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Lowland antpittas (1 Viewer)

Daniel Philippe

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Carneiro L., Bravo G.A., Aristizábal N., Cuervo A.M. & Aleixo A., in press. Molecular systematics and biogeography of lowland antpittas (Aves, Grallariidae): The role of vicariance and dispersal in the diversification of a widespread Neotropical lineage. Mol. Phylogen. Evol.

Abstract
We infer phylogenetic relationships, divergence times, and the diversification history of the avian Neotropical antpitta genera Hylopezus and Myrmothera (Grallariidae), based on sequence data (3139 base pairs) from two mitochondrial (ND2 and ND3) and three nuclear markers (TGFB2, MUSK and FGB-I5) from 142 individuals of the 12 currently recognized species in Hylopezus and Myrmothera and 5 outgroup species. Phylogenetic analyses recovered 19 lineages clustered into two major clades, both distributed in Central and South America. Hylopezus nattereri, previously considered a subspecies of H. ochroleucus, was consistently recovered in a separate clade of uncertain phylogenetic relationships within the Grallaricula/Hylopezus/Myrmothera clade. Ancestral range estimation suggested that modern lowland antpittas probably originated in the Amazonian Sedimentary basin during the middle Miocene, and that most lineages within the Hylopezus/Myrmothera clade appeared in the Plio- Pleistocene. However, the rate of diversification in the Hylopezus/Myrmothera clade appeared to have remained constant through time, with no major shifts over the 20 million years. Although the timing when most modern lineages of the Hylopezus/Myrmothera clade coincides with a period of intense landscape changes in the Neotropics (Plio-Pleistocene), the absence of any significant shifts in diversification rates over the last 20 million years challenges the view that there is a strict causal relationship between intensification of landscape changes and cladogenesis. The relative old age of the Hylopezus/Myrmothera clade coupled with an important role ascribed to dispersal for its diversification, favor an alternative scenario whereby long-term persistence and dispersal across an ever-changing landscape might explain constant rates of cladogenesis through time.
 
I'm not against an expanded Myrmothera , which absorb Hylopezus and Grallaricula, because there are no generic names available for dives, nattereri and fulviventris/berlepschi clade.
 
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I don't know if I can post this now because it's in review

Carneiro, L., G.A. Bravo, A. Aleixo. Phenotypic similarity leads to taxonomic inconsistency: a revision of the genera Hylopezus and Myrmothera (Passeriformes, Grallariidae), with the description of a new genus from the Atlantic Forest. In review.
 
If anyone yet has access to this paper can they please advise the name of the new grallarid genus and its type species. All info gratefully acknowledged in the Key.
 
If anyone yet has access to this paper can they please advise the name of the new grallarid genus and its type species. All info gratefully acknowledged in the Key.


Will be published in Zoologica scripta but I can't find it in the website

Of course, the type species is ''Hylopezus'' nattereri
 
I don't know if I can post this now because it's in review

Carneiro, L., G.A. Bravo, A. Aleixo. Phenotypic similarity leads to taxonomic inconsistency: a revision of the genera Hylopezus and Myrmothera (Passeriformes, Grallariidae), with the description of a new genus from the Atlantic Forest. In review.

First published: 24 November 2018

Abstract:

A comprehensive molecular phylogeny of lowland antpittas in the genera Hylopezus and Myrmothera indicated that Hylopezus, as currently defined, is paraphyletic with respect to Myrmothera and Grallaricula. Specifically, both species now placed in Myrmothera, Hylopezus dives, Hylopezus fulviventris and Hylopezus berlepschi form a strongly supported clade that is sister to a clade comprised by Hylopezus perspicillatus, Hylopezus auricularis, Hylopezus ochroleucus, Hylopezus whittakeri, Hylopezus paraensis, Hylopezus macularius, and Hylopezus dilutus. Furthermore, Hylopezus nattereri is sister to a clade glade grouping Myrmothera, Hylopezus, and Grallaricula, representing the most divergent lineage in this complex. Our approach to assess diagnosability and define generic boundaries among these taxa integrates phylogenetic relationships with morphological and acoustic traits. Given that phenotypic and ecological differences do not warrant merging H. nattereri into any other genus, and because there is no generic name available for H. nattereri, we describe herein a new genus for this Atlantic Forest endemic lineage, Cryptopezus gen. n. We also redefine generic limits in Myrmothera and Hylopezus to have a taxonomic classification concordant with their phylogenetic relationships.
 
The diagnosis of Cryptopezus is in the supporting information

Family Grallariidae

Cryptopezus gen. n.
Type species. Grallaria nattereri Pinto, 1937 by original description.

Included species. Cryptopezus nattereri (Pinto, 1937) comb. nov. Speckle-breasted Antpitta.

Diagnosis. Distinguished from other genera in Grallariidae by breast, upper belly and flanks spotted dusky, forming a particular pattern that is fully distinguishable from stripes and spots present on the other species of lowland’s antpittas; bare orbital skin buffy white. Longer tarsi than Hylopezus sensu stricto and shorter tarsi than Myrmothera sensu lato. Genetically distinct. Loudsongs structurally distinct, show whistled notes, steadily increasing in amplitude, first few slightly falling, but thereafter rising in pitch from c. 2 to c. 2·5 kHz, notes changing shape through the series.
Habitat: Ground and lower growth in humid and montane forest, mature secondary woodland, and borders; often in very densely tangled vegetation and bamboo.
Distribution: Restricted to the southern Atlantic Forest between 1200–1900 m, but it may occur at lower elevations in the southern part of its range.
Etymology. The masculine generic name is taken from the Greek kryptós (hidden) and pezos (walking, that walks) < patéō (to walk, to step), meaning “the one that walks hidden.” This name is an allusion to the secretive habits and the difficulty of locating this bird even when it is active and vocalizing.
Origin and phenotypic evolution. The origin of Cryptopezus predates that of its closest relatives and was estimated as dating back to the Early Miocene (Fig. 1). Recent studies showed that the Atlantic Forest holds ancient lineages that date to the mid-Tertiary, as verified for birds (Derryberry et al., 2011), mammals (Fabre, Galewski, Tilak, & Douzery, 2013; Galewski, Mauffrey, Leite, Patton, & Douzery, 2005) and frogs (Fouquet et al., 2012). This endemic Atlantic Forest lineage seems to have originated from Andean ancestors, and probably reached southeastern South America through the southern Andes, as it is restricted to humid subtropical and montane forests (Krabbe & Schulenberg, 2003). Given the phylogenetic distance recovered between Cryptopezus and H. ochroleucus, their phenotypic similarities seem to be result of either convergence or retention of ancestral characters (Carneiro et al., 2018). These results can also be related to the broad variation of the phenotypic measurements of these lineages (Tables 1 and 2), or to the niche conservatism reported for some Grallariidae species (Stratford & Stouffer, 2015).
 
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Dear birdforum colleagues,

Upon working on the update of the Brazilian checklist, I have finally decided to act with respect to the nomenclatural validity of Cryptopezus, as advised by my friend and colleague Vitor Piacentini.

As you know, I have published along with two other colleagues a new bird genus description (Cryptopezus gen. nov.) in the January 2019 issue of Zoologia Scripta (see: https://doi.org/10.1111/
zsc.12324).

However, as raised above on this thread, there seems to be consensus among some zoological nomenclature experts, including a ICZN commissar, that the name is unfortunately not valid (it is a nomen nudum), because the actual full description took place in the supplementary materials of our paper. Indeed, there is no link to the supplementary materials in the body of our published paper, but just in the Zoologia Scripta web site, where all materials related to the paper can be found.

Back then, we had registered the new name and the associated Zoologica Scripta publication in Zoobank (see:
urn:lsid:zoobank.org:act:23976C51-E056-491F-B475-E69450CC4D5D), and the publication has been registered at the British Library Online Archive ([http://www.bl.uk/aboutus/legaldeposit/websites/elecpubs/] for perpetuity as the new rules of the ICZN require, but apparently NOT along with the supplementary files. As a matter of fact, the following statement can be found in the Zoologia Scripta web site alongside with the supplementary files of our publication: "Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article." And this is the main reason for Cryptopezus being regarded nowadays as nomen nudum, I believe.

Because of that, as of today, I went ahead and uploaded all the supplementary materials associated with the paper (except for the main published PDF text, which is the only file linked to the Zoologica Scripta assigned DOI) in Zenodo, a public open data repository based in the EU (as some of you probably know), see the link: https://doi.org/10.5281/zenodo.3741124

Once materials are uploaded under a Zenodo DOI, they cannot be altered in any way. You may add different versions of the same data, publication, or document, but in this case every time you make any changes, a new DOI will be generated, and the thread of changes will be documented "forever". Therefore, this process assures that all materials associated under a particular DOI cannot be changed in any way after closing any given uploading session. I have also associated clearly the Zenodo link to the taxon name Cryptopezus in Zoobank, so now both the original Zoologica Scripta publication (and its respective DOI) and the Zenodo open "publication" DOI are associated with nomenclatural acts under Cryptopezus. In my view, this satisfies the provisions of the Code, but I would love to receive your thoughts on this. This is uncharted territory to me and I dare to say that we ornithologists´as a community are still in the process of learning and assimilating all the new code provisions.

If this turns out not to be an acceptable solution to "rescue" the name Cryptopezus, I am already working with the editorial board of Zoologica Scripta on the possibility of publishing the PDF with the full Cryptopezus description (published originally as a supplementary file) as an addendum in the main body of a future issue of Zoologica Scripta.

Irrespective of the closing of this story, Cryptopezus seems a case in point that could help streamline the whole process of publishing names in online venues.

Thanks in advance for any comments!

Sincerely,


Alex Aleixo
 
Cryptopezus is not the only case, unfortunately, in which new taxa of birds were "described" not in accord with the rules of the Code. There are four cases in 2018 alone, so it seems that the new regulations in connection with electronic only publication are not well known, despite their publication in 2012 already. Several parts of the Code are difficult to understand and interpret, but the new Article 8.5. Works issued and distributed electronically, is not among them. The Amendments of the Code have been published in Zootaxa 3450 (2012): 1-7, and are available on the ICZN website, so every author intending to publish on nomenclatural matters should easily be able to check the rules.
In any case, a subsequent registration in ZooBank or other institutions does not make a nomenclatural act available. Authors have no other option but to republish the nomenclatural part(s) of their work according to the rules if they failed to do so in their original, electronically published work.
In addition to the authors, the reviewers should also pay more attention to compliancewith the rules. And finally, national and international checklist committees should be aware of their responsibilities and ensure that they only recognize taxa which have been described according to the ICZN rules.
 
Lord -- how on Earth was this conclusion reached...?

A paper or nomenclatural act being registered on ZooBank is absolutely no guarantee of availability. (Authors register their papers themselves, there is no systematic control process going on.)

An online-only work must have been registered in ZooBank before being issued to be published in the sense of the Code, and the work must include evidence that this registration had occurred.

Here, the original registration (the one that appears in the paper) was:
http://zoobank.org/References/BDD3A461-3253-492C-91F0-C76D2901FF5F
This is still not publicly visible (clicking the link above yields a blank page), which means that, although the registration was made, the process was not fully completed or went wrong in some way. (We have seen this happening before, when the final date of publication -- which of course can only be added once known, thus after actual publication has occurred -- had not been added yet.)

The registration given in the comments to the SACC proposal is:
http://zoobank.org/References/533674EE-6734-4B37-A7D1-30523E62016A
This is a registration of pp. 46-56 in Vol. 48 of Zoologica Scripta, with nothing suggesting it was intended to cover an online-only supplement.
This is a brand new registration as compared to the original one, which was done on 4 March 2020 (hover over the orange "LSID" with your mouse to see this), thus more than a year after the date of online publication of the paper, as given in the ZooBank record itself.
There is (for obvious reasons) no evidence that this registration had occurred, be it in the .pdf file which includes the description of the new genus (https://onlinelibrary.wiley.com/act...c.12324&file=zsc12324-sup-0006-AppendixS1.pdf), which, as per the file's metadata was created on Fri 30 Nov 2018, or even in the main article .pdf, which was published online 6 days earlier.

(This supplementary file also still does not "state the date of publication in the work itself" (Art. 8.5.2). Although a date is embedded in the metadata, it is not "stated", and metadata cannot be understood as being "in the work itself" -- otherwise, they would be part of the content, and, as such, they would have to be fixed before the work is published : this would make any "advance online publication" of a paper before its insertion in a volume impossible, because metadata at this point are bound to change, and would exclude entirely a number of publishers, who use systems that add new metadata to their files at each download, from being published online.)

I agree with what Norbert explained above: there is in principle no way that a work can be made published retroactively if it was not published when it appeared originally. (Except possibly through an action of the Commission under the Plenary Powers.) The only thing that can be done is to republish.
 
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However at this point it appears that the SACC committee members, for better or worse, have accepted Cryptopezus as a valid name. I think that it's unlikely that anybody is going to unravel this mess in the future, it's just going to be written off as "Mistakes Were Made".
 
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