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Anatidae (9 Viewers)

Here an unexpected question

The Southern Pochard (Phaeoaythia erythrophthalma) looks very similar to the genus Aythya and I would not be surprised if a study shows that it belongs to this genus

So, do you know if this species has already been analyzed in a phylogeny and, if so, what would be its position?
 
The only genetic data from this species that I'm aware of is an hba2 (haemoglobin αA subunit) sequence in GenBank, with which I once computed the tree attached here.
I have not seen anything published, so far as I can remember.
If I trust your tree, and I don't know the degree of support of the relationship, I would make it a member of the genus Aythya. Aythya erythrophthalma, a good new combination, no ?
 
If I trust your tree, and I don't know the degree of support of the relationship, I would make it a member of the genus Aythya. Aythya erythrophthalma, a good new combination, no ?
Support is rather poor within the Aythya group, and it's only one gene, which might not represent the species relationships faithfully. (Note that the only node with rather good support in this clade unites Asarcornis to Aythya and former Netta spp to the exclusion of Netta rufina; this conflicts with mtDNA trees, which make Asarcornis sister to [Aythya + Netta], including N. rufina.)

The species has been placed in Aythya (or Nyroca) quite frequently in the past, so it wouldn't really be 'new'.
 
Irina V. Kulikova, Sergei V. Shedko, Yury N. Zhuravlev, Philip Lavretsky, and Jeffrey L. Peters (2022) Z-chromosome outliers as diagnostic markers to discriminate Mallard and Chinese Spot-billed Duck (Anatidae). Zoologica Scripta 51: 401-404/
First published: 28 April 2022
https://doi.org/10.1111/zsc.12540


Abstract
Closely related bird species often exhibit elevated differentiation in the Z-chromosome. Genetic differentiation is repeatedly found in so-called ‘islands of differentiation’ that might contain loci under selection that contribute to reproductive isolation. Using double-digest restriction-associated DNA sequencing (ddRAD-seq), we examined genomic divergence of Mallard (Anas platyrhynchos) and Chinese Spot-billed Duck (A. zonorhyncha), two closely related species of ducks that occasionally hybridize. The taxa were distinguishable based on overall ddRAD-seq allele frequency differences. However, differentiation on the Z-chromosome was about 4.5 times greater than observed for autosomal DNA and included three fixed differences in SNPs. These SNPs are the first species-specific molecular markers revealed among mallard group species. The causes of elevated Z-chromosome divergence are discussed, including the possibility that Z-linked loci are resistant to introgression and potentially linked to phenotypic differences between the species.
 
Ng, C.S., C.-K. Lai, H.-M. Ke, H.-H. Lee, C.-F. Chen, P.-C. Tang, H.-C. Cheng, M.J. Lu, W.-H. Li, and I.J. Tsai (2022)
Genome assembly and evolutionary analysis of the mandarin duck Aix galericulata reveal strong genome conservation among ducks
Genome Biology and Evolution 14: evac083
doi: 10.1093/gbe/evac083

The mandarin duck, Aix galericulata, is popular in East Asian cultures and displays exaggerated sexual dimorphism, especially in feather traits during breeding seasons. We generated and annotated the first mandarin duck de novo assembly, which was 1.08 Gb in size and encoded 16,615 proteins. Using a phylogenomic approach calibrated with fossils and molecular divergences, we inferred that the last common ancestor of ducks occurred 13.3–26.7 Ma. The majority of the mandarin duck genome repetitive sequences belonged to the chicken repeat 1 (CR1) retroposon CR1-J2_Pass, which underwent a duck lineage-specific burst. Synteny analyses among ducks revealed infrequent chromosomal rearrangements in which breaks were enriched in LINE retrotransposons and DNA transposons. The calculation of the dN/dS ratio revealed that the majority of duck genes were under strong purifying selection. The expanded gene families in the mandarin duck are primarily involved in olfactory perception as well as the development and morphogenesis of feather and branching structures. This new reference genome will improve our understanding of the morphological and physiological characteristics of ducks and provide a valuable resource for functional genomics studies to investigate the feather traits of the mandarin duck.
 
Karawita, A.C., Y. Cheng, K.Y. Chew, A. Challagulla, R. Kraus, R.C. Mueller, M.Z.W. Tong, K.D. Hulme, H. Bielefeldt-Ohmann, L.E. Steele, M. Wu, J. Sng, E. Noye, T.J. Bruxner, G.G. Au, S. Lowther, J. Blommaert, A. Suh, A.J. McCauley, P. Kaur, O. Dudchenko, E. Aiden, O. Fedrigo, G. Formenti, J. Mountcastle, W. Chow, F.J. Martin, D.N. Ogeh, F. Thiaud-Nissen, K. Howe, A. Tracey, J. Smith, R.I. Kuo, M.B. Renfree, T. Kimura, Y. Sakoda, M. McDougall, H.G. Spencer, M. Pyne, C. Tolf, J. Waldenström, E.D. Jarvis, M.L. Baker, D.W. Burt, and K.R. Short (2023)
The swan genome and transcriptome, it is not all black and white
Genome Biology 24: 13
doi: 10.1186/s13059-022-02838-0

Background
The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information.

Results
Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan.

Conclusion
Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.
 
Karawita, A.C., Y. Cheng, K.Y. Chew, A. Challagulla, R. Kraus, R.C. Mueller, M.Z.W. Tong, K.D. Hulme, H. Bielefeldt-Ohmann, L.E. Steele, M. Wu, J. Sng, E. Noye, T.J. Bruxner, G.G. Au, S. Lowther, J. Blommaert, A. Suh, A.J. McCauley, P. Kaur, O. Dudchenko, E. Aiden, O. Fedrigo, G. Formenti, J. Mountcastle, W. Chow, F.J. Martin, D.N. Ogeh, F. Thiaud-Nissen, K. Howe, A. Tracey, J. Smith, R.I. Kuo, M.B. Renfree, T. Kimura, Y. Sakoda, M. McDougall, H.G. Spencer, M. Pyne, C. Tolf, J. Waldenström, E.D. Jarvis, M.L. Baker, D.W. Burt, and K.R. Short (2023)

Is this a list of authors or a list of fans who backed the paper on Patreon? 😳🤪
 
Seibert, S.R., L. Joseph, J. Bowers, P. Lavretsky, A. Drew, I. Mason, D.A. Roshier, B. Iova, and J.L. Peters (2023)
Population genomics and phylogeography of four Australasian waterfowl
Emu (advance online publication)
doi: 10.1080/01584197.2023.2173611

Biogeographic barriers can restrict gene flow, but variation in ecological drivers of dispersal influences the effectiveness of these barriers among different species. Detailed information about the genetic connectivity and movement of waterfowl across biogeographic barriers in northern Australia and Papua New Guinea is limited. We compared genetic connectivity for four species of Australasian waterfowl that vary in their capacity and predisposition for dispersal: Radjah Shelduck (Radjah radjah), Wandering Whistling Duck (Dendrocygna arcuata), Green Pygmy Goose (Nettapus pulchellus), and Pacific Black Duck (Anas superciliosa). We obtained >3,700 loci from double-digest restriction-associated DNA sequencing for 15 to 40 individuals per species and found idiosyncratic patterns of population structure among the four species. The mostly sedentary Radjah Shelduck exhibited clear genetic differences between New Guinea and Australia as well as among locations within Australia. Although the population structure was consistent with isolation by distance, the Torres Strait and Carpentaria Barrier contributed more to genetic differences than geographic distance alone. In contrast, the presumed sedentary Green Pygmy Goose did not show obvious structure. Likewise, populations of the more dispersive Wandering Whistling Duck and Pacific Black Duck were unstructured and genetically indistinguishable between southern New Guinea and northern Australia. Our data suggest that some Australo-Papuan biogeographical barriers are insufficient to impede gene flow in waterfowl species capable of dispersing great distances. In sedentary species like the Radjah Shelduck, these barriers, perhaps coupled with its ecology and natural history, restrict gene flow. Our findings bring new insight into the population ecology of Australo-Papuan waterfowl.
 
Donegan, Thomas M. (2023) Towards a more rational and stable nomenclature for Mallard Anas platyrhynchos, Greylag Goose Anser anser and their domesticates, including various priority issues, designation of lectotypes, and a First Reviser act. Bulletin of the British Ornithologists' Club 143: 406-423, 4 December 2023.
Towards a more rational and stable nomenclature for Mallard Anas platyrhynchos, Greylag Goose Anser anser and their domesticates, including various priority issues, designation of lectotypes, and a First Reviser act

Abstract:
Three competing names were introduced by Linnaeus (1758) for Mallard, based on males (Anas boschas), females (A. platyrhynchos) and the hook-billed domestic breed (A. adunca). A. domestica (often attributed to J. F. Gmelin, 1789, but arguably better to Brünnich, 1764) was described later for domestic ducks. A. platyrhynchos was selected as having priority over its contemporaneous synonyms via First Reviser actions. Priority of widely used A. p. domestica remains threatened by the senior A. adunca and potentially by the mixed type series of A. boschas (comprising wild male Mallards and ducks of mixed or domestic origin). Lectotypes are designated here for A. boschas Linnaeus, 1758 (and its synonym A. boschas fera Brünnich, 1764, or Bechstein, 1792), using the same male Mallard specimen of wild phenotype illustrated by Albin (1734). This clarifies these names as objective synonyms of one another and as junior synonyms of A. platyrhynchos, as all three would then have a type series exclusively of wild Mallards from Western Europe. Garsault and Brünnich both named Anser domesticus in the same year, just three weeks apart—on 30 June 1764 and 23 July 1764, respectively. Garsault thus has priority. Consequently, Brünnich's Anas anser domesticus represents subsequent usage and his A. boschas domestica is not a homonym. Brünnich's A. anser ferus and A. boschas fera for wild geese and Mallards, respectively, if available, would be primary homonyms of one another. Acting as First Reviser, the latter name is here selected as having priority. Authorship of Anser ferus should be attributed to S. G. Gmelin (1770), whose locality of the Caspian Sea results in a potential threat to the priority heretofore afforded to A. anser rubrirostris Swinhoe, 1871, for the Eastern Greylag Goose. Brünnich's names Anser boschas domestica and Anas boschas fera were introduced as apparent trinominals; they were already in widespread use by 1764. In all likelihood Brünnich thought they had been described already, citing Linnaeus (1746, 1758) and Brisson (1760), but neither made these names available under the Code. Brünnich's names for domestics may not have been recognised because the same font was used in his work to denote distinct male and female plumages as for his domesticus/a and ferus/a, potentially denoting infrasubspecific variation. There is competing evidence as to whether or not he intended to name these units. Irrespective, under Art. 45.6.4 infrasubspecific names later adopted as valid are available. Regarding priority of A. adunca, I will separately be asking the Commission to endorse either Brünnich (1764) or J. F. Gmelin (1789) as author of Anas boschas domestica. Reversal of priority of A. adunca Linnaeus, 1758, vs. A. boschas domestica (Brünnich, 1764, or J. F. Gmelin, 1789), reversal of precedence of Anser ferus S. G. Gmelin, 1770, vs. A. anser rubrirostris Swinhoe, 1871, resolution of the type series for A. anser Linnaeus, 1758, and typification of the genus Anser Brisson, 1760, also all require ICZN attention.
 
Dendrocygna viduata lives in Africa and South America. The type locality of viduata is Carthagena in Colombia and I wondered why the species was not divided into subspecies. Do you know if a name was available for African populations?
 
personata has been used for African birds.
This name appeared first in a text by Hartlaub (here), where it was attributed to the "Duke of Würtemburg" (= Paul Wilhelm von Württemberg, with whom Hartlaub corresponded); but Hartlaub did not accept it as valid and did not associate any description to it, hence I would tend to make it unavailable there.
The name was subsequently used as valid and is certainly available from somewhere, though.
 
personata has been used for African birds.
This name appeared first in a text by Hartlaub (here), where it was attributed to the "Duke of Würtemburg" (= Paul Wilhelm von Württemberg, with whom Hartlaub corresponded); but Hartlaub did not accept it as valid and did not associate any description to it, hence I would tend to make it unavailable there.
The name was subsequently used as valid and is certainly available from somewhere, though.
The names Anas personata and Dendrocygna personata are mentioned in several works but I have not seen a formal description of this taxon. 🤷
 
The names Anas personata and Dendrocygna personata are mentioned in several works but I have not seen a formal description of this taxon. 🤷

Hartlaub 1854 would be sufficient, I believe.
The name was still not used as valid there, but it was subsequently used as a valid name quite a few times, perhaps first in Ibis in 1864, which makes it available from its introduction in synonymy (Art. 11.5 is not fulfilled, but Art. 11.6.1 is).
 
Hartlaub 1854 would be sufficient, I believe.
There is a short description that helps distinguish it from viduata : " ...(A. personata Herz. v. Würtenb.) das Weiss der Kehle und des Vorderhalsfleckens nicht wie bei viduata durch eine schwarze Querbinde getrennt ist, sondern viel- mehr fortlaufend und zusammenhängend erscheint, wobei indessen das Weiss an der Stelle der schwarzen Binde nicht ganz rein ist und einige schwarze Flecken zeigt. " [...(A. personata Herz. v. Würtenb.) the white of the throat and the front neck patch is not separated by a black cross band as in viduata, but rather appears continuous and connected, although the white at the location of the black band is not complete is clean and shows some black spots.]
 
There is a short description that helps distinguish it from viduata : " ...(A. personata Herz. v. Würtenb.) das Weiss der Kehle und des Vorderhalsfleckens nicht wie bei viduata durch eine schwarze Querbinde getrennt ist, sondern viel- mehr fortlaufend und zusammenhängend erscheint, wobei indessen das Weiss an der Stelle der schwarzen Binde nicht ganz rein ist und einige schwarze Flecken zeigt. " [...(A. personata Herz. v. Würtenb.) the white of the throat and the front neck patch is not separated by a black cross band as in viduata, but rather appears continuous and connected, although the white at the location of the black band is not complete is clean and shows some black spots.]

The case of names introduced in synonymy is always a bit odd, and not easily apprehended...

It is my understanding that some description or indication is needed, because Art. 12 (which concerns "every new name published before 1931") must be satisfied in addition to Art. 11. As a name introduced in synonymy does not inherit the nominal type of the name in the synonymy of which it is originally place (see Art. 72.4.3 for the type series of species-group names introduced in synonymy), such a name can in no event be interpreted as a having been proposed as a nomen novum. Some kind of description / definition / illustration must therefore be associated to the new name in the OD, either directly or through a bibliographic reference -- or the name fails to satisfy Art. 12 and should be unavailable.
However, if the new name and the valid name are treated as synonymous, they must be understood as denoting the same taxonomic taxon : any description/indication associated to this taxon in the OD is thus arguably de facto also associated to both names. Thus, in the present case, Hartlaub's 1854 Latin diagnosis of Dendrocygna viduata could be viewed as applying to the synonym personata as well, which would actually be sufficient to make it available.
(In 1850, Hartlaub described neither personata nor viduata; if he had cited an authority for the latter, this could -perhaps- have been interpreted as a reference to a published description -- but he did not even do this.)
 
The case of names introduced in synonymy is always a bit odd, and not easily apprehended...

It is my understanding that some description or indication is needed, because Art. 12 (which concerns "every new name published before 1931") must be satisfied in addition to Art. 11. As a name introduced in synonymy does not inherit the nominal type of the name in the synonymy of which it is originally place (see Art. 72.4.3 for the type series of species-group names introduced in synonymy), such a name can in no event be interpreted as a having been proposed as a nomen novum. Some kind of description / definition / illustration must therefore be associated to the new name in the OD, either directly or through a bibliographic reference -- or the name fails to satisfy Art. 12 and should be unavailable.
However, if the new name and the valid name are treated as synonymous, they must be understood as denoting the same taxonomic taxon : any description/indication associated to this taxon in the OD is thus arguably de facto also associated to both names. Thus, in the present case, Hartlaub's 1854 Latin diagnosis of Dendrocygna viduata could be viewed as applying to the synonym personata as well, which would actually be sufficient to make it available.
(In 1850, Hartlaub described neither personata nor viduata; if he had cited an authority for the latter, this could -perhaps- have been interpreted as a reference to a published description -- but he did not even do this.)
I could ask the same question for Fulica cristata because its type locality is Madagascar and there is a good chance that authors named the European populations with a different name, saying that they were different species. Maybe Fulica mitrata Lichtenstein 🤷
 
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