ORCID Profile
0000-0002-0650-1282
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Publisher: Springer Science and Business Media LLC
Date: 07-09-2020
Publisher: Cold Spring Harbor Laboratory
Date: 26-04-2018
DOI: 10.1101/308742
Abstract: Phylogenetic analysis algorithms require the assumption of character independence - a condition generally acknowledged to be violated by morphological data. Correlation between characters can originate from intra-organismal features, shared phylogenetic history or forced by particular character-state coding schemes. Although the two first sources can be investigated by biologists a posteriori and the third one can be avoided a priori with good practices, phylogenetic software do not distinguish between any of them. In this study, we propose a new metric of raw character difference as a proxy for character correlation. Using thorough simulations, we test the effect of increasing or decreasing character differences on tree topology. Overall, we found an expected positive effect of reducing character correlations on recovering the correct topology. However, this effect is less important for matrices with a small number of taxa (25 in our simulations) where reducing character correlation is not more effective than randomly drawing characters. Furthermore, in bigger matrices (350 characters), there is a strong effect of the inference method with Bayesian trees being consistently less affected by character correlation than maximum parsimony trees. These results suggest that ignoring the problem of character correlation or independence can often impact topology in phylogenetic analysis. However, encouragingly, they also suggest that, unless correlation is actively maximised or minimised, probabilistic methods can easily accommodate for a random correlation between characters.
Publisher: Cold Spring Harbor Laboratory
Date: 10-06-2020
DOI: 10.1101/2020.06.09.132027
Abstract: Endochondral bone is the main internal skeletal tissue of nearly all osteichthyans—the group comprising more than 60,000 living species of bony fishes and tetrapods. Chondrichthyans (sharks and their kin) are the living sister group of osteichthyans and have cartilaginous endoskeletons, long considered the ancestral condition for all jawed vertebrates (gnathostomes). The absence of bone in modern jawless fishes and the absence of endochondral ossification in early fossil gnathostomes appears to lend support to this conclusion. Here we report the discovery of extensive endochondral bone in Minjinia turgenensis , a new genus and species of ‘placoderm’-like fish from the Early Devonian (Pragian) of western Mongolia described using x-ray computed microtomography (XR-µCT). The fossil consists of a partial skull roof and braincase with anatomical details providing strong evidence of placement in the gnathostome stem group. However, its endochondral space is filled with an extensive network of fine trabeculae resembling the endochondral bone of osteichthyans. Phylogenetic analyses place this new taxon as a proximate sister group of the gnathostome crown. These results provide direct support for theories of generalised bone loss in chondrichthyans. Furthermore, they revive theories of a phylogenetically deeper origin of endochondral bone and its absence in chondrichthyans as a secondary condition.
No related grants have been discovered for Martin Brazeau.