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Zong-Ji Wang, Guang-Ji Chen, Guo-Jie Zhang, Qi Zhou. Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. Zoological Research, 2021, 42(1): 51-61. doi: 10.24272/j.issn.2095-8137.2020.175

Abstract:

Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution. Here, we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories, which are presently unknown. We found that most species showed a reduction of population size since the beginning of the last glacial period, except for those species distributed in Australasia and in the far south of South America. Different degrees of contraction and expansion of transposable elements (TE) have shaped the paleognathous genome architecture, with a higher transposon removal rate in tinamous than in ratites. One repeat family, AviRTE, likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago. Our analysis of gene families identified rapid turnover of immune and reproduction-related genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites. We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites, with the former also showing more degenerated W chromosomes. This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria. Overall, we reconstructed the evolutionary history of the Palaeognathae populations, genes, and TEs. Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.
 
Wang, Z., J. Zhang, X. Xu, C. Witt, Y. Deng, G. Chenc, G. Meng, S. Feng, L. Xu, T. Szekely, G. Zhang, and Q. Zhou (2021)
Phylogeny and sex chromosome evolution of Palaeognathae
Journal of Genetics and Genomics (advance online publication)
doi: 10.1016/j.jgg.2021.06.013

Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for different tempo of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of ‘evolutionary strata’. Nine of the 15 studied species’ sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending over half of the entire chromosome length. We found that in older strata, the W-chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared to other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly-expressed progenitors. We speculate the ‘de-feminization’ of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females that evolved in their common ancestors.
 
Takezaki, N. (2023)
Effect of different types of sequence data on palaeognath phylogeny
Genome Biology and Evolution (advance online publication)
doi: 10.1093/gbe/evad092

Palaeognathae consists of five groups of extant species: flighted tinamous (1) and four flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular studies supported the groupings of extinct moas with tinamous and elephant birds with kiwi as well as ostriches as the group that diverged first among the five groups. However, phylogenetic relationships among the five groups are still controversial. Previous studies showed extensive heterogeneity in estimated gene tree topologies from conserved nonexonic elements (CNEEs), introns, and ultraconserved elements (UCEs). Using the non-coding loci together with protein-coding loci this study investigated the factors that affected gene tree estimation error and the relationships among the five groups. Using closely related ostrich rather than distantly related chicken as the outgroup, concatenated and gene-tree based approaches supported rheas as the group that diverged first among groups (1) - (4). While gene tree estimation error increased using loci with low sequence divergence and short length, topological bias in estimated trees occurred using loci with high sequence divergence and/or nucleotide composition bias and heterogeneity, which more occurred in trees estimated from coding loci than non-coding loci. Regarding the relationships of (1) - (4) the site patterns by parsimony criterion appeared less susceptible to the bias than tree construction assuming stationary time-homogenous model and suggested the clustering of kiwi and cassowaries and emu the most likely with approximately 40% support rather than the clustering of kiwi and rheas and that of kiwi and tinamous with 30% support each.
 
Prŷs-Jones, R.P. and J. White (2023)
On the name Struthio australis Gurney Sr, 1868, and its type specimens
Bulletin of the British Ornithologists’ Club 143: 257–259
doi: 10.25226/bboc.v143i2.2023.a9

The name Struthio australis Gurney Sr, 1868, was based on three captive birds that arrived at the Zoological Society of London in November 1861. A skeleton of one of these is shown to survive in the bird collection of the Natural History Museum, but whether the other two syntypes still exist is doubtful.
 
Very interesting paper. Rothschild in 1899 used the skeleton to revive Struthio meridionalis.
"I feel justified in reviving Dr. Sclater's Struthio meridionalis [90] on account of the many marked peculiarities which the skull and the trunk of this skeleton presents"
v.15 (1898-1901) - Transactions of the Zoological Society of London - Biodiversity Heritage Library .
The paper mentions Warren Type-specimens of birds in the British Museum (Natural History), vol. 1. but I would like to see Warren's
Notes on specimens and illustrations of Cassowaries, mainly in the British Museum
https://www.tandfonline.com/doi/abs/10.1080/00222935608655892?journalCode=tnah18 .
 

Aves—A Taxonomy in Flux: Recent Changes

Avian Taxonomy
jboyd.net


Rheas: After the Ostriches, the Paleognaths split into three groups, the (1) rheas, (2) tinamous (and the recently extinct moas), and (3) cassowaries, emus, and kiwis. These groups all separated over a short time period near the beginning of the Paleogene. The next question is which of the three groups separated first? Previously, I went with a coalescent tree rather than a concatenated tree, on the grounds they they are coalescent tree more reliable. That showed the Rheas grouping with group (3), sister to group (2). Further analysis has shown that for once, the coalescent method got it wrong, with incomplete lineage sorting playing a role. The rheas separated first, with groups (2) and (3) sister to each other.
[Rheas?, Palaeognathae: Ratites and Tinamous, 3.04]

Kiwis: I've added a tree for the Kiwis.
[Apterygiformes, Palaeognathae: Ratites and Tinamous, 3.04]
Click to expand...

Tinamous, type of Tinamus: The big change is that I now strictly follow the ICZN Code for Tinamus. This means the type is soui, not major. As a result, the new Tinamus contains most of the species previously included in Crypturellus, but none that previously in Tinamus. The old Tinamus is now Cryptura. For the present, this will unfortunately cause some confusion when comparing with other lists.

I've added a species level phylogenetic tree for the Tinamous. Among other changes, I have followed Figure S4 for the taxa that have available DNA, and have added the taxa without DNA based on the trees including morphological data — Figure 2 and Figures S6-S9. E.g., berlepschi is placed sister to cinereus as the genus Crypturus. These are the two former Crypturellus species that did not move to Tinamus. The only species that was not placed this way was the Gray-legged Tinamou, Tinamus duidae, where I had to make an educated guess to place it.
[Tinamiformes, Palaeognathae: Ratites and Tinamous, 3.04]
Click to expand...
Boyd can't do that because this would create big taxonomic instability in two already well-established genera. Only ICZN can decide under plenary power to suppress Hermann (1783) as original author to the benefit of Latham (1790). He must reinstated traditional genera Tinamus and Crypturellus and their traditional species.
 
Last edited:
Jim LeNomenclatoriste said:
Boyd can't do that because this would create big taxonomic instability in two already well-established genera. Only ICZN can decide under plenary power to suppress Hermann (1783) as original author to the benefit of Latham (1790). He must reinstated traditional genera Tinamus and Crypturellus and their traditional species.
Click to expand...

What constitutes a "big instability" is completely subjective (and arguably varies between groups -- more instability will typically be tolerated in more obscure groups). The Code provisions that apply here are :
70.2. Type fixation overlooked
If it is found that an earlier type species fixation has been overlooked, the overlooked fixation is to be accepted and any later fixations are invalid. If this is considered to cause instability or confusion the case is to be referred to the Commission for a ruling.
Click to expand...
Article 82. Status of case under consideration.
82.1. Maintenance of prevailing usage. When a case is under consideration by the Commission, prevailing usage (see Glossary) of names is to be maintained until the ruling of the Commission is published.
82.2. Date when consideration is deemed to begin. A case is deemed to be under consideration by the Commission from the date of publication in the Bulletin of Zoological Nomenclature of the notice of receipt of the case.
Click to expand...

This leaves the choice between two options : either you accept the fixation as per 70.2, and you change usage accordingly (what Boyd did); or you refer the case to the Commission asking them to preserve usage. Once the case is under consideration -- i.e., once a notice of receipt has been published in BZN, see 82.2 -- prevailing usage becomes protected by 82.1.

As long as no notice of receipt of a case has been published in BZN, any use of the name in a sense that conflicts with the earliest type fixation is a violation of the Code.
 
l_raty said:
What constitutes a "big instability" is completely subjective (and arguably varies between groups -- more instability will typically be tolerated in more obscure groups). The Code provisions that apply here are :
Click to expand...
When genera with many species have been unanimously used by all authorities and books for decades, you can imagine that such a change would risk causing a big upheaval, especially among South American ornithologists. We should talk to ICZN about it first.

Whether Boyd is right or wrong is beside the point, but shouldn't we wait for a final decision from the relevant authorities?
 
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Jim LeNomenclatoriste said:
When genera with many species have been unanimously used by all authorities and works for decades, you can imagine that such a change would risk causing a big upheaval, especially among South American ornithologists. We should talk to ICZN about it first.
Click to expand...

Perhaps, but it remains that the only Code-compliant way that allows maintaining usage is to have the notice of receipt of a case published in BZN. If you want to "talk to ICZN first" and don't want to start using the name in the sense of the earliest type fixation, fine -- but, according to the word of the Code, you should then in principle refrain from using this name until the notice of receipt of the case has been published.

(I'm not saying this is what people do... In practice, people violate the Code all the time. However, I don't believe that you can use the Code to conclude that Boyd was not entitled to do what he did.)
 
Jim LeNomenclatoriste said:
It would be a lot of work for him.
Click to expand...
Perhaps, but a Code-compliant nomenclature would be freed of the sword of Damocles that will always be hanging above a non-Code-compliant nomenclature.

____
Just one more comment (hadn't seen this line when I answered post #50) :
Jim LeNomenclatoriste said:
Whether Boyd is right or wrong is beside the point, but shouldn't we wait for a final decision from the relevant authorities?
Click to expand...
Only the submission of a case would make the Commission the relevant authority on this case.
Until this happens, the only "relevant authorities" are supposed to be the authors, who use the name and all apply the Code individually -- which, in an ideal world, should always produce the same result.
 
l_raty said:
Only the submission of a case would make the Commission the relevant authority on this case.
Until this happens, the only "relevant authorities" are supposed to be the authors, who use the name and all apply the Code individually -- which, in an ideal world, should always produce the same result.
Click to expand...
Boyd could also extend that to the Sulidae, except that I spoke about it with Richard Pyle who will discuss it with his colleagues 🤔
 

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