Emberizidae) and phylogenetic relationships within the genus Emberiza. Journal of Genetics, Accepted article.

The data have problems. If you check my recent Emberiza barcode tree [here]:
- The complete mitochondrial genome of E. chrysphrys is HQ896034 in GenBank, and labelled "Emberiza_chrysophrys_HQ896034_CYTC3660-12_maybeChina" in the tree. The barcode region of this sequence forms a clade with two Korean "E. elegans" barcodes from BOLD, completely away from both the 10 other E. elegans, and the 4 other E. chrysophrys. I don't know for sure what these three barcodes are, but I would regard all three as spurious.
- The complete mitochondrial genome of E. aureola is KF111713 in GenBank, and labelled "Emberiza_aureola_KF111713_maybeChina" in the tree. The barcode region of this sequence is basically identical to 7 sequences of E. rutila and completely different from 15 other sequences of E. aureola. Either this bird was misidentified, or the sample was contaminated with rutila DNA.

 

[Peter Kovalik]

Emberiza jankowskii

Yun-Jiao Zhao, Dan Li, Shi Li, Yan-Yang Xi, and Yun-Lei Jiang. Mitochondrial genome of the Emberiza jankowskii (Emberizidae: Emberiza). Mitochondrial DNA, Posted online on April 14, 2015. (doi:10.3109/19401736.2015.1033696).

Abstract

Emberiza jankowskii is an Endangered species, whose population quantity decreased year by year in the limited distribution areas. The complete mitochondrial genome of E. jankowskii (16,776 bp in length) consists of 37 genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and a non-coding region (D-loop), which is similar to the typical mtDNA of vertebrates. All the protein-coding genes in E. jankowskii are distributed on the H-strand, except the ND6 subunit gene and ten tRNA genes, which are encoded on the L-strand. A preliminary phylogenetic analysis has been carried out with eight bunting species and other related species.

 

[Marek K]

M. PÄCKERT, YUE-HUA S., P. STRUTZENBERGER, O. VALCHUK, D. TIETZE & J. MARTENS. 2015. Phylogenetic relationships of a Qinghai-Tibet Plateau endemic bunting, Emberiza koslowi (Aves, Passeriformes, Emberizidae)
and intraspecific lineage separation of Asian bunting species at the plateau margins. Vert. Zool. 65 (1): 135-150. PDF

 

[Richard Klim]

M. PÄCKERT, YUE-HUA S., P. STRUTZENBERGER, O. VALCHUK, D. TIETZE & J. MARTENS. 2015. Phylogenetic relationships of a Qinghai-Tibet Plateau endemic bunting, Emberiza koslowi (Aves, Passeriformes, Emberizidae) and intraspecific lineage separation of Asian bunting species at the plateau margins. Vert. Zool. 65 (1): 135-150. PDF

Marek, thanks for posting, and welcome to BirdForum. :t:

 

[l_raty]

M. PÄCKERT, YUE-HUA S., P. STRUTZENBERGER, O. VALCHUK, D. TIETZE & J. MARTENS. 2015. Phylogenetic relationships of a Qinghai-Tibet Plateau endemic bunting, Emberiza koslowi (Aves, Passeriformes, Emberizidae)
and intraspecific lineage separation of Asian bunting species at the plateau margins. Vert. Zool. 65 (1): 135-150. PDF

Thanks indeed :t:

Would anyone know where the electronic supplement files are? The paper says:

at http://www.senckenberg.de/vertebrate-zoology (“Contents”)
File 1: paeckert&al-buntingphylogeny-asp2015-electronicsupplement-1.pdf (Table, origin of samples for genetic analysis)
File 2: paeckert&al-buntingphylogeny-asp2015-electronicsupplement-2.pdf (Table, PCR primer combinations for PCR with toe pad samples from museum specimens).

...but so far I've failed to find anything.

 

[Richard Klim]

Would anyone know where the electronic supplement files are?

Electronic supplement files have previously been included explicitly in the issue table of contents, eg Vert Zool 64(2): Fritz et al 2014.

But not (yet?) for Vert Zool 65(1).

 

[Richard Klim]

Päckert et al 2015

Would anyone know where the electronic supplement files are?

Now online...

1. paeckertal-buntingphylogeny-asp2015-electronicsupplement-1.pdf
2. paeckertal-buntingphylogeny-asp2015-electronicsupplement-2.pdf

 

[l_raty]

Thanks Richard :t:

Waiting for the sequences, now...

That they had problems with E. affinis in the multi-locus tree, if they used the cox1 sequence referenced in the appendix, is not very surprising. EU847699 may be labelled "Emberiza affinis" in GenBank, in Liang et al. 2008 [pdf] it is called Mycerobas affinis... And Mycerobas affinis it is. (If it is correct, that is--it has lots of duplicated nucleotides which, if real, would disturb the reading frame. This type of thing can as well just be imperfect sequencing, though.) This should not have affected the cytb tree (Fig.4), though.

 

[Richard Klim]

TiF

M. PÄCKERT, YUE-HUA S., P. STRUTZENBERGER, O. VALCHUK, D. TIETZE & J. MARTENS. 2015. Phylogenetic relationships of a Qinghai-Tibet Plateau endemic bunting, Emberiza koslowi (Aves, Passeriformes, Emberizidae) and intraspecific lineage separation of Asian bunting species at the plateau margins. Vert. Zool. 65 (1): 135-150. PDF

John Boyd (TiF):
www.jboyd.net/Taxo/changes.html (8 May 2015)
www.jboyd.net/Taxo/List30.html#emberizidae
www.jboyd.net/Taxo/Emberizidae.pdf

 

[l_raty]

Waiting for the sequences, now...

I see nothing clearly problematic in the cytb sequence of E. affinis, but it appears very distant from everything else in the data set, which makes it hard to assess. In some non-bootstrapped ML reconstructions, I actually recover it basal in the African clade (see cytb tree, first attachment), but support for this (or any alternative) position is lacking, and the position is probably best regarded as unresolved. In bootstrapped reconstructions, it appears as one of 6 lineages that, in an unresolved polytomy, make up Old World buntings.
(BOLD has a few more sequences of African emberizines, including sequences of E. affinis, but these are still kept private and cannot be seen. Yet:
- there are three E. flaviventris in the database: submitting the E. flaviventris sequence produced by Päckert et al. (KP877699) to the ID engine shows that they are congruent with this sequence; their sister group is made of three identical sequences of E. cabanisi; however, no sequences of E. affinis pop up in ID trees produced by submitting this sequence;
- there are five E. affinis in the database (which are not similar to the GenBank "Emberiza" (= Mycerobas) affinis sequence (EU847699)); these do pop up in ID trees produced by submitting Päckert et al.'s E. impetuani sequence (KP877686), albeit they are >10% away from this sequence; these 5 sequences are congruent.
This doesn't say much about who the closest relatives of affinis are but, all in all, this supports the idea that affinis is in any case quite distant from the other African yellow-breasted species.)


There is one sequence in Päckert et al.'s data set which I think is wrong: this is the Emberiza calandra myoglobin; this sequence ends up embedded in yellow-breasted African buntings (flaviventris / cabanisi), far away from another sequence of the same species, produced by Barker et al. 2013 [pdf], which falls down exactly where expected (close to fucata, basal in Emberiza s.s.; see myo tree, second attachment). This myo sequence is probably what takes E. calandra to a fully basal position within Emberiza s.s. in Päckert et al.'s multi-gene tree. In my reconstructions, using the Barker et al. sequence, calandra is sister to fucata.


I have further joined:
- a bootstrapped tree based on the five genes used by Päckert et al.;
- another boostrapped tree based on a data set to which I added nd2 and odc data taken from various other studies;
- a last tree based on the same data set, from which I removed the two species that are represented by nothing more than a single cytb sequence (E. affinis and E. poliopleura) -- the effect on the resolution of internal nodes in the phylogeny is rather dramatic .

 

[Peter Kovalik]

Laurent respect to you.

 

[Peter Kovalik]

Emberiza siemsseni

Qiang Shi, Yang Liu & Hong-Feng Zhao. Characterization of the complete mitochondrial genome of slaty bunting Emberiza siemsseni (Passeriformes: Fringillidae). Conservation Genet Resour (2016). doi:10.1007/s12686-016-0632-x

[abstract]

 

[Peter Kovalik]

Melophus lathami

Yu Zhang, Kai Li, Tao Pan, Zhaojie Peng, Xiaonan Sun, Xing Kang, Yanan Zhang & Baowei Zhang (2016) Mitochondrial genome of the Melophus lathami, Mitochondrial DNA Part B, 1:1, 929-930

[pdf]