Towards a theoretical basis of paleoecology: concepts of community dynamics

The science of paleoecology suffers from a lack of conceptual frameworks. Paleoecologists have been overconcerned with the inadequacies of the fossil record: as a result, community palmecology has historically developed very slowly. At the community ecosystem level, the need for a theoretical framework is so great that paleoecology must 'borrow' the hypotheses of modem ecology. Consideration of the stability-time hypothesis of Sanders in conjunction with the physical setting of transgression and regression has permitted the structuring of three community types and the interpretation of their behavior under variations in the physical environment. These community types (opportunistic. stable mature, relict mature) are recognizable in the fossil record and examples are given from the Upper Pennsylvanian of the Appalachian Basin.     

Positive interactions in communities

Current concepts of the role of interspecific interactions in communities have been shaped by a profusion of experimental studies of interspecific competition over the past few decades. Evidence for the importance of positive interactions - facilitations - in community organization and dynamics has accrued to the point where it warrants formal inclusion into community ecology theory, as it has been in evolutionary biology.     

H. A. GLEASON'S 'INDIVIDUALISTIC CONCEPT' AND THEORY OF ANIMAL COMMUNITIES: A CONTINUING CONTROVERSY

A tradition of natural history and of the lore of early twentieth-century ecology was that organisms lived together and interacted to form natural entities or communities. Before there was a recognizable science of ecology, Mobius (1877) had provided a name ‘biocoenosis’ for such entities. This concept persisted in the early decades of ecological science; at an extreme it was maintained that the community had integrating capabilities and organization like those of an individual organism, hence the term organismic community. In the 1950s- 1970s an alternative individualist concept, derived from the ideas of H. A. Gleason (1939), gained credence which held that communities were largely a coincidence of individualistic species characteristics, continuously varying environments and different probabilities of a species arriving on a given site. During the same period, however, a body of population based theory of animal communities became dominant which perpetuated the idea of patterns in nature based on biotic interactions among species resulting in integrated communities. This theory introduced an extended terminology and mathematical models to explain the organization of species into groups of compatible species governed by rules. In the late 1970s the premises and methods of the theory came under attack and a vigorous debate ensued. The alternatives proposed were, at an extreme, null models of random aggregations of species or stochastic, individualistic aggregations of species, sensu Gleason. Extended research and debate ensued during the 1980s resulting in an explosion of studies of animal communities and a plethora of symposia and volumes of collected works concerning the nature of animal communities. The inherent complexity of communities and the traditional differences among animal ecologists about how they should be defined and delimited, at what scale of taxa, space and time to study them, and appropriate methods of study and analysis have resulted in extended and as yet inconclusive discussions. Recent differences and discussions are considered under five general categories, evolution and community theory, individualistic concept, community definition, questions from community ecology and empirical studies. Communities are seen by some ecologists as entities of coevolving species and, in any case, it is necessary to integrate evolutionary ideas with the varied concepts of community. The individualistic concept of community, as a relative latecomer to discussions of animal community, is sometimes misconstrued as holding that communities are random assemblages of organisms without biotic interactions among species. Nevertheless, it has increasingly been accepted as supported by studies of diverse taxa and habitats. However, many other ecologists continue to argue for integrated, biotically controlled and evolved communities. Among the major difficulties of addressing the problems of community are problems of definition and terminology. One commentator noted that community ecology may be unique in the sciences because there is no consensus definition of community. One consequence of the lack of consensus definition is evident in the varied and diffuse questions posed in studies of community. Some critics of community ecology fault it for posing unanswerable questions. Recent empirical studies include various assessments about community ranging from deterministic, integrated and organismic to individualistic with various suggestions for compromise. The early emphasis on birds in studies of animal communities has expanded to obviate the argument that any position is constrained by the taxon studied. Insects, in general, are more prone to give rise to interpretation of a nonintegrated community. Parasite community studies have given rise to some distinctive categories and terminology. However, consensus is not achieved either within or among taxonomic groups or habitat groups. The extreme heterogeneity and complexity of communities (and of ecologists) has produced extended discussions of how to approach such multidimensional complexity. These discussions often turn on polarized positions of reductionism and experiment versus holism. Proponents of reductionism asserted that natural communities cannot be understood or their structure and organization predicted until experimental communities, or models thereof, are understood. Holists insisted that the inherent complexity and variability of communities cannot be elucidated in simplified experimental communities or in models. A more recent trend has urged pluralism, or, at least, mutual respect and dialogue, which are sometimes lacking, between proponents of these divergent approaches to communities. Recent work perpetuates the original dichotomy between integrated organismic community concept and individualistic non-integrated concept. The hope for a rule-governed community has extended to metarules and a new theory of community as divided into core species and satellite species is called into question. The problems of distinguishing between determinism and chance effects in community organization continue and the lost or fading hope of a general theory of community is revived in a search for rules that govern their assembly.     

Increase of body size in sixgill sharks with change in diet as a possible background of their evolution

Body size variation of a predator is a simple way to follow the main changes in its food source during its life history or along its evolution in ecology and paleoecology, respectively. Here, we present possible first evidence of such predator-prey co-evolution through the study of the body size evolution among sixgill sharks (genus Hexanchus) inferred from their fossil record and by comparison to the life history of its two recent species. As for the observed ontogenic diet change of the living bluntnose sixgill shark (H. griseus), its ancestors appear to have developed a similar penchant for dining on marine mammals at the end of the Paleogene with a remarkably well-correlated timing.     

Community ecology of the Middle Miocene primates of La Venta,Colombia: the relationship between ecological diversity,divergence time,and phylogenetic richness

It has been suggested that the degree of ecological diversity that characterizes a primate community correlates positively with both its phylogenetic richness and the time since the members of that community diverged (Fleagle and Reed in Primate communities. Cambridge University Press, New York, pp 92–115, 1999). It is therefore questionable whether or not a community with a relatively recent divergence time but high phylogenetic richness would be as ecologically variable as a community with similar phylogenetic richness but a more distant divergence time. To address this question, the ecological diversity of a fossil primate community from La Venta, Colombia, a Middle Miocene platyrrhine community with phylogenetic diversity comparable with extant platyrrhine communities but a relatively short time since divergence, was compared with that of modern Neotropical primate communities. Shearing quotients and molar lengths, which together are reliable indicators of diet, for both fossil and extant species were plotted against each other to describe the dietary “ecospace” occupied by each community. Community diversity was calculated as the area of the minimum convex polygon encompassing all community members. The diversity of the fossil community was then compared with that of extant communities to test whether the fossil community was less diverse than extant communities while taking phylogenetic richness into account. Results indicate that the La Ventan community was not significantly less ecologically diverse than modern communities, supporting the idea that ecological diversification occurred along with phylogenetic diversification early in platyrrhine evolution.     

The environmental background of hominid emergence and the appearance of the genusHomo

The human biologist usually considers ecology of recent humanity. This essay explores the question of whether the human biologist specialising in the ecology of living peoples has anything to learn from the palaeo-anthropologist, studying ancient hominids andtheir adaptive mechanisms over a deep time dimension. Since the Hominidae are under discussion, the definition of the hominids is reviewed. Historically, three phases are recognised. A rethinking of the classification of the hominoids has become necessary for the old and classical systematics, which divided this superfamily into the Hominidae and the Pongidae, is now outmoded. Since no consensus on such a re-classification has yet been reached, the author adheres to the classical system for the time being. The Hominidae emerged between about 8 and 5 million years ago. At that time, Africa was subject to major cooling and aridification and considerable changes in the flora and fauna were occurring. Wet forests were retreating, savanna was spreading and the animals of Africa were undergoing many changes, partly by faunal interchange with Asia following the drying up of the Mediterranean, and partly by autochthonous evolution among the pre-existing species of the continent. The Hominidae could well have emerged from the striking environmental modifications of this late Miocene phase. Critical changes occurred in hominid evolution between 3 and 2 million years before the present. The pre-existing speciesAustralopithecus africanus acquired the form of a postulated derivedA. africanus; the hominid lineage underwent cladogenetic splitting into robust and hyper-robust australopithecines and the genusHomo; Homo babilis appeared; stone tools are first found in the archaeological record; spoken language seems to have been acquired. These sensational events, within the space of one million years, took place against the background of conspicuous changes in the climate and physical geography of Africa, the flora and non-hominid fauna. Mankind became increasingly dependent upon stone culture. Hence a new element was added to the range of modes of adjustment, an element which must have greatly increased the ecological flexibility of the hominids. From the end of the Pliocene era onwards, culture should be seen as a constituent of man's environment and, at the same time, a highly advantageous component of human adaptational processes. In later and recent mankind, it may be difficult to extricate the respective roles of biological, social and physical factors, on the one hand, and cultural aspects on the other, as mechanisms and facilitators of adaptation to diverse econiches.     

The ecostratigraphic paradigm

What can distinguish ecostratigraphy from other stratigraphic concepts stems not so much from its specific methods as from the theoretical background proposed here and called the ecostratigraphic paradigm. This theory claims that the fossil record of evolution at the community, taxocoene, and/or species group level displays a more or less discrete pattern, with discontinuities imposed mostly by extrinsic, geologic events. This pattern may constitute a base for natural stratigraphic classification of rocks using coenozonal schemes. The ecostratigraphic paradigm may or may not refer to communities as distinct and real biologic units. The greatest advantage of the ecostratigraphic approach is that the resultant set of time-planes is much more informative about the course of geobiologic evolution than the traditionally used chronostratigraphic one. Stratigraphial theory. ecostratigraphy. chronostratigraphy. paleoecology. coenozones. communities, evolution .     

Paleoecology of benthic community replacement

The literature of community paleoecology is filled with examples in which long-term environmentally-controlled faunal transitions are misidentified as forms of ecologic succession. This has obscured a fundamental community-level process - community replacement - involving gradual to abrupt substitution of one benthic community for another as a result of subtle to sharp changes in habitats over subevolutionary time. In gradually changing environments, replacement takes place through conformational reorganization of species-abundance distributions within established communities, yielding sequences of slightly different fossil associations. Environments that change very rapidly drastically feature a different type of community replacement involving species turnover, wherein environmental tolerance limits of community members are closely approached or exceeded. Paleoecologists should be alert to the strong likelihood that many temporal transitions involving autochthonous fossil associations are, in fact, community replacement sequences.     

Fossil apes from the vallès‐penedès basin

Currently restricted to Southeast Asia and Africa, extant hominoids are the remnants of a group that was much more diverse during the Miocene. Apes initially diversified in Africa during the early Miocene, but by the middle Miocene they extended their geographical range into Eurasia, where they experienced an impressive evolutionary radiation. Understanding the role of Eurasian hominoids in the origin and evolution of the great‐ape‐and‐human clade (Hominidae) is partly hampered by phylogenetic uncertainties, the scarcity and incompleteness of fossil remains, the current restricted diversity of the group, and pervasive homoplasy. Nevertheless, scientific knowledge of the Eurasian hominoid radiation has significantly improved during the last decade. In the case of Western Europe, this has been due to the discovery of new remains from the Vallès‐Penedès Basin (Catalonia, Spain). Here, I review the fossil record of Vallès‐Penedès apes and consider its implications. Although significant disagreements persist among scholars, some important lessons can be learned regarding the evolutionary history of the closest living relatives of humans. © 2012 Wiley Periodicals, Inc.     

Evolutionary community ecology of plant-associated arthropods in terrestrial ecosystems

In the 21st century, researchers have attempted a synthesis between community ecology and evolutionary biology. This emerging research area, which aims to synthesize community ecology and evolutionary biology, is evolutionary community ecology. Evolutionary community ecology addresses how intraspecific trait variation in community members is essential for predicting community properties and, how community properties are a key component of the selective forces that determine genetic and phenotypic variation in a community member. In this paper, I review recent findings in evolutionary community ecology in plant-associated arthropods in terrestrial ecosystems. I discuss roles of both genetic variation and phenotypic plasticity as a source of trait variation in plants in shaping plant-associated arthropod communities. Also, I discuss effects of genetic variation in herbivores on plant-associated arthropod communities. Furthermore, I highlight community context evolution in which multiple species interactions and community composition affect trait evolution of a community member. Finally, I argue that future studies should investigate a feedback loop between community and evolutionary dynamics beyond unidirectional studies on effects of evolution on a community or vice versa. This approach will provide major insights into mechanistic principles for making predictions of community ecology.     

The developing relationship between the study of fungal communities and community ecology theory

Plant and animal systems had a head start of several decades in community ecology and have largely created the theoretical framework for the field. I argue that the lag in fungal community ecology was largely due to the microscopic nature of fungi that makes observing species and counting their numbers difficult. Thus the basic patterns of fungal occurrence were, until recently, largely invisible. With the development of molecular methods, especially high-throughput sequencing, fungal communities can now be “seen”, and the field has grown dramatically in response. The results of these studies have given us unprecedented views of fungal communities in novel habitats and at broader scales. From these advances we now have the ability to see pattern, compare it to existing theory, and derive new hypotheses about the way communities are assembled, structured, and behave. But can fungal systems contribute to the development of theory in the broader realm of community ecology? The answer to this question is yes! In fact fungal systems already have contributed, because in addition to many important natural fungal communities, fungi also offer exceptional experimental communities that allow one to manipulate, control, isolate and test key mechanisms. I discuss five well-developed systems and some of the contributions they have made to community ecology, and I briefly mention one additional system that is amenable to development.     

Eco-evolutionary dynamics in herbivorous insect communities mediated by induced plant responses

It is increasingly recognized that the ecology of communities and evolution of species within communities are interdependent, and researchers have been paying attention to this rapidly emerging field of research, i.e., through studies on eco-evolutionary dynamics. Most of the studies on eco-evolutionary dynamics have been concerned with direct trophic interactions. However, community ecologists have shown that trait-mediated indirect effects play an important role in shaping the structure of natural communities. In particular, in terrestrial plant–insect systems, indirect effects mediated through herbivore-induced plant responses are common and have a great impact on the structure of herbivore communities. This review describes eco-evolutionary dynamics in herbivorous insect communities, and specifically focuses on the key role of herbivore-induced plant responses in eco-evolutionary dynamics. First, I review studies on the evolution of herbivore traits relevant to plant induction and discuss evolution in a community context mediated by induced plant responses. Second, I highlight how intraspecific genetic variation or evolution in herbivore traits can influence herbivore community structure. Finally, I propose the hypothetical model that induced plant responses supports eco-evolutionary feedback in herbivore communities. In this review, I argue that the application of the indirect interaction web approaches into studies on eco-evolutionary will provide profound insights into understanding of mechanisms of the generation and maintenance of biodiversity.     

A fossil record for trematodes: extent and potential uses

Some extant parasitic flatworms (Phylum Platyhelminthes, Class Trematoda, Order Digenea) produce pits on the interior shell surface of their molluscan bivalve hosts. Based on comparisons of pits in Tertiary and Quaternary Gemma, Parastarte and Transennella (Family Veneridae), we establish a history of association between trematodes and these host genera spanning over 5 My in North America. This is the first report of a fossil record for the Trematoda. Similar pits are also present in many other bivalve genera (both fossil and living species), indicating that a substantial fossil record may exist for parasitic flatworms. The identification of parasitic infections from fossil shells may provide a new dimension for the study of the evolutionary biology, paleoecology and biogeography of host-parasite associations. □ Trematoda, trace fossils, Veneridae, paleoecology. life-history evolution, parasites.     

Vertebrate palaeohistology: Past and future

Vertebrate palaeohistology has been considered for a long time as a modest subdivision of Palaeontology. Starting in the 1930s and 1940s, comparative bone tissue histology and palaeohistology progressively demonstrated the multiple correlations between bone tissue distribution and numerous biological variables, such as ontogenetic origin, growth, size, shape, biomechanics, physiology, and ecology. During the last three decades, Palaeohistology has focussed on deciphering the numerous, complex causes explaining the patterns and processes of Vertebrate evolution. Palaeohistology is a powerful tool, in connection with Biology, for the reconstruction of fossil Vertebrates as living organisms.     

An emerging synthesis between community ecology and evolutionary biology

A synthesis between community ecology and evolutionary biology is emerging that identifies how genetic variation and evolution within one species can shape the ecological properties of entire communities and, in turn, how community context can govern evolutionary processes and patterns. This synthesis incorporates research on the ecology and evolution within communities over short timescales (community genetics and diffuse coevolution), as well as macroevolutionary timescales (community phylogenetics and co-diversification of communities). As we discuss here, preliminary evidence supports the hypothesis that there is a dynamic interplay between ecology and evolution within communities, yet researchers have not yet demonstrated convincingly whether, and under what circumstances, it is important for biologists to bridge community ecology and evolutionary biology. Answering this question will have important implications for both basic and applied problems in biology.     

Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition

Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen and endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To address this gap, we used genome‐wide association mapping with a population of 445 aspen (Populus tremuloides) genets to identify the genes governing variation in plant traits (defence chemistry, bud phenology, leaf morphology, growth) and insect community composition. We found 49 significant SNP associations in 13 Populus genes that are correlated with chemical defence compounds and insect community traits. Most notably, we identified an early nodulin‐like protein that was associated with insect community diversity and the abundance of interacting foundation species (ants and aphids). These findings support the concept that particular plant traits are the mechanistic link between plant genes and the composition of associated insect communities. In putting the “genes” into “genes to ecosystems ecology”, this work enhances understanding of the molecular genetic mechanisms that underlie plant–insect associations and the consequences thereof for the structure of ecological communities.     

The return of the variance: intraspecific variability in community ecology

Despite being recognized as a promoter of diversity and a condition for local coexistence decades ago, the importance of intraspecific variance has been neglected over time in community ecology. Recently, there has been a new emphasis on intraspecific variability. Indeed, recent developments in trait-based community ecology have underlined the need to integrate variation at both the intraspecific as well as interspecific level. We introduce new T-statistics ('T' for trait), based on the comparison of intraspecific and interspecific variances of functional traits across organizational levels, to operationally incorporate intraspecific variability into community ecology theory. We show that a focus on the distribution of traits at local and regional scales combined with original analytical tools can provide unique insights into the primary forces structuring communities.     

寒武纪大爆发——来自贵州的化石证据*

寒武纪展示了生物演化和生态创新最为关键的一段历史, 在此期间发生了后生动物快速的辐射性演化事件, 被称为“寒武纪大爆发”。近四十年来, 基于寒武纪特异埋藏生物群的大量研究为解密寒武纪大爆发具体过程、主要动物类群起源与生态演化作出了重要贡献。贵州素有古生物王国之称, 在寒武系地层中不仅保存了大量解剖学细节精美的化石资源, 也在多个地区产出时间连续的生物组合演化序列, 在探讨动物起源与演化、全球地层对比及群落古生态学等方面具有极其重要的科研价值。近年来, 以小壳动物群、牛蹄塘生物群、杷榔生物群、剑河生物群、凯里生物群等多个生物群在贵州的发现提供了早期后生生物的新信息, 加密了中国乃至全球早期后生生物特异埋藏化石群的演化链, 为全面揭示寒武纪生物群落面貌、早期多门类后生动物的辐射演化和海洋生物群落演替提供了独特的意义, 最终为深入解读寒武纪大爆发的过程与发生机制提供重要实证。本文简要总结了贵州地区在该领域的主要学术贡献, 结合全球研究进展, 对目前存在的问题和未来研究方向提出展望。     

Fossils of parasites: what can the fossil record tell us about the evolution of parasitism?

Parasites are common in many ecosystems, yet because of their nature, they do not fossilise readily and are very rare in the geological record. This makes it challenging to study the evolutionary transition that led to the evolution of parasitism in different taxa. Most studies on the evolution of parasites are based on phylogenies of extant species that were constructed based on morphological and molecular data, but they give us an incomplete picture and offer little information on many important details of parasite–host interactions. The lack of fossil parasites also means we know very little about the roles that parasites played in ecosystems of the past even though it is known that parasites have significant influences on many ecosystems. The goal of this review is to bring attention to known fossils of parasites and parasitism, and provide a conceptual framework for how research on fossil parasites can develop in the future. Despite their rarity, there are some fossil parasites which have been described from different geological eras. These fossils include the free‐living stage of parasites, parasites which became fossilised with their hosts, parasite eggs and propagules in coprolites, and traces of pathology inflicted by parasites on the host's body. Judging from the fossil record, while there were some parasite–host relationships which no longer exist in the present day, many parasite taxa which are known from the fossil record seem to have remained relatively unchanged in their general morphology and their patterns of host association over tens or even hundreds of millions of years. It also appears that major evolutionary and ecological transitions throughout the history of life on Earth coincided with the appearance of certain parasite taxa, as the appearance of new host groups also provided new niches for potential parasites. As such, fossil parasites can provide additional data regarding the ecology of their extinct hosts, since many parasites have specific life cycles and transmission modes which reflect certain aspects of the host's ecology. The study of fossil parasites can be conducted using existing techniques in palaeontology and palaeoecology, and microscopic examination of potential material such as coprolites may uncover more fossil evidence of parasitism. However, I also urge caution when interpreting fossils as examples of parasites or parasitism‐induced traces. I point out a number of cases where parasitism has been spuriously attributed to some fossil specimens which, upon re‐examination, display traits which are just as (if not more) likely to be found in free‐living taxa. The study of parasite fossils can provide a more complete picture of the ecosystems and evolution of life throughout Earth's history.     

Transgression, regression and fossil community succession

Recent paleoecological studies have emphasized the recognition of successional stages of level-bottom communities, but have neglected to point out techniques for distinguishing succession within a fossil community from the temporal and spatial replacement of one fossil community by another. The physical integrity of a marine level-bottom community is discernible, in most instances, through careful temporal and spatial study, and one community can be distinguished from another by judicious application of the 'end-member' concept. Community boundaries are only as distinct as the associated environmental stress gradient. Of first-order significance in understanding fossil community succession and replacement is appreciation of the basic asymmetry of the community dynamics involved in transgression-regression events. Of second-order importance is appreciation of the nature of the onshore-offshore environmental stress gradient, which, in turn, is controlled by the physical setting of transgression-regression (e.g. progradation versus eustatic control; high topographic relief versus low topographic relief, etc.). The application of the preceding concepts is shown by detailed study of community succession and replacement in the Cambridge Limestone (Upper Pennsylvanian), Guernsey County, Ohio.