Fred Ruhe
Well-known member
Naoko Takezaki, 2023
Effect of different types of sequence data on palaeognath phylogeny
Genome Biology and Evolution, evad092
doi: https://doi.org/10.1093/gbe/evad092
Abstract and free pdf: https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evad092/7179533
Abstract
Palaeognathae consists of five groups of extant species: flighted tinamous (1) and four flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular studies supported the groupings of extinct moas with tinamous and elephant birds with kiwi as well as ostriches as the group that diverged first among the five groups. However, phylogenetic relationships among the five groups are still controversial. Previous studies showed extensive heterogeneity in estimated gene tree topologies from conserved nonexonic elements (CNEEs), introns, and ultraconserved elements (UCEs). Using the non-coding loci together with protein-coding loci this study investigated the factors that affected gene tree estimation error and the relationships among the five groups. Using closely related ostrich rather than distantly related chicken as the outgroup, concatenated and gene-tree based approaches supported rheas as the group that diverged first among groups (1) - (4). While gene tree estimation error increased using loci with low sequence divergence and short length, topological bias in estimated trees occurred using loci with high sequence divergence and/or nucleotide composition bias and heterogeneity, which more occurred in trees estimated from coding loci than non-coding loci. Regarding the relationships of (1) - (4) the site patterns by parsimony criterion appeared less susceptible to the bias than tree construction assuming stationary time-homogenous model and suggested the clustering of kiwi and cassowaries and emu the most likely with approximately 40% support rather than the clustering of kiwi and rheas and that of kiwi and tinamous with 30% support each.
Enjoy,
Fred
Effect of different types of sequence data on palaeognath phylogeny
Genome Biology and Evolution, evad092
doi: https://doi.org/10.1093/gbe/evad092
Abstract and free pdf: https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evad092/7179533
Abstract
Palaeognathae consists of five groups of extant species: flighted tinamous (1) and four flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular studies supported the groupings of extinct moas with tinamous and elephant birds with kiwi as well as ostriches as the group that diverged first among the five groups. However, phylogenetic relationships among the five groups are still controversial. Previous studies showed extensive heterogeneity in estimated gene tree topologies from conserved nonexonic elements (CNEEs), introns, and ultraconserved elements (UCEs). Using the non-coding loci together with protein-coding loci this study investigated the factors that affected gene tree estimation error and the relationships among the five groups. Using closely related ostrich rather than distantly related chicken as the outgroup, concatenated and gene-tree based approaches supported rheas as the group that diverged first among groups (1) - (4). While gene tree estimation error increased using loci with low sequence divergence and short length, topological bias in estimated trees occurred using loci with high sequence divergence and/or nucleotide composition bias and heterogeneity, which more occurred in trees estimated from coding loci than non-coding loci. Regarding the relationships of (1) - (4) the site patterns by parsimony criterion appeared less susceptible to the bias than tree construction assuming stationary time-homogenous model and suggested the clustering of kiwi and cassowaries and emu the most likely with approximately 40% support rather than the clustering of kiwi and rheas and that of kiwi and tinamous with 30% support each.
Enjoy,
Fred
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