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Galliformes (1 Viewer)

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.
 
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 ?
 
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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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.
 
uses coturnicini
uses tetraogallini for this clade

which one is correct?
 
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:
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
 
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)
 
Zohreh Aliakbari, Nasrin Kayvanfar, Hassan Rajabi-Maham, and Seyed Mahmoud Ghasempouri. 2021. Evidence for introgressive hybridization of wild black-necked pheasant with the exotic ring-necked pheasant during the past 50 years in the Hyrcanian zone, an integrative molecular and morphological approach. Journal of Zoological Systematics and Evolutionary Research.
First published: 18 November 2021
https://doi.org/10.1111/jzs.12548

Abstract
Hybridization with non-native-related taxa, especially with introgression, is a major conservation problem, as it may disturb local adaptations, resulting in population decline and biodiversity loss. It is important to identify hybrid individuals, which can be difficult to break up morphologically. Using morphometric and genetic approaches [multivariate analysis, microsatellites, and amplified fragment length polymorphism (AFLP)], this research attempts to classify the interaction and the prevalence of introgressive hybridization in four native pheasant subspecies of Phasianus colchicus with non-native P. c. torquatus. According to principal component analysis and canonical discriminant function results, hybrid individuals are placed between these two major groups of native and exotic birds. Also, we assessed the population structure, genetic variation, and gene flow between native subspecies and exotic pheasants using 16 microsatellite loci in 129 samples. Our findings revealed that hybridization occurred between two native subspecies, P. c. talischensis and P. c. persicus, and exotic subspecies (P. c. torquatus). Observation of hybrids in P. c. persicus were almost three times higher than P. c. talischensis. The levels of the genetic variation within and among the natural populations were investigated using the AFLP markers method to identify hybrids. A total of 202 distinct bands were amplified using four primer combinations, with 179 of them being polymorphic. AMOVA analysis revealed a low degree of genetic differentiation among the populations. The hybrid samples were closely related to the P. c. talischensis and P. c. persicus populations, according to the UPGMA clusters and discriminant analysis of principal components. It appears that disruption of gene flow between pheasant populations in the Hyrcanian zone is a serious issue. The data from molecular markers prompted us to raise a concern about the genetic integrity in some native subspecies in the Iranian plateau. As a result, a clear cut-level can now be used to differentiate the hybrids, which is also supported by morphological evidence. A direct relationship was found between farmed pheasants and hybrid frequency. Farmed individuals should be closely monitored, and non-native taxa should not be released into the wild.
 
Chen, D., P.A. Hosner, D.L. Dittmann, J.P. O’Neill, S.M. Birks, E.L. Braun, and R.T. Kimball (2021)
Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements
BMC Ecology and Evolution 21: 209
doi: 10.1186/s12862-021-01935-1

Background
Divergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results.

Results
In this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different “gene shopping” schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partitioning (e.g., PartitionFinder) and selection of tree-like partitions may be good strategies to select a subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree.

Conclusions
We provide a robust galliform backbone time tree that can be combined with more fossil records to further facilitate our understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.
 
Interesting that the divergence between Cracidae and later diverging Galliformes is so old, while the divergence times estimates within Cracidae are fairly young. Must be a hell of a lot of ghost lineages for that clade.
 
Interesting that the divergence between Cracidae and later diverging Galliformes is so old, while the divergence times estimates within Cracidae are fairly young. Must be a hell of a lot of ghost lineages for that clade.
The oldest Cracidae I have in my notes is Taoperdix sp. from the Late Eocene of France.

Fred
 
I tried to understand the biogeographic patterns lying behind the cladogramm by comparing divergence times to continental drift (I used a video on Youtube). Most of the processes are easy to understand, but the placement of some taxa really fucks with my head (though I guess others have been surprised by these too):
  • Forest specialists Xenoperdix and Afropavo within otherwise mostly eastern Asiatic groups having diverged only ca. 30 mya ago
  • The sudden appearance of Meleagris in central America
 
Li, X.-J., X.-Y. Wang, C. Yang, L.-L. Lin, L. Zhao, X.-P. Yu, F.-M. Lei, and Y. Huang (2021)
The de novo genome sequencing of silver pheasant (Lophura nycthemera)
Genome Biology and Evolution 13: evab275
doi: 10.1093/gbe/evab275

Silver pheasant (Lophura nycthemera) belongs to Phasianidae, Galliformes, which exhibits high subspecific differentiation. In this study, we assembled a novel genome based on 98.42 Gb of Illumina sequencing data and 30.20 Gb of PacBio sequencing data. The size of the final assembled genome was 1.01 Gb, with a contig N50 of 6.96 Mb. Illumina paired-end reads (94.96%) were remapped to the contigs. The assemble genome shows high completeness, with a complete BUSCO score of 92.35% using the avian data set. A total of 16,747 genes were predicted from the generated assembly, and 16,486 (98.44%) of the genes were annotated. The average length of genes, exons, and introns were 19,827.53, 233.69, and 1841.19 bp, respectively. Noncoding RNAs included 208 miRNAs, 40 rRNAs, and 264 tRNAs, and a total of 189 pseudogenes were identified; 116.31 Mb (11.47%) of the genome consisted of repeat sequences, with the greatest proportion of LINEs. This assembled genome provides a valuable reference genome for further studies on the evolutionary history and conversion genetics of L. nycthemera and the phylogenomics of the Galliformes lineage.
 
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.
how to get the supplementary files from this article?
 

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