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Phylogeny of birds (3 Viewers)

Peter Kovalik

Well-known member
Slovakia
Evolution of nest characters

Yi-Ting Fang, Mao-Ning Tuanmu & Chih-Ming Hung. Asynchronous evolution of interdependent nest characters across the avian phylogeny. Nature Communications, Volume 9, Article number: 1863 (2018).

Abstract:

Nest building is a widespread behavior among birds that reflects their adaptation to the environment and evolutionary history. However, it remains unclear how nests evolve and how their evolution relates to the bird phylogeny. Here, by examining the evolution of three nest characters—structure, site, and attachment—across all bird families, we reveal that nest characters did not change synchronically across the avian phylogeny but had disparate evolutionary trajectories. Nest structure shows stronger phylogenetic signal than nest site, while nest attachment has little variation. Nevertheless, the three characters evolved interdependently. For example, the ability of birds to explore new nest sites might depend on the emergence of novel nest structure and/or attachment. Our results also reveal labile nest characters in passerines compared with other birds. This study provides important insights into avian nest evolution and suggests potential associations between nest diversification and the adaptive radiations that generated modern bird lineages.

[pdf]
 

Daniel Philippe

Well-known member
Tracking avifaunal change

Winker K., in press. Systematics, population genetics, and taxonomy, and their importance for tracking avifaunal change. In: Shuford W.D., Gill R. & Handel C. (Eds.) Avifaunal Change in Western North America. Studies of Western Birds 2. Western Field Ornithologists.

PDF
 

Peter Kovalik

Well-known member
Slovakia
Yang Liu, Simin Liu, Chia-Fen Yeh, Nan Zhang, Guoling Chen, Pinjia Que, Lu Dong & Shou-hsien Li. The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies. Scientific Reportsvolume 8, Article number: 15723 (2018). Published: 24 October 2018

Abstract:

Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.

[pdf]
 

Peter Kovalik

Well-known member
Slovakia
Kimball RT, Oliveros CH, Wang N, White ND, Barker FK, Field DJ, Ksepka DT, Chesser RT, Moyle RG, Braun MJ, Brumfield RT, Faircloth BC, Smith BT, Braun EL (2019). A phylogenomic supertree of birds. Diversity. Accepted, under revision.
 

RSN

Rafael Nascimento
Brazil
Kimball RT, Oliveros CH, Wang N, White ND, Barker FK, Field DJ, Ksepka DT, Chesser RT, Moyle RG, Braun MJ, Brumfield RT, Faircloth BC, Smith BT, Braun EL (2019). A phylogenomic supertree of birds. Diversity. Accepted, under revision.

Rebecca T. Kimball , Carl H. Oliveros, Ning Wang, Noor D. White, F. Keith Barker, Daniel J. Field, Daniel T. Ksepka, R. Terry Chesser, Robert G. Moyle, Michael J. Braun, Robb T. Brumfield, Brant C. Faircloth, Brian Tilston Smith and Edward L. Braun

A Phylogenomic Supertree of Birds

Diversity 2019, 11(7), 109
https://doi.org/10.3390/d11070109

Abstract
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

https://www.mdpi.com/1424-2818/11/7/109
 

albertonykus

Well-known member
Kuhl, H., C. Frankl-Vilches, A. Bakker, G. Mayr, G. Nikolaus, S.T. Boerno, S. Klages, B. Timmermann, M. Gahr (2020)
An unbiased molecular approach using 3’UTRs resolves the avian family-level tree of life
Molecular Biology and Evolution (advance online publication)
doi: 10.1093/molbev/msaa191
https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa191/5891114

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 for the non-passerines and 115 for 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 non-passerine 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 non-passeriform 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. Since 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
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
It's surprising and unexpected this close relationship between the hoazin and the Strisores. He is so unique that it made sense to me that he was the only member of his lineage, not related to other group, following Prum & Al., 2015
 

Xenospiza

Distracted
Supporter
The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of non-passeriform 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.
Or the threshold to claim a family in the Passeriformes is just a lot lower...

Anyway, they should switch the tit and the pitta in the tree.
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
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 ??
 

Xenospiza

Distracted
Supporter
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 ??
Or resurrect the Metaves for the last group?
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
What do you think of the trees available on bird tree/vertlife, are they reliable ?, can we learn something from them? I'm looking at them all on figtree and, I don't know, I'm puzzled because many contradict several studies that have been published. :brains:
 

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