taxonID	type	format	identifier	references	title	description	created	creator	contributor	publisher	audience	source	license	rightsHolder	datasetID
4F15D51915034567FD067555FC5BFF56.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/13350305/files/figure.png	https://doi.org/10.5281/zenodo.13350305	FIGURE 5 | Optimal cladogram resulting from the partitioned-likelihood analysis of the Sanger and UCE dataset of the family-level 57 taxa and 279.979 nucleotide characters. Clades with ≥95% bootstrap support are identified with a black circle, clades with 70–94% bootstrap support are identified with a gray circle, and clades with ≥50–69% bootstrap support are identified with a white circle.	FIGURE 5 | Optimal cladogram resulting from the partitioned-likelihood analysis of the Sanger and UCE dataset of the family-level 57 taxa and 279.979 nucleotide characters. Clades with ≥95% bootstrap support are identified with a black circle, clades with 70–94% bootstrap support are identified with a gray circle, and clades with ≥50–69% bootstrap support are identified with a white circle.	2022-09-12	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.		Zenodo	biologists	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.			
4F15D51915034567FD067555FC5BFF56.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/13350299/files/figure.png	https://doi.org/10.5281/zenodo.13350299	FIGURE 2 | Hypotheses of relationships among the Acropomatiformes based on the following studies: Smith, Wheeler (2006); Smith, Craig (2007); Betancur-R et al. (2013b); Near et al. (2013, 2015); Thacker et al. (2015); Davis et al. (2016); Mirande (2016); Sanciangco et al. (2016); Ghedotti et al. (2018); Rabosky et al. (2018); Satoh (2018). The asterisk in Mirande refers to the polyphyly of Malakichthyidae, where some members of the family were resolved outside of the Acropomatiformes.	FIGURE 2 | Hypotheses of relationships among the Acropomatiformes based on the following studies: Smith, Wheeler (2006); Smith, Craig (2007); Betancur-R et al. (2013b); Near et al. (2013, 2015); Thacker et al. (2015); Davis et al. (2016); Mirande (2016); Sanciangco et al. (2016); Ghedotti et al. (2018); Rabosky et al. (2018); Satoh (2018). The asterisk in Mirande refers to the polyphyly of Malakichthyidae, where some members of the family were resolved outside of the Acropomatiformes.	2022-09-12	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.		Zenodo	biologists	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.			
4F15D51915034567FD067555FC5BFF56.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/13350301/files/figure.png	https://doi.org/10.5281/zenodo.13350301	FIGURE 3 | Optimal cladogram resulting from the partitioned-likelihood analysis of the Sanger and UCE dataset of the 54 core taxa and 279.979 nucleotide characters. Clades with ≥95% bootstrap support are identified with a black circle, clades with 70–94% bootstrap support are identified with a gray circle, and clades with ≥50–69% bootstrap support are identified with a white circle.	FIGURE 3 | Optimal cladogram resulting from the partitioned-likelihood analysis of the Sanger and UCE dataset of the 54 core taxa and 279.979 nucleotide characters. Clades with ≥95% bootstrap support are identified with a black circle, clades with 70–94% bootstrap support are identified with a gray circle, and clades with ≥50–69% bootstrap support are identified with a white circle.	2022-09-12	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.		Zenodo	biologists	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.			
4F15D51915034567FD067555FC5BFF56.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/13350303/files/figure.png	https://doi.org/10.5281/zenodo.13350303	FIGURE 4 | Optimal cladogram resulting from the species-tree analysis of the Sanger and UCE dataset composed of the 54 core taxa and 466 loci. Clades with ≥95% LPP support are identified with a black circle, clades with 70–94% LPP support are identified with a gray circle, and clades with ≥50–69% LPP support are identified with a white circle.	FIGURE 4 | Optimal cladogram resulting from the species-tree analysis of the Sanger and UCE dataset composed of the 54 core taxa and 466 loci. Clades with ≥95% LPP support are identified with a black circle, clades with 70–94% LPP support are identified with a gray circle, and clades with ≥50–69% LPP support are identified with a white circle.	2022-09-12	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.		Zenodo	biologists	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.			
4F15D51915034567FD067555FC5BFF56.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/13350311/files/figure.png	https://doi.org/10.5281/zenodo.13350311	FIGURE 6 | Simplified 57-taxon maximum-likelihood phylogeny of major acropomatiform clades with the maximum-likelihood optimization of depth illustrated as pie charts on the nodes (black: fishes that live in the deep sea; white: fishes that exclusively live in shallow water) and of bioluminescence on the branches (blue: clade includes bioluminescent fishes; black: clade does not include bioluminescent fishes). The depth ranges of the different acropomatiform clades (standard deviation from the mean) are plotted in gray and the depth mean values are represented by the colored silhouettes (blue: families with bioluminescent fishes; pink non-bioluminescent families).	FIGURE 6 | Simplified 57-taxon maximum-likelihood phylogeny of major acropomatiform clades with the maximum-likelihood optimization of depth illustrated as pie charts on the nodes (black: fishes that live in the deep sea; white: fishes that exclusively live in shallow water) and of bioluminescence on the branches (blue: clade includes bioluminescent fishes; black: clade does not include bioluminescent fishes). The depth ranges of the different acropomatiform clades (standard deviation from the mean) are plotted in gray and the depth mean values are represented by the colored silhouettes (blue: families with bioluminescent fishes; pink non-bioluminescent families).	2022-09-12	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.		Zenodo	biologists	Smith, W. Leo;Ghedotti, Michael J.;Domínguez-Domínguez, Omar;McMahan, Caleb D.;Espinoza, Eduardo;Martin, Rene P.;Girard, Matthew G.;Davis, Matthew P.			
