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Phylogeny of birds (2 Viewers)

Peter Kovalik

Well-known member
Slovakia
Heiner Kuhl, Carolina Frankl-Vilches, Antje Bakker, Gerald Mayr, Gerhard Nikolaus, Stefan T Boerno, Sven Klages, Bernd Timmermann, Manfred Gahr, An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life, Molecular Biology and Evolution, , msaa191, https://doi.org/10.1093/molbev/msaa191

Abstract:

Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life.
 

Fred Ruhe

Well-known member
Netherlands
Heiner Kuhl, Carolina Frankl-Vilches, Antje Bakker, Gerald Mayr, Gerhard Nikolaus, Stefan T Boerno, Sven Klages, Bernd Timmermann, Manfred Gahr, An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life, Molecular Biology and Evolution, , msaa191, https://doi.org/10.1093/molbev/msaa191

Abstract:

Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life.

Also see https://www.birdforum.net/showthread.php?t=396374

Fred
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
It's a big file but this is how I see the phylogeny of all orders and families of birds.
 

Attachments

  • [#phylogénie des ordres et des familles des oiseaux].pdf
    73.8 KB · Views: 30

Peter Kovalik

Well-known member
Slovakia
Braun, E.L.; Kimball, R.T. Data Types and the Phylogeny of Neoaves. Preprints 2020, 2020110423 (doi: 10.20944/preprints202011.0423.v1).

Abstract:

The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. The difficulty associated with resolving the early branches in Neoaves is likely driven by the rapid radiation of this group. However, conflicts among studies may be exacerbated by the hypothesis that relationships are sensitive to the data type analyzed. For example, analyses of coding exons typically yield trees that place Strisores (nightjars and allies) sister to the remaining Neoaves, while analyses of non-coding data typically yield trees where Mirandornites (flamingos and grebes) is the sister of the remaining Neoaves. Our understanding of data type effects is hampered by the fact that previous analyses have used different taxa, loci, and types of non-coding data. Herein, we provide strong corroboration of the data type effects hypothesis for Neoaves by comparing trees based on coding and non-coding data derived from the same taxa and gene regions. A simple analytical method known to minimize biases due to base composition (coding nucleotides as purines and pyrimidines) resulted in coding exon data with increased congruence to the non-coding topology using concatenated analyses. These results improve our understanding of the resolution of neoavian phylogeny and point to a challenge - data type effects - that is likely to be an important factor in phylogenetic analyses of birds (and many other taxonomic groups). Using our results, we provide a summary phylogeny that identifies well-corroborated relationships and highlights specific nodes where future efforts should focus.

pdf here
 

Peter Kovalik

Well-known member
Slovakia
WINK M, COLE TCH, FERNANDES AM (2020) TREE OF BIRDS – AVIAN PHYLOGENY POSTER (Neornithes, Aves), Systematics, Classification, Features • hypothetical tree based on phylogenetic data (as of 2020) • branch lengths deliberate, not reflecting true time spans; figures at nodes are approx. divergence times (shaded circles: x Mya = million years ago) from Prum et al. (2015) • features at nodes (incomplete) do not necessarily apply to all members of a group • this poster presents an overview of the 40 orders currently accepted by the IOC • classification and species numbers (in gray) according to IOC World Bird List, Vers. 10.1 (2020) • tree topology based on Prum et al. (2015); differing from Suh et al. 2015/16 who agrue for a polytomy at the level of Neoaves, i.e., there is uncertainty of relationships in that part of the tree • features from Sibley & Ahlquist (1990) Phylogeny and Classification of Birds, Yale Univ. Press and Billerman et al. (eds.) (2020) Birds of the World, Cornell Lab. of Ornithology, Ithaca, NY

[poster]
 

Peter Kovalik

Well-known member
Slovakia
Braun, E.L.; Kimball, R.T. Data Types and the Phylogeny of Neoaves. Preprints 2020, 2020110423 (doi: 10.20944/preprints202011.0423.v1).

Abstract:

The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. The difficulty associated with resolving the early branches in Neoaves is likely driven by the rapid radiation of this group. However, conflicts among studies may be exacerbated by the hypothesis that relationships are sensitive to the data type analyzed. For example, analyses of coding exons typically yield trees that place Strisores (nightjars and allies) sister to the remaining Neoaves, while analyses of non-coding data typically yield trees where Mirandornites (flamingos and grebes) is the sister of the remaining Neoaves. Our understanding of data type effects is hampered by the fact that previous analyses have used different taxa, loci, and types of non-coding data. Herein, we provide strong corroboration of the data type effects hypothesis for Neoaves by comparing trees based on coding and non-coding data derived from the same taxa and gene regions. A simple analytical method known to minimize biases due to base composition (coding nucleotides as purines and pyrimidines) resulted in coding exon data with increased congruence to the non-coding topology using concatenated analyses. These results improve our understanding of the resolution of neoavian phylogeny and point to a challenge - data type effects - that is likely to be an important factor in phylogenetic analyses of birds (and many other taxonomic groups). Using our results, we provide a summary phylogeny that identifies well-corroborated relationships and highlights specific nodes where future efforts should focus.

pdf here
Braun, E.L.; Kimball, R.T. Data Types and the Phylogeny of Neoaves. Birds 2021, 2, 1-22.

[link]
 

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