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PubMed2004

Error in estimation of rate and time inferred from the early amniote fossil record and avian molecular clocks.

The best reconstructions of the history of life will use both molecular time estimates and fossil data. Errors in molecular rate estimation typically are unaccounted for and no attempts have been made to quantify this uncertainty comprehensively. Here, focus is primarily on fossil calibration error because this error is least well understood and nearly universally disregarded. Our quantification of errors in the synapsid-diapsid calibration illustrates that although some error can derive from geological dating of sedimentary rocks, the absence of good stem fossils makes phylogenetic error the most critical. We therefore propose the use of calibration ages that are based on the first undisputed synapsid and diapsid. This approach yields minimum age estimates and standard errors of 306.1 +/- 8.5 MYR for the divergence leading to birds and mammals. Because this upper bound overlaps with the recent use of 310 MYR, we do not support the notion that several metazoan divergence times are significantly overestimated because of serious miscalibration (sensuLee 1999). However, the propagation of relevant errors reduces the statistical significance of the pre-K-T boundary diversification of many bird lineages despite retaining similar point time estimates. Our results demand renewed investigation into suitable loci and fossil calibrations for constructing evolutionary timescales.

Animals↗

PubMed1987

Adaptation, plant evolution, and the fossil record.

The importance of adaptation in determining patterns of evolution has become an important focus of debate in evolutionary biology. As it pertains to paleobotany, the issue is whether or not adaptive evolution mediated by natural selection is sufficient to explain the stratigraphic distributions of taxa and character states observed in the plant fossil record. One means of addressing this question is the functional evaluation of stratigraphic series of plant organs set in the context of paleoenvironmental change and temporal patterns of floral composition within environments. For certain organ systems, quantitative estimates of biophysical performance can be made on the basis of structures preserved in the fossil record. Performance estimates for plants separated in time or space can be compared directly. Implicit in different hypotheses of the forces that shape the evolutionary record (e.g. adaptation, mass extinction, rapid environmental change, chance) are predictions about stratigraphic and paleoenvironmental trends in the efficacy of functional performance. Existing data suggest that following the evolution of a significant structural innovation, adaptation for improved functional performance can be a major determinant of evolutionary changes in plants; however, there are structural and development limits to functional improvement, and once these are reached, the structure in question may no longer figure strongly in selection until and unless a new innovation evolves. The Silurian-Devonian paleobotanical record is consistent with the hypothesis that the succession of lowland floodplain dominants preserved in the fossil record of this interval was determined principally by the repeated evolution of new taxa that rose to ecological importance because of competitive advantages conferred by improved biophysical performance. This does not seem to be equally true for Carboniferous-Jurassic dominants of swamp and lowland floodplain environments. In these cases, environmental disruption appears to have been a major factor in shaping the fossil record. This does not mean that continuing adaptation was not important during this interval, but it may indicate that adaptive evolution was strongest in environments other than those best represented in the paleobotanical record.

Adaptation, Biological↗

PubMed2004

Adolescent archaics or adult moderns? Le Moustier 1 as a model for estimating the age at death of fragmentary supraorbital fossils in the modern human origins debate.

This study documents and examines selected implications of the adolescent supraorbital anatomy of the Le Moustier 1 Neandertal. Le Moustier's supraorbital morphology conforms to that expected of an adolescent Neandertal but indicates that significant development of the adult Neandertal torus occurs late in ontogeny. As the best preserved adolescent from the Late Pleistocene, Le Moustier 1's anatomy is used to help distinguish adolescent from adult anatomy in two cases of fragmentary supraorbital fossils, the Vindija late Neandertals and KRM 16425 from Klasies River Mouth (South Africa). It has been suggested that the modern-like aspects of the Vindija and Klasies supraorbital fossils are a function of developmental age rather than evolution. Although Le Moustier 1's anatomy does indicate that two of the Vindija fossils are adolescent; these two fossils have already been excluded from studies that demonstrate transitional aspects of the Vindija adult supraorbitals. Results of an analysis of KRM 16425 in light of Le Moustier 1 are more ambiguous. KRM 16425 is clearly not a Neandertal, but its morphology suggests that it may be an adolescent form of such late archaic Africans like Florisbad or Ngaloba. Both the Vindija and Klasies River Mouth cases highlight the need to be wary of confusing adolescent anatomy with modernity.

Adolescent↗

PubMed2004

New discoveries and interpretations of hominid fossils and artifacts from Vindija Cave, Croatia.

Beginning with excavations during the 1970s, Vindija Cave (Croatia) has yielded significant Middle and Upper Paleolithic fossil and archaeological finds. We report on seven recently identified hominid fossils, a newly associated partial hominid cranial vault from level G(3), nine possible bone retouchers, and a revised interpretation of the Mousterian artifact assemblage from the site. This new information reinforces our knowledge of the complex biocultural phenomena revealed in unit G and earlier deposits at Vindija. Six of the new hominid fossils derive from stratigraphic units G and I, while one lacks exact provenience. All specimens preserving diagnostic anatomy are from Neandertals. One of the postcranial remains, a radius fragment which exhibits Neandertal-like anatomy, comes from level G(1)and is congruent with the previously established association of Neandertals with an early Upper Paleolithic industry at the site. The partial cranial vault represents the most complete Neandertal from Vindija. The possible retouchers derive from unit G. Our analysis of these artifacts suggests that both percussion and pressure techniques may have been used by Neandertals in the final stage of tool production (retouching). This paper also presents a revision of the artifact analysis for late Mousterian level G(3). We separated raw materials into two main groups due to the differing ways that the materials fracture and the differing morphology of the debitage. The use of raw material in level G(3)is different from earlier Middle Paleolithic levels at Vindija. This indicates that the G(3)late Neandertals were making choices regarding source material somewhat more like the Upper Paleolithic people at the site. When interpreted within a larger regional framework, the Vindija archaeological and hominid fossil remains demonstrate a complex, mosaic pattern of biocultural change in the Late Pleistocene of south-central Europe.

Animals↗

PubMed2006

A fossil hominoid proximal femur from Kikorongo Crater, southwestern Uganda.

The external morphology of a fragmentary right proximal femur from southwestern Uganda is described here. Discovered in the Kikorongo Crater of Queen Elizabeth National Park in 1961, this specimen was informally assigned to Homo sapiens (although never described) and tentatively dated to the late Pleistocene. However, because aspects of the external morphology of the femur align the fossil with the African great apes, we suggest that the Kikorongo femur may be the first postcranial fossil of the genus Pan. Like the African apes, the Kikorongo specimen lacks both an obturator externus groove and an intertrochanteric line. It has a short femoral neck with a circular cross section, and a narrow and deep superior notch. Using resampling statistics and discriminant function analysis, the Kikorongo femur clustered with the genus Pan, as opposed to Gorilla or Homo. However, if the specimen is from Pan, it would be large for this taxon. Furthermore, features that clearly distinguish the external morphology of Plio-Pleistocene hominin proximal femora from African ape femora, such as the shape of the femoral neck in cross section and femoral neck length, have converged in Holocene humans and African apes. Unfortunately, the internal morphology of the femoral neck of the Kikorongo fossil was not discernable. Although we hypothesize that the Kikorongo femur is from the genus Pan, there is such variability in the proximal femora of modern humans that, although it would be an unusual human, it remains possible that this fossil represents H. sapiens.

Animals↗

PubMed2004

Can extinction rates be estimated without fossils?

There is considerable interest in the possibility of using molecular phylogenies to estimate extinction rates. The present study aims at assessing the statistical performance of the birth-death model fitting approach to estimate speciation and extinction rates by comparison to the approach considering fossil data. A simulation-based approach was used. The diversification of a large number of lineages was simulated under a wide range of speciation and extinction rate values. The estimators obtained with fossils performed better than those without fossils. In the absence of fossils (e.g. with a molecular phylogeny), the speciation rate was correctly estimated in a wide range of situations; the bias of the corresponding estimator was close to zero for the largest trees. However, this estimator was substantially biased when the simulated extinction rate was high. On the other hand the estimator of extinction rate was biased in a wide range of situations. Surprisingly, this bias was lesser with medium-sized trees. Some recommendations for interpreting results from a diversification analysis are given.

Animals↗

PubMed2004

The Elgin marvel: using magnetic resonance imaging to look at a moldic fossil from the Permian of Elgin, Scotland, UK.

The successful use of magnetic resonance imaging (MRI) of a moldic fossil dicynodont from the Permian aeolian Hopeman Sandstone Formation of Elgin, Scotland, UK, provides paleontologists with a nondestructive technique for examining fossils preserved in this fashion. For large moldic fossils, medical scanners such as the Phillips Gyroscan MRI, provide adequate resolution for gross morphologic determination. The 3-D rendered images using software such as Philips Easivision allows the fossil to be examined and dissected without causing any physical damage to the original material. From the scans it is also possible to produce 3-D stereolithographs for a more tactile manipulation of the renderings.

Animals↗

PubMed2005

A chemical signal possibly related to physiology in fossil cells detected by energy dispersive X-ray microanalysis.

Energy dispersive X-ray microanalysis (EDXMA) is a widely used tool employed to detect elemental composition and its spatial distribution in a sample without causing damage. Charcoalified cytoplasm is a new type of fossil material that came to people's attention only recently. In this paper, EDXMA is used for the first time to detect the spatial elemental distribution in charcoalified cytoplasm of two fossil plants that are more than 100 million years old. The results demonstrate certain elemental distribution patterns within charcoalified cytoplasm and the surrounding cell walls. Based on the results from cytological studies of extant material, the heterogeneous spatial elemental distribution within the charcoalified cytoplasm has the potential to be related to the maturation of cells, the presence of certain organelles, and the physiology of these organelles. This is the first chemical signal detected in cytoplasm residue that can possibly be related to plant physiology. This paves the way for further research on fossil cytoplasm, which will better our understanding on the physiology of fossil plants.

Carbon↗

PubMed2005

Rise from the ashes - the reconstruction of charcoal fossil flowers.

The fossil record provides a unique opportunity to study the evolutionary history and past diversity of life. Without making use of palaeontological data, a comprehensive understanding of the phylogeny and present diversity of life would remain elusive. Angiosperms (flowering plants) are the largest and most diverse group of land plants. Our understanding of their evolution has in recent years profited immensely from the discovery and study of three-dimensionally preserved fossil flowers. Descriptions of such fossil flowers are in many respects equivalent to those of extant plants. Here, I provide background information about this type of angiosperm fossils and give special attention to the techniques used to reconstruct their three-dimensional shape and organization.

Charcoal↗

PubMed2003

The thermal history of human fossils and the likelihood of successful DNA amplification.

Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.

Animals↗

PubMed2005

The Paleogene fossil record of birds in Europe.

The Paleogene (Paleocene-Oligocene) fossil record of birds in Europe is reviewed and recent and fossil taxa are placed into a phylogenetic framework, based on published cladistic analyses. The pre-Oligocene European avifauna is characterized by the complete absence of passeriform birds, which today are the most diverse and abundant avian taxon. Representatives of small non-passeriform perching birds thus probably had similar ecological niches before the Oligocene to those filled by modern passerines. The occurrence of passerines towards the Lower Oligocene appears to have had a major impact on these birds, and the surviving crown-group members of many small arboreal Eocene taxa show highly specialized feeding strategies not found or rare in passeriform birds. It is detailed that no crown-group members of modern 'families' are known from pre-Oligocene deposits of Europe, or anywhere else. The phylogenetic position of Paleogene birds thus indicates that diversification of the crown-groups of modern avian 'families' did not take place before the Oligocene, irrespective of their relative position within Neornithes (crown-group birds). The Paleogene fossil record of birds does not even support crown-group diversification of Galliformes, one of the most basal taxa of neognathous birds, before the Oligocene, and recent molecular studies that dated diversification of galliform crown-group taxa into the Middle Cretaceous are shown to be based on an incorrect interpretation of the fossil taxa used for molecular clock calibrations. Several taxa that occur in the Paleogene of Europe have a very different distribution than their closest extant relatives. The modern survivors of these Paleogene lineages are not evenly distributed over the continents, and especially the great number of taxa that are today restricted to South and Central America is noteworthy. The occurrence of stem-lineage representatives of many taxa that today have a restricted Southern Hemisphere distribution conflicts with recent hypotheses on a Cretaceous vicariant origin of these taxa, which were deduced from the geographical distribution of the basal crown-group members.

Animals↗

PubMed1999

Absolute measures of the completeness of the fossil record.

Measuring the completeness of the fossil record is essential to understanding evolution over long timescales, particularly when comparing evolutionary patterns among biological groups with different preservational properties. Completeness measures have been presented for various groups based on gaps in the stratigraphic ranges of fossil taxa and on hypothetical lineages implied by estimated evolutionary trees. Here we present and compare quantitative, widely applicable absolute measures of completeness at two taxonomic levels for a broader sample of higher taxa of marine animals than has previously been available. We provide an estimate of the probability of genus preservation per stratigraphic interval, and determine the proportion of living families with some fossil record. The two completeness measures use very different data and calculations. The probability of genus preservation depends almost entirely on the Palaeozoic and Mesozoic records, whereas the proportion of living families with a fossil record is influenced largely by Cenozoic data. These measurements are nonetheless highly correlated, with outliers quite explicable, and we find that completeness is rather high for many animal groups.

Animals↗

PubMedDate not supplied

A fossil owl monkey from La Venta, Colombia.

Knowledge of the evolutionary history of living New World anthropoids is limited by a relatively poor fossil record. The discovery in 1986 of a new fossil monkey from the middle Miocene deposits of La Venta, Colombia, 12-15 million years ago (Myr BP), is the first example of a living New World monkey genus appearing in Tertiary rocks. Including anatomical evidence of the dentition and facial skull, it provides an unambiguous link between a Neogene fossil and the owl monkey, Aotus, the only modern crepuscular-nocturnal anthropoid primate. This new form brings to three the number of La Venta fossil monkeys which preserve excellent dentitions sharing extensive similarities with modern genera. All of these species are potentially ancestral to their extant relatives. The La Ventan Aotus is additional support for the idea that the modern platyrrhine radiation includes long-lived genera or generic lineages, some of which may be traceable to the early Miocene, 20 Myr BP.

Animals↗

PubMed2001

Fossil evidence of water lilies (Nymphaeales) in the Early Cretaceous.

Phylogenetic analyses have identified the water lilies (Nymphaeales: Cabombaceae and Nymphaeaceae), together with four other small groups of flowering plants (the 'ANITA clades': Amborellaceae, Illiciales, Trimeniaceae, Austrobaileyaceae), as the first diverging lineages from the main branch of the angiosperm phylogenetic tree, but evidence of these groups in the earliest phases of the angiosperm fossil record has remained elusive. Here we report the earliest unequivocal evidence, based on fossil floral structures and associated pollen, of fossil plants related to members of the ANITA clades. This extends the history of the water lilies (Nymphaeales) back to the Early Cretaceous (125-115 million years) and into the oldest fossil assemblages that contain unequivocal angiosperm stamens and carpels. This discovery adds to the growing congruence between results from molecular-based analyses of relationships among angiosperms and the palaeobotanical record. It is also consistent with previous observations that the flowers of early angiosperms were generally very small compared with those of their living relatives.

Biological Evolution↗

PubMed2004

On the evolutionary history of Ephedra: Cretaceous fossils and extant molecules.

Gnetales comprise three unusual genera of seed plants, Ephedra, Gnetum, and Welwitschia. Their extraordinary morphological diversity suggests that they are survivors of an ancient, more diverse group. Gnetalean antiquity is also supported by fossil data. Dispersed "ephedroid" (polyplicate) pollen first appeared in the Permian >250 million years ago (Myr), and a few megafossils document the presence of gnetalean features in the early Cretaceous. The Cretaceous welwitschioid seedling Cratonia cotyledon dates the split between Gnetum and Welwitschia to before 110 Myr. Ages and character evolution of modern diversity are, however, controversial, and, based on molecular data, it has recently been suggested that Ephedra is very young, only 8-32 Myr. Here, we present data on the evolutionary history of Ephedra. Fossil seeds from Buarcos, Portugal, unequivocally link one type of Cretaceous polyplicate pollen to Ephedra and document that plants with unique characters, including the peculiar naked male gametophyte, were established already in the Early Cretaceous. Clades in our molecular phylogeny of extant species correspond to geographical regions, with African species in a basal grade/clade. The study demonstrates extremely low divergence in both molecular and morphological characters in Ephedra. Features observed in the fossils are present in all major extant clades, showing that modern species have retained unique reproductive characters for >110 million years. A recent origin of modern species of Ephedra would imply that the Cretaceous Ephedra fossils discussed here were members of widespread, now extinct sister lineage(s), and that no morphological innovations characterized the second diversification.

Base Sequence↗

PubMed2001

Integrated fossil and molecular data reconstruct bat echolocation.

Molecular and morphological data have important roles in illuminating evolutionary history. DNA data often yield well resolved phylogenies for living taxa, but are generally unattainable for fossils. A distinct advantage of morphology is that some types of morphological data may be collected for extinct and extant taxa. Fossils provide a unique window on evolutionary history and may preserve combinations of primitive and derived characters that are not found in extant taxa. Given their unique character complexes, fossils are critical in documenting sequences of character transformation over geologic time and may elucidate otherwise ambiguous patterns of evolution that are not revealed by molecular data alone. Here, we employ a methodological approach that allows for the integration of molecular and paleontological data in deciphering one of the most innovative features in the evolutionary history of mammals-laryngeal echolocation in bats. Molecular data alone, including an expanded data set that includes new sequences for the A2AB gene, suggest that microbats are paraphyletic but do not resolve whether laryngeal echolocation evolved independently in different microbat lineages or evolved in the common ancestor of bats and was subsequently lost in megabats. When scaffolds from molecular phylogenies are incorporated into parsimony analyses of morphological characters, including morphological characters for the Eocene taxa Icaronycteris, Archaeonycteris, Hassianycteris, and Palaeochiropteryx, the resulting trees suggest that laryngeal echolocation evolved in the common ancestor of fossil and extant bats and was subsequently lost in megabats. Molecular dating suggests that crown-group bats last shared a common ancestor 52 to 54 million years ago.

Animals↗

PubMed1992

Molecular phylogenetic inference from saber-toothed cat fossils of Rancho La Brea.

A method for the successful extraction of sequestered cellular DNA from 14,000-year-old fossil bones was developed and applied to asphalt-preserved specimens of the extinct saber-toothed cat, Smilodon fatalis. Two distinct gene segments, the mitochondrial gene for 12S rRNA and nuclear FLA-I (the feline class I major histocompatibility complex gene), from three different individual fossil specimens were cloned and sequenced after PCR amplification. Comparison of fossil-derived DNA sequences to homologous regions in 15 living carnivorous species, including 9 species of Felidae and 6 nonfelids, affirmed the phylogenetic placement of Smilodon within the modern radiation of Felidae distinct from the Miocene paleofelid (Nimravidae) saber-toothed "cat" species. These results raise the prospect of obtaining genetically informative DNA from preserved bones of extinct fossil species, particularly among the 2 million specimens excavated from the asphaltic sediments at Rancho La Brea in metropolitan Los Angeles.

Animals↗

PubMed2006

Uncertainty in the age of fossils and the stratigraphic fit to phylogenies.

The ages of first appearance of fossil taxa in the stratigraphic record are inherently associated to an interval of error or uncertainty, rather than being precise point estimates. Contrasting this temporal information with topologies of phylogenetic relationships is relevant to many aspects of evolutionary studies. Several indices have been proposed to compare the ages of first appearance of fossil taxa and phylogenies. For computing most of these indices, the ages of first appearance of fossil taxa are currently used as point estimates, ignoring their associated errors or uncertainties. The effect of age uncertainty on measures of stratigraphic fit to phylogenies is explored here for two indices based on the extension of ghost lineages (MSM* and GER). A solution based on randomization of the ages of terminal taxa is implemented, resulting in a range of possible values for measures of stratigraphic fit to phylogenies, rather than in a precise but arbitrary stratigraphic fit value. Sample cases show that ignoring the age uncertainty of fossil taxa can produce misleading results when comparing the stratigraphic fit of competing phylogenetic hypotheses. Empirical test cases of alternative phylogenies of two dinosaur groups are analyzed through the randomization procedure proposed here.

Animals↗