Peter Kovalik
Well-known member
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Ratites (1 Viewer)
- Thread starter Daniel Philippe
- Start date
Fred Ruhe
Well-known member
Peter Kovalik
Well-known member
Richard Klim
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Peter Kovalik
Well-known member
Richard Klim
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Richard Klim
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Mitchell et al 2014
Greg Laden, 10,000 Birds, 17 Jun 2014: Being A Living Fossil Evolved Multiple Times.
Peter Kovalik
Well-known member
Richard Klim
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Fred Ruhe
Well-known member
Alison Cloutier, Timothy B. Sackton, Phil Grayson, Michele Clamp, Allan J. Baker4, Scott V. Edwards, 2018
Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
bioRxiv doi:10.1101/262949
Free pdf: https://www.biorxiv.org/content/biorxiv/early/2018/02/09/262949.1.full.pdf
Enjoy,
Fred
Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
bioRxiv doi:10.1101/262949
Free pdf: https://www.biorxiv.org/content/biorxiv/early/2018/02/09/262949.1.full.pdf
Enjoy,
Fred
Peter Kovalik
Well-known member
Ostrich
Eckhart J Buchmann & Colleen T Downs (2018) Ostrich, Southern Ostrich or Common Ostrich? The ‘eternal vexed question’ of English bird names and name changes in southern Africa through eight editions of Roberts field guides, 1940–2016, Ostrich, DOI: 10.2989/00306525.2018.1460408
Abstract:
A set of stable simple common bird names helps non-ornithologist birders, who contribute to conservation by visiting protected areas and participating in citizen science projects. Changes in English bird names have caused discomfort in the local birding community, especially those that followed international standardisation of common bird names between 2000 and 2005. To understand the extent and nature of English bird name changes, an analysis was done of all southern African bird names through the eight editions of Roberts Birds of South/Southern Africa field guides published from 1940 to 2016. Of 813 species listed in both the first and the latest of the field guides, 453 (55.7%) had their names changed, among which 108 (13.3%) had changes in both the group name and the species epithet. The greatest single wave of changes (31.4%) occurred in the first ‘Roberts bird guide’ (the seventh field guide) in 2007, following international standardisation. Mean word and syllable counts of bird names also increased significantly in that edition. Name changes were associated with new authorships, taxonomic changes and use of geographic species epithets. There was a trend towards name stability for southern African endemic species. Further name changes should be kept to a minimum, shortening and simplifying wherever possible.
Eckhart J Buchmann & Colleen T Downs (2018) Ostrich, Southern Ostrich or Common Ostrich? The ‘eternal vexed question’ of English bird names and name changes in southern Africa through eight editions of Roberts field guides, 1940–2016, Ostrich, DOI: 10.2989/00306525.2018.1460408
Abstract:
A set of stable simple common bird names helps non-ornithologist birders, who contribute to conservation by visiting protected areas and participating in citizen science projects. Changes in English bird names have caused discomfort in the local birding community, especially those that followed international standardisation of common bird names between 2000 and 2005. To understand the extent and nature of English bird name changes, an analysis was done of all southern African bird names through the eight editions of Roberts Birds of South/Southern Africa field guides published from 1940 to 2016. Of 813 species listed in both the first and the latest of the field guides, 453 (55.7%) had their names changed, among which 108 (13.3%) had changes in both the group name and the species epithet. The greatest single wave of changes (31.4%) occurred in the first ‘Roberts bird guide’ (the seventh field guide) in 2007, following international standardisation. Mean word and syllable counts of bird names also increased significantly in that edition. Name changes were associated with new authorships, taxonomic changes and use of geographic species epithets. There was a trend towards name stability for southern African endemic species. Further name changes should be kept to a minimum, shortening and simplifying wherever possible.
Daniel Philippe
Well-known member
Yonezawa T., Segawa T., Mori H., Campos P.F., Hongoh Y., Endo H., Akiyoshi A., Kohno N., Nishida S., Wu J., Jin H., Adachi J., Kishino H., Kurokawa K., Nogi Y., Tanabe H., Mukoyama H., Yoshida K., Rasoamiaramanana A., Yamagishi S., Hayashi Y., Yoshida A., Koike H., Akishinonomiya F., Willerslev E. & Hasegawa M., 2017. Phylogenomics and morphology of extinct Paleognaths reveal the origin and evolution of the Ratites. Current Biol. 27: 1-10.
Access to PDF
Access to PDF
Fred Ruhe
Well-known member
A great find Daniel,
The paper is based on fossil Palaeognathae (Lithornithidae, Aepyornis, Mullerornis, Dinornithiformes and so on), and that is important (you should have posted it on the bird paleontoligy subforum).
But unfortunately, I already posted this paper on the 16th december 2016, see https://www.birdforum.net/showthread.php?t=336534&highlight=Yonezawa
Fred
The paper is based on fossil Palaeognathae (Lithornithidae, Aepyornis, Mullerornis, Dinornithiformes and so on), and that is important (you should have posted it on the bird paleontoligy subforum).
But unfortunately, I already posted this paper on the 16th december 2016, see https://www.birdforum.net/showthread.php?t=336534&highlight=Yonezawa
Fred
Last edited:
Daniel Philippe
Well-known member
Sorry Fred, missed it. |8(|
Peter Kovalik
Well-known member
Alison Cloutier, Timothy B Sackton, Phil Grayson, Michele Clamp, Allan J Baker, Scott V Edwards, Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone, Systematic Biology, , syz019, https://doi.org/10.1093/sysbio/syz019
Abstract:
Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totalling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4,274 CR1 retroelements identified from multi-species whole genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other non-ostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.
Abstract:
Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totalling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4,274 CR1 retroelements identified from multi-species whole genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other non-ostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.
Fred Ruhe
Well-known member
They must be very clever. I don't understand a word they say. Who does and can explain to me what they are saying?
Fred
mb1848
Well-known member
Fred.
I am using genome-scale data to reconstruct the phylogenetic history of this group [palaeognaths] with both sequence-based approaches and presence/absence characters such as retroelement insertions. Hope that helps.
Me neither but, the lead author says on her webpage :
I am using genome-scale data to reconstruct the phylogenetic history of this group [palaeognaths] with both sequence-based approaches and presence/absence characters such as retroelement insertions. Hope that helps.
I am reading the abstract to be technical more than biological: more than half is comparisons of different analysis methods.
Biologically, the important sentence is Rhea as sister to Kiwi and Emu + Cassowary. I am not sure where that places Ostrich.
Niels
Biologically, the important sentence is Rhea as sister to Kiwi and Emu + Cassowary. I am not sure where that places Ostrich.
Niels
albertonykus
Well-known member
Urantówka, A.D., A. Kroczak, and P. Mackiewicz (2020)
New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves
BMC Genomics 21: 874
doi: 10.1186/s12864-020-07284-5
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07284-5
Background
Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans.
Results
Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication.
Conclusions
The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves
BMC Genomics 21: 874
doi: 10.1186/s12864-020-07284-5
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07284-5
Background
Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans.
Results
Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication.
Conclusions
The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
