Peter Kovalik
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Emberiza (1 Viewer)
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Peter Kovalik
Well-known member
Peter Kovalik
Well-known member
Emberiza godlewskii
Jiande Li, Gang Song, Naifa Liu, Yongbin Chang and Xinkang Bao. Deep south-north genetic divergence in Godlewski’s bunting (Emberiza godlewskii) related to uplift of the Qinghai-Tibet Plateau and habitat preferences. BMC Evolutionary Biology 19: 161 (2019).
Abstract:
Background
Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski’s Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species.
Results
A phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2–6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth.
Conclusions
Our results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.
[full article]
Jiande Li, Gang Song, Naifa Liu, Yongbin Chang and Xinkang Bao. Deep south-north genetic divergence in Godlewski’s bunting (Emberiza godlewskii) related to uplift of the Qinghai-Tibet Plateau and habitat preferences. BMC Evolutionary Biology 19: 161 (2019).
Abstract:
Background
Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski’s Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species.
Results
A phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2–6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth.
Conclusions
Our results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.
[full article]
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
I'm too lazy to write the full reference. Here a new phylogeny of Emberizidae.
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Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Ils sont forts ces chinoisFull resolution of all the basal nodes in 9-pp oscines (ML BS = 100) with almost every single gene ??
You are the full paper?
l_raty
laurent raty
I'd be interested to see it. (I am a human being, though
)For comparison: the last tree I attached here is a ML tree based on the same genes, which (even though it is not entirely based on the same individual sequences and the choice of outgroups is not identical) should be fully equivalent to the first tree shown in Fig. S1 of the supplementary material of Cai et al.
(Note that I recovered Arremonidae sister to Emberiza, albeit with mixed support (BS = 85), while in the new study, Calcariidae are are consistently sister to Emberiza with BS = 100, in all trees, be them based on one or more gene(s).)
This new study uses sequences that I regard as obviously problematic, such Päckert et al.'s myoglobin sequence KP877878 (see my comments above) and the "Emberiza aureola" NC_022150 mitogenome, which is obviously wrong and mostly E. rutila (cox1 is rutila; cytb is rutila; 16s is rutila; nd2 is partly rutila (the 360 first bp or so), partly highly divergent (9-10% from both rutila and aureola; doesn't match anything else in GenBank closely)).
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Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
It is the position of Emberiza affinis that intrigues meI'd be interested to see it. (I am a human being, though
For comparison: the last tree I attached here is a ML tree based on the same genes, which (even though it is not entirely based on the same individual sequences and the choice of outgroups is not identical) should be fully equivalent to the tree shown in Fig. S1.
(Note that I recovered Arremonidae sister to Emberiza, albeit with mixed support (BS = 85), while in the new study, Calcariidae are are consistently sister to Emberiza with BS = 100, in all trees, be them based on one or more gene(s).)
This new study uses sequences that I regard as obviously problematic, such Päckert et al.'s myoglobin sequence KP877878 (see my comments above) and the "Emberiza aureola" NC_022150 mitogenome, which is obviously wrong and mostly E. rutila (cox1 is rutila; cytb is rutila; 16s is rutila; nd2 is partly rutila (the 360 first bp or so), partly highly divergent (9-10% from both rutila and aureola; doesn't match anything else in GenBank closely)).
l_raty
laurent raty
They used the cytb sequence of Päckert et al 2015 (here, see Fig. 4 in particular), and nothing else, hence the position was rather expected. Whether it is correct or not, is another issue. The signal in this sequence has always been surprising, but nothing else is available to confirm or infirm it.
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l_raty
laurent raty
Cai T, Wu G, Sun L, Zhang Y, Peng Z, Guo Y, Liu X, Pan T, Chang J, Sun Z, Zhang B. 2021. Biogeography and diversification of Old World buntings (Aves:
Emberizidae): radiation in open habitats. J. Avian Biol., e02672: 1-14. DOI: 10.1111/jav.02672
Full text here: https://www.researchgate.net/publication/351825272
No news on affinis then, other than its position as sister to Black-headed Bunting and the lot probably is wrong. The divergence times are interesting, certainly an argument for breaking up Emberiza into four neat genera, considering the first split is about the same age as Phaenicophilidae-Parulidae and almost as old as Cardinalidae-Thraupidae!
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Affinis is in the supplementary files
From the text: "Unfortunately, the phylogenetic positions of the African species E. affinis and E. vincenti were not determined in our study."
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Not determined in the sense of uncertain
Which in my world means "no news".
DDonsker
David Donsker
Emberiza spodocephala split
The IOC World Bird List has just posted the proposed split of monotypic Masked Bunting E. personata from Black-faced Bunting E. spodocephala.
We are looking for a copy of the following paper that may help us in our assessment. Do any of you have a copy you could provide to us?
Weissensteimer, M.H., Koblmüller, S. and Sefc, K.M. (2014). The Emberiza spodocephala subspecies complex: new insights into taxonomy and phylogeography. 26th International Ornithological Congress 2014, Tokyo, 18-24 Aug 2014.
Thank you in advance.
David
The IOC World Bird List has just posted the proposed split of monotypic Masked Bunting E. personata from Black-faced Bunting E. spodocephala.
We are looking for a copy of the following paper that may help us in our assessment. Do any of you have a copy you could provide to us?
Weissensteimer, M.H., Koblmüller, S. and Sefc, K.M. (2014). The Emberiza spodocephala subspecies complex: new insights into taxonomy and phylogeography. 26th International Ornithological Congress 2014, Tokyo, 18-24 Aug 2014.
Thank you in advance.
David
mb1848
Well-known member
Abstract at page 778 of:
https://www.internationalornithology.org/PDF/IOCTokyo_Abstracts.pdf .
Page 393 shows this was a Poster presentation not a paper.
https://www.researchgate.net/profile/Stephan-Koblmueller .
Kristina M Sefc .
https://www.internationalornithology.org/PDF/IOCTokyo_Abstracts.pdf .
Page 393 shows this was a Poster presentation not a paper.
https://www.researchgate.net/profile/Stephan-Koblmueller .
Kristina M Sefc .
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DDonsker
David Donsker
mb1848
Well-known member
The IOC cites Päckert et al. 2015 for the split and that paper cites Weissensteiner, M. (2013): Morphological and genetical differences of two subspecies of the masked bunting Emberiza spodocephala in Far Eastern Russia. – Master thesis at the KarlFranzens University of Graz, Austria .
https://unipub.uni-graz.at/obvugrhs/download/pdf/232438?originalFilename=true .
Päckert et al. 2015
(PDF) Phylogenetic relationships of endemic bunting species (Aves, Passeriformes, Emberizidae, Emberiza koslowi ) from the eastern Qinghai-Tibet Plateau .
https://unipub.uni-graz.at/obvugrhs/download/pdf/232438?originalFilename=true .
Päckert et al. 2015
(PDF) Phylogenetic relationships of endemic bunting species (Aves, Passeriformes, Emberizidae, Emberiza koslowi ) from the eastern Qinghai-Tibet Plateau .
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