Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

Sansom, Robert S.; Choate, Peter G.; Keating, Joseph N.; Randle, Emma

doi:10.1098/rsbl.2018.0263

Cited by 55 publications

(47 citation statements)

References 30 publications

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“…A, boxplots of the distributions of MIG scores, as in Sansom et al . (2018). B, the same data, but as a violin plot with points overlain.…”

Section: Resultsmentioning

confidence: 99%

“…Empirical datasets were downloaded from http://www.graemetlloyd.com/matr.html, the starting repository used by Sansom et al . (2018). We initially excluded anything molecular, phenetic, ontogenetic or meta‐analytical as these do not represent data sets intended for morphological phylogenetic inference (our focus here).…”

Section: Methodsmentioning

confidence: 99%

“…The same XML files contain taxonomic reconciliations; links between OTU names used in the trees with taxa entered into the Paleobiology Database (PaleoDB), the source used for our age data (and that of Sansom et al . 2018). Using the PaleoDB API (Peters & McClennen 2016) we further filtered the data down to just those where all taxa are both reconciled and have age data available in the database (i.e.…”

Section: Methodsmentioning

confidence: 99%

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Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample

Wright

Lloyd

2020

Palaeontology

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Establishing hypotheses of relationships is a critical prerequisite for any macroevolutionary analysis, but different approaches exist for achieving this goal. Amongst palaeontologists using morphological data the Bayesian approach is increasingly preferred over parsimony, but this shift also alters the way we think about samples of trees. Here we revisit stratigraphic congruence as a comparator between Bayesian and parsimony samples, but in a new visual context: treespace. Such spaces represent an ordination of unique topologies that can also be extended to create a ‘landscape’ where altitude represents some comparative measure (here congruence with stratigraphy). By co‐opting existing visualization tools and applying them to a meta‐analysis of 128 cladistic data sets we show that there is no consistent favouring of either Bayesian or parsimony according to stratigraphic congruence metrics, and further that empirical treespace visualizations suggest a complex variety of topological landscapes. We conclude by arguing that treespaces should become a standard exploratory tool in phylogenetic analysis.

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“…A, boxplots of the distributions of MIG scores, as in Sansom et al . (2018). B, the same data, but as a violin plot with points overlain.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample

Wright

Lloyd

2020

Palaeontology

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“…These characters were not definitely confirmed in our observations and therefore were not scored in our morphological matrix and were instead coded as ‘?’. It is also noted, however, that Bayesian trees may exhibit significantly lower stratigraphic congruence than the equivalent parsimony trees; and therefore, parsimony analyses are more accurate for phylogenetic reconstruction of morphological data (Sansom et al ., ).…”

Section: Discussionmentioning

confidence: 97%

First and oldest Leptochirini rove beetles illuminate diverse cephalic structures in the Cretaceous (Coleoptera: Staphylinidae: Osoriinae)

Yamamoto

Takahashi²

2019

Systematic Entomology

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Osoriinae is a highly diverse, globally distributed subfamily of rove beetles (Staphylinidae), but only a single Mesozoic species, Mesallotrochus longiantennatus Cai & Huang, in mid-Cretaceous Burmese amber is known (age c. 99 Ma). Leptochirini, which is primarily found in decaying wood in the tropics, is one of the four tribes of osoriine rove beetles. The diversity of cephalic tooth shapes in adults has attracted special research attention with regard to the evolution and classification of this group. Here, we report two well-preserved fossils of Leptochirini for the first time from Burmese amber. Together with M. longiantennatus, they represent the oldest osoriines, highlighting the palaeodiversity of the subfamily in Burmese amber. Based on our observations and phylogenetic analyses, a remarkable new genus and species, †Cretochirus newtoni Yamamoto gen. et sp.n., is described. Additionally, a new species, †Priochirus thayerae Yamamoto sp.n., is also described and placed in the extant genus Priochirus Sharp.†Cretochirus gen.n. has a typical body plan of Leptochirini, but it retains several primitive features that have rarely, or never, been known from modern leptochirine taxa, including simple cephalic structures with a largely depressed dorsum, undeveloped cephalic teeth, and the absence of a longitudinal median sulcus of the head, together with the only slightly crenulate external margins of the protibiae. These findings demonstrate the antiquity of Leptochirini rove beetles and even suggest a much older origin of the subfamily. Morphologically diverse leptochirines from Burmese amber also illuminate the remarkable cephalic diversity of the tribe during the Mesozoic. They were already diversified during the mid-Cretaceous in the tropical forests of Myanmar, and possibly living underneath the bark of rotten wood and logs.This published work has been registered in ZooBank, http://zoobank.org/urn:lsid: zoobank.org:pub

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“…There has been much debate on whether parsimony or Bayesian approaches are most suitable for the analysis of morphological data [1][2][3][4][5][6][7][8]. These debates focused on results from simulations, discussions of model assumptions and stratigraphic fit.…”

Section: Introductionmentioning

confidence: 99%

Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans

King

2019

Biol. Lett.

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There has been much recent debate about which method is best for reconstructing the tree of life from morphological datasets. However, little attention has been paid to which characters, if any, are responsible for topological differences between trees recovered from competing methods on empirical datasets. Indeed, a simple procedure for finding characters supporting conflicting tree topologies is available in a parsimony framework, but an equivalent procedure in a model-based framework is lacking. Here, I introduce such a procedure and apply it to the problem of the ‘psarolepid’ osteichthyans. The ‘psarolepids’, which include the earliest known osteichthyans, are weakly supported as stem osteichthyans under parsimony but strongly supported as sarcopterygians in Bayesian analysis. The Bayesian result is driven by just two characters, both of which relate to the intracranial joint of sarcopterygians. Important characters that support a stem osteichthyan affinity for ‘psarolepids’, such as the absence of tooth enamel, have virtually no effect in a Bayesian framework. This is because of a bias towards characters with relatively complete sampling, a bias that has previously been reported for molecular data. This has important implications for Bayesian analysis of morphological datasets in general, as characters from different body parts commonly have different levels of coding completeness. Methods to critically appraise character support for conflicting phylogenetic hypotheses, such as that used here, should form an important part of phylogenetic analyses.

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Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

Cited by 55 publications

References 30 publications

Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample

Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample

First and oldest Leptochirini rove beetles illuminate diverse cephalic structures in the Cretaceous (Coleoptera: Staphylinidae: Osoriinae)

Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans

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