The phylogenetic position of the Pterosauria within the Archosauromorpha

In recent years the hypothesis that pterosaurs were the major sister-group of dinosaurs and a closely-linked hypothesis that pterosaurs evolved flight from the ground up have gained general acceptance. A cladistic analysis of the Archosauromorpha using characters presented by previous workers results in a single most parsimonious tree with the Pterosauria as the major sister-group of the Dinosauria. However, that sister-group relationship is supported only by a suite of hindlimb characters that are correlated with bipedal digitigrade locomotion in dinosaurs. In pterosaurs the characters have been interpreted as correlates of bipedal cursorial locomotion, arboreal leaping, or involvement of the hindlimb in the wing. The homology of those characters in dinosaurs and pterosaurs cannot be supported. Reanalysis of the data after exclusion of those hindlimb characters results in most parsimonious trees with the Pterosauria as the sister-group of the Erythrosuchidae + Proterochampsidae + Euparkeria + Archosauria, in that order. This sister-group relationship is supported by a diverse assemblage of functionally independent skeletal characters from all regions of the skeleton. The results of the analysis cast doubt on the hypothesis that pterosaurs evolved flight from the ground up.     

Evolution of metatherian and eutherian (mammalian) characters: a review based on cladistic methodology

Cladistic methodology is used to test the hypothesis that three major monophyletic groups exist among living mammals–the oviparous monotremes (Prototheria), and the viviparous marsupials (Metatheria) and placentals (Eutheria). Evaluation is made of the polarity (i.e. the direction of change in a primitive-to-derived sequence) of numerous characters which distinguish some or all of these groups, and of the usefulness of these characters in phylogenetic inference. An attempt is made to establish the state of these characters in the common Late Jurassic-Early Cretaceous therian ancestor of marsupials and placentals.
It is concluded that the most basic division of the Mammalia is the dichotomy into the subclasses Prototheria (including Monotremata, Multituberculata, Triconodonta, Docodonta) and Theria (including Metatheria, Eutheria, Pantotheria and Symmetrodonta). Two major groups exist among living viviparous mammals, the Metatheria and Eutheria; in a cladistic framework these are sister-groups. It is demonstrated that there is no special (sister-group) relationship between monotremes and marsupials, and there is no justification for placing them in a group Marsupionta.     

Evolutionary analysis of the middle and inner ear of Late Jurassic multituberculates

We describe three previously unreported specimens of petrosal bones of paulchoffatiid multituberculate mammals, collected from strata of Late Jurassic age in the Guimarota lignite mine of Leiria, west-central Portugal. The new fossils allow correction, supplementation, and confirmation of anatomical details, thus refining knowledge of general adaptation in the ear region among Jurassic multituberculates. Virtually all observed characters in the paulchoffatiid otic region are primitive relative to homologous features seen among Late Cretaceous and younger representatives of the Multituberculata; we recognize few unique otic specializations in paulchoffatiids that would preclude ancestry to later multituberculates. The plesiomorphic nature of paulchoffatiid ear regions provides no evidence in support of the hypothesis of a special, sister-group relationship between multituberculates and Late Cretaceous/Cenozoic marsupials plus placentals. Used in isolation, objective evidence derived from paulchoffatiid ear regions is consistent with interpretation of multituberculate divergence from other mammals predating the stem to living monotremes and postdating the stem to extinct morganucodontids. More broadly based comparative studies among Mesozoic mammals, however, suggest that independent acquisition of similarly advanced mammalian features was a pervasive theme among evolutionary histories of early mammals, probably including multituberculates. Although the phylogenetic position of multituberculates relative to other mammalian groups has yet to be unequivocally resolved, we suggest that a very early divergence of the group remains a distinct possibility.     

Phylogeny and classification, origins, and evolution of host associations of lice

Lice are highly successful ectoparasites. Most species of mammals and birds are infested by at least 1 but up to 6 species of lice. Current opinion is that lice evolved from free-living Psocoptera (booklice, barklice and psocids). It is generally agreed that there are 4 main groups of lice: Anoplura, Amblycera, Ischnocera and Rhyncophthirina. In contrast, there is no agreement on the phylogenetic relationships of these groups and their classification. In particular, there is much debate over the validity of the taxon Mallophaga, which is almost certainly paraphyletic. For many years the sister-group of the Boopiidae, which almost exclusively infest Australasian marsupials, was thought to be a group of lice that now infest marsupials in South America. This, however, is almost certainly incorrect; the sister-group of the Boopiidae probably contains bird-infesting lice from the Menoponidae (Amblycera). Thus, menoponid lice transferred from birds to mammals and from these arose the Boopiidae. Transfers of lice between mammals and birds have occurred on other occasions during the evolution of the lice; 2 of the 4 main groups of lice, the Ischnocera and Amblycera, contain families that infest birds and families that infest mammals. Strict cospeciation and coevolution was thought to predominate among the lice; however, detailed studies indicate this to be incorrect. Consequently, the axiom that lice and their hosts invariably coevolve should be abandoned. Ironically, biologists may learn more about the evolutionary biology of hosts when host-switching has occurred. Some evidence exists for competition between species of lice; this interaction may determine whether or not the transfer of a species of louse to an atypical hose (a potential host-switch) is successful. Thus, the extincion of populations of lice (that result in uninfested hosts) may facilitate host-switching and perhaps the evolution of new taxa of lice. In contrast, extinction of hosts unfortunately often leads to the extinction of species of lice.     

Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships [published erratum appears in Mol Biol Evol 1991 May;8(3):398]

The 18S ribosomal RNAs of 21 tetrapods were sequenced and aligned with five published tetrapod sequences. When the coelacanth was used as an outgroup, Lissamphibia (living amphibians) and Amniota (amniotes) were found to be statistically significant monophyletic groups. Although little resolution was obtained among the lissamphibian taxa, the amniote sequences support a sister-group relationship between birds and mammals. Portions of the 28S ribosomal RNA (rRNA) molecule in 11 tetrapods also were sequenced, although the phylogenetic results were inconclusive. In contrast to previous studies, deletion or down- weighting of base-paired sites were found to have little effect on phylogenetic relationships. Molecular evidence for amniote relationships is reviewed, showing that three genes (beta-hemoglobin, myoglobin, and 18S rRNA) unambiguously support a bird-mammal relationship, compared with one gene (histone H2B) that favors a bird- crocodilian clade. Separate analyses of four other genes (alpha- crystallin A, alpha-hemoglobin, insulin, and 28S rRNA) and a combined analysis of all sequence data are inconclusive, in that different groups are defined in different analyses and none are strongly supported. It is suggested that until sequences become available from a broader array of taxa, the molecular evidence is best evaluated at the level of individual genes, with emphasis placed on those studies with the greatest number of taxa and sites. When this is done, a bird-mammal relationship is most strongly supported. When regarded in combination with the morphological evidence for this association, it must be considered at least as plausible as a bird-crocodilian relationship.      

Phylogeny and classification of the Psocodea, with particular reference to the lice (Psocodea: Phthiraptera)

ABSTRACT. Apomorphies that have been proposed for the Psocodea, Psocoptera, Phthiraptera and superfamilial groups within the Phthiraptera are enumerated and evaluated. The Psocodea and Phthiraptera are considered to be holophyletic, but the sister-group of the Phthiraptera lies within the Psocoptera. Within the Phthiraptera the Anoplura and Rhyncophthirina form a holophyletic group whose sister-group is the Ischnocera, and the Amblycera is the sister-group of this assemblage. The common ancestor of the Phthiraptera is suggested to have been parasitic, and all lice are believed to have evolved under environmental constraints similar to those operating today. On the evidence provided by host relationships the origin of the lice is dated as the Cretaceous, but the host of the ancestor of the order is not identified. The lice of marsupials in South America and Australia are not considered to comprise a holophyletic group.     

CHARACTER DIAGNOSIS, FOSSILS AND THE ORIGIN OF TETRAPODS

I. The traditional view of the origin of tetrapod vertebrates is that they are descendants of fossil osteolepiform fish, of which Eusthenopteron is best known. In recent years both that conclusion and the methodology by which it has been reached have been challenged by practitioners of cladistic analysis. Particularly a recent review by Rosen et al. (1981) claims that Dipnoi (lungfish) are the sister-group of the Tetrapoda, that Osteolepiformes is a non-taxon and that Eusthenopteron is more distant from tetrapods than are Dipnoi, coelacanths and probably the fossil Porolepiformes. We attempt to refute all these concludions by use of the same cladistic technique. 2. We accept that all the above-mentioned groups, together with some less well-known taxa, can be united as Sarcopterygii by means of shared derived (apomorph) characters. We also agree that Porolepiformes and Actinistia (coelacanths) can be characterized as valid taxa. The primitive and enigmatic fossil fish Powichthys is accepted as representing the plesiomorph sister-group of true porolepiforms. 3. Only two apomorph features, the course of the jaw adductor muscles and the position of incurrent and excurrent nostrils, appear to unite all the fish, living and fossil, currently regarded as Dipnoi. The characteristic tooth plates and the presence of petrodentine both exclude important primitive fossil forms. 4. Contrary to the opinion of Rosen et al., Osteolepiformes can be characterized — by the arrangement of bones forming the cheek plate, the presence of basal scutes to the fins and by the unjointed radials of the median fins. However, if these are true autapomorphies they exclude any osteolepiform from direct tetrapod ancestry. 5. Tetrapoda is a monophyletic group characterized by ten or more autapomorphies, including the bones of the cheek plate, a stapes and fenestra ovalis, and a series of characters of the appendicular skeleton. 6. Tetrapods have a true choana (internal nostril). We accept that the posterior (excurrent) nostril of Dipnoi is the homologue of the tetrapod choana. However, we assert that the posterior nostril of all bony fish is the homologue of the choana. This assertion would be refuted if any fish showed separate posterior nostril and choana. We reject the claim that this ‘three nostril condition’ occurred in porolepiforms and osteolepiforms. The evidence for a choana in porolepiforms is inadequate. Osteolepiforms had a true choana, characterized as in tetrapods by its relationship to the bones of the palate, but no third nostril. Dipnoans are not choanate. 7. Following cladistic practice, the relationship of the extant taxa is established first. Dipnoi are thus shown to be the living sister-group of tetrapods, but only on ‘soft anatomy’ characters unavailable in fossils. Coelacanths are the living sister-group of the taxon so formed. 8. The relationship of the fossil taxa to the extant sarcopterygians is then considered. The synapomorphy scheme proposed by Rosen et al. is discussed at length. Virtually all the characters they use to exclude close relationship of Eusthenopteron (and hence all osteolepiforms) to tetrapods, in favour of coelacanths and dipnoans, are invalid. 9. A series of synapomorphies uniting osteolepiforms and tetrapods is proposed, including a true choana (hence the taxon Choanata), the histology of the teeth, and a number of characters of the humerus. The recently discovered fossil Youngolepis, which lacks a choana, represents the sister-group of the Choanata, and is not uniquely close to Powichthys. The latter, as a porolepiform (s.l.) is a member of the sister-group to Choanata plus Youngolepis. 10. Our cladistic analysis suggests that all the extinct taxa considered are more closely related to tetrapods than are the Dipnoi. Moreover fossil evidence suggests that Dipnoi, considered as an extant taxon, may not even be the living sister-group of Tetrapoda. Early fossil dipnoans appear to have been marine fish without specific adaptations for air breathing. If so the apparent synapomorphies of Dipnoi and Tetrapoda may be homoplastic — the insistence on grouping extant taxa first would then have yielded an invalid inference.     

Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals

Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years.     

The relationships of the major group of mammals: New approaches

Systematically, mammals must be the most intensively studied group of organisms. Yet the relationships between the major orders - bats, whales, primates, rodents, insectivores, elephants, and so on - are still controversial. New systematic approaches, including molecular sequencing studies and cladisitic analyses of morphological data, have given rise to a number of new phylogenetic hypotheses, but only a few sister-group relationships seem to have general support. These hypotheses are depicted in the accompanying centre-page diagram.     

Parasitological evidence pertaining to the phylogeny of the hominoid primates

A systematic review of parasitological data pertaining to the phylogeny of hominoid primates revealed considerable internal consistency and congruence with non-parasitological data. Hylobatids are supported as the sister-group of Pongo + Pan + Gorilla , the 'Great Apes'. Within the Great Apes, Pan + Gorilla are sister taxa. Multiple analyses of presence/absence data place Homo with cercopithecids, probably an artefact of humans' widespread occurrence and polymorphic feeding and living habits. Explicit phylogenetic hypotheses are available for only two parasite groups. Hookworms of the genus Oesophagostomum subgenus Conoweberia place Homo as the sister-group of Pan + Gorilla , whereas pinworms of the genus Enterobius place Homo as the sister-group of Pongo + Pan + Gorilla . This disagreement among data sets with regards to the placement of Homo , combined with the complete agreement about the placement of the other hominoids, is consistent with uncertainties in current findings from other sets of data.     

On the Relationship of Pinnipeds to Other Carnivores

The paper discusses Tedford's (1976) hypothesis concerning a sister-group relationship of the otariids with the ursids and the phocids with the mustelids, based on a cladistic analysis. It is concluded that because Tedford has used at most branching points in his cladogram the opposite character states as synapomorphies as those used in the sister-group, his hypothesis is put forward in conflict with the premises of the cladistic method. It must therefore be rejected.     

Classification and phylogeny of the diapsid reptiles

Reptiles with two temporal openings in the skull are generally divided into two groups–the Lepidosauria (lizards, snakes, Sphenodon , 'eosuchians') and the Archosauria (crocodiles, thecodontians, dinosaurs, pterosaurs). Recent suggestions that these two are not sister-groups are shown to be unproven, whereas there is strong evidence that they form a monophyletic group, the Diapsida, on the basis of several synapomorphies of living and fossil forms. A cladistic analysis of skull and skeletal characters of all described Permo-Triassic diapsid reptiles suggests some significant rearrangements to commonly held views. The genus Petrolacosaurus is the sister-group of all later diapsids which fall into two large groups–the Archosauromorpha (Pterosauria, Rhynchosauria, Prolacertiformes, Archosauria) and the Lepidosauromorpha (Younginiformes, Sphenodontia, Squamata). The pterosaurs are not archosaurs, but they are the sister-group of all other archosauromorphs. There is no close relationship between rhynchosaurs and sphenodontids, nor between Prolacerta or Tanystropheus and lizards. The terms 'Eosuchia', 'Rhynchocephalia' and 'Protorosauria' have become too wide in application and they are not used. A cladistic classification of the Diapsida is given, as well as a phylogenetic tree which uses cladistic and stratigraphic data.     

Interrelationships of the ostariophysan fishes (Teleostei)

The history of ostariophysan classification is summarized and it is noted that traditional concepts of relationships have never been supported by characters found to be unique to the taxa. We present a new hypothesis of relationships among four of the five major ostariophysan lineages: Cypriniformes, Characiformes, Siluroidei, and Gymnotoidei (Otophysi). Cypriniforms are the sister-group of the remaining three (Characiphysi), and characiforms are the sister-group of siluroids plus gymnotoids (Siluriformes). Placement of the Gonorynchiformes as the sister-group of the Otophysi is supported by additional evidence. Each of the five lineages is monophyletic. Analysis was concentrated upon species thought to be the least specialized within each lineage; choices of these species are discussed. Chanos is determined to be a relatively primitive gonorynchiform morphologically and the sister-group of all other Recent members of the order. Opsariichthys and Zacco are found to be morphologically primitive cypriniforms. We propose that a monophyletic group comprising the Citharinidae and Distichodontidae forms the sister-group of all other characiforms. Within the two families, Xenocharax is the least specialized. We suggest that Hepsetus, the erythrinids, and the ctenoluciids are more derived than the distichodontids and citharinids, and may form a monophyletic group within die characiforms. The traditional hypothesis that Diplomystes is the primitive sister-group of all Recent siluroids is substantiated. Our evidence suggests that Sternopygus is the most primitive gymnotoid morphologically; but rather than being the sister-group of all other gymnotoids, it is the primitive sister-group within a lineage called the Sternopygidae by Mago-Leccia. Previous explanations of otophysan distribution have been based on notions of relationships which are unsupported by the evidence presented herein. Our own analysis of relationships serves primarily to make clear the extent of sympatry, and therefore the probability of dispersal, among the major ostariophysan lineages. The extent of sympatry, together with the widespread distribution of ostariophysans, suggests that the group is older than previously supposed, and our hypotheses of relationships among the characiforms implies that many of the extent characiform lineages evolved before the separation of Africa and South America. Further understanding of ostariophysan distribution must await phylogenetic analysis within each of the five major lineages so that distributions linked with vicariance patterns and dispersal events can be sorted out.     

Dimetrodon Is Not a Dinosaur: Using Tree Thinking to Understand the Ancient Relatives of Mammals and their Evolution

The line of descent that includes all living mammals extends back in time over 300 million years. Many of the ancient relatives of mammals that fall along this line are very different in appearance from living mammals and are frequently mistaken for reptiles such as dinosaurs. This misconception is reinforced by the fact that these animals are often referred to as “mammal-like reptiles,” a term reflecting outdated methods for classifying organisms. In reality, these ancient mammal-relatives, known as synapsids, are more closely related to living mammals than they are to any reptiles. Evolutionary trees, which depict patterns of descent from common ancestors among organisms, are very useful for understanding why this is the case and for reconstructing the evolutionary histories of many of the unique characters found in mammals. Here, I provide an introduction to evolutionary trees and their implications for understanding the relationships between mammals, synapsids, and reptiles. This is followed by a review of synapsid diversity and a discussion of how evolutionary trees can be used to investigate when in synapsid history different mammalian characteristics first appeared.     

Reptile phylogeny and the interrelationships of turtles

A comprehensive analysis of amniote interrelationships is presented in an attempt to test turtle interrelationships. The results refute earlier hypotheses that turtles are related to parareptiles, i.e. to procolophonids or pareiasaurs. Instead, turtles are shown to be the sister-group of Sauropterygia, the two clades being nested within Sauria as sister-group of Lepidosauriformes. This scenario is also supported by several developmental and soft tissue characters which are shown to be congruent with the current phylogeny. The analysis strongly supports a monophyletic Parareptilia, sister-group of a monophylctic Eurcptilia. The Diapsida, however, is paraphyletic unless it includes turtles and sauropterygians. Additionally, the position of turtles within Diapsida has major implications for the evolutionary history and/or significance of many characters, i.e. temporal fenestration.     

Phylogenetic position of the monogeneans Sundanonchus, Thaparocleidus, and Cichlidogyrus inferred from 28S rDNA sequences

A molecular phylogeny was inferred from newly obtained partial 28S rRNA gene sequences of Sundanonchus micropeltis (Sundanonchidae), Thaparocleidus siamensis and Cichlidogyrus sp. (Ancyrocephalidae), and other already available sequences. Although sequences are lacking for several families, the following phylogenetic relationships could be inferred. The Diplectanidae were the sister-group to a clade including Sundanonchus and the Ancyrocephalidae; Sundanonchus was the sister-group to the Ancyrocephalidae, therefore suggesting validity of the Sundanonchidae, which include this single genus; within the Ancyrocephalidae, Thaparocleidus (Ancylodiscoidinae) was the sister-group to the four other taxa, though with relatively low support, suggesting that the Ancylodiscoidinae are the sister-group to the Ancyrocephalinae.     

Intrinsic hand proportions of euarchontans and other mammals: implications for the locomotor behavior of plesiadapiforms

Arboreal primates have distinctive intrinsic hand proportions compared with many other mammals. Within Euarchonta, platyrrhines and strepsirrhines have longer manual proximal phalanges relative to metacarpal length than colugos and terrestrial tree shrews. This trait is part of a complex of features allowing primates to grasp small-diameter arboreal substrates. In addition to many living and Eocene primates, relative elongation of proximal manual phalanges is also present in most plesiadapiforms. In order to evaluate the functional and evolutionary implications of manual similarities between crown primates and plesiadapiforms, we measured the lengths of the metacarpal, proximal phalanx, and intermediate phalanx of manual ray III for 132 extant mammal species (n=702 individuals). These data were compared with measurements of hands in six plesiadapiform species using ternary diagrams and phalangeal indices. Our analyses reveal that many arboreal mammals (including some tree shrews, rodents, marsupials, and carnivorans) have manual ray III proportions similar to those of various arboreal primates. By contrast, terrestrial tree shrews have hand proportions most similar to those of other terrestrial mammals, and colugos are highly derived in having relatively long intermediate phalanges. Phalangeal indices of arboreal species are significantly greater than those of the terrestrial species in our sample, reflecting the utility of having relatively long digits in an arboreal context. Although mammals known to be capable of prehensile grips demonstrate long digits relative to palm length, this feature is not uniquely associated with manual prehension and should be interpreted with caution in fossil taxa. Among plesiadapiforms, Carpolestes, Nannodectes, Ignacius, and Dryomomys have manual ray III proportions that are unlike those of most terrestrial species and most similar to those of various arboreal species of primates, tree shrews, and rodents. Within Euarchonta, Ignacius and Carpolestes have intrinsic hand proportions most comparable to those of living arboreal primates, while Nannodectes is very similar to the arboreal tree shrew Tupaia minor. These results provide additional evidence that plesiadapiforms were arboreal and support the hypothesis that Euarchonta originated in an arboreal milieu.     

Interrelationships of lower actinopterygian fishes

The lower actinopterygian fishes are classified using dermal skull roof pattern, in particular the various configurations displayed by the bones on the otic branch of the infraorbital canal (dermosphenotic, intertemporal-supratemporal/dermopterotic). Where possible these patterns are related to the sequential acquisition of derived features, and the resulting cladogram represents a synthesis of dermal bone pattern and endochondral and dermal skeletal characters. We have proposed 27 terminal groups which we tentatively regard as monophyletic and have concluded that Polypterus is the most primitive living taxon, that the Chondrostei is the sister-group of Saurichthys and Luganoia the most derived stem-group neopterygian.     

A reevaluation of early amniote phylogeny

A new phylogenetic analysis of early amniotes based on 124 characters and 13 taxa (including three outgroups) indicates that synapsids are the sister-group of all other known amniotes. The sister-group of Synapsida is Sauropsida, including Mesosauridae and Reptilia as its two main subdivisions. Reptilia is divided into Parareptilia and Eureptilia. Parareptilia includes Testudines and its fossil relatives (Procolophonidae, Pareiasauria and Millerettidae), while Eureptilia includes Diapsida and its fossil relatives (Pakothyris and Captorhinidae). Parts of the phylogeny are robust, such as the sister-group relationship between procolophonids and testudines, and between pareiasaurs and the testudinomorphs (the clade including procolophonids and testudines). Other parts of the new tree are not so firmly established, such as the position of mesosaurs as the sister-group of reptiles. The new phylogeny indicates that three major clades of amniotes extend from the present to the Palaeozoic. These three clades are the Synapsida (including Mammalia), Parareptilia (including Testudines), and Eureptilia (including Sauria). In addition, the Procolophonidae, a group of Triassic parareptiles, are the sister-group of Testudines.