DOI: 10.5061/dryad.s1rn8pk7s
title: Data from: Validating marine Devonian biogeography: a study in bioregionalization

description: The Devonian record presents an opportunity to test and validate an
 existing marine bioregionalisation. This study is the first to use
 comparative biogeography and phylogenetic data to test Devonian
 bioregionalisation. Proposed in the 1960’s the Old World, Eastern
 Americas, and Malvinokaffric realms have been the functional standard
 within marine Devonian Biogeography. Data from 32 published phylogenies of
 Devonian marine taxa and a database of c.800 occurrences were analysed
 using phylogenetic software to test for area monophyly. The taxic
 occurrences within the current database were then tested against total
 fauna Devonian occurrences with the Palaeobiology Database to indicate
 differences in sampling. Results indicate that the current Devonian
 bioregionalisation is not representative of natural areas and requires
 revision. The result highlights areas that are most robust from which the
 study makes recommendations to improve the process and diagnosis of
 Devonian biogeographic areas. We found that legacy issues within
 palaeontology are evident within the results and their interpretation. The
 validation of bioregionalisation and process is critical to the
 advancement of biogeography and palaeontology. The sensitivity of
 bioregionalisation shows biotic and geographical relationships, how life
 and earth evolved together, and how geographic bias is evident in
 scientific process.
description: Database of 475 taxa from
 32 published phylogenies was created from the primary literature (Table
 1). Distributional data was taken from the published database of Dowding
 and Ebach (2019) and supplemented by the Palaeobiology database(PBDB;
 www.paleobiodb.org). Trees were selected based on the Devonian occurrence
 of the taxa and then polytomies were removed following the Paralogy-free
 Subtree Method (PFS; Nelson and Ladiges, 1996; Murphy et al, 2019).The PFS
 resulted in ten reduced phylogenies which were then converted to areagrams
 using the units, both spatial and temporal, from the bioregionalisation of
 Dowding and Ebach (2018; Figure 1). Vertebrate fauna (labelled ‘fish’)
 were separated from invertebrate trees and each (fish, invertebrates, and
 both) were converted into a paralogy free, uniformly weighted three-taxon
 statement (3TS) matrices (reviewed by Kitching et al., 1998; Williams and
 Ebach, 2008) using the program TAXODIUM version 1.2 (Mavrodiev and
 Madorsky, 2012) (command: inputfilename –ib –ob –og –phy). As a next step,
 the 3TS matrices were established as an arrays of the minimal trees using
 script FORESTER version 1.0 (Mavrodiev et al., 2017) (command: ruby ruby
 seedlings.rb –inputfilename). A 3TS matrix retains a
 hierarchical structure, thereby rooting all 3TSs as individual trees.
 Subsequently, the arrays of the rooted minimal trees were imported to
 Clann version 4.1.5 (Creevey, 2004; Creevey and McInerney, 2009) to
 calculate the average consensuses. All average consensus analyses were
 performed in PAUP* 4.0a (Swofford, 2002) as described by Mavrodiev et al.
 (2017, 2019). In all cases, the optimality criterion of the best tree is
 defined in the simplest way – as a ‘distance with non-weighted least
 squares’ (Lapointe and Cucumel, 1997;  Lapointe and Levasseur, 2004;
 Creevey, 2004; Swofford, 2002). Proportions of vertebrate and
 invertebrate data within the study were tested against the proportions
 within the Palaeobiology Database. The data were downloaded from the
 Paleobiology Database using the group name 'marine', type
 Occurrences’ and parameters: time interval = Devonian, paleoenvironment =
 marine, taxa = chordata, trilobita, brachiopoda, phyllocarida, and
 chelicertata. Results were sorted into chordata and invertebrata.  A Chi
 Squared statistic
 (<i>X</i><sup><i>2</i></sup>) and Yates continuity correction <i>(</i><i>X</i><sup><i>2</i></sup><i>Yates)</i>  was applied to the data using R (R Core Team 2020).
description: The data should be substituted by newer phylogenies. There is a
 bias toward OWR and EAR units over Malvinokaffric/Malvinoxhosan and
 Gondwanan areas.