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The origin and early evolution of birds: discoveries, disputes, and perspectives from fossil evidence.

The study of the origin and early evolution of birds has never produced as much excitement and public attention as in the past decade. Well preserved and abundant new fossils of birds and dinosaurs have provided unprecedented new evidence on the dinosaurian origin of birds, the arboreal origin of avian flight, and the origin of feathers prior to flapping flight. The Mesozoic avian assemblage mainly comprises two major lineages: the prevalent extinct group Enantiornithes, and the Ornithurae, which gave rise to all modern birds, as well as several more basal taxa. Cretaceous birds radiated into various paleoecological niches that included fish- and seed-eating. Significant size and morphological differences and variation in flight capabilities, ranging from gliding to powerful flight among early birds, highlight the diversification of birds in the Early Cretaceous. There is little evidence, however, to support a Mesozoic origin of modern avian groups. Controversy and debate, nevertheless, surround many of these findings, and more details are needed to give a better appreciation of the significance of these new discoveries.

Animals↗

Fossil insect evidence for the end of the Western Settlement in Norse Greenland.

The fate of Norse farming settlements in southwest Greenland has often been seen as one of the great mysteries of North Atlantic colonization and expansion. Preservation of organic remains in the permafrost of the area of the Western Settlement, inland from the modern capital Nuuk, allowed very detailed study of the phases of occupation. Samples were taken from house floors and middens during the process of archaeological excavations and from insect remains were abstracted and identified in the laboratory. In this study, we present a new paleoecological approach principally examining the fossil fly faunas from house floors. The results of our study provide contrasting detailed pictures of the demise of two neighboring farms, Gården under Sandet and Nipaatsoq, one where abandonment appears as part of a normal process of site selection and desertion, and the other where the end was more traumatic. The level of detail, which was obtained by analysis of the dipterous (true fly) remains, exceeds all previous work and provides insights otherwise unobtainable.

Animals↗

Origin of Metazoa: sponges as living fossils.

The phylogenetic position of the phylum Porifera (sponges) is at the base of the kingdom Metazoa. During the past few years not only rDNA sequences but--and this was a major advance--even cDNAs/genes have been isolated and characterized from sponges, especially from the marine demosponge Geodia cydonium, which code for proteins. The analyses of their deduced amino acid sequences allowed a molecular biological approach to solve the problem of monophyly of Metazoa. Molecules of the extracellular matrix/basal lamina, with the integrin receptor, fibronectin, and galectin as prominent examples, cell-surface receptors (tyrosine kinase receptor), elements of sensory systems (crystallin, metabotropic glutamate receptor), and homologs/modules of an immune system (immunoglobulin like molecules, scavenger receptor cysteine-rich, and short consensus repeats, rhesus system) classify the Porifera as true Metazoa. As living fossils, provided with simple, primordial molecules allowing cell-cell and cell-matrix adhesion as well as processes of signal transduction as known in a more complex manner from higher Metazoa, they also show peculiarities not known in other metazoan phyla. Tissues of sponges are rich in telomerase activity, suggesting a high plasticity in the determination of cell lineages. It is concluded that molecular biological studies with sponges as model will not only help to understand the evolution of Protoctista to Metazoa but also the complex, hierarchial regulatory network of cells in higher Metazoa.

Amino Acid Sequence↗

Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.

Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.

Animals↗

The phylogenetic history of the MHC class I gene families in pig, including a fossil gene predating mammalian radiation.

More than 990 kb of the 1200 kb in the SLA class I region of the pig major histocompatibility complex (MHC) have been sequenced. The present study was designed to establish the evolution of this region which was best understood by distinguishing three periods. The most recent period, which extended from 40 to 15 mya, probably corresponded to five rounds of duplication of a basic unit. This unit consisted of a single class I gene linked to widely dispersed repeats, and one SLA-specific repeat motif. The duplications gave rise to six SLA classical class I genes. The second evolutionary period corresponded to the emergence of the SLA nonclassical class I genes, i.e. after the suidae separated from the other artiodactyl species about 65 mya. The third period appeared to correspond to a much more remote age when the ancestor of the gene SLA-11 existed. Comparative studies of the human and pig sequences of the class I-containing segments indeed revealed the presence within the human HSR1-ZNF segment of relics of a human class I fossil gene which appeared to be orthologous to the 5' moiety of the SLA-11 pseudogene. This was the first evidence that a class I gene existed in this location at least 110-120 mya in the MHC class I region of the precursor of the mammalian species. Human/pig sequence comparison also revealed that the presumably functional pig MIC2 gene was probably orthologous to the human functional MICA or MICB genes.

Animals↗

The hemocyanin from a living fossil, the cephalopod Nautilus pompilius: protein structure, gene organization, and evolution.

By electron microscopic and immunobiochemical analyses we have confirmed earlier evidence that Nautilus pompilius hemocyanin (NpH) is a ring-like decamer (M(r) = approximately 3.5 million), assembled from 10 identical copies of an approximately 350-kDa polypeptide. This subunit in turn is substructured into seven sequential covalently linked functional units of approximately 50 kDa each (FUs a-g). We have cloned and sequenced the cDNA encoding the complete polypeptide; it comprises 9198 bp and is subdivided into a 5' UTR of 58 bp, a 3' UTR of 365 bp, and an open reading frame for a signal peptide of 21 amino acids plus a polypeptide of 2903 amino acids (M(r) = 335,881). According to sequence alignments, the seven FUs of Nautilus hemocyanin directly correspond to the seven FU types of the previously sequenced hemocyanin "OdH" from the cephalopod Octopus dofleini. Thirteen potential N-glycosylation sites are distributed among the seven Nautilus hemocyanin FUs; the structural consequences of putatively attached glycans are discussed on the basis of the published X-ray structure for an Octopus dofleini and a Rapana thomasiana FU. Moreover, the complete gene structure of Nautilus hemocyanin was analyzed; it resembles that of Octopus hemocyanin with respect to linker introns but shows two internal introns that differ in position from the three internal introns of the Octopus hemocyanin gene. Multiple sequence alignments allowed calculation of a rather robust phylogenetic tree and a statistically firm molecular clock. This reveals that the last common ancestor of Nautilus and Octopus lived 415 +/- 24 million years ago, in close agreement with fossil records from the early Devonian.

Amino Acid Sequence↗

Fossil woods from Janggi Group (Early Miocene) in Pohang Basin, Korea.

Sixty-four silicified fossil woods were collected from the Early Miocene Upper Coal-bearing Formation of Janggi Group in Pohang City, the Korean Peninsula. Out of them 23 specimens were identified as gymnosperms and 27 specimens as dicotyledons. The taxa identified include Picea palaeomaximowiczii Watari, Taxodioxylon cunninghamioides (Watari) Watari, T. sequoianum (Merckl.) Gothan, Fagus hondoensis (Watari) Watari, Cercidiphyllum sp., Camellia japonoxyla Suzuki et Terada, Distylium chiharu-hirayae Suzuki et Terada, Aesculus sp., Wataria miocenica (Watari) Terada et Suzuki and W. parvipora Terada et Suzuki. All of these species are reported for the first time from the Tertiary basins of Korea. Compared with those of the Miocene Formations in Japan, most taxa we found are common between the paleo-floras in Korea and Japan during the Early to Middle Miocene.

Cycadopsida↗

Isolation of proline and hydroxyproline from fossil bone.

We describe a simple and rapid procedure for the isolation of proline and hydroxyproline from fossil bone based on the isolation of gelatin, hydrolysis, purification with XAD-2, deamination of primary amino acids with aqua regia, and separation of the imino acids by cation exchange chromatography. This procedure will provide material for accurate bone carbon dating, and stable carbon isotope ratio determinations for the evaluation of paleodiets.

Animals↗

Trace metal levels in fossil human bone from the Bezdanjaca necropolis in Croatia.

Elemental analysis of prehistoric human bone for the reconstruction of past environmental conditions, diets and migrations is a relatively new concept and can be a helpful tool in palaeoanthropology. The contents of Pb, Cu, Cd, Zn, Ca, Sr and Ba in fossil and recent human bone were determined by inductively coupled plasma atomic emission spectrometry (ICP-AES) and differential pulse anodic stripping voltammetry (DPASV). Some variation among the measured elements was established, but strontium was found to be a suitable tracer for such bioanthropological investigations. The applied analytical techniques are suitable for such investigations because of the comparatively small amount of material required and great analytical precision.

Bone and Bones↗

Chromosome aberrations in employees from fossil-fueled and nuclear-power plants.

Chromosome aberrations were scored in 59 persons from fossil-fueled plants, in 89 persons from nuclear-power plants and in 23 controls. A significant increase in acentric chromosome fragments and dicentric chromosomes compared to the control group was observed in both types of workers. Moreover, the number of abnormal cells was significantly greater in workers of conventional plants than in those of nuclear-power plants. When adjusted for loss of lymphocytes according to a half-life of 3 years, this difference was also significant for the number of dicentric chromosomes observed. A significant effect of length of exposure or of frequency of radiological examinations could be discerned only in the group of workers from conventional plants.

Adult↗

Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record.

Recent geological treatises have presented three alternative models of the origins of eukaryotes as if they merited equal treatment. However, modern biological techniques, especially nucleic acid and protein sequencing, have clearly established the validity of the symbiotic theory of the origin of eukaryotic organelles. The serial endosymbiotic theory in its most extreme form states that three classes of eukaryotic cell organelles (mitochondria, plastids and undulipodia) originated as free-living bacteria (aerobic respirers, phototrophic bacteria and spirochetes respectively) in association with hosts that become the nucleocytoplasm (Thermoplasma-like archaebacterial hosts). Molecular biological information, primarily derived from ribosomal RNA nucleotide sequencing studies leads to the conclusion that the symbiotic origin theory for both mitochondria and plastids has been proven. The probability of an ancestral archaebacterial-Thermoplasma-like host for the nucleocytoplasm has been rendered more likely by discoveries by Dennis Searcy and his colleagues and Carl Woese and his colleagues. The most equivocal postulate of the symbiotic theory, the origin of undulipodia (cilia and other organelles of motility that develop from kinetosomes is under investigation now. The status of these postulates, as well as their implications for the fossil record, is briefly summarized here.

Bacteria↗

Evaluation on estrogenicity and oxidative hepatotoxicity of fossil fuel industrial wastewater before and after the powdered activated carbon treatment.

There are 10 manufacturers who produce fossil fuel products in the Da-Hse Industrial District, Kaohsiung County, southwestern Taiwan. Before discharging the wastewater into the nearby aquatic environment, the pretreated wastewater from these manufacturers must be processed in a treatment plant which includes four major processing units: equalization, a primary clarifier, an aeration basin, and a final clarifier. In order to estimate the potential environmental risks of industrial wastewater from each manufacturer and the treatment efficiency of the powdered activated carbon treatment (PACT) system used in this wastewater treatment plant, in vitro bioassays for estrogenicity and oxidative hepatotoxicity were carried out using a stably transfected human breast cancer cell line, MVLN, and a human hepatocellular carcinoma cell line, HepG2, respectively. Estrogenic substances occurred in nine of 10 pretreated wastewaters from these manufacturers in which the relative luciferase activity ranged from 18.9% to 98.0% for 1-fold-condensed wastewaters corresponding to the concentration of the original wastewater. The estrogenicity was highest at the influent of the treatment plant and decreased through the treatment process. About 81% estrogenicity clearance was found through all processing units. On the other hand, oxidative hepatotoxic substances existed in seven of 10 pretreated wastewaters from these manufacturers in which relative TBARs activity ranged from 18.5% to 43.0% for 1-fold-condensed wastewater. The TBARs of influent samples apparently decreased through the processing units until the aeration basin, but abruptly rose in the final clarifier, which was a result of the addition of an active charcoal-retrieving agent with the molecular formula of (C(2)H(3))(n)CONHCH(2)N(CH(3))(3)Cl and which had high TBARs activity. No TBARs activity being found in effluent samples could be a consequence of allowing sufficient time for coagulation between the active charcoal and its retrieval agent which decreased the residual active charcoal-retrieving agent. We concluded that the industrial wastewater treatment plant using the PACT system in the Da-Hse Industrial District is suitable for removing estrogenic substances and oxidative hepatotoxic substances discharged from these industrial manufacturers.

Biological Assay↗

Microbial biocatalyst developments to upgrade fossil fuels.

Steady increases in the average sulfur content of petroleum and stricter environmental regulations concerning the sulfur content have promoted studies of bioprocessing to upgrade fossil fuels. Bioprocesses can potentially provide a solution to the need for improved and expanded fuel upgrading worldwide, because bioprocesses for fuel upgrading do not require hydrogen and produce far less carbon dioxide than thermochemical processes. Recent advances have demonstrated that biodesulfurization is capable of removing sulfur from hydrotreated diesel to yield a product with an ultra-low sulfur concentration that meets current environmental regulations. However, the technology has not yet progressed beyond laboratory-scale testing, as more efficient biocatalysts are needed. Genetic studies to obtain improved biocatalysts for the selective removal of sulfur and nitrogen from petroleum provide the focus of current research efforts.

Fossil Fuels↗

Environmental evidence of fossil fuel pollution in Laguna Chica de San Pedro lake sediments (Central Chile).

This paper describes lake sediment spheroidal carbonaceous particle (SCP) profiles from Laguna Chica San Pedro, located in the Biobío Region, Chile (36 degrees 51' S, 73 degrees 05' W). The earliest presence of SCPs was found at 16 cm depth, corresponding to the 1915-1937 period, at the very onset of industrial activities in the study area. No SCPs were found at lower depths. SCP concentrations in Laguna Chica San Pedro lake sediments were directly related to local industrial activities. Moreover, no SCPs were found in Galletué lake (38 degrees 41' S, 71 degrees 17.5' W), a pristine high mountain water body used here as a reference site, suggesting that contribution from long distance atmospheric transport could be neglected, unlike published data from remote Northern Hemisphere lakes. These results are the first SCP sediment profiles from Chile, showing a direct relationship with fossil fuel consumption in the region. Cores were dated using the 210Pb technique.

Air Pollutants↗

Beyond leopards: tooth marks and the contribution of multiple carnivore taxa to the accumulation of the Swartkrans Member 3 fossil assemblage.

The ca. 1.0 myr old fauna from Swartkrans Member 3 (South Africa) preserves abundant indication of carnivore activity in the form of tooth marks (including pits) on many bone surfaces. This direct paleontological evidence is used to test a recent suggestion that leopards, regardless of prey body size, may have been almost solely responsible for the accumulation of the majority of bones in multiple deposits (including Swartkrans Member 3) from various Sterkfontein Valley cave sites. Our results falsify that hypothesis and corroborate an earlier hypothesis that, while the carcasses of smaller animals may have been deposited in Swartkrans by leopards, other kinds of carnivores (and hominids) were mostly responsible for the deposition of large animal remains. These results demonstrate the importance of choosing appropriate classes of actualistic data for constructing taphonomic inferences of assemblage formation. In addition, they stress that an all-encompassing model of assemblage formation for the hominid-bearing deposits of the Sterkfontein Valley is inadequate and that each must be evaluated individually using not just analogical reasoning but also incorporating empirical data generated in the preserved fossil samples.

Animals↗

Was Australopithecus anamensis ancestral to A. afarensis? A case of anagenesis in the hominin fossil record.

We tested the hypothesis that early Pliocene Australopithecus anamensis was ancestral to A. afarensis by conducting a phylogenetic analysis of four temporally successive fossil samples assigned to these species (from earliest to latest: Kanapoi, Allia Bay, Laetoli, Hadar) using polarized character-state data from 20 morphological characters of the dentition and jaws. If the hypothesis that A. anamensis is ancestral to A. afarensis is true, then character-state changes between the temporally ordered site-samples should be congruent with hypothesized polarity transformations based on outgroup (African great ape) conditions. The most parsimonious reconstruction of character-state evolution suggests that each of the hominin OTUs shares apomorphies only with geologically younger OTUs, as predicted by the hypothesis of ancestry (tree length=31; Consistency Index=0.903). This concordance of stratigraphic and character-state data supports the idea that the A. anamensis and A. afarensis samples represent parts of an anagenetically evolving lineage, or evolutionary species. Each site-sample appears to capture a different point along this evolutionary trajectory. We discuss the implications of this conclusion for the taxonomy and adaptive evolution of these early-middle Pliocene hominins.

Animals↗

Recent and fossil nematode parasites (Nematoda: Mermithidae) of neotropical ants.

The following new recent species of mermithid (Nematoda) parasites of Neotropical ants are described: Meximermis ectatommi n.gen., n. sp. from workers of Ectatomma ruidum Roger in Southern Mexico, Agamomermis cephaloti n. sp. from a worker of Cephalotes minutus (Fab.) collected in Brazil, Agamomermis ecitoni n. sp. from a worker of Eciton burchellii Westwood collected in Venezuela and Agamomermis costaricensis n. sp. from a worker of Odontomachus hastatus (Fab.) collected in Costa Rica. In addition, a fossil mermithid parasite of a worker of Linepithema sp. from Dominican amber is described as Heydenius myrmecophila n. sp. These parasites represent the first descriptions of Neotropical ant mermithids and together with previous records listed here, show that ant infection by mermithids in the Neotropics is widespread and has occurred for at least 20-30 million years.

Animals↗

The influence of weather and environment on pulmonary embolism: pollutants and fossil fuels.

Previous publications have highlighted seasonal variations in the incidence of thrombosis and pulmonary embolism, and that weather patterns can influence these. While medical risk factors for pulmonary thrombo-embolism such as age, obesity, hypercoagulable states, cancer, previous thrombo-embolism, immobility, limb paralysis, surgery, major illness, trauma, hypotension, tachypnoea and right ventricular hypokinesis are not directly implicated regarding environmental factors such as weather, they could be influenced indirectly by these. This would be especially relevant in polluted areas that are associated with a higher pulmonary embolism risk. Routine nuclear medicine lung ventilation/perfusion studies (V/Q scans) of 2071 adult patients referred to the nuclear medicine department of the Royal Surrey County Hospital in Guildford, UK, between January 1998 and October 2002 were reviewed and 316 of these patients were classified as positive for pulmonary embolism with high probability scan on PIOPED criteria. The occurrence of positive scans was compared to environmental factors such as temperature, humidity, vapour pressure, air pressure and rainfall. Multiple linear regression was used to establish the significance of these relations. The incidence of pulmonary embolism was positively related to vapour pressure and rainfall. The most significant relation was to vapour pressure (p=0.010) while rainfall was less significant (p=0.017). There was no significant relation between pulmonary embolism and air pressure, humidity or temperature. It is postulated that rainfall and water vapour may be contributary factors in thrombosis and pulmonary embolism by way of pollutants that are carried as condensation nuclei in micro-droplets of water. In particular, fossil fuel pollutants are implicated as these condensation nuclei. Pollutants may be inhaled by populations exposed to windborne vapour droplets in cities or airports. Polluted vapour droplets may be absorbed by the lung to hasten coagulation cascades in the blood. This may lead to thrombosis and increased pulmonary embolism under high vapour pressure conditions. With combined factors such as pre-existing ill health or immobility on long flights, the risk of thrombosis and consequent embolism might increase substantially.

Adult↗