Extinct Clade Research Articles

Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: the giant moas of New Zealand.

The tempo and mode of evolution of the extinct giant moas of New Zealand remain obscure because the number of lineages and their divergence times cannot be estimated reliably by using fossil bone characters only. We therefore extracted ancient DNA from 125 specimens and genetically typed them for a 658-bp mtDNA control region sequence. The sequences detected 14 monophyletic lineages, 9 of which correspond to currently recognized species. One of the newly detected lineages was a genetically divergent form of Megalapteryx originally described as a separate species, two more were lineages of Pachyornis in southern and northeastern New Zealand, and two were basal lineages of South Island Dinornis. When results from genetic typing and previous molecular sexing were combined, at least 33.6% of the specimens were incorrectly classified. We used longer sequences of the control region and nine other mtDNA genes totaling 2,814 base pairs to derive a strongly supported phylogeny of the 14 moa lineages. Molecular dating estimated the most recent common ancestor of moas existed after the Oligocene drowning of New Zealand. However, a cycle of lineage-splitting occurred approximately 4-10 million years ago, when the landmass was fragmented by tectonic and mountain-building events and general cooling of the climate. These events resulted in the geographic isolation of lineages and ecological specialization. The spectacular radiation of moa lineages involved significant changes in body size, shape, and mass and provides another example of the general influence of large-scale paleoenvironmental changes on vertebrate evolutionary history.

The histology of ossified tendon in dinosaurs

ABSTRACT Intratendinous ossification is widespread in dinosaurs (including birds). Although intratendinous ossification in living birds is well understood, the physiological process of tendon metaplasia and associated histological variability in Dinosauria are not. Therefore, ossified tendons were histologically sampled across extinct dinosaurian clades. Tendons of living birds and alligators were also sampled. Despite various anatomical locations and large differences in body size, ossified tendons were found to possess uniform microstructure even in specimens that do not normally experience intratendinous ossification (such as Spinostropheus and Camarasaurus). The ossified tendons of non-avian dinosaurs are largely indistinguishable from skeletal bone with respect to microanatomical features. However, ossified tendons in birds lack periosteal bone and associated fibrolamellar structures associated with ornithischian dinosaur tendons. Variation in periosteal bone occurs along the length of individual tendons. Ossified tendons from marginocephalians are unique in that they have large quantities of anisotropic fibrolamellar bone, while those from pachycephalosaurids have radial vascularity.

Trilobite body patterning and the evolution of arthropod tagmosis.

Preservation permitting patterns of developmental evolution can be reconstructed within long extinct clades, and the rich fossil record of trilobite ontogeny and phylogeny provides an unparalleled opportunity for doing so. Furthermore, knowledge of Hox gene expression patterns among living arthropods permit inferences about possible Hox gene deployment in trilobites. The trilobite anteroposterior body plan is consistent with recent suggestions that basal euarthropods had a relatively low degree of tagmosis among cephalic limbs, possibly related to overlapping expression domains of cephalic Hox genes. Trilobite trunk segments appeared sequentially at a subterminal generative zone, and were exchanged between regions of fused and freely articulating segments during growth. Homonomous trunk segment shape and gradual size transition were apparently phylogenetically basal conditions and suggest a single trunk tagma. Several derived clades independently evolved functionally distinct tagmata within the trunk, apparently exchanging flexible segment numbers for greater regionally autonomy. The trilobite trunk chronicles how different aspects of arthropod segmentation coevolved as the degree of tagmosis increased.

The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization1

SYNOPSIS. A recent total evidence analysis of the position of cetaceans (whales, dolphins and porpoises and extinct relatives) among mammals indicated that the phylogeny of these taxa remains poorly resolved. Molecular data show that 1) the order Artiodactyla (even-toed ungulates) is paraphyletic unless whales are included within it and 2) that the traditional relationships of clades within Artiodactyla are not supported. This controversy also affects the position of a wholly extinct clade, Mesonychia, which has been argued to be the group of terrestrial mammals most closely related to whales. Here I update a previous total evidence analysis by adding several hundred new informative molecular characters from the literature. Even with the addition of these characters the phylogeny remains unresolved. All most parsimonious trees, however, indicate a paraphyletic Artiodactyla with conflict existing over the exact sister taxon of Cetacea. Congruence between different equally parsimonious cladograms and the stratigraphic record as measured using the modified Manhattan Stratigraphic Measure shows that all of the competing topologies, including those with a paraphyletic Artiodactyla, are significantly congruent with the stratigraphic record. In fossil taxa cladistic optimization can be used as an alternative to ‘‘argument from design’’ (Lauder, 1996) to reconstruct behavior and soft tissues that do not fossilize or osteological characters that have not preserved. In certain scenarios of cetacean phylogeny, optimization indicates that taxa such as the archaic whales Ambulocetus and Pakicetus, and possibly mesonychians, are more correctly reconstructed without hair.

The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization

A recent total evidence analysis of the position of cetaceans (whales, dolphins and porpoises and extinct relatives) among mammals indicated that the phylogeny of these taxa remains poorly resolved. Molecular data show that 1) the order Artiodactyla (even-toed ungulates) is paraphyletic unless whales are included within it and 2) that the traditional relationships of clades within Artiodactyla are not supported. This controversy also affects the position of a wholly extinct clade, Mesonychia, which has been argued to be the group of terrestrial mammals most closely related to whales. Here I update a previous total evidence analysis by adding several hundred new informative molecular characters from the literature. Even with the addition of these characters the phylogeny remains unresolved. All most parsimonious trees, however, indicate a paraphyletic Artiodactyla with conflict existing over the exact sister taxon of Cetacea. Congruence between different equally parsimonious cladograms and the stratigraphic record as measured using the modified Manhattan Stratigraphic Measure shows that all of the competing topologies, including those with a paraphyletic Artiodactyla, are significantly congruent with the stratigraphic record. In fossil taxa cladistic optimization can be used as an alternative to “argument from design” (Lauder, 1996) to reconstruct behavior and soft tissues that do not fossilize or osteological characters that have not preserved. In certain scenarios of cetacean phylogeny, optimization indicates that taxa such as the archaic whales Ambulocetus and Pakicetus, and possibly mesonychians, are more correctly reconstructed without hair.

Prickly Paleozoic Animals

PALEONTOLOGY/EVOLUTION Were the flattened, asymmetric Paleozoic animals known as stylophorans in fact early chordates. This calcichordate hypothesis requires that chordates originally possessed calcite skeletons made of stereom (a microscopic mesh embedded in mesodermal tissues). But, traditionally, stereom has been seen as diagnostic of the echinoderms, and most paleontologists have interpreted stylophorans accordingly. Because they and the other homalozoans lack the fivefold symmetry so characteristic of living echinoderms (such as sea urchins), all four classes of homalozoans usually are placed together near the base of the phylum Echinodermata. Recently, researchers have combined ontogenetic, embryologic, and molecular evidence to identify body-wall homologies among extant echinoderms. David et al. have applied these findings to reinterpret homalozoan morphologies (in particular, the thecal walls, stems, arms, and brachioles). They conclude that homalozoans comprise independently evolved groups of echinoderms, whose asymmetry is derived rather than representative of the phylum's original morphology. Three classes possess brachioles and are placed within the blastozoans (an extinct Paleozoic clade). The controversial stylophorans are most closely releated to crinoids (sea lilies). This new phylogeny is more congruent with the known fossil record. — SJS Paleobiology 26 , 529 (2000).

New teleostean fishes from the Jurassic of southern Germany and the systematic problems concerning the ‘pholidophoriforms’

A new genus,Siemensichthys, from the Upper Jurassic of southern Germany is described. The new genus includes two species,S. macrocephalus (Agassiz) which was formerly in the genusPholidophorus, andS. siemensi n. sp. The two species share synapomorphies such as only one supramaxillary bone covering the dorsal margin of the maxilla. Both species are described, and their phylogenetic position is analyzed. The phylogenetic analyses, based on 27 taxa and 141 characters, show thatAnkylophorus from the Kimmeridgian of Cerin,Siemensichthys andEurycormus from the Solnhofen Lithographic Limestone of Bavaria, form a monophyletic group. The new extinct clade (preliminarily identified as theSiemensichthys- group) is proposed as the sister-group ofPholidophorus s. str. plus more advanced teleosts. This sister-group relationship is supported by eight characters (e.g., supraoccipital bone extending forward in the roof of the otic region; articular bone fused with both the angular and retroarticular; presence of an elongated posteroventral process of quadrate; presence of dorsal processes at the base of the innermost caudal rays of upper lobe; mobile premaxillary bone). Comparisons with species ofPholidophorus s. str. provide a new understanding of the genusPholidophorus. At least four synapomorphies are proposed to support the monophyly ofPholidophorus. As a consequence of this new interpretation, the European Late Jurassic species previously assigned to the Pholidophoridae and to the genusPholidophorus (e.g., ‘Ph.’armatus, ‘Ph.’ falcifer, ‘Ph.’ micronyx, ‘Ph.’ microps) should be reexamined because they do not belong to the family nor to the genus. The order PholidophoriformesBerg is not a monophyletic group as currently constructed. Therefore, all so-called pholidophoriforms are in need of revision.

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa.

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.

The time of origin of whales and the role of behavioral changes in the terrestrial-aquatic transition

Addition of the recently discovered fossil Nalacetus to a phylogenetic analysis of basicranial, cranial, dental, postcranial, and soft morphological characters reveals that it is the most basal cetacean, and that mesonychians form the monophyletic sister group to Cetacea. The molars of Nalacetus elucidate transformations in dental morphology that occurred early in the cetacean radiation and clarify certain derived differences in molar cusp position between cetaceans and the extinct clade, Mesonychia, hypothesized to be their sister taxon. Nalacetus and other archaic cetaceans share derived vertically elongate shearing facets on the lower molars. Applying the Extant Phylogenetic Bracket, we advance the hypothesis that these facets are an osteological correlate of aquatic predation. Our functional interpretation of this character and its distribution within Cetacea indicates that a behavioral change in tooth use characterized the origin of the clade. Comparison of the transformation of this dental character with that of the cetacean pelvis indicates that a change in tooth use (feeding behavior) occurred before loss of the ability to engage in terrestrial locomotion.The most parsimonious phylogenetic hypothesis presented here has a significant fit with the stratigraphic record as determined by the Manhattan Stratigraphic Measure, which is corroborated by retention indices of stratigraphic data. Ghost lineages necessitated by the phylogenetic hypothesis extend the stratigraphic range of Cetacea into the middle Paleocene (Torrejonian), ten million years earlier than the oldest cetacean fossil currently known. Primitive features of Nalacetus, the large number of synapomorphies diagnosing Cetacea, and the implied ghost lineage suggest that the early cetacean radiation was much more extensive than has been previously recognized.

The Fossil History of the Gnetales

The fossil record of dispersed pollen documents that the extant genera Ephedra, Welwitschia, and Gnetum are the relictual extant remnants of a group of plants that was once more widespread and much more diverse. Unfortunately, macrofossils corresponding to these dispersed palynomorphs remain sparse, and only scattered information on other organs of fossil Gnetales are available Late Triassic and Early Jurassic fossils provide the most radical additions to knowledge of morphological diversity among probable extinct Gnetales, but more detailed information is needed to reliably and accurately establish their systematic affinities. In the long term, detailed morphological data from such fossils will be crucial for understanding morphological homologies between the reproductive structures of Gnetales and those of other plants. However, in the short term, studies of well-preserved material from Cretaceous mesofloras may be more informative Among the recent results of such studies has been the identification of small dispersed seeds with ephedroid pollen in the micropyle, and increased knowledge of the plants that produced the widespread and distinctive Mesozoic pollen grains assigned to the genus Eucommiidites. These data indicate that Eucommiidites producers (Erdtmanithecaceae) comprise an extinct clade with probable close affinities to the Gnetales.

The shape of evolution: a comparison of real and random clades

The history of life is replete with apparent order. Much of this order may reflect the deterministic causes conventionally invoked, but we cannot be sure until we measure and subtract the order that arises in simple random systems. Consequently, we have constructed a random model that builds evolutionary trees by allowing lineages to branch and become extinct at equal probabilities. We proceed by dividing our simulated tree into clades and by comparing their sizes and shapes with the patterns exhibited by “real” clades as recorded by fossils.We regard the similarity of real and random clades as the outstanding result of this comparison. In both real and random systems, extinct clades arising after an “ecological barrel” had been filled have their maximum diversity at the midpoint of their duration; clades arising during the initial “filling” reach an earlier climax during this preequilibrial period of rapid diversification. However, some potential differences also emerge. Clades still living are much larger than extinct clades. We may attribute this to the morphological superiority of survivors, but we can also simulate it in a model that chooses the originators of clades at random. Real clades undergo greater fluctuations in diversity than do random clades, but the effect is not marked.