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On the origin of animals and placental mammals: a critique of literalist readings of the fossil record.

The fossil record is incomplete, as evidenced by the pervasive presence of ghost lineages throughout the Tree of Life. For example, across placental mammals, at least 720 Myr of basal lineages are ghost lineages, that is, lineages that have left no fossil evidence of their past history. In contrast, some studies have suggested that the fossil record is a faithful temporal archive of evolutionary history and thus the times of diversification of clades must be close to the ages of their oldest fossils. Such literalist interpretations have been contradicted by analysis of molecular datasets which, in many cases, indicate that groups including placental mammals and animals may have originated at times substantially older than their fossil records. Some of those studies have further argued that, in the case of animals and placental mammals, molecular clocks are uninformative, suffer from characteristic pathologies, and thus cannot distinguish between recent and ancient hypotheses of diversification. Here, we reexamine these two cases and show, using Bayesian model selection theory, that the explosive diversification models previously proposed for animals and placental mammals have a posterior probability of ∼0. We show the characteristic pathologies purportedly discovered do not exist, highlight errors in previous analyses, and provide advice on best practice for molecular-clock dating analysis.

Animals

Methods of preparation of fossil bone samples for light and transmission electron microscopy.

The methods described make possible the preparation of fossil samples for light nad transmission electron microscopy. To obtain good images with ground sections of bone, both the grinding process and classical bone staining techniques were modified, the latter by staining already made ground sections. Ground sections of suitable thickness were etched with a 4:1 mixture of 5% HNO3 and 2% OsO4 at a lowered temperature, thereby obtaining isolated osteocytes with a complete network of processes. Using the same method with thicker ground sections, the contents of vascular canals were isolated. The contents retained spatial relations permitting complete reconstruction of the vascular system of the bone in question. The isolated osteocytes, the vascular canal contents, and the isolated remnants of the intercellular organic part of this bone, subsequently embedded in Epon 812 and in methacrylate, made possible sections suitable for detailed analysis of the image of the surfaces of these elements. Polished surfaces of the fossil bone were replicated by the so-called clearing replicas technique adapted to fossil bone. The latter facilitated analysis of the ultrastructure of the surfaces of the vascular canals, isolated osteocytes and their processes, and analysis of the immediate proximity of these elements, since the technique preserves the mutual spatial relations intact.

Animals

Evolutionary legacy of the "living fossil" genus Parrotia (Hamamelidaceae): genomic insights into species divergence and polygenic adaptation.

Despite their long evolutionary history, the genomic basis of adaptation and speciation in "living fossil" plants remain largely unexplored. Parrotia, a Tertiary relict tree genus with two extant species, P. subaequalis and P. persica, exhibits a disjunct distribution between East Asia and West Asia. Here, we present the first chromosome-level assemblies for both species, confirmed their sibling relationship, and dated the speciation event to the early Miocene. The recent proliferation of long-terminal repeat retrotransposons has driven the genome expansion in P. subaequalis. We detected widespread heterogeneous genomic differentiation between species. Extensive signals of divergent selection, local adaptation, and elevated Ka/Ks ratios in Parrotia indicate that this genus has undergone adaptive evolution in distinct refugia, challenging the notion of it as an "evolutionary dead end". Our findings provide new insights into the genomic evolution, environmental adaptation, and speciation of this "living fossil" tree genus.

Genome, Plant

New fossil hominids from Laetolil, Tanzania.

New fossil hominid specimens from the Laetolili fossil locality in Tanzania are described. The material includes mandibles and teeth derived from reliably-dated deposits of Pliocene age. Preliminary descriptions, measurements and illustrations are presented.

Dentition

Computed tomography and biomechanical analysis of fossil long bones.

Computerized transverse axial scanning (computed tomography) is a relatively new radiographic technique designed to recover precise cross-sectional images (tomograms) of 3-dimensional objects. This highly sensitive process permits tissues of similar density to be separated and displayed unambiguously. These special features are, therefore, ideal for analyzing the cross-sectional geometry of intact fossil long bones, even when they are highly mineralized and their medullary cavities are occluded by matrix. In order to demonstrate the utility of this method in assessing the complex relationship between fossil structure and probable function, geometrical and biomechanical properties of midshaft tomograms of femora and tibiae have been analyzed for a comparative primate sample consisting of Megaladapis edwardsi (an extinct giant prosimian from Madagascar), Indri indri (the largest extant prosimian), and Homo sapiens.

Animals

Fossil reptilian gelatins.

1. Studies have been made of products obtained by treating several reptilian fossil bones with dilute formic acid. 2. Their amounts and compositions have been compared with those of similarly treated fresh and Pleistocene bones. 3. Fewer and small peptides are obtained from the older fossils but in only one instance was the composition significantly different from that of the total protein. 4. For the collagenous proteins aspartic acid was the most readily freed by hydrolysis; for these older proteins it is alanine. 5. Unlike the Pleistocene proteins, the chromatograms from these older proteins have always had peaks in the position of beta-alanine, and usually others of unidentified origin.

Amino Acids

Morphological differentiation of the fossil dinosaur bone cells. Light, transmission electron-, and scanning electron-microscopic studies.

The investigation was carried out on the fossil dinosaur bone from before 80 million years. Samples for examination were prepared with specially elaborated methods. Thus the isolated osteocytes of the dinosaur bone, which had previously undergone natural fossilizing processes, were obtained. This permitted their morphological assessment. On the basis of the images obtained in the light, transmission electron, and scanning electron microscopes, two types of osteocytes were distinguished. Type I was characterized by an elongated shape, its length exceeding the width several times; the mean dimensions of this osteocyte amounted to 28.8/7.03 micron. Type II was shorter, its mean dimensions being equal to 20.28/6.88 micron. Moreover, two types of osteocytes processes were differentiated: the first was represented by thick processes, so-called 'axial processes', whose diameter ranged from 0.5 to 1.5 micron, and which, as a rule, departed from the pole of the cell. They ran farther from the mother cell body to more distant osteocytes. The other type consisted of thin processes departing from various points of the cell body in no particular arrangement but always extrapolarly. They branched off in a close vicinity of the mother osteocyte. Their diameter ranged between 0.076 and 0.35 micron.

Animals

Studies on the condition and structure of bone of the Saldanha fossil cranium.

The external surface of the Saldanha cranium shows extensive exfoliation and cracking. In a few places remnants of the probable original bone surfaces can be observed. These are orange-brown in color, contrasting with the nearly white color of exposed deeper layers, and are subdivided into small segments with pits in their centers. Causes of the color differences are uncertain but merit investigation. The surface cracking and exfoliation probably result from weathering before fossilization. This conclusion is based on the observation that the endocranial surfaces show no such effects, despite the scattering of the cranial fragments at the time of discovery. A depressed fracture in the frontal bone indicates a heavy blow at or shortly after the time of death. This blow probably created some of the fragments, but there are also incomplete fracture cracks which may have resulted from the blow. Unresolved taphonomic problems include the manner in which the cranium held together after decay of soft tissues allowed weathering, and the manner in which the fragments were subsequently scattered. Chips from the cranial vault indicate that the outer table was very thick, tending to support recent proposals that the specimen and assoicated fauna and tools are from a considerably earlier time period than originally believed. The surface damage to the brow ridges gives information on the structure of deeper layers. These are lacking orientation, supporting the hypothesis that hominid brow ridges are not primarily a response to masticatory forces, but may afford protection for the eyes.

Animals

Interpretation of the results of investigating molecular fossils.

The difficulties and possible errors in interpreting the results of investigating molecular fossils within the scope of the problem of chemical evolution and origin of life on the earth are examined. These difficulties can be largely overcome on the basis of modeling processes of the transformation of organic matter under different geological conditions.

Amino Acids

Regional variation in tooth size and pathology in fossil hominids.

Tooth size and dental pathology in fossil hominids were studied to test for regional differences in these parameters. The results showed little regional variation in tooth size for the Middle and Upper Pleistocene sites compared (except for Krapina) but considerable differences in the severity of attrition and dental pathology. These differences were considered indicative of regional differences in the functional load borne by the teeth, and in view of the similar technological status of the groups studied, were attributed to environmental differences in the diet. Since, in all regions, reduction in tooth size appeared to continue at the same rate for the periods investigated, no association can be established between presumed selective pressures related to differences in functional demands made on the dentition, and tooth reduction.

Adult

A fossil skull probably of the genus Homo from Sterkfontein, Transvaal.

A skull with numerous Homo features was discovered at Sterkfontein, near Krugersdorp, Transvaal, in August 1976. It stems from member 5 of the Sterkfontein Formation, with stone tools and with fauna pointing to an age of 2.0-1.5 Myr. The underlying member 4 contains Australopithecus africanus, no stone tools, and fauna dated 3.0-2.5 Myr. The new find supports the view that the Sterkfontein toolmaker was not the earlier A. africanus, but a later hominid related to Homo habilis. By a remarkable double coincidence, the first pieces of the new skull, Stw 53, were found on August 9, 1976, 40 years to the day after Robert Broom's first visit to Sterkfontein, while the last part came to light on August 17, the 40th anniversary of Broom's first discovery of a hominid cranium at Sterkfontein. Although most of the fragments were found in a decalcified pocket of cave earth, one large part of the calvaria was still present in the calcified wall of the pocket, thus establishing indisputably the provenance of the specimen.

Craniology