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Galliformes (1 Viewer)

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
Rebecca T. Kimball, Peter A. Hosner, Edward L. Braun. A Phylogenomic Supermatrix Of Galliformes (Landfowl) Reveals Biased Branch Lengths. Molecular Phylogenetics and Evolution, In Press, Journal Pre-proof, Available online 2 February 2021.

Abstract:

Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology (“legacy” markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
Agelastes, Pauxi and Perdicula are not monophyletic.

Agelastes niger is sister to Numida meleagris while A. meleagrides is sister to Guttera and Acryllium. So, I have put A. niger in Phasidus as Phasidus niger

Perdicula
is formed of two distinct lineage, one with P. erythrorhyncha (now Cryptoplectron erythrorhyncha), and one other with P. asiatica (include but not analyzed the following species manipurensis and argoondah which share same morphological features with asiatica).

Pauxi pauxi is close to Nothocrax ururmutum but with weak support. I didn't touch them. I don't know where placed Pauxi koepckeae.

I have placed Excalfactoria in synonymy with Synoicus, resulting this new combination Synoicus adansonii and S. chinensis.
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
Rebecca T. Kimball, Peter A. Hosner, Edward L. Braun. A Phylogenomic Supermatrix Of Galliformes (Landfowl) Reveals Biased Branch Lengths. Molecular Phylogenetics and Evolution, In Press, Journal Pre-proof, Available online 2 February 2021.

Abstract:

Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology (“legacy” markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
Who has the paper plz ?
 

Acanthis

Well-known member
Wow! "Erectile clade" & "Non-erectile clade"!
Hopefully without any dysfunctional taxa😁

So if you wished to divide Phasianidae into 2 subfamilies based on this feature the name available for the non-erectiles would be Pavoninae?
Is that right?
 
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l_raty

laurent raty
So if you wished to divide Phasianidae into 2 subfamilies based on this feature the name available for the non-erectiles would be Pavoninae?
Is that right?
That is what I would do as well.

Bock 1994 claimed this name from:
"Pavosia"; subfamily; Rafinesque-Schmaltz CS. 1815. Analyse de la nature, ou tableau de l'univers et des corps organisés. S.n., Palerme.; p. 70; 1815 - Analyse de la nature : - Biodiversity Heritage Library
...but as I already wrote elsewhere, Rafinesque's family and subfamily names were explicitly not plural (1815 - Analyse de la nature : - Biodiversity Heritage Library ), thus they all fail to meet Art. 11.7.1.1 of the ICZN and (unless explicitly attributed to this source on the Official List as a result of an action by the Commission) they all are objectively unavailable.
In my list, I take it from:
Pavonidae; family; Horsfield T. 1821. Systematic arrangement and description of birds from the Island of Java. (Read 18 April 1820). Trans. Linn. Soc. London, 13: 133-200.; p. 185; v.13 (1822) - Transactions of the Linnean Society of London - Biodiversity Heritage Library
...which does not affect its precedence.
 

TomDerutter

Well-known member
uses coturnicini
uses tetraogallini for this clade

which one is correct?
 

albertonykus

Well-known member
Kimball, R.T., M. Guido, P.A. Hosner, and E.L. Braun (2021)
When good mitochondria go bad: cyto-nuclear discordance in landfowl (Aves: Galliformes)
Gene 801: 145841
doi: 10.1016/j.gene.2021.145841

Mitochondrial sequences were among the first molecular data collected for phylogenetic studies and they are plentiful in DNA sequence archives. However, the future value of mitogenomic data in phylogenetics is uncertain, because its phylogenetic signal sometimes conflicts with that of the nuclear genome. A thorough understanding of the causes and prevalence of cyto-nuclear discordance would aid in reconciling different results owing to sequence data type, and provide a framework for interpreting megaphylogenies when taxa which lack substantial nuclear data are placed using mitochondrial data. Here, we examine the prevalence and possible causes of cyto-nuclear discordance in the landfowl (Aves: Galliformes), leveraging 47 new mitogenomes assembled from off-target reads recovered as part of a target-capture study. We evaluated two hypotheses, that cyto-nuclear discordance is “genuine” and a result of biological processes such as incomplete lineage sorting or introgression, and that cyto-nuclear discordance is an artifact of inaccurate mitochondrial tree estimation (the “inaccurate estimation” hypothesis). We identified seven well-supported topological differences between the mitogenomic tree and trees based on nuclear data. These well-supported topological differences were robust to model selection. An examination of sites suggests these differences were driven by small number of sites, particularly from third-codon positions, suggesting that they were not confounded by convergent directional selection. Hence, the hypothesis of genuine discordance was supported.
 
Last edited:

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
Kimball, R.T., M. Guido, P.A. Hosner, and E.L.Braun (2021)
When good mitochondria go bad: cyto-nuclear discordance in landfowl (Aves: Galliformes)
Gene 801: 145841
doi: 10.1016/j.gene.2021.145841

Mitochondrial sequences were among the first molecular data collected for phylogenetic studies and they are plentiful in DNA sequence archives. However, the future value of mitogenomic data in phylogenetics is uncertain, because its phylogenetic signal sometimes conflicts with that of the nuclear genome. A thorough understanding of the causes and prevalence of cyto-nuclear discordance would aid in reconciling different results owing to sequence data type, and provide a framework for interpreting megaphylogenies when taxa which lack substantial nuclear data are placed using mitochondrial data. Here, we examine the prevalence and possible causes of cyto-nuclear discordance in the landfowl (Aves: Galliformes), leveraging 47 new mitogenomes assembled from off-target reads recovered as part of a target-capture study. We evaluated two hypotheses, that cyto-nuclear discordance is “genuine” and a result of biological processes such as incomplete lineage sorting or introgression, and that cyto-nuclear discordance is an artifact of inaccurate mitochondrial tree estimation (the “inaccurate estimation” hypothesis). We identified seven well-supported topological differences between the mitogenomic tree and trees based on nuclear data. These well-supported topological differences were robust to model selection. An examination of sites suggests these differences were driven by small number of sites, particularly from third-codon positions, suggesting that they were not confounded by convergent directional selection. Hence, the hypothesis of genuine discordance was supported.
I want it too please
 

andrew147

Well-known member
anyone care to describe if there are any new phylogenetic findings?
Not really anything novel. Their overall phylogeny is "largely congruent" with (e.g.) Shen et al 2014, Hosner et al 2016/2017. They identify seven areas where mitochondrial topology differs from nuclear topology, specifically:

(i) subgroups of Lophura (6 spp)
(ii) whether Pucrasia is closer to core pheasants or to grouse/turkeys
(iii) position of Lagopus within grouse
(iv) relationships within Gallus (all 4 spp)
(v) inter-relationships of the erectile/non-erectile clades
(vi) if Philortyx is closer to Callipepla or to Colinus
(vii) inter-relationships of guineafowl (4 spp)
 

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