Spatial competition among clonal organisms in extant and selected paleozoic reef communities

Summary Occurrences of densely packed benthic organisms in extant reefs are of two types: 1) live-live interactions, where two living organisms interact, and 2) live-dead associations, where only one is alive and uses the other as a substrate. The latter are common in reef deposits due to biostratinomic feedback, i.e. dense skeletal accumulations provide hard substrates for clonal recruitment, thus facilitating greater frequency of live-dead encounters than in lower biomass level-bottom communities dominated by solitary organisms. Differentiating between these two types in ancient reefs is difficult, often impossible. Most live-live interactions among clones in extant reef communities involve competition for space. Clonal spatial competition is divisible into four types: 1) direct-aggressive: encrusting overgrowth; 2) indirect-passive: depriving neighbors of resources, chiefly sunlight, by growth above them; 3) stand-off: avoidance of competition by organisms adopting positions that avoid or minimize direct polyp/zooid contact; and 4) overwhelming: one clone/ species volumetrically or numerically overwhelms the other, meeting minimal resistance. Despite class-order level differences in taxa, our results indicate that extant analogs, based on the arrangement and distortion of skeletons, are valuable for recognizing live-live interactions in Silurian and Carboniferous reefs and interpreting the types of spatial competition represented. Comparison of overhead (plan) views of live-live coral competition in Polynesian reefs with vertical sections of Silurian and Carboniferous sponge-dominated reefs and biostromes suggests that direct-aggressive competition is more common among extant than among Paleozoic reef-builders. Stand-offs showing clone margin distortion and overwhelming with minor skeletal distortion are most common in our fossil examples and probably relate to the dominance of these reefs by sponges. Success by extant sponges in spatial competition is largely due to allelochemical deterrence which may explain the predominance of stand-off and overwhelming confrontations in fossil sponges rather than tentacle-mesentery based direct aggression among extant corals and bryozoans.     

Relationships among extant and fossil echimyids (Rodentia: Hystricognathi)

The echimyid rodents are the most diverse group of Neotropical hystricognaths, with approximately 40 extant and fossil genera. Craniodental characters are proposed in order to formulate hypotheses of phylogenetic relationships within the Echimyidae. A data matrix of 54 taxa and 50 characters is constructed and submitted to parsimony analyses using PAUP and WinClada programs. Analysis of the complete data set results in 47 448 most parsimonious trees 107 steps long. These trees are summarized in a strict consensus tree, which is taken as the main phylogenetic hypothesis resulting from this study. The monophyly of several currently recognized supraspecific taxa is not corroborated. These are: the subfamilies Eumysopinae, Echimyinae, Myocastorinae and Adelphomyinae; and the genera Proechimys , Echimys and Makalata . Conversely, the monophyly of Dactylomyinae and Trinomys is supported. New associations are proposed: (1) a clade comprising the extant Carterodon , Clyomys and Euryzygomatomys and the fossil Pampamys and Theridomysops placed at the base of the crown-group Echimyidae; (2) a clade uniting Proechimys , Hoplomys and Trinomys , which is the sister-taxon of (3) a clade including Mesomys , Lonchothrix , Myocastor and a clade with extant dactylomyines and echimyines and associated fossil taxa. Based on this phylogenetic hypothesis, patterns of tooth evolution in Echimyidae are discussed, and minimum ages for the divergence events within the family are estimated.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 142 , 445–477.     

Paranasal pneumatization in extant and fossil Cercopithecoidea

Unlike most primates, extant cercopithecoids lack maxillary sinuses, which are pneumatic spaces in the facial skeleton lateral of the nasal cavity proper. Character state analysis of living cercopithecoids across well-supported topologies suggests that the sinus was lost at the origin of the superfamily, only to have evolved again convergently in extant macaques. Recent work has shown that a) the 'early loss' hypothesis is supported by the lack of any pneumatization in Victoriapithecus, a stem cercopithecoid, b) like extant macaques, the fossil cercopithecine Paradolichopithecus shows evidence of presence of the maxillary sinus (MS), and c) unlike extant colobines, the fossil colobine Libypithecus also possesses a maxillary sinus. To more fully assess the pattern of cercopithecoid sinus evolution, fossil taxa from both subfamilies (Colobinae, Cercopithecinae) were examined both visually and by computed tomography (CT). The observations were evaluated according to standard anatomical criteria for defining sinus spaces, and compared with data from all extant Old World monkey genera. Most taxa examined conformed to the pattern already discerned from extant cercopithecoids. Maxillary sinus absence in Theropithecus oswaldi, Mesopithecus, and Rhinocolobus is typical for all extant cercopithecids except Macaca. The fossil macaque Macaca majori possesses a well-developed maxillary sinus, as do all living species of the genus. Cercopithecoides, on the other hand, differs from all extant colobines in possessing a maxillary sinus. Thus, paranasal pneumatization has reemerged a minimum of two and possibly three times in cercopithecoids. The results suggest that maxillary sinus absence in cercopithecoids is due to suppression, rather than complete loss.     

Resistant macromolecules of extant and fossil microalgae

The occurrence and composition of macromolecular resistant walls of microalgae and their fossil macromolecular counterparts are reviewed. To date, several algal groups have been identified to produce fossilizable biomacromolecules. Only two biosynthetic pathways seem to be responsible for this, of which the acetate/malate pathway used by Chlorophyta, Eustigmatophyta and Dinophyta is considered to lead to a series of closely related resistant biomacromolecules, called algaenans. Algaenans consist of a network of predominantly linear carbon chains. A different, as yet unidentified, pathway is used by the Dinophyta to produce the aromatic walls of their cysts. The poly‐ketide or acetogenic pathway may have been responsible for resorcinol‐based algae or bacteria‐derived microfossils of the acritarch Gloeocapsamorpha prisca, either through synthesis of the biomacromolecule or through a third pathway, the post‐mortem polymerization of its resorcinol lipids. The postmortem polymerization of lipids also appears to be responsible for the formation of fatty acid‐based macromolecules in Eocene dinoflagellate‐shaped remains from Pakistan. Finally, there is a clear need for elucidating the chemical differences between the biomacromolecules produced by the algae and their fossil analogs in the sediments. This notably applies to the release and condensation of aliphatic and aromatic moieties both at normal and at elevated temperature and pressure conditions.     

Cladistic relationships of extant and fossil hominoids

There is general agreement that the hominoid primates form a monophyletic group, that the extant great apes and humans form a second clade within that group with the gibbons as the sister group, and that the African apes and humans form a third clade. Although it has recently been proposed that humans and orang utans are sister taxa and also that the great apes form a clade to the exclusion of humans, our analysis, particularly of the molecular evidence, supports the existence of an African ape and human clade. The major problem in hominoid phylogeny at present is the relationships of the species within this clade: morphological data generally support the existence of an African ape clade which is the sister group to humans; some molecular data also support this conclusion, but most molecular evidence indicates the existence of a chimpanzee/human clade. We have cladistically re-analysed the DNA and protein sequence data for which apomorphic character states can be assessed. It is clear that there is a high degree of homoplasy whichever branching pattern is produced, with some characters supporting the existence of a chimpanzee/human clade and others supporting an African ape clade. When the cladistic analyses of morphological and molecular data are combined we believe that the most parsimonious interpretation of the data is that the African apes form a clade which is the sister taxon of the human (i.e., Australopithecus, Homo and Paranthropus) clade.This paper is not intended as a survey of all hominoid fossils but as a study of branching points in hominoid evolution and fossils are included which are relevant to this branching pattern. The analysis of fossil taxa in this study leads us to conclude that Proconsul is the sister taxon to the later Hominoidea. A number of middle Miocene forms such as Dryopithecus, Kenyapithecus, Heliopithecus and Afropithecus are shown to share derived characters with great apes and humans and provide evidence for the divergence of that clade from the gibbon lineage prior to 18 Ma. The position that Sivapithecus represents the sister group of the orang utan clade is supported here and shows that the orang utan lineage had diverged from the African ape and human lineage prior to 11·5 Ma. There is unfortunately no definitive fossil cvidence on branching sequences within the African ape and human clade, although a new specimen from Samburu, Kenya may be related to the gorilla.     

The fossil record of extant elasmobranchs

Sharks and their relatives (Elasmobranchii) are highly threatened with extinction due to various anthropogenic pressures. The abundant fossil record of fossil taxa has allowed the tracing of the evolutionary history of modern elasmobranchs to at least 250 MYA; nonetheless, exactly how far back the fossil record of living taxa goes has never been collectively surveyed. In this study, the authors assess the representation and extent of the fossil record of elasmobranchs currently living in our oceans by collecting their oldest records and quantifying first appearance dates at different taxonomic levels (i.e., orders, families, genera and species), ecological traits (e.g., body size, habitat and feeding mechanism) and extinction risks (i.e., threatened, not threatened and data deficient). The results of this study confirm the robust representation of higher taxonomic ranks, with all orders, most of the families and over half of the extant genera having a fossil record. Further, they reveal that 10% of the current global species diversity is represented in the geological past. Sharks are better represented and extend deeper in time than rays and skates. While the fossil record of extant genera (e.g., the six gill sharks, Hexanchus) goes as far back as c. 190 MYA, the fossil record of extant species (e.g., the sand shark, Carcharias taurus Rafinesque 1810) extends c. 66 MYA. Although no significant differences were found in the extent of the fossil record between ecological traits, it was found that the currently threatened species have a significantly older fossil record than the not threatened species. This study demonstrate that the fossil record of extant elasmobranchs extends deep into the geologic time, especially in the case of threatened sharks. As such, the elasmobranch geological history has great potential to advance the understanding of how species currently facing extinction have responded to different stressors in the past, thereby providing a deep-time perspective to conservation.     

Gaps and nodes between fossil and extant insects

Traditional contributions of the insect fossil record are listed. Fossil material indicates the earliest occurrence of a group, which in turn is useful for inferring clade divergence dates and net diversification rates. Fossil material provides complementary information on the dynamics of taxonomic diversity. Geographical occurrences outside the extant range of a taxon can be used to infer climatic macro‐fluctuations. In short, the fossil record of insects is essential for pointing out the major factors responsible for the mega‐diversity of the group, and of some of its internal lineages. Reliable taxonomic assignments and phylogenetic hypotheses underpin broader generalizations. In that respect, a problem is the inadequate integration of data from fossil and extant insect taxa in phylogenetic investigations. Stumbling blocks lie at various systematic levels. Unreliability of specimen‐based data, of species delimitation, and of homology assumptions, might have been responsible for a disdain by some entomologists for palaeoentomological literature. Idiosyncratic (and in cases flawed) methods aimed at investigating phylogenetic relationships used by a fraction of the palaeoentomological community might also have contributed to this situation. Concurrently, the traditional nomenclatural procedure might prevent effective communication between neo‐ and palaeoentomologists. Augmenting the available information on the wing venation of extant taxa would significantly advance palaeoentomology, and provide a relevant broad‐scale character system. Furthermore, the entomological community should contribute to experimentations of various nomenclatural procedures, with the aim of developing an optimal approach in terms of communication and information retrieval.     

Flavonoids of fossil miocene Platanus and its extant relatives

Flavonoids of seven extant Platanus species and a fossil Platanus species from the Miocene Clarkia Flora of northern Idaho were compared. Sixteen flavonoids were isolated of which 15 were either wholly or partially identified. Flavonoids of Platanus are based on kaempferol and quercetin and most glycosides are linked at position 3. Because of an extremely high degree of overall chemical similarity and the presence of minor variation within some species, flavonoid data were of limited value in clarifying relationships among extant species. Flavonoid data suggest a closer chemical similarity of the fossil Platanus species to the Asiatic P. orientalis, rather than to the six investigated North American species. Morphologically, however, the fossil Platanus is very similar to P.occidentalis from eastern North America. These findings are similar to those reported in a paleobiochemical study of a fossil Liriodendron species from the same Miocene Flora.     

Tackling the population genetics of clonal and partially clonal organisms

Many clonal organisms experience occasional events of sexual recombination, with profound consequences for their population dynamics and evolutionary trajectories. With the recent development of polymorphic genetic markers and new statistical methods, we now have an unprecedented ability to detect recombination in organisms that are thought to reproduce strictly, or essentially asexually. However, it is not always obvious which methodology to apply. Consequently, biologists might decide how to analyse their data without clear guidelines. Here, we discuss the available methods, focusing on those best suited when working with limited genetic information, such as a few genetic markers or DNA sequences. We conclude by commenting on the prospects offered by some recent conceptual advances and the access to high throughput technologies in an increasing number of model organisms.     

DNA fingerprinting in clonal organisms

The use of DNA fingerprinting to identify members of the same clone in completely or partially asexual organisms requires that the individuals within a clone share a recent common ancestor. By considering the expected distributions of band–sharing values in asexual and sexual organisms, it is shown that DNA fingerprinting may be effective in distinguishing members of the same clone, provided that the frequency of sexual reproduction is considerably greater than the minisatellite mutation rate.     

Morphological variation in the nasal region of extant and fossil hominids

We describe here the mid-facial region of a skull of anatomically modern Homo sapiens (FAI 3/2/1) that exhibits upwardly divergent nasal bones. In previous literature, that pattern has been described as a diagnostic character state for the robust early hominid taxon Paranthropus. This specimen supports our viewpoint that nasal region morphology varies extensively within and between living hominoid primate taxa, in patterns that provide a basis for understanding how microevolutionary variation serves as the basis for macroevolutionary transformations.     

Generalized individual dental age stages for fossil and extant placental mammals

The traditional age stages for eutherian mammals (infant, juvenile, adult, senile) can be difficult to apply in the fossil record. Based on the tooth eruption and wear of the cheek teeth we propose six “individual dental age stages” (IDAS) that can be applied to almost all fossil and extant mammalian dentitions. The six stages of IDAS cover the entire life span. Traditional terms can be correlated to the IDAS stages and thus redefined based on the dentition: IDAS 0—prenatal, IDAS 1—infant, IDAS 2—juvenile, IDAS 3—adult, IDAS 4—late adult, and IDAS 5—senile. Furthermore IDAS enables comparison between individuals, characterizing the mortality in monospecific populations, and even of entire communities composed of various species. The data obtained can be used for paleoecological interpretations. The varying duration of different stages in the IDAS pattern during the life history forms an additional way to characterize mammalian groups by development and wear of their dentition.     

Morphology of the hallucial phalanges in extant anthropoids and fossil hominoids

Pedal phalanges of living anthropoids and several Miocene fossil hominoid taxa were studied to reveal functional adaptations of living anthropoid feet and to infer positional behavior of fossil hominoids. Among the examined living anthropoids, Pan has a very developed (long and robust) hallux. Proconsul and Nacholapithecus, a large hominoid from Nachola, northern Kenya, display a moderately long hallux like Alouatta and Cebus, suggesting the well-developed capability of a hallux-assisted power grip. Allometric analyses revealed that the Miocene hominoids examined (mainly from East Africa) as a whole displayed a different scaling pattern about the width of the proximal articular surface of the hallucial terminal phalanx from that of living anthropoids. Larger-sized hominoids display a wider articular surface than comparable-sized living anthropoids while smaller-sized fossil hominoids do the reverse. Such a difference was less marked for the height of the articular surface. These results may suggest that positional adaptations of Miocene hominoids are not merely resultants of a common body size function that is observed in living anthropods. The wide articular surface of fossil hominoid hallucial terminal phalanges suggests an adaptation for vertical climbing and clinging, in which the hallux is kept perpendicularly to the long axis of the vertical support.     

Identifying metameric variation in extant hominoid and fossil hominid mandibular molars

Landmark data were collected from cross sections and occlusal images of mandibular molar crowns, and Euclidean distance matrix analysis (EDMA) was used to identify metameric morphological variation between the first and second mandibular molars of living taxa: Gorilla gorilla (n = 30), Pan troglodytes (n = 34), and Homo sapiens (n = 26). Two patterns of metameric variation were identified, one unique to humans and the other shared by chimpanzees and gorillas. In order to assess the utility of this type of analysis for the interpretation of the hominid fossil record, 19 mandibular molars from Sterkfontein Member 4, South Africa, were examined. The pattern of metameric variation of the Sterkfontein molars resembled that of the African great apes, and differed from the modern human pattern. These results demonstrate that data on metameric variation may provide information regarding function or developmental processes previously indiscernible from fossil material.     

Resurrecting extinct interactions with extant substitutes

There is increasing evidence that restoration ecologists should be most concerned with restoring species interactions rather than species diversity per se [1]. Rewilding with taxon substitutes, the intentional introduction of exotic species to replace the ecosystem functions of recently extinct species, is one way to reverse ecosystem dysfunction following the loss of species interactions [2]. This is highly controversial [3], in part because of a lack of rigorous scientific studies [4]. Here we present the first empirical evidence of an in situ rewilding project undertaken as a hypothesis-driven ecosystem management option. On Ile aux Aigrettes, a 25-hectare island off Mauritius, the critically endangered large-fruited endemic ebony, Diospyros egrettarum (Ebenaceae), was seed-dispersal limited after the extinction of all native large-bodied frugivores, including giant tortoises. We introduced exotic Aldabra giant tortoises, Aldabrachelys gigantea, to disperse the ebony seeds. Not only did the tortoises ingest the large fruits and disperse substantial numbers of ebony seeds, but tortoise gut passage also improved seed germination, leading to the widespread, successful establishment of new ebony seedlings. Our results demonstrate that the introduction of these exotic frugivores is aiding the recovery of ebonies. We argue for more reversible rewilding experiments to investigate whether extinct species interactions can be restored.     

A morphometric analysis of extant and early miocene fossil hominoid maxillo-dental specimens

It is demonstrated in this paper that before we can hope to formulate phylogenetic relationships between and amongst fossil hominoid material it is first necessary to sex the material accurately. In order to determine whether the morphological and morphometrical variability seen in fossil specimens is due to sexual or inter species dimorphism, it is necessary to calibrate fossil specimens against extant hominoid species' morphologies. Only after fossil specimens have been sexed is it possible to differentiate between morphologies that are related to sex and those that are species specific. This will help reduce fossil misallocation. A morphometric analysis of extant and fossilProconsul hominoid material is presented. Each fossil specimen has been sexed according to symplesiomorphic sex morphologies as defined in this paper. After the fossil specimens have been sexed they are analyzed using multivariate statistics. The identification of differing sex patterns within the specimens examined here suggests that a new species ofProconsul may have to be considered.     

High-resolution computed tomography for the comparative study of fossil and extant bone

Special methods have been developed to use computed tomography (CT) for 3-dimensional imaging of both fossil and extant bones. Most commercial CT scanners cannot display the internal structure of fossils because the very high density is beyond the upper limits of the normal CT number scale (Hounsfield scale) of the scanners. X-ray projections from CT scans of fossils were modified by scaling the data to provide an expanded CT number scale, allowing the internal structure of highly fossilized objects to be visualized. These images were compared with state-of-the-art, high-resolution CT images of extant bone. Special image reformatting software was used to provide qualitative and quantitative 3-dimensional imaging. The recent rapid advances in CT technology have made this imaging modality the procedure of choice in much of diagnostic radiology. Use of this tool in paleoanthropology has been limited in the past by restricted access to scanners. However, new developments in CT will make this technique available to many researchers in the near future.     

Functional morphology of the asterionic region in extant hominoids and fossil hominids

Asterionic sutural patterns in Plio-Pleistocene hominid crania have never been examined in detail. We present an analysis of this anatomical region in Australopithecus and Homo and relate different sutural patterns to functional changes in the masticatory apparatus. The great apes and A. afarensis share the common adult higher primate sutural pattern referred to as the "asterionic notch," which develops in response to the hypertrophy of posterior temporalis muscle fibers and the consequent formation of compound temporal/nuchal crests. This sutural configuration also appears to be present on the early Homo cranium KNM-ER 1805. In contrast, adult male A. boisei crania exhibit a unique pattern where the temporal squama overlaps the parietal which, in turn, overlaps the par mastoidea and the upper scale of the occipital bone. We relate this arrangement to the need to reinforce the rear of a thin-walled braincase against the net tensile forces exerted by the temporalis and nuchal muscles. The common juvenile hominoid edge-to-edge asterionic articulation is maintained in adult A. africanus, A. robustus, female A. boisei, and most Homo crania. We discuss the latter pattern in regard to anterior temporalis hypertrophy in A. africanus, A. robustus, and A. boisei and to craniofacial paedomorphosis in Homo.     

Articular morphology of the proximal ulna in extant and fossil hominoids and hominins

Extant hominoids share similar elbow joint morphology, which is believed to be an adaptation for elbow stability through a wide range of pronation-supination and flexion-extension postures. Mild variations in elbow joint morphology reported among extant hominoids are often qualitative, where orangutans are described as having keeled joints, and humans and gorillas as having flatter joints. Although these differences in keeling are often linked to variation in upper limb use or loading, they have not been specifically quantified. Many of the muscles important in arboreal locomotion in hominoids (i.e., wrist and finger flexors and extensors) take their origins from the humeral epicondyles. Contractions of these muscles generate transverse forces across the elbow, which are resisted mainly by the keel of the humeroulnar joint. Therefore, species with well-developed forearm musculature, like arboreal hominoids, should have more elbow joint keeling than nonarboreal species. This paper explores the three- and two-dimensional morphology of the trochlear notch of the elbow of extant hominoids and fossil hominins and hominoids for which the locomotor habitus is still debated. As expected, the elbow articulation of habitually arboreal extant apes is more keeled than that of humans. In addition, extant knuckle-walkers are characterized by joints that are distally expanded in order to provide greater articular surface area perpendicular to the large loads incurred during terrestrial locomotion with an extended forearm. Oreopithecus is characterized by a pronounced keel of the trochlear notch and resembles Pongo and Pan. OH 36 has a morphology that is unlike that of extant species or other fossil hominins. All other hominin fossils included in this study have trochlear notches intermediate in form between Homo and Gorilla or Pan, suggesting a muscularity that is less than in African apes but greater than in humans.     

Permian macroburrows as microhabitats for meiofauna organisms: an ancient behaviour common in extant organisms

Meiofaunal organisms are indirectly influenced by the activity of benthic macroinvertebrates within the sediment, which plays a role in modifying physical and chemical characteristics of the habitat. The association of meiofaunal organisms and macroburrows is well known in modern environments, but the record of this relationship in the geological record is still incipient. This study documents diminutive burrows (Helminthoidichnites tenuis) associated with the surface of macroburrows (Palaeophycus tubularis) in Early Permian deposits. The cylindrical shape and meandering to loop trajectory of the diminutive burrows indicate that they were produced by small free‐living meiofaunal nematodes. Apparently, P. tubularis (open burrow) constituted a favourable microhabitat for nematodes, providing the following: (1) protection against erosive processes and meiofauna predators; (2) oxygen access to more in‐depth layers within the sediment; (3) temperature stabilization; and (4) food supply due to mucus impregnation in the macroburrow walls by the Palaeophycus tracemaker. The association between H. tenuis and P. tubularis constitutes the first fossil record of a symbiotic relationship between meiofaunal nematodes and macrobenthic organisms (polychaetes). It also suggests that ecological strategies such as mutualism or commensalism, which are common between extant nematodes and macrobenthic invertebrates, were available in the behavioural programme of these organisms since the Early Permian.