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PubMed1999

Recognizing species diversity among large-bodied hominoids: a simulation test using missing data finite mixture analysis.

A persistent problem in paleoanthropology is the recognition of intra- vs. inter-specific differences within fossil samples. Exacerbating this situation is the often fragmentary nature of the fossils themselves, thus precluding rote applications of many multivariate approaches designed for complete case analyses. In this paper we apply finite mixture analysis to samples of large-bodied hominoids to test this procedure's efficacy in clustering individuals by species without a priori knowledge of group membership. In addition, we stochastically remove individual specimens and measurements, simulating small, incomplete fossil samples, and re-apply the finite mixture procedure to test how often it correctly assigns these "fragmentary" specimens. Finite mixture analysis can be highly accurate, even when confronted with small sample sizes and missing data. For example, a combination of 124 chimpanzees and humans are correctly identified in one analysis, and the accuracy drops only 2% to become 98% when the total sample size is reduced to 16 and missing data patterns are applied. In comparisons to better known methods that have been used to recognize groups in the fossil record, such as k-means, the benefits of finite mixture analysis are readily apparent. First, k-means is unable to accommodate missing data, an obvious deficiency when investigating the fossil record. Second, in direct comparisons of their ability to accurately assign "unknowns" to taxa, finite mixture performed at least as well as, and often better than, k-means in our analyses. A potential test that can be used to identify species in the fossil record, derived from comparisons of results generated from a general vs. a restricted (isometry-corrected) finite mixture analysis, is presented.

Animals↗

PubMedDate not supplied

The human cranial remains from Gran Dolina Lower Pleistocene site (Sierra de Atapuerca, Spain).

In this article we study the cranial remains of the late Lower Pleistocene human fossils from Gran Dolina (Sierra de Atapuerca, Spain), assigned to the new species Homo antecessor. The cranial remains belong to at least five individuals, both juveniles and adults. The most outstanding feature is the totally modern human morphology of the very complete face ATD6-69, representing the earliest occurrence of the modern face in the fossil record. The Gran Dolina fossils show in the face a suite of modern human apomorphies not found in earlier hominids nor in contemporary or earlier Homo erectus fossils. There are also traits in the Gran Dolina fossils shared with both Neandertals and modern humans, which reinforce the hypothesis that Neandertals and modern humans form a clade, and that the Gran Dolina fossils are a common ancestor to both lineages.

Age Determination by Teeth↗

PubMedDate not supplied

Stratigraphy, age and environments of the late Miocene Mpesida Beds, Tugen Hills, Kenya.

Interpretations of faunal assemblages from the late Miocene Mpesida Beds in the Tugen Hills of the Central Kenyan Rift Valley have figured prominently in discussions of faunal turnover and establishment of the modern East African communities. These faunal changes have important implications for the divergence of the human lineage from the African apes ca. 8-5 Ma. While fossil material recovered from the Mpesida Beds has traditionally been analyzed collectively, accumulating evidence indicates that Mpesida facies span the 7-6 Ma interval and are scattered more than 25 km along the eastern flanks of the Tugen Hills. Stratigraphic distinctions between Mpesida facies and younger sediments in the sequence, such as the Lukeino Formation, are not yet fully resolved, further complicating temporal assessments and stratigraphic context of Mpesida facies. These issues are discussed with specific reference to exposures of Mpesida facies at Rurmoch, where large fossil tree fragments were swept up in an ancient ash flow. Preserved anatomical features of the fossil wood as well as estimated tree heights suggest a wet, lowland rainforest in this portion of the rift valley. Stable isotopic analyses of fossil enamel and paleosol components indicate the presence of more open habitats locally. Overlying air-fall tuffs and epiclastic debris, possibly associated with the ash flow, have yielded an assemblage of vertebrate fossils including two teeth belonging to one of the earliest colombines of typical body size known from Africa, after the rather small Microcolobus. Single-crystal, laser-fusion,(40)Ar/(39)Ar dates from a capping trachyte flow as well as tuffs just below the lava contact indicate an age of greater than 6.37 Ma for the fossil material.

Animals↗

PubMed1994

Implications of ancient DNA for phylogenetic studies.

The utility of DNA sequence characters from fossil specimens is examined from a phylogenetic perspective. Four ways that fossil characters can alter phylogenetic hypotheses are discussed. Two empirical examples and a third hypothetical example concerning amber-preserved insects are presented to illustrate these phenomena. Fossil DNA sequences as characters will be affected by the problem of missing data and missing taxa. In general, cladogram accuracy will be more greatly affected by missing taxa and cladogram resolution will be affected more acutely by missing data. Due to these points, an examination of the importance of the phylogenetic question being addressed, the utility of the fossil DNA sequences and the rarity of the fossil should be considered before damage of a fossil is undertaken.

Animals↗

PubMed2006

Examining affinities of the Taung child by developmental simulation.

As a well-preserved juvenile and the type specimen of Australopithecus africanus, the Taung child figures prominently in taxonomic, ontogenetic, and phylogenetic analyses of fossil hominins. Despite general agreement about allocation of Sterkfontein and Makapansgat fossils to this species, limited morphological comparisons have been possible between these adult specimens and the juvenile Taung. Here, we used developmental simulation to estimate the adult form of the Taung child, and directly compare its morphology to that of other fossil hominins. Specimens were represented by 50 three-dimensional landmarks superimposed by generalized Procrustes analysis. The simulation process applied developmental trajectories from extant hominine species to the Taung fossil in order to generate its adult form. Despite differences found in the developmental patterns of these modern species, simulations tested on extant juveniles-transforming them into "adults" using trajectories from other species-revealed that these differences have negligible impact on adult morphology. This indicates that morphology already present by occlusion of the first permanent molar is the primary determinant of adult form, thereby supporting use of extant trajectories to estimate the morphology of an extinct species. The simulated Taung adult was then compared to other adult fossils. As these comparisons required assumptions about the pattern and magnitude of developmental change, additional analyses were performed to evaluate these two parameters separately. Results of all analyses overwhelmingly rejected the possibility that the Taung child was a juvenile robust australopith, but were consistent with the hypothesis that the Taung and Sterkfontein fossils are conspecific. Between Sts 5 and Sts 71, the latter is more likely to resemble the adult form of the Taung child.

Animals↗

PubMed2002

Amber: the organic gemstone.

Resins are produced by woody plants on a worldwide basis. We have found several distinct classes of modern diterpenoid resins based phenomenologically on the solid-state (13)C NMR spectra of the bulk material. Resin fossilizes over millions of years into a robust material sometimes called amber. We have characterized several hundred samples of fossil resin by solid-state (13)C NMR spectroscopy. We can relate one globe-spanning group of fossil resins to the modern genus Agathis, based on spectral evolution over time. A second large group has not been related with certainty to specific modern plants. Fossil resins from Europe fall into two categories, the famous Baltic ambers and another that resembles the Agathis group. Fossil resins from the Americas and Africa are closely related to the modern genus Hymenaea. Based on spectral distinctions, fossil resin found in an archaeological context sometimes can be assigned to a specific geographical origin on the basis of its (13)C NMR spectrum.

Amber↗

PubMed2000

Investigating human evolutionary history.

We rely on fossils for the interpretation of more than 95% of our evolutionary history. Fieldwork resulting in the recovery of fresh fossil evidence is an important component of reconstructing human evolutionary history, but advances can also be made by extracting additional evidence for the existing fossil record, and by improving the methods used to interpret the fossil evidence. This review shows how information from imaging and dental microstructure has contributed to improving our understanding of the hominin fossil record. It also surveys recent advances in the use of the fossil record for phylogenetic inference.

Animals↗

PubMed2004

Cretaceous flowers of Nymphaeaceae and implications for complex insect entrapment pollination mechanisms in early angiosperms.

Based on recent molecular systematics studies, the water lily lineage (Nymphaeales) provides an important key to understanding ancestral angiosperm morphology and is of considerable interest in the context of angiosperm origins. Therefore, the fossil record of Nymphaeales potentially provides evidence on both the timing and nature of diversification of one of the earliest clades of flowering plants. Recent fossil evidence of Turonian age (approximately 90 million years B.P.) includes fossil flowers with characters that, upon rigorous analysis, firmly place them within Nymphaeaceae. Unequivocally the oldest floral record of the Nymphaeales, these fossils are closely related to the modern Nymphaealean genera Victoria (the giant Amazon water lily) and Euryale. Although the fossils are much smaller than their modern relatives, the precise and dramatic correspondence between the fossil floral morphology and that of modern Victoria flowers suggests that beetle entrapment pollination was present in the earliest part of the Late Cretaceous.

Animals↗

PubMed1976

Characterization of 80-million-year-old mollusk shell proteins.

Fossil glycoproteins of the soluble organic matrix are present in an 80-million-year-old mollusk shell from the Late Cretaceous Period. Discrete molecular weight components, as determined by gel electrophoresis, are preserved. The fossil organic matrix was compared with the organic matrix of a living representative species of the same superfamily. A particular repeating amino acid sequence, found in contemporary mollusk shell proteins, was identified in the fossil glycoproteins. The ultrastructure, mineralogy, and chemistry of the inorganic components of the fossil and contemporary shells provide information on the state of preservation of the fossil. The use of fossil shell proteins to further our understanding of molecular evolution is discussed.

Amino Acids↗

PubMed2004

Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification.

We present a phylogenetic dating of asterids, based on a 111-taxon tree representing all major groups and orders and 83 of the 102 families of asterids, with an underlying data set comprising six chloroplast DNA markers totaling 9914 positions. Phylogenetic dating was done with semiparametric rate smoothing by penalized likelihood. Confidence intervals were calculated by bootstrapping. Six reference fossils were used for calibration. To explore the effects of various sources of error, we repeated the analyses with alternative dating methods (nonparametric rate smoothing and the Langley-Fitch clock-based method), alternative tree topologies, reduced taxon sampling (22 of the 111 taxa deleted), partitioning the data into three genes and three noncoding regions, and calibrating with single reference fossils. The analyses with alternative topologies, reduced taxon sampling, and coding versus noncoding sequences all yielded small or in some cases no deviations. The choice of method influenced the age estimates of a few nodes considerably. Calibration with reference fossils is a critical issue, and use of single reference fossils yielded different results depending on the fossil. The bootstrap confidence intervals were generally small. Our results show that asterids and their major subgroups euasterids, campanulids, and lamiids diversified during the Early Cretaceous. Cornales, Ericales, and Aquifoliales also have crown node ages from the Early Cretaceous. Dipsacales and Solanales are from the Mid-Cretaceous, the other orders of core campanulids and core lamiids from the Late Cretaceous. The considerable diversity exhibited by asterids almost from their first appearance in the fossil record also supports an origin and first phase of diversification in the Early Cretaceous.

DNA, Chloroplast↗

PubMed2006

Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata).

The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.

Animals↗

PubMed2005

Ancient DNA from pollen: a genetic record of population history in Scots pine.

Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100-year old and 10 000-year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.

Base Sequence↗

PubMed2006

Comparative anatomy and histology of xenarthran osteoderms.

Reconstruction of soft tissues in fossil vertebrates is an enduring challenge for paleontologists. Because inferences must be based on evidence from hard tissues (typically bones or teeth), even the most complete fossils provide only limited information about certain organ systems. Osteoderms ("dermal armor") are integumentary bones with high fossilization potential that hold information about the anatomy of the skin in many extant and fossil amniotes. Their importance for functional morphology and phylogenetic research has recently been recognized, but studies have focused largely upon reptiles, in which osteoderms are most common. Among mammals, osteoderms occur only in members of the clade Xenarthra, which includes armadillos and their extinct relatives: glyptodonts, pampatheres, and, more distantly, ground sloths. Here, I present new information on the comparative morphology and histology of osteoderms and their associated soft tissues in 11 extant and fossil xenarthrans. Extinct mylodontid sloths possessed simple, isolated ossicles, the presence of which is likely plesiomorphic for Xenarthra. More highly derived osteoderms of glyptodonts, pampatheres, and armadillos feature complex articulations and surface ornamentation. Osteoderms of modern armadillos are physically associated with a variety of soft tissues, including nerve, muscle, gland, and connective tissue. In some cases, similar osteological features may be caused by two or more different tissue types, rendering soft-tissue inferences for fossil osteoderms equivocal. Certain osteological structures, however, are consistently associated with specific soft-tissue complexes and therefore represent a relatively robust foundation upon which to base soft-tissue reconstructions of extinct xenarthrans.

Anatomy, Comparative↗

PubMed2007

Ethanol production: energy, economic, and environmental losses.

The prime focus of ethanol production from corn is to replace the imported oil used in American vehicles, without expending more fossil energy in ethanol production than is produced as ethanol energy. In a thorough and up-to-date evaluation of all the fossil energy costs of ethanol production from corn, every step in the production and conversion process must be included. In this study, 14 energy inputs in average U.S. corn production are included. Then, in the fermentation/distillation operation, 9 more identified fossil fuel inputs are included. Some energy and economic credits are given for the by-products, including dried distillers grains (DDG). Based on all the fossil energy inputs, a total of 1.43 kcal fossil energy is expended to produced 1 kcal ethanol. When the energy value of the DDG, based on the feed value of the DDG as compared to that of soybean meal, is considered, the energy cost of ethanol production is reduced slightly, to 1.28 kcal fossil energy input per 1 kcal ethanol produced. Several proethanol investigators have overlooked various energy inputs in U.S. corn production, including farm machinery, processing machinery, and the use of hybrid corn. In other studies, unrealistic, low energy costs were attributed to such inputs as nitrogen fertilizer, insecticides, and herbicides. Controversy continues concerning the energy and economic credits that should be assigned to the by-products. The U.S. Department of Energy reports that 17.0 billion L ethanol was produced in 2005. This represents only less than 1% of total oil use in the U.S. These yields are based on using about 18% of total U.S. corn production and 18% of cornland. Because the production of ethanol requires large inputs of both oil and natural gas in production, the U.S. is importing both oil and natural gas to produce ethanol. Furthermore, the U.S. Government is spending about dollar 3 billion annually to subsidize ethanol production, a subsidy of dollar 0.79/L ethanol produced. With the subsidy, plus the cost of production, the cost of ethanol is calculated to be dollar 1.21/L. The subsidy for a liter of ethanol is 45-times greater than the subsidy per liter of gasoline. The environmental costs associated with producing ethanol are significant but have been ignored by most investigators in terms of energy and economics. The negative environmental impacts on cropland, and freshwater, as well as air pollution and public health, have yet to be carefully assessed. These environmental costs in terms of energy and economics should be calculated and included in future ethanol analyses. General concern has been expressed about taking 18% of U.S. corn, and more in the future, to produce ethanol for burning in automobiles instead of using the corn as food for the many malnourished people in the world. The World Health Organization reports that more than 3.7 billion humans are currently malnourished in the world--the largest number ever in history.

Bioelectric Energy Sources↗

PubMed2001

A study of amber and copal samples using FT-Raman spectroscopy.

FT-Raman spectra were collected from fossil resins originating from a variety of geographical locations. The spectral profiles of most of the fossil resins could be related to modern resins containing diterpenoid components with predominantly labdane skeletons. The spectra collected from the fossil resin sample from Borneo differed from other fossil resins and was found to contain triterpenoid components. The differences in the spectral profile of fossil resins containing diterpenoid components are shown to relate to differences in level of maturation rather than geographical origin. FT-Raman spectra of fossil resins cannot be used to distinguish source although the degree of maturation can be used as an indicator to narrow the range of possible geographical origins.

Amber↗

PubMedDate not supplied

Evolution and development of teeth.

Teeth as a feeding mechanism in an oral cavity (mouth) are functionally and locationally linked with jaws. In fossils, teeth found in the oral cavity are usually linked with jaws, although mineralised structures with the same histology as teeth are known in fossils before jaws appeared. Denticles in the skin occur in both fossil and extant fish. Pharyngeal denticles also occur in both extant and fossil gnathostomes but in only a few fossil agnathans (thelodonts). Complex structures with dentine and enamel have been described in the earliest jawless vertebrates, conodonts. Such fossils have been used to suggest that teeth and jaws have evolved and developed independently. Our understanding of the developmental biology of mammalian tooth development has increased greatly in the last few years to a point where we now understand some of the basic genetic interactions controlling tooth initiation, morphogenesis and patterning. The aim of this review is to see what this developmental information can reveal about evolution of the dentition.

Animals↗

PubMed2004

The colonization of land by animals: molecular phylogeny and divergence times among arthropods.

BACKGROUND: The earliest fossil evidence of terrestrial animal activity is from the Ordovician, approximately 450 million years ago (Ma). However, there are earlier animal fossils, and most molecular clocks suggest a deep origin of animal phyla in the Precambrian, leaving open the possibility that animals colonized land much earlier than the Ordovician. To further investigate the time of colonization of land by animals, we sequenced two nuclear genes, glyceraldehyde-3-phosphate dehydrogenase and enolase, in representative arthropods and conducted phylogenetic and molecular clock analyses of those and other available DNA and protein sequence data. To assess the robustness of animal molecular clocks, we estimated the deuterostome-arthropod divergence using the arthropod fossil record for calibration and tunicate instead of vertebrate sequences to represent Deuterostomia. Nine nuclear and 15 mitochondrial genes were used in phylogenetic analyses and 61 genes were used in molecular clock analyses. RESULTS: Significant support was found for the unconventional pairing of myriapods (millipedes and centipedes) with chelicerates (spiders, scorpions, horseshoe crabs, etc.) using nuclear and mitochondrial genes. Our estimated time for the divergence of millipedes (Diplopoda) and centipedes (Chilopoda) was 442 +/- 50 Ma, and the divergence of insects and crustaceans was estimated as 666 +/- 58 Ma. Our results also agree with previous studies suggesting a deep divergence (approximately 1100 - 900 Ma) for arthropods and deuterostomes, considerably predating the Cambrian Explosion seen in the animal fossil record. CONCLUSIONS: The consistent support for a close relationship between myriapods and chelicerates, using mitochondrial and nuclear genes and different methods of analysis, suggests that this unexpected result is not an artefact of analysis. We propose the name Myriochelata for this group of animals, which includes many that immobilize prey with venom. Our molecular clock analyses using arthropod fossil calibrations support earlier studies using vertebrate calibrations in finding that deuterostomes and arthropods diverged hundreds of millions of years before the Cambrian explosion. However, our molecular time estimate for the divergence of millipedes and centipedes is close to the divergence time inferred from fossils. This suggests that arthropods may have adapted to the terrestrial environment relatively late in their evolutionary history.

Animals↗

PubMed2000

Makers of the early Aurignacian of Europe.

Despite intensive study and a number of remarkable discoveries in the last two decades of the 20th century, our understanding of the cultural and biological processes that resulted in the emergence of the Upper Paleolithic and the establishment of modern humans in Interpleniglacial Europe remains far from complete. There is active debate concerning the timing and location of the origins of the Aurignacian, the nature of the origins of Initial Upper Paleolithic industries (whether by autochthonous development or through acculturation by Aurignacian peoples), the timing of the appearance of early modern humans and the disappearance of the Neandertals, and the relationship of archeologically defined cultures to these different types of hominids. Frustrating our attempts to address these latter two questions is a general paucity of taxonomically diagnostic human fossil material from early Upper Paleolithic contexts. We undertake here a review of the human fossil record of Interpleniglacial Europe, and its archeological and chronological context, to clarify to the extent possible the nature of the relationship between hominid groups and the earliest Upper Paleolithic artifact industries, particularly the early Aurignacian. Although substantial difficulties involved in interpreting the fossil, archeological, and geochronological records of this time period prohibit making any definitive statements, a number of observations are suggested by the current data: 1) the Middle Paleolithic of Europe appears to have been made exclusively by Neandertals; 2) Initial Upper Paleolithic industries (with the exception of the Bachokirian) appear to have their roots in the late Middle Paleolithic industries of their respective regions; 3) all of the human fossils yet recovered from Initial Upper Paleolithic (except the Bachokirian) contexts for which any diagnostic morphology is present have their greatest morphological affinities with Neandertals and not early modern humans; 4) modern humans were almost certainly established in Europe by ca. 32 ky BP, with a strong possibility that they were there by ca. 36 ky BP. Claims for an appearance before 36 ky BP cannot be substantiated with currently available evidence; 5) the hypothesis that modern humans are uniquely associated with the Aurignacian cannot yet be refuted. Aurignacian-associated human fossils (including those from the Bachokirian) for which any diagnostic morphology is present have their greatest affinities with early modern Europeans and not Neandertals; and 6) Neandertals and modern humans coexisted in Europe for at least 2,000-4,000 years, and perhaps for 8,000-10,000 years or longer. The overall picture is one of an extended period of cultural contact, involving some degree of genetic exchange, between Neandertals and early modern Europeans.

Animals↗