Molecular Phylogenies Map to Biogeography Better than Morphological Ones

Oyston, Jack; Wilkinson, Mark; Ruta, Marcello; Wills, Matthew A.

doi:10.21203/rs.3.rs-846195/v1

Cited by 3 publications

(3 citation statements)

References 81 publications

(73 reference statements)

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“…They were able to show that morphological data were more prone to convergence than amino acid sites, in large part due to the small number of character states defined for discretized morphological characters. Similarly, in the case of biogeography, a recent meta-analysis of morphological and molecular phylogenies showed that molecular phylogenies exhibit better congruence to biogeographic distributions than their counterpart morphological trees [87], suggesting that homoplasy in morphological trees obscures inference of macroevolutionary processes.…”

Section: Morphology In the Era Of Phylogenomicsmentioning

confidence: 99%

“…Yet few published works arrive at this explicit conclusion. The archetypal conclusions postulated by phylogenetic workers that compare data classes to the detriment of morphology are (1) the importance of fossils and an integrated understanding of evolutionary history, which substantiates the continued relevance of morphology (e.g., [67,87,88]); and/or (2) a call for collecting more morphological data, despite the molecular data usually having resolved most of the relationships in question more efficiently and more reproducibly (e.g., [60]). Given the comparatively greater epistemological and practical challenges to collecting, interpreting, and analyzing morphological data in the context of phylogenetic inference, it is not surprising that morphological datasets have taken on an ancillary role by comparison to molecular data, in deciphering evolutionary relationships of extant taxa.…”

Section: Morphology In the Era Of Phylogenomicsmentioning

confidence: 99%

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What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

2021

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The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.

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Section: Morphology In the Era Of Phylogenomicsmentioning

confidence: 99%

Section: Morphology In the Era Of Phylogenomicsmentioning

confidence: 99%

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

2021

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“…Morphological affinities are considered insufficient for testing evolutionary hypotheses because of interference from homoplasy and convergence 65 . The scarcity of genetic data in our research, which could serve for haplotype and private allele inquiry, hamper inferences concerning the radiation of taxa grouped in specific clades.…”

Section: Phylogenymentioning

confidence: 99%

Diversity under a magnifier lens: The case of Typhlotanaidae in N Atlantic

Gellert

Błażewicz

Mamos

et al. 2022

Preprint

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Research focusing on ‘stout-bodied’ typhlotanaids collected from several sites around Iceland and adjacent northern seas has resulted in the description of 15 species new to science, as well as the creation of eight new genera. Typhlotanais eximius Hansen, 1913 was redescribed and transferred to a new genus, while Typhlotanais crassus and Peraeospinosus adipatus are transferred to the genus Larsenotanais. The morphological and the molecular data were combined to consolidate and confirm the validity of the results obtained from both approaches. The polyphyletic nature of Typhlotanaidae and its serious underestimation was emphasized. Molecular analysis revealed that the ’stout-bodied‘ Typhlotanaidae are monophyletic. Depth, temperature, and salinity were identified as the main environmental parameters determining the distribution of this group of Typhlotanaidae. Several species were clearly associated with shelf and upper bathyal of Iceland. The Greenland-Iceland-Faroe ridge is shown to be a distinct zoogeographical barrier for typhlotanaids inhabiting the deeper slope and abyssal around Iceland.

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Observations on Paleospecies Determination, With Additional Data on Tyrannosaurus Including Its Highly Divergent Species Specific Supraorbital Display Ornaments That Give T. rex a New and Unique Life Appearance

Paul¹

2022

Preprint

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Intrageneric dinosaur species have been being named for decades without either significant examination of the methods and standards used to do so, or widely publicized controversy over the results. The long standing assumption that all large known specimens of the iconic North American Tyrannosaurus consisted of just the one popular species T. rex was recently challenged with the first comprehensive test of the question. The result was the diagnosing and naming of two additional taxa, T. imperator and T. regina, based on a number of species levels characters regarding robustness and tooth proportions in the context of their stratigraphic distribution. In association a rare in-depth look was taken at the current state of naming vertebrate paleospecies, which it turns out are not highly rigorous because of inherent problems with the species concept and other matters. The results of the paper were severely criticized in in a manner never seen before for new dinosaur species even when based on less evidence. This study takes another look as the determination of paleospecies, and shows that many of the claims made in the criticisms regarding the Tyrannosaurus species work were inaccurate. New data on the proportions of strength bars in Tyrannosaurus skulls reinforces the basing of the three species in part on robustness factors, and allows all but one skull to be assigned to one of the species. These results allow the first detailed systematic examination of the supraorbital display bosses of the genus. They sort out as visually distinctive species specific ornaments based on both stratigraphic and taxonomic factors, strongly affirm that Tyrannosaurus was multispecific, and the species probably dimorphic. New skulls of T. rex show that the species sported, males probably, striking display bosses not yet observed in other tyrannosaurids.

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Molecular Phylogenies Map to Biogeography Better than Morphological Ones

Cited by 3 publications

References 81 publications

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

Diversity under a magnifier lens: The case of Typhlotanaidae in N Atlantic

Observations on Paleospecies Determination, With Additional Data on Tyrannosaurus Including Its Highly Divergent Species Specific Supraorbital Display Ornaments That Give T. rex a New and Unique Life Appearance

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