Phylogeny of birds (1 Viewer)

Tif checklist is my reference for birds checklisting. ^^ (attendons, attendons.....)

For those of that need pretty diagrams...
http://www.sci-news.com/biology/science-avian-tree-life-03326.html

edit: the paper direct from Prum for those without a sub to Nature
http://prumlab.yale.edu/sites/default/files/prum_et_al_2015.pdf
http://prumlab.yale.edu/sites/default/files/prum_et_al_2015_supplement.pdf

Telephoto Paul said:

...the paper direct from Prum for those without a sub to Nature
http://prumlab.yale.edu/sites/default/files/prum_et_al_2015.pdf
http://prumlab.yale.edu/sites/default/files/prum_et_al_2015_supplement.pdf

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Peter Kovalik also gave a link to the Prum Lab website...

Peter Kovalik said:

Prum R.O, Berv J.S, Dornburg A., Field D.J, Townsend J.P, Lemmon E.M, Lemmon A.R. 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature. 526:5pp..

PDF here

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Sorry, missed that. Blame it on being past my bedtime!

Toews et al 2016

Toews, Campagna, Taylor, Balakrishnan, Baldassarre, Deane-Coe, Harvey, Hooper, Irwin, Judy, Mason, McCormack, McCracken, Oliveros, Safran, Scordato, Stryjewski, Tigano, Uy & Winger 2016. Genomic approaches to understanding population divergence and speciation in birds. Auk 133(1): 13–30. [abstract] [pdf]

Publications Blog: The Auk & The Condor, 21 Oct 2015: Advances in Genetic Studies of Birds Are Changing Ornithology Research.

Daniela Almeida, Emanuel Maldonado, Imran Khan, Liliana Silva, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O’Brien, Warren E. Johnson and Agostinho Antunes. Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds. Genome Biol Evol (2016).
doi: 10.1093/gbe/evw041. First published online: March 14, 2016

[PDF]

Erich D. Jarvis. Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class. Annu. Rev. Anim. Biosci. 2016. 4:45–59.

[PDF]

Alexander Suh. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. Zoologica Scripta, Volume 45, Issue S1, October 2016, Pages: 50–62.

[pdf]

Peter Kovalik said:

Alexander Suh. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. Zoologica Scripta, Volume 45, Issue S1, October 2016, Pages: 50–62.

[pdf]

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Wow, that's truly fascinating. Not only is it hard to figure out the tree at the Neoaves root, it's essentially impossible. Sure answers which of the robust phylogenies are correct: they're all wrong.

One question though. Let's say this is the last word of the matter, that the root of Neoaves is not possible to resolve. How do we arrange the pieces to a straight list? From species poorness to species richness? As traditional as possible? Any thoughts?

gusasp said:

How do we arrange the pieces to a straight list? From species poorness to species richness? As traditional as possible? Any thoughts?

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Alphabetical? :-O

I'd go with 'As traditional as possible'

probably easiest in this case to just keep the the three divisions in as traditional an organization as possible (although within each of those three divisions you would probably have to move stuff around still).

Masami Hasegawa, Sayako Kuroda. Phylogeny Mandalas of Birds using the Lithographs of John Gould’s Folio Bird Books. Molecular Phylogenetics and Evolution. In Press, Accepted Manuscript, Available online 9 December 2016.

[abstract]

Peter Kovalik said:

Alexander Suh. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. Zoologica Scripta, Volume 45, Issue S1, October 2016, Pages: 50–62.

[pdf]

Click to expand...

TiF Update December 11, 2016

Mousebirds: Based on Suh et al. (2015) and Suh (2016), the Coliiformes have been moved to a basal position in Afroaves. Yes, there are more changes from Suh (2016) to come. There may be some minor inconsistencies until these changes are all made.

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Peter Kovalik said:

Alexander Suh. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. Zoologica Scripta, Volume 45, Issue S1, October 2016, Pages: 50–62.

[pdf]

Click to expand...

TiF Update December 15, 2016

Higher Taxonomy: I have made some changes to the sequence of bird orders as a result of Suh et al. (2015) and Suh (2016). Suh (2016) makes the case for a hard polytomy at the base of Neoaves. I think there is still some information there, and the sequence I use reflects this. As a result, Mirandornithes has been moved to follow Opisthocomiformes (Hoatzin) and Charadriiformes now follows Ardeiformes. See the text for more information.
[The 46 Orders, Paleognathae, 3.01]

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It's surprising that Boyd didn't follow the phylogeny based on Prum & al.

Accepted ms:

Reddy, S., Kimball, R. T., Pandey, A., Hosner, P. A., Braun, M. J., Hackett, S. J., Han, K.-L., Harshman, J., Huddleston, C.J., Kingston, S., Marks, B.D., Miglia, K.J., Moore, W.S., Sheldon, F.H., Witt, C.C., Yuri, T. & Braun, E.L. (2017). Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling. Systematic Biology. doi: 10.1093/sysbio/syx041

bioRxiv preprint:

Brown, J., Wang, N. & Smith, S. (2017). The development of scientific consensus: analyzing conflict and concordance among Avian phylogenies. bioRxiv, 123034. doi:10.1101/123034

Brown, J.W., Wang, N., Smith, S.A., The development of scientific consensus: analyzing conflict and concordance among avian phylogenies, Molecular Phylogenetics and Evolution (2017), doi: http://dx.doi.org/10.1016/j.ympev.2017.08.002

Abstract:

Recent developments in phylogenetic methods and data acquisition have allowed for the construction of large and comprehensive phylogenetic relationships. Published phylogenies represent an enormous resource that not only facilitates the resolution of questions related to comparative biology, but also provides a resource on which to gauge the development of concordance across the tree of life. From the Open Tree of Life, we gathered 290 avian phylogenies representing all major groups that have been published over the last few decades and analyzed how concordance and conflict develop among these trees through time. Nine large scale phylogenetic hypotheses (including a new synthetic tree from this study) were used for comparisons. We found that conflicts were over-represented both along the backbone (higher-level neoavian relationships) and within the oscine Passeriformes. Importantly, although we have made major strides in the resolution of major clades, recent published comprehensive trees, as well as trees of individual clades, continue to contribute significantly to the resolution of relationships throughout the avian phylogeny. Our analyses highlight the need for continued research into the resolution of avian relationships.

Springer, Gatesy. 2017. On the importance of homology in the age of phylogenomics. Syst. Biodiv.
[abstract & supp. mat.]

Abstract
Homology is perhaps the most central concept of phylogenetic biology. Molecular systematists have traditionally paid due attention to the homology statements that are implied by their alignments of orthologous sequences, but some authors have suggested that manual gene-by-gene curation is not sustainable in the phylogenomics era. Here, we show that there are multiple ways to efficiently screen for and detect homology errors in phylogenomic data sets. Application of these screening approaches to two phylogenomic data sets, one for birds and another for mammals, shows that these data are replete with homology errors including alignments of different exons to each other, alignments of exons to introns, and alignments of paralogues to each other. The extent of these homology errors weakens the conclusions of studies based on these data sets. Despite advances in automated phylogenomic pipelines, we contend that much of the long, difficult, and sometimes tedious work of systematics is still required to guard against pervasive homology errors. This conclusion is underscored by recent studies that show that just a few outlier genes can impact phylogenetic results at short, tightly spaced internodes that are deep in the Tree of Life. The view that widespread DNA sequence alignment errors are not a major concern for rigorous systematic research is not tenable. If a primary goal of phylogenomics is to resolve the most challenging phylogenetic problems with the abundant data that are now available, researchers must employ effective procedures to screen for and correct homology errors prior to performing downstream phylogenetic analyses.
Key words: Gene trees, homology, orthology, phylogenomics, phylogeny, sequence alignment

(The bird data set was that of Jarvis et al. 2014 [pdf].)

Princess S. Gilbert, Jing Wu, Margaret W. Simon, Janet S. Sinsheimer, Michael E. Alfaro. Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements. Molecular Phylogenetics and Evolution. In Press, Accepted Manuscript, Available online 4 April 2018.

Abstract:

Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.

Princess S. Gilbert, Jing Wu, Margaret W. Simon, Janet S. Sinsheimer & Michael E. Alfaro, 2018

Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.

Molecular Phylogenetics and Evolution (advance online publication)

doi: https://doi.org/10.1016/j.ympev.2018.03.033
https://www.sciencedirect.com/science/article/pii/S1055790317308539

Highlights

Filtering Ultraconserved Elements (UCEs) for sites with the highest phylogenetic signal to noise ratio produces datasets that are able recover relationships that would otherwise require intronic and exonic data in birds.

Filtering UCEs results in UCE-only phylogenetic reconstructions that support the Columbea+ Passerea sister relationship, Phaethontimorphae + Aequornithia sister relationship, the Eucavitaves clade.

Filtering UCEs for sites with the highest signal to noise ratio can lead to increases in node support for some clades supported by Total Evidenced datasets (i.e the Pelecanidae + Ardeidae sister relationship, and the Otidiformes + Musophagiformes sister relationship) and decreases in node support for some clades supported by Total Evidenced datasets (i.e. the Hoatzin + Cursorimorphae clade and the Columbea clade)

Our automated site filtering approach which uses signal to noise estimates (Townsend et al. 2012) is applicable to large genome-wide studies that seek to resolve difficult phylogenetic questions.

Abstract:

Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.

Enjoy,

Fred