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Corvidae

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Old Wednesday 19th April 2017, 11:36   #26
gusasp
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Originally Posted by l_raty View Post
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)
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?
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Old Wednesday 19th April 2017, 12:22   #27
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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?
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).
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Old Tuesday 28th November 2017, 20:20   #28
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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

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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.
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Old Sunday 24th June 2018, 19:44   #29
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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

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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.
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Old Tuesday 11th December 2018, 16:34   #30
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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). "
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Old Tuesday 11th December 2018, 19:38   #31
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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). "
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."
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Old Tuesday 11th December 2018, 20:50   #32
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Also, it's nice to see the term "reticulate evolution" taking the place of the backward-sounding "reverse speciation."
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!”..'
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Old Thursday 13th December 2018, 15:19   #33
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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!”..'
Certainly a pioneering taxonomy joke, though I suspect the flight speed difference between H.r. rustica and savignii is "wafer thin."
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Old Thursday 13th December 2018, 16:05   #34
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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!"
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