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At least 145 records · Page 8Linked to original sources

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↗

PubMed2004

Ferns diversified in the shadow of angiosperms.

The rise of angiosperms during the Cretaceous period is often portrayed as coincident with a dramatic drop in the diversity and abundance of many seed-free vascular plant lineages, including ferns. This has led to the widespread belief that ferns, once a principal component of terrestrial ecosystems, succumbed to the ecological predominance of angiosperms and are mostly evolutionary holdovers from the late Palaeozoic/early Mesozoic era. The first appearance of many modern fern genera in the early Tertiary fossil record implies another evolutionary scenario; that is, that the majority of living ferns resulted from a more recent diversification. But a full understanding of trends in fern diversification and evolution using only palaeobotanical evidence is hindered by the poor taxonomic resolution of the fern fossil record in the Cretaceous. Here we report divergence time estimates for ferns and angiosperms based on molecular data, with constraints from a reassessment of the fossil record. We show that polypod ferns (> 80% of living fern species) diversified in the Cretaceous, after angiosperms, suggesting perhaps an ecological opportunistic response to the diversification of angiosperms, as angiosperms came to dominate terrestrial ecosystems.

Biodiversity↗

PubMed2006

Bird evolution in the Eocene: climate change in Europe and a Danish fossil fauna.

The pattern of the evolutionary radiation of modern birds (Neornithes) has been debated for more than 10 years. However, the early fossil record of birds from the Paleogene, in particular, the Lower Eocene, has only recently begun to be used in a phylogenetic context to address the dynamics of this major vertebrate radiation. The Cretaceous-Paleogene (K-P) extinction event dominates our understanding of early modern bird evolution, but climate change throughout the Eocene is known to have also played a major role. The Paleocene and Lower Eocene was a time of avian diversification as a result of favourable global climatic conditions. Deteriorations in climate beginning in the Middle Eocene appear to be responsible for the demise of previously widespread avian lineages like Lithornithiformes and Gastornithidae. Other groups, such as Galliformes display replacement of some lineages by others, probably related to adaptations to a drier climate. Finally, the combination of slowly deteriorating climatic conditions from the Middle Eocene onwards, appears to have slowed the evolutionary rate in Europe, as avian faunas did not differentiate markedly until the Oligocene. Taking biotic factors in tandem with the known Paleogene fossil record of Neornithes has recently begun to illuminate this evolutionary event. Well-preserved fossil taxa are required in combination with ever-improving phylogenetic hypotheses for the inter-relationships of modern birds founded on morphological characters. One key avifauna of this age, synthesised for the first time herein, is the Lower Eocene Fur Formation of Denmark. The Fur birds represent some of the best preserved (often in three dimensions and with soft tissues) known fossil records for major clades of modern birds. Clear phylogenetic assessment of these fossils will prove critical for future calibration of the neornithine evolutionary timescale. Some early diverging clades were clearly present in the Paleocene as evidenced directly by new fossil material alongside the phylogenetically constrained Lower Eocene taxa. A later Oligocene radiation of clades other than Passeriformes is not supported by available fossil data.

Animals↗

PubMed2004

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes.

We estimated the dates of the monocot-dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li-Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot-dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li-Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li-Tanimura method, we propose that monocots branched off from dicots 140-150 Myr ago (late Jurassic-early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100-115 Myr ago (Albian-Aptian of the Cretaceous). These estimates indicate that both the monocot-dicot divergence and the core eudicot's age are older than their respective fossil records.

Chloroplasts↗

PubMed2003

The evolution of body size in extant groups of North American freshwater fishes: speciation, size distributions, and Cope's rule.

Change in body size within an evolutionary lineage over time has been under investigation since the synthesis of Cope's rule, which suggested that there is a tendency for mammals to evolve larger body size. Data from the fossil record have subsequently been examined for several other taxonomic groups to determine whether they also displayed an evolutionary increase in body size. However, we are not aware of any species-level study that has investigated the evolution of body size within an extant continental group. Data acquired from the fossil record and data derived from the evolutionary relationships of extant species are not similar, with each set exhibiting both strengths and weaknesses related to inferring evolutionary patterns. Consequently, expectation that general trends exhibited in the fossil record will correspond to patterns in extant groups is not necessarily warranted. Using phylogenetic relationships of extant species, we show that five of nine families of North American freshwater fishes exhibit an evolutionary trend of decreasing body size. These trends result from the basal position of large species and the more derived position of small species within families. Such trends may be caused by the invasion of small streams and subsequent isolation and speciation. This pattern, potentially influenced by size-biased dispersal rates and the high percentage of small streams in North America, suggests a scenario that could result in the generation of the size-frequency distribution of North American freshwater fishes.

Animals↗

PubMed1996

Fossil preservation and the stratigraphic ranges of taxa.

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.

Animals↗

PubMed1974

Nonasymptotic species richness models and the insects of british trees.

Nonasymptotic models of species diversity are those that do not consider negative feedback between number of species in a biota and the net rate of species addition. These models propose species richness differences to be primarily the product of geologic age differences among biotas. Nonasymptotic explanations are traditional for various diversity difference spectra, including latitudinal diversity gradients and the greater species richness of ancient compared to young lakes. I review new evidence that renders these nonasymptotic explanations doubtful.The only uncontested evidence in favor of nonasymptotic species accumulation is Southwood's correlation between the number of insect species associated with British tree taxa and the number of Quaternary fossil records of these taxa. I show that nonasymptotic explanations of species richness variation are unacceptable for this system also. The variation in insect species richness among these taxa is well accounted for by a species-area relationship. The species richness asymptote is attained within a few hundred years, and the influence of cumulative host taxon abundance (number of fossil records) upon insect species richness is insignificant after the statistical influence of present-day host plant range is removed. I conclude Southwood's correlation to lack causality; it probably derives from a correlation between the number of fossil records of the host taxa and their present range.

Journal Article↗

PubMed2002

Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils.

Many efforts to date evolutionary divergences by using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies often are attributed to the inadequacy of the fossil record, but many potential sources of error can affect molecular-based estimates. In this study, we minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes. Age estimates varied because of gene effects, codon position, lineage effects, method of inferring branch lengths, and whether or not rate constancy was assumed. However, even methods designed to ameliorate the effects of rate heterogeneity among lineages could not accommodate the substantially slower rates observed in Marattia + Angiopteris and in the tree ferns. Both of these clades of ferns have undergone dramatic decelerations in their rates of molecular evolution and are "molecular living fossils," consistent with their relative morphological stasis for the past 165-200 million years. Similar discrepancies between the fossil record and molecular-based age estimates noted in other studies may also be explained in part by violations of rate constancy among lineages.

Journal Article↗

PubMed2002

Identification of immunoreactive material in mammoth fossils.

The fossil record represents a history of life on this planet. Attempts to obtain molecular information from this record by analysis of nucleic acids found within fossils of extreme age have been unsuccessful or called into question. However, previous studies have demonstrated the long-term persistence of peptides within fossils and have used antibodies to extant proteins to demonstrate antigenic material. In this study we address two questions: Do immunogenic/antigenic materials persist in fossils? and; Can fossil material be used to raise antibodies that will cross-react with extant proteins? We have used material extracted from a well-preserved 100000-300000-year-old mammoth skull to produce antisera. The specificity of the antisera was tested by ELISA, western blotting, and immunohistochemistry. It was demonstrated that antisera reacted specifically with the fossils and not the surrounding sediments. Reactivity of antisera with modern proteins and tissues was also demonstrated, as was the ability to detect evolutionary relationships via antibody-antigen interactions. Mass spectrometry demonstrated the presence of amino acids and specific peptides within the fossil. Peptides were purified by anion-exchange chromatography and sequenced by tandem mass spectrometry. The collagen-derived peptides may have been the source of at least some of the immunologic reactivity, but the antisera identified molecules that were not observed by mass spectrometry, indicating that immunologic methods may have greater sensitivity. Although the presence of peptides and amino acids was demonstrated, the exact nature of the antigenic material was not fully clarified. This report demonstrates that antibodies may be used to obtain information from the fossil record.

Amino Acid Sequence↗

PubMed1996

Paleobiology, community ecology, and scales of ecological pattern.

The fossil record provides a wealth of data on the role of regional processes and historical events in shaping biological communities over a variety of time scales. The Quaternary record with its evidence of repeated climatic change shows that both terrestrial and marine species shifted independently rather than as cohesive assemblages over scales of thousands of years. Larger scale patterns also show a strong individualistic component to taxon dynamics; assemblage stability, when it occurs, is difficult to separate from shared responses to low rates of environmental change. Nevertheless, the fossil record does suggest that some biotic interactions influence large-scale ecological and evolutionary patterns, albeit in more diffuse and protracted fashions than those generally studied by community ecologists. These include: (1) the resistance by incumbents to the establishment of new or invading taxa, with episodes of explosive diversification often appearing contingent on the removal of incumbents at extinction events; (2) steady states of within-habitat and global diversity at longer time scales (10(7)-l0(8) yr), despite enormous turnover of taxa; and (3) morphological and biogeographic responses to increased intensities of predation and substratum disturbance over similarly long time scales. The behavior of species and communities over the array of temporal and spatial scales in the fossil record takes on additional significance for framing conservation strategies, and for understanding recovery of species, lineages, and communities from environmental changes.

Animals↗

PubMed1997

Molecular systematics of the Canidae.

Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canidae fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canidae species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canidae endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canidae clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets.

Animals↗

PubMed2002

The Scaphopoda.

The Scaphopoda are marine infaunal carnivores that feed on foraminiferans and other microorganisms selected and manipulated by their unique feeding tentacles or captacula. Their tusk-like shell is open at both ends; the burrowing foot and captacula protrude anteriorly, while respiratory currents pass through the posterior opening. Although the scaphopods comprise one of the smallest molluskan classes in terms of species diversity, they have a worldwide distribution ranging from intertidal to depths in excess of 6000 m. Despite detailed monographic work from the late nineteenth and early twentieth centuries, however, the biology of scaphopods is today among the least understood of mollusks. To some extent, this is related to a significant departure from more typical molluscan organization inferred from studies of the larger classes. For example, the mantle cavity is elongate and restricted in space, and several associated organs are lost, including the osphradium and ctenidia; the latter is associated with the loss of auricles from the scaphopod heart. There is also little record of ontogeny in the adult shell, as the older portion is periodically decollated to maintain the posterior aperture for passage of inhalant and exhalant currents. This and other constraints on scaphopod diversification are reflected in the range limits of shell shape within the class. In contrast, the "Dentalium" egg has been a model system for experimental embryology, particularly in studies of cell lineage and early morphogenesis. Later larval development and most organogenesis is nonetheless poorly known, although recent studies have considerably enhanced our knowledge in this area. Global biogeographic patterns of scaphopod diversity have been studied only preliminarily. A general decrease in diversity with depth is broken by small diversity peaks at bathyal depths. There is also evidence for a marked latitudinal diversity gradient in the world's oceans, near equatorial in the Pacific but at approximately 20 degrees N in the Atlantic. Scaphopods have a wide diversity of ecto- and endo-symbiotic associations with other organisms, including commensal bacteria and ciliates, mutualistic anemones and corals, and parasitic algae and platyhelminths. Other documented associations include predation by naticid gastropods and ratfish, and the inhabitation of empty scaphopod shells by a variety of sipunculans and hermit crabs. Phylogeny within the class is still unresolved, although significant progress has been made recently in documenting morphological variation among families, genera, and species for application in a cladistic context. The evolutionary relationships of Scaphopoda within Mollusca are farther from resolution, with every conchiferan class a proposed sister group among modern analyses. Molecular avenues should provide significant progress in scaphopod phylogenetics, as indicated by recent comparative sequence analysis and gene expression patterns. Scaphopods comprise the most recent class of mollusks to appear in the fossil record, dating at least from the Mississippian Carboniferous (362.5 My). They appear from first-order occurrence data to have a substantially documented fossil record, with several sharp extinction and radiation events evident during their comparatively short geologic history. The unresolved position of the Scaphopoda within molluscan phylogeny, and their relatively limited range of morphological disparity but substantial derivation from other conchiferans, renders the scaphopods an enigmatic group. They represent a significant evolutionary avenue within the Mollusca, but one that is poorly examined. Nonetheless, comprehensive phylogenetic analysis and documentation of diversity within this small, monophyletic, class-level taxon, well-preserved in the fossil record, is imminently tractable, and presents a singular opportunity in the study of molluscan evolution.

Animals↗

PubMed2002

Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the isthmus of panama.

Calibration of nucleotide sequence divergence rates provides an important method by which to test many hypotheses of evolution. In the absence of an adequate fossil record, geological events, rather than the first appearances of sister taxa in the geological record, are often used to calibrate molecular clocks. The formation of the Isthmus of Panama, which isolated the tropical western Atlantic and eastern Pacific oceans, is one such event that is frequently used to infer rates of nucleotide sequence divergence. Isthmian calibrations assume that morphologically similar "geminate" species living now on either side of the isthmus were isolated geographically by the latest stages of seaway closure 3.1-3.5 MYA. Here, I have applied calibration dates from the fossil record to cytochrome c oxidase-1 (CO1) and nuclear histone-3 (H3) divergences among six pairs of geminates in the Arcidae to test this hypothesis. Analysis of CO1 first and third positions yield geminate divergences that predate final seaway closure, and on the basis of CO1 first positions, times for all six geminates are significantly greater than 3.5 Myr. H3 sequences produce much more recent geminate divergences, some that are younger than 3.1 Myr. But H3-derived estimates for all arcid geminates are not significantly different from both 0 and 15 Myr. According to CO1, one of the two most divergent pairs, Arca mutabilis and A. imbricata, split more than 30 MYA. This date is compatible with the fossil record, which indicates that these species were morphologically distinct at least 16-21 MYA. Across all CO1 nucleotide sites, divergence rates for arcids are slower than the rates reported for other taxa on the basis of isthmian calibrations, with the exception of rates determined from the least divergent species pair in larger surveys of multiple transisthmian pairs. Rate differences between arcids and some taxa may be real, but these data suggest that divergence rates can be greatly overestimated when dates corresponding to final closure of the Central American Seaway are used to calibrate the molecular clocks of marine organisms.

Animals↗

PubMed2004

Plant cytoplasm preserved by lightning.

Usually only an organism with hard parts may be preserved in the fossil record. Cytoplasm, which is a physiologically active part of a plant, is rarely seen in the fossil record. Two Cretaceous plant fossils older than 100 million years with exceptional preservation of cytoplasm are reported here. Some cytoplasm is well preserved with subcellular details while other cytoplasm is highly hydrolyzed in the cortex of the same fossil even though both of preservations may be less than 2 microm away. The unique preservation pattern, sharp contrast of preservation in adjacent cells and the exceptional preservation of cytoplasm in the cortex suggest that lightning should play an important role in the preservation of cytoplasm and that cytoplasmic membranes may be more stable than the cell contents. Interpreting the preservation needs knowledge scattering in several formerly unrelated fields of science, including geophysics, botany, biophysics, cytology and microwave fixation technology. This new interpretation of fossilization will shed new light on preservation of cytoplasm and promote cytoplasm fossils from a position of rarity to a position of common research objects available for biological research. The importance of the identification of cytoplasm in fossil lies not in itself but in how much it influences the future research in paleobotany.

Cytoplasm↗

PubMed2006

Snake fangs from the Lower Miocene of Germany: evolutionary stability of perfect weapons.

There is a general consensus that most of today's nonvenomous snakes are descendants of venomous snakes that lost their venomous capabilities secondarily. This implies that the evolutionary history of venomous snakes and their venom apparatus should be older than the current evidence from the fossil record. We compared some of the oldest-known fossil snake fangs from the Lower Miocene of Germany with those of modern viperids and elapids and found their morphology to be indistinguishable from the modern forms. The primary function of recent elapid and viperid snake fangs is to facilitate the extremely rapid, stab-like application of highly toxic venoms. Our findings therefore indicate that the other components of the venom-delivery system of Early Miocene vipers and elapids were also highly developed, and that these snakes used their venom in the same way as their modern relatives. Thus, the fossil record supports the view that snakes used their venoms to rapidly subdue prey long before the mid-Tertiary onset of the global environmental changes that seem to have supported the successful radiation of venomous snakes.

Animals↗

PubMed2004

Rapid recovery from the Late Ordovician mass extinction.

Understanding the evolutionary role of mass extinctions requires detailed knowledge of postextinction recoveries. However, most models of recovery hinge on a direct reading of the fossil record, and several recent studies have suggested that the fossil record is especially incomplete for recovery intervals immediately after mass extinctions. Here, we analyze a database of genus occurrences for the paleocontinent of Laurentia to determine the effects of regional processes on recovery and the effects of variations in preservation and sampling intensity on perceived diversity trends and taxonomic rates during the Late Ordovician mass extinction and Early Silurian recovery. After accounting for variation in sampling intensity, we find that marine benthic diversity in Laurentia recovered to preextinction levels within 5 million years, which is nearly 15 million years sooner than suggested by global compilations. The rapid turnover in Laurentia suggests that processes such as immigration may have been particularly important in the recovery of regional ecosystems from environmental perturbations. However, additional regional studies and a global analysis of the Late Ordovician mass extinction that accounts for variations in sampling intensity are necessary to confirm this pattern. Because the record of Phanerozoic mass extinctions and postextinction recoveries may be compromised by variations in preservation and sampling intensity, all should be reevaluated with sampling-standardized analyses if the evolutionary role of mass extinctions is to be fully understood.

Biodiversity↗

PubMed1992

Evolution and environment in the Hominoidea.

Between 10 and 20 million years ago, a variety of hominoid primates lived in Africa, Europe and Asia. The question of which of these, if any, lie closest to the ancestries of humans and modern apes remains a lively source of debate. Recent fossil discoveries, though, shed light on the environments in which the various groups of hominoid emerged and, it is hoped, on their evolution. But the lack of a hominid fossil record before about 5 million years ago--and any fossil record for the African apes--is still a frustrating barrier.

Animals↗

PubMed2006

Oldest coelacanth, from the Early Devonian of Australia.

Coelacanths are well-known sarcopterygian (lobe-finned) fishes, which together with lungfishes are the closest extant relatives of land vertebrates (tetrapods). Coelacanths have both living representatives and a rich fossil record, but lack fossils older than the late Middle Devonian (385-390 Myr ago), conflicting with current phylogenies implying coelacanths diverged from other sarcopterygians in the earliest Devonian (410-415 Myr ago). Here, we report the discovery of a new coelacanth from the Early Devonian of Australia (407-409 Myr ago), which fills in the approximately 20 Myr 'ghost range' between previous coelacanth records and the predicted origin of the group. This taxon is based on a single lower jaw bone, the dentary, which is deep and short in form and possesses a dentary sensory pore, otherwise seen in Carboniferous and younger taxa.

Animals↗