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[dinosaur] Feduccia on bird evolution + genetics of flight origins + morphological phylogenetics (free pdfs)



Some recent(ish) papers that have not yet been posted on the DML:


Feduccia's reply to Smith et al.'s (2015) critique of his writings on the origin of birds (see http://dml.cmnh.org/2015Mar/msg00067.html):

Feduccia A 2016 Fantasy vs reality: a critique of Smith et al.'s bird origins. Open Ornithol J 9: 14–38
http://benthamopen.com/contents/pdf/TOOENIJ/TOOENIJ-9-14.pdf

Adherents of the current orthodoxy of a derivation of birds from theropod dinosaurs, criticize the commentary by Feduccia (2013, Auk, 130) [1 - 12] entitled “Bird Origins Anew” as well as numerous papers by Lingham-Soliar on theropod dermal fibers, using numerous mischaracterizations and misstatements of content, and illustrate their own misconceptions of the nature of the debate, which are here clarified. While there is general agreement with the affinity of birds and maniraptorans, the widely accepted phylogeny, advocating derived earth-bound maniraptorans giving rise to more primitive avians (i.e. Archaeopteryx), may be “topsy-turvy.” The current primary debate concerns whether maniraptorans are ancestral or derived within the phylogeny, and whether many maniraptorans and birds form a clade distinct from true theropods. Corollaries of the current scheme show largely terrestrial maniraptoran theropods similar to the Late Cretaceous Velociraptor giving rise to avians, and flight originating via a terrestrial (cursorial) “gravity-resisted,” as opposed to an arboreal “gravity-assisted” model. The current dogma posits pennaceous flight remiges in earth-bound theropods having evolved in terrestrial theropods that never flew. As part of the orthodoxy, fully feathered maniraptorans such as the tetrapteryx gliders Microraptor and allies, are incorrectly reconstructed as terrestrial cursors, when in reality their anatomy and elongate hindlimb feathers would be a hindrance to terrestrial locomotion.The same is true of many early birds, exemplified by reconstruction of the arboreally adapted Confuciusornis as a terrestrial predator, part of the overall theropodan scheme of birds evolving from terrestrial dinosaurs, and flight from the ground up. Both sides of this contentious debate must be constantly aware that new fossil or even molecular discoveries on birds may change current conclusions.


A new paper making use of the whole-genome data assembled by the Avian Phylogenomics Project consortium:

Machado JP, Johnson WE, Gilbert MTP, Zhang G, Jarvis ED, O’Brien SJ, Antunes A 2016 Bone-associated gene evolution and the origin of flight in birds. BMC Genom 17: 371
http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2681-7

Background 

Bones have been subjected to considerable selective pressure throughout vertebrate evolution, such as occurred during the adaptations associated with the development of powered flight. Powered flight evolved independently in two extant clades of vertebrates, birds and bats. While this trait provided advantages such as in aerial foraging habits, escape from predators or long-distance travels, it also imposed great challenges, namely in the bone structure. 

Results 

We performed comparative genomic analyses of 89 bone-associated genes from 47 avian genomes (including 45 new), 39 mammalian, and 20 reptilian genomes, and demonstrate that birds, after correcting for multiple testing, have an almost two-fold increase in the number of bone-associated genes with evidence of positive selection (~52.8 %) compared with mammals (~30.3 %). Most of the positive-selected genes in birds are linked with bone regulation and remodeling and thirteen have been linked with functional pathways relevant to powered flight, including bone metabolism, bone fusion, muscle development and hyperglycemia levels. Genes encoding proteins involved in bone resorption, such as TPP1, had a high number of sites under Darwinian selection in birds. 

Conclusions 

Patterns of positive selection observed in bird ossification genes suggest that there was a period of intense selective pressure to improve flight efficiency that was closely linked with constraints on body size.


Two papers exploring the performance of different phylogenetic methods when applied to morphological data:

Congreve CR, Lamsdell JC 2016 Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices. Palaeontol 59(3): 447–62
http://onlinelibrary.wiley.com/doi/10.1111/pala.12236/abstract
http://www.academia.edu/25653840/Implied_weighting_and_its_utility_in_palaeontological_datasets_a_study_using_modelled_phylogenetic_matrices?auto=view&campaign=weekly_digest

Implied weighting, a method for phylogenetic inference that actively seeks to downweight supposed homoplasy, has in recent years begun to be widely utilized in palaeontological datasets. Given the method's purported ability at handling widespread homoplasy/convergence, we investigate the effects of implied weighting on modelled phylogenetic data. We generated 100 character matrices consisting of 55 characters each using a Markov Chain morphology model of evolution based on a known phylogenetic tree. Rates of character evolution in these datasets were variable and generated by pulling from a gamma distribution for each character in the matrix. These matrices were then analysed under equal weighting and four settings of implied weights (k = 1, 3, 5, and 10). Our results show that implied weighting is inconsistent in its ability to retrieve a known phylogenetic tree. Equally weighted analyses are found to generally be more conservative, retrieving higher frequency of polytomies but being less likely to generate erroneous topologies. Implied weighting is found to generally resolve polytomies while also propagating errors, resulting in an increase in both correctly and incorrectly resolved nodes with a tendency towards higher rates of error compared to equal weighting. Our results suggest that equal weights may be a preferable method for parsimony analysis.


O'Reilly JE, Puttick MN, Parry L, Tanner AR, Tarver JE, Fleming J, Pisani D, Donoghue PCJ 2016 Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data. Biol Lett 12(4): 20160081
http://rsbl.royalsocietypublishing.org/content/12/4/20160081 
http://www.researchgate.net/publication/301568607_Bayesian_methods_outperform_parsimony_but_at_the_expense_of_precision_in_the_estimation_of_phylogeny_from_discrete_morphological_data

Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphological data, we demonstrate that the Mk-model outperforms equal-weights parsimony in terms of topological accuracy, and implied-weights performs the most poorly. However, the Mk-model produces phylogenies that have less resolution than parsimony methods. This difference in the accuracy and precision of parsimony and Bayesian approaches to topology estimation needs to be considered when selecting a method for phylogeny reconstruction.


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David Černý