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Rallidae (1 Viewer)

Thanks for the Kirchman paper.

So there is pretty good agreement on the subfamily/tribe topology (just need to debock the names). The two differences are the addition of Gynnocrex as an additional tribe (Gymnocrecini) and the position of Fulicini. Kirchman's ML analysis (Fig 1) has Gymnocrecini as sister to Himantornithini with Fulicini sister to the remainder of the subfamily, while Kirchman's species tree (Fig 2) matches the Garcia-R et al (2020; Fig1) topology. The disagreement on position of Fulicini is a good reason for the two subfamily approach over three.
My current taxonomy is based on Garcia & al which show the existence of three subfamilies. I don't know who to believe and who to follow finally šŸ§šŸ˜•
 
Thanks for the Kirchman paper.

So there is pretty good agreement on the subfamily/tribe topology (just need to debock the names). The two differences are the addition of Gynnocrex as an additional tribe (Gymnocrecini) and the position of Fulicini. Kirchman's ML analysis (Fig 1) has Gymnocrecini as sister to Himantornithini with Fulicini sister to the remainder of the subfamily, while Kirchman's species tree (Fig 2) matches the Garcia-R et al (2020; Fig1) topology. The disagreement on position of Fulicini is a good reason for the two subfamily approach over three.
Based on Garcia-R et al and this paper I'm going to sit down later and divvy this family up into a whole bunch of little pieces that make sense to me, without giving them taxonomic ranks, and see how it all shakes out.

"debock"! :LOL:
To de-Bock a name.
Is that a thing now?
Hahaha
 
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šŸ˜² Bock is like some kind of taxonomic 'Lord of chaos'!
The late Storrs Olson famously tore into Bock's monograph in a review in the Auk (Review: [Untitled] on JSTOR). The brilliance of this review is famously reflected is this gem of a passage:

"Unfortunately, in this instance the Teutonic fountain of omniscience has spewed forth a sphagnum opus that is a bog of fatuous and sometimes inexplicable errors that can only be regarded as mire. Because this work is one of the most meretricious and fallacious documents ever produced in the history of zoological nomenclature, a frank caveat lector must be issued lest it be accepted and its myriad errors perpetuated."

Read the whole review for more chuckles.
Andy
 
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The late Storrs Olsen famously tore into Bock's monograph in a review in the Auk (Review: [Untitled] on JSTOR). The brilliance of this review is famously reflected is this gem: of a passage:

"Unfortunately, in this instance the Teutonic fountain of omniscience has spewed forth a sphagnum opus that is a bog of fatuous and sometimes inexplicable errors that can only be regarded as mire. Because this work is one of the most meretricious and fallacious documents ever produced in the history of zoological nomenclature, a frank caveat lector must be issued lest it be accepted and its myriad errors perpetuated."

Read the whole review for more chuckles.
Andy
Whether you criticize him positively or negatively, it is through his work that I have been able to make discoveries, and not the least
 
Kirchman, J.J., N.R. McInerney, T.C. Giarla, S.L. Olson, E. Slikas, and R.C. Fleischer (2021)
Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification
Ornithology (advance online publication)
doi: 10.1093/ornithology/ukab042

The rails (Family Rallidae) are the most diverse and widespread group in the Gruiformes. Their extensive fossil history, global geographic distribution, and tendency to rapidly evolve flightless species on islands make them an attractive subject of evolutionary studies, but the rarity of modern museum specimens of so many rail species has, until recently, limited the scope of molecular phylogenetics studies. As a result, the classification of rails remains one of the most unsettled among major bird radiations. We extracted DNA from museum specimens of 82 species, including 27 from study skins collected as long ago as 1875, and generated nucleotide sequences from thousands of homologous ultra-conserved elements (UCEs). Our phylogenetic analyses, using both concatenation and multispecies coalescent approaches, resulted in well-supported and highly congruent phylogenies that resolve the major lineages of rails and reveal several currently recognized genera to be polyphyletic. A fossil-calibrated time tree is well-resolved and supports the hypothesis that rails split into 2 major lineages (subfamilies Himantornithinae and Rallinae) ~34 mya, but clade age estimates have wide confidence intervals. Our results, combined with results of other recently published phylogenomics studies of rails and other Gruiformes, form the basis for a proposed classification of the Rallidae that recognizes 40 genera in 9 tribes.

I just wish to say thank you to Kirchman et al and Garcia-R et al for their excellent efforts.

I spent a most enjoyable afternoon sifting through it all.
Now if I could just have all the Rail plates in ICBW vol.1 in the new taxonomic order....šŸ˜
 
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I just wish to say thank you to Kirchman et al and Garcia-r et al for their excellent efforts.

I spent a most enjoyable afternoon sifting through it all.
Now if I could just have all the Rail plates in ICBW vol.1 in the new taxonomic order....šŸ˜
Two studies which contradict each other on the number of sub-families, 3 on one side, 2 on the other.
 
Two studies which contradict each other on the number of sub-families, 3 on one side, 2 on the other.
Yes, but nice to see them all in their 'kin groups' without having to make personal decisions around taxonomic ranks.
Also, I'm trying to avoid thinking about the fin-footed 'elephant in the room'.šŸ˜
 
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Did Garcia-R make taxonomic subfamily and tribe recommendations? .
No, but we can adapt our taxonomy according to their result. If we follow Garcia-R, I think we won't have the choice to recognize three sub-families : Himantornithinae (Himantornis and Gymnocrex), Fulicinae (Crake, Moorhen and Coot), Rallinae (true rails). Or we merge the last two subfamilies into one šŸ¤”šŸ§šŸ˜•


The problem for me is the classification at the generic level within these subfamilies, depending on whether we follow Garcia or Kirchman
 

August 20​

Rails: We start with a split. Based on Ridgely and Greenfield (2001) and the fact that the birds in Ecuador sound quite different from those in North America, the Virginia Rail, Rallus limicola, is split into:

  • Virginia Rail, Rallus limicola
  • Ecuadorian Rail, Rallus aequatorialis, including meyerdeschauenseei
[Rallidae Gruae I, 3.07]

I've reorganized the rails using Garcia-R. and Matzke (2021), Kirchman et al. (2021), Garcia-R. et al. (2020), Boast et al. (2019) and an number of other papers. Details are in the rail section. Here I will just list the generic changes, which are numerous.

  • The Colombian Crake, Mustelirallus colombiana and Paint-billed Crake, Mustelirallus erythrops are transferred to genus Neocrex (Sclater and Salvin, 1869), type erythrops.
  • The Zapata Rail, Mustelirallus cerverai returns to the monotypic genus Cyanolimnas (Barbour and JL Peters, 1927).
  • The African Crake, Crex egregia, is not sister to the Corn Crake, so it moves to the monotypic genus Crecopsis (Sharpe, 1893).
  • The Snoring Rail, Lewinia plateni has moved away from Lewinia to become the monotypic genus Aramidopsis (Sharpe, 1893).
  • The Invisible Rail, Gallirallus wallacii is now in the monotypic genus Habroptila (Gray, 1861).
  • Hawkins's Rail, Gallirallus hawkinsi has become the monotypic genus Diaphorapteryx (Forbes, 1892).
  • The Calayan Rail, Gallirallus calayanensis becomes genus Aptenorallus (Kirchman et al., 2021).
  • The Chestnut Rail, Gallirallus castaneoventris becomes genus Eulabeornis (Gould, 1844).
  • The New Caledonian Rail, Gallirallus lafresnayanus becomes Tricholimnas (Sharpe, 1893).
  • The Chatham Rail, Gallirallus modestus joins Aphanapteryx (Frauenfeld, 1868), type bonasia.
  • The Okinawa Rail, Gallirallus okinawae, Barred Rail, Gallirallus torquatus, and Pink-legged Rail, Gallirallus insignis are all moved to Habropteryx (Stresemann, 1932), type insignis.
  • The rest of Gallirallus is transferred to genus Hypotaenidia (Reichenbach, 1853), type philippensis.
  • The American purple gallinules: Allen's Gallinule, Porphyrio alleni, Purple Gallinule, Porphyrio martinica, and Azure Gallinule, Porphyrio flavirostris, have been transferred to genus Porphyrula (Blyth, 1852), type alleni.
  • The Rusty-flanked Crake, Laterallus levraudi, joins Rufirallus (Bonaparte, 1856), type viridis.
  • The Ascension Crake, Mundia elpenor joins the black rail genus Creciscus (Cabanis, 1857), type jamaicensis.
  • The White-throated Crake, Limnocrex albigularis, is transferred to Laterallus (GR Gray, 1855), type melanophaius.
  • The Gray-breasted Crake, Laterallus exilis is sister to the Yellow-breasted Crake, Hapalocrex flaviventer. However, they are distant relations, so a new genus is needed. I don't know of any with exilis as type, so a temporary name must be used. Gray-breasted Crake becomes "Hapalocrex" exilis.
  • The Isabelline Bush-hen, Amaurornis isabellina, seems a bit distant from the other Amaurornis and becomes the monotypic genus Oenolimnas (Sharpe, 1853).
  • The Brown Crake, Zapornia akool, is transferred to Limnocorax (W Peters, 1854), type flavirostra.
  • Finally, a group of former Zapornia (and before that Porzana) have been separated as the genus Pennula (Dole, 1878), type sandwichensis. They are:
    • Sakalava Rail, Zapornia olivieri
    • Black-tailed Crake, Zapornia bicolor
    • Hawaiian Rail, Zapornia sandwichensis
    • Red-eyed Crake, Zapornia atra
    • Spotless Crake, Zapornia tabuensis
    • Kosrae Crake, Zapornia monasa
    • Tahiti Crake, Zapornia nigra
[Rallidae Gruae I, 3.07]
The last taxonomy adopted by Boyd (in red) doesn't really match with the result of Gracia-R. & al (2021)

One clade is composed by atra, bicolor, flavirostra, monasa, nigra, olivieri, and tabuensis, and the second by akool, fusca, isabellina, palmeri, parva, paykullii, pusilla, and sandwichensis. It's surprinsing that isabellina is a part of Zapornia. I would like to have an explanation as to the position of this species in this genus. And also know in which study Amaurornis isabellina was analyzed

In blue, just yes
 
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Kirchman, J.J., N.R. McInerney, T.C. Giarla, S.L. Olson, E. Slikas, and R.C. Fleischer (2021)
Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification
Ornithology (advance online publication)
doi: 10.1093/ornithology/ukab042

The rails (Family Rallidae) are the most diverse and widespread group in the Gruiformes. Their extensive fossil history, global geographic distribution, and tendency to rapidly evolve flightless species on islands make them an attractive subject of evolutionary studies, but the rarity of modern museum specimens of so many rail species has, until recently, limited the scope of molecular phylogenetics studies. As a result, the classification of rails remains one of the most unsettled among major bird radiations. We extracted DNA from museum specimens of 82 species, including 27 from study skins collected as long ago as 1875, and generated nucleotide sequences from thousands of homologous ultra-conserved elements (UCEs). Our phylogenetic analyses, using both concatenation and multispecies coalescent approaches, resulted in well-supported and highly congruent phylogenies that resolve the major lineages of rails and reveal several currently recognized genera to be polyphyletic. A fossil-calibrated time tree is well-resolved and supports the hypothesis that rails split into 2 major lineages (subfamilies Himantornithinae and Rallinae) ~34 mya, but clade age estimates have wide confidence intervals. Our results, combined with results of other recently published phylogenomics studies of rails and other Gruiformes, form the basis for a proposed classification of the Rallidae that recognizes 40 genera in 9 tribes.
Jeremy J Kirchman, Nancy Rotzel McInerney, Thomas C Giarla, Storrs L Olson, Elizabeth Slikas, Robert C Fleischer, Corrigendum to: Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification, Ornithology, 2021;, ukab065, https://doi.org/10.1093/ornithology/ukab065

Since the publication of our paper (Kirchmann et al. 2021), we have learned that our classification of the rails incorrectly attributed the genus name Rufirallus to Statius Muller, 1776, who named the type species Rallus viridis. The names Rufirallus and Micropygia were introduced in the same paper by Bonaparte (1856) and, therefore, have equal priority for the name of the group that we proposed that includes both Rufirallus viridis and Micropygia schomburgkii. We herein take the formal step, required by the International Code of Zoological Nomenclature, to act as First Reviser and assign precedence to Rufirallus over Micropygia. We regret the error, and that we failed to take this First Reviser action in the text of our paper. We thank Edward Dickinson, Paul Scofield, and Steven Gregory for bringing the matter to our attention. We also herein provide notification that two newly erected taxon names in our paper have been registered with the Official Register of Zoological Nomenclature (ZooBank; urn:lsid:zoobank.org:pub:C6B6ACB3-6B92-4E7F-9D4E-FA3BE40376E9) and include the information necessary to establish the new names here:

Aptenorallus, genus nov.

Type species.
Gallirallus calayanensis Allen, Oliveros, EspaƱola, Broad, and Gonzalez, 2004.

Included species.Aptenorallus calayanensis (Allen, Oliveros, EspaƱola, Broad, and Gonzalez, 2004) comb.nov., Calayan Rail.

Diagnosis. A stocky, medium-sized (~245 g) flightless rail with red bill and legs, uniform dark olive to blackish brown plumage, and light barring on underwing coverts. Differs from Gallirallus and Hypotaenidia by the absence of barring on the remiges or flanks. Differs from Habroptila by its smaller size and the absence of a frontal shield. In phylogenetic analyses of DNA sequence data (herein, Garcia-R et al. 2014a, Garcia-R et al. 2020), it occupies a long, well-supported phylogenetic branch basal to Habroptila, Eulabeornis, Gallirallus, and Hypotaenidia. In our UCE dataset (Taxon Sets A and F) it is approximately equally divergent from species in Habroptila, Gallirallus, and Hypotaenidia, from which it differs by an average of 2,697, 3,430, and 3,340 sites, respectively (out of 610,351 in the Set F alignment).

Etymology. Greek adjective aptenos, unable to fly + New Latin masculine noun rallus. Thus ā€œflightless rail from Calayan.ā€

Tribe Laterallini, New Taxon

Type genus.
Laterallus G.R. Gray, 1855

Diagnosis. Small (14ā€“19 cm in length) and very small (12 cm) rails with short bills and no frontal shield. The group comprises 18 extant species in 4 genera (Coturnicops, Hapalocrex, Laterallus, Rufirallus) and is the least inclusive crown clade that includes Rufirallis viridis and C. noveboracensis. The taxa in this tribe form a well-defined monophyletic clade that has received high node support under a variety of phylogenetic reconstruction methods and DNA sequence datasets (herein, Garcia-R et al. 2014a, Garcia-R et al. 2020). Species in this tribe occupy a wide variety of habitats in North and South America, the Galapagos, and the South Atlantic Islands. One species occurs in northeast Asia. Based on our UCE dataset (Taxon Set B) we estimate that the Laterallini diverged from its sister clade (Amaurornithini + Zapornini) ~12 mya.
 
This should ultimately lead to the ZooBank entry for the Corrigendum : http://zoobank.org/urn:lsid:zoobank.org:pub:C6B6ACB3-6B92-4E7F-9D4E-FA3BE40376E9
(Right now, this leads to a blank page, so I can't check if things are OK or not.)

Small (14ā€“19 cm in length) and very small (12 cm) rails with short bills and no frontal shield.
So we have to understand that this is "a statement of the characters purported to differentiate the taxon" (i.a., from Zaporniini which are part of the taxon's sister group, and which are, well, small rails with short bills and no frontal shields). Is it ? (It's a genuine question. My inclination would be to say no, but I'm rather convinced some will say yes.) The rest of the diagnosis fulfills no ICZN requirement, so far as I can assess, so the name must stand on this single sentence alone.

(Is Amaurornithini really available ? It was certainly nude in Livezey 1998, where it was taken in the paper. But this name had been used elsewhere before this.)
 
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Amaurornithini cited to Grizmek 1969 and Makatsch 1969 on internet
https://archive.org/stream/revuesuissedez821975schw/revuesuissedez821975schw_djvu.txt /
Yes, Makatsch in Grzimek 1969 is the earliest use I have seen.
(You need to register and to "borrow" the book to see it in full; it cannot be downloaded.)
But all you get there is a list of the content of the group, with a few characters listed randomly for a couple of the included genera, and nothing generalizable to the group as a whole.

There's also an English version of the same work from 1972, but it's not really better.

One problem is that the publications from the period ranging from the 1960s to the 1980s are quite poorly represented on the Internet (particularly books -- think, e.g., Wolters; the coverage for non-international journals is also quite irregular), which makes it difficult to be sure you have seen everything.
 
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Alex F. Brown, Thomas J. Shannon, J. Martin Collinson, Guy M. Kirwan, Arturo Kirkconnell, and Martin Stervander. 2022. First genetic data for the Critically Endangered Cuban endemic Zapata Rail Cyanolimnas cerverai, and the taxonomic implications. bioRxiv preprint.
First genetic data for the Critically Endangered Cuban endemic Zapata Rail Cyanolimnas cerverai, and the taxonomic implications

Abstract
The taxonomic affinity of the near-flightless Zapata Rail Cyanolimnas cerverai, a Critically Endangered and highly localized species endemic to Cuba, has long been debated. Morphological analyses have suggested that this species, which constitutes a monotypic genus, could be related either to the extinct Tahitian Cave Rails (Nesotrochis sp.) or to the South American rail tribe Pardirallini, i.e., the genera Neocrex, Mustelirallus, and Pardirallus. Whilst pronounced phenotypic convergenceā€”and divergenceā€”among rails have repeatedly proven morphology-based phylogenies unreliable, thus far no attempt to sequence DNA from the enigmatic Cyanolimnas has succeeded. In this study, we extracted historic DNA from a museum specimen collected in 1927 and sequenced multiple short fragments that allowed us to assemble a partial sequence of the mitochondrial cytochrome oxidase I gene. Phylogenetic analyses confirm that Cyanolimnas belongs in tribe Pardirallini as sister to genus Neocrex, from which it diverged about six million years ago. Their divergence from Mustelirallus was estimated at about eight million years ago. Based on morphology and our mitochondrial phylogeny, we conclude that it is unjustified to retain the monotypic genus Cyanolimnas and tentatively recommend that C. cerverai and the two Neocrex species are ascribed to genus Mustelirallus.
 
Alex F. Brown, Thomas J. Shannon, J. Martin Collinson, Guy M. Kirwan, Arturo Kirkconnell, and Martin Stervander. 2022. First genetic data for the Critically Endangered Cuban endemic Zapata Rail Cyanolimnas cerverai, and the taxonomic implications. bioRxiv preprint.
First genetic data for the Critically Endangered Cuban endemic Zapata Rail Cyanolimnas cerverai, and the taxonomic implications

Abstract
The taxonomic affinity of the near-flightless Zapata Rail Cyanolimnas cerverai, a Critically Endangered and highly localized species endemic to Cuba, has long been debated. Morphological analyses have suggested that this species, which constitutes a monotypic genus, could be related either to the extinct Tahitian Cave Rails (Nesotrochis sp.) or to the South American rail tribe Pardirallini, i.e., the genera Neocrex, Mustelirallus, and Pardirallus. Whilst pronounced phenotypic convergenceā€”and divergenceā€”among rails have repeatedly proven morphology-based phylogenies unreliable, thus far no attempt to sequence DNA from the enigmatic Cyanolimnas has succeeded. In this study, we extracted historic DNA from a museum specimen collected in 1927 and sequenced multiple short fragments that allowed us to assemble a partial sequence of the mitochondrial cytochrome oxidase I gene. Phylogenetic analyses confirm that Cyanolimnas belongs in tribe Pardirallini as sister to genus Neocrex, from which it diverged about six million years ago. Their divergence from Mustelirallus was estimated at about eight million years ago. Based on morphology and our mitochondrial phylogeny, we conclude that it is unjustified to retain the monotypic genus Cyanolimnas and tentatively recommend that C. cerverai and the two Neocrex species are ascribed to genus Mustelirallus.
Curious the placement of Eurypyga within Gruiformes
 
Curious the placement of Eurypyga within Gruiformes

In my experience, this level of divergence is much too deep for a cox1 tree to be reliable, and support is poor for the critical nodes (see the colour of the node uniting Rallidae to Eurypigidae).
This probably makes the time calibration a bit pointless, however.
 
Alex F. Brown, Thomas J. Shannon, J. Martin Collinson, Guy M. Kirwan, Arturo Kirkconnell, and Martin Stervander. 2022. First genetic data for the Critically Endangered Cuban endemic Zapata Rail Cyanolimnas cerverai, and the taxonomic implications. bioRxiv preprint.
First genetic data for the Critically Endangered Cuban endemic Zapata Rail Cyanolimnas cerverai, and the taxonomic implications

Abstract
The taxonomic affinity of the near-flightless Zapata Rail Cyanolimnas cerverai, a Critically Endangered and highly localized species endemic to Cuba, has long been debated. Morphological analyses have suggested that this species, which constitutes a monotypic genus, could be related either to the extinct Tahitian Cave Rails (Nesotrochis sp.) or to the South American rail tribe Pardirallini, i.e., the genera Neocrex, Mustelirallus, and Pardirallus. Whilst pronounced phenotypic convergenceā€”and divergenceā€”among rails have repeatedly proven morphology-based phylogenies unreliable, thus far no attempt to sequence DNA from the enigmatic Cyanolimnas has succeeded. In this study, we extracted historic DNA from a museum specimen collected in 1927 and sequenced multiple short fragments that allowed us to assemble a partial sequence of the mitochondrial cytochrome oxidase I gene. Phylogenetic analyses confirm that Cyanolimnas belongs in tribe Pardirallini as sister to genus Neocrex, from which it diverged about six million years ago. Their divergence from Mustelirallus was estimated at about eight million years ago. Based on morphology and our mitochondrial phylogeny, we conclude that it is unjustified to retain the monotypic genus Cyanolimnas and tentatively recommend that C. cerverai and the two Neocrex species are ascribed to genus Mustelirallus.
Why the name Tahitian Cave Rails for Nesotrochis, arenā€™t they all Caribbean?
 

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