The Phylogeny and Classification of Tapiromorph Perissodactyls (Mammalia)

Despite an excellent fossil record, the phylogeny of Perissodactyla is not well understood, in terms of both the relationships within Perissodactyla and the position of the Perissodactyla among the orders of mammals. This paper provides a phylogenetic analysis of one major perissodactyl lineage, the Tapiromorpha. This analysis combines a more comprehensive sampling of characters and taxa with rigorous tree-searching methods to create a new hypothesis of tapiromorph relationships. The phylogeny of tapiromorph perissodactyls is analyzed using 45 characters of the skull, postcranial skeleton, and dentition scored for 29 taxa, including three nontapiromorph outgroups. Phylogenetic taxonomic definitions are constructed for suprageneric taxa. According to the results of this analysis, the Chalicotherioidea cannot be unequivocally assigned to the Tapiromorpha, nor can Homogalax or Cardiolophus. Isectolophus , Tapiroidea, and Rhinocerotoidea are unequivocal members of the Tapiromorpha. Heptodon is included in a monophyletic Tapiroidea. Amynodontid rhinocerotoids come out as the sister group to rhinocerotids, and indricotheres do not fall within the Hyracodontidae. The results of this study provide further arguments that tapiromorphs (and putative tapiromorphs) may be important for understanding the ancestral morphology of Perissodactyla.     

Anthracobunids from the Middle Eocene of India and Pakistan Are Stem Perissodactyls

Anthracobunidae is an Eocene family of large mammals from south Asia that is commonly considered to be part of the radiation that gave rise to elephants (proboscideans) and sea cows (sirenians). We describe a new collection of anthracobunid fossils from Middle Eocene rocks of Indo-Pakistan that more than doubles the number of known anthracobunid fossils and challenges their putative relationships, instead implying that they are stem perissodactyls. Cranial, dental, and postcranial elements allow a revision of species and the recognition of a new anthracobunid genus. Analyses of stable isotopes and long bone geometry together suggest that most anthracobunids fed on land, but spent a considerable amount of time near water. This new evidence expands our understanding of stem perissodactyl diversity and sheds new light on perissodactyl origins.     

The evolution of pelvic osteology and soft tissues on the line to extant birds (Neornithes)

Substantial differences in pelvic osteology and soft tissues separate crown group crocodylians (Crocodylia) and birds (Neornithes). A phylogenetic perspective including fossils reveals that these disparities arose in a stepwise pattern along the line to extant birds, with major changes occurring both within and outside Aves. Some character states that preceded the origin of Neornithes are only observable or inferable in extinct taxa. These transitional states are important for recognizing the derived traits of neornithines. Palaeontological and neontological data are vital for reconstructing the sequence of pelvic changes along the line to Neornithes. Soft tissue correlation with osteological structures allows changes in soft tissue anatomy to be traced along a phylogenetic framework, and adds anatomical significance to systematic characters from osteology. Explicitly addressing homologies of bone surfaces reveals many subtleties in pelvic evolution that were previously unrecognized or implicit. I advocate that many anatomical features often treated as independent characters should be interpreted as different character states of the same character. Relatively few pelvic character states are unique to Neornithes. Indeed, many features evolved quite early along the line to Neornithes, blurring the distinction between 'avian' and 'non-avian' anatomy.     

A primitive ceratomorph (Perissodactyla, Mammalia) from the early Tertiary of Europe

Hyracotherium cuniculus Owen, 1842, from Palaeocene–Eocene boundary strata in NW Europe, was formerly considered to be an equoid. It is here placed in Cymbalophus gen. nov. , in the perissodactyl suborder Ceralomorpha, which comprises tapiroids and rhinocerotoids, as one of its most primitive and earliest members. This revised classification is based on an evaluation of its advanced versus primitive character states, and comparison with a variety of other primitive perissodactyls. Cheek tooth occlusal relationships in the early stages of ceratomorph evolution are discussed and contrasted with the fundamental perissodactyl morphotype as represented in Hyracotherium. It is suggested that the Lophiodontidae (formerly considered to be ceratomorphs; may be more closely related to chalicotheres; that the Isectolophidae may be the sister-group of chalicotheres and lophiodonts plus ceratomorplis; and that Cymbalophus is the most primitive known member of the newly restricted Ceratomorpha. Cymbalophus is placed tentatively in the family Helaletidae.     

Ankle morphology of the earliest Cetaceans and its implications for the phylogenetic relations among ungulates

Recent molecular studies are inconsistent with ungulate phylogenetic trees that are based on morphological traits. These inconsistencies especially relate to the position of cetaceans and perissodactyls. Evaluation of the close phylogenetic ties between artiodactyls and cetaceans has been hampered by the absence of tarsal bones of primitive cetaceans, as artiodactyls are often diagnosed on the basis of their tarsus. We here describe newly discovered tarsal bones that are the oldest cetacean tarsals known. We present a character analysis for primitive ungulate tarsals and evaluate their impact on the ungulate phylogenetic tree. Tarsal data are consistent with some molecular studies in suggesting that the extant sister group of Cetacea is Artiodactyla or that Cetacea should be included within the latter order. Tarsal data do not support Cete (Mesonychia plus Cetacea) and are consistent with the exclusion of perissodactyls from paenungulates as suggested by some molecular studies.     

Phylogenetics of Perissodactyla and Tests of the Molecular Clock

Two mitochondrial genes, the protein-coding cytochrome c oxidase subunit II (COII) gene and a portion of the 12S rRNA gene, were used for phylogenetic investigation of the mammalian order Perissodactyla. The primary objective of the study was to utilize the extensive fossil record of perissodactyls for calibrating molecular clocks and comparing estimates of divergence times using both genes and two fossil calibration points. Secondary objectives included clarification of previously unresolved relationships within Tapiridae and comparison of the results of separate and combined analyses of two genes. Analyses included several perissodactyl lineages representing all three families (Tapiridae, Equidae, and Rhinocerotidae), most extant genera, all four species of tapirs, two to four species of rhinoceros, and two species of Equus. The application of a relatively recent fossil calibration point and a relatively ancient calibration point produced greatly different estimates of evolutionary rates and divergence times for both genes, even though a relative rates test did not find significant rate differences among taxa. A likelihood-ratio test, however, rejected a molecular clock for both genes. Neither calibration point produced estimates of divergence times consistent with paleontological evidence over a range of perissodactyl radiations. The combined analysis of both genes produces a well-resolved phylogeny with Perissodactyla that conforms to traditional views of interfamilial relationships and supports monophyly of neotropical tapirs. Combining the data sets increases support for most nodes but decreases the support for a neotropical tapir clade because the COII and 12S rRNA data sets are in conflict for tapir relationships. Received: 6 January 1999 / Accepted: 2 August 1999     

A statistical approach to the evaluation of characters to estimate evolutionary relationships among the species of the aquatic subterranean genus, Iberobathynella (Crustacea, Syncarida)

The 13 known species of the genus Iberobathynella were studied. Twenty-six characters with usually two or three states were revealed to have low within-species variability but show clear differences among some species. These characters were hypothesized to have states convex on the branching pattern of the phylogenetic lines that gave rise to these 13 species (i.e. be uniquely derived). Each pair of these hypotheses was tested for logical compatibility; then, for each character, a new character was created by choosing equiprobably one of the possible permutations of the 13 species to rename the species in each state. Characters created in this random way would have convex states only by chance, not by evolution. This random character was tested with each of the remaining 25 for logical compatibility as hypotheses of convexity. For each character, one thousand such random characters were created and tested. Sixteen observed characters were compatible with more other observed characters than 90% of their randomly generated counterparts, and so were considered plausibly non-random. They were used to speculate on branching patterns of the phylogenetic lines among the 13 species.     

Cranial shape and correlated characters in crocodilian evolution

Crocodilians show a high degree of cranial variation and convergence throughout their 80 million-year fossil record that complicates their phylogenetic reconstruction. Conflicting phylogenetic results from different data partitions and character homoplasies typify crocodilian phylogeny, and differences between molecular and morphological phylogenetic hypotheses are believed to be associated with the slender-snout skull shape of Gavialis gangeticus and Tomistoma schlegelii. Slender-snout skulls are one of five identified eusuchian cranial ecomorph shape categories (ESCs) thought to reflect functional or ecological specialization. This paper tested the effect of transitions among general, blunt and slender ESCs on cranial character-state distributions in phylogeny using the concentrated changes test. In addition, 'tree-free' character compatibility analysis of character independence was conducted on the morphological character matrix to determine if character correlations are observed independent of specific tree topologies. Results suggest cranial ESCs do affect cranial character-state gains in phylogeny. Concentrated changes identify a broad suite of character-state changes that significantly correlate with transitions to slender, general and blunt ESCs on morphological, molecular and combined-data tree topologies, but numbers of correlated characters for each category differ according to topology. Character compatibility analysis results do not mirror the concentrated changes test results and reflect hierarchically distributed support throughout the data. As cranial ESCs affect character-state transitions, it is possible that nonphylogenetic variables could affect inferences of crocodilian phylogeny by affecting cranial morphology.     

First phylogenetic analysis of the tribe Phyllotini (Rodentia: Sigmodontinae) combining morphological and molecular data

Previous phylogenetic analyses of the tribe Phyllotini, one of the largest components of the subfamily Sigmodontinae, have been based on a single source of evidence. In particular, morphological analyses were largely based on craniodental data, almost neglecting the potential phylogenetic information present in the postcranium. Despite the significant advances made in relation to the knowledge of phyllotine phylogeny in recent times, there are several unsolved issues that highlight the importance of a phylogenetic analysis that integrates multiple sources of evidence, including previously considered sources as well as new sources of data. We present here the first combined phylogenetic analysis (morphological and molecular) of phyllotines, which includes the widest taxon and character sampling to date. Our dataset includes 164 morphological characters, of which 83 are postcranial characters, plus 3561 molecular characters, scored for 52 species from 34 genera of Oryzomyalia. In this study 75 postcranial characters not previously considered in this group are thoroughly described, and their utility for solving the relationships within Phyllotini is evaluated by means of different complementary analyses. Phyllotini was retrieved as a monophyletic clade in the combined analysis, with a composition that matches that obtained in most other recent analyses. All genera of phyllotines were monophyletic and show high support values. Abrotrichini, Akodontini and Oryzomyini were also monophyletic. The inclusion of postcranial data appears to be of limited utility to solve the phylogenetic relationships within Phyllotini.     

Measuring the phylogenetic randomness of biological data sets

Two qualitative taxonomic characters are potentially compatible if the states of each can be ordered into a character state tree in such a way that the two resulting character state trees are compatible. The number of potentially compatible pairs (NPCP) of qualitative characters from a data set may be considered to be a measure of its phylogenetic randomness. The value of NPCP depends on the number of evolutionary units (EUs), the number of characters, the number of states in the characters, the distributions of EUs among these states, and the amount and distribution of missing information and so does not directly indicate degree of phylogenetic randomness. Thus, for an observed data set, we used Monte Carlo methods to estimate the probability that a data set chosen equiprobably from among those identical (with respect to all the other above determining features) to the observed data set would have as high (or low) an NPCP as the observed data set. This probability, the realized significance of the observed NPCP, is attractive as an indication of phylogenetic randomness because it does not require the assumptions made by other such methods: No character state trees are assumed and consequently, only potential compatibility can be determined; no particular method of phylogenetic estimation is assumed; and no phylogenetic trees are constructed. We determined the values and significances of NPCP for analyses of 57 data sets taken from 53 published sources. All data sets from 37 of those sources exhibited realized significances of < 0.01, indicating high levels of phylogenetic nonrandomness. From each of the remaining 16 sources, at least one data set was more phylogenetically random. Inclusion of outgroups changed significance in some cases, but not always in the same direction. Data sets with significantly low NPCP may be consistent with an ancient hybrid origin (or other ancient polyphyletic gene exchange, crossing over, viral transfer, etc.) of the study group.     

A New Fulmarine Petrel (Aves: Procellariiformes) from the Upper Miocene of the Western Mediterranean

A new sea bird, Pterodromoides minoricensis gen. et sp. nov., similar in size and proportions to species of the modern genus Pterodroma , is described from Late Miocene breccias situated on the north-west coast of Menorca. The cranial osteology is similar to that of fulmarine petrels, but the large orbitonasal opening and characters of the postcranial skeleton justify its classification as a separate genus. At least one other species of procellariid occurs in the accompanying fossil asemblage, suggesting that Late Tertiary ecological conditions favoured sea bird populations in this area of the Mediterranean.     

Postcranial skeleton of Pistosaurus and interrelationships of the Sauropterygia (Diapsida)

Postcranial remains referable to the enigmatic sauropterygian Pistosaurus longaevus , from the Hauptmuschelkalk (Middle Triassic) of southern Germany, are described and comparisons are made with other sauropterygian groups. A phylogenetic hypothesis of sauropterygian interrelationships is presented. The Sauropterygia are most closely related to the Lepidosauromorpha. Pislosaurus most closely resembles the Plesiosauria in a number of cranial and postcranial features.     

A primitive ornithischian dinosaur from the Late Triassic of South Africa, and the early evolution and diversification of Ornithischia

Although the group played an important role in the evolution of Late Mesozoic terrestrial ecosystems, the early evolutionary history of the ornithischian dinosaurs remains poorly understood. Here, we report on a new primitive ornithischian, Eocursor parvus gen. et sp. nov., from the Late Triassic (?Norian) Lower Elliot Formation of South Africa. Eocursor is known from a single specimen comprising substantial cranial and postcranial material and represents the most complete Triassic member of Ornithischia, providing the earliest evidence for the acquisition of many key ornithischian postcranial characters, including an opisthopubic pelvis. A new phylogenetic analysis positions this taxon near the base of Ornithischia, as the sister taxon to the important and diverse clade Genasauria. The problematic clade Heterodontosauridae is also positioned basal to Genasauria, suggesting that an enlarged grasping manus may represent a plesiomorphic ornithischian condition. This analysis provides additional phylogenetic support for limited ornithischian diversity during the Late Triassic, and suggests that several major ornithischian clades may have originated later than generally believed. There are few morphological differences between Late Triassic and Early Jurassic ornithischians, supporting previous suggestions that the Early Jurassic ornithischian radiation may simply represent the filling of vacant ecological space following Late Triassic terrestrial extinctions.     

Muscles of the masticatory apparatus in two genera of hyraces (Procavia and Heterohyrax)

Subungulate hyraces are similar to the condition assumed to have characterized primitive ungulates and subungulates by virtue of their small body size, relatively unspecialized cranial and postcranial anatomy, and primitive type of lophodont dentition. The muscles of mastication of Procavia habessinica and Heterohyrax brucei are here compared with those of other mammals, both with ungulates, as an example of more specialized mammals, and with opossums, as an example of more generalized mammals, to determine aspects of hyrax myology that represent the retention of a condition primitive for herbivorous mammals. The masticatory muscles of hyraces retain the primitive ungulate/subungulate condition in the large, complexly subdivided temporalis, and in the enlarged, pinnated, bilayered medial pterygoid. The medial pterygoid originates from the pterygoid hamulus, a condition that may also be primitive for this assemblage. The large complex superficial masseter is derived compared with the condition in ruminant artiodactyls, but may represent the condition primitive for perissodactyls. The architectural modifications of this muscle in hyraces may represent adaptations to allow a wide gape threat display. Hyraces possess a posterior belly of the digastric alone, paralleling the condition in some perissodactyls. They possess a large and complexly subdivided styloglossus, which may be a shared derived character of subungulates. Hyraces are unique among ungulates and subungulates in the extreme reduction of the anterior hyoid cornua, and may be unique among mammals in the development of paired lingual processes from the ceratohyal ossifications.     

Use of mitochondrial DNA sequences to test the Ceratomorpha (Perissodactyla:Mammalia) hypothesis

Wood (J. Mamm. 18, 106–118; 1937) united the superfamilies Tapiroidea sensu stricto and Rhinocerotoidea in the suborder Ceratomorpha and aligned the Ceratomorpha with the suborder Hippomorpha within the order Perissodactyla. Although the monophyly of the Ceratomorpha appears now well-supported in paleontological and morphological analyses, the molecular relationship among the three extant superfamilies Tapiroidea, Rhinocerotoidea, and Equoidea has not yet been examined due to the limited amount of molecular information on tapirs. In the present study, we examined the phylogenetic position of Tapiroidea, represented by the complete mitochondrial cytochrome b gene (1140 bp) of a lowland tapir ( Tapirus terrestris ), and a Indian tapir ( Tapirus indicus ), relative to modern horses, zebras, donkeys, and rhinoceroses. The phylogenetic analyses using standard parsimony, neighbour-joining and maximum likelihood algorithms revealed monophyly of the Perissodactyla and three clearly distinct lineages: the modern horses, tapirs, and rhinoceroses. However, the sister-taxon relationship of the tapirs to either the rhinoceroses or the horses was not resolved conclusively in the bootstrap analysis. Spectral analysis, in which phylogenetic information is displayed independently of any selected tree, revealed that the DNA sequences available do not contain enough phylogenetic signal for any of the alternative hypotheses on the basal diversification of perissodactyls. The short branch lengths among the three perissodactyl lineages suggest that they diverged within a relatively short period, a finding consistent with molecular divergence datings and the fossil evidence that indicates a major radiation of the early perissodactyls approximately 54–50 million years ago.     

Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice

We consider the problem of reconstructing near-perfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states that is computationally efficient but not robust to imperfections in real data. A near-perfect phylogeny relaxes the perfect phylogeny assumption by allowing at most a constant number of additional mutations. We develop two algorithms for constructing optimal near-perfect phylogenies and provide empirical evidence of their performance. The first simple algorithm is fixed parameter tractable when the number of additional mutations and the number of characters that share four gametes with some other character are constants. The second, more involved algorithm for the problem is fixed parameter tractable when only the number of additional mutations is fixed. We have implemented both algorithms and shown them to be extremely efficient in practice on biologically significant data sets. This work proves the BNPP problem fixed parameter tractable and provides the first practical phylogenetic tree reconstruction algorithms that find guaranteed optimal solutions while being easily implemented and computationally feasible for data sets of biologically meaningful size and complexity.