Phylogeny of birds (2 Viewers)

[Peter Kovalik]

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]

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

 

[Ben Wielstra]

Feng et al 2020 Nature

Dense sampling of bird diversity increases power of comparative genomics

 

[Jim LeNomenclatoriste]

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

 

[Peter Kovalik]

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]

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]

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]

 

[Jim LeNomenclatoriste]

Cariama to passerine : Australaves

Higher landbird : Afroaves

Aquatic and semi-aquatic bird : Aequornithes and Eurypygimorphae

Grebes and flamingos : Mirandornithes

But, dove, gruiformes, shorebirds, cuckoo, hoazin : Columbaves ??

Cf. Kuhl & al , 2020

I wonder if the name Terrestrornithes could not be redefined to be applied to the lineage containing the shorebirds, the Gruiformes, Cuculiformes, Nightjar, Hoazin etc. ?

 

[Peter Kovalik]

Wink, Michael: DNA analyses have revolutionized studies on the taxonomy and evolution in birds. IntechOpen (2021).

[pdf]

 

[jts1882]

Neither link works for me (one gave a security warning).

The full text is here though.

Chapter: DNA Analyses Have Revolutionized Studies on the Taxonomy and Evolution in Birds

Whereas Linné aimed to classify all species of our planet by a unique binomial Latin name, later generations of taxonomists and systematicists intended to place the taxa in a natural system according

www.intechopen.com

 

[albertonykus]

Bravo, G.A., C.J. Schmitt, and S.V. Edwards (2021)
What have we learned from the first 500 avian genomes?
Annual Review of Ecology, Evolution, and Systematics (advance online publication)
doi: 10.1146/annurev-ecolsys-012121-085928

The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.

 

[Jim LeNomenclatoriste]

Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are...

www.mdpi.com

 

[George Sangster]

Sangster, G, Braun, EL, Johansson, US, Kimball, RT, Mayr, G & Suh, A 2022. Phylogenetic definitions for 25 higher-level clade names of birds. Avian Research 13, 100027.

Knowledge of the higher-level phylogenetic relationships of birds has grown substantially during the past two decades due to the application of genomic data. However, the nomenclature of higher-level taxa has not become more stable, due to the lack of regulation of taxon names above the level of superfamily by the ICZN, and the usage of rank-based nomenclature, which is not tied to clades in a phylogeny. Lack of regulation and the instability of rank-based nomenclature impede effective communication among systematists. Here we review support for higher-level avian clades using a set of 10 phylogenomic data sets, and identify clades that are supported by congruency of at least four of these. We provide formal definitions of the names of these clades based on the rules of the recently published PhyloCode. The names of 25 clades are here defined using minimum-crown-clade (n = 23), minimum-clade (n = 1) and maximum-crown-clade (n = 1) definitions. Five new names are introduced here: Dinocrypturi, Pteroclimesites, Musophagotides, Phaethoquornithes and Pelecanes. We also review diagnostic apomorphies of the relevant clades, and identify known synonyms and homonyms. By establishing a formal link between higher-level taxon names and well-supported phylogenetic hypotheses, our phylogenetic definitions will provide a solid basis for the stabilization of avian higher-level nomenclature.

 

[Jim LeNomenclatoriste]

What's the difference between Phoenicopterimorphae and Mirandornithes ?

 

[l_raty]

What's the difference between Phoenicopterimorphae and Mirde Queiroz, Cantino & Gauthier 2020 ?

The two names are parts of two distinct (competing) naming systems.

The first is the name of a taxon ranked as a superorder, formed according to a convention (internal to ornithology) which requires that superorder names be made of the stem of the name of an included genus with the addition of the standardized suffix -imorphae. This name is implicitly defined as applying to the taxon that includes Phoenicopterus ruber Linnaeus 1758 (the type species of Phoenicopterus Linnaeus 1758) and that is (subjectively) ranked as a superorder.

The other is the name of an unranked clade, established according to the rules of the PhyloCode (and registered under this Code with number 281). This name was originally defined as applying to "the least inclusive clade comprising Phoenicopterus ruber Linnaeus, 1758 and Podiceps cristatus (Linnaeus, 1758)" (Sangster 2005), but was redefined as applying to "the smallest crown clade containing Phoenicopterus chilensis Molina 1782 and Podiceps (originally Colymbus) auritus (Linnaeus 1758)" when the PhyloCode took effect in 2020 (Sangster in de Queiroz, Cantino & Gauthier 2020, pp. 1265-1267) - under the current PhyloCode, this is the definition that matters.

So far as extant birds are concerned and under currently accepted phylogenetic hypotheses, the two names denote the same group. Their content might conceivably be made different in terms of fossils (the stem-group is excluded from Mirandornithes by definition, but might be included in Phoenicopterimorphae if this was felt necessary); changes, either in ranking criteria, or in accepted phylogenetic hypotheses, might also potentially affect the contents of the two taxa differently and make them diverge.

 

[Jim LeNomenclatoriste]

The two names are parts of two distinct (competing) naming systems.

The first is the name of a taxon ranked as a superorder, formed according to a convention (internal to ornithology) which requires that superorder names be made of the stem of the name of an included genus with the addition of the standardized suffix -imorphae. This name is implicitly defined as applying to the taxon that includes Phoenicopterus ruber Linnaeus 1758 (the type species of Phoenicopterus Linnaeus 1758) and that is (subjectively) ranked as a superorder.

The other is the name of an unranked clade, established according to the rules of the PhyloCode (and registered under this Code with number 281). This name was originally defined as applying to "the least inclusive clade comprising Phoenicopterus ruber Linnaeus, 1758 and Podiceps cristatus (Linnaeus, 1758)" (Sangster 2005), but was redefined as applying to "the smallest crown clade containing Phoenicopterus chilensis Molina 1782 and Podiceps (originally Colymbus) auritus (Linnaeus 1758)" when the PhyloCode took effect in 2020 (Sangster in de Queiroz, Cantino & Gauthier 2020, pp. 1265-1267) - under the current PhyloCode, this is the definition that matters.

So far as extant birds are concerned and under currently accepted phylogenetic hypotheses, the two names denote the same group. Their content might conceivably be made different in terms of fossils (the stem-group is excluded from Mirandornithes by definition, but might be included in Phoenicopterimorphae if this was felt necessary); changes, either in ranking criteria, or in accepted phylogenetic hypotheses, might also potentially affect the contents of the two taxa differently and make them diverge.

I know one is ranked and the other isn't, so I figured they were almost synonymous, thinking these two terms defined the same lineage. When I see the number of clade within the dinosaurs (birds excluded), I wondered if this multiplication of terms didn't complicate things.

I also had the idea that a clade opposed another. Why a clade for sandgrouse and mesites (Pteroclimesites) lineage, but not one for pigeons ? Or by choosing either Columbaves or Columbea for the latter, by redefining this clade

 

[Mysticete]

There is a clade for pigeons: Columbidae. Unless you define it differently, like make it a broader clade that includes taxa not placed in Columbidae but on the stem, it would be redundant to create a new name.

 

[Jim LeNomenclatoriste]

There is a clade for pigeons: Columbidae.

I meant, an unranked clade, you understood x)

Superordo Columbimorphae
Clade Pteroclimesites
Family Pteroclidae
Family Mesitornithidae
Clade ??? 🤔🤔
Family Columbidae

 

[l_raty]

Superordo Columbimorphae
Clade Pteroclimesites
Family Pteroclidae
Family Mesitornithidae
Clade ??? 🤔🤔
Family Columbidae

• Clade Columbimorphae
  • Clade Pteroclimesites
    • Clade Pteroclidae
    • Clade Mesitornithidae
  • Clade Columbidae

In phylogenetic nomenclature, all recognized taxa are clades, and there are no ranks at all. One of the declared purposes is to remove redundancy, which is present in ranked nomenclature, where different names are applied to the same monophyletic group when it is treated at different ranks.
Besides, as the system involves the official 'conversion' of 'preexisting' names traditionally regulated by the ICZN (or used under ICZN-like informal rules traditionally applied to ranked names above the family-group), and applies precedence among clade names based on the date of conversion irrespective of their original rank, things might become much more 'heterogeneous' than the above, where the three 'preexisting' names used in the classification are all names in -idae (originally ranked as family). Depending on which name would have been converted first, the sister clade of Pteroclidae might end up named, e.g., Mesithornithiformes, and the sister clade of Pteroclimesites might be Columbinae.

(Ending up with the same names being regulated simultaneously by two sets of rules (ICZN[-like] rules for a 'preexisting' version of the name and PhyloCode for a 'converted' version), which will potentially respond very differently to the addition of new data, is particularly problematic in my opinion.)

 

[Jim LeNomenclatoriste]

• Clade Columbimorphae
  • Clade Pteroclimesites
    • Clade Pteroclidae
    • Clade Mesitornithidae
  • Clade Columbidae

In phylogenetic nomenclature, all recognized taxa are clades, and there are no ranks at all. One of the declared purposes is to remove redundancy, which is present in ranked nomenclature, where different names are applied to the same monophyletic group when it is treated at different ranks.
Besides, as the system involves the official 'conversion' of 'preexisting' names traditionally regulated by the ICZN (or used under ICZN-like informal rules traditionally applied to ranked names above the family-group), and applies precedence among clade names based on the date of conversion irrespective of their original rank, things might become much more 'heterogeneous' than the above, where the three 'preexisting' names used in the classification are all names in -idae (originally ranked as family). Depending on which name would have been converted first, the sister clade of Pteroclidae might end up named, e.g., Mesithornithiformes, and the sister clade of Pteroclimesites might be Columbinae.

But it's suck ! It's awfully awful. It's decadenceennh ! The wrath of Linnaeus will descend on the world !