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Identifying Heterogeneity in Rates of Morphological Evolution: Discrete Character Change in the Evolution of Lungfish (Sarcopterygii; Dipnoi)

ORIGINAL ARTICLE doi:10.1111/j.1558-5646.2011.01460.x IDENTIFYING HETEROGENEITY IN RATES OF MORPHOLOGICAL EVOLUTION: DISCRETE CHARACTER CHANGE IN THE EVOLUTION OF LUNGFISH (SARCOPTERYGII; DIPNOI) Graeme T. Lloyd,1,2 Steve C. Wang,3 and Stephen L. Brusatte4,5 1Department of Palaeontology, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom 2E-mail: [email protected] 3Department of Mathematics and Statistics, Swarthmore College, Swarthmore, Pennsylvania 19081 4Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024 5Department of Earth and Environmental Sciences, Columbia University, New York, New York 10025 Received February 9, 2010 Accepted August 15, 2011 Data Archived: Dryad: doi:10.5061/dryad.pg46f Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a cladogram (branches or entire clades) that are characterized by significantly high or low rates of change. These methods include a randomization approach that identifies branches with significantly high rates and likelihood ratio tests that pinpoint either branches or clades that have significantly higher or lower rates than the pooled rate of the remainder of the tree. As a test case for these methods, we analyze a discrete character dataset of lungfish, which have long been regarded as “living fossils” due to an apparent slowdown in rates since the Devonian.
MATT FRIEDMAN [email protected]

MATT FRIEDMAN [email protected] Lecturer in Palaeobiology, Deparment of Earth Sciences Tutor in Earth Sciences, St. Hugh’s College University of Oxford and Research Associate Department of Vertebrate Paleontology American Museum of Natural History EDUCATION 2003-2009 Committee on Evolutionary Ph.D., Evolutionary Biology Biology University of Chicago Chicago, Illinois 2003-2005 Committee on Evolutionary S.M., Evolutionary Biology Biology University of Chicago Chicago, Illinois 2002-2003 Department of Zoology and M.Phil., Zoology University Museum of Zoology University of Cambridge Thesis Title: “New elements of the Late Cambridge, UK Devonian lungfish Soederberghia groenlandica (Sarcopterygii: Dipnoi) 1998-2002 Department of Earth and B.S., Geological Sciences (Bio-geology) Environmental Sciences University of Rochester Rochester, NY EMPLOYMENT/INSTITUTIONAL AFFILIATIONS 2010-present Department of Paleontology Research Associate American Museum of Natural History New York, NY 2009-present Department of Earth Sciences Lecturer in Palaeobiology University of Oxford Oxford, UK 2009-present St. Hugh’s College Tutor in Earth Sciences Oxford, UK M. Friedman: curriculum vitae EMPLOYMENT/TEACHING EXPERIENCE 2012-present Department of Earth Sciences Course developer and instructor: Vertebrate University of Oxford Palaeobiology Oxford, UK 2011-present Department of Earth Sciences Course developer and instructor: Evolution University of Oxford Oxford, UK Course co-developer and instructor: Fossil Records 2010 Department of Ecology and Guest lecturer:
The Relationship Between Branchiosomatic and Pulmosomatic Indices in the African Lungfish, Protopterus Annectens of Anambra River, Nigeria

Journal of Biology and Life Science ISSN 2157-6076 2014, Vol. 5, No. 1 The Relationship between Branchiosomatic and Pulmosomatic Indices in the African Lungfish, Protopterus Annectens of Anambra River, Nigeria Anthony I. Okafor Department of Animal and Environmental Biology Abia State University, Uturu-Nigeria E-mail: [email protected] Received: November 22, 2012 Accepted: December 6, 2013 doi:10.5296/jbls.v5i1.5213 URL: http://dx.doi.org/10.5296/jbls.v5i1.5213 Abstract The relationship between Branchiosomatic indices (BSI) and Pulmosomatic indices (PSI) in various sizes of the African lungfish, Protopterus annectens procured from Anambra River was determined. There was an inverse relationship between BSI and PSI. Mean BSI exhibited highest values of between 0.90 and 0.96 in the fingerlings, then began to decrease as the fish grew until it reached minimum values of between 0.36 and 0.44 in the large sized P. annectens. Conversely, mean PSI showed minimum values of between 0.32 and 0.48 in the fingerlings, then rose to a peak of between 0.88 and 1.06 in the large sized P. annectens. The study tends to support the palaeontological evidence which states that the Amphibians evolved from some now extinct fish groups related to the lungfishes during the Devonian period. Keywords: Branchiosomatic, Pulmosomatic, Inverse relationship, Devonian period. 1. Introduction The African lungfish, Protopterus is amphibious using its gills to absorb oxygen whilst immersed in water and its lungs for absorption of atmospheric oxygen.(Okafor,2012) It inhabits shallow and swampy parts of some Rivers and Lakes of some African countries during the wet season (Giusi et al, 2011; Icardo et al, 2011,2012; Laberge and Walsh, 2011;) However, during the dry season, when the ambient water has totally dried up, Protopterus excavates a burrow in the soil where it resides in a dormant state until the end of the season.
A Redescription of the Lungfish Eoctenodus Hills 1929, with Reassessment of Other Australian Records of the Genus Dipterns Sedgwick & Murchison 1828

Ree. West. Aust. Mus. 1987, 13 (2): 297-314 A redescription of the lungfish Eoctenodus Hills 1929, with reassessment of other Australian records of the genus Dipterns Sedgwick & Murchison 1828. J.A. Long* Abstract Eoctenodus microsoma Hills 1929 (= Dipterus microsoma Hills, 1931) from the Frasnian Blue Range Formation, near Taggerty, Victoria, is found to be a valid genus, differing from Dipterus, and other dipnoans, by the shape of the parasphenoid and toothplates. The upper jaw toothp1ates and entopterygoids, parasphenoid, c1eithrum, anoc1eithrum and scales of Eoctenodus are described. Eoctenodus may represent the earliest member of the Ctenodontidae. Dipterus cf. D. digitatus. from the Late Devonian Gneudna Formation, Western Australia (Seddon, 1969), is assigned to Chirodipterus australis Miles 1977; and Dipterus sp. from the Late Devonian of Gingham Gap, New South Wales (Hills, 1936) is thought to be con generic with a dipnoan of similar age from the Hunter Siltstone, New South Wales. This form differs from Dipterus in the shape of the parasphenoid. The genus Dipterus appears to be restricted to the Middle-Upper Devonian of Europe, North America and the USSR (Laurasia). Introduction Although Hills (1929) recognised a new dipnoan, Eoctenodus microsoma, in the Late Devonian fish remains from the Blue Range Formation, near Taggerty, he later (Hills 1931) altered the generic status of this species after a study trip to Britain in which D,M.S. Watson pointed out similarities between the Australian form and the British genus Dipterus Sedgwick and Murchison 1828. Studies of the head of Dipterus by Westoll (1949) and White (1965) showed the structure of the palate and, in particular, the shape of the parasphenoid which differs from that in the Taggerty dipnoan.
A Lungfish Survivor of the End-Devonian Extinction and an Early Carboniferous Dipnoan

1 A Lungfish survivor of the end-Devonian extinction and an Early Carboniferous dipnoan 2 radiation. 3 4 Tom J. Challands1*, Timothy R. Smithson,2 Jennifer A. Clack2, Carys E. Bennett3, John E. A. 5 Marshall4, Sarah M. Wallace-Johnson5, Henrietta Hill2 6 7 1School of Geosciences, University of Edinburgh, Grant Institute, James Hutton Road, Edinburgh, 8 EH9 3FE, UK. email: [email protected]; tel: +44 (0) 131 650 4849 9 10 2University Museum of Zoology Cambridge, Downing Street, Cambridge CB2 3EJ, UK. 11 12 3Department of Geology, University of Leicester, Leicester LE1 7RH, UK. 13 14 4School of Ocean & Earth Science, University of Southampton, National Oceanography Centre, 15 European Way, University Road, Southampton, SO14 3ZH , UK. 16 17 5Sedgwick Museum, Department of Earth Sciences, University of Cambridge, Downing St., 18 Cambridge CB2 3EQ, UK 1 19 Abstract 20 21 Until recently the immediate aftermath of the Hangenberg event of the Famennian Stage (Upper 22 Devonian) was considered to have decimated sarcopterygian groups, including lungfish, with only 23 two taxa, Occludus romeri and Sagenodus spp., being unequivocally recorded from rocks of 24 Tournaisian age (Mississippian, Early Carboniferous). Recent discoveries of numerous 25 morphologically diverse lungfish tooth plates from southern Scotland and northern England indicate 26 that at least ten dipnoan taxa existed during the earliest Carboniferous. Of these taxa, only two, 27 Xylognathus and Ballgadus, preserve cranial and post-cranial skeletal elements that are yet to be 28 described. Here we present a description of the skull of a new genus and species of lungfish, 29 Limanichthys fraseri gen.
I Ecomorphological Change in Lobe-Finned Fishes (Sarcopterygii

Ecomorphological change in lobe-finned fishes (Sarcopterygii): disparity and rates by Bryan H. Juarez A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science (Ecology and Evolutionary Biology) in the University of Michigan 2015 Master’s Thesis Committee: Assistant Professor Lauren C. Sallan, University of Pennsylvania, Co-Chair Assistant Professor Daniel L. Rabosky, Co-Chair Associate Research Scientist Miriam L. Zelditch i © Bryan H. Juarez 2015 ii ACKNOWLEDGEMENTS I would like to thank the Rabosky Lab, David W. Bapst, Graeme T. Lloyd and Zerina Johanson for helpful discussions on methodology, Lauren C. Sallan, Miriam L. Zelditch and Daniel L. Rabosky for their dedicated guidance on this study and the London Natural History Museum for courteously providing me with access to specimens. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS ii LIST OF FIGURES iv LIST OF APPENDICES v ABSTRACT vi SECTION I. Introduction 1 II. Methods 4 III. Results 9 IV. Discussion 16 V. Conclusion 20 VI. Future Directions 21 APPENDICES 23 REFERENCES 62 iv LIST OF TABLES AND FIGURES TABLE/FIGURE II. Cranial PC-reduced data 6 II. Post-cranial PC-reduced data 6 III. PC1 and PC2 Cranial and Post-cranial Morphospaces 11-12 III. Cranial Disparity Through Time 13 III. Post-cranial Disparity Through Time 14 III. Cranial/Post-cranial Disparity Through Time 15 v LIST OF APPENDICES APPENDIX A. Aquatic and Semi-aquatic Lobe-fins 24 B. Species Used In Analysis 34 C. Cranial and Post-Cranial Landmarks 37 D. PC3 and PC4 Cranial and Post-cranial Morphospaces 38 E. PC1 PC2 Cranial Morphospaces 39 1-2.
The Salmon, the Lungfish (Or the Coelacanth) and the Cow: a Revival?

Zootaxa 3750 (3): 265–276 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Editorial ZOOTAXA Copyright © 2013 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3750.3.6 http://zoobank.org/urn:lsid:zoobank.org:pub:0B8E53D4-9832-4672-9180-CE979AEBDA76 The salmon, the lungfish (or the coelacanth) and the cow: a revival? FLÁVIO A. BOCKMANN1,3, MARCELO R. DE CARVALHO2 & MURILO DE CARVALHO2 1Dept. Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo. Av. dos Bandeirantes 3900, 14040-901 Ribeirão Preto, SP. Brazil. E-mail: [email protected] 2Dept. Zoologia, Instituto de Biociências, Universidade de São Paulo. R. Matão 14, Travessa 14, no. 101, 05508-900 São Paulo, SP. Brazil. E-mails: [email protected] (MRC); [email protected] (MC) 3Programa de Pós-Graduação em Biologia Comparada, FFCLRP, Universidade de São Paul. Av. dos Bandeirantes 3900, 14040-901 Ribeirão Preto, SP. Brazil. In the late 1970s, intense and sometimes acrimonious discussions between the recently established phylogeneticists/cladists and the proponents of the long-standing ‘gradistic’ school of systematics transcended specialized periodicals to reach a significantly wider audience through the journal Nature (Halstead, 1978, 1981; Gardiner et al., 1979; Halstead et al., 1979). As is well known, cladistis ‘won’ the debate by showing convincingly that mere similarity or ‘adaptive levels’ were not decisive measures to establish kinship. The essay ‘The salmon, the lungfish and the cow: a reply’ by Gardiner et al. (1979) epitomized that debate, deliberating to a wider audience the foundations of the cladistic paradigm, advocating that shared derived characters (homologies) support a sister- group relationship between the lungfish and cow exclusive of the salmon (see also Rosen et al., 1981; Forey et al., 1991).
A Primitive Megalichthyid Fish (Sarcopterygii, Tetrapodomorpha)

A primitive megalichthyid fi sh (Sarcopterygii, Tetrapodomorpha) from the Upper Devonian of Turkey and its biogeographical implications Philippe JANVIER UMR 5143 du CNRS, Département Histoire de la Terre, Muséum national d’Histoire naturelle, case postale 38, 57 rue Cuvier, F-75231 Paris cedex 05 (France) [email protected] and Department of Palaeontology, The Natural History Museum, Cromwell Road, London SW7 5BD (United Kingdom) Gaël CLÉMENT UMR 5143 du CNRS, Département Histoire de la Terre, Muséum national d’Histoire naturelle, case postale 38, 57 rue Cuvier, F-75231 Paris cedex 05 (France) [email protected] Richard CLOUTIER Département de Biologie, Université du Québec à Rimouski, 300 allée des Ursulines, Rimouski, Québec, G5L 3A1 (Canada) [email protected] Janvier P., Clément G. & Cloutier R. 2007. — A primitive megalichthyid fi sh (Sarcopterygii, Tetrapodomorpha) from the Upper Devonian of Turkey and its biogeographical implications. Geodiversitas 29 (2) : 249-268. ABSTRACT KEY WORDS Sarcopterygii, Th e vertebrate fauna of the red sandstone of Pamucak-Sapan Dere Unit of Tetrapodomorpha, the Upper Antalya Nappe (Frasnian?, Turkey) is reviewed on the basis of new Megalichthyidae, “Osteolepiformes”, material. Th e association of the phyllolepid Placolepis with the arthrodire Holo- Devonian, nema in this fauna strongly suggests a Frasnian age or, at any rate, older than Turkey, the Famennian. Th e unique osteolepiform sarcopterygian of this fauna is here biogeography, new genus, described in detail and referred to Sengoerichthys ottoman n. gen., n. sp., which new species. is considered as the most generalized megalichthyid known to date. GEODIVERSITAS • 2007 • 29 (2) © Publications Scientifi ques du Muséum national d’Histoire naturelle, Paris.
Table of Contents Introduction 5 Acknowledgments 5 Arrangement of Catalogue 6 Taxa Listed 6 Presentation of Taxa 6 Systematics O

Table of Contents Page Introduction 5 Acknowledgments 5 Arrangement of Catalogue 6 Taxa listed 6 Presentation of taxa 6 Systematics of Dipnoi 7 Depository of types 9 Catalogus 12 Class Osteichthyes 12 Subclass Sarcopterygii 12 Infraclass Dipnoiformes 12 Order Diabolepidida 12 Family Diabolepididae 12 Genus Diabolepis 12 Order Dipnoi 13 "Suborder" Dipnorhynchoidei 13 Family Uranolophidae 13 Genus Uranolophus 13 Family Dipnorhynchidae 18 Genus Dipnorhynchus 18 Genus Speonesydrion 27 ?Genus Melanognathus 31 Suborder Dipteroidei 32 Family Dipteridae 32 Genus Dipterus 32 Genus Grossipterus 71 Genus Rhinodipterus 72 Family Chirodipteridae 78 Genus Chirodipterus 78 ?Genus Conchodus 87 ?Genus Nielsenia 92 Genus Palaedaphus 92 http://d-nb.info/99340605X Family Phaneropleuridae 97 Genus Phaneropleuron 97 Genus Oervigia 104 Genus Pentlandia 105 Genus Scaumenacia 108 Family Stomiahykidae 117 Genus Stomiahykus 117 Genus A rchaeonectes 118 Family indet 119 Genus Dongshanodus 119 Genus Iranorhynchus 119 Suborder Holodontoidei 120 Family Holodontidae 120 Genus Holodipterus 120 ?Genus Devonosteus 125 ?Genus Ganorhynchus 126 Genus Sunwapta 132 Family Fleurantiidae 133 Genus Fleurantia 133 Genus Andreyevichthys 137 Genus Jarvikia 138 Family Rhynchodipteridae 140 Genus Rhynchodipterus 140 Genus Griphognathus 142 ?Genus Orlovichthys 149 Genus Soederberghia 150 "Suborder" Uronemoidei 153 Family Uronemidae , 153 Genus Ganopristodus .. 153 Family Conchopomatidae 160 Genus Conchopoma 160 Suborder Ctenodontoidei 168 Family Ctenodontidae 168 Genus Ctenodus 168
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Records of the Western Australian Museum 21: 167-201 (2002). The axial postcranial structure of Griphognathus whitei from the Upper Devonian Gogo Formation of Western Australia: comparisons with other Devonian Dipnoans K.S.W. Campbell and R.E. Barwick Geology Department, Australian National University, Canberra, 0200, Australia. e-mail [email protected]@anu.edu.au Abstract - The skeleton of the pectoral and pelvic girdles, the foremost axial region, and the scales of Griplwgnathus whitei, and the pectoral and pelvic girdles and scales of Chirodipterus australis, have been described previously. The posterior parts of the postcranial skeleton of these fishes have been commented on in passing, but new material permits a description of the centra, the neural and haemal arches and the incomplete medial fins of G. whitei. The limb skeletons have not been preserved in our material. The new material of G. whitei adds considerably to the information available on the axial skeleton and the medial fins of Devonian dipnoans. Of these dipnoans, only Dipterus has the axial skeleton without the centra well preserved, though fragments of the centra of some of the other genera are poorly preserved. The new specimens of G. whitei have well preserved centra along the full length of the body of the animal. The neural and haemal arches give the best information available on Devonian species. The medial fins are sufficiently well preserved to compare with those of Fleurantia and Scaumenacia from the Upper Devonian of Canada, and the Australian Barwickia and Howidipterus from the Givetian of Victoria. Gross differences occur between all the above genera in the structure of the medial fins.
A High Latitude Devonian Lungfish, from the Famennian of South Africa

A high latitude Devonian lungfish, from the Famennian of South Africa Robert W. Gess1,2,3,* and Alice M. Clement4,* 1 Geology Department, Rhodes University, Makhanda/Grahamstown, South Africa 2 Albany Museum, Makhanda/Grahamstown, South Africa 3 Wits University, DST-NRF Centre of Excellence in Palaeosciences (CoE-Pal), Johannesburg, South Africa 4 College of Science and Engineering, Flinders University, Adelaide, SA, Australia * These authors contributed equally to this work. ABSTRACT New fossil lungfish remains comprising two parasphenoids, tooth plates and scales from the Famennian Witpoort Formation of South Africa are described. From the parasphenoid material, which bears similarity to Oervigia and Sagenodus but is nevertheless unique, a new genus, Isityumzi mlomomde gen. et sp. nov. is erected. Tooth plates and scales from the same locality may be conspecific but are not yet assigned until further material becomes available. The tooth plates closely resemble those of some taxa in the Carboniferous genus Ctenodus. The new taxon is significant as only the second Devonian lungfish described from the African continent, and for hailing from the high-latitude (polar) Waterloo Farm environment situated close to 70 south during the Famennian. Subjects Paleontology, Taxonomy Keywords Waterloo farm, Witpoort formation, Dipnoi, Famennian, South Africa, Western Gondwana, Sarcopterygii, Palaeozoic INTRODUCTION Lungfish (Dipnoi) are a clade of sarcopterygian (lobe-finned) fishes with their origins Submitted 30 July 2019 stretching back to the Early Devonian, over 410 million years ago (Campbell & Barwick, Accepted 21 October 2019 Published 4 December 2019 1983; Chang & Yu, 1984; Denison, 1968; Wang et al., 1993). They reached a peak of diversity and abundance throughout the Devonian with close to 100 species described Corresponding author Alice M.
Graeme T. Lloyd <[email protected]>

Can palaeobiogeography explain low rates of morphological evolution in ‘living fossil’ lungfish? Graeme T. Lloyd <[email protected]> n=124 Introduction Methods and Materials A B In a classic work Westoll (1949) used a character-taxon matrix to show that Aside from the inevitable addition of new taxa and refinements to the lungfish underwent rapid morphological evolution early in their history geological timescale since 1949 there are some significant flaws in No followed by an extended period of morphological stagnation (Figure 1): a Westoll’s method: 1) the ancestor is purely hypothetical, 2) a selective Change textbook example (literally) of evolution in a ‘living fossil’. Here I update suite of taxa was used, 3) error bars (missing data) constrain Contraction 45 Westoll’s method for use with cladistic datasets and place it in its correct interpretation, 4) a stratigraphically ordered ancestor-descendant 55.5 phylogenetic context. One proposed explanation for the existence of living sequence was assumed, and 5) reversal (character loss) wasn’t taken into fossils is geographic isolation in refugia, where lack of competition negates account. Although modern cladistic matrices are more inclusive and more Expansion the need for morphological change. Here this hypothesis is tested by often contain a real outgroup (answering points 1 and 2 above) missing 23.5 C comparing lungfish dispersal patterns during their rapid Devonian phase data is still a major issue. To overcome this the internal nodes (rather than with their slower post-Devonian phase of evolution. the taxa themselves) were scored as these are complete under a given phylogenetic hypothesis.