Phalacrocoracidae (1 Viewer)

Peter Kovalik said:

Martyn Kennedy, Hamish G. Spencer. Classification of the Cormorants of the World. Molecular Phylogenetics and Evolution. In Press.

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Kennedy M, Spencer HG. 2014. Classification of the Cormorants of the World. Mol. Phylogenet. Evol. 79: 249-257.
The full paper (with--unusual, and definitely to be applauded--the supplementary material added at the end of the pdf) is obtainable [here].

I played a bit with the data, they seem clean, and the relationships generally robust.
I have some reservations, however, about the position of Phalacrocorax gaimardi. The dataset the study was based on included sequences of four mitochondrial (12s, atp8-6, cox1, nd2) and 5 nuclear (bfib7, cryaa, irf2, park7, rapgef1) markers. Unfortunately, for gaimardi, besides the mtDNA, they obtained only irf2, which is the shortest of the five nuclear markers. This would not be a problem if the signal in irf2 was congruent with the signal present in the mtDNA--however, it is not: instead of making it highly distinct, irf2 places gaimardi within Phalacrocorax sensu stricto with a support that, although not huge, is nevertheless disturbingly high (see the attached nDNA tree). Of course, when the complete dataset is analyzed, 645bp of slow-evolving nDNA are unable to offset the signal brought by >3500bp of fast-evolving mtDNA, and the position of the taxon is in effect entirely determined by the mtDNA. But the conflict remains, and is unexplained. I'd really love to see more data from this species (particularly more nDNA, but mtDNA from other individuals, that might confirm what we currently have, would be a good thing as well).
(Incidentally: note also that this much more limited amount of nDNA for gaimardi makes the distances involving Poikilocarbo in Table 5 much higher than the rest, for a reason that has nothing to do with evolutionary distinctness. In all the other groups, the values are taken down by the inclusion of more slow-evolving nDNA.)

All that being said, I'm afraid that I remain to be convinced that so much splitting is really the best way to go. A rapid look at the attached mtDNA tree suggests that, if the distance separating Leucocarbo from Nannopterum marks a generic limit, then we should also split Gavia in two, Sula s.s. (Morus and Papasula already excluded) in three, Anhinga in three, and Pelecanus in four... Not to mention that, as indeed noted by the authors, the distance between the two sampled Microcarbo is also larger than between these two "genera". And the distances withing Phalacrocorax s.s. are dangerously close as well.
Personally, I'm happy with the two genera recognized in H&M4.

SACC proposal

Peter Kovalik said:

Proposal (648) to SACC:
Revise the classification of the Phalacrocoracidae

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Proposal #648B passed, 22 Jan 2016: Recent changes.

Phalacrocorax aristotelis - citation

Phalacrocorax aristotelis (Linnaeus, 1761), is cited (e.g. zoonomen, Lynx HBW): Fauna svecica ed.2: [23], 51.

But page 23 doesn't mention it at all, and page 51 (#146) doesn't say "aristotelis" as a species name, just PELECANUS and then some phrase descriptions (unlike e.g. PELECANUS Carbo, next above, or PELECANUS Bassanus, next below).

So why is the species validly published there? Or is there a more correct citation elsewhere?

It is there on page 51 6th line from the bottom. "Graculus palmipes aristotelis"

This is one of those cases where Linnaeus "validates" the work of others - i.e. he takes a name someone else used and by the rules of the ICZN he becomes the author.

Aldr. orn. Means that this species was originally described in Aldrovandis's Ornithologiae (1599-1603).

I am not familiar enough with this publication to find the actual reference - although it is near pg 759.

I suspect there is a degree of interpretation by the subsequent (or revising) authors (probably also Linnaeus) that has lead to us actually using aristotelis however.

Paul

"Fauna svecica ed.2: [23]" is not page 23.
It is the 23rd unpaginated page, counted from the first leaf that follows the one that includes the title page: [this].
There, you do have a "Pelecanus 146 aristotelis 117" -- which is a binominal name applying to the "146. PELECANUS subtus fuscus, rectricibus duodecim. Fn. 117." of page 51.

(References cited by Linnaeus:
- Ulyssis Aldrovandi Ornithologiae tomus alter, liber XIX, caput LVIII: [here].
- Francisci Willughbeii Ornithologiae libri tres, pagina 249: [here]; tabula LXIII: [here]. English translation of the text: [here].
- Joannis Raji Synopsis methodica avium, pagina 123: [here].
- Eleazar Albin's "Ornithologia" (= A natural history of birds), tomus 2, pagina 74 & tabula 81: [here].
The last one is obviously a cormorant, not a shag, and was probably cited in error. (Albin was mainly a painter, and many of his texts were taken almost verbatim from the English version of Willughby's Ornithology; here, Albin's description is that of Willughby's "Cormorant Corvus aquaticus" [here]; this reference conflicts objectively with the second one, which is to another species in Willughby's work; Linnaeus cited Willughby's Corvus aquaticus under his PELECANUS Carbo.) That being said, Linnaeus himself was evidently uncertain about the status of the bird he described. ("Forte haec avis vel junior vel Carbonis femina.": "Perhaps this bird is either the young or the female of Carbo."))

Excellent, thanks!

Harell. 2016. Comparative ecomorphology of cormorants (Phalacrocoracidae). Waterbirds 39:136-145. [abstract]

(Harell. 2012. Comparative ecomorphology of cormorants (Phalacrocoracidae) from three Mediterranean regions. Master thesis, California State University. [pdf])

Phalacrocorax carbo

Letong Zhang, Ming Zhang, and Shiyang He. The complete mitochondrial genome of great cormorant, Phalacrocorax carbo (Phalacrocorax, Phalacrocoracidae). Mitochondrial DNA Part A, Published online: 26 Oct 2016

[abstract]

King Shag

Rawlence, N.J., et al. Speciation, range contraction and extinction in the endemic New Zealand King Shag complex. Mol. Phylogenet. Evol. (2017), http://dx.doi.org/10.1016/j.ympev.2017.07.011

Abstract:

New Zealand’s endemic King Shag (Leucocarbo carunculatus) has occupied only a narrow portion of the northeastern South Island for at least the past 240 years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications. Our analyses show that the King Shag was formerly widespread around southern coasts of the North Island and the northern parts of the South Island but experienced population and lineage extinctions, and range contraction, probably after Polynesian arrival. This history parallels range contractions of other New Zealand seabirds. Conservation management of the King Shag should take into account this species narrow distribution and probable reduced genetic diversity. Moreover, combined genetic, morphometric and osteological analyses of prehistoric material from mainland New Zealand suggest that the now extinct northern New Zealand Leucocarbo populations comprised a unique lineage. Although these distinctive populations were previously assigned to the King Shag (based on morphological similarities and geographic proximity to modern Leucocarbo populations), we herein describe them as a new species, the Kohatu Shag (Leucocarbo septentrionalis). The extinction of this species further highlights the dramatic impacts Polynesians and introduced predators had on New Zealand’s coastal and marine biodiversity. The prehistoric presence of at least four species of Leucocarbo shag on mainland NZ further highlights its status as a biodiversity hotspot for Phalacrocoracidae.

Phalacrocorax harrisi

Alejandro Burga, Weiguang Wang, Eyal Ben-David, Paul C. Wolf, Andrew M. Ramey, Claudio Verdugo, Karen Lyons, Patricia G. Parker, Leonid Kruglyak. A genetic signature of the evolution of loss of flight in the Galapagos cormorant. Science 02 Jun 2017: Vol. 356, Issue 6341, eaal3345

[abstract]

[pdf]

Peter Kovalik said:

Alejandro Burga, Weiguang Wang, Eyal Ben-David, Paul C. Wolf, Andrew M. Ramey, Claudio Verdugo, Karen Lyons, Patricia G. Parker, Leonid Kruglyak. A genetic signature of the evolution of loss of flight in the Galapagos cormorant. Science 02 Jun 2017: Vol. 356, Issue 6341, eaal3345

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Mark J. Berger & Gill Bejerano. Comment on "A genetic signature of the evolution of loss of flight in the Galapagos cormorant". bioRxiv preprint first posted online Sep. 8, 2017

[pdf]

It would be interesting to see if flightless Steller's Cormorant, extinct in 19. century, had the same genetic signature of loss of flight.

Phalacrocorax perspicillatus

Junya Watanabe, Hiroshige Matsuoka and Yoshikazu Hasegawa. Pleistocene fossils from Japan show that the recently extinct Spectacled Cormorant (Phalacrocorax perspicillatus) was a relict. The Auk 135: 895–907.

See also Fred's post here

Martyn Kennedy, Sampath S. Seneviratne, Nicolas J. Rawlence, Shakila Ratnayake, Hamish G. Spencer (2018) The phylogenetic placement of the enigmatic Indian Cormorant, Phalacrocorax fuscicollis (Phalacrocoracidae). Molecular Phylogenetics and Evolution. Available online 25 October 2018. In Press, Accepted Manuscript
https://www.sciencedirect.com/science/article/pii/S1055790318304275

Abstract
The Indian Cormorant (Phalacrocorax fuscicollis) is a common avian piscivore that occurs throughout the Indian subcontinent and east to southern Vietnam. Its evolutionary relationships, however, have remained obscure, largely because of a lack of material available for either osteological or genetic analysis. Here we show using DNA-sequence data from both nuclear and mitochondrial genes that this species is sister to the allopatric Little Black Cormorant (P. sulcirostris), which occurs from Java in the west through southern Indonesia and New Guinea to Australia and New Zealand in the south. We estimate this split to have happened 2.5-3.2 million years ago, during the late Pliocene. We also report on genetic variation within the mitochondrial control region, which suggests that this part of the genome may be useful in investigating if there is genetic structure across the geographical range of the Indian Cormorant.



I hate taxonomy only based on phylogeny without take into account morphological peculiarities. Phalacrocorax, as currently defined, forms a disparate and superficial group. For me , Phalacrocorax should be restricted to the type species (including lucidus, maroccanus). The remaining taxon being moved in their own genus : Pseudocarbo for capensis, Hypoleucus for varius and fuscescens, Mesocarbo for sulcirostris and fuscicollis (thanks Laurent) Stictocarbo for punctatus and featherstoni and 1 new genus : "Nesonastes" (Island inhabitant) for nigrogularis.

If I had the means to write a worldwide checklist of birds......

LeNomenclatoriste said:

and "Leptohalieus" (thin shag) for sulcirostris and fuscicollis.

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Mesocarbo Mathews & Iredale 1913 has Carbo sulcirostris Brandt 1837 as its type : https://biodiversitylibrary.org/page/26514655
(Not sure it'll please you overly, if you like creative names, though .)

How did I miss this name? Thks

Phalacrocorax punctatus

Nicolas J Rawlence, Matt J Rayner, Tim G Lovegrove, Debbie Stoddart, Melanie Vermeulen, Luke J Easton, Alan J D Tennyson, R Paul Scofield, Martyn Kennedy, Hamish Spencer, Jonathan M Waters, Archival DNA reveals cryptic biodiversity within the Spotted Shag (Phalacrocorax punctatus) from New Zealand, The Condor, , duz029, https://doi.org/10.1093/condor/duz029

Abstract:

Genetic data are increasingly being used to prioritize species conservation in a fiscally constrained age of seemingly boundless conservation crises. Such data can also reveal previously cryptic biodiversity requiring further revision of conservation management guidelines. Using a combination of mitochondrial (control region) and nuclear (beta fibrinogen intron 7) DNA, and morphology, we reveal that the endemic New Zealand Spotted Shag (Phalacrocorax punctatus) complex exhibits phylogenetic structure that is decoupled from previously recorded qualitative morphological variation. Crucially, the most genetically distinct populations within P. punctatus are from northern New Zealand; recent surveys show that these populations, which house important genetic diversity within Spotted Shags, are in danger of being extirpated. In contrast, we find the previously phenotypically differentiated nominate (P. punctatus punctatus) and Blue (P. punctatus oliveri) Shag subspecies show no genetic and morphological separation, and are of least conservation concern.

A query arising out of side discussion in this thread - what is the type locality and precise [subspecific] identity of Linnaeus's Phalacrocorax carbo? All that Linnaeus says about location is 'Europe', but also that it is nidificat in altis arboribus, "nesting in tall trees". I've not seen any subsequent reference restricting the location at all; given Linnaeus's nationality, one might expect that (like many other familiar N European birds) it would be Sweden, likely not far from Uppsala. The species is currently common around nearby Stockholm, where they nest in trees. According to some authors (though not others!) this is a defining behavioural character of what is now called P. c. sinensis with nominate carbo, contrary to Linnaeus's statement, largely restricted to ground nesting on marine islands. Is there any designated type specimen on which the gular angle can be measured?

Nutcracker said:

A query arising ... what is the type locality and precise [subspecific] identity of Linnaeus's Phalacrocorax carbo?
[...]

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As Linnaeus's Phalacrocorax carbo (1758) is the nominate itself I assume it must be of ssp. P. c. carbo. .

Nutcracker said:

... All that Linnaeus says about location is 'Europe', but also that it is nidificat in altis arboribus, "nesting in tall trees". I've not seen any subsequent reference restricting the location at all; given Linnaeus's nationality, one might expect that (like many other familiar N European birds) it would be Sweden, likely not far from Uppsala. The species is currently common around nearby Stockholm, ... [...]. Is there any designated type specimen on which the gular angle can be measured?

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As far as I know there's no "designated type specimen" (nor a Type locality) of this species [alt. (nominate) subspecies, neither of (the "Chinese" ssp.) P. c. sinensis (Staunton, 1796)]. At least not in the Type collection at Naturhistoriska riksmuseet [Swedish (Royal) Museum of Natural History] in Stockholm (here).

Linnaeus' first reference in the OD of "[Pelecanus] Carbo" [later moved into Phalacrocorax Brisson, 1760 (not Moering/Möhring, 1758)], in the long list of references (all earlier pre-Linnaean/pre-1758 works), takes us back to his own: "Fn. Svec. 116" [Fauna Svecica, 1746, here; listed as No. 116 (thus, not page 116), it's found on p.42], which (only) states (re. distribution/habitat/location): "Habitat in maris Scopulis, arboribusque insidet", which, to me (a non-Latin scholar) says something like "Inhabits rocky shores, situated upon trees" (or similar).

Either way, I think you can lean back. This certain bird (and topic) has been looked at, and dealt with, in the most minute detail, by several (many) acknowledged ornithologist and scientists.

Though, it's true that these Cormorants are "currently common around nearby Stockholm", but it was a completely different situation back in the mid-1700's. In those days Cormorants were a Rare sight (and certainly so in the vicinity of Stockholm and Uppsala).

In that Era Great Cormorants were mainly found in the southernmost parts of the country [even if it's known/listed as a "Swedish" bird/species, present in Sweden, far, far earlier; known in Swedish literature since 1555, as well as verified, confirmed from/in archeological (Viking Age) findings, dug up just outside Stockholm].

Björn

PS. Allow me to share a short birding memory (even if of no taxonomic value what-so-ever), simply as this certain species was my very first finding of a "rarity", my own first (proud) mark in the local Bird Club community, back in the 1970's, when I was a teenager, a mere beginner, a novice with my first pair of binoculars, I had spotted three Great Cormorants (storskarv, in Swedish), in Lake Möckeln, inland Southern Sweden. When I told my older, far more experienced, birding pals about this observation, they shook their heads, and replied with skepticism; "No no no, you mean you've seen a storskrake [Common/Eurasian Merganser/Goosander Mergus merganser]". But nope, such they were not.

Linnaeus worked a long while in The Netherlands, where it was common by then.