Peter Kovalik
Well-known member
-
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Corvidae (2 Viewers)
- Thread starter Peter Kovalik
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Peter Kovalik
Well-known member
New Zealand Ravens
R. Paul Scofield, Kieren J. Mitchell, Jamie R. Wood, Vanesa L. De Pietri, Scott Jarvie, Bastien Llamas, Alan Cooper. The Origin and Phylogenetic Relationships of the New Zealand Ravens. Molecular Phylogenetics and Evolution, Accepted Manuscript, Available online 24 September 2016.
[abstract]
R. Paul Scofield, Kieren J. Mitchell, Jamie R. Wood, Vanesa L. De Pietri, Scott Jarvie, Bastien Llamas, Alan Cooper. The Origin and Phylogenetic Relationships of the New Zealand Ravens. Molecular Phylogenetics and Evolution, Accepted Manuscript, Available online 24 September 2016.
[abstract]
Peter Kovalik
Well-known member
l_raty
laurent raty
Corvus convergence
Laiolo. 2017. Phenotypic similarity in sympatric crow species: Evidence of social convergence? Evolution 71:1051–1060.
[abstract & supp.mat.]
Laiolo. 2017. Phenotypic similarity in sympatric crow species: Evidence of social convergence? Evolution 71:1051–1060.
[abstract & supp.mat.]
l_raty
laurent raty
Huang, Ruan. [in press.] DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes). Mitoch DNA (A).
[abstract & supp.mat.]
[tree on Figshare] (same as in the supp. mat. of the paper)
[abstract & supp.mat.]
[tree on Figshare] (same as in the supp. mat. of the paper)
Whoa, some real weird stuff here: Cyanopica basal, Pinyon Jay with Pica, Fish Crow more basal in Corvus than jackdaws and Urocissa wedged in the American jays. How trustworthy is this?
l_raty
laurent raty
If there is no support value next to a given node, this node is not trustworthy. (Even if the text says that it is. At best you might look at it as a hypothesis to be tested with more data; not as a conclusion to be accepted.)
The outgroups they used were Chrysolophus pheasants, a choice (very !!) hard to understand--much too far from the ingroup, resulting in a very poorly supported rooting (cf. Cyanopica basal).
Peter Kovalik
Well-known member
Corvus splendens
Urszula Krzemińska, Hernán E. Morales, Chris Greening, Árpád S. Nyári, Robyn Wilson, Beng Kah Song, Christopher M. Austin, Paul Sunnucks, Alexandra Pavlova & Sadequr Rahman. Population mitogenomics provides insights into evolutionary history, source of invasions acnd diversifying selection in the House Crow (Corvus splendens). Heredity (2017)
doi:10.1038/s41437-017-0020-7
Abstract:
The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.
Urszula Krzemińska, Hernán E. Morales, Chris Greening, Árpád S. Nyári, Robyn Wilson, Beng Kah Song, Christopher M. Austin, Paul Sunnucks, Alexandra Pavlova & Sadequr Rahman. Population mitogenomics provides insights into evolutionary history, source of invasions acnd diversifying selection in the House Crow (Corvus splendens). Heredity (2017)
doi:10.1038/s41437-017-0020-7
Abstract:
The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.
Peter Kovalik
Well-known member
Garrulus glandarius
Aoki, D., Kinoshita, G., Kryukov, A.P. et al. Quaternary-related genetic differentiation and parallel population dynamics of the Eurasian Jay (Garrulus glandarius) in the circum-Japan Sea region. J Ornithol (2018). First Online: 22 June 2018. https://doi.org/10.1007/s10336-018-1573-9
Abstract:
The circum-Japan Sea region (CJSR) greatly impacted animal diversity in the Eastern Palearctic during the Quaternary. However, its role in avian diversification has been underestimated because of the high dispersal capabilities of birds over the sea. We investigated the phylogeographic and demographic history of the Eurasian Jay (Garrulus glandarius), focusing on CJSR populations. We sequenced a total of 1744 bp of mitochondrial DNA (cytochrome b and control region) from 73 samples. Together with the database sequences, we reconstructed a phylogenetic tree for the Eurasian Jay over the Palearctic. The earliest phylogenetic divergence was inferred to be related to geological vicariance between the Japanese archipelago and Eurasian mainland around the Pliocene–Pleistocene boundary. Several demographic analyses have suggested that there are two divergent subspecies across the CJSR, G. g. brandtii on the mainland, Sakhalin, and Hokkaido and G. g. japonicus in the archipelago. These simultaneously experienced population contractions to independent refugia and subsequent expansions around the last glacial period, i.e., parallel population dynamics. We suggest that the two landmasses of the CJSR were important for generating and preserving the phylogenetic structure of the Eurasian Jay.
Aoki, D., Kinoshita, G., Kryukov, A.P. et al. Quaternary-related genetic differentiation and parallel population dynamics of the Eurasian Jay (Garrulus glandarius) in the circum-Japan Sea region. J Ornithol (2018). First Online: 22 June 2018. https://doi.org/10.1007/s10336-018-1573-9
Abstract:
The circum-Japan Sea region (CJSR) greatly impacted animal diversity in the Eastern Palearctic during the Quaternary. However, its role in avian diversification has been underestimated because of the high dispersal capabilities of birds over the sea. We investigated the phylogeographic and demographic history of the Eurasian Jay (Garrulus glandarius), focusing on CJSR populations. We sequenced a total of 1744 bp of mitochondrial DNA (cytochrome b and control region) from 73 samples. Together with the database sequences, we reconstructed a phylogenetic tree for the Eurasian Jay over the Palearctic. The earliest phylogenetic divergence was inferred to be related to geological vicariance between the Japanese archipelago and Eurasian mainland around the Pliocene–Pleistocene boundary. Several demographic analyses have suggested that there are two divergent subspecies across the CJSR, G. g. brandtii on the mainland, Sakhalin, and Hokkaido and G. g. japonicus in the archipelago. These simultaneously experienced population contractions to independent refugia and subsequent expansions around the last glacial period, i.e., parallel population dynamics. We suggest that the two landmasses of the CJSR were important for generating and preserving the phylogenetic structure of the Eurasian Jay.
ntbirdman
Well-known member
David L Slager, Kevin L Epperly, Renee R Ha, Sievert Rohwer, Chris Wood, Caroline Van Hemert, John Klicka. Cryptic and extensive hybridization between ancient lineages of American crows. bioRxiv preprint: https://www.biorxiv.org/content/early/2018/12/10/491654
Twitter summary thread: https://twitter.com/dlslager/status/1072353359041085440
Seems like good evidence for a lump of Northwestern Crow: "Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, consistent with potentially recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). "
Twitter summary thread: https://twitter.com/dlslager/status/1072353359041085440
Seems like good evidence for a lump of Northwestern Crow: "Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, consistent with potentially recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). "
Kirk Roth
Rarely to be taken seriously
They use stronger statements in the paper: " In light of our results, past claims of distinct crow species breeding assortatively in sympatry appear to have been in error, seemingly arising from overzealous or imaginative use of subjective identification criteria."
I'd love to see a similar study centered on the Great Plains.
Also, its nice to see the term "reticulate evolution" taking the place of the backward-sounding "reverse speciation."
MJB
Well-known member
Almost Pythonesque,** one might say...
MJB
**For example, this ornithological gem:
'Bridgekeeper: “What… is the air-speed velocity of an unladen swallow?”
King Arthur: “What do you mean? An African or a European swallow?”
Bridgekeeper: “I don’t know that. Aaaaaaaaagh!”..'
James Jobling
Well-known member
Apologies, but I cannot resist posting this from the Key; "EOS (Psittacidae; Ϯ Red-and-blue Lory E. histrio) L. Eos East, Orient < Gr. εως eōs or ηως ēōs eastern, oriental; reflecting an elegy by Ovid (Amores,VI, c. 15 BC) lamenting the death of the parrot he had given to Corinna, his mistress: "Psittacus, Eois imitatrix ales ab Indis, occidit" ("The parrot, oriental wingèd mimic from India, is dead"). The shades of an early Monty Python sketch!"
Jacana
Will Jones
David L. Slager, Kevin L. Epperly, Renee R. Ha, Sievert Rohwer, Chris Wood, Caroline Van Hemert & John Klicka (2020). Cryptic and extensive hybridization between ancient lineages of American crows. Molecular Ecology. https://doi.org/10.1111/mec.15377
https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15377
Prepare to take NW Crow of your lists...
https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15377
Prepare to take NW Crow of your lists...
Jacana
Will Jones
Twitter thread by first author here: https://twitter.com/dlslager/status...Crm5mCUyn9Ks5ns0yTh6iKMPmAXF7kjqa9EVG-OULp4b8
Mysticete
Well-known member
Been preparing for that for years now...
Nutcracker
Stop Brexit!
And if you want to keep it at least for the time being, make sure you've seen one in Alaska, as the Canadian and NW Washington ones are all hybrids . . .
Jacana
Will Jones
With the disclaimer that I haven't read the whole paper yet, so it might have been covered already...
But the lack of F1s suggests to me that they can tell each other apart now, but that they couldn't in the past. This suggests some sort of reinforcement pattern happening in this system, which would be very neat!
