Palaeomorphology: fossils and the inference of cladistic relationships

Edgecombe, G.D. 2010. Palaeomorphology: fossils and the inference of cladistic relationships. —Acta Zoologica (Stockholm) 91 : 72–80 Twenty years have passed since it was empirically demonstrated that inclusion of extinct taxa could overturn a phylogenetic hypothesis formulated upon extant taxa alone, challenging Colin Patterson’s bold conjecture that this phenomenon ‘may be non‐existent’. Suppositions and misconceptions about missing data, often couched in terms of ‘wildcard taxa’ and ‘the missing data problem’, continue to cloud the literature on the topic of fossils and phylogenetics. Comparisons of real data sets show that no a priori (or indeed a posteriori) decisions can be made about amounts of missing data and most properties of cladograms, and both simulated and real data sets demonstrate that even highly incomplete taxa can impact on relationships. The exclusion of fossils from phylogenetic analyses is neither theoretically nor empirically defensible.     

Cranial anatomy and phylogenetic position of Suminia getmanovi, a basal anomodont (Amniota: Therapsida) from the Late Permian of Eastern Europe

Suminia getmanovi , a recently discovered basal anomodont from the Late Permian of Russia, is characterized by robust, 'leaf-shaped' teeth, and a masticatory architecture that is similar to that of the highly diverse and cosmopolitan group of Permo-Triassic herbivores, Dicynodontia (Anomodontia). Based on new material, the skull is reconstructed in three dimensions and described in detail. A cladistic analysis of the basal anomodonts, Patranomodon, Galeops, Otsheria, Ulemica , and Suminia , using 37 cranial characters, resulted in a single most parsimonious tree, in which Suminia is united with the Russian taxa, Ulemica and Otsheria. This clade, diagnosed by four unambiguous characters, is designated as Venyukovioidea. The South African anomodont, Galeops , appears as the sister taxon to Dicynodontia. Patranomodon is the most basal anomodont. The cladistic analysis suggests that a 'dicynodont-type' masticatory architecture, with an expanded adductor musculature and sliding jaw articulation, may have originated prior to the advent of the (Venyukovioidea + ( Galeops + Dicynodontia)) clade.     

Reconsidering the status and affinities of the ornithischian dinosaur Tatisaurus oehleri Simmons, 1965

The early Mesozoic fossil fauna collected from the Lower Lufeng Formation of Yunnan Province, China, has attracted considerable interest and attention since its discovery in the late 1930s. Its importance reflected a combination of its comparatively remote geographical position and, more particularly, the similarities of its fauna compared with approximately contemporary discoveries from Europe, North and South America, and southern Africa. The fragmentary and poorly preserved Lufeng ornithischian dinosaur Tatisaurus oehleri was described in 1965 and proved taxonomically and systematically enigmatic from the start. Originally assigned, with some noted ambivalence, to the basal ('primitive') group of ornithischians known as hypsilophodontids, since 1965 Tatisaurus has been variously ignored, assigned to a more rigorously defined Hypsilophodontidae, referred to both of the armoured (thyreophoran) ornithischian dinosaur clades (Stegosauria and Ankylosauria), or referred to a more basal position within the thyreophoran lineage. In 1996 the holotype of Tatisaurus was renamed Scelidosaurus oehleri , and the genus Scelidosaurus was proposed as an index fossil of the ' Scelidosaurus biochron' with the potential to be used for the global stratigraphic correlation of Early Jurassic (early Sinemurian) rocks. Because of this chequered history Tatisaurus oehleri Simmons, 1965 has been re-examined and is redescribed so that its taxonomic status and systematic position could be reassessed. Tatisaurus is identified as a basal thyreophoran (armoured ornithischian dinosaur); there is no basis for amalgamating it in synonymy with the genus Scelidosaurus , and the proposed creation of a ' Scelidosaurus biochron' for the purposes of biostratigraphic correlation of Lower Jurassic outcrops has no utility whatever. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 865–874.     

Skeletal ultrastructure and phylogeny of cyclostome bryozoans

Recent research on the ultrastructure of the calcareous skeleton in the bryozoan order Cyclostomata is summarized and updated, based on field emission SEM studies of 87 species. Six fundamental ultrastructural fabrics are recognized which differ in the crystallographic orientations, shapes and prevailing growth directions of the constituent crystallites. During the growth of individual walls a succession of fabrics is secreted, defining a fabric suite. Five fabric suites are described in interior walls and four in exterior walls. Nine ultrastructural characters were combined with 37 other skeletal characters in a PAUP analysis of the relationships between 28 post-Palaeozoic cyclostomes chosen to include representatives of all suborders. A single tree of length 142 steps was found. Comparison of tree statistics for three categories of characters showed ultrastructural characters to be more homoplastic than zooidal characters, and the latter more homoplastic than colonial characters. Rooting the tree on the paleotubuliporine Cuffeyella gave four transitions from fixed- to free-walled organization and no reversals. With respect to the five extant suborders of cyclostomes, this first, preliminary analysis implies that Rectangulata and Cancellata are monophyletic groups, whereas Articulata are diphyletic, and both Tubuliporina and Cerioporina paraphyletic.     

The phylogenetic relationships of sauropod dinosaurs

A data-matrix of 205 osteological characters for 26 sauropod taxa is subjected to cladistic analysis. Two most parsimonious trees are produced, differing only in the relationships between Euhelopus, Omeisaurus and Mamenchisaurus. The monophyly of the Euhelopodidae (including Shunosaurus) is supported by seven synapomorphies. The Cetiosauridae (Patagosaurus, Cetiosaurus and Haplocanthosaurus) is paraphyletic with respect to the Neosauropoda. The latter clade divides into two major radiations–the ‘Brachiosauria’ (Camarasaurus, brachiosaurids and titanosauroids), and the Diplodocoidea (nemegtosaurids, dicraeosaurids, diplodocids and Rebbachisaurus). Further evidence for the inclusion of Opisthocoelwaudia in the Titanosauroidea is presented. Phuwiangosaurus, a problematic sauropod from Thailand, may represent one of the most plesiomorphic titanosauroids. ‘Peg’-like teeth have evolved at least twice within the Sauropoda. The postspinal lamina, on the neural spines of middle and caudal dorsal vertebrae, represents a neomorph rather than a fusion of pre-existing structures. Forked chevrons may have evolved convergently in the Euhelopodidae and the diplodocid-dicraeosaurid clade, or they may have been acquired early in sauropod evolution and subsequently lost in the ‘Brachiosauria’. The strengths and weaknesses of the data-matrix and tree topologies are explored using bootstrapping, decay analysis and randomization tests. Several nodes are only poorly supported, but this seems to reflect the large proportion of missing data in the matrix (～46%), rather than an abnormally high level of homoplasy. The results of the randomization tests indicate that the ‘data-matrix’ probably contains a strong phylogenetic ‘signal’. The relationships of some forms, such as Haplocanthosaurus, are influenced by the inclusion or exclusion of certain taxa with unusual combinations of character states. Such a result suggests that there are dangers inherent in the view that ‘higher’ level sauropod phylogeny can be accurately reconstructed using only a small number of well-known taxa.     

The phylogeny and taxonomy of Hippopotamidae (Mammalia: Artiodactyla): a review based on morphology and cladistic analysis

The phylogeny and taxonomy of the whole family Hippopotamidae is in need of reconsideration, the present confusion obstructing palaeoecology and palaeobiogeography studies of these Neogene mammals. The revision of the Hippopotamidae initiated here deals with the last 8 Myr of African and Asian species. The first thorough cladistic analysis of the family is presented here. The outcome of this analysis, including 37 morphological characters coded for 15 extant and fossil taxa, as well as non-coded features of mandibular morphology, was used to reconstruct broad outlines of hippo phylogeny. Distinct lineages within the paraphyletic genus Hexaprotodon are recognized and characterized. In order to harmonize taxonomy and phylogeny, two new genera are created. The genus name Choeropsis is re-validated for the extant Liberian hippo. The nomen Hexaprotodon is restricted to the fossil lineage mostly known in Asia, but also including at least one African species. The genus Hippopotamus is confirmed. These changes represent substantial advances for understanding the evolutionary history of the Hippopotamidae, and provide a new framework for future studies.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 1–26.     

Killer sperm whale: a new basal physeteroid (Mammalia, Cetacea) from the Late Miocene of Italy

Zygophyseter varolai , a new genus and species of Physeteroidea (Cetacea, Odontoceti), is based on an almost complete skeleton from the Late Miocene (Tortonian) in southern Italy. The extreme elongation of the zygomatic process of the squamosal and the circular supracranial basin (probably for housing the spermaceti organ) delimited by a peculiar anterior projection of the supraorbital process of the right maxilla are the most distinctive features of this bizarre sperm whale. Large body size, large teeth present in both lower and upper jaw, and anteroposteriorly elongated temporal fossa and zygomatic process of the squamosal indicate that this cetacean (for which we suggest the English common name killer sperm whale) was an active predator adapted to feeding on large prey, similarly to the extant killer whale ( Orcinus orca ). A phylogenetic analysis reveals that Zygophyseter belongs to a Middle–Late Miocene clade of basal physeteroids, together with Naganocetus (new genus for the type of ' Scaldicetus ' shigensis ). Moreover, the phylogenetic analysis shows evidence of a wide physeteroid radiation during the Miocene and that the extant Physeter and Kogia belong to two distinct families that form a clade representing the crown-group Physeteroidea.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 103–131.     

Revision and cladistic analysis of Isoctenus and description of a new neotropical genus (Araneae,Ctenidae, Cteninae)

A cladistic analysis was applied to test the monophyly of the genus Isoctenus. The data matrix comprised 28 taxa scored for 53 morphological and two behavioural characters. The analysis resulted in two equally parsimonious trees of 89 steps. The strict consensus was used to discuss the relationships of Isoctenus and related Cteninae genera. Ctenopsis Schmidt is synonymized with Isoctenus. Isoctenus foliifer Bertkau, I. strandi Mello‐Leitão, I. eupalaestrus Mello‐Leitão, I. janeirus (Walckenaer), I. coxalis (Pickard‐Cambridge), I. corymbus Polotow, Brescovit & Pellegatti‐Franco and I. malabaris Polotow, Brescovit & Ott are maintained in Isoctenus. Four species currently included in Ctenus are transferred to Isoctenus: I. griseolus (Mello‐Leitão) comb. nov., I. taperae (Mello‐Leitão) comb. nov., I. herteli (Mello‐Leitão) comb. nov. and I. minusculus (Keyserling) comb. nov. The following specific names are synonymized: Ctenus sanguineus Walckenaer, C. semiornatus Mello‐Leitão and Ctenopsis stellata Schmidt with Isoctenus janeirus (Walckenaer), Ctenus mourei Mello‐Leitão with Isoctenus herteli (Mello‐Leitão) and Ctenus pauper Mello‐Leitão with Isoctenus strandi Mello‐Leitão. Isoctenus sigma Schenkel, described from French Guiana, is transferred to Ctenus. Four species are newly described: Isoctenus areia sp. nov. from Paraíba, Brazil, I. charada sp. nov. and I. segredo sp. nov. from Paraná, Brazil, and I. ordinario sp. nov. from south and south‐eastern Brazil and north‐eastern Argentina. Isoctenus latevittatus Caporiacco is considered species inquirenda. Parabatinga gen. nov. is proposed to include Ctenus brevipes Keyserling. The following synonymies are established: Ctenus taeniatus Keyserling, C. tatarandensis Tullgren, C. anisitsi Strand, C. atrivulvus Strand, C. mentor Strand, C. brevipes brevilabris Strand, Isoctenus masculus Mello‐Leitão and Ctenus birabeni Mello‐Leitão with Parabatinga brevipes (Keyserling) comb. nov. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 583–614.     

Turbellaria Lecithoepitheliata: morphology,systematics, phylogeny

A review of the literature on the world fauna of lecithoepitheliata and Prolecithophora and extensive observations by the author on species of the Prorhynchidae, including cosmopolitan species as well as some endemic to Lake Baikal, and on endemic species of Baicalarctiinae (Prolecithophora) show that the Prorhynchidae and Gnosonesimidae are properly classified in the Neoophora. The morphological similarity of the Prorhynchidae and Prolecithophora proves these taxa are closely related. A hypothesis relating the Lecithoepitheliata Prorhynchidae to primitive prolecithophorans appears to be the only tenable hypothesis on the phylogeny of Lecithoepitheliata. The question of whether the Lecithoepitheliata is monophyletic still needs investigation; more evidence on the phylogeny of the Gnosonesimidae is needed.     

Skull anatomy of the Oligocene toothed mysticete Aetioceus weltoni (Mammalia; Cetacea): implications for mysticete evolution and functional anatomy

Toothed mysticetes of the family Aetiocetidae from Oligocene rocks of the North Pacific play a key role in interpretations of cetacean evolution because they are transitional in grade between dorudontine archaeocetes and edentulous mysticetes. The holotype skull of Aetiocetus weltoni from the late Oligocene (28–24 Ma) of Oregon, USA, has been further prepared, revealing additional morphological features of the basicranium, rostrum and dentary that have important implications for mysticete evolution and functional anatomy. The palate of Aetiocetus weltoni preserves diminutive lateral palatal foramina and associated delicate sulci which appear to be homologous with the prominent palatal foramina and sulci that occur along the lateral portion of the palate in extant mysticetes. In modern baleen whales these foramina allow passage of branches of the superior alveolar artery, which supplies blood to the epithelia of the developing baleen racks. As homologous structures, the lateral palatal foramina of A. weltoni suggest that baleen was present in this Oligocene toothed mysticete. Cladistic analysis of 46 cranial and dental characters supports monophyly of the Aetiocetidae, with toothed mysticetes Janjucetus and Mammalodon positioned as successive sister taxa. Morawanacetus is the earliest diverging aetiocetid with Chonecetus as sister taxon to Aetiocetus species. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 308–352.     

Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters

Of the basal clades of extant birds (Neornithes) the 'landfowl' or galliforms (Aves, Galliformes) are the most speciose. Cladistic analysis of more than 100 morphological characters coded at the generic level for most putative galliform genera confirms that the megapodes ('mound builders'; Megapodiidae) are the most basal clade within the order. They are followed successively by the curassows, guans and chachalacas (Cracidae), which comprise the sister-group to all other extant Galliformes (i.e. Phasianoidea). Within this large 'phasianoid' clade, analyses suggest that the guineafowl (Numididae) are the most basal taxon, although monophyly of this 'family' is not strictly supported on the basis of the morphological characters employed. An additional major clade within the phasianoid Galliformes is recovered by this analysis, comprising the traditional groupings of New World quails (Odontophoridae) and Old World quails ('Perdicini'), yet only monophyly of the former is supported unambiguously by morphological characters. Relationships within the remainder of the phasianoid taxa, including the grouse (Tetraonidae), turkeys (i.e. Meleagris / Agriocharus spp.) as well as other 'pavonine' galliforms (i.e. peafowl; Pavo , Afropavo , Rheinardia , Argusianus and Polyplectron spp.) remain largely unresolved on the basis of morphological characters, yet monophyly of the major subdivisions is supported here. Although there are a number of important differences, especially with regard to relationships within the nonquail phasianoids, the results of this morphological phylogenetic (cladistic) analysis are broadly congruent both with traditional classifications and existing molecular hypotheses of galliform phylogenetic relationships.     

Relationships among extant and fossil echimyids (Rodentia: Hystricognathi)

The echimyid rodents are the most diverse group of Neotropical hystricognaths, with approximately 40 extant and fossil genera. Craniodental characters are proposed in order to formulate hypotheses of phylogenetic relationships within the Echimyidae. A data matrix of 54 taxa and 50 characters is constructed and submitted to parsimony analyses using PAUP and WinClada programs. Analysis of the complete data set results in 47 448 most parsimonious trees 107 steps long. These trees are summarized in a strict consensus tree, which is taken as the main phylogenetic hypothesis resulting from this study. The monophyly of several currently recognized supraspecific taxa is not corroborated. These are: the subfamilies Eumysopinae, Echimyinae, Myocastorinae and Adelphomyinae; and the genera Proechimys , Echimys and Makalata . Conversely, the monophyly of Dactylomyinae and Trinomys is supported. New associations are proposed: (1) a clade comprising the extant Carterodon , Clyomys and Euryzygomatomys and the fossil Pampamys and Theridomysops placed at the base of the crown-group Echimyidae; (2) a clade uniting Proechimys , Hoplomys and Trinomys , which is the sister-taxon of (3) a clade including Mesomys , Lonchothrix , Myocastor and a clade with extant dactylomyines and echimyines and associated fossil taxa. Based on this phylogenetic hypothesis, patterns of tooth evolution in Echimyidae are discussed, and minimum ages for the divergence events within the family are estimated.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 142 , 445–477.     

The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa

The monophyly and phylogeny of the adaptive radiation of Hawaiian finches (Fringillidae: Drepanidini; honeycreepers, auct.) were studied using parsimony analysis of comparative osteology, combined with Templeton (Wilcoxon signed‐ranks) tests of alternative phylogenetic hypotheses. Eighty‐four osteological characters were scored in 59 terminal taxa of drepanidines, including 24 fossil forms, and in 30 outgroup species. The optimal phylogenetic trees show considerable agreement, and some conflict, with independently derived ideas about drepanidine evolution. The monophyly of a large Hawaiian radiation was upheld, although one fossil taxon from Maui fell outside the drepanidine clade. The finch‐billed species were placed as basal drepanidine taxa, and continental cardueline finches (Carduelini) were identified as the radiation's closest outgroups. The study found anatomical as well as phylogenetic evidence that the radiation had a finch‐billed ancestor. The optimal trees identify the red‐and‐black plumage group as a clade, and suggest that the tubular tongue evolved only once in the radiation. Because comparative osteology provides too few characters to strongly support all the nodes of the tree, it was helpful to evaluate statistical support for alternative hypotheses about drepanidine relationships using the Templeton test. Among the alternatives that received significant statistical support are a relationship of the drepanidines with cardueline finches rather than with the Neotropical honeycreepers (Thraupini), classification of the controversial genera Paroreomyza and Melamprosops as drepanidines, and a secondary loss of the tubular tongue in Loxops mana. The hypothesis of monophyly for all the Hawaiian taxa in the study was not rejected statistically. The study provides a framework for incorporating morphological and palaeontological information in evolutionary studies of the Drepanidini. © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society, 2004, 141 , 207–255.