Palaeobiotechnology

The majority of organisms that ever lived on the Earth, and hence the majority of evolutionary innovations, are now extinct. Only fragments of this past diversity are observable in the form of the fossil record. Biomimicry and biotechnology seek to utilize the astonishing diversity of living organism's solutions to complex biological problems as inspiration for human technology. This feature reviews the potential industrial applications of fossil-inspired technologies, an emerging area of research here referred to as ‘palaeobiotechnology’ or ‘brown biotechnology’. Examples from vertebrate, invertebrate and molecular palaeontology illustrate the diverse potential applications of extinct organisms, including the design of new materials such as bone substitutes, development of pharmaceuticals, robots and anchoring devices for submarines. Palaeobiotechnological approaches are able to both inspire modern sustainable technologies and at the same time illuminate the biology of ancient organisms.     

From bone to pixel—fossil restoration and reconstruction with digital techniques

Fossils represent the only physical evidence for the existence of extinct life, and hold a vast potential to reconstruct organisms and ecosystems vanished a long time ago. Yet fossils are not as complete as they might appear in museum exhibits, documentaries or Hollywood blockbusters. Millions of years of fossilization have left their marks on the fossils, which might no longer resemble the condition of the organism when it was alive. A key challenge in palaeontology is therefore to restore and reconstruct the morphology of fossils. Luckily, novel digital visualization and reconstruction techniques offer powerful tools to bring extinct organisms back to life in unprecedented detail.     

From clergymen to computers—the advent of virtual palaeontology

Palaeontology was established as a science in the Victorian era, yet has roots that stretch deeper into the recesses of history. More than 2000 years ago, the Greek philosopher Aristotle deduced that fossil sea shells were once living organisms, and around 500 ad Xenophanes used fossils to argue that many areas of land must have previously been submarine. In 1027, the Persian scholar Avicenna suggested that organisms were fossilized by petrifying fluids; this theory was accepted by most natural philosophers up until the eighteenth century Enlightenment, and even beyond. The late 1700s were notable for the work of Georges Cuvier who established the reality of extinction. This, coupled with advances in the recognition of faunal successions made by the canal engineer William Smith, laid the framework for the discipline that would become known as palaeontology. As the nineteenth century progressed, the scientific community became increasingly well organized. Most fossil workers were gentleman scientists and members of the clergy, who self‐funded their studies in a new and exciting field. Many of the techniques used to study fossils today were developed during this ‘classical’ period. Perhaps the most fundamental of these is to expose a fossil by splitting the rock housing it, and then conduct investigations based upon the exposed surface ( Fig. 1 ). This approach has served the science well in the last two centuries, having been pivotal to innumerable advances in our understanding of the history of life. Nevertheless, there are many cases where splitting a rock in this way results in incomplete data recovery; those where the fossils are not flattened, but are preserved in three‐dimensions. Even the ephemeral soft‐tissues of organisms are occasionally preserved in a three‐dimensional state, for example in the Herefordshire, La Voulte Sûr Rhone and Orsten ‘Fossil Lagerstätten’ (sites of exceptional fossil preservation). These rare and precious deposits provide a wealth of information about the history of life on Earth, and are perhaps our most important resource in the quest to understand the palaeobiology of extinct organisms. With the aid of twenty‐first century technology, we can now make the most of these opportunities through the field of ‘virtual palaeontology’—computer‐aided visualization of fossils.

Figure 1 Open in figure viewer PowerPoint A split nodule showing the fossil within, in this case a cockroachoid insect. Fossil 4 cm long (From Garwood & Sutton, in press ).     

Preservation of the shell matrix protein dermatopontin in 1500 year old land snail fossils from the Bonin islands

Organic molecules such as proteins can be preserved in certain fossils. The bulk properties of fossil proteins of both vertebrates and invertebrates have been studied for over half a century. Named proteins have so far been identified, however, only in vertebrate fossils, such as collagen from mammoth bones. Using immunological assays, we examined 1500 year old fossils of the extinct land snail Mandarina luhuana from the Bonin islands for the presence of dermatopontin, a molluscan shell matrix protein. First, we examined the shell microstructure and mineralogy of the fossil shells using scanning electron microscopy (SEM) and powder X-ray diffraction (XRD) in order to estimate the extent of diagenetic alteration. The results suggest that the original microstructure and mineralogy of the shells are preserved. Antiserum raised against the Type-1 dermatopontin fragment of the living land snail Euhadra brandtii showed significant immunological reactivity with the extracts from the fossil shells of M. luhuana. Immunological binding curves drawn for the shell extracts of extant M. aureola and the extinct M. luhuana confirmed the presence of dermatopontin in the fossil shells and provided an estimate that about 75–98% of the original dermatopontin was lost from the M. luhuana fossils. This is the first report of a named protein being identified in invertebrate fossils.     

Microconchids

Microconchids are a group of tiny, encrusting tubeworms. They appeared in the Late Ordovician, some 450 Myr ago, flourished during the rest of Palaeozoic and Triassic, and became extinct in the Middle Jurassic. Their morphological resemblance to the sedentary polychaete genus Spirorbis, very common in marine environments, misled various authors for decades. This mistake originally gave the genus Spirorbis an enormous stratigraphical range, from Ordovician to Recent. Indeed, microconchids provide an excellent example of evolutionary convergence with respect to both their morphology and ecology. In the late 1970s these ‘spirorbids’ were interpreted as vermetid gastropods on the basis of the inner architecture and microstructure of their tubes. This idea, however, was challenged in the 1990s when detailed microstructural investigation showed them to be neither polychaetes nor gastropods, but closely related to an extinct Palaeozoic enigmatic group of organisms called tentaculitids. No thorough investigation of their origin, phylogeny and ecology has ever been conducted, but new data concerning their palaeobiology has come to the light during the last few years.     

Arctic plesiosaurs from the Lower Cretaceous of Melville Island,Nunavut, Canada

An expedition to Melville Island in Nunavut, Canada, recovered the fragmentary fossils of several plesiosaurs from non-marine deposits of the Hauterivian–Aptian Isachsen Formation. These plesiosaur fossils are some of the oldest Early Cretaceous records of the group in North America, and they likely predate the formation of a continuous Western Interior Seaway. The plesiosaurs from Melville Island appear to be primarily juveniles, and would have been living in a region that experienced at least seasonally cool temperatures. The presence of these fossils in a fluvial deposit support previous suggestions that juvenile plesiosaurs may have preferentially inhabited shallower waters rather than open marine environments. These fossils also show that polycotylid plesiosaurs were able to rapidly disperse and colonize high latitude coastal regions, as their occurrence in Arctic Canada only slightly postdates the first confirmed appearance of the group in Australia.     

Extinctions, Morphological Gaps, Major Transitions, Stem Groups, and the Origin of Major Clades, with a Focus on Early Animals

Systematic extinctions can leave major morphological gaps between living crown-group clades. Such morphological gaps would be perceived, from a neontological point of view, as major evolutionary transitions. In order to fill these morphological gaps and to map the evolutionary steps toward major evolutionary transitions, we need to integrate extinct stem-group taxa in phylogenetic studies. However, the recognition of stem group has not been widely adopted in the study of early animal fossils, despite that all fossils are stem groups at one level or another. Part of the difficulty is that stem groups may not have all features that collectively diagnose the respective crown group, and they can have unique (autapomorphic) features, making them tantalizingly similar to and frustratingly different from the crown group (e.g., stem-group eukaryotes can be prokaryotic and stem-group animals can be protistan). The need to embrace stem groups and to implement the PhyloCode, in order to achieve phylogenetic clarity and to offer key paleontological insights into the origin and early animal evolution, is illustrated in debates on several controversial Ediacaran and Cambrian fossils.     

On the experimental silicification of microorganisms. III. Implications of the preservation of the green prokaryotic alga prochloron and other coccoids for interpretation of the microbial fossil record

Evidence for Precambrian fossil eukaryotic microorganisms has been based on: (1) the presence of internal ‘spots’ which have been variously interpreted to be remains of nuclei or pyrenoids of photosynthetic plastids or other organelles; (2) tetrahedral tetrad arrangement of cells; (3) trilete scars interpreted to be indicative of meiotic division: (4) large cell diameters; and (5) putative mitotic cell divisions. These features have been reported in fossils preserved in Precambrian cherts. We have studied modern microbial mats, thought to be analogues of Precambrian fossil communities, and found they may be silicified by laboratory procedures. In microbial mats from Baja California we have found many ‘spot cells’ that we could identify as remains of cyanophytes. We have silicified the newly discovered large prokaryotic coccoid green alga Prochloron and have found that it, like many cyanophytes previously silicified, preserves its structure and maintains its initial dimensions. In laboratory-silicified prokaryotic organisms we have found that all of the above criteria, supposedly characteristic of eukaryotes, can be observed. We conclude that there is no compelling morphological evidence for fossil eukaryotic microbes from Precambrian cherts.     

广西恭城奥陶纪含笔石地层

桂北恭城奥陶纪含笔石地层过去因缺乏生物化石证据将其划归于寒武系清溪组。1997年在其中发现笔石后重新将时代确定为奥陶纪,整套地层可划分为8个笔石带.自上而下为:8.Nemagraptus gracilis带;7.Ptero-graptus elegans带;6.Nicholsonograptus fasciculatus带;5.Acrograptus ellesae带;4.Undulograptus austroden-tatus带;3.Exigraptus clavus带;2.Isograptus caduceus cf.imitatus带;1.Didymograptus(Expansograptus)abnormis带。该地层与我国广东、浙江、江西、安徽等地区,以及澳大利亚、北美、英国等的相应层位可以对比。     

Spirits of Yokokurayama: shrine of the Japanese trilobites

‘We are such stuff as dreams are made on, and our little life is rounded with a sleep’. So sleep the trilobites of Yokokurayama, a sacred mountain hidden within the beautiful landscape of Japan’s Shikoku’s island. And though Prospero may have been speaking to his daughter and her fiancé (in William Shakespeare’s The Tempest), he might well have been contemplating the magnificent trilobite fossils of Yokokurayama. Japan may be better known for its sweeping volcanic landscapes, majestic castles, Shinto shrines and bullet trains, but it is also home to important collections of Silurian and Devonian trilobites.     

Identifying remains of extinct kangaroos in Late Pleistocene deposits using collagen fingerprinting

Our knowledge of past animal populations, including the geographical ranges of extinct species, has largely been derived from morphological analyses of skeletal fossil remains. However, a major barrier to the identification of the remains of extinct megafaunal species in archaeological and palaeontological sites is the highly fragmented nature of the material, which often precludes confident taxonomic identifications based on morphology. Biomolecular techniques are able to go beyond these limitations and are increasingly being used to make such identifications. Protein analysis offers a promising alternative to DNA techniques because they can be much cheaper, more amenable to high‐throughput processing and work on much older specimens. Here we demonstrate the potential of collagen fingerprinting in an Australian context by extracting collagen from 50‐ka kangaroo fossils from two caves in Tasmania, and identify several species including the extinct short‐faced kangaroo Simosthenurus occidentalis . Importantly, of the five fossil bones sampled that had hitherto been ascribed morphology‐based identifications below the family level, three had been incorrectly identified during an initial assessment of photographs taken in the field. Our results highlight the utility of using protein‐based methods for making genus‐level identification of marsupial bone, especially those that may form a basis for broader arguments such as that of late‐surviving megafaunal species.

     

Dinosaur material from the Lower Greensand Group of Upware,Cambridgeshire, and the age of ‘Wealden’ vertebrates from the ‘Bedfordshire Straits’

Post-Wealden dinosaur remains are rare in the UK, so any material from late Early or Late Cretaceous deposits is potentially of palaeoecological and palaeobiogeographical significance. Four dinosaur specimens collected from the Woburn Sands Formation (Aptian) of Upware, Cambridgeshire were described briefly by Walter Keeping in 1883, but have not been reappraised since. These specimens are identified herein as a ?turiasaurian sauropod tooth and indeterminate iguanodontian ornithopod remains (a tooth, middle caudal vertebra, pollex ungual). Although collected from the Woburn Sands Formation, it is likely that all of these fossils were reworked from older (now absent) sediments and they have usually been regarded as either ‘Wealden’ or Neocomian in age, presumably due to previous identifications of some of these specimens as Iguanodon. However, consideration of UK dinosaur faunas and regional geology indicates that these fossils could potentially be older. Further work is needed on the derived terrestrial fossils of the Lower Greensand Group in order to constrain their ages more precisely so that they can be incorporated into broader studies of regional diversity and palaeoecology.     

中国扬子海盆奥陶纪末期生物集群绝灭事件

<正> 近年来,奥陶纪末期生物集群绝灭事件的研究,越来越为人们所关注。Raup和Sepkoski(1982)认为,在晚奥陶世大约有22％科的生物绝灭,是显生宙生物集群绝灭5个最大幕之一。这次事件造成了所有海洋无脊椎动物的分异度和丰度的降低。Brenchley(1990)把晚奥陶世绝灭的若干类群的重要变化作了如下概述:阿什极尔中期的38科三叶虫,仅有14科存活到志留纪;在或接近奥陶-志留系界线,有13科腕足类绝灭,27科穿     

A renaissance in studies of ancient life

In the Origin of Species, published a century‐and‐a‐half ago, Darwin was mystified by the lack of a ‘pre‐Cambrian’ fossil record, the existence of which he regarded as pivotal to his theory of evolution. For the next 100 years, this ‘missing’ fossil record—unknown and thought unknowable'stood out as arguably the single greatest blemish to Darwin's theory. Beginning in the 1950s, the answer to Darwin's problem began to be unearthed, a Precambrian record of flourishing communities of microscopic organisms now known to extend to 3500 million years ago. During recent years, studies of such ancient microbes have markedly increased, spurred by an influx of new workers and, especially, by the introduction of new analytical techniques, three of which are featured here: confocal laser scanning microscopy, and Raman‐spectral and fluorescence‐spectral imagery. Used together, these techniques provide evidence of the three‐dimensional form, cellular anatomy, and molecular structure of rock‐embedded microscopic fossils and of the minerals in which they are entombed that is unavailable by any other means.     

Defining organominerals: Comment on ‘Defining biominerals and organominerals: Direct and indirect indicators of life’ by Perry et al. (2007, Sedimentary Geology, 201, 157–179)

The paper by Perry et al. (2007, Defining biominerals and organominerals: Direct and indirect indicators of life, Sedimentary Geology, 201, 157–179) proposes to introduce “the new term ‘organomineral’” to describe mineral products whose formation is induced by by-products of biological activity, dead and decaying organisms, or nonbiological organic compounds, to be distinguished from the biomineral components of living organisms. The substantive ‘organomineral’, however, is not new: it was first introduced in 1993, with basically the same definition and distinction from biominerals, at the 7th International Symposium on Biomineralization (Défarge and Trichet, 1995, From biominerals to ‘organominerals’: The example of the modern lacustrine calcareous stromatolites from Polynesian atolls, Bulletin de l'Institut Océanographique de Monaco, n° spéc. 14, vol. 2, pp. 265–271). Thereafter, more than twenty-five papers by various authors have been devoted to organominerals and organomineral formation (‘organomineralization’) processes. Only two of these papers are cited by Perry et al., and without any reference to the definitions, or even the terms ‘organomineral’ or ‘organomineralization’, which they included. Moreover, Perry et al. tend to enlarge the original concept of organomineral to encompass all minerals containing organic matter, whether these organic compounds are active or passive in the mineralization, which introduces ambiguities detrimental to a fine understanding of present and past geobiological processes. Finally, Perry et al. propose to consider organominerals as indirect biosignatures that could be used in the search for evidence of life in the geological record and extraterrestrial bodies. This latter proposition also is problematical, in that organominerals may be formed in association with prebiotic or abiotic organic matter.     

New insights into the nature of the Late Riphean Eosolenides

Studies of a morphologically diverse population of Eosolenides, organic-walled macrofossils from the Upper Mesoproterozoic (1015–1025 Ma) Lakhanda Group of southeastern Siberia, suggest that these elongate fossils may be remains of soft-bodied organisms having tube-grade organization. The compressed, originally cylindrical fossils, of more or less constant diameter along their length, are subdivided by transverse membranes into a regular series of distinct chamber-like segments. The lateral walls of the segmented tubes are double-layered, the outer sheath- or cuticle-like layer of which was originally flexible and commonly exhibits very fine and closely spaced transverse striations. The presence of structures inferred to be basal attachment disks suggests a benthic habit, whereas the morphological variability of the population can be interpreted as showing that their body shape changed as the organisms grew and increased markedly in length. Reproduction may have been by budding. An important peculiarity exhibited by these tubular fossils is the presence within many specimens of small spherical unicells, interpreted possibly to be algal endosymbionts. Although in some respects these fossils resemble cnidarians, the biological affinities of Eosolenides tubes remain enigmatic.     

Plesiosaurs

Plesiosaurs are an unusual and intriguing group of extinct aquatic reptiles ( Fig. 1 ). They are sauropterygians, a group known from an array of semi‐aquatic forms during the Triassic period: placodonts, pachypleurosaurs and nothosaurs. The first plesiosaurs are known from the very latest Triassic, but by the Early Jurassic plesiosaurs were cosmopolitan in distribution and lasted successfully to the latest Cretaceous, when they became victims of the K‐T extinction event. Plesiosaurs were predominantly marine organisms, although their fossils are not uncommon in brackish or even fresh water deposits. We know that all plesiosaurs were carnivorous; many of them were top predators in their respective ecosystems. But with no living descendants (or analogues) plesiosaurs are mysterious fossil organisms—as we will see, many questions regarding their biology remain unanswered or contentious. However, plesiosaurs are currently undergoing renewed scientific attention.

Figure 1 Open in figure viewer PowerPoint The beautifully preserved skeleton of the plesiosaur Rhomaleosaurus victor seen in ventral view, from the Lower Jurassic (Toarcian) of Holzmaden, Germany (total length 3.44 m). Redrawn from Fraas (1910).     

Quaternary fossil fauna from the Luangwa Valley,Zambia

This paper describes a large collection of Quaternary fossil fauna from the Luangwa Rift Valley, Zambia. Stone Age artefacts have been recovered from stratified fluvial contexts, but no in situ fossil faunas have yet been recovered. We report on 500 fossil specimens collected from the surface of point bars exposed seasonally along the banks of the main Luangwa River channel. We used non‐destructive X‐ray fluorescence analysis of the fossils' chemical signatures to determine whether they derive from one or many primary contexts, and the relationship between chemical signature and state of preservation. Specimens are identified to taxon (genus) to reconstruct palaeoenvironments and biochronology. A relatively wide range of taxa is identified, including a fossil hominin talus, described here. None of the fossils is positively attributable to extinct species, except a femur of an extinct Theropithecus reported in 2003. Although no additional extinct taxa were identified, some of the remains were attributable to genera that are not currently found in this region. The results suggest that most of the assemblage derives from sediments which are Middle Pleistocene or later, and that past environments in the Luangwa Valley may have differed from the habitat availability found today.     

Ostracods: The ultimate survivors

Ostracods are tiny crustacean arthropods just a few millimetres long, with a bivalved carapace made of calcium carbonate that covers the whole body, and into which the animal can retreat from the world outside. Because of their diminutive size they are largely overlooked as fossils, but they have a fascinating history. Silent witnesses to life in the seas since the time of trilobites, they have a fossil record extending back to the Early Ordovician, and possibly the Cambrian. Ostracods have survived nearly 500 million years of Earth history including the ‘big five’ mass extinctions of the Phanerozoic Eon; they are true survivors. They are almost perfectly adapted for the aquatic environments in which they live, and can be found from the ocean abyssal plains to damp leaf litter. The ostracod carapace is a triumph of biological engineering that has been re‐configured into myriad different morphologies according to environment. Streamlined and agile species plough through the ocean water column, sometimes reaching a ‘giant’ size of a centimetre in length, whilst their tinier sea bottom cousins make elaborately ornamented carapaces to withstand the pressures of living at the seabed, or shape their carapaces into forms that facilitate burrowing into sediment. Ostracods are key components of aquatic ecosystems. As primary consumers they are food for larger animals both in seabed and planktonic habitats, and they recycle much of the organic detritus produced by larger animals and plants. Delve into the history of ostracods and it is possible to find pioneers who triumphed in the plankton, early colonisers of terrestrial aquatic ecosystems, and ostracods that literally conquered the land. And in more recent times, ostracods have even hitched rides on rockets into space.     

Enigmatic ribbon-like fossil from Early Cambrian of Yunnan,China

During the Late Neoproterozoic and Early Cambrian, a series of paleogeographic and paleoecological events occurred associated with deglaciations and the evolution of life. The appearance of fossils representing diverse phyla, novel body plans and complex ecologies in Ediacaran and Cambrian sedimentary successions has sparked diverse hypotheses about potential drivers for the radiation of early animals during this interval. Recently, new macroscopic fossils of carbonaceous compressions with unique features have been found in Anning, Yunnan, China. The fossils’ bodies are ribbon-shaped and bilaterally symmetric, with dense longitudinal features and transversal features. The fossils occur 0.68 m below a bentonite interlayer which has been dated 535.2 ± 1.7 Ma by Ri-xiang Zhu and his team in 2009. The relatively simply morphology of these fossils, coupled with a lack of preserved internal structures challenge efforts taxonomically identify the precursor organism and definitively ally it to a living group. However, the symmetry and unusual features of the body are analogous to members of Platyzoa. The presence of ribbon-shaped fossils in the Zhongyicun Member in Anning indicates that these organisms were at least a locally significant component of Cambrian seafloor ecosystems, and may hold important implications for our understanding of the early evolution of Bilateria.