Journal Article
An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)
Gierl, C., Dohrmann, M., Keith, P., Humphreys, W.J., Esmaeili, H.R., Vukić, J., Radek, S. and ReichenbacherI, B.
Record Number:
5885
Year:
2022
Journal:
PLoS ONE 17(7): e0271121.
Pages:
1-29
Volume:
17(7):e0271121
Notes:
This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited
Abstract:
The suborder Gobioidei is among the most diverse groups of vertebrates, comprising about
2310 species. In the fossil record gobioids date back to the early Eocene (c. 50 m.y. ago),
and a considerable increase in numbers of described species is evident since the middle
Miocene (c. 16 m.y. ago). About 40 skeleton-based gobioid species and > 100 otolith-based
species have been described until to date. However, assignment of a fossil gobioid species
to specific families has often remained tentative, even if well preserved complete specimens
are available. The reasons are that synapomorphies that can be recognized in a fossil skele-
ton are rare (or absent) and that no phylogenetic framework applicable to gobioid fossils
exists. Here we aim to overcome this problem by developing a phylogenetic total evidence
framework that is suitable to place a fossil skeleton-based gobioid at family level. Using both
literature and newly collected data we assembled a morphological character matrix (48
characters) for 29 extant species, representing all extant gobioid families, and ten fossil
gobioid species, and we compiled a multi-gene concatenated alignment (supermatrix; 6271
bp) of published molecular sequence data for the extant species. Bayesian and Maximum
Parsimony analyses revealed that our selection of extant species was sufficient to achieve a
molecular ‘backbone’ that fully conforms to previous molecular work. Our data revealed that
inclusion of all fossil species simultaneously produced very poorly resolved trees, even for
some extant taxa. In contrast, addition of a single fossil species to the total evidence data
set of the extant species provided new insight in its possible placement at family level, espe-
cially in a Bayesian framework. Five out of the ten fossil species were recovered in the same
family as had been suggested in previous works based on comparative morphology. The
remaining five fossil species had hitherto been left as family incertae sedis. Now, based on
our phylogenetic framework, new and mostly well supported hypotheses to which clades
they could belong can be presented. We conclude that the total evidence framework presented here will be beneficial for all future work dealing with the phylogenetic placement
of a fossil skeleton-based gobioid and thus will help to improve our understanding of the evo-
lutionary history of these fascinating fishes. Moreover, our data highlight that increased
sampling of fossil taxa in a total-evidence context is not universally beneficial, as might be
expected, but strongly depends on the study group and peculiarities of the morphological
data
Times Cited:
5
Relevent Species:
Related Records:
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Samonds K.E., Godfrey L.R., Ali J.R., Goodman S.M., Vences M., Sutherland, M.R. Irwin, M.T. and Krause, D.W. (2013)Imperfect isolation: Factors and filters shaping Madagascar’s extant vertebrate fauna
Humphreys, G., Alexander, J., Harvey, M.S. and Humphreys, W.F. (2013)The subterranean fauna of Barrow Island, northwestern Australia: 10 years on
Tornabene, L., Chen, Y.G. and Pezold, F. (2013)Gobies are deeply divided: phylogenetic evidence from nuclear DNA (Teleostei: Gobioidei: Gobiidae)
Unmack, P.J. (2013)Biogeography
Unmack, P.J. (2013)Biogeography
Tornabene, L., Chen, Y.G. and Pezold, F. (2013)Gobies are deeply divided: phylogenetic evidence from nuclear DNA (Teleostei: Gobioidei: Gobiidae)
Halse, S., Scanlon, M., Cocking, J., Barron, H., Richardson, J. and Eberhard, S. (2014)Pilbara stygofauna: deep groundwater of an arid landscape contains globally significant radiation of biodiversity
Morgan, D.L., Unmack, P.J., Beatty, S.J., Ebner, B.C., Allen, M.G., Keleher, J., Donaldson, J.A. and Murphy, J. (2014)An overview of the 'freshwater fishes' of Western Australia
Morgan, D.L., Unmack, P.J., Beatty, S.J., Ebner, B.C., Allen, M.G., Keleher, J., Donaldson, J.A. and Murphy, J. (2014)An overview of the 'freshwater fishes' of Western Australia
Halse, S., Scanlon, M., Cocking, J., Barron, H., Richardson, J. and Eberhard, S. (2014)Pilbara stygofauna: deep groundwater of an arid landscape contains globally significant radiation of biodiversity
Dworak, L., Rasoloariniaina, J.R., Raminosoa, N. and Englert, A. (2015)Hydrogéologie dans le sud-ouest de Madagascar.
Dworak, L., Rasoloariniaina, J.R., Raminosoa, N. and Englert, A. (2015)Hydrogéologie dans le sud-ouest de Madagascar.
Dworak, L., Rasoloariniaina, J.R., Raminosoa, N. and Englert, A. (2015)Hydrogéologie dans le sud-ouest de Madagascar.
Bishop, R.E., Humphreys, W.F., Cukrov, N., Zic, V., Boxshall, G.A., Cukrov, M., Iliffe, T.M., Krsinic, F., Moore, W.S., Pohlman, J.W., and Sket, B. (2015)‘Anchialine’ redefined as a subterranean estuary in a crevicular or cavernous geological setting
Bishop, R.E., Humphreys, W.F., Cukrov, N., Zic, V., Boxshall, G.A., Cukrov, M., Iliffe, T.M., Krsinic, F., Moore, W.S., Pohlman, J.W., and Sket, B. (2015)‘Anchialine’ redefined as a subterranean estuary in a crevicular or cavernous geological setting
Rasoloariniaina, J.R., Ganzhorn, J.U., Riemann, J.C. and Raminosoa, N. (2016)Water quality and biotic interaction of two cavefish species: Typhleotris madagascariensis Petit, 1933 and Typhleotris maraybe Sparks and Chakrabarty, 2012, in the Mahafaly Plateau groundwater syste, Madagascar
Rasoloariniaina, J.R., Ganzhorn, J.U., Riemann, J.C. and Raminosoa, N. (2016)Water quality and biotic interaction of two cavefish species: Typhleotris madagascariensis Petit, 1933 and Typhleotris maraybe Sparks and Chakrabarty, 2012, in the Mahafaly Plateau groundwater syste, Madagascar
Rasoloariniaina, J.R., Ganzhorn, J.U., Riemann, J.C. and Raminosoa, N. (2016)Water quality and biotic interaction of two cavefish species: Typhleotris madagascariensis Petit, 1933 and Typhleotris maraybe Sparks and Chakrabarty, 2012, in the Mahafaly Plateau groundwater syste, Madagascar
Rasoloariniaina, J.R., Ganzhorn, J.U., Riemann, J.C. and Raminosoa, N. (2016)Water quality and biotic interaction of two cavefish species: Typhleotris madagascariensis Petit, 1933 and Typhleotris maraybe Sparks and Chakrabarty, 2012, in the Mahafaly Plateau groundwater syste, Madagascar
Humphreys, W. F. (2017)Australasian subterranean biodiversity
Laumanns, M. (2017)Atlas of the great caves and the karst of Africa. Part 1. Introduction and Algeria to Madagascar
Laumanns, M. (2017)Atlas of the great caves and the karst of Africa. Part 1. Introduction and Algeria to Madagascar
Laumanns, M. (2017)Atlas of the great caves and the karst of Africa. Part 1. Introduction and Algeria to Madagascar
Humphreys, W. F. (2017)Australasian subterranean biodiversity
Page, T.J.,Stevens, M.I., Adams, M., Foster, R. Velasco-Castrillón, A. and Humphreys, W.F. (2018)Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)
Perina, G., Camacho, A.I., Huey, J., Horwitz, P., and Koenders, A. (2018)Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach
Perina, G., Camacho, A.I., Huey, J., Horwitz, P., and Koenders, A. (2018)Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach
Fricke, R.,Mahafina, J.J., Behivoke, F., Jaonalison, H. Leopold, M. and Ponton, D. (2018)Annotated checklist of the fishes of Madagascar, southwestern Indian Ocean, with 158 new records
Fricke, R.,Mahafina, J.J., Behivoke, F., Jaonalison, H. Leopold, M. and Ponton, D. (2018)Annotated checklist of the fishes of Madagascar, southwestern Indian Ocean, with 158 new records
Fricke, R.,Mahafina, J.J., Behivoke, F., Jaonalison, H. Leopold, M. and Ponton, D. (2018)Annotated checklist of the fishes of Madagascar, southwestern Indian Ocean, with 158 new records
Moore, G.I. (2018)New morphological data and live photographs of the rare subterranean blind cave eel Ophisternon candidum (Synbranchidae) from north‑western Australia
Moore, G.I., Humphreys, W.F. and Foster, R. (2018)New populations of the rare subterranean Blind Cave Eel Ophisternon candidum (Synbranchidae) reveal recent historical connections throughout northwestern Australia
Moore, G.I. (2018)New morphological data and live photographs of the rare subterranean blind cave eel Ophisternon candidum (Synbranchidae) from north‑western Australia
Moore, G.I., Humphreys, W.F. and Foster, R. (2018)New populations of the rare subterranean Blind Cave Eel Ophisternon candidum (Synbranchidae) reveal recent historical connections throughout northwestern Australia
Kuang, T., Tornabene, L., Lia, J., Jiang, J., Chakrabarty, P., Sparks, J.S., Naylor, G.J.P. and Lia, C. (2018)Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
Kuang, T., Tornabene, L., Lia, J., Jiang, J., Chakrabarty, P., Sparks, J.S., Naylor, G.J.P. and Lia, C. (2018)Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
Kuang, T., Tornabene, L., Lia, J., Jiang, J., Chakrabarty, P., Sparks, J.S., Naylor, G.J.P. and Lia, C. (2018)Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
Vences, M., Rasoloariniaina, J.R. and Riemann, J.C. (2018)A preliminary assessment of genetic divergence and distribution of Malagasy cave fish in the genus Typhleotris (Teleostei: Milyeringidae)
Page, T.J., Hughes, J.M., Real, K.M., Stevens, M.I., King, R.A. and Humphreys, W.F. (2018)Allegory of a cave crustacean: systematic and biogeographic reality of Halosbaena (Peracarida: Thermosbaenacea) sought with molecular data at multiple scales
Kuang, T., Tornabene, L., Lia, J., Jiang, J., Chakrabarty, P., Sparks, J.S., Naylor, G.J.P. and Lia, C. (2018)Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
Vences, M., Rasoloariniaina, J.R. and Riemann, J.C. (2018)A preliminary assessment of genetic divergence and distribution of Malagasy cave fish in the genus Typhleotris (Teleostei: Milyeringidae)
Page, T.J., Hughes, J.M., Real, K.M., Stevens, M.I., King, R.A. and Humphreys, W.F. (2018)Allegory of a cave crustacean: systematic and biogeographic reality of Halosbaena (Peracarida: Thermosbaenacea) sought with molecular data at multiple scales
Vences, M., Rasoloariniaina, J.R. and Riemann, J.C. (2018)A preliminary assessment of genetic divergence and distribution of Malagasy cave fish in the genus Typhleotris (Teleostei: Milyeringidae)
Halse, S. (2018)Subterranean fauna of the arid zone
Halse, S. (2018)Subterranean fauna of the arid zone
Page, T.J.,Stevens, M.I., Adams, M., Foster, R. Velasco-Castrillón, A. and Humphreys, W.F. (2018)Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)
Matthews, E.F., Abrams, K.M., Cooper, S.J.B., Huey, J.A., Hillyer, M.J., Humphreys, W.F., Austin, A.D. and Guzik, M.T. (2019)Scratching the surface of subterranean biodiversity: molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia
Matthews, E.F., Abrams, K.M., Cooper, S.J.B., Huey, J.A., Hillyer, M.J., Humphreys, W.F., Austin, A.D. and Guzik, M.T. (2019)Scratching the surface of subterranean biodiversity: molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia
Perina, G. (2019)Ancient origins of a diverse stygofaunal group: The Australian Bathynellidae (Crustacea)
Perina, G. (2019)Ancient origins of a diverse stygofaunal group: The Australian Bathynellidae (Crustacea)
Moore, G. (2019)Milyeringa justitia. Barrow Island cave gudgeon. The IUCN Red List of Threatened Species 2019: e.T128969918A128970120
Perina, G., Camacho, A.I., Huey, J., Horwitz, P. and Koenders, A. (2019)New Bathynellidae (Crustacea) taxa and their relationships in the Fortescue catchment aquifers of the Pilbara region, Western Australia, Systematics and Biodiversity
Perina, G., Camacho, A.I., Huey, J., Horwitz, P. and Koenders, A. (2019)New Bathynellidae (Crustacea) taxa and their relationships in the Fortescue catchment aquifers of the Pilbara region, Western Australia, Systematics and Biodiversity
Perina, G., Camacho, A., Huey, J., Horwitz, P. and Koenders, A. (2019)The role of allopatric speciation and ancient origins of Bathynellidae (Crustacea) in the Pilbara (Western Australia): two new genera from the De Grey River catchment
Perina, G., Camacho, A., Huey, J., Horwitz, P. and Koenders, A. (2019)The role of allopatric speciation and ancient origins of Bathynellidae (Crustacea) in the Pilbara (Western Australia): two new genera from the De Grey River catchment
Lintermans, M., Geyle, H.M., Beatty, S., Brown, C., Ebner, B.C., Freeman, R., Hammer, M.P., Humphreys, W.F., Kennard, M.J., Kern, P., Martin, K., Morgan, D.L., Raadik, T.A., Unmack, P.J., Wager, R., Woinarski, J.C.Z. and Garnett, S.T. (2020)Big trouble for little fish: identifying Australian freshwater fishes in imminent risk of extinction
Lintermans, M., Geyle, H.M., Beatty, S., Brown, C., Ebner, B.C., Freeman, R., Hammer, M.P., Humphreys, W.F., Kennard, M.J., Kern, P., Martin, K., Morgan, D.L., Raadik, T.A., Unmack, P.J., Wager, R., Woinarski, J.C.Z. and Garnett, S.T. (2020)Big trouble for little fish: identifying Australian freshwater fishes in imminent risk of extinction
White, N.E., Guzik, M.T., Austin, A.D., Moore, G.I. Humphreys, W.F., Alexander, J. and Bunce, M. (2020)Detection of rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments
White, N.E., Guzik, M.T., Austin, A.D., Moore, G.I. Humphreys, W.F., Alexander, J. and Bunce, M. (2020)Detection of rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments
Shelley, J.J., Swearer, S.E., Dempster, T., Adams, M., Le Feuvre, M.C., Hammer, M.P. and Unmack, P.J. (2020)Plio-Pleistocene sea-level changes drive speciation of freshwater fishes in north-western Australia
Shelley, J.J., Swearer, S.E., Dempster, T., Adams, M., Le Feuvre, M.C., Hammer, M.P. and Unmack, P.J. (2020)Plio-Pleistocene sea-level changes drive speciation of freshwater fishes in north-western Australia
Eberhard, S.M. and Howarth, F.G. (2021)Undara lava cave fauna in tropical Queensland with an annotated list of Australian subterranean biodiversity hotspots
Eberhard, S.M. and Howarth, F.G. (2021)Undara lava cave fauna in tropical Queensland with an annotated list of Australian subterranean biodiversity hotspots
Saccò, M., Blyth, A.J., Douglas, G., Humphreys, W.F., Hose, G.C., Davis, J., Guzik, M.T., Martínez, A., Eberhard, S.M. and Halse, S.A. (2022)Stygofaunal diversity and ecological sustainability of coastal groundwater ecosystems in a changing climate: The Australian paradigm
Saccò, M., Blyth, A.J., Douglas, G., Humphreys, W.F., Hose, G.C., Davis, J., Guzik, M.T., Martínez, A., Eberhard, S.M. and Halse, S.A. (2022)Stygofaunal diversity and ecological sustainability of coastal groundwater ecosystems in a changing climate: The Australian paradigm
Gierl, C., Dohrmann, M., Keith, P., Humphreys, W.J., Esmaeili, H.R., Vukić, J., Radek, S. and ReichenbacherI, B. (2022)An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)
Gierl, C., Dohrmann, M., Keith, P., Humphreys, W.J., Esmaeili, H.R., Vukić, J., Radek, S. and ReichenbacherI, B. (2022)An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)
Gierl, C., Dohrmann, M., Keith, P., Humphreys, W.J., Esmaeili, H.R., Vukić, J., Radek, S. and ReichenbacherI, B. (2022)An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)
Gierl, C., Dohrmann, M., Keith, P., Humphreys, W.J., Esmaeili, H.R., Vukić, J., Radek, S. and ReichenbacherI, B. (2022)An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)
Gierl, C., Dohrmann, M., Keith, P., Humphreys, W.J., Esmaeili, H.R., Vukić, J., Radek, S. and ReichenbacherI, B. (2022)An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)
Sparks, J.S. and Chakrabarty, P. (2022)Milyeringidae: Typhleotris
Sparks, J.S. and Chakrabarty, P. (2022)Milyeringidae: Typhleotris
Sparks, J.S. and Chakrabarty, P. (2022)Milyeringidae: Typhleotris
Saccò, M., Guzik, M.T., van der Heyde, M., Nevill, P., Cooper, S.J.B., Austin, A.D., Coates, P.J. and Allentoft, M.E. (2022)eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects
Saccò, M., Guzik, M.T., van der Heyde, M., Nevill, P., Cooper, S.J.B., Austin, A.D., Coates, P.J. and Allentoft, M.E. (2022)eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects
van der Heyde, M., Alexander, J., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Rapid detection of subterranean fauna from passive sampling of groundwater eDNA
van der Heyde, M., White, N.E., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater
van der Heyde, M., White, N.E., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater
Thacker, C.E., McCraney, W.T., Harrington, R.C., Near, T.J., Shelley, J.J., Adams, M., Hammer, M.P. and Unmack, P.J. (2023)Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families
Thacker, C.E., McCraney, W.T., Harrington, R.C., Near, T.J., Shelley, J.J., Adams, M., Hammer, M.P. and Unmack, P.J. (2023)Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families
Thacker, C.E., McCraney, W.T., Harrington, R.C., Near, T.J., Shelley, J.J., Adams, M., Hammer, M.P. and Unmack, P.J. (2023)Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families
Thacker, C.E., McCraney, W.T., Harrington, R.C., Near, T.J., Shelley, J.J., Adams, M., Hammer, M.P. and Unmack, P.J. (2023)Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families
Thacker, C.E., McCraney, W.T., Harrington, R.C., Near, T.J., Shelley, J.J., Adams, M., Hammer, M.P. and Unmack, P.J. (2023)Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families
Webb, J.A., White, S.Q. and Smith, G.K. (2023)Australian caves and karst systems
Webb, J.A., White, S.Q. and Smith, G.K. (2023)Australian caves and karst systems
White, S.Q., Brooks, D. and Webb, J.A. (2023)Cape Range
White, S.Q., Brooks, D. and Webb, J.A. (2023)Cape Range
van der Heyde, M., Alexander, J., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T. (2023)Rapid detection of subterranean fauna from passive sampling of groundwater eDNA