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Data from: The amphibamiform Nanobamus macrorhinus from the early Permian of Texas

Cite this dataset

Gee, Bryan M. (2024). Data from: The amphibamiform Nanobamus macrorhinus from the early Permian of Texas [Dataset]. Dryad. https://doi.org/10.5061/dryad.mq385f0

Abstract

Nanobamus macrorhinus is a small amphibamiform temnospondyl from the early Permian Arroyo Formation of Texas. It is most readily characterized by an elongate and partially subdivided naris. This condition is superficially reminiscent of that seen in the coeval trematopids, the group to which N. macrorhinus was originally referred to under an interpretation of the holotype as a larval form. This was discounted by later workers, but the amphibamiform affinities of the specimen were not formalized until recently. The specimen has never been described in the context of its amphibamiform affinities and remains poorly characterized, never having been sampled in a phylogenetic analysis. Here we present a complete, updated osteological description of N. macrorhinus, including an improved characterization of its unique mosaic of plesiomorphic and apomorphic features and clarification of the taxon’s autapomorphies. Our analysis of the taxon’s phylogenetic position within Amphibamiformes shows that N. macrorhinus is recovered as diverging after basal amphibamiforms such the micropholids and before derived amphibamiforms such as the amphibamids. This is supported by the unique mixture of retained plesiomorphies such as non-foreshortened postparietals and an oval choana and apomorphies such as a narrow interorbital region and slender palatal rami of the pterygoid. These results reflect the complexity of terrestrial amphibamiform diversity and provide further insight into the evolutionary history of the lissamphibian stem in terrestrial environments.

README: Data from: The amphibamiform Nanobamus macrorhinus from the early Permian of Texas

https://doi.org/10.5061/dryad.mq385f0

GENERAL INFORMATION

Title of Dataset: Phylogenetic data for: The amphibamiform Nanobamus macrorhinus from the early Permian of Texas

First/Corresponding Author Information

Name: Bryan M. Gee

ORCID: 0000-0003-4517-3290

Institution: University of Toronto

Email: bryangee.temnospondyli@gmail.com

Geographic location of data collection: Mississauga, ON, Canada

Information about funding sources that supported the collection of the data: Natural Sciences and Engineering Research Council (NSERC) Discovery Grant to RRR, an Ontario Graduate Scholarship (OGS) grant to BMG, and the University of Toronto.

SHARING/ACCESS INFORMATION

Licenses/restrictions placed on the data: CC0 license waiver (https://creativecommons.org/public-domain/cc0/)

Links to publications that cite or use the data: none

Links to other publicly accessible locations of the data: This dataset is also deposited on MorphoBank as Project #4605: http://dx.doi.org/10.7934/P4605

Links/relationships to ancillary data sets: N/A

Was data derived from another source? Yes

If yes, list source(s):

Primary source: Schoch, R. R. (2019). The putative lissamphibian stem-group: phylogeny and evolution of the dissorophoid temnospondyls. Journal of Paleontology, 93(1), 137–156.

Recommended citation for this dataset: Gee, B. M. (2024). Phylogenetic data for: The amphibamiform Nanobamus macrorhinus from the early Permian of Texas. Dataset.

DATA & FILE OVERVIEW

April 2024 version

This dataset is not modified in any sense with respect to the character scores, but it adds all of the character states to the NEXUS file and provides .tre files of MPTs for each analysis that was performed. MPTs were not originally saved as part of the analyses conducted for the article in 2019, and it should be noted that three analyses (the permutations with character removal) recovered MPTs with a length of one step greater than those reported by Gee & Reisz in the article (but the same number of MPTs and the same consensus trees). The source for this discrepancy is not clearly typographic given that three analyses had their MPT length misreported by 1 step, but it does not appear to be an issue of using a slightly different version of the matrix, as the two permutations with the full character sample (select multistate ordered vs. all multistate unordered) recovered the same length of MPTs (as well as the same number of MPTs and the same consensus trees). I (BMG) believe that the MPT lengths reported for those three permutations are outdated and represent the result of a preliminary analysis in which the one scoring change for Georgenthalia was not implemented (character 39, 0 -> 1). Analyzing the matrix without that change and the specific character removals does recover the sets of slightly shorter MPTs.

File List:

  1. Gee & Reisz_2019_J Paleo matrix.nex: modified character matrix from Schoch (2019)
  2. Gee & Reisz_2019_multistate ordered_106 char.tre: resultant MPTs from the iteration with 106 characters (characters 17 and 30 omitted) and select multistate characters ordered
  3. Gee & Reisz_2019_multistate ordered_107 char_c17 removed.tre: resultant MPTs from the iteration with 107 characters (character 17 omitted) and select multistate characters ordered
  4. Gee & Reisz_2019_multistate ordered_107 char_c30 removed.tre: resultant MPTs from the iteration with 107 characters (character 30 omitted) and select multistate characters ordered
  5. Gee & Reisz_2019_multistate ordered_108 char.tre: resultant MPTs from the iteration with 108 characters (no characters omitted) and select multistate characters ordered
  6. Gee & Reisz_2019_multistate ordered_108 char.tre: resultant MPTs from the iteration with 108 characters (no characters omitted) and no multistate characters ordered
  7. Gee & Reisz_Supp Fig 1.tif: Results of phylogenetic analysis of Nanobamus macrorhinus in the matrix of Schoch (2019) (35 taxa, 108 characters); tree visually pruned to focus on Amphibamiforms: (1) majority rule consensus of the first 107-character (removal of character 17) sampling permutation; (2) strict con- sensus tree of the same permutation with bootstrap support and Bremer decay indices (the latter in parentheses); (3) majority rule consensus of the second 107-character sampling (removal of character 30) permutation; (4) strict consensus tree of the same permutation with bootstrap support and Bremer decay indices.

Relationship between files, if important: N/A

Additional related data collected that was not included in the current data package: None.

Are there multiple versions of the dataset? No.

METHODOLOGICAL INFORMATION

Description of methods used for collection/generation of data:

Matrices were downloaded from the source literature and compiled in Mesquite v. 3.6 build 917 for MacOS on a Mid 2015 MacBook Pro running Mojave v. 10.14.6.

Methods for processing the data:

  1. Following Schoch (2019), six multistate characters were ordered: 1, 45, 53, 67, 75, 94. Following Schoch (2019), three additional permutations (with all multistage characters ordered) were run:
  • Removal of character 17
  • Removal of character 30
  • Removal of characters 17 and 30

The following software packages were used for this analysis:

This matrix has been superseded by other derivates in this family of matrices (not all with the exact same taxon sample) and should only be reused for the express purpose of reproducing the results of Gee & Reisz (2020). For more recent versions, see the following:

  • Schoch, R. R., Henrici, A. C., & Hook, R. W. (2021). A new dissorophoid temnospondyl from the Allegheny Group (late Carboniferous) of five points, Mahoning County, Ohio (USA). Journal of Paleontology, 95(3), 638-651. https://doi.org/10.1017/jpa.2020.101
  • Schoch, R. R. (2022). Phylogeny of the amphibamiform temnospondyls: the relationship of taxa known by adults, larvae and neotenes. Journal of Systematic Palaeontology, 20(1), 1-30. https://doi.org/10.1080/14772019.2022.2113831
  • Schoch, R. R., & Sues, H. D. (2022). The dissorophoid temnospondyl Parioxys ferricolus from the early Permian (Cisuralian) of Texas. Journal of Paleontology, 96(4), 950-960. https://doi.org/10.1017/jpa.2022.10
  • Werneburg, R., Schneider, J. W., Štamberg, S., Legler, B., & Schoch, R. R. (2022). A new amphibamiform (Temnospondyli: Branchiosauridae) from the lower Permian of the Czech Boskovice Basin. Journal of Vertebrate Paleontology, 42(6), e2231994. https://doi.org/10.1080/02724634.2023.2231994
  • Schoch, R. R., & Werneburg, R. (2023). Adult branchiosaurid temnospondyls: the life cycle of Xerodromeus gracilis. Papers in Palaeontology, 9(4), e1513. https://doi.org/10.1002/spp2.1513
  • So, C., Pardo, J. D., & Mann, A. (2024). A new amphibamiform from the Early Permian of Texas elucidates patterns of cranial diversity among terrestrial amphibamiforms. Zoological Journal of the Linnean Society, zlae012. https://doi.org/10.1093/zoolinnean/zlae012

Methods

To test the relationships of Nanobamus macrorhinus within Dissorophoidea at large and more specifically within Amphibamiformes, we utilized the matrix of Schoch (2019), which originally included 34 taxa and 108 characters. Nanobamus could be coded for 65 of the total 108 characters (60% completeness); no postcranial characters could be coded. One coding was changed from that of Schoch (2019): for character 39 (external narial opening), we changed Georgenthalia clavinasica from 0 to 1, reflecting the ‘keyhole-shaped’ naris described by Anderson et al. (2008a) that is shared with N. macrorhinus. We performed a maximum parsimony analysis in PAUP 4.0b164 for Macintosh (Swofford, 2002) with multistate characters ordered, a heuristic search, simple stepwise addition, and Dendrysekos helogenes Steen, 1934 as the outgroup. As with Schoch (2019), changing all multistate characters to be unordered did not produce any changes to the strict consensus, so these characters were maintained as ordered in all subsequent permutations and in the supplemental data matrix. Following a reviewer’s suggestion, we also ran the analysis with random addition sequence stepwise addition (10,000 reps), which resulted in the strict consensus tree remaining the same. A bootstrap analysis with 1,000 replicates was also performed. Following Schoch (2019), three permutations with slightly reduced character sampling were performed: (1) the removal of character 17 (postparietal length); (2) the removal of character 30 (a second postparietal length character); and (3) the removal of both characters, with bootstrap analyses performed on each permutation. Schoch’s original analysis examined these permutations because of previous concerns over the independence or redundancy of these characters.

Usage notes

This matrix has been superseded by other derivates in this family of matrices and should only be reused for the express purpose of reproducing the results of Gee & Reisz (2020). Any other form of reuse risks incorporation of erroneous or outdated information. For more recent derivates, see the following:

  • Schoch, R. R., Henrici, A. C., & Hook, R. W. (2021). A new dissorophoid temnospondyl from the Allegheny Group (late Carboniferous) of five points, Mahoning County, Ohio (USA). Journal of Paleontology, 95(3), 638-651. https://doi.org/10.1017/jpa.2020.101
  • Schoch, R. R. (2022). Phylogeny of the amphibamiform temnospondyls: the relationship of taxa known by adults, larvae and neotenes. Journal of Systematic Palaeontology, 20(1), 1-30.  https://doi.org/10.1080/14772019.2022.2113831
  • Schoch, R. R., & Sues, H.-D. (2022). The dissorophoid temnospondyl Parioxys ferricolus from the early Permian (Cisuralian) of Texas. Journal of Paleontology, 96(4), 950-960. https://doi.org/10.1017/jpa.2022.10
  • Werneburg, R., Schneider, J. W., Štamberg, S., Legler, B., & Schoch, R. R. (2022). A new amphibamiform (Temnospondyli: Branchiosauridae) from the lower Permian of the Czech Boskovice Basin. Journal of Vertebrate Paleontology, 42(6), e2231994. https://doi.org/10.1080/02724634.2023.2231994
  • Schoch, R. R., & Werneburg, R. (2023). Adult branchiosaurid temnospondyls: the life cycle of Xerodromeus gracilis. Papers in Palaeontology, 9(4), e1513. https://doi.org/10.1002/spp2.1513 
  • So, C., Pardo, J. D., & Mann, A. (2024). A new amphibamiform from the Early Permian of Texas elucidates patterns of cranial diversity among terrestrial amphibamiforms. Zoological Journal of the Linnean Society, zlae012. https://doi.org/10.1093/zoolinnean/zlae012

Funding

Natural Sciences and Engineering Research Council, Award: Discovery Grant

Government of Ontario, Award: Ontario Graduate Scholarship

University of Toronto

Location

Texas
North America