The proterozoic and earliest cambrian trace fossil record; patterns, problems and perspectives

The increase in trace fossil diversity across the Neoproterozoic-Cambrianboundary often is presented in terms of tabulations of ichnogenera.However, a clearer picture of the increase in diversity andcomplexity can be reached by combining trace fossils into broadgroups defined both on morphology and interpretation. This alsofocuses attention on looking for similarites between Neoproterozoicand Cambrian trace fossils. Siliciclastic sediments of the Neoproterozoicpreserve elongate tubular organisms and structures of probablealgal origin, many of which are very similar to trace fossils.Such enigmatic structures include Palaeopascichnus and Yelovichnus,previously thought to be trace fossils in the form of tightmeanders. A preliminary two or tripartite terminal Neoproterozoic tracefossil zonation can be be recognized. Possibly the earliesttrace fossils are short unbranched forms, probably younger thanabout 560 Ma. Typical Neoproterozoic trace fossils are unbranchedand essentially horizontal forms found associated with diverseassemblages of Ediacaran organisms. In sections younger thanabout 550 Ma a modest increase in trace fossil diversity occurs,including the appearance of rare three-dimensional burrow systems(treptichnids), and traces with a three-lobed lower surfaces.     

Theoretical morphology of developmental asymmetries

Morphospaces are theoretical tools to explore the morphological organization of living and fossil organisms. They have been used mostly by the paleontological community in an effort to get the most out of one of the only pieces of evidence that fossil material usually provide: the morphology of hard parts. The expectation with the establishment of theoretical morphospaces is that, by abstracting and modeling the fundamental parts of form, the multiple processes that generate the phenotypes of embryonic and adult structures will be better understood. In this essay, we suggest that ontogenetic trajectories can be used as the generative functions that build morphospaces, and propose approaches to build theoretical models for the establishment of left-right asymmetries during vertebrate heart embryogenesis.     

Molecular and Paleontological Evidence for a Post-Cretaceous Origin of Rodents

The timing of the origin and diversification of rodents remains controversial, due to conflicting results from molecular clocks and paleontological data. The fossil record tends to support an early Cenozoic origin of crown-group rodents. In contrast, most molecular studies place the origin and initial diversification of crown-Rodentia deep in the Cretaceous, although some molecular analyses have recovered estimated divergence times that are more compatible with the fossil record. Here we attempt to resolve this conflict by carrying out a molecular clock investigation based on a nine-gene sequence dataset and a novel set of seven fossil constraints, including two new rodent records (the earliest known representatives of Cardiocraniinae and Dipodinae). Our results indicate that rodents originated around 61.7–62.4 Ma, shortly after the Cretaceous/Paleogene (K/Pg) boundary, and diversified at the intraordinal level around 57.7–58.9 Ma. These estimates are broadly consistent with the paleontological record, but challenge previous molecular studies that place the origin and early diversification of rodents in the Cretaceous. This study demonstrates that, with reliable fossil constraints, the incompatibility between paleontological and molecular estimates of rodent divergence times can be eliminated using currently available tools and genetic markers. Similar conflicts between molecular and paleontological evidence bedevil attempts to establish the origination times of other placental groups. The example of the present study suggests that more reliable fossil calibration points may represent the key to resolving these controversies.     

How Accurate are Paleoecological Reconstructions of Early Paleontological and Archaeological Sites?

Paleoecology allows construction of paleoenvironmental models, faunal changes and evolutionary trends of paleontological taxa using modern analogs. However, when linking modern analogs to paleontological taxa in paleoecological reconstruction, differential taxonomic preservation in the fossil record has to be taken into account. Paleontologists have known the biased nature of the fossil record since Efremov’s publication on taphonomy in 1940, yet many ecological models of habitats associated with hominins in paleontological and archaeological sites in Africa and elsewhere barely address the complexity of the fossil record. We use randomly sampled ungulates from modern biomes in a comparative taxonomic abundance to demonstrate how the combination of modern thanatocoenoses and taphocoenoses, when used in reference to habitat-specific biocoenosis, produce better inferences of past habitats in paleontological and archaeological sites than approaches currently used.     

Paleontological completeness of the record of lower tertiary mollusks,U.S. Gulf and Atlantic coastal plains: Implications for phylogenetic studies

Choice of method in phylogenetic analysis should involve some consideration of the quality or completeness of the available fossil record. If it is poor, cladistic methods are preferable; if it is good, stratophenetic methods may be valid. A concept of paleontological completeness, defined herein, is useful for judging the quality of a given fossil record. This paper considers eight possible measures of paleontological completeness, and evaluates their value as phylogenetically useful estimates of the quality of the fossil record. Of the eight measures, Sadler‐Schindel type analysis of stratigraphic completeness and analysis of geographic ranges appear to be the most useful and reliable. The remaining six are useful only as rough approximations of the quality of the record, or as supporting evidence for conclusions based on other methods. Use of these eight measures on the lower Tertiary molluscan record of the U.S. Gulf and Atlantic coastal plains indicates that this record is approximately 30–50% complete. This is probably not complete enough to trust purely stratophenetic approaches to phylogenetic analysis, but is too complete to ignore the record in favor of a purely atemporal, cladistic approach. The concept of paleontological completeness may be useful in estimating the quality of this and other fossil records for non‐phylogenetic purposes, such as studies of evolutionary rates and diversity and extinction patterns.     

Evolution in fossil lineages: paleontology and The Origin of Species

Of all of the sources of evidence for evolution by natural selection, perhaps the most problematic for Darwin was the geological record of organic change. In response to the absence of species-level transformations in the fossil record, Darwin argued that the fossil record was too incomplete, too biased, and too poorly known to provide strong evidence against his theory. Here, this view of the fossil record is evaluated in light of 150 years of subsequent paleontological research. Although Darwin's assessment of the completeness and resolution of fossiliferous rocks was in several ways astute, today the fossil record is much better explored, documented, and understood than it was in 1859. In particular, a reasonably large set of studies tracing evolutionary trajectories within species can now be brought to bear on Darwin's expectation of gradual change driven by natural selection. An unusually high-resolution sequence of stickleback-bearing strata records the transformation of this lineage via natural selection. This adaptive trajectory is qualitatively consistent with Darwin's prediction, but it occurred much more rapidly than he would have guessed: almost all of the directional change was completed within 1,000 generations. In most geological sequences, this change would be too rapid to resolve. The accumulated fossil record at more typical paleontological scales (10(4)-10(6) years) reveals evolutionary changes that are rarely directional and net rates of change that are perhaps surprisingly slow, two findings that are in agreement with the punctuated-equilibrium model. Finally, Darwin's view of the broader history of life is reviewed briefly, with a focus on competition-mediated extinction and recent paleontological and phylogenetic attempts to assess diversity dependence in evolutionary dynamics.     

Ediacaran microbial colonies

Enigmatic discoidal fossils are common in Neoproterozoic sedimentary sequences and in the stratigraphic record pre-date the first appearance of diverse Ediacaran fossil assemblages. Termed 'medusoids', these Neoproterozoic discoidal fossils have generally been interpreted as coelenterate-grade organisms implying a radially symmetrical body plan for ancestral eumetazoans. Analysis of exceptionally preserved discoidal fossils from the White Sea area, however, indicates that most of these discoidal forms represent colonial microbes. Localized pyritization, for example, reveals the presence of a conspicuous filamentous substructure in Ediacaria , whereas concentric rings, radial sectors and central structures in Cyclomedusa and Paliella compare directly with Recent microbial colonies growing in a nutritionally heterogeneous environment. At least some Ediacaran discoids can be compared with extant concentric ring-shaped microbial colonies that grow in hypersaline microbial mats. Insofar as most of the remaining record of Ediacaran discoids can be attributed to the holdfast structures of non-radiate modular organisms, there is no support from the fossil record for identifying a radiate ancestry for the Metazoa.     

Functional Morphology in Paleobiology: Origins of the Method of ‘Paradigms’

From the early nineteenth century, the successful use of fossils in stratigraphy oriented paleontology (and particularly the study of fossil invertebrates) towards geology. The consequent marginalising of biological objectives was countered in the twentieth century by the rise of ‘Paläobiologie’, first in the German cultural area and only later, as ‘paleobiology’, in the anglophone world. Several kinds of paleobiological research flourished internationally after the Second World War, among them the novel field of ‘paleoecology’. Within this field there were attempts to apply functional morphology to the problematical cases of fossil organisms, for which functions cannot be observed directly. This article describes the origins of the kind of functional inference for fossils that I proposed in 1961 as the method of ‘paradigms’ (a year before Thomas Kuhn made that word more widely familiar with a quite different meaning). Here I summarize some of my ‘worked exemplars’, which were intended to show the paradigm method in action. These case-studies were all taken from the paleontologically important phylum of the Brachiopoda, but the method was claimed to have much wider implications for the interpretation of the fossil record in terms of adaptive evolution. This article takes the history of the paradigm method as far as the late 1960s. I hope to trace, in a sequel, its ambivalent fate during the 1970s and beyond, when for example Gould’s critique of ‘the adaptationist programme’ and the rise of computer-based quantitative methods for the evolutionary interpretation of the fossil record led to the relative eclipse of functional morphology in paleontology.     

Towards “A Natural History of Data”: Evolving Practices and Epistemologies of Data in Paleontology, 1800–2000

The fossil record is paleontology’s great resource, telling us virtually everything we know about the past history of life. This record, which has been accumulating since the beginning of paleontology as a professional discipline in the early nineteenth century, is a collection of objects. The fossil record exists literally, in the specimen drawers where fossils are kept, and figuratively, in the illustrations and records of fossils compiled in paleontological atlases and compendia. However, as has become increasingly clear since the later twentieth century, the fossil record is also a record of data. Paleontologists now routinely abstract information from the physical fossil record to construct databases that serve as the basis for quantitative analysis of patterns in the history of life. What is the significance of this distinction? While it is often assumed that the orientation towards treating the fossil record as a record of data is an innovation of the computer age, it turns out that nineteenth century paleontology was substantially “data driven.” This paper traces the evolution of data practices and analyses in paleontology, primarily through examination of the compendia in which the fossil record has been recorded over the past 200 years. I argue that the transition towards conceptualizing the fossil record as a record of data began long before the emergence of the technologies associated with modern databases (such as digital computers and modern statistical methods). I will also argue that this history reveals how new forms of visual representation were associated with the transition from seeing the fossil record as a record of objects to one of data or information, which allowed paleontologists to make new visual arguments about their data. While these practices and techniques have become increasingly sophisticated in recent decades, I will show that their basic methodology was in place over a century ago, and that, in a sense, paleontology has always been a “data driven” science.     

Early origins of modern birds and mammals: molecules vs. morphology

Recent claims from molecular evidence that modern orders of birds and mammals arose in the Early Cretaceous, over 100 million years (Myr) ago, are contrary to palaeontological evidence. The oldest fossils generally fall in the time range from 70-50 Myr ago, with no earlier finds. If the molecular results are correct, then the first half of the fossil record of modern birds and mammals is missing. Suggestions that this early history was played out in unexplored parts of the world, or that the early progenitors were obscure forms, are unlikely. Intense collecting over hundreds of years has failed to identify these missing fossils. Control experiments, in the form of numerous Cretaceous-age fossil localities which yield excellently preserved lizards, salamanders, birds, and mammals, fail to show the modern forms. The most likely explanation is that they simply did not exist, and that the molecular clock runs fast during major radiations.     

Rangeomorphs,Thectardis (Porifera?) and dissolved organic carbon in the Ediacaran oceans

The mid-Ediacaran Mistaken Point biota of Newfoundland represents the first morphologically complex organisms in the fossil record. At the classic Mistaken Point localities the biota is dominated by the enigmatic group of "fractally" branching organisms called rangeomorphs. One of the few exceptions to the rangeomorph body plan is the fossil Thectardis avalonensis, which has been reconstructed as an upright, open cone with its apex in the sediment. No biological affinity has been suggested for this fossil, but here we show that its body plan is consistent with the hydrodynamics of the sponge water-canal system. Further, given the habitat of Thectardis beneath the photic zone, and the apparent absence of an archenteron, movement, or a fractally designed body plan, we suggest that it is a sponge. The recognition of sponges in the Mistaken Point biota provides some of the earliest body fossil evidence for this group, which must have ranged through the Ediacaran based on biomarkers, molecular clocks, and their position on the metazoan tree of life, in spite of their sparse macroscopic fossil record. Should our interpretation be correct, it would imply that the paleoecology of the Mistaken Point biota was dominated by sponges and rangeomorphs, organisms that are either known or hypothesized to feed in large part on dissolved organic carbon (DOC). The biology of these two clades gives insight into the structure of the Ediacaran ocean, and indicates that a non-uniformitarian mechanism delivered labile DOC to the Mistaken Point seafloor.     

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.     

Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards

Background  

Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates.     

DNA and Morphology Unite Two Species and 10 Million Year Old Fossils

Species definition and delimitation is a non-trivial problem in evolutionary biology that is particularly problematic for fossil organisms. This is especially true when considering the continuity of past and present species, because species defined in the fossil record are not necessarily equivalent to species defined in the living fauna. Correctly assigned fossil species are critical for sensitive downstream analysis (e.g., diversification studies and molecular-clock calibration). The marine snail genus Alcithoe exemplifies many of the problems with species identification. The paucity of objective diagnostic characters, prevalence of morphological convergence between species and considerable variability within species that are observed in Alcithoe are typical of a broad range of fossilised organisms. Using a synthesis of molecular and morphometric approaches we show that two taxa currently recognised as distinct are morphological variants of a single species. Furthermore, we validate the fossil record for one of these morphotypes by finding a concordance between the palaeontological record and divergence time of the lineage inferred using molecular-clock analysis. This work demonstrates the utility of living species represented in the fossil record as candidates for molecular-clock calibration, as the veracity of fossil species assignment can be more rigorously tested.     

Characterization of Isoforms of Pectin Methylesterase of Linum usitatissimum Using Polyclonal Antibodies

In flax (Linum usitatissimum, c.v. Ariane) pectin methylesterase(PME) (EC 3.1.1.11 [EC] ), ionically bound to cell-wall, was composedmainly of forms with isoelectric points (pIs) of 7.1, 7.6 and9.6. Minor forms, with acid pIs (4.5, 4.8 and 6.3), were detectedduring the purification of two of these forms. Polyclonal antibodieswere raised against the isoenzymes presenting pIs of 7.1 and7.6. Antibodies recognized antigenic forms and two close proteinsin the basic range which could be associated to the PME activitywith pI of 9.6. Antibodies did not recognize any acid formsand exhibited no cross-reactivity with proteins resolved inthe cellular content. Antigenicity was related mainly to theprotein part of the glycosylated enzyme. The antibodies againstflax PME did not cross-react with PMEs from Citrus and tomatoand with glycosylated proteins of various sources. Specificityof anti-PME antibodies was judged sufficient to localize therecognized forms on tissue prints of flax hypocotyls. AlthoughPME was distributed in the whole parts of hypocotyl, stainingwas not homogeneous and appeared reinforced in the apical zone.In the basal part, epidermis was more contrasted than internaltissues. (Received August 2, 1994; Accepted January 3, 1995)     

Simulations of the Ontogeny of Spongiophyton, a Devonian Plant

Mathematical representations of the cellular organization anddimensions of Spongiophyton Krusel, a Middle Devonian thallophytewere projected by means of a computer to simulate patterns ofdevelopment and organization. Extrapolation of the cellularpatterns observed on the surface of the fossil may be comparedwith those derived from living plants of which the ontogenycan be directly observed. Spongiophyton is compared in thisrespect with the growth of Protosalvinia (an Upper Devonianplant of enigmatic affinity), Pellia (a thallose liverwort)and Cutleria (a brown alga). The growth pattern of Spongiophytondeveloped by computer shows a closer similarity to that of thepseudoparenchymatous alga Cutleria than to the truly parenchymatousPellia or the fossil Protosalvinia. Computer simulations ofthe growth process throw light on the affinity of Spongiophytonwhich cannot be derived from direct observation of the fossil.Broader applications of computer simulations of tissue organizationand gross morphology are suggested with regard to the studyof living and fossil plants.     

Rewilding the tropics,and other conservation translocations strategies in the tropical Asia‐Pacific region

Alarm over the prospects for survival of species in a rapidly changing world has encouraged discussion of translocation conservation strategies that move beyond the focus of ‘at‐risk’ species. These approaches consider larger spatial and temporal scales than customary, with the aim of recreating functioning ecosystems through a combination of large‐scale ecological restoration and species introductions. The term ‘rewilding’ has come to apply to this large‐scale ecosystem restoration program. While reintroductions of species within their historical ranges have become standard conservation tools, introductions within known paleontological ranges—but outside historical ranges—are more controversial, as is the use of taxon substitutions for extinct species. Here, we consider possible conservation translocations for nine large‐bodied taxa in tropical Asia‐Pacific. We consider the entire spectrum of conservation translocation strategies as defined by the IUCN in addition to rewilding. The taxa considered are spread across diverse taxonomic and ecological spectra and all are listed as ‘endangered’ or ‘critically endangered’ by the IUCN in our region of study. They all have a written and fossil record that is sufficient to assess past changes in range, as well as ecological and environmental preferences, and the reasons for their decline, and they have all suffered massive range restrictions since the late Pleistocene. General principles, problems, and benefits of translocation strategies are reviewed as case studies. These allowed us to develop a conservation translocation matrix, with taxa scored for risk, benefit, and feasibility. Comparisons between taxa across this matrix indicated that orangutans, tapirs, Tasmanian devils, and perhaps tortoises are the most viable taxa for translocations. However, overall the case studies revealed a need for more data and research for all taxa, and their ecological and environmental needs. Rewilding the Asian‐Pacific tropics remains a controversial conservation strategy, and would be difficult in what is largely a highly fragmented area geographically.     

The origin of mammalian endothermy: a paradigm for the evolution of complex biological structure

Several mutually incompatible theories exist about how and why endothermy evolved in mammals and birds. Some take the primary function to have been thermoregulation, selected for one adaptive purpose or another. Others take the high aerobic metabolic rate to have been primary. None of these theories is incontrovertibly supported by evidence, either from the fossil record of the synapsid amniotes or from observations and experiments on modern organisms. Furthermore, all are underpinned by the tacit assumption that endothermy must have evolved in a stepwise pattern, with an initial adaptive function followed only later by the addition of further functions. It is argued that this assumption is unrealistic and that the evolution of endothermy can be explained by the correlated progression model. Each structure and function associated with endothermy evolved a small increment at a time, in loose linkage with all the others evolving similarly. The result is that the sequence of organisms maintained functional integration throughout, and no one of the functions of endothermy was ever paramount over the others. The correlated progression model is tested by the nature of the integration between the parts as seen in living mammals, by computer simulations of the evolution of complex, multifunctional, multifactorial biological systems, and by reference to the synapsid fossil record, which is fully compatible with the model. There are several potentially important implications to be drawn from this example concerning the study of the evolution of complex structure and the new higher taxa that manifest it.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 147 , 473–488.     

Historical Zoogeography of the Eusuchian Crocodilians: A Physiological Perspective

The historical zoogeography of eusuchian crocodilians has rarelybeen reviewed in any detail and yet is of increasing interestto students of crocodilian biology as large amounts of comparativeinformation on a wide range of species come to hand. Previousinterpretations of crocodilian zoogeography have been basedon one or another of two assumptions–that the major continentalland masses have remained more or less fixed in position, andthat the eusuchians have had only very limited powers of dispersalacross marine barriers. Both of these assumptions are inappropriatein light of our present knowledge of continental drift and crocodilianphysiology. In this paper we attempt a reinterpretation of eusuchian zoogeographybased on new information on their systematic relationships,physiological capacity for marine dispersal, and fossil history.We postulate that anatomical and physiological adaptations toa marine existence have played an important role in eusuchianhistory. We propose that Gavialis and Tomistoma, now restrictedto fresh waters, may have been derived secondarily from ancestorsadapted to salt water. In the case of Tomistoma, similaritiesin lingual gland and buccal cavity anatomy to the true crocodiles(Crocodylus and Osteolaemus) suggest that marine adaptationspredated the divergence of tomistomine and crocodyline stocks.The buccal morphology of Gavialis suggests it also has a marineancestry. Its systematic affinities are uncertain, lying perhapswith Tomistoma or, on other interpretations, with the Mesosuchia.In both cases, the fossil record is not inconsistent with thispossibility. Palaeontological information now available is inadequate toreconstruct the evolutionary history of the Eusuchia in detail.However, saltwater adapted eusuchians are more common in thefossil record than is widely recognized and the likelihood ofdispersal across marine "barriers" by non-alligatorid crocodilianscannot be ignored.