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PubMed1991

Phylogenetic and functional affinities of Babakotia (primates), a fossil lemur from northern Madagascar.

Recent paleontological expeditions to the Ankarana range of northern Madagascar have recovered the partial remains of four individuals of a newly recognized extinct lemur, Babakotia radofilai. Craniodental and postcranial material serve to identify Babakotia as a member of the palaeopropithecids (also including the extinct genera Palaeopropithecus, Archaeoindris, and Mesopropithecus). Living indrids form the sister group to this fossil clade. The postcranial anatomy indicates that Babakotia was a medium-sized (approximately 15 kg) indroid whose inferred positional behaviors were primarily slow climbing and hanging. Although it is probable that a leaping component typified the ancestral positional repertoire of all Malagasy lemurs, the mosaic nature of the locomotor skeleton of Babakotia further suggests that vertical climbing and hang-feeding rather than ricochetal leaping were primitive for indrids and palaeopropithecids and that the dramatic saltatory adaptations of the living indrids postdate the divergence of these two lineages.

Animals↗

PubMed1994

Indigeneity of organic matter in fossils: a test using stable isotope analysis of amino acid enantiomers in Quaternary mollusk shells.

Comparison of the delta 13C values of D and L enantiomers of individual amino acids was used to evaluate the presence of amino acid contaminants in Quaternary land snails. Measurements of delta 13C values of amino acid D and L enantiomers determined by combined gas chromatography, combustion, isotope-ratio mass spectrometry are reported. Conventional combustion techniques, following separation of aspartic acid and glutamic acid enantiomers by liquid chromatography, were also used to determine delta 13C as well as delta 15N values. Thoroughly cleaned samples ranging in age from 7000 to > 100,000 yr B.P. are shown to have analytically identical delta 13C values for the D and L enantiomers of each amino acid, thus confirming that the amino acids are indigenous to the shells, even in Pleistocene samples. On the other hand, partially cleaned material shows divergence of isotopic values, thus indicating the presence of amino acid contaminants and emphasizing the importance of proper cleaning procedures. This approach provides a powerful method for assessing the indigeneity of amino acids in fossils.

Amino Acids↗

PubMed1996

Phylogenetic resolution within the Elephantidae using fossil DNA sequence from the American mastodon (Mammut americanum) as an outgroup.

DNA was extracted from the extinct American mastodon, the extinct woolly mammoth, and the modern Asian and African elephants to test the traditional morphologically based phylogeny within Elephantidae. Phylogenetic analyses of the aligned sequences of the mitochondrial gene cytochrome b support a monophyletic Asian elephant-woolly mammoth clade when the American mastodon is used as an outgroup. Previous molecular studies were unable to resolve the relationships of the woolly mammoth, Asian elephant, and African elephant because the sequences appear to have evolved at heterogeneous rates and inappropriate outgroups were used for analysis. The results demonstrate the usefulness of fossil molecular data from appropriate sister taxa for resolving phylogenies of highly derived or early radiating lineages.

Africa↗

PubMed2001

Electricity from fossil fuels without CO2 emissions: assessing the costs of carbon dioxide capture and sequestration in U.S. electricity markets.

The decoupling of fossil-fueled electricity production from atmospheric CO2 emissions via CO2 capture and sequestration (CCS) is increasingly regarded as an important means of mitigating climate change at a reasonable cost. Engineering analyses of CO2 mitigation typically compare the cost of electricity for a base generation technology to that for a similar plant with CO2 capture and then compute the carbon emissions mitigated per unit of cost. It can be hard to interpret mitigation cost estimates from this plant-level approach when a consistent base technology cannot be identified. In addition, neither engineering analyses nor general equilibrium models can capture the economics of plant dispatch. A realistic assessment of the costs of carbon sequestration as an emissions abatement strategy in the electric sector therefore requires a systems-level analysis. We discuss various frameworks for computing mitigation costs and introduce a simplified model of electric sector planning. Results from a "bottom-up" engineering-economic analysis for a representative U.S. North American Electric Reliability Council (NERC) region illustrate how the penetration of CCS technologies and the dispatch of generating units vary with the price of carbon emissions and thereby determine the relationship between mitigation cost and emissions reduction.

Air Pollution↗

PubMed2000

The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity.

Because phylogenies can be estimated without stratigraphic data and because estimated phylogenies also infer gaps in sampling, some workers have used phylogeny estimates as templates for evaluating sampling from the fossil record and for "correcting" historical diversity patterns. However, it is not known how sampling intensity (the probability of sampling taxa per unit time) and completeness (the proportion of taxa sampled) affect the accuracy of phylogenetic inferences, nor how phylogenetically inferred estimates of sampling and diversity respond to inaccurate estimates of phylogeny. Both issues are addressed with a series of simulations using simple models of character evolution, varying speciation patterns, and various rates of speciation, extinction, character change, and preservation. Parsimony estimates of simulated phylogenies become less accurate as sampling decreases, and inaccurate trees chronically underestimate sampling. Biotic factors such as rates of morphologic change and extinction both affect the accuracy of phylogenetic estimates and thus affect estimated gaps in sampling, indicating that differences in implied sampling need not reflect actual differences in sampling. Errors in inferred diversity are concentrated early in the history of a clade. This, coupled with failure to account for true extinction times (i.e., the Signor-Lipps effect), inflates relative diversity levels early in clade histories. Because factors other than differences in sampling predict differences in the numbers of gaps implied by phylogeny estimates, inferred phylogenies can be misleading templates for evaluating sampling or historical diversity patterns.

Fossils↗

PubMed2006

The phylogeny of early eureptiles: comparing parsimony and Bayesian approaches in the investigation of a basal fossil clade.

For the first time the phylogenetic relationships of early eureptiles, consisting of captorhinids, diapsids, and protorothyridids, are investigated in a modern phylogenetic context using both parsimony and Bayesian approaches. Ninety parsimony-informative characters and 25 taxa were included in the analyses. The Bayesian analysis was run with and without a gamma-shape parameter allowing for variable rates across characters. In addition, we ran two more Bayesian analyses that included 42 autapomorphies and thus parsimony-uninformative characters in order to test the effect of variable branch lengths. The different analyses largely converged to the same topology, suggesting that the "protorothyridid" Coelostegus is the sister taxon of all other eureptiles and that the remaining "protorothyridids" are paraphyletic. Also, there is a close relationship between diapsids and Anthracodromeus, Cephalerpeton, and Protorothyris, a grouping of Thuringothyris with captorhinids, and a variable position of the "protorothyridids" Brouffia, Hylonomus, and Paleothyris. The lack of resolution in some parts of the tree might be due to "hard polytomies" and short divergence times between the respective taxa. The tree topology is consistent with the hypothesis that the temporal fenestrations of diapsid reptiles appear to be the consequence of a more lightly built skeleton, indicating a significant ecological shift in the early stages of diapsid evolution. Bayesian analysis is a very useful additional approach in studies of fossil taxa in which more traditional statistical support like the bootstrap is often weak. However, the exclusive use of the Mk model appears suitable only if autapomorphic characters are included, whereas the Mk+gamma model performed well with or without autapomorphies.

Animals↗

PubMed1999

The fossil record of North American mammals: evidence for a Paleocene evolutionary radiation.

Paleontologists long have argued that the most important evolutionary radiation of mammals occurred during the early Cenozoic, if not that all eutherians originated from a single common post-Cretaceous ancestor. Nonetheless, several recent molecular analyses claim to show that because several interordinal splits occurred during the Cretaceous, a major therian radiation was then underway. This claim conflicts with statistical evidence from the well-sampled latest Cretaceous and Cenozoic North American fossil record. Paleofaunal data confirm that there were fewer mammalian species during the latest Cretaceous than during any interval of the Cenozoic, and that a massive diversification took place during the early Paleocene, immediately after a mass extinction. Measurement data show that Cretaceous mammals were on average small and occupied a narrow range of body sizes; after the Cretaceous-Tertiary mass extinction, there was a rapid and permanent shift in the mean. The fact that there was an early Cenozoic mammalian radiation is entirely compatible with the existence of a few Cretaceous splits among modern mammal lineages.

Animals↗

PubMed2003

Exploring developmental modes in a fossil arthropod: growth and trunk segmentation of the trilobite Aulacopleura konincki.

Trilobites offer the opportunity to explore postembryonic development within the fossil record of arthropod evolution. In contrast to most trilobites, the Silurian proetid Aulacopleura konincki from the Czech Republic exhibits marked variation in the mature number of thoracic segments, with five morphs with 18-22 thoracic segments. The combination of abundant articulated specimens available from a narrow stratigraphic interval and segmental intraspecific variation makes this trilobite singularly useful for studying postembryonic growth and segmentation. Trunk segmentation followed a hemianamorphic pattern, as seen in other arthropods and as characteristic of the Trilobita; during a first anamorphic phase, segments were accreted, while in the subsequent epimorphic phase, segmentation did not proceed further despite continued growth. Size increment during the anamorphic phase was targeted and followed Dyar's rule, a geometric progression typical of many arthropods. We consider alternative hypotheses for the control of the switch from anamorphic to epimorphic phases of development. Our analysis favors a scenario in which the mature number of thoracic segments was determined quite early in development rather than at a late stage in association with a critical size threshold. This study demonstrates that hypotheses concerning developmental pattern and control can be tested in organisms belonging to an extinct clade.

Animals↗

PubMed2004

A test of Simpson's "rule of the survival of the relatively unspecialized" using fossil crinoids.

Temporally long-ranging (=long-lived) taxa have been postulated to have unusual properties that aid their prolonged geologic survival. Past studies have examined dispersal capabilities, geographic ranges, and single-character morphological adaptations as factors that may contribute to geologic longevity. Here, I test whether long-lived fossil crinoid taxa are morphologically unusual using a whole suite of morphological characters. I define long-lived taxa in several explicit, comparative ways. I find that long-lived crinoid genera and families are often less distant from mean morphologies of their crinoid orders than their shorter-lived relatives; that is, they are relatively less specialized. I also compare the morphology of crinoid genera relative to basal members of their respective orders; mean morphological distances of long-lived genera from basal morphologies are seldom distinct from those of their shorter-lived relatives. I observe that long-lived crinoid genera are less distant from mean morphologies of their temporal cohorts compared with shorter-lived genera but not in a statistically significant manner. I conclude that long-lived crinoids are relatively unspecialized, in the sense that they are relatively closer to mean morphologies of their taxonomic groups.

Animals↗

PubMed2003

A hydrothermal system associated with the Siljan impact structure, Sweden--implications for the search for fossil life on Mars.

The Siljan ring structure (368 +/- 1.1 Ma) is the largest known impact structure in Europe. It isa 65-km-wide, eroded, complex impact structure, displaying several structural units, including a central uplifted region surrounded by a ring-shaped depression. Associated with the impact crater are traces of a post-impact hydrothermal system indicated by precipitated and altered hydrothermal mineral assemblages. Precipitated hydrothermal minerals include quartz veins and breccia fillings associated with granitic rocks at the outer margin of the central uplift, and calcite, fluorite, galena, and sphalerite veins associated with Paleozoic carbonate rocks located outside the central uplift. Two-phase water/gas and oil/gas inclusions in calcite and fluorite display homogenization temperatures between 75 degrees C and 137 degrees C. With an estimated erosional unloading of approximately 1 km, the formation temperatures were probably not more than 10-15 degrees C higher. Fluid inclusion ice-melting temperatures indicate a very low salt content, reducing the probability that the mineralization was precipitated during the Caledonian Orogeny. Our findings suggest that large impacts induce low-temperature hydrothermal systems that may be habitats for thermophilic organisms. Large impact structures on Mars may therefore be suitable targets in the search for fossil thermophilic organisms.

Awards and Prizes↗

PubMed2003

The application of a molecular clock based on molecular sequences and the fossil record to explain biogeographic distributions within the Alexandrium tamarense "species complex" (Dinophyceae).

The cosmopolitan dinoflagellate genus Alexandrium, and especially the A. tamarense species complex, contain both toxic and nontoxic strains. An understanding of their evolution and paleogeography is a necessary precursor to unraveling the development and spread of toxic forms. The inclusion of more strains into the existing phylogenetic trees of the Alexandrium tamarense species complex from large subunit rDNA sequences has confirmed that geographic distribution is consistent with the molecular clades but not with the three morphologically defined species that constitute the complex. In addition, a new clade has been discovered, representing Mediterranean nontoxic strains. The dinoflagellates fossil record was used to calibrate a molecular clock: key dates used in this calibration are the origins of the Peridiniales (estimated at 190 MYA), Gonyaulacaceae (180 MYA), and Ceratiaceae (145 MYA). Based on the data set analyzed, the origin of the genus Alexandrium was estimated to be around late Cretaceous (77 MYA), with its earliest possible origination in the mid Cretaceous (119 MYA). The A. tamarense species complex potentially diverged around the early Neogene (23 MYA), with a possible first appearance in the late Paleogene (45 MYA). A paleobiogeographic scenario for Alexandrium is based on (1) the calculated possible ages of origination for the genus and its constituent groups; (2) paleogeographic events determined by plate movements, changing ocean configurations and currents, as well as climatic fluctuations; and (3) the present geographic distribution of the various clades of the Alexandrium tamarense species complex.

Animals↗

PubMed2006

A genomic fossil reveals key steps in hemoglobin loss by the antarctic icefishes.

Antarctic icefishes are the only vertebrates that do not have hemoglobin and erythrocytes in their blood. These startling phenotypes are associated in several icefish species with deletions of juvenile and adult globin loci, which in red-blooded teleosts are typically composed of tightly linked pairs of alpha- and beta-globin genes. It is unknown if the loss of hemoglobin expression in icefishes was the direct result of such deletions or if other mutational events compromised globin chain synthesis prior to globin gene loss. In this study, we show that 15 of the 16 icefish species have lost the adult beta-globin gene but retain a truncated alpha-globin pseudogene. Surprisingly, a phylogenetically derived icefish species, Neopagetopsis ionah, possesses a complete, but nonfunctional, adult alphabeta-globin complex. This cluster contains 2 distinct beta-globin pseudogenes whose phylogenetic origins span the entire Antarctic notothenioid radiation, consistent with an origin via introgression. Maximum likelihood ancestral state reconstruction supports a scenario of icefish globin gene evolution that involves a single loss of the transcriptionally active adult alphabeta-globin cluster prior to the diversification of the extant species in the clade. Through lineage sorting of ancestral polymorphism, 2 types of alleles became fixed in the clade: 1) the alpha-globin pseudogene of the majority of species and 2) the inactive alphabeta-globin complex of N. ionah. We conclude that the globin pseudogene complex of N. ionah is a "genomic fossil" that reveals key intermediate steps on the pathway to loss of hemoglobin expression by all icefish species.

Animals↗

PubMed2000

Mutagenicity of diesel exhaust particles from two fossil and two plant oil fuels.

Particulate matter of diesel engine exhaust from four different fuels was studied for content of polynuclear aromatic compounds and mutagenic effects. Two so-called biodiesel fuels, rapeseed oil methylesters (RME) and soybean oil methylesters (SME), were compared directly with two fossil diesel fuels with the normal (DF) and a low sulfur content (LS-DF). Diesel exhaust particles were sampled on filters from the diluted and cooled exhaust of a test engine at five different speeds and loads. Filters were weighed for total particulate matter, Soxhlet extracted with dichloromethane and the content of insoluble material determined. The soluble organic fraction was analysed for polynuclear aromatic compounds. Mutagenicity was determined using the Salmonella typhimurium/mammalian microsome assay with strains TA98 and TA100. Compared with DF, the exhaust particles of LS-DF, RME and SME contained less insoluble material, which consisted mainly of the carbon cores of diesel exhaust particles. The concentrations of individual polynuclear aromatic compounds varied widely among the different exhaust extracts, but total concentrations of the compounds were approximately double for DF and SME compared with LS-DF and RME. In TA98 significant increases in mutation rates were obtained for the soluble organic fractions of all fuels for engines running at full speed (load modes A and D), but for DF revertants were 2- to 10-fold more frequent as compared with LS-DF, RME and SME. Revertant frequencies for DF and partly for LS-DF were also elevated in TA100, while RME and SME gave no significant increase in mutations. The results indicate that diesel exhaust particles from RME, SME and LS-DF contain less black carbon and total polynuclear aromatic compounds and are significantly less mutagenic in comparison with DF. A high sulfur content of the fuel and high engine speeds (rated power) and loads are associated with an increase in mutagenicity of diesel exhaust particles.

Chromatography, High Pressure Liquid↗

PubMed1993

Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology.

Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the available character evidence. Explicit or implicit use of taxonomic congruence is usually employed when an investigator either has both molecular and morphological data sets or has different gene-, rRNA-, or protein-sequence data sets available. Indeed, a taxonomic congruence rationale is frequently used as the basis for exploring classes of data, thus allowing comparison between the phylogenetic signal emerging from a particular data set and those of other such classes. Problematic aspects of employing the taxonomic congruence approach include the potentially misleading and arbitrary choices of both a consensus method and the division of characters into subsets. If the goal of an analysis is to provide the best estimate of genealogy afforded by the available character evidence, then taxonomic congruence is substantially more arbitrary than a total evidence approach. The theoretical advantages of phylogenetic estimates based on total evidence are argued in the present study and are illustrated with an example of amniote relationships. We report conflicting results from total evidence and taxonomic congruence approaches, with analyses of previously reported data from both fossil and living amniotes and from both morphology and molecules, the latter including available 18S rRNA, 28S rRNA, and protein sequences. We conclude that a more highly resolved and robust phylogenetic hypothesis of amniotes, the traditional one, emerges when a total evidence approach is employed.

Animals↗

PubMed2005

Cyclicity in the fossil record mirrors rock outcrop area.

In a recent article, Rohde & Muller (Rohde & Muller 2005 Nature 434, 208-210) identified a strong 62 Myr cyclicity in the history of marine diversity through the Phanerozoic. The data they presented were highly convincing, yet they were unable to explain what process might have generated this pattern. A significant correlation between observed genus-level diversity (after removal of long-term trends) and the amount of marine sedimentary rock measured at a surface outcrop in Western Europe is demonstrated. This suggests that cyclicity originates from long-term changes in sedimentary depositional and erosional regimes, and raises the strong possibility that the cyclicity apparent in the record of marine fossils is not a biological signal but a sampling signal.

Biodiversity↗

PubMed2006

Comparing amber fossil assemblages across the Cenozoic.

To justify faunistic comparisons of ambers that differ botanically, geographically and by age, we need to determine that resins sampled uniformly. Our pluralistic approach, analysing size distributions of 671 fossilized spider species from different behavioural guilds, demonstrates that ecological information about the communities of two well-studied ambers is retained. Several lines of evidence show that greater structural complexity of Baltic compared to Dominican amber trees explains the presence of larger web-spinners. No size differences occur in active hunters. Consequently, we demonstrate for the first time that resins were trapping organisms uniformly and that comparisons of amber palaeoecosystem structure across deep time are possible.

Amber↗

PubMed2002

Origin of the tooth-replacement pattern in therian mammals: evidence from a 110 Myr old fossil.

Living placental and marsupial mammals (therians) use distinctive tooth-replacement patterns that have not yet been traced back fully to their time of divergence in the Early Cretaceous (>100 Myr ago). Slaughteria eruptens, a small 110 Myr old fossil mammal from Texas, USA, is near the base of that divergence. Using ultra-high-resolution X-ray CT analysis we demonstrate that Slaughteria preserves an unrecognized pattern of tooth replacement with simple posterior premolars replacing molariform precursors. Differing from both placentals that have a more complex posterior adult premolar, and from marsupials, in which only one premolar is replaced, Slaughteria provides the first direct evidence of a tooth-replacement pattern that is plausible for the common ancestor of all therians. By our interpretation Slaughteria has only one adult molar in place and contains two mental foramina in the jaw, thus changing characters that are critical to reconstruction of mammalian relationships and to species discrimination and interpretations of diversity for Early Cretaceous mammals.

Animals↗

PubMed2002

Major adaptive radiation in neritopsine gastropods estimated from 28S rRNA sequences and fossil records.

A well-supported phylogeny of the Neritopsina, a gastropod superorder archaic in origin, radiated ecologically and diverse in morphology, is reconstructed based on partial 28S rRNA sequences. The result (Neritopsidae (Hydrocenidae (Helicinidae + Neritiliidae) (Neritidae + Phenacolepadidae))) is highly congruent with the fossil records and the character distribution of reproductive tracts in extant taxa. We suggest that the Neritopsina originated in subtidal shallow waters, invaded the land and became fully terrestrial at least three times in different clades, by the extinct Dawsonellidae in the Late Palaeozoic and by the Helicinidae and Hydrocenidae in the Mesozoic. Invasion of fresh- and brackish waters is prevalent among the Neritopsina as the Jurassic and freshwater ancestory is most probable for helicinids. The Phenacolepadidae, a group exclusively inhabiting dysoxic environments, colonized deep-sea hydrothermal vents and seeps in the Late Cretaceous or Early Cenozoic. Submarine caves have served as refuges for the archaic Neritopsidae since the Early to Middle Cenozoic, and the marine neritopsine slug Titiscania represents a highly specialized but relatively recent offshoot of this family. The Neritiliidae is another clade to be found utilizing submarine caves as shelter by the Oligocene; once adapted to the completely dark environment, but some neritiliids have immigrated to surface freshwater habitats.

Adaptation, Physiological↗