Ancient Fossil Research Articles

Comparison and Development of A Rapid Extraction Methods of DNA from Ancient Human Skeletal Remains of Turkey

The use of genetic technology in forensic science is applied primarily to distinguish between individials who may be the source of biological material associated with archeological remains. DNA sequences from ancient fossils have great potential for studies of phylogeny, biogeography and molecular evolution. DNA from fossils also facilitates the rigorous testing and calibration of mutation rates among related taxa, sex test and molecular divergence time. In this study, a rapid and quantitative aDNA extaction methods from human skeletal remains was developed for application of forensic science and archeometry. For that reason, DNA was extracted from ancient human bones from Mugla in Turkey. Extraction of DNA was carried out using the laboratuary handling and cleaning protocol. After cleaning of bone, small piece of ancient bones were ground to powder with a mixer mill. Aliquots of the powder were subjected to a calfication method and extracted with 0.5 M EDTA (pH 8.3) for 48 hours at 56 ∞ C. After addition of proteinase K, solution of bone was incubated at 37 ∞ C. Genomic DNA from supernatant was extracted automatically by using EZ1 Automatic Nucleic Acid Isolation System (Qiagen, Germany) with investigator kit (Qiagen, Ilden, Germany) and different DNA extraction methods which are modified by researcher from ancient bones. EZ1 Nucleic acid isolation method; This tehnique is quite useful for high yield and quality of aDNA isolation from human skeletal remains. In this methods, no further purification was needed for molecular analysis. Amount and purity of extracted DNA from ancient bones were measured by Spectrophotometer. In addition to spectrophotometric measurement, extracted DNA was applied to 1 % agarose gel, stained and imaged under ultraviolet (UV) irradiation. As a result, 50 ng pure DNA was extracted from ancient bones, approximately 1.8. This protocol proved to be advantageous because of its simplicity, quickness and affordable reagents, besides the high molecular weight DNA and purity achieved in a variety of fosil bone tissues from the total set obtained from Mugla in Turkey.

Key Morphological Alterations in the Evolution of Leaves

Evolution of plant form proceeds through sequential alterations in the development of plant organs. Leaves (or fronds) are organs that have diagnostic characteristics, including definite arrangement on a stem, bilateral symmetry (abaxial/adaxial identity), and determinate growth. Evolution of those diagnostic characteristics represents a series of critical steps in plant evolution that resulted from specific developmental alterations. The fossil record reveals a transformational series in leaf evolution that highlights steps that have occurred in parallel but independently in both leptosporangiate ferns and seed plants, resulting in superficially similar frond morphologies. In this study, the fronds of the most ancient fossil fern, Psalixochlaena antiqua, and the most ancient reconstructed seed plant, Elkinsia polymorpha, are characterized and compared with leaves of modern plants in order to identify the sequence in which features of leaves in two distinct clades of euphyllophytes arose. While both fronds show a combination of characters attributable to ancestral vegetative axes and characters attributable to leaves, each plant displays different combinations of those characters. These data document dissimilar sequences of character originations and, therefore, the independent evolution of developmental mechanisms in seed plants and ferns.

Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis

Molecular preservation in non-avian dinosaurs is controversial. We present multiple lines of evidence that endogenous proteinaceous material is preserved in bone fragments and soft tissues from an 80-million-year-old Campanian hadrosaur, Brachylophosaurus canadensis [Museum of the Rockies (MOR) 2598]. Microstructural and immunological data are consistent with preservation of multiple bone matrix and vessel proteins, and phylogenetic analyses of Brachylophosaurus collagen sequenced by mass spectrometry robustly support the bird-dinosaur clade, consistent with an endogenous source for these collagen peptides. These data complement earlier results from Tyrannosaurus rex (MOR 1125) and confirm that molecular preservation in Cretaceous dinosaurs is not a unique event.

Beyond the Age of Fishes

Discovery of an unusually intact and ancient fossil fish provides further evidence that the search for modern vertebrate origins requires breaking out of the Devonian and into the preceding period.

Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are

There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms. Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The findings here do not conform to these predictions. Neanderthals are more distant to chimpanzees and gorillas than modern humans are. Dinosaurs are more distant to frogs than extant birds are. Mastodons are more distant to opossums than other placental mammals are. The genetic distance between dinosaurs and mastodons is greater than that between extant birds and mammals. Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient fossils. Far more damaging to the hypothesis than data from extant organisms, which merely question the constancy of mutation rate, the study of ancient fossil organisms here challenges for the first time the fundamental premise of modern evolution theory that genetic distances had always increased with time in the past history of life on Earth.

Mars before the Space Age

AbstractMars has surely been scrutinised since the dawn of humankind. Its appearance every couple of years like a drop of blood in the sky led to warlike attributes in the ancient world. In the 16th century Tycho Brahe made accurate observations of the position of Mars that enabled Johannes Kepler to obtain his first two laws of planetary motion. These in turn were explained by Newton's laws of motion and gravity. In the 17th century the first telescope observations were made, but Mars is small and very little surface detail could be discerned.Throughout the 18th and 19th centuries telescopes improved, revealing many dark areas on the red tinted surface. During the close opposition of 1877 sufficient detail could be seen that enabled Giovanni Schiaparelli to announce that he could see about 40 canali on Mars. This led to the saga of the canals of Mars, finally laid to rest in 1971 when Mariner 9 made observations from Martian orbit showing that the canali/canals do not exist.Belief that there was life on Mars was widespread in the 19th century. However, the majority of astronomers never believed in Martian intelligence. Least controversial was the view that the dark areas were some form of plant life. This view persisted until Mariner 4 flew past Mars in 1965 and discovered a far thinner atmosphere than previously thought. This was a low point, with impact craters dominating the images. It was Mariner 9 that revealed much more promising landscapes, including volcanic features, and others indicating that water had flowed across the surface, particularly when Mars was young. Thus, the contemporary era of Mars exploration began.Our picture of Mars today is not only much more complete than that before Mariner 4, in several ways it is quite different. The belief, however, that there might be life on Mars persists – subsurface life cannot be ruled out and, failing that, there might be ancient fossils on Mars.

Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are

AbstractThere exists a remarkable correlation between genetic distance and time of species divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies on extant organisms. Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The findings here did not support these predictions. Neanderthals are more distant to chimpanzees and gorillas than modern humans are. Dinosaurs are more distant to frogs than extant birds are. Mastodons are more distant to opossums than other placental mammals are. The genetic distance between dinosaurs and mastodons is greater than that between extant birds and mammals. Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient fossils.

Interpreting Sequences from Mastodon and T. rex

J. Asara et al. reported that collagen proteins from well-preserved ancient fossil bones from a 160,000- to 600,000-year-old mastodon and a 68-million-year-old T. rex can be extracted and sequenced (“Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry,” 13 April,

Ancient fossil forest found by accident

Ancient fossil forest found by accident

From Fossils to Molecules: Phylogeny and the Core Eudicot Floral Groundplan in Hamamelidoideae (Hamamelidaceae, Saxifragales)

Most floral diversity in the core eudicots is based on a groundplan that includes among its most distinctive elements a bipartite perianth and pentamerous merosity combined with a bicarpellate gynoecium. To obtain insights into the origins of this groundplan, the evolution of its structural components in Hamamelidoideae (Hamamelidaceae, Saxifragales, core eudicots) is explored. Phylogenetic hypotheses were obtained from independent analyses of morphological and molecular data, and from two alternative approaches to integrating morphological and molecular data from living and fossil taxa. In spite of the large numbers of missing data cells, fossils were unambiguously placed within particular clades in the well resolved but poorly supported trees obtained from morphological data. Phylogenetic analyses of individual and combined molecular data sets using different optimization criteria resulted in congruent trees that share most strongly supported nodes. No well-supported incongruence existed among the morphological and molecular trees. A total evidence analysis including only complete taxa was congruent with molecular trees, but resolution decreased substantially as incomplete taxa and incomplete characters were included. A parsimony analysis of morphological data constrained with the strongly supported nodes from the total evidence tree resulted in the same backbone relationships as the molecular trees and in the unambiguous placement of fossil taxa; however, relationships within some clades were unique. The floral characters of ancient fossils and their nested placement in the phylogeny indicate stasis in floral structure since the origin of major lineages of Hamamelidoideae. Individual elements of floral structure display independent evolutionary histories, suggesting that the core eudicot floral groundplan evolved through the accretion of components which originated at different points during angiosperm history: some outside the eudicots, and others, namely the bipartite perianth and the pentamerous merosity, most likely within core eudicots.

A redescription of ‘Plesiochelys’ tatsuensis from the Late Jurassic of China, with comments on the antiquity of the crown clade Cryptodira

ABSTRACT A reexamination of the holotype of ‘Plesiochelys’ tatsuensis Yeh, 1963, from the Late Jurassic of China, allows us to establish previously unknown characters of this species. A phylogenetic analysis places ‘P.’ tatsuensis on the stem of Trionychia, near the clades Adocidae and Nanhsiungchelyidae. Given the hypothesized phylogenetic position of ‘P.’ tatsuensis, a new genus, Yehguia gen. nov., is erected for this species. The phylogenetic position of Y. tatsuensis pushes the origin of the crown clade Cryptodira into the Late Jurassic. This is remarkable in light of recent studies that moved the origin of crown group turtles (Testudines) from the Triassic to the Late Jurassic. This means that the establishment of basal cryptodiran lineages must have quickly followed the origin of Testudines in the Late Jurassic. The fact that the most ancient fossil Cryptodira is hypothesized to be on the stem of Trionychia is concordant with recent molecular hypotheses that place Trionychia as the most basal extant lineage of Cryptodira. Finally, our results further highlight that the Late Jurassic of China is important for understanding the earliest evolution of cryptodiran turtles.

Late Tertiary origins of the Arctic beetle fauna

During the past 30 years, Quaternary insect paleontologists working in the Arctic have studied rare deposits of fossil insects that date back millions of years. Some of these fossils may be as old as the Late Miocene. The fossils have been preserved mostly in permafrost environments, and their state of preservation is often exceptional. The vast majority of identifiable beetle specimens appear to match modern, extant species. This morphological constancy through time appears to reflect constancy of physiological adaptations, as well. The latter aspect is demonstrated indirectly through the ecological compatibility of species found in the ancient fossil assemblages. While most of the species themselves appear to have remained constant, the biological communities in which they lived have shifted dramatically through time. Based on both insect and plant fossil data, Late Tertiary environments of the Arctic were substantially warmer than they are today, supporting the growth of coniferous forests, up to the shores of the ancient Arctic Ocean. By about 2 million years ago (my) or shortly thereafter, Arctic tundra communities came into existence in parts of Beringia. Arctic insect faunal diversity declined markedly with the onset of Quaternary cooling.

Stromatolite reef from the Early Archaean era of Australia

The 3,430-million-year-old Strelley Pool Chert (SPC) (Pilbara Craton, Australia) is a sedimentary rock formation containing laminated structures of probable biological origin (stromatolites). Determining the biogenicity of such ancient fossils is the subject of ongoing debate. However, many obstacles to interpretation of the fossils are overcome in the SPC because of the broad extent, excellent preservation and morphological variety of its stromatolitic outcrops--which provide comprehensive palaeontological information on a scale exceeding other rocks of such age. Here we present a multi-kilometre-scale palaeontological and palaeoenvironmental study of the SPC, in which we identify seven stromatolite morphotypes--many previously undiscovered--in different parts of a peritidal carbonate platform. We undertake the first morphotype-specific analysis of the structures within their palaeoenvironment and refute contemporary abiogenic hypotheses for their formation. Finally, we argue that the diversity, complexity and environmental associations of the stromatolites describe patterns that--in similar settings throughout Earth's history--reflect the presence of organisms.

Genetic evidence for complex speciation of humans and chimpanzees

The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human-chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human-chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.

Hanskerpiagen. nov. and phylogenetic relationships among the most ancient conifers (Voltziales)

AbstractA new fossilized walchian (Voltziales) conifer plant from the Late Pennsylvanian Hamilton Quarry of Kansas, U.S.A. combines morphological characters of the morphogenusWalchiaand the fossil plant genusOtovicia, with cuticular characters like those of the fossil plant genusErnestiodendron, and seed cone morphology like that of the fossil plant genusEmporia. Internal anatomical characters are basically similar to the other walchian genera for which such features are known, but some are taxonomically informative. Numerical cladistic analysis reveals that this novel combination of characters defines a new fossil plant genus and species of walchian conifersHanskerpia hamiltonensis. This analysis provides a test of hypotheses for relationships among walchian and other ancient conifers. Results of this analysis support some previously proposed relationships among the most primitive conifers and other Paleozoic coniferophytes. However, the analysis also calls to question the validity of all previously proposed familial circumscriptions for walchian conifers, and highlights the perplexing systematic challenges posed by the most ancient fossil conifers. The unexpected species richness of voltzialean conifers is interpreted as having resulted from the evolutionary ecology of unstable environments.

Building Virtual Hominids: Musical Duo Reconstructs Ancient Fossils

PONCE DE LEON AND ZOLLIKOFER PROFILEZURICH, SWITZERLAND-- A pair of researchers team up professionally and personally to perfect the art of putting distorted fossils back together in the computer.

Clues to occludin. Focus on “Knockdown of occludin expression leads to diverse phenotypic alterations in epithelial cells”

FOR MANY YEARS AFTER ITS SYSTEMATIC morphological description by Farquhar and Palade in 1963 (7), the tight junction remained a puzzle. The freeze-fracture knife exposed anastomosing ridges in platinum/carbon replicas resembling the bones of ancient fossils, and, like fossils, provided few clues to living, breathing function. Speculation abounded about the true nature of the tight junction, with those favoring protein or lipid structures squared off in competing camps (14) while others counted strands and developed models, waiting for new breakthroughs (4). All of this began to change in 1986 with the identification of ZO-1 (15), proudly named as the first bona fide component of the zonula occludens, as tight junctions were formally bestowed by Farquhar and Palade (7). Enthusiasm was tempered, however, with the recognition that ZO-1 was not an integral membrane protein, but one that associated with the cytoplasmic face of the tight junction and thus could not account for the intercellular seal or the intramembrane ridges.

W poszukiwaniu „brakującego ogniwa”

Eighty years ago Raymond A. Dart wrote the papers about Australopithecus africanus and decided to classify it as a “missing link". The creature from Taung represented an ultra-simian and pre-human stock. Therefore, he proposed a new family Homo - simiadae. Nowadays, scientists on the occasion of this anniversary publish, many papers about this event. They want to remind discussion about Taung's child and in homage to Raymond A. Dart. Surprisingly, the discussion which took place in the thirties and forties was an exact repetition of the earlier debate about Trinil's fossil! In 1890/91 Dubois had found already ancient fossils in Java which classified as Pithecanthropidae - this new family was an evolutionary "bridge" between apes and man. However, despite the fact that anthropologists wanted to find a “missing link” they rejected those interpretations! Some of them thought that fossil form Taung and Trinil belonged to a true ape. Whereas the others believed that remains should have been classified as a hominid family. Those two debates indicate one scheme of thinking: 1. theoretical view of “missing link”; 2. empirical researching; 3. taxonomic debate about fossil; and 4. rejecting the idea of “missing link”.

Archaeobotanic evidence of the preincaic Chiribaya culture. Determination of capsaicinoids in archaeological samples of Capsicum frutescens and votive foods.

The lack of Capsicum species or paprika (a basic ingredient of Peruvian foodstuff) in preincaic archaeological samples and votive foods, as evidenced by archaeobotanic studies, has stimulated the chemical analyses of these samples by HPLC methods. The results confirmed the absence of capsaicinoids in these samples whereas they were detected in more ancient fossil fruit.

Laser--Raman imagery of Earth's earliest fossils.

Unlike the familiar Phanerozoic history of life, evolution during the earlier and much longer Precambrian segment of geological time centred on prokaryotic microbes. Because such microorganisms are minute, are preserved incompletely in geological materials, and have simple morphologies that can be mimicked by nonbiological mineral microstructures, discriminating between true microbial fossils and microscopic pseudofossil 'lookalikes' can be difficult. Thus, valid identification of fossil microbes, which is essential to understanding the prokaryote-dominated, Precambrian 85% of life's history, can require more than traditional palaeontology that is focused on morphology. By combining optically discernible morphology with analyses of chemical composition, laser--Raman spectroscopic imagery of individual microscopic fossils provides a means by which to address this need. Here we apply this technique to exceptionally ancient fossil microbe-like objects, including the oldest such specimens reported from the geological record, and show that the results obtained substantiate the biological origin of the earliest cellular fossils known.