Phylogeny of birds (6 Viewers)

[jurek]

Cladistics has a not immediately visible property. It allows creation of many times more taxonomic units than rank-based taxonomy.

If anybody considers that defining and naming 25 bird clades in a row might be considered, in some sense, excessive, this is only scratching the surface. Working with 9000 bird species, one can define over 80 million (80,911,000) least inclusive clades linking two different species of birds, every clade with a separate name. By comparison, Webster's International Dictionary has less than 0,5 million of entries. The number of exclusive clades and names linking three bird species is over 700 billion (7.28757e+11). Check the formula for mathematical permutations if in doubt.

I propose a very simple method of stabilization of zoological nomenclature:

1. A new clade for a bigger taxonomic unit should be normally defined by the type species of the type genus of the type family.
2. A clade should be named by combining the type genera, e.g. a flamingo-grebe clade as “Phoenicopterus-Podiceps clade”.
3. The exception are clades which names were used in at least 25 different publications until 22. April 2022., called established clades, for example Dinosauria or Galloanserae.

This will make clade names possible to remember for people other than authors of a particular publication. It will also contribute to quality of taxonomy by making researchers discover new biological facts, rather than dwelling on names, definitions etc.

 

[mb1848]

The wrath of Linnaeus will descend on the world !
We really do not want that. An early cladist Dr. Nils Rosen made fun of Carl's classification system. "No wonder if the wrath of Linnaeus burst forth in a
most unbounded manner. The wild-beast vein of the
ancient Goth rose in him. In the tempest of his passion he forgot himself, his future happiness, and every moral consideration, but ' who ever saw far in a storm ' ? Boiling with pugnacity and rage, with flaming eyes more
piercing than his knife, he swore ' By all the Valkyrs ! '
he would slay his foe. When Rosen left the senate Linnaeus waited for
him, and with desperate fury drew his sword, and would
have run it through the body of his enemy had not the
bystanders fortunately wrested it from him. He flew at
Rosen's throat and grappled with him in a fierce struggle.
He was with difficulty separated from his prey. Rosen,
who was a member of the academy, complained of this
gross assault and of this daring violation of the laws of
public safety."

 

[Mysticete]

I don't really see an issue with clade names. They are a tool of convenience, a way for me to label a group using shorthand rather than a long complicated description. Delphinoidea is a lot easier and faster to say than "Clade including Monodontidae, Phocoenidae, and Delphinidae, and all fossil taxa more closely related to them then other crown whales".

Yeah, you could go ahead and create a bazillion names, but if they are not actually useful or stable, no one will use them. Sangster can go ahead an name these clades, but its up to the folks who use taxonomy to decide to use them.

 

[Snapdragyn]

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.

Or if you were to split the clade into multiple family-level groups. In that case, a clade uniting those families would be needed to distinguish this group from the mesites + sandgrouse group.

 

[Jim LeNomenclatoriste]

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

I may be exaggerating but what scares me is the possibility of the disappearance of taxon units (order, family, genus..) in favor of "Clade" (with a capital C). There would be a kind of disequilibrium and a lack of harmony that would disturb me, and I like how there is a semblance of equilibrium (Palaeognathae vs Neognathae, Galloanseres vs Neoaves).
Crazy like POV, isn't it ?

 

[l_raty]

I don't really see an issue with clade names. They are a tool of convenience, a way for me to label a group using shorthand rather than a long complicated description. Delphinoidea is a lot easier and faster to say than "Clade including Monodontidae, Phocoenidae, and Delphinidae, and all fossil taxa more closely related to them then other crown whales".

Delphinoidea Gray 1821 (*) stands for "the superfamily with Delphinus Linnaeus 1758 (the type of which is (by Linnaean tautonymy) Delphinus delphis Linnaeus 1758) as its type". This name (including its ending) is fully governed by the ICZN.

Is there a phylogenetic definition for this name ? Should there be one : what if an author wishes to recognize, e.g., a group a bit more inclusive at the rank of superfamily ? Should he refrain from doing so because the name he would have to use under the ICZN has been "high-jacked" and frozen with a more restricted circumscription under the rules of another naming system ?

*) This is the usual attribution.
Gray 1821 used the name at family rank (as "Delphinidae"). As a superfamily name, it is sometimes (incl. on Wikipidia) attributed to Flower 1865, who effectively use a name spelled "Delphinoidea", but : (1) by virtue of the Principle of Coordination, Gray must be deemed the author of the name at all ranks of the family group, which includes all supra-generic names up to superfamily; and (2) infering the rank of a taxon from the ending of its name in the early literature can be deceptive: a name "Delphinoidea" had already been used before in the German literature (e.g. Leiblein 1839) but at family rank, and Flower actually ranked his "Balaenoidea" and "Delphinoidea" explicitly as suborders, which places them entirely outside of the family-group.
As an aside, it's interesting that mammalogists do not take Delphinidae/Delphinoidea from Rafinesque 1815, who had a family "Delphinia" which included Delphinus Linnaeus 1758. (I agree with this -- Rafinesque's suprageneric names do not fulfill ICZN 11.7.1.1, because they are, explicitly, not "nouns in the nominative plural" -- but it departs strikingly from what has been done in ornithology in recent decades.)

 

[James Lowther]

Cladistics has a not immediately visible property. It allows creation of many times more taxonomic units than rank-based taxonomy.

If anybody considers that defining and naming 25 bird clades in a row might be considered, in some sense, excessive, this is only scratching the surface. Working with 9000 bird species, one can define over 80 million (80,911,000) least inclusive clades linking two different species of birds, every clade with a separate name. By comparison, Webster's International Dictionary has less than 0,5 million of entries. The number of exclusive clades and names linking three bird species is over 700 billion (7.28757e+11). Check the formula for mathematical permutations if in doubt.
, rather than dwelling on names, definitions etc.

I can’t check your formulae as I don’t really understand what you mean by “least inclusive” and “exclusive”, but for practical purposes this is surely an exaggeration.
The number of monophyletic clades required to fully describe phylogeny of 9000 species is 8999, not including the 9000 clades comprising single species.
I don’t think anyone is proposing e.g. naming a clade comprising all species except rockhopper penguin, snail kite and Scottish crossbill

Cheers
James

 

[Peter Kovalik]

Lum, Deon, Frank E. Rheindt, and Ryan A. Chisholm (2022) Tracking scientific discovery of avian phylogenetic diversity over 250 years. Proceedings of the Royal Society B. Published 20 April 2022.
https://doi.org/10.1098/rspb.2022.0088

Abstract
Estimating the total number of species on Earth has been a longstanding pursuit. Models project anywhere between 2 and 10 million species, and discovery of new species continues to the present day. Despite this, we hypothesized that our current knowledge of phylogenetic diversity (PD) may be almost complete because new discoveries may be less phylogenetically distinct than past discoveries. Focusing on birds, which are well studied, we generated a robust phylogenetic tree for most extant species by combining existing published trees and calculated each discovery's marginal contribution to known PD since the first formal species descriptions in 1758. We found that PD contributions began to plateau in the early 1900s, about half a century earlier than species richness. Relative contributions of each phylogenetic order to known PD shifted over the first 150 years, with a growing contribution of the hyper-diverse perching birds (Passeriformes) in particular, but after the early 1900s this has remained relatively stable. Altogether, this suggests that our knowledge of the evolutionary history of extant birds is mostly complete, with few discoveries of high evolutionary novelty left to be made, and that conclusions of studies using avian phylogenies are likely to be robust to future species discoveries.

 

[Jim LeNomenclatoriste]

Ning Wang, Edward L. Braun, Bin Liang, Joel Cracraft, & Stephen A.Smith, 2022.
Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree. Molecular Phylogenetics and Evolution, Available online 9 June 2022, 107550. In press, journal pre-proof

Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree

Phylogenetic analyses fail to yield a satisfactory resolution of some relationships in the tree of life even with genome-scale datasets, so the failur…

www.sciencedirect.com

Abstract

Phylogenetic analyses fail to yield a satisfactory resolution of some relationships in the tree of life even with genome-scale datasets, so the failure is unlikely to reflect limitations in the amount of data. Gene tree conflicts are particularly notable in studies focused on these contentious nodes, and taxon sampling, different analytical methods, and/or data type effects can further confound analyses. Although many efforts have been made to incorporate biological conflicts, few studies have curated individual genes for their efficiency in phylogenomic studies. Here, we conduct an edge-based analysis of Neoavian evolution, examining the phylogenetic efficacy of two recent phylogenomic bird datasets and three datatypes (ultraconserved elements [UCEs], introns, and coding regions). We assess the potential causes for biases in signal-resolution for three difficult nodes: the earliest divergence of Neoaves, the position of the enigmatic Hoatzin (Opisthocomus hoazin), and the position of owls (Strigiformes). We observed extensive conflict among genes for all data types and datasets even after meticulous curation. Edge-based analyses (EBA) increased congruence and provided information about the impact of data type, GC content variation (GCCV), and outlier genes on each of nodes we examined. First, outlier gene signals appeared to drive different patterns of support for the relationships among the earliest diverging Neoaves. Second, the placement of Hoatzin was highly variable, although our EBA did reveal a previously unappreciated data type effect with an impact on its position. It also revealed that the resolution with the most support here was Hoatzin + shorebirds. Finally, GCCV, rather than data type (i.e., coding vs non-coding) per se, was correlated with a signal that supports monophyly of owls + Accipitriformes (hawks, eagles, and New World vultures). Eliminating high GCCV loci increased the signal for owls + mousebirds. Categorical EBA was able to reveal the nature of each edge and provide a way to highlight especially problematic branches that warrant a further examination. The current study increases our understanding about the contentious parts of the avian tree, which show even greater conflicts than appreciated previously.

 

[jts1882]

I can't access the article, but there is a preprint.

Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree

Phylogenetic analyses of large-scale datasets sometimes fail to yield a satisfactory resolution of the relationships among taxa for a number of nodes in the tree of life. This has even been true for genome-scale datasets, where the failure to resolve relationships is unlikely to reflect...

www.biorxiv.org

https://www.researchgate.net/publication/351673309_Categorical_edge-based_analyses_of_phylogenomic_data_reveal_conflicting_signals_for_difficult_relationships_in_the_avian_tree

 

[albertonykus]

Gatesy, J. and M.S. Springer (2022)
Phylogenomic coalescent analyses of avian retroelements infer zero-length branches at the base of Neoaves, emergent support for controversial clades, and ancient introgressive hybridization in Afroaves
Genes 13: 1167
doi: 10.3390/genes13071167

Retroelement insertions (RIs) are low-homoplasy characters that are ideal data for addressing deep evolutionary radiations, where gene tree reconstruction errors can severely hinder phylogenetic inference with DNA and protein sequence data. Phylogenomic studies of Neoaves, a large clade of birds (>9000 species) that first diversified near the Cretaceous–Paleogene boundary, have yielded an array of robustly supported, contradictory relationships among deep lineages. Here, we reanalyzed a large RI matrix for birds using recently proposed quartet-based coalescent methods that enable inference of large species trees including branch lengths in coalescent units, clade-support, statistical tests for gene flow, and combined analysis with DNA-sequence-based gene trees. Genome-scale coalescent analyses revealed extremely short branches at the base of Neoaves, meager branch support, and limited congruence with previous work at the most challenging nodes. Despite widespread topological conflicts with DNA-sequence-based trees, combined analyses of RIs with thousands of gene trees show emergent support for multiple higher-level clades (Columbea, Passerea, Columbimorphae, Otidimorphae, Phaethoquornithes). RIs express asymmetrical support for deep relationships within the subclade Afroaves that hints at ancient gene flow involving the owl lineage (Strigiformes). Because DNA-sequence data are challenged by gene tree-reconstruction error, analysis of RIs represents one approach for improving gene tree-based methods when divergences are deep, internodes are short, terminal branches are long, and introgressive hybridization further confounds species–tree inference.

 

[Jim LeNomenclatoriste]

Gatesy, J. and M.S. Springer (2022)
Phylogenomic coalescent analyses of avian retroelements infer zero-length branches at the base of Neoaves, emergent support for controversial clades, and ancient introgressive hybridization in Afroaves
Genes 13: 1167
doi: 10.3390/genes13071167

Retroelement insertions (RIs) are low-homoplasy characters that are ideal data for addressing deep evolutionary radiations, where gene tree reconstruction errors can severely hinder phylogenetic inference with DNA and protein sequence data. Phylogenomic studies of Neoaves, a large clade of birds (>9000 species) that first diversified near the Cretaceous–Paleogene boundary, have yielded an array of robustly supported, contradictory relationships among deep lineages. Here, we reanalyzed a large RI matrix for birds using recently proposed quartet-based coalescent methods that enable inference of large species trees including branch lengths in coalescent units, clade-support, statistical tests for gene flow, and combined analysis with DNA-sequence-based gene trees. Genome-scale coalescent analyses revealed extremely short branches at the base of Neoaves, meager branch support, and limited congruence with previous work at the most challenging nodes. Despite widespread topological conflicts with DNA-sequence-based trees, combined analyses of RIs with thousands of gene trees show emergent support for multiple higher-level clades (Columbea, Passerea, Columbimorphae, Otidimorphae, Phaethoquornithes). RIs express asymmetrical support for deep relationships within the subclade Afroaves that hints at ancient gene flow involving the owl lineage (Strigiformes). Because DNA-sequence data are challenged by gene tree-reconstruction error, analysis of RIs represents one approach for improving gene tree-based methods when divergences are deep, internodes are short, terminal branches are long, and introgressive hybridization further confounds species–tree inference.

Who understood the article? it's just geneticist gibberish 🤣

 

[ornithociencia]

Who understood the article? it's just geneticist gibberish 🤣

I do but I agree with you.

 

[jts1882]

It seems to just add another analysis to the many showing different datasets and analysis methods get different results. Their retroelement results reproduce a tree with some oddities, but when combined with introns and UCEs is confirms some of the clades in the Jarvis TENT tree (ML). Total evidence trees flock together, it seems.

What I want to know is what is going on with Jarvis II. The Jarvis phylogeny came out at the same time as the genomics companion paper (Zhang et al, 2014). The genomics paper of stage two (family level, Feng et al, 2020) came out almost a couple of years ago, but the phylogeny paper is yet to appear. Is it that the computers are chugging away in the background because there is so much data? In the meantime we have seen several reanalyses of Jarvis and Prum. Are these reanalyses attempting to find the optimum for running the phylogenomic analysis of the stage II dataset?

 

[Mysticete]

It seems to just add another analysis to the many showing different datasets and analysis methods get different results. Their retroelement results reproduce a tree with some oddities, but when combined with introns and UCEs is confirms some of the clades in the Jarvis TENT tree (ML). Total evidence trees flock together, it seems.

What I want to know is what is going on with Jarvis II. The Jarvis phylogeny came out at the same time as the genomics companion paper (Zhang et al, 2014). The genomics paper of stage two (family level, Feng et al, 2020) came out almost a couple of years ago, but the phylogeny paper is yet to appear. Is it that the computers are chugging away in the background because there is so much data? In the meantime we have seen several reanalyses of Jarvis and Prum. Are these reanalyses attempting to find the optimum for running the phylogenomic analysis of the stage II dataset?

It's definitely not a case of the computers are still running. I've been part of some studies with enormous datasets, and while they can take weeks, I am unaware of any analysis that has taken years to run, at least with modern cloud computing technology. Not to mention, the longer it takes to run a computer analysis, the more likely something is going to happen to abort it by accident!

There are innumerable number of reasons why papers get "stuck" and not submitted/published, ranging from the authors being sidetracked by other projects, lack of research time, key people leaving the project, waiting for crucial data that sometimes never shows up, or simple frustration over a project.

 

[albertonykus]

Zelentsova, E.A., L.V. Yanshole, Y.P. Tsentalovich, K.A. Sharshov, and V.V. Yanshole (2022)
The application of quantitative metabolomics for the taxonomic differentiation of birds
Biology 11: 1089
doi: 10.3390/biology11071089

In the current pilot study, we propose the use of quantitative metabolomics to reconstruct the phylogeny of vertebrates, namely birds. We determined the concentrations of the 67 most abundant metabolites in the eye lenses of the following 14 species from 6 orders of the class Aves (Birds): the Black kite (Milvus migrans), Eurasian magpie (Pica pica), Northern raven (Corvus corax), Eurasian coot (Fulica atra), Godlewski’s bunting (Emberiza godlewskii), Great crested grebe (Podiceps cristatus), Great tit (Parus major), Hawfinch (Coccothraustes coccothraustes), Hooded crow (Corvus cornix), House sparrow (Passer domesticus), Rock dove (Columba livia), Rook (Corvus frugilegus), Short-eared owl (Asio flammeus) and Ural owl (Strix uralensis). Further analysis shows that the statistical approaches generally used in metabolomics can be applied for differentiation between species, and the most fruitful results were obtained with hierarchical clustering analysis (HCA). We observed the grouping of conspecific samples independently of the sampling place and date. The HCA tree structure supports the key role of genomics in the formation of the lens metabolome, but it also indicates the influence of the species lifestyle. A combination of genomics-based and metabolomics-based phylogeny could potentially resolve arising issues and yield a more reliable tree of life.

 

[Fred Ruhe]

Thomas Guillerme, Natalie Cooper, Andrew P Beckerman & Gavin Huw Thomas, 2022

Innovation and elaboration on the avian tree of life

bioRxiv 2022.08.12.503188 (preprint)
doi: https://doi.org/10.1101/2022.08.12.503188
https://www.biorxiv.org/content/10.1101/2022.08.12.503188v1

Abstract

Patterns of biological diversity across the tree of life are the result of millions of years of evolutionary history and are shaped by natural selection. A long-standing proposal is that most morphological diversity among species arises along “an evolutionary line of least resistance”, where new phenotypes arise primarily by elaboration - evolution along this line of least resistance. At macro and mega-evolutionary scales, however, we frequently observe major shifts in phenotypes among lineages [1, 2]. The presence of distinct morphological forms suggests instead that diversity can arise via innovation - where species evolve away from the line of least resistance [3, 4]. Here we apply new multi-trait methods to evaluate the magnitude and distribution of elaboration and innovation in the evolution of bird beaks. Our analyses show that elaboration is a common feature at all scales, consistent with theory. We also find that innovation is a common and major contributor to avian morphological diversity among clades. Furthermore, we show that these patterns of innovation are replicated hierarchically throughout avian evolutionary history. These results suggest that both elaboration and innovation are ubiquitous from macro- to mega-evolutionary scales, and that macroevolutionary axes of multivariate evolution are frequently reoriented throughout the history of life, opening up new avenues for evolution to explore.

Enjoy,

Fred

 

[Peter Kovalik]

van den Burg, M.P. and Vieites, D.R. (2022), Bird genetic databases need improved curation and error reporting to NCBI. Ibis. https://doi.org/10.1111/ibi.13143

The ongoing biodiversity crisis is causing rapid species losses faster than taxonomists’capacity to describe new species. Integrative taxonomic approaches need robust taxo-nomic baseline data to correctly describe and conserve global species diversity, in whichgenetic data are one of the pillars. However, despite their broad use throughout the bio-logical sciences, the quality of genetic data within public repositories is still not guaran-teed. Here, we curated GenBank Cytochrome-b records of Aves, a well-known taxonundergoing continuous taxonomic changes, and provide a curated database to aid taxo-nomic and conservation efforts. After curation of 54 114 records, the database represents50 280 sequences from 6867 species (63% of current bird biodiversity), with a per-genusmedian of two species (50% interquartile ranges of 1–4) and three sequences (1–9). Over-all, 4469 bird species have≥2 sequences representing 91.7% and 97.5% of currentlyknown families and orders, respectively. Weflagged 1336 erroneous records (2.5% of AvesCytochrome-b records) in need of taxonomic curation (71%) or removal, 45% of whichlack any voucher information preventing a proper taxonomic assignation. Compared withAmphibia, a group for which a similar analysis was recently published, Aves records haveafive-fold higher prevalence of errors caused by contamination, sequencing errors ordiverging mutation patterns. We provide a species-level taxonomic update for 839 Gen-Bank records, including changes at the genus (76), family (21) and order (16) levels. Sci-entific conclusions from the manuscripts that have ever used those data might becompromised. A further concern is the current availability of GenBank records previouslyidentified as erroneous in published manuscripts, demonstrating the need for improvedcommunication between NCBI and the community. We call for caution when utilizingGenBank records without curation of retrieved data, despite new improvements.

[pdf]

 

[Peter Kovalik]

Thomas Guillerme, Jen A. Bright, Christopher R. Cooney, Emma C. Hughes, Zoë K. Varley, Natalie Cooper, Andrew P. Beckerman, Gavin H. Thomas. Innovation and elaboration on the avian tree of life. bioRxiv 2022.08.12.503188; doi: https://doi.org/10.1101/2022.08.12.503188

 

[albertonykus]

Wu, S., F.E. Rheindt, J. Zhang, J. Wang, L. Zhang, C. Quan, Z. Li, M. Wang, F. Wu, Y. Qu, S.V. Edwards, Z. Zhou, and L. Liu (2024)
Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous
PNAS 121: e2319696121
doi: 10.1073/pnas.2319696121

The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, and 2,384 intergenic segments. We conducted a comprehensive sensitivity analysis to account for the heterogeneity across different DNA classes, leading to an optimal tree of Neoaves with high resolution. This phylogeny features a novel Neoavian dichotomy comprising two monophyletic clades: a previously recognized Telluraves (land birds) and a newly circumscribed Aquaterraves (waterbirds and relatives). Molecular dating analyses with 20 fossil calibrations indicate that the diversification of modern birds began in the Late Cretaceous and underwent a constant and steady radiation across the KPg boundary, concurrent with the rise of angiosperms as well as other major Cenozoic animal groups including placental and multituberculate mammals. The KPg catastrophe had a limited impact on avian evolution compared to the Paleocene–Eocene Thermal Maximum, which triggered a rapid diversification of seabirds. Our findings suggest that the evolution of modern birds followed a slow process of gradualism rather than a rapid process of punctuated equilibrium, with limited interruption by the KPg catastrophe. This study places bird evolution into a new context within vertebrates, with ramifications for the evolution of the Earth’s biota.