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Arborophila partridge Q

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Old Thursday 13th September 2012, 10:44   #1
Larry Sweetland
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Arborophila partridge Q

Looking for some clarification of where species limits fall according to latest IOC list, with "Scaly-breasted" type partridge.

Which are the forms at Cuc Phuong (northern Vietnam), Cat Tien (south Vietnam) and Khao Yai (Thailand)? Think there's been some reshuffling since the Robson?

Cheers,

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Old Thursday 13th September 2012, 13:18   #2
James Eaton
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Hi Larry,

Cuc Phoung = tonkinensis
Cat Tien = cognacqi
Khao Yai = chloropus

What's Clements done with them out of interest? tonkinensis is a Chestnut-necklaced in Robson, though I tend to split it as Tonkin Partridge - it's certainly more distinct than the dodgy Annam Partridge...

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Old Thursday 13th September 2012, 14:07   #3
Larry Sweetland
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cheers James. As far as I can make out from this: http://www.worldbirdnames.org/n-pheasants.html

tonkinensis, cognacqi and chloropus are now all within A. chloropus (Green-legged Partridge). Tonkinensis is put under A. charltonii on the list, but there's a tax note saying it should be under chloropus??

tonkinensis also spelt 2 ways (tonkiniensis too) unless they're two taxa?

Basically in Robson as I unsderstood it, the Cuc phuong birds are lumped with the allopatric peninsular Chestnut-necklaced, but I'm guessing this is no more, and they're now lumped with the Cat Tien and Khao Yai birds all as Green-legged (following IOC)?
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Old Thursday 13th September 2012, 15:13   #4
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all three in chloropus in Clements

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Old Thursday 13th September 2012, 15:35   #5
Richard Klim
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Madge & McGowan 2002

Here's the overview from Madge & McGowan 2002 (Pheasants etc), which recognised three species (A charltonii, A merlini, A chloropus)...
Quote:
Subgenus TROPICOPERDIX: scaly-breasted hill-partridges
... Their relationships are extremely confused; some authorities treat all taxa within A. charltonii (e.g. Johnsgard 1988, Inskipp et al. 1996), and others consider them to involve two species (merlini being included within chloropus, e.g. Peters 1934 and Davison 1982). A move to recognise three species was promulgated by del Hoyo et al. (1994), although the intermediate nature of tonkinensis is a major stumbling block to this treatment. The latter has been considered a form of A. chloropus, primarily on geography, or within A. charltonii on morphological features. In view of the already disjunct distribution of A. charltonii it appears logical to align tonkinensis with that form (C. Robson in litt.).
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Old Thursday 13th September 2012, 17:43   #6
Larry Sweetland
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Thanks guys. Looks like I'm a tick down then IOC-wise .....but hopefully just til James's suggested split comes into play one day!
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Old Friday 12th October 2012, 08:44   #7
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IOC World Bird List

Quote:
Originally Posted by Larry Wheatland View Post
Tonkinensis is put under A. charltonii on the list, but there's a tax note saying it should be under chloropus??
v3.2 (Oct 2012): "Add Arborophila chloropus tonkinensis reassigned from Arborophila charltonii (Clements 2006, Rheindt unpubl.)"
www.worldbirdnames.org/updates/subspecies
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Old Sunday 17th August 2014, 11:11   #8
Daniel Philippe
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Hainan & Taiwan

The exposed continental shelf in the ice age as a long distance colonization route? The southeastern Asian origin of Hainan and Taiwan Hill Partridges

De Chen, Jiang Chang, Shou-Hsien Li, Yang Liu, Wei Liang, Cheng-Te Yao & Zhengwang Zhang

Research on island biotas has greatly contributed to the development of modern evolutionary and biogeographic theories. Until now, most studies have suggested that continental islands received their biotas directly from the adjacent mainland. However, a few studies have indicated that species on continental islands might originate from other distant regions. Here, we used the hill partridges (genus Arborophila) that are widely distributed on the southwest and southeast China mainland, Indochina, Hainan and Taiwan islands to test whether species on continental islands might originate from distant regions rather than the adjacent mainland. Based on a molecular phylogeny inferred from three mitochondrial fragments and three nuclear DNA loci, together with an ancestral area reconstruction, we find that the ancestors of the endemic Hainan and Taiwan Hill Partridges (A. ardens and A. crudigularis) likely came from Indochina, rather than the adjacent southeast China mainland. Divergence time estimates demonstrate that their ancestors probably colonized Hainan and Taiwan using the long exposed continental shelf between Indochina, Hainan and Taiwan during glacial periods, which had not been shown before. Thus, integrating distribution data with phylogenetic information can shed new lights on historical biogeography of continental islands and surrounding mainland regions.

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Old Thursday 23rd April 2015, 21:38   #9
Peter Kovalik
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Tropicoperdix

Quote:
Originally Posted by Richard Klim View Post
Here's the overview from Madge & McGowan 2002 (Pheasants etc), which recognised three species (A charltonii, A merlini, A chloropus)...
Quote:
Subgenus TROPICOPERDIX: scaly-breasted hill-partridges
... Their relationships are extremely confused; some authorities treat all taxa within A. charltonii (e.g. Johnsgard 1988, Inskipp et al. 1996), and others consider them to involve two species (merlini being included within chloropus, e.g. Peters 1934 and Davison 1982). A move to recognise three species was promulgated by del Hoyo et al. (1994), although the intermediate nature of tonkinensis is a major stumbling block to this treatment. The latter has been considered a form of A. chloropus, primarily on geography, or within A. charltonii on morphological features. In view of the already disjunct distribution of A. charltonii it appears logical to align tonkinensis with that form (C. Robson in litt.).
-Chen D., Liu Y., Geoffrey D., Dong L., Chang J., Gao S.H., Li S.H., and Zhang Z.W. Revival of the genus Tropicoperdix Blyth 1859 (Phasianidae, Aves) using multilocus sequence data, Zoological Journal of Linnean Society, accepted.
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Old Friday 24th April 2015, 06:49   #10
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Tropicoperdix

Quote:
Originally Posted by Richard Klim View Post
Here's the overview from Madge & McGowan 2002 (Pheasants etc), which recognised three species (A charltonii, A merlini, A chloropus)...
Also...
Quote:
Members of this group differ from other hill-partridges in being primarily lowland species, with overall scaly or mottled plumages without strong patterning, and yellowish or greenish legs.
It'll be interesting to see whether Chen et al (in press) supports the HBW/BirdLife (Tobias criteria) species-level taxonomy: Arborophila tonkinensis (monotypic), A charltonii (incl ssp atjenensis), A graydoni (monotypic), A chloropus (other sspp). [H&M4 lumps all as A chloropus.]

Last edited by Richard Klim : Friday 24th April 2015 at 10:26.
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Old Friday 15th May 2015, 05:14   #11
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Quote:
...our results contradict the prevailing view that places Tropicoperdix within Arborophila (Davison, 1982; Johnsgard, 1988; Madge & McGowan, 2002; Zheng et al., 2002; Dickinson & Remsen, 2013; Clements et al., 2014; del Hoyo & Collar, 2014; Gill & Donsker, 2014), but support the revival of Tropicoperdix as a separate genus (Blyth, 1859; Ogilvie-Grant, 1895; Morony et al., 1975). More interestingly, our analyses indicate that Tropicoperdix and Arborophila are distinct and distantly related taxa, residing in two different major Phasianid clades...
Quote:
...T. charltonii and T. chloropus should be considered as two separate species. Their genetic distance is much greater than that between sister species of Arborophila, and COI divergence between T. charltonii and T. chloropus is 7.70%, far higher than the 3% threshold of COI sequence divergence typically used to characterize different species...

Last edited by Peter Kovalik : Friday 15th May 2015 at 05:28.
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Old Tuesday 26th May 2015, 06:00   #12
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Tropicoperdix

TiF Update May 25:

The Chestnut-necklaced Partridge and Green-legged Partridge have been moved out of Arborophila and Rollulinae to become genus Tropicoperdix in Pavoninae. It is uncertain exactly where they belong in Pavoninae. One possibility is that they are basal in Pavonini. For now, they are left incertae sedis in Pavoninae (Chen et al., 2015).
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Old Monday 1st June 2015, 10:45   #13
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Arborophila rufipectus

Jie Huang, Dan Zhu, Xuhao Song, Benping Chen, Chenjuan Zeng, Timothy Moermond, Xiuyue Zhang, Bisong Yue. High-throughput microsatellite markers discovery for the Sichuan Hill Partridge (Arborophila rufipectus) and assessment of genetic diversity in the Laojunshan population. Biochemical Systematics and Ecology, Volume 60, June 2015, Pages 266-272.

[Abstract]
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Old Thursday 21st January 2016, 06:35   #14
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White-necklaced Partridge

Chen, Liu, Chang, Jiang, Zhou, Zhang & Zhang 2016. Multi-locus analysis supports the taxonomic validity of Arborophila gingica guangxiensis Fang Zhou & Aiwu Jiang, 2008. ZooKeys 555: 125–136. [article & pdf]

McGowan et al 2014 (HBW Alive).

Last edited by Richard Klim : Thursday 21st January 2016 at 07:10. Reason: OD link.
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Old Tuesday 1st March 2016, 11:12   #15
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Arborophila rufipectus

Yaoyao Cui, Chaochao Yan, Tianlin Sun, Jing Li, Bisong Yue, Xiuyue Zhang and Jing Li. Identification of CR1 Retroposons in Arborophila rufipectus and their application to Phasianidae Phylogeny. Molecular Ecology Resources, Accepted article.

[Abstract]
[Supporting Information]
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Old Saturday 12th August 2017, 10:06   #16
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Yan, Mou, Meng, Tu, Fan, Price, Yue, Zhang. 2017. A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history. PLoS ONE 12(7): e0181649.
[whole paper]
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Old Saturday 8th September 2018, 11:23   #17
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Tropicoperdix

De Chen, Edward L. Braun, Michael Forthman, Rebecca T. Kimball, Zhengwang Zhang. A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: placement of the partridge genus Tropicoperdix within the Galliformes. Molecular Phylogenetics and Evolution, Available online 7 September 2018, In Press, Accepted Manuscript.

Abstract:

Next-generation DNA sequencing (NGS) offers a promising way to obtain massive numbers of orthologous loci to understand phylogenetic relationships among organisms. Of particular interest are old museum specimens and other samples with degraded DNA, where traditional sequencing methods have proven to be challenging. Low coverage shotgun sequencing and sequence capture are two widely used NGS approaches for degraded DNA. Sequence capture can yield sequence data for large numbers of orthologous loci, but it can only be used to sequence genomic regions near conserved sequences that can be used as probes. Low coverage shotgun sequencing has the potential to yield different data types throughout the genome. However, many studies using this method have often generated mitochondrial sequences, and few nuclear sequences, suggesting orthologous nuclear sequences are likely harder to recover. To determine the phylogenetic position of the galliform genus Tropicoperdix, whose phylogenetic position is currently uncertain, we explored two strategies to maximize data extraction from low coverage shotgun sequencing from approximately 100-year-old museum specimens from two species of Tropicoperdix. One approach, a simple read mapping strategy, outperformed the other (a reduced complexity assembly approach), and allowed us to obtain a large number of ultraconserved element (UCE) loci, relatively conserved exons, more variable introns, as well as mitochondrial genomes. Additionally, we demonstrated some simple approaches to explore possible artifacts that may result from the use of degraded DNA. Our data placed Tropicoperdix within a clade that includes many taxa characterized with ornamental eyespots (peafowl, argus pheasants, and peacock pheasants), and established relationships among species within the genus. Therefore, our study demonstrated that low coverage shotgun sequencing can easily be leveraged to yield substantial amounts and varying types of data, which opens the door for many research questions that might require information from different data types from museum specimens.
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