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At least 19 recordsLinked to original sources
PubMed2004

Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection.

Estimates of species divergence times using DNA sequence data are playing an increasingly important role in studies of evolution, ecology and biogeography. Most work has centred on obtaining appropriate kinds of data and developing optimal estimation procedures, whereas somewhat less attention has focused on the calibration of divergences using fossils. Case studies with multiple fossil calibration points provide important opportunities to examine the divergence time estimation problem in new ways. We discuss two cross-validation procedures that address different aspects of inference in divergence time estimation. 'Fossil cross-validation' is a procedure used to identify the impact of different individual calibrations on overall estimation. This can identify fossils that have an exceptionally large error effect and may warrant further scrutiny. 'Fossil-based model cross-validation' is an entirely different procedure that uses fossils to identify the optimal model of molecular evolution in the context of rate smoothing or other inference methods. Both procedures were applied to two recent studies: an analysis of monocot angiosperms with eight fossil calibrations and an analysis of placental mammals with nine fossil calibrations. In each case, fossil calibrations could be ranked from most to least influential, and in one of the two studies, the fossils provided decisive evidence about the optimal molecular evolutionary model.

Animals↗
PubMed2002

Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils.

Many efforts to date evolutionary divergences by using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies often are attributed to the inadequacy of the fossil record, but many potential sources of error can affect molecular-based estimates. In this study, we minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes. Age estimates varied because of gene effects, codon position, lineage effects, method of inferring branch lengths, and whether or not rate constancy was assumed. However, even methods designed to ameliorate the effects of rate heterogeneity among lineages could not accommodate the substantially slower rates observed in Marattia + Angiopteris and in the tree ferns. Both of these clades of ferns have undergone dramatic decelerations in their rates of molecular evolution and are "molecular living fossils," consistent with their relative morphological stasis for the past 165-200 million years. Similar discrepancies between the fossil record and molecular-based age estimates noted in other studies may also be explained in part by violations of rate constancy among lineages.

Journal Article↗
PubMed1976

Are the oldest 'fossils', fossils?

A comparative statistical study has been carried out on populations of modern algae, of Precambrian algal microfossils, of the 'organized elements' of the Orgueil carbonaceous meteorite, and of the oldest microfossil-like objects now known (spheroidal bodies from the Fig Tree and Onverwacht Groups of the Swaziland Supergroup, South Africa). The distribution patterns exhibited by the greater than 3000 m.y.-old Swaziland microstructures bear considerable resemblance to those of the abiotic 'organized elements' but rather markedly differ from those exhibited by younger, assuredly biogenic, populations. Based on these comparisons it is concluded that the Swaziland spheroids could be, at least in part, of non-biologic origin; these oldest known fossil-like micro-structures should not be regarded as constituting firm evidence of Archean life.

Biological Evolution↗
PubMed1989

Correlation between occurrence of leprosy and fossil fuels: role of fossil fuel bacteria in the origin and global epidemiology of leprosy.

On the basis of correlative data on the global distribution of leprosy, its bacteria metabolizing fossil fuels (FF), and the FF themselves, the origin of leprosy in the world as a whole, and in the leprosy-free countries, in particular, as indigenous cases, appeared to be primarily due to a soil-to-man, and secondarily due to a man-to-man infection. These findings helped to elucidate similar problems of animal leprosies and nocardial diseases.

Animals↗
PubMed1997

Short-term improvements in public health from global-climate policies on fossil-fuel combustion: an interim report. Working Group on Public Health and Fossil-Fuel Combustion.

BACKGROUND: Most public-health assessments of climate-control policies have focused on long-term impacts of global change. Our interdisciplinary working group assesses likely short-term impacts on public health. METHODS: We combined models of energy consumption, carbon emissions, and associated atmospheric particulate-matter (PM) concentration under two different forecasts: business-as-usual (BAU); and a hypothetical climate-policy scenario, where developed and developing countries undertake significant reductions in carbon emissions. FINDINGS: We predict that by 2020, 700,000 avoidable deaths (90% CI 385,000-1,034,000) will occur annually as a result of additional PM exposure under the BAU forecasts when compared with the climate-policy scenario. From 2000 to 2020, the cumulative impact on public health related to the difference in PM exposure could total 8 million deaths globally (90% CI 4.4-11.9 million). In the USA alone, the avoidable number of annual deaths from PM exposure in 2020 (without climate-change-control policy) would equal in magnitude deaths associated with human immunodeficiency diseases or all liver diseases in 1995. INTERPRETATION: The mortality estimates are indicative of the magnitude of the likely health benefits of the climate-policy scenario examined and are not precise predictions of avoidable deaths. While characterized by considerable uncertainty, the short-term public-health impacts of reduced PM exposures associated with greenhouse-gas reductions are likely to be substantial even under the most conservative set of assumptions.

Air Pollutants↗
PubMed2005

Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei: Centrarchidae).

Molecular clock methods allow biologists to estimate divergence times, which in turn play an important role in comparative studies of many evolutionary processes. It is well known that molecular age estimates can be biased by heterogeneity in rates of molecular evolution, but less attention has been paid to the issue of potentially erroneous fossil calibrations. In this study we estimate the timing of diversification in Centrarchidae, an endemic major lineage of the diverse North American freshwater fish fauna, through a new approach to fossil calibration and molecular evolutionary model selection. Given a completely resolved multi-gene molecular phylogeny and a set of multiple fossil-inferred age estimates, we tested for potentially erroneous fossil calibrations using a recently developed fossil cross-validation. We also used fossil information to guide the selection of the optimal molecular evolutionary model with a new fossil jackknife method in a fossil-based model cross-validation. The centrarchid phylogeny resulted from a mixed-model Bayesian strategy that included 14 separate data partitions sampled from three mtDNA and four nuclear genes. Ten of the 31 interspecific nodes in the centrarchid phylogeny were assigned a minimal age estimate from the centrarchid fossil record. Our analyses identified four fossil dates that were inconsistent with the other fossils, and we removed them from the molecular dating analysis. Using fossil-based model cross-validation to determine the optimal smoothing value in penalized likelihood analysis, and six mutually consistent fossil calibrations, the age of the most recent common ancestor of Centrarchidae was 33.59 million years ago (mya). Penalized likelihood analyses of individual data partitions all converged on a very similar age estimate for this node, indicating that rate heterogeneity among data partitions is not confounding our analyses. These results place the origin of the centrarchid radiation at a time of major faunal turnover as the fossil record indicates that the most diverse lineages of the North American freshwater fish fauna originated at the Eocene-Oligocene boundary, approximately 34 mya. This time coincided with major global climate change from warm to cool temperatures and a signature of elevated lineage extinction and origination in the fossil record across the tree of life. Our analyses demonstrate the utility of fossil cross-validation to critically assess individual fossil calibration points, providing the ability to discriminate between consistent and inconsistent fossil age estimates that are used for calibrating molecular phylogenies.

Animals↗
PubMed2006

Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for pinus.

Silent mutation rate estimates for Pinus vary 50-fold, ranging from angiosperm-like to among the slowest reported for plants. These differences either reflect extraordinary genomic processes or inconsistent fossil calibration, and they have important consequences for population and biogeographical inferences. Here we estimate mutation rates from 4 Pinus species that represent the major lineages using 11 nuclear and 4 chloroplast loci. Calibration was tested at the divergence of Pinus subgenera with the oldest leaf fossil from subg. Strobus (Eocene; 45 MYA) or a recently published subg. Strobus wood fossil (Cretaceous; 85 MYA). These calibrations place the origin of Pinus 190-102 MYA and give absolute silent rate estimates of 0.70-1.31x10(-9) and 0.22-0.42x10(-9).site-1.year-1 for the nuclear and chloroplast genomes, respectively. These rates are approximately 4- to 20-fold slower than angiosperms, but unlike many previous estimates, they are more consistent with the high per-generation deleterious mutation rates observed in pines. Chronograms from nuclear and chloroplast genomes show that the divergence of subgenera accounts for about half of the time since Pinus diverged from Picea, with subsequent radiations occurring more recently. By extending the sampling to encompass the phylogenetic diversity of Pinus, we predict that most extant subsections diverged during the Miocene. Moreover, subsect. Australes, Ponderosae, and Contortae, containing over 50 extant species, radiated within a 5 Myr time span starting as recently as 18 MYA. An Eocene divergence of pine subgenera (using leaf fossils) does not conflict with fossil-based estimates of the Pinus-Picea split, but a Cretaceous divergence using wood fossils accommodates Oligocene fossils that may represent modern subsections. Because homoplasy and polarity of character states have not been tested for fossil pine assignments, the choice of fossil and calibration node represents a significant source of uncertainty. Based on several lines of evidence (including agreement with ages inferred using calibrations outside of Pinus), we conclude that the 85 MYA calibration at the divergence of pine subgenera provides a reasonable lower bound and that further refinements in age and mutation rate estimates will require a synthetic examination of pine fossil history.

Chloroplasts↗
PubMed2002

Morphology-based systematics (MBS) and problems with fossil hominoid and hominid systematics.

The generalized/primitive nature of the hominoid dentition and often fragmentary nature of fossils, coupled with enthusiastic optimism for making revolutionary finds, has wreaked havoc with recognition of early human ancestors and reconstruction of fossil hominoid phylogeny. As such, the history of paleoanthropology is one of repeated misidentification of fossil ancestors and of occasional fraud. Although this history has led many workers to lose confidence in morphology based systematics (MBS), past and present misidentifications are actually due to a disregard of systematic methodology. Systematics depends on the continuity of life and gains its objectivity largely from the order alpha taxonomy imposes on morphologic discontinuities in closely related taxa (i.e., species and genera). Transformation of characters fixed in species into character complexes, as manifested in taxa nested at different levels of relationship, form the foundation for higher-level taxonomy and for phylogeny. Because in most cases, hominoid fossils are unable to provide the data needed to resolve alpha taxonomy, classification and phylogeny of fossil taxa must be guided by analogies to living taxa. Hominid and hominoid fossil taxonomy and phylogeny, however, has been based largely on preevolutionary notions and on misinterpretations of the polarity of assumed diagnostic characters. More often than not, fossils lack resolution for the taxonomic level or rank they are assigned to and taxa are erected without appropriate analogies to living forms. As such, phylogenies based on these classifications are unlikely to be correct. More in-depth anatomical studies that are in accordance with systematic methodology are likely to hold the key to correctly classifying fossils and unraveling hominoid and hominid phylogeny.

Animals↗
PubMed2006

Analysis of fluorescence from algae fossils of the Neoproterozoic Doushantuo formation of China by confocal laser scanning microscope.

Chinese algae fossils can provide unique information about the evolution of the early life. Thin sections of Neoproterozoic algae fossils, from Guizhou, China, were studied by confocal laser scanning microscopy, and algae fossils were fluorescenced at different wavelengths when excited by laser light of 488 nm, 476 nm, and 568 nm wavelength. When illuminated by 488 nm laser light, images of the algae fossils were sharper and better defined than when illuminated by 476 nm and 568 nm laser light. The algae fossils fluoresce at a wide range of emission wavelengths. The three-dimensional images of the fluorescent algae fossils were compared with the transmission images taken by light microscope. We found that the fluorescence image of the confocal laser scanning microscope in a single optical section could pass for the transmission image taken by a light microscope. We collected images at different sample depths and made a three-dimensional reconstruction of the algae fossils. And on the basis of the reconstruction of the three-dimensional fluorescent images, we conclude that the two algae fossils in our present study are red algae.

Cell Wall↗
PubMed2002

Identification of immunoreactive material in mammoth fossils.

The fossil record represents a history of life on this planet. Attempts to obtain molecular information from this record by analysis of nucleic acids found within fossils of extreme age have been unsuccessful or called into question. However, previous studies have demonstrated the long-term persistence of peptides within fossils and have used antibodies to extant proteins to demonstrate antigenic material. In this study we address two questions: Do immunogenic/antigenic materials persist in fossils? and; Can fossil material be used to raise antibodies that will cross-react with extant proteins? We have used material extracted from a well-preserved 100000-300000-year-old mammoth skull to produce antisera. The specificity of the antisera was tested by ELISA, western blotting, and immunohistochemistry. It was demonstrated that antisera reacted specifically with the fossils and not the surrounding sediments. Reactivity of antisera with modern proteins and tissues was also demonstrated, as was the ability to detect evolutionary relationships via antibody-antigen interactions. Mass spectrometry demonstrated the presence of amino acids and specific peptides within the fossil. Peptides were purified by anion-exchange chromatography and sequenced by tandem mass spectrometry. The collagen-derived peptides may have been the source of at least some of the immunologic reactivity, but the antisera identified molecules that were not observed by mass spectrometry, indicating that immunologic methods may have greater sensitivity. Although the presence of peptides and amino acids was demonstrated, the exact nature of the antigenic material was not fully clarified. This report demonstrates that antibodies may be used to obtain information from the fossil record.

Amino Acid Sequence↗
PubMed2004

Sr/Ca and early hominin diets revisited: new data from modern and fossil tooth enamel.

A previous study of strontium/calcium (Sr/Ca) ratios in Paranthropus suggested that it consumed more animal foods than was previously believed. However, that study looked at Sr/Ca in fossil bone, which is known to be highly susceptible to diagenesis. Enamel, in contrast, is resistant to post-mortem alteration making it a more appropriate material for Sr/Ca analysis of Plio-Pleistocene fossils. Yet, we know virtually nothing about Sr/Ca in the enamel of modern African mammals, much less fossil taxa. To address this gap, we studied Sr/Ca in tooth enamel from modern mammals in the greater Kruger National Park, South Africa, as well as fossil fauna from the Sterkfontein Valley. Grazing herbivores have the highest Sr/Ca, followed by browsers and carnivores in both modern and fossil fauna. This similarity in ecological Sr/Ca patterning between modern and fossil fauna shows that diagenesis has not obscured the primary dietary signals. Australopithecus has significantly higher Sr/Ca than Paranthropus, and higher Sr/Ca than fossil papionins, browsers, and carnivores. Paranthropus has lower Sr/Ca than grazers, but its Sr/Ca is higher or equal to that of fossil papionins, browsers, and carnivores. Thus, Sr/Ca for both hominins is relatively high, and provides no direct evidence for omnivory in either taxon. The consumption of underground resources or insects are among the possible explanations for the highly elevated Sr/Ca in Australopithecus.

Animals↗
PubMed1997

Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis.

Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved.

Alligators and Crocodiles↗
PubMed1976

African fossil tali: further multivariate morphometric studies.

Analysis of measurements from the tali of 21 individual fossil primates from Africa shows that the specimens fall into five clearly defined groups. Accordingly, these specimens have been included as groups along with extant species in a subsequent canonical analysis thus allowing the fossils to play their part in the determination of the canonical separations. The results of this procedure show that the five fossil groups lie in a part of the canonical space not occupied by any extant African primate. Their positions are between the envelope of Asiatic apes (Hylobates and Pongo) and the envelope of African forms near the edge which contains Pan and Papio. One fossil group is so similar to Hylobates that its talus may have functioned in locomotion in a parallel manner. Others lie near to Pongo in directions proceeding towards Pan and Papio and it is possible that this similarity may indicate remnants of morphological adaptation for climbing in these fossils. At the same time, however, individual specimens are closer to one or another of the extant groups and this considerable spread suggests that the locomotor adaptations as evidenced by talar morphology, of the primate fauna in Africa, may have been very different from those of the present day. This would not the inconsistent with the different habitats, floras and non-primate faunas that may have characterized the East African scene at these earlier times. Particular fossils from Olduvai and Kromdraai that are supposed to be australopithecine and therefore bipeds, are confirmed (Oxnard, '72; Lisowski et al., '74) as being totally different from man in their talar morphology and essentially rather similar to the majority of the other fossil tali examined.

Africa↗
PubMed1984

Additional fossil Theropithecus from Hopefield, South Africa: a comparison with other African sites and a reevaluation of its taxonomic status.

Additional fossil Theropithecus remains, recovered from mid to late Pleistocene deposits near Hopefield , South Africa, include portions of the jaws of at least five individuals. Extensive comparisons with fossil Theropithecus from other African sites, including Makapan , Swartkrans , Kanjera , Olorgesailie , and Olduvai , reveal few morphological differences, especially when variation in modern gelada baboons ( Theropithecus gelada ) and savannah baboons (Papio) is considered. The most pronounced differences between fossil forms are overall size and relative P3 length. However, these traits do not separate the fossil forms either chronologically or geographically. Other traits, such as depth of the fossa of the mandibular corpus, slope of the upper symphyseal shelf, and variation in the depth of the mandibular corpus, do not distinguish alleged primitive forms ( Makapan and lower beds at Olduvai ) from remains found at Hopefield , Swartkrans , Kanjera , Olorgesailie , Olduvai Bed IV, or the lower Ndutu Beds. Other traits, such as canine crown height and incisor size, are poorly documented for fossil Theropithecus . Thus, the available evidence suggests that Theropithecus darti and its successional species, T. oswaldi , can best be considered as a single fossil species, T. oswaldi , of which the remains from Hopefield are a late representative. Furthermore, lack of morphological differences dictates that Hopefield Theropithecus not be considered a distinct subspecies. Variation within the Hopefield sample shows that only one taxa is found at this site. Hypothesized physical and climatic conditions at Hopefield during the Pleistocene suggest that T. oswaldi lived near vleis or fresh water lagoons. Comparisons with modern T. gelada suggest a graminivorous diet for the fossil form.

Animals↗
PubMed1991

Proteins in the fossil bone of the dinosaur, Seismosaurus.

Proteins have been successfully extracted from the fossil vertebra of a 150-million-year-old sauropod dinosaur ("Seismosaurus") recently excavated from the Morrison Formation of New Mexico. HCl and guanidine.HCl extracts of the fossil bone and its sandstone matrix were concentrated, demineralized, and resolved into a number of different protein fractions by reversed-phase high-performance liquid chromatography (HPLC). One of these fractions had the same retention time as collagen. Amino acid analysis (Pico-Tag method) of these fractions confirmed they were proteins. Comparison of the correlation coefficients of the amino acid analyses with that of collagen standards indicated that none of the fractions contained significant amounts of collagen. Similar HPLC profiles were obtained for the HCl extracts of fossil bone and its sandstone matrix suggesting they contained the same proteins. However, different HPLC profiles were obtained when these HCl extracts were dried and reextracted with guanidine.HCl. These different fractions represent proteins unique to the fossil and were not found in the sandstone matrix. These differences were confirmed by amino acid analysis. Such information on fossil bone proteins might provide useful knowledge concerning the evolution of skeletal molecules and the fossilization process. Similar information on the proteins from the geological matrix might provide useful fingerprints for reconstructing ancient environments and for assessing sedimentary rocks for fossil fuel exploration.

Amino Acids↗
PubMed1990

The fossil record and estimating divergence times between lineages: maximum divergence times and the importance of reliable phylogenies.

Bounded estimates on divergence times between lineages are crucial to the calculation of absolute rates of molecular evolution. Upper (minimum) bounds on divergence times are easily estimated based on earliest fossil finds. Lower (maximum) bounds are more difficult to estimate; the age of putative ancestors may be used, though in practice it is virtually impossible to distinguish ancestors from primitive sister groups, which do not, of logical necessity, constitute lower bounds on divergence times. Two relatively new approaches to estimating lower bounds directly assess the incompleteness of the fossil record. The first uses taphonomic control groups to distinguish real absences from nonpreservation, while the second, and probably more powerful, uses the quality of the fossil record to estimate confidence intervals on the bases of stratigraphic ranges. For some groups, especially vertebrates, the inclusion or exclusion of problematic fossils can dramatically affect estimated lower bounds on divergence times, often swamping the uncertainties due to the incompleteness of the fossil record and/or correlation and dating errors. When datable paleogeographic events reflect ancient divisions of faunas, a lower bound on the divergence time of species within a fauna can be established based on the geologic, rather than fossil, record. The fossil records of hominids, eutherian mammals, echinoids, and geese are used as examples.

Animals↗