Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals.
Some molecular clock estimates of divergence times of taxonomic groups undergoing evolutionary radiation are much older than the groups' first observed fossil record. Mathematical models of branching evolution are used to estimate the maximal rate of fossil preservation consistent with a postulated missing history, given the sum of species durations implied by early origins under a range of species origination and extinction rates. The plausibility of postulated divergence times depends on origination, extinction, and preservation rates estimated from the fossil record. For eutherian mammals, this approach suggests that it is unlikely that many modern orders arose much earlier than their oldest fossil records. (+info)
X chromosome evidence for ancient human histories.
Diverse African and non-African samples of the X-linked PDHA1 (pyruvate dehydrogenase E1 alpha subunit) locus revealed a fixed DNA sequence difference between the two sample groups. The age of onset of population subdivision appears to be about 200 thousand years ago. This predates the earliest modern human fossils, suggesting the transformation to modern humans occurred in a subdivided population. The base of the PDHA1 gene tree is relatively ancient, with an estimated age of 1.86 million years, a late Pliocene time associated with early species of Homo. PDHA1 revealed very low variation among non-Africans, but in other respects the data are consistent with reports from other X-linked and autosomal haplotype data sets. Like these other genes, but in conflict with microsatellite and mitochondrial data, PDHA1 does not show evidence of human population expansion. (+info)
Predicting protein decomposition: the case of aspartic-acid racemization kinetics.
The increase in proportion of the non-biological (D-) isomer of aspartic acid (Asp) relative to the L-isomer has been widely used in archaeology and geochemistry as a tool for dating. the method has proved controversial, particularly when used for bones. The non-linear kinetics of Asp racemization have prompted a number of suggestions as to the underlying mechanism(s) and have led to the use of mathematical transformations which linearize the increase in D-Asp with respect to time. Using one example, a suggestion that the initial rapid phase of Asp racemization is due to a contribution from asparagine (Asn), we demonstrate how a simple model of the degradation and racemization of Asn can be used to predict the observed kinetics. A more complex model of peptide bound Asx (Asn + Asp) racemization, which occurs via the formation of a cyclic succinimide (Asu), can be used to correctly predict Asx racemization kinetics in proteins at high temperatures (95-140 degrees C). The model fails to predict racemization kinetics in dentine collagen at 37 degrees C. The reason for this is that Asu formation is highly conformation dependent and is predicted to occur extremely slowly in triple helical collagen. As conformation strongly influences the rate of Asu formation and hence Asx racemization, the use of extrapolation from high temperatures to estimate racemization kinetics of Asx in proteins below their denaturation temperature is called into question. In the case of archaeological bone, we argue that the D:L ratio of Asx reflects the proportion of non-helical to helical collagen, overlain by the effects of leaching of more soluble (and conformationally unconstrained) peptides. Thus, racemization kinetics in bone are potentially unpredictable, and the proposed use of Asx racemization to estimate the extent of DNA depurination in archaeological bones is challenged. (+info)
Preservation of key biomolecules in the fossil record: current knowledge and future challenges.
We have developed a model based on the analyses of modern and Pleistocene eggshells and mammalian bones which can be used to understand the preservation of amino acids and other important biomolecules such as DNA in fossil specimens. The model is based on the following series of diagenetic reactions and processes involving amino acids: the hydrolysis of proteins and the subsequent loss of hydrolysis products from the fossil matrix with increasing geologic age; the racemization of amino acids which produces totally racemized amino acids in 10(5)-10(6) years in most environments on the Earth; the introduction of contaminants into the fossil that lowers the enantiomeric (D:L) ratios produced via racemization; and the condensation reactions between amino acids, as well as other compounds with primary amino groups, and sugars which yield humic acid-like polymers. This model was used to evaluate whether useful amino acid and DNA sequence information is preserved in a variety of human, amber-entombed insect and dinosaur specimens. Most skeletal remains of evolutionary interest with respect to the origin of modern humans are unlikely to preserve useful biomolecular information although those from high latitude sites may be an exception. Amber-entombed insects contain well-preserved unracemized amino acids, apparently because of the anhydrous nature of the amber matrix, and thus may contain DNA fragments which have retained meaningful genetic information. Dinosaur specimens contain mainly exogenous amino acids, although traces of endogenous amino acids may be present in some cases. Future ancient biomolecule research which takes advantage of new methologies involving, for example, humic acid cleaving reagents and microchip-based DNA-protein detection and sequencing, along with investigations of very slow biomolecule diagenetic reactions such as the racemization of isoleucine at the beta-carbon, will lead to further enhancements of our understanding of biomolecule preservation in the fossil record. (+info)
Early medieval cattle remains from a Scandinavian settlement in Dublin: genetic analysis and comparison with extant breeds.
A panel of cattle bones excavated from the 1000-year-old Viking Fishamble Street site in Dublin was assessed for the presence of surviving mitochondrial DNA (mtDNA). Eleven of these bones gave amplifiable mtDNA and a portion of the hypervariable control region was determined for each specimen. A comparative analysis was performed with control region sequences from five extant Nordic and Irish cattle breeds. The medieval population displayed similar levels of mtDNA diversity to modern European breeds. However, a number of novel mtDNA haplotypes were also detected in these bone samples. In addition, the presence of a putative ancestral sequence at high frequency in the medieval population supports an early post-domestication expansion of cattle in Europe. (+info)
New evidence from Le Moustier 1: computer-assisted reconstruction and morphometry of the skull.
In this study, we present a new computerized reconstruction of the Le Moustier 1 Neanderthal skull and discuss its significance for Neanderthal growth and variability. Because of the precarious state of preservation of the original material, we applied entirely noninvasive methods of fossil reconstruction and morphometry, using a combination of computed tomography, computer graphics, and stereolithography. After electronic restoration, the isolated original pieces were recomposed on the computer screen using external and internal anatomical clues to position the bone fragments and mirror images to complete missing parts. The inferred effects of general compressive deformation that occurred during fossilization were corrected by virtual decompression of the skull. The resulting new reconstruction of the Le Moustier 1 skull shows morphologic features close to the typical Neanderthal adult state. Residual asymmetry of skeletal parts can be traced to in vivo skeletal modification: the left mandibular joint shows signs of a healed condylar fracture, and the anatomy of the occipital region suggests mild plagiocephaly. Using micro-CT analysis, the left incus could be recovered from the matrix filling of the middle ear cavity. Its morphometric dimensions are similar to those of the La Ferrassie III incus. The morphometric characteristics of the inner ear deviate substantially from the condition reported as typical for Neanderthals and fall within the range of modern human variability. (+info)
Evolutionary patterns from mass originations and mass extinctions.
The Fossil Record 2 database gives a stratigraphic range of most known animal and plant families. We have used it to plot the number of families extant through time and argue for an exponential fit, rather than a logistic one, on the basis of power spectra of the residuals from the exponential. The times of origins and extinctions, when plotted for all families of marine and terrestrial organisms over the last 600 Myr, reveal different origination and extinction peaks. This suggests that patterns of biological evolution are driven by its own internal dynamics as well as responding to upsets from external causes. Spectral analysis shows that the residuals from the exponential model of the marine system are more consistent with 1/f noise suggesting that self-organized criticality phenomena may be involved. (+info)
Environment and behavior of 2.5-million-year-old Bouri hominids.
The Hata Member of the Bouri Formation is defined for Pliocene sedimentary outcrops in the Middle Awash Valley, Ethiopia. The Hata Member is dated to 2.5 million years ago and has produced a new species of Australopithecus and hominid postcranial remains not currently assigned to species. Spatially associated zooarchaeological remains show that hominids acquired meat and marrow by 2.5 million years ago and that they are the near contemporary of Oldowan artifacts at nearby Gona. The combined evidence suggests that behavioral changes associated with lithic technology and enhanced carnivory may have been coincident with the emergence of the Homo clade from Australopithecus afarensis in eastern Africa. (+info)