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At least 55 records · Page 3Linked to original sources

PubMed2005

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.

We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.

Animals↗

PubMed2006

Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution.

Testing models of macroevolution, and especially the sufficiency of microevolutionary processes, requires good collaboration between molecular biologists and paleontologists. We report such a test for events around the Late Cretaceous by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describe the gradual decline of pterosaurs at the same time modern birds radiate. The penguin fossils comprise four naturally associated skeletons from the New Zealand Waipara Greensand, a Paleocene (early Tertiary) formation just above a well-known Cretaceous/Tertiary boundary site. The fossils, in a new genus (Waimanu), provide a lower estimate of 61-62 Ma for the divergence between penguins and other birds and thus establish a reliable calibration point for avian evolution. Combining fossil calibration points, DNA sequences, maximum likelihood, and Bayesian analysis, the penguin calibrations imply a radiation of modern (crown group) birds in the Late Cretaceous. This includes a conservative estimate that modern sea and shorebird lineages diverged at least by the Late Cretaceous about 74 +/- 3 Ma (Campanian). It is clear that modern birds from at least the latest Cretaceous lived at the same time as archaic birds including Hesperornis, Ichthyornis, and the diverse Enantiornithiformes. Pterosaurs, which also coexisted with early crown birds, show notable changes through the Late Cretaceous. There was a decrease in taxonomic diversity, and small- to medium-sized species disappeared well before the end of the Cretaceous. A simple reading of the fossil record might suggest competitive interactions with birds, but much more needs to be understood about pterosaur life histories. Additional fossils and molecular data are still required to help understand the role of biotic interactions in the evolution of Late Cretaceous birds and thus to test that the mechanisms of microevolution are sufficient to explain macroevolution.

Animals↗

PubMed1999

Fossil fuel biomarkers in sewage sludges: environmental significance

Fossil fuel biomarkers, or "molecular fossils," are specific organic substances found in coals, petroleums, and sedimentary rocks. They are formed during millions of years of sedimentary burial by geochemical alteration of biological molecules, such as cholesterol, under the effect of biodegradation, temperature, pressure, and mineral catalysis, to produce geochemically mature molecules, for example, aromatic steroids (Fig. 1). Since fossil fuel biomarkers have a very specific molecular structure betraying fossil fuel sources, such markers should be useful in assessing the fossil fuel contamination of various modern media such as soils, plants, waters, and modern sediments. Here the identification of fossil fuel biomarkers of high geothermal maturity in sewage sludges provides evidence of the contamination of sludges by petroleum products. The most likely sources of contamination are contaminated vegetal food, road dust, and soil particles carried by rain water.http://link. springer.de/link/service/journals/00114/bibs/9086010/90860484. htm</HEA

Journal Article↗

PubMed1999

Study of fossil tracks due to 50 < or = Z < or = 92 galactic cosmic ray nuclei in meteoritic crystals: results and perspectives.

A new approach to the problem of investigation of charge and energy spectra of ultra heavy Galactic cosmic ray nuclei, based on fossil track study of extraterrestrial olivine crystals has been developed. The results of an investigation of ultra heavy Galactic cosmic ray nuclei (Z=50-92) in meteoritic olivine crystals are presented. The technique was based on calibration of olivine crystals with accelerated Xe, Au, Pb and U ions and well-controlled partial annealing of "fresh" and "fossil" tracks. It allows us to determine the charge spectra and abundances of cosmic ray nuclei based on fossil track length study in meteoritic and Moon crystals. The comparative studies of the spectra of "fossil' tracks and tracks due to 208Pb and 238U nuclei have shown that the group of 210 micrometers "fossil" tracks, first observed in 1980 at JINR is due to Th-U nuclei-products of recent r-process nucleosynthesis in our Galaxy. The method in principle allows one to resolve Pt-Pb peaks in fossil tracks, to establish the upper limit of the abundance of Z>110 nuclei in the Galactic cosmic rays at the level < or = 10(-3) to the abundance of actinide nuclei and to get information on the history of Z>50 cosmic ray nuclei in time interval up to 220 M.Y.

Calibration↗

PubMed1992

Oldest fossil flowers of hamamelidaceous affinity, from the Late Cretaceous of New Jersey.

Exceptionally well-preserved staminate inflorescences, pistillate inflorescences, and detached stamens with important phylogenetic and paleoecological implications have been discovered from the Turonian (ca. 88.5-90.4 million years B.P.) Raritan Formation of New Jersey. The fossils have a combination of floral and pollen characters found in various genera of modern entomophilous and anemophilous Hamamelidaceae and anemophilous Platanus (Platanaceae). The floral characters of the fossils, including a sepal cup, staminal tube, and apparently nectariferous staminodes, indicate that this taxon was probably insect pollinated. The juxtaposition of character complexes in an extinct taxon from disparate modern taxa provides an interesting phylogenetic perspective on the origins of Hamamelidaceae and is a striking example of a fossil that is a mosaic of familial level characters relative to modern taxa. Of even broader interest, however, is the occurrence of staminodal nectaries that have structural characters intermediate between the fossil's functional stamens and modern hamamelidaceous petals. This transitional staminode morphology in the context of the other fossil characters suggests a staminodal origin of petals in the hamamelid-rosid lineage. This hypothesis is supported by the apparent staminode position within the fossil flowers where petals are found in modern genera. The character complex of morphologically transitional staminodes, a staminal tube, and sepal cup can be viewed as prehypanthial, lacking only fusion of the staminal tube to the sepal cup. The appearance of the character complex embodied in these flowers during the late mid-Cretaceous may signal the early stages of the relationship between specialized pollinators, such as bees, and the hamamelid-rosid-asterid lineage of angiosperms, arguably one of the most important events in angiosperm radiation.

Journal Article↗

PubMed2026

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↗

PubMed1987

Rates of evolution: is there a conflict between neo-darwinian evolutionary theory and the fossil record?

Neo-darwinian and population genetics theory assumes that the necessary and sufficient set of conditions for all genetic, therefore evolutionary, change has been identified. Punctuationalists have assumed the opposite and cite the fossil record as evidence for change too rapid to be explained in neo-darwinian theory. Data is given here to provide estimates of the rate of evolution in hominid fossils, in living populations, and of that rate which would qualify as punctuational in the hominid fossil record. Evolution in living populations is orders of magnitude greater than that found in the fossil record and far greater than necessary to create apparently instantaneous saltations in the fossil record. It is suggested that such saltations may not represent more rapid rates of evolution but, rather, the persistence of evolutionary change in a given direction for a longer than normal period.

Animals↗

PubMed2006

Computerized restoration of nonhomogeneous deformation of a fossil cranium based on bilateral symmetry.

We developed a computerized method of correcting plastic deformation of a fossil skull, based on bilateral symmetry with respect to the midsagittal plane, and applied this method to reconstruction of a fossilized Proconsul heseloni cranium (KNM-RU-7290A). A three-dimensional (3D) model of the fossil was generated using consecutive cross-sectional images retrieved from computed tomography. 3D coordinates of anatomical landmarks that should be located on the midsagittal plane and pairs of landmarks that should be symmetrical with respect to this plane were acquired. These landmarks were then repositioned so that geometrical constraints were satisfied, while translated distances of landmarks were minimized. We adopted a thin-plate spline function to mathematically describe the 3D nonlinear volumetric transformation between acquired and repositioned landmarks. Using this function, the entire fossil shape was transformed, and the effect of reversing the deformation could be visualized. The results indicated that the proposed method was effective in eliminating nonhomogeneous deformation of the fossil skull. The antemortem appearance of the skull cannot be completely restored by this method alone, due to methodological limitations. However, the presented method has a role as an adjunct in complementing conventional restoration techniques on account of its objective nature.

Animals↗

PubMed2002

Is paleoanthropology science? Naming new fossils and control of access to them.

Progress in paleoanthropology is impeded when new fossil materials are published but unavailable for comparative study, as is too often the case. In this commentary, we review the stages of description and analysis that new fossils must undergo and conclude that it is disingenuous to argue that fossils have not been properly "published" when descriptions and new names formulated in accordance with the International Code of Zoological Nomenclature have appeared in leading scientific journals. Once such names and descriptions have been published, it is imperative that the original fossils concerned be available to the scientific community for comparative analysis, for by the very nature of science, no statement about such fossils, however carefully prepared by the original describers (or anyone else), can be regarded as definitive. Science is a system of provisional knowledge that constantly requires re-examination and testing. It cannot function as a system in which assertions have to be left unchallenged for want of free access to the primary data.

Animals↗

PubMed2005

Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates.

Recent controversy about the use of the vertebrate fossil record for external calibration of molecular clocks centers on two issues, the number of dates used for calibration and the reliability of the fossil calibration date. Viewing matters from a palaeontological perspective, we propose three qualitative, phylogenetic criteria that can be used within a comparative framework for the selection of well-constrained calibration dates from the vertebrate fossil record. On the basis of these criteria, we identify three highly suitable new fossil calibration dates for molecular clock estimates: the lungfish-tetrapod split (between 419 and 408 Ma), the bird-crocodile split (between 251 and 243 Ma), and the alligator-caiman split (between 71 and 66 Ma). Together with our previously suggested bird-lizard split (between 252 and 257 Ma), these four fossil dates span a range of very different ages. They are, in our opinion, more suitable for molecular clock calibration than the traditionally used mammal-bird split, which is less well constrained. We plea for closer interactions between paleontologists and molecular biologists in studying the timescale of vertebrate evolution.

Animals↗

PubMed2007

Is Palaeospondylus gunni a fossil larval lungfish? Insights from Neoceratodus forsteri development.

The enigmatic Devonian fossil Palaeospondylus gunni was identified as a larval form, metamorphosing into the lungfish Dipterus valenciennesi. Morphological features used to identify P. gunni as a larval lungfish include enlarged cranial ribs, rudimentary limb girdles, and absence of teeth. However, this combination of features does not characterize the extant lungfish Neoceratodus forsteri, even at very young stages, nor early stages of Devonian and younger fossil lungfish. Absence of teeth is problematic because early ontogenetic stages of fossil and living lungfish possess full dentitions including marginal teeth. Also problematic are cranial ribs as a defining character of lungfish, as these also occur in certain actinopterygians. It is argued that Neoceratodus is an obligate neotene (reproductively mature larva), with the implication that metamorphosis was a feature of the ontogeny of early lungfish. Pedomorphic characters have been recognized in Neoceratodus and other post-Devonian lungfish, including large cells and correspondingly large genome size; these latter characters correlate with neoteny in salamanders. Small cells preserved in fossil bone suggest that Devonian lungfish had a smaller genome than post-Devonian lungfish, implying that they were not neotenic. As fossil lungfish cell sizes (and genomes) increased in the late Paleozoic, the diversity of lungfish morphologies decreased, so that taxa like Sagenodus and Conchopoma show morphological similarity to Neoceratodus, marking a point in phylogeny at which metamorphosis was potentially lost. Since ancestral larval characters are retained in neotenic adults, we predict that Devonian larvae should resemble these post-Devonian taxa, a prediction which Palaeospondylus does not fulfill.

Animals↗

PubMed2001

Taphonomy of the fossil hominid bones from the Acheulean site of Castel di Guido near Rome, Italy.

Castel di Guido near Rome is one of the few open air Middle Pleistocene European sites that has yielded hominid skeletal remains associated with fossil fauna and Acheulean implements. The fossil hominid bones include two femoral shafts, respectively designated Castel di Guido-1 (CdG-1) and CdG-2, an occipital fragment (CdG-3), a right maxilla lacking teeth (CdG-4), a portion of right parietal (CdG-5), a right temporal (CdG-6), and a fragment of left parietal vault (CdG-7). CdG-1 through CdG-4 were collected in 1979-1982 on the surface, together with fossil fauna, where ploughing incised fossiliferous tuffaceous sands. Excavations conducted in the same area from 1980 to 1990 led to the discovery of CdG-5, CdG-6 and CdG-7 within the tuffaceous sands, which were shown to overlay a bone-bearing paleosurface, with abundant evidence of hominid activities. The Castel di Guido hominid assemblage poses intriguing taphonomic questions. The analysis of the physical evidence offered by the bone surfaces, reported in the present study, indicates that the hominid skeletal remains were heavily fragmented before fossilization and exposed to carnivores and rodents, as well as to trampling and/or friction in abrasive sediment. Although definitive conclusions cannot be reached on the basis of the available evidence, it is possible that clusters of incisions localized on specific regions of the Castel di Guido fossil hominid bones might reflect deliberate human manipulations.

Animals↗

PubMed2004

Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa.

Recent discoveries of new fossil hominid species have been accompanied by several phylogenetic hypotheses. All of these hypotheses are based on a consideration of hominid craniodental morphology. However, Collard and Wood (2000) suggested that cladograms derived from craniodental data are inconsistent with the prevailing hypothesis of ape phylogeny based on molecular data. The implication of their study is that craniodental characters are unreliable indicators of phylogeny in hominoids and fossil hominids but, notably, their analysis did not include extinct species. We report here on a cladistic analysis designed to test whether the inclusion of fossil taxa affects the ability of morphological characters to recover the molecular ape phylogeny. In the process of doing so, the study tests both Collard and Wood's (2000) hypothesis of character reliability, and the several recently proposed hypotheses of early hominid phylogeny. One hundred and ninety-eight craniodental characters were examined, including 109 traits that traditionally have been of interest in prior studies of hominoid and early hominid phylogeny, and 89 craniometric traits that represent size-corrected linear dimensions measured between standard cranial landmarks. The characters were partitioned into two data sets. One set contained all of the characters, and the other omitted the craniometric characters. Six parsimony analyses were performed; each data set was analyzed three times, once using an ingroup that consisted only of extant hominoids, a second time using an ingroup of extant hominoids and extinct early hominids, and a third time excluding Kenyanthropus platyops. Results suggest that the inclusion of fossil taxa can play a significant role in phylogenetic analysis. Analyses that examined only extant taxa produced most parsimonious cladograms that were inconsistent with the ape molecular tree. In contrast, analyses that included fossil hominids were consistent with that tree. This consistency refutes the basis for the hypothesis that craniodental characters are unreliable for reconstructing phylogenetic relationships. Regarding early hominids, the relationships of Sahelanthropus tchadensis and Ardipithecus ramidus were relatively unstable. However, there is tentative support for the hypotheses that S. tchadensis is the sister taxon of all other hominids. There is support for the hypothesis that A. anamensis is the sister taxon of all hominids except S. tchadensis and Ar. ramidus. There is no compelling support for the hypothesis that Kenyanthropus platyops shares especially close affinities with Homo rudolfensis. Rather, K. platyops is nested within the Homo + Paranthropus + Australopithecus africanus clade. If K. platyops is a valid species, these relationships suggest that Homo and Paranthropus are likely to have diverged from other hominids much earlier than previously supposed. There is no support for the hypothesis that A. garhi is either the sister taxon or direct ancestor of the genus Homo. Phylogenetic relationships indicate that Australopithecus is paraphyletic. Thus, A. anamensis and A. garhi should be allocated to new genera.

Animals↗

PubMed2006

Revised stratigraphy of Area 123, Koobi Fora, Kenya, and new age estimates of its fossil mammals, including hominins.

Recent geologic study shows that all hominins and nearly all other published mammalian fossils from Paleontological Collection Area 123, Koobi Fora, Kenya, derive from levels between the KBS Tuff (1.87+/-0.02 Ma) and the Lower Ileret Tuff (1.53+/-0.01 Ma). More specifically, the fossils derive from 53 m of section below the Lower Ileret Tuff, an interval in which beds vary markedly laterally, especially those units containing molluscs and algal stromatolites. The upper Burgi Member (approximately 2.00-1.87 Ma) crops out only in the southwestern part of Area 123. Adjacent Area 110 contains larger exposures of the member, and there the KBS Tuff is preserved as an airfall ash in lacustrine deposits and also as a fluvially redeposited ash. We observed no mammalian fossils in situ in this member in Area 123, but surface specimens have been documented in some monographic treatments. Fossil hominins from Area 123 were attributed to strata above the KBS Tuff in the 1970s, but later they were assigned to strata below the KBS Tuff (now called the upper Burgi Member). This study definitively places the Area 123 hominins in the KBS Member. Most of these hominins are between 1.60 and 1.65 myr in age, but the youngest may date to only 1.53 Ma, and the oldest, to 1.75 Ma. All are 0.15-0.30 myr younger than previously estimated. The new age estimates, in conjunction with published taxonomic attributions of fossils, suggest that at least two species of Homo coexisted in the region along with A. boisei until at least 1.65 Ma. Comparison of crania KNM-ER 1813 and KNM-ER 1470, which were believed to be of comparable age, is at the focus of the debate over whether Homo habilis sensu lato is in fact composed of two species: Homo habilis and Homo rudolfensis. These two crania are separated in time by approximately 0.25 myr, and therefore, arguments for their conspecificity no longer need to confront the issue of unusually high contemporaneous variation within a single species.

Animals↗

PubMed2002

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.

Archaea↗

PubMed2005

First fossil chimpanzee.

There are thousands of fossils of hominins, but no fossil chimpanzee has yet been reported. The chimpanzee (Pan) is the closest living relative to humans. Chimpanzee populations today are confined to wooded West and central Africa, whereas most hominin fossil sites occur in the semi-arid East African Rift Valley. This situation has fuelled speculation regarding causes for the divergence of the human and chimpanzee lineages five to eight million years ago. Some investigators have invoked a shift from wooded to savannah vegetation in East Africa, driven by climate change, to explain the apparent separation between chimpanzee and human ancestral populations and the origin of the unique hominin locomotor adaptation, bipedalism. The Rift Valley itself functions as an obstacle to chimpanzee occupation in some scenarios. Here we report the first fossil chimpanzee. These fossils, from the Kapthurin Formation, Kenya, show that representatives of Pan were present in the East African Rift Valley during the Middle Pleistocene, where they were contemporary with an extinct species of Homo. Habitats suitable for both hominins and chimpanzees were clearly present there during this period, and the Rift Valley did not present an impenetrable barrier to chimpanzee occupation.

Animals↗

PubMed2006

Assessing the fidelity of the fossil record by using marine bivalves.

Taxa that fail to become incorporated into the fossil record can reveal much about the biases of this record and provide the information needed to correct such biases in empirical analyses of the history of life. Yet little is known about the characteristics of taxa missing from the fossil record. For the marine Bivalvia, which have become a model system for macroevolutionary and macroecological analysis in the fossil record, 308 of the 1,292 living genera and subgenera (herein termed "taxa") are not recorded as fossils. These missing taxa are not a random sample of the clade, but instead tend to have small body size, reactive shell structures, commensal or parasitic habit, deep-sea distribution, narrow geographic range, restriction to regions exposing few Neogene marine sediments, or recent date of formal taxonomic description in the neontological literature. Most missing taxa show two or more of these features and tend to be concentrated in particular families. When we exclude the smallest taxa (<1 cm) and deep-sea endemics, date of published description and geographic range become the strongest predictors of the missing taxa; other factors are statistically insignificant or have relatively small effects. These biases might influence a variety of analyses including the use of fossil data in support of phylogenetic analyses, molecular clock calibrations, and analyses of spatial and temporal dynamics of clades and biotas. Clade inventories such as these can be used to develop protocols that minimize the biases imposed by sampling and preservation.

Animals↗

PubMed2002

Atomic force microscopy of Precambrian microscopic fossils.

Atomic force microscopy (AFM) is a technique used routinely in material science to image substances at a submicron (including nm) scale. We apply this technique to analysis of the fine structure of organic-walled Precambrian fossils, microscopic sphaeromorph acritarchs (cysts of planktonic unicellular protists) permineralized in approximately 650-million-year-old cherts of the Chichkan Formation of southern Kazakhstan. AFM images, backed by laser-Raman spectroscopic analysis of individual specimens, demonstrate that the walls of these petrified fossils are composed of stacked arrays of approximately 200-nm-sized angular platelets of polycyclic aromatic kerogen. Together, AFM and laser-Raman spectroscopy provide means by which to elucidate the submicron-scale structure of individual microscopic fossils, investigate the geochemical maturation of ancient organic matter, and, potentially, distinguish true fossils from pseudofossils and probe the mechanisms of fossil preservation by silica permineralization.

Animals↗