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Phasianidae

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Old Thursday 9th February 2012, 10:33   #1
Daniel Philippe
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Phasianidae

Zhao Senlin et al., 2012. Molecular phylogeny of major lineages of the avian family Phasianidae inferred from complete mitochondrial genome sequences. J. Nat. Hist. 46 (11-12): 757-767.


http://www.tandfonline.com/doi/abs/1...33.2011.653588

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Old Thursday 13th September 2012, 07:13   #2
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"Tetraonidae"

Xiao-QI CAI, Su-Ying BAI & YU JIN, 2012. COI SEQUENCE VARIATIONS AND PHYLOGENETIC RELATIONSHIPS AMONG 13 SPECIES OF TETRAONIDAE BIRDS. Acta Zootaxonomica Sinica. Vol. 37 (2).
Abstract:
The mtDNA cytochrome c-oxidase (COI), an important gene as DNA barcodes, is a very good tool for species identification. Now it has been widely used for phylogeny studies of birds. The COI sequences of the Tetrastes bonasia and Lyrurus tetrix were sequenced in this study. The COI sequence variations and phylogenetic relationships of 13 species of Tetraonidae were analyzed, combined with homologous sequences from GenBank. The results show that variations of interspecies is higher than that of intraspecies in Tetraonidae. Sequence variations and phylogenetic relationships show that the Tetrastes bonasia belongs to Tetrastes of Tetraonidae.The variations among Lyrurus tetrix and other species of Tetrao genus is lower than that among other genus in Tetraonidae. The Lyrurus tetrix was clustered in Tetrao genus in phylogeny tree. The results suggest Lyrurus tetrix belongs to Tetrao genus.
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Old Thursday 13th September 2012, 08:53   #3
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Hazel & Black Grouse

Quote:
Originally Posted by Peter Kovalik View Post
Xiao-QI CAI, Su-Ying BAI & YU JIN, 2012. COI SEQUENCE VARIATIONS AND PHYLOGENETIC RELATIONSHIPS AMONG 13 SPECIES OF TETRAONIDAE BIRDS. Acta Zootaxonomica Sinica. Vol. 37 (2).

... The COI sequences of the Tetrastes bonasia and Lyrurus tetrix were sequenced in this study. ... Sequence variations and phylogenetic relationships show that the Tetrastes bonasia belongs to Tetrastes of Tetraonidae. ... The results suggest Lyrurus tetrix belongs to Tetrao genus.
A quick survey of recent treatments...
  • Tetrastes bonasia: Madge & McGowan 2002 (Pheasants etc), H&M3, Zoonomen, IOC, TiF, King 1997, Dutch Birding, OSME, OBC, China Bird Report.
  • Bonasa bonasia: de Juana 1994 (HBW 2), Monroe & Sibley 1993, BirdLife, Cornell (Clements/eBird), Beaman 1994, AERC.

  • Lyrurus tetrix: Madge & McGowan 2002 (Pheasants etc), H&M3, Zoonomen, IOC, TiF, King 1997, OSME, China Bird Report.
  • Tetrao tetrix: de Juana 1994 (HBW 2), Monroe & Sibley 1993, BirdLife, Cornell (Clements/eBird), Beaman 1994, AERC, BOU, CSNA/Dutch Birding, OBC.
No consensus there!

Last edited by Richard Klim : Thursday 13th September 2012 at 11:57. Reason: typo.
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Old Thursday 13th September 2012, 21:21   #4
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Just for comparison two older papers:
Gutiérrez, R.J., Barrowclough, G.F. & Groth, J.G. 2000: A classification of the grouse (Aves: Tetraoninae) based on mitochondrial DNA sequences. - Wildl. Biol. 6: 205-211.
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Vittorio Lucchini, Jacob Hoglund, Siegfried Klaus, Jon Swenson and Ettore Randi, 2001. Historical Biogeography and a Mitochondrial DNA Phylogeny of Grouse and Ptarmigan. Molecular Phylogenetics and Evolution, Vol. 20, No. 1, July, pp. 149–162.
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Old Monday 21st October 2013, 20:49   #5
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HUANG Zuhao, KE Zuohua, LIAO Xinjun. MOLECULAR PHYLOGENETICS OF FOUR TRIBES IN PHASIANIDAE. Journal of Jinggangshan University (Natural Sciences Edition) 2013 Vol. Issue 2.
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Old Monday 21st October 2013, 21:03   #6
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BaoXinKang, 2010. Molecular Phylogeny of the Alpine Partridges in China. PhD thesis.

Executive Summary
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Old Friday 10th January 2014, 16:06   #7
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Indian Peafowl

Zhou, Sha, Irwin & Zhang (in press). Complete mitochondrial genome of the Indian peafowl (Pavo cristatus), with phylogenetic analysis in phasianidae. Mitochondrial DNA. [abstract]
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Old Friday 10th January 2014, 16:14   #8
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Koklass Pheasant

Huang & Ke (in press). Phylogenetic relationship of Pucrasia (Aves: Galliformes) based on complete mitochondrial genome sequences. Mitochondrial DNA. [abstract]
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Old Wednesday 12th March 2014, 06:55   #9
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Mitochondrial DNA

Huang & Ke (in press). Structure and evolution of the Phasianidae mitochondrial DNA control region. Mitochondrial DNA. [abstract]
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Old Saturday 19th April 2014, 07:16   #10
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Updated phylogenies

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Originally Posted by Peter Kovalik View Post
Yong-Yi Shen et al. 2010. A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the phasianidae. BMC Evolutionary Biology 10:132.
Provisional pdf here
Shen, Dai, Cao, Murphy, Shen & Zhang 2014. The updated phylogenies of the Phasianidae based on combined data of nuclear and mitochondrial DNA. PLoS ONE 9(4): e95786. [article] [pdf]

Last edited by Richard Klim : Saturday 19th April 2014 at 07:21.
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Old Tuesday 22nd April 2014, 07:38   #11
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Domestic Chicken

Girdland Flink, Allen, Barnett, Malmström, Peters, Eriksson, Andersson, Dobney & Larson (in press). Establishing the validity of domestication genes using DNA from ancient chickens. PNAS. [abstract] [pdf]

ScienceDirect, 18 Apr 2014: Ancient DNA: Barnyard chickens living just a few hundred years ago looked far different from today's chickens.

Last edited by Richard Klim : Tuesday 22nd April 2014 at 15:09. Reason: ScienceDirect.
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Old Tuesday 24th June 2014, 10:51   #12
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Ocelli

Kimball, Sun, Meiklejohn, Braun, Faircloth & Glenn. Testing Darwin's hypothesis on the evolution of ornamental eyespots in peafowl and their relatives. Evolution 2014. (p238)
Quote:
The most striking feature of peafowl (Pavo) is the males’ elaborate train, which exhibits ocelli (ornamental eyespots) that are under sexual selection. Two additional genera within the Phasianidae (Polyplectron and Argusianus) exhibit ocelli, but the appearance and location of these ornamental eyespots exhibits substantial variation among these genera, raising the question of whether ocelli are homologous. Within Polyplectron, ocelli are ancestral, suggesting ocelli may have evolved even earlier, prior to the divergence among genera. However, it remains unclear whether Pavo, Polyplectron, and Argusianus form a monophyletic clade in which ocelli evolved once. We estimated the phylogeny of the ocellated species using sequences from 1966 ultraconserved elements (UCEs) and three mitochondrial regions. The three ocellated genera did form a strongly supported clade, but each ocellated genus was sister to at least one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus not previously suggested to be related to any ocellated taxon, were sister genera. The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation.
[With thanks to Nick Sly.]

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Old Wednesday 16th July 2014, 08:06   #13
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Ocelli

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Kimball, Sun, Meiklejohn, Braun, Faircloth & Glenn. Testing Darwin's hypothesis on the evolution of ornamental eyespots in peafowl and their relatives. Evolution 2014. (p238)
Sun, Meiklejohn, Faircloth, Glenn, Braun & Kimball 2014. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proc R Soc B 281(1790): 20140823. [abstract] [data suppl]
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Old Thursday 17th July 2014, 07:51   #14
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Sun, Meiklejohn, Faircloth, Glenn, Braun & Kimball 2014. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proc R Soc B 281(1790): 20140823. [abstract] [data suppl]
John Boyd (TiF):
www.jboyd.net/Taxo/changes.html (16 Jul 2014)
www.jboyd.net/Taxo/List2.html#phasianidae
Quote:
Based on Sun et al. (2014), Galloperdix has been moved to Polyplectronini.
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Old Saturday 26th July 2014, 19:41   #15
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Quote:
Originally Posted by Richard Klim View Post
Kimball, Sun, Meiklejohn, Braun, Faircloth & Glenn. Testing Darwin's hypothesis on the evolution of ornamental eyespots in peafowl and their relatives. Evolution 2014. (p238)
[With thanks to Nick Sly.]
Does anyone know what's going on with the link to the paper?
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Old Monday 28th July 2014, 14:27   #16
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Proc R Soc B

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Does anyone know what's going on with the link to the paper?
The Royal Society Publishing website now seems to be functioning correctly again (after a couple of days of problems).
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Old Tuesday 29th July 2014, 06:58   #17
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Chinese Grouse

Xue-Juan Li, Yuan Huang, Fu-Min Lei, 2014. Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis. Zoological Systematics (formerly Acta Zootaxonomica Sinica), Vol.39 (3).

Abstract:
Bonasa sewerzowi, the smallest and most southerly distributed grouse species in the world, is a bird endemic to China. The population of B. sewerzowi had shown a declining trend, which made it to be the endangered species in the China Red Data Book and Category I of nationally protected animals. So far, however, most studies about this species were mainly focused on the morphological and ecological aspects. In order to further study the feature of B. sewerzowi, the complete mitochondrial genome (mitogenome) of B. sewerzowi was sequenced by Illumina Hiseq 2000 high-throughput sequencing. Then, we focused on comparative genomics of two Bonasa species to find their characteristics. Finally, phylogenetic position of Bonasa was made based on the mitogenome dataset. Our results revealed that: (1) the mitogenome of B. sewerzowi, consisting of 16 658 bp, displayed typical genome organization and gene order found in other previously determined Galliformes mitogenomes; (2) the structure and composition of mitogenomes were similar between B. sewerzowi and B. bonasia; (3) the monophyly of Bonasa was well supported, which had a closer phylogenetic relationship with Meleagris gallopavo.

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Old Tuesday 12th August 2014, 12:18   #18
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Quote:
Originally Posted by Richard Klim View Post
Sun, Meiklejohn, Faircloth, Glenn, Braun & Kimball 2014. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proc R Soc B 281(1790): 20140823. [abstract] [data suppl]
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Old Wednesday 13th August 2014, 18:44   #19
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Syrmaticus humiae

Yongjian Bei, Weicai Chen, Binghua Sun, Jinhua Li, Jieling Lai, Shaoquan Meng. Population structure of the endangered Hume's pheasant (Syrmaticus humiae) inferred from a partial sequence of the mitochondrial DNA control region. Biochemical Systematics and Ecology. Volume 57, December 2014, Pages 69–77.

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Old Wednesday 22nd October 2014, 07:05   #20
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Z.H. Huang and D.H. Ke, 2014. DNA barcoding and evolutionary relationships of the Phasianidae family in China. Genet. Mol. Res. 13 (3): 7411-7419.

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Old Wednesday 4th March 2015, 12:45   #21
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Argusianus

Jiří Mlíkovský, 2015. The correct generic name for the Great Argus (Aves: Phasianidae). RAFFLES BULLETIN OF ZOOLOGY 63: 66–68.

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Old Sunday 8th March 2015, 19:30   #22
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Syrmaticus humiae

Chen W, Bei Y, Li H (2015) Genetic Variation of the Major Histocompatibility Complex (MHC Class II B Gene) in the Threatened Hume’s Pheasant, Syrmaticus humiae. PLoS ONE 10(1): e0116499. doi:10.1371/journal.pone.0116499

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Old Thursday 26th March 2015, 11:22   #23
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Chrysolophus pheasants

Lyu, Päckert, Tietze & Sun (in press). Uncommon paleodistribution patterns of Chrysolophus pheasants in East Asia: explanations and implications. J Avian Biol. [abstract]

McGowan & Kirwan 2013/2014 (HBW Alive):
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Old Tuesday 31st March 2015, 10:21   #24
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Tibetan Snowcock

An, Zhang, Liu & Wang 2015. Refugia persistence of Qinghai-Tibetan Plateau by the cold-tolerant bird Tetraogallus tibetanus (Galliformes: Phasianidae). PLoS ONE 10(3): e0121118. [article] [pdf]

McGowan & Kirwan 2013 (HBW Alive).
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Old Thursday 26th November 2015, 07:03   #25
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Tetraonini

Kozma, Melsted, Magnússon & Höglund (in press). Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences. Mol Ecol. [abstract]
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