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Ploceidae

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Old Thursday 22nd December 2016, 13:25   #26
l_raty
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Quote:
Originally Posted by Peter Kovalik View Post
De Silva, T.N., Townsend Peterson, A., Fernando, S.W., Bates, J.M., Marks, B.D., Girard, M., Phylogenetic relationships of weaverbirds (Aves: Ploceidae): A first robust phylogeny based on mitochondrial and nuclear markers, Molecular Phylogenetics and Evolution (2016), doi: http://dx.doi.org/10.1016/j.ympev. 2016.12.013 In Press, Accepted Manuscript, Available online 21 December 2016.
(http://dx.doi.org/10.1016/j.ympev.2016.12.013 it should be -- no space after 'ympev.')
[Fig. 1]
[Fig. 2]
A long-awaited one .

This nicely confirms and expands what we suspected/knew already (cf. above, and also [here]) -- Ploceus must be restricted to the four Asian spp; the Madagascan Ploceus spp are sister to the African typical weaver/malimbe radiation; in this African radiation, the species usually placed in Ploceus (i.e., Textor sensu TiF) are paraphyletic wrt Malimbus.
The authors suggest lumping the entire African radiation (Malimbus, Anaplectes, Textor sensu TiF) into a quite (too?) broad Malimbus. (Which at least has the advantage that we don't need to worry too much about which subclade most unsampled species fall in.)

(Main remaining "mysteries", in my view: Brachycope anomala/Ploceus anomalus [looks like it might be a bishop, based on two very short (100bp) published cox1 sequences, but I wouldn't bet too much on this] and Pachyphantes/Ploceus superciliosus [seems pretty distinct, based on a single 297bp-long published cox1 sequence; can't really say more; and of course one single sequence can always 'be wrong' for one or another reason].)

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Old Thursday 22nd December 2016, 18:47   #27
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It's lacking some data to conclude to an enlarged Malimbus , the following species : ( flavipes, angolensis, sanctithomae... ) are not sampled and are sometimes placed in distinct genera (respectively Rhinoploceus, Notiospiza and Thomasophantes), it's too early for a complete review of these genera.

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Old Friday 23rd December 2016, 12:34   #28
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I would definitely not base any taxonomic recommendation on this but, for the entertainment, I have attached an unbootstrapped tree including all available cox1 Ploceidae sequences. I used the same colour codes for the clades as in the [graphical abstract] of the recent paper.

Many of these sequences are from Sonet et al. 2011 [pdf here] (pp.117-131): these are short (~300bp) to very short (100bp) sequences obtained from old to very old museum specimens; some of them may have problems -- in fact for some of them I see a strong suggestion that they do have problems. Almost all the sequences in the data set include the region corresponding to the 100bp of the shortest ones (the two that do not only lack a couple of bases at the start of this region), hence artefacts associated to some sequences having no overlapping DNA at all should at least be absent. Due to the shortness of many of the sequences, bootstrapping this data set would largely destroy the structure that can be seen in the unbootstrapped tree; this structure is not to be regarded as having received statistical support; yet, it does reflect the divergence levels that are present between the sequences of the data set.

The length of each sequence is given in parentheses, in the tip label, before the GenBank/BOLD accession number.
Attached Files
File Type: pdf Ploceidae-cox1.no-support.pdf (11.3 KB, 159 views)

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Old Friday 23rd December 2016, 16:12   #29
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I would definitely not base any taxonomic recommendation on this but, for the entertainment, I have attached an unbootstrapped tree including all available cox1 Ploceidae sequences. I used the same colour codes for the clades as in the [graphical abstract] of the recent paper.

Many of these sequences are from Sonet et al. 2011 [pdf here] (pp.117-131): these are short (~300bp) to very short (100bp) sequences obtained from old to very old museum specimens; some of them may have problems -- in fact for some of them I see a strong suggestion that they do have problems. Almost all the sequences in the data set include the region corresponding to the 100bp of the shortest ones (the two that do not only lack a couple of bases at the start of this region), hence artefacts associated to some sequences having no overlapping DNA at all should at least be absent. Due to the shortness of many of the sequences, bootstrapping this data set would largely destroy the structure that can be seen in the unbootstrapped tree; this structure is not to be regarded as having received statistical support; yet, it does reflect the divergence levels that are present between the sequences of the data set.

The length of each sequence is given in parentheses, in the tip label, before the GenBank/BOLD accession number.
Laurent, I appreciate your input, as always.
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Old Friday 23rd December 2016, 16:27   #30
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Many of these sequences are from Sonet et al. 2011 [pdf here] (pp.117-131):
Link leads to a study of genus Accipiter
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Old Friday 23rd December 2016, 16:30   #31
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Link leads to a study of genus Accipiter
Scroll to p.117.
(It's an entire issue of Bonn Zool Monogr, minus the cover.)
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Old Friday 23rd December 2016, 16:46   #32
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Old Thursday 5th January 2017, 05:46   #33
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De Silva, T.N., Townsend Peterson, A., Fernando, S.W., Bates, J.M., Marks, B.D., Girard, M., Phylogenetic relationships of weaverbirds (Aves: Ploceidae): A first robust phylogeny based on mitochondrial and nuclear markers, Molecular Phylogenetics and Evolution (2016), doi: http://dx.doi.org/10.1016/j.ympev. 2016.12.013 In Press, Accepted Manuscript, Available online 21 December 2016.

[abstract]
TiF Update January 4, 2017

Weavers: The weavers have been rearranged based mainly on De Silva et al. (2017), with some help from the barcoding results of Sonet et al. (2011), who did not provide a tree. Raty did, but cautions that the barcoding data is quite limited and that the result has has no real statistical support. Indeed, when compared to De Silva et al. (2017), there are some odd placements. Nonetheless, I have treated close relationships as having some meaning. When combined with traditional taxonomy, this has allowed me to regroup Textor (formerly the African Ploceus). Keep in mind that I previously restricted the name Ploceus to the Asian species. The two Madagascan weavers are separated as Nelicurvius, with some of the African Textor being moved to Malimbus. Although Sonet et al.'s data indicate that the Golden Palm Weaver is close to Nelicurvius, I have considerable doubts about this and have retained it in Textor.

I have merged Pseudonigrita into Philetairus as they are closely related. Note that the main time-calibration in De Silva et al. (2017) is way too old as the whole family is probably not more than 20 million years old. I have separated Pachyphantes from Textor and placed it near Quela based on the barcoding data. I have also merged Brachycope into Euplectes, again based on the barcoding data, and merged Anaplectes into Malimbus based on De Silva et al. (2017).

The tree in De Silva et al. (2017) encouraged me to acknowledge the split of Aldabra Fody, Foudia aldabrana, from Comoros Fody, Foudia eminentissima.

I have also removed the alternate English name African Golden-Weaver from Southern Masked Weaver, Textor velatus and removed the hyphens from Masked and Golden Weavers.
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Old Thursday 5th January 2017, 15:36   #34
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The two Madagascan weavers are separated as Nelicurvius
I would prefer to separate the Sakalava Weaver in the genus Saka Roberts, 1947 , based only on appearance.
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Old Friday 6th January 2017, 20:15   #35
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Hi guys,
The complete phylogeny is being worked on. I'm doing the lab work these days using ancient DNA. Pretty soon I'll be able to complete the weaver phylogeny hopefully.
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Old Friday 6th January 2017, 20:21   #36
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Hi guys,
The complete phylogeny is being worked on. I'm doing the lab work these days using ancient DNA. Pretty soon I'll be able to complete the weaver phylogeny hopefully.
Good news.
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Old Wednesday 11th January 2017, 05:00   #37
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LeNomenclatoriste said "I would prefer to separate the Sakalava Weaver in the genus Saka Roberts, 1947 , based only on appearance." Wolters in Die Vogelarten der Erde 4 lieferung page 290 puts N. sakalava in subgenus Saka Austin Roberts 1947 Ostrich. He puts N. nelicourvi in subgenus Nelicurvius Bonaparte 1850 the genus name also.
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Old Wednesday 11th January 2017, 07:24   #38
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LeNomenclatoriste said "I would prefer to separate the Sakalava Weaver in the genus Saka Roberts, 1947 , based only on appearance." Wolters in Die Vogelarten der Erde 4 lieferung page 290 puts N. sakalava in subgenus Saka Austin Roberts 1947 Ostrich. He puts N. nelicourvi in subgenus Nelicurvius Bonaparte 1850 the genus name also.
According to HBW , P. sakalava and nelicourvi were considered conspecifics in the past.

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Old Saturday 1st July 2017, 11:22   #39
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IOC Updates

IOC Updates Diary June 30

Move sparrow-weavers (Plocepasser) from Passeridae to Ploceidae
Move Rufous-tailed Weaver (Histurgops) from Passeridae to Ploceidae
Move social-weavers (Pseudonigrita) from Passeridae to Ploceidae
Move Sociable Weaver (Philetairus) from Passeridae to Ploceidae
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Old Sunday 2nd July 2017, 17:54   #40
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IOC Updates Diary June 30

Move sparrow-weavers (Plocepasser) from Passeridae to Ploceidae
Move Rufous-tailed Weaver (Histurgops) from Passeridae to Ploceidae
Move social-weavers (Pseudonigrita) from Passeridae to Ploceidae
Move Sociable Weaver (Philetairus) from Passeridae to Ploceidae
Isn't that just reversing a move they did in the opposite direction a few years ago?
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Old Saturday 6th January 2018, 14:21   #41
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Twyman H, Prager M, Mundy NI, Andersson S. Expression of a carotenoid-modifying gene and evolution of red coloration in weaverbirds (Ploceidae). Mol Ecol. 2017;00:1–10. https://doi.org/10.1111/mec.14451

[abstract]
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Old Wednesday 7th February 2018, 18:55   #42
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Thilina N. de Silva, John M. Bates, A. Townsend Peterson. Getting the Ploceidae Tree Right. Molecular Phylogenetics and Evolution. In Press, Accepted Manuscript, Available online 7 February 2018

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Prager (2017) offered a series of criticisms of our recent publication providing a first phylogenetic hypothesis for the Ploceidae (De Silva et al., 2017). We were chagrined to note her correct indication that we misinterpreted the taxonomic identity of samples to which we referred as Northern Red Bishop (Euplectes franciscanus) versus Southern Red Bishop (E. orix), Montane Widowbird (E. psammocromius) versus Marsh Widowbird (E. hartlaubi), and Fan-tailed Widowbird (Euplectes axillaris) versus Long-tailed Widowbird (E. progne). We accept these three corrections fully: we overlooked differing taxonomic concepts between holdings of museum collections (the first two cases), and did not catch a misidentification of a specimen in one museum collection (the latter case). A fourth criticism was odd, involving a problem with the taxon labels of the ND2 sequences that we deposited in Genbank, which are scrambled— Prager (2017) admitted that our figures and conclusions are not affected; we have verified that the Genbank accession numbers reported in our paper are correct, although the names in the Genbank data records are not. We are in the process of correcting the problems with the Genbank data records.

We suggest that such issues of sequence metadata could be addressed much more flexibly if Genbank were to create a comments and feedback section, so that persons other than the creator of the record can provide input. Such comments can be offered, for example, for auditory submissions to a public database of avian vocalizations, Xeno-canto (http://www.xeno-canto.org/). In our case, thanks to Prager’s comment, we are addressing making the appropriate changes in Genbank. However, such corrections are not always made, so Genbank metadata often remain uncorrected in spite of some researcher knowing that problems exist.

After the factual documentation of the problems with our publication, however, Prager (2017) proceeded to make remarks that are more ad hominem in nature. She asserted that we have been “careless” in our literature review, but no documentation is offered. She suggested that, because she found problems in Euplectes, problems are probably rife across our ploceid work—indeed, we have checked each taxonomic name used, and can confirm that no further problems of this sort exist. A final comment, directed at co-author Peterson (although co-author Bates is equally guilty!), was about our focus on the need for museum vouchers in phylogenetic studies ( Bates et al., 2004; Peterson et al., 2007). Prager (2017) says that she appreciates the importance of museum collections and voucher samples in such research, but that a voucher is no substitute for knowledge of the studied organisms. We agree, and for that reason have sustained long field careers, but we remind Prager that vouchered samples can be revisited and re-examined, as she was able to request in the case of our misidentification of E. axillaris). Yes, perhaps a mistake was made (not by us, but by the source museum); however, thanks only to the existence of voucher specimens, it can be revisited and verified; with non-vouchered material (see, for example, the sampling in Prager et al., 2008), such repeatability of scientific results is not possible, and corrections are possible only via inference and supposition.

On a more fundamental level, we consider it rather sad that Prager (2017) saw it necessary to publish an aggressive critique of our paper. We were in friendly communication with her group soon after publication of our paper, exploring possible coordination and/or cooperation, yet no mention of problems was made. The problems pointed out could easily have been corrected as a “friendly amendment,” rather than as an attack. Science can, and should, proceed in a more civilized fashion, but the present interchange is not an example of that possibility.
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Old Thursday 8th February 2018, 06:01   #43
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Prager M. [in press.] Unweaving a taxon tangle: Comments on De Silva et al. (2017). Letter to the Editor. Mol. Phylogenet. Evol.
https://doi.org/10.1016/j.ympev.2018.02.005
(No abstract.)

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Old Friday 9th February 2018, 02:29   #44
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I am rooting for team de Silva!! Because he posted to this forum. Laurent do you have an opinion on his proposal for others to comment on Genbank?
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Old Saturday 13th October 2018, 08:01   #45
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Golden-naped & Yellow-legged Weavers

Fishpool LDC, Collar NJ. 2018. On the validity of the Golden-naped Weaver Ploceus aureonucha and the Yellow-legged Weaver P. flavipes, with comments on forest ‘nuthatch-weavers’. ABC Bulletin, 25: 159-179.

Summary. Propositions are tested that Golden-naped Weaver Ploceus aureonucha (known from seven specimens) represents undescribed immature plumage stages of Yellow-mantled Weaver P. tricolor or, alternatively, a hybrid between P. tricolor and Vieillot’s Black Weaver P. nigerrimus, and that Yellow-legged Weaver P. flavipes (known from nine specimens) is a hybrid between P. nigerrimus and Maxwell’s Black Weaver P. albinucha. Morphological and morphometric evidence from all museum specimens of both contested species was compared with equivalent data from the putative parents, as well as from several other selected forest weaver species. Plumages of P. aureonucha grouped by sex and age prove to be consistent, but descriptions of them have varied confusingly. Its smaller size and much shorter tail than those of the proposed parent species render a hybrid origin for P. aureonucha entirely implausible. Moreover these differences, and the fact that the entire sequence of age-related plumages is known in P. tricolor, discredit the proposition that P. aureonucha is an immature P. tricolor. The nasal structure of P. flavipes, combined with its yellow legs, speaks for its taxonomic authenticity, while the case for a hybrid origin founders not just on these characters but also on the far greater size of of P. nigerrimus, one of the supposed parents. The geographical restriction of both taxa, when the suggested parent species are much more widely spread, further undermines the hybrid hypothesis. Mensural data show that forest ‘nuthatch-weavers’ have distinctively long hind toes and claws as well as narrow bills, modifications likely to be associated with their specialised foraging behaviour. Despite some field observations to the contrary, measurements indicate that P. aureonucha is unlikely to be a nuthatch-weaver
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Old Sunday 25th November 2018, 11:34   #46
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Ploceus philippinus

H. D. Oschadleus. Type locality of the Baya Weaver Ploceus philippinus (Passeriformes, Ploceidae). Zootaxa, Vol 4524, No 3: 22 Nov. 2018.

Abstract:

The Baya Weaver Ploceus philippinus (Linnaeus, 1766) was one of the first weaverbirds to be described, and although Linnaeus (1766) provided its specific epithet and the type locality of the Philippines, the Baya Weaver does not occur there. Hartert (1902, p. 577) thus restricted the locality to Ceylon (now Sri Lanka), and this locality has been used in all major references since, in spite of Stresemann (1952) showing that the type was most probably collected by Pierre Poivre in India. This paper draws attention to this error so that avian handbooks and taxonomic works may refer to the correct type locality of the Baya Weaver as Puducherry (previously Pondicherry), Puducherry district, India.
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Old Wednesday 12th June 2019, 23:33   #47
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Hi guys,
Finally my paper got published!!
So I present to you, a first near species-level molecular phylogeny of the family Ploceidae. Thank you!!
https://academic.oup.com/auk/advance...cgVMUPwsLnryq4
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Old Thursday 13th June 2019, 05:40   #48
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Hi guys,
Finally my paper got published!!
So I present to you, a first near species-level molecular phylogeny of the family Ploceidae. Thank you!!
https://academic.oup.com/auk/advance...cgVMUPwsLnryq4
Awesome work!

My suggestion :

I divided Ploceus into 3 subgenera (Deignaniplectes, Ploceela, Ploceus) ;

Quelea into 2 subgenera (Quelea and Queleopsis);

5 subgenera under Euplectes (Taha, Paraplectes, Euplectes, Brachycope and Coliuspasser)

[That said, taking into account the time of divergence of each genus , I could eventually raise them to generic rank]

I recognise 2 genera within the African weavers, Malimbus and Textor.

Clarification is needed for some Plocepasser species and Pseudonigrita cabanisi. However, I reinstate Whitellus for cabanisi

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Old Thursday 13th June 2019, 06:12   #49
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Hi guys,
Finally my paper got published!!
So I present to you, a first near species-level molecular phylogeny of the family Ploceidae. Thank you!!
https://academic.oup.com/auk/advance...cgVMUPwsLnryq4
Fantastic work and a great read!

Just a couple of questions:

I notice in the tree that both Southern Red Bishop and Fan-tailed Widowbird seem to be paraphyletic, something you don’t comment on in text. What are your thoughts on that?

Also, I lack a rationale of a large Malimbus vs keeping the savanna Ploceus in a separate genus. As you state in the text, they seem to form two morphologic and ecologic separate clades.
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Old Thursday 13th June 2019, 07:40   #50
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Fantastic work and a great read!

Just a couple of questions:

I notice in the tree that both Southern Red Bishop and Fan-tailed Widowbird seem to be paraphyletic, something you don’t comment on in text. What are your thoughts on that?

Also, I lack a rationale of a large Malimbus vs keeping the savanna Ploceus in a separate genus. As you state in the text, they seem to form two morphologic and ecologic separate clades.
Thanks for the compliments.
Subspecies genetic data for most widowbird taxa were extracted from Prager's work, thus I didn't go on to interpret paraphyly observed within those clades.
Maybe yours is a good suggestion, I was trying to do minimal changes to the existing nomenclature while playing by the rule book. Thanks for your thoughts!!
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