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Understanding the role of humans as ‘ecosystem engineers’ requires a deep-time perspective rooted in evolutionary history and the fossil record. However, no con-ceptual framework exists for studying the rise of ecosystem engineering in deep time, requiring us to consider effects that fall outside the scope of traditional defini-tions. Here, we present a new framework applicable to both modern and ancient engineering-type effects. We propose a new term – ‘Earth system engineering’ – to describe biological processes that alter the structure and function of planetary spheres, and which combines core tenets of ecosystem engineering, niche construction, and legacy effects. We illustrate this framework using the fossil record, and show how it can be applied across the tree of life, and throughout Earth history. 

Ecosystem structure—that is the species present, the functions they represent, and how those functions interact—is an important determinant of community stability. This in turn affects how ecosystems respond to natural and anthropogenic crises, and whether species or the ecological functions that they represent are able to persist. Here we use fossil data from museum collections, literature, and the Paleobiology Database to reconstruct trophic networks of Tethyan paleocommunities from the Anisian and Carnian (Triassic), Bathonian (Jurassic), and Aptian (Cretaceous) stages, and compare these to a previously reconstructed trophic network from a modern Jamaican reef community. We generated model food webs consistent with functional structure and taxon richnesses of communities, and compared distributions of guild level parameters among communities, to assess the effect of the Mesozoic Marine Revolution on ecosystem dynamics. We found that the trophic space of communities expanded from the Anisian to the Aptian, but this pattern was not monotonic. We also found that trophic position for a given guild was subject to variation depending on what other guilds were present in that stage. The Bathonian showed the lowest degree of trophic omnivory by top consumers among all Mesozoic networks, and was dominated by longer food chains. In contrast, the Aptian network displayed a greater degree of short food chains and trophic omnivory that we attribute to the presence of large predatory guilds, such as sharks and bony fish. Interestingly, the modern Jamaican community appeared to have a higher proportion of long chains, as was the case in the Bathonian. Overall, results indicate that trophic structure is highly dependent on the taxa and ecological functions present, primary production experienced by the community, and activity of top consumers. Results from this study point to a need to better understand trophic position when planning restoration activities because a community may be so altered by human activity that restoring a species or its interactions may no longer be possible, and alternatives must be considered to restore an important function. Further work may also focus on elucidating the precise roles of top consumers in moderating network structure and community stability. 

The Earth has been beset by many crises during its history, and yet comparing the ecological impacts of these mass extinctions has been difficult. Key questions concern the kinds of species that go extinct and survive, how communities rebuild in the post-extinction recovery phase, and especially how the scaling of events affects these processes. Here, we explore ecological impacts of terrestrial and freshwater ecosystems in three mass extinctions through the mid-Phanerozoic, a span of 121 million years (295–174 Ma). This critical duration encompasses the largest mass extinction of all time, the Permian–Triassic (P–Tr) and is flanked by two smaller crises, the Guadalupian–Lopingian (G–L) and Triassic–Jurassic (T–J) mass extinctions. Palaeocommunity dynamics modelling of 14 terrestrial and freshwater communities through a long sedimentary succession from the lower Permian to the lower Jurassic in northern Xinjiang, northwest China, shows that the P–Tr mass extinction differed from the other two in two ways: (i) ecological recovery from this extinction was prolonged and the three post-extinction communities in the Early Triassic showed low stability and highly variable and unpredictable responses to perturbation primarily following the huge losses of species, guilds and trophic space; and (ii) the G–L and T–J extinctions were each preceded by low-stability communities, but post-extinction recovery was rapid. Our results confirm the uniqueness of the P–Tr mass extinction and shed light on the trophic structure and ecological dynamics of terrestrial and freshwater ecosystems across the three mid-Phanerozoic extinctions, and how complex communities respond to environmental stress and how communities recovered after the crisis. Comparisons with the coeval communities from the Karoo Basin, South Africa show that geographically and compositionally different communities of terrestrial ecosystems were affected in much the same way by the P–Tr extinction. 

A thorough understanding of how communities respond to extreme changes, such as biotic invasions, is essential to manage ecosystems today. Here we constructed fossil food webs to identify changes in Late Ordovician (Katian) shallow-marine paleocommunity structure and functioning before and after the Richmondian invasion, a well-documented ancient invasion. Food webs were compared using descriptive metrics and cascading extinction on graphs models. Richness at intermediate trophic levels was underrepresented when using only data from the Paleobiology Database relative to museum collections, resulting in a spurious decrease in modeled paleocommunity stability. Therefore, museum collections and field sampling may provide more reliable sources of data for the reconstruction of trophic organization in comparison to online data repositories. The invasion resulted in several changes in ecosystem dynamics. Despite topological similarities between pre- and postinvasion food webs, species loss occurred corresponding to a minor decrease in functional groups. Invaders occupied all of the preinvasion functional guilds, with the exception of four incumbent guilds that were lost and one new guild, corroborating the notion that invaders replace incumbents and fill preexisting niche space. Overall, models exhibited strong resistance to secondary extinction, although the postinvasion community had a lower threshold of collapse and more variable response to perturbation. We interpret these changes in dynamics as a decrease in stability, despite similarities in overall structure. Changes in food web structure and functioning resulting from the invasion suggest that conservation efforts may need to focus on preserving functional diversity if more diverse ecosystems are not inherently more stable. 

The emergence of an ecological community in evolutionary time is the result of species evolution and coevolution. In species rich and functionally diverse communities, there are a multitude of alternative pathways along which emergence could proceed. Nevertheless, analysis of alternative pathways for paleocommunities spanning more than 13 million years of the Permian-Triassic of the Karoo Basin of South Africa, suggests that pathways actually taken represent a small subset of the total available. This leads to a narrow representation of the total number of communities possible given a specific number of species and level of functional diversity. Furthermore, the paleocommunities were always superior to structural alternatives of equal complexity, in terms of community global stability (the number of species that can coexist stably and indefinitely). Such optimization could indicate a selective process during the formation of types of communities, or simply be emergent from the coevolutionary framework. Here we present ongoing work to support an emergent process by which many alternative types of communities may form constantly on ecological timescales, but where few are stable and persistent on longer timescales. This leads to the compositional stability of paleoecological units often noted in the fossil record, and the apparent incumbency of long-lasting lineages. The aftermath of mass extinctions present opportunities to test this hypothesis, because previously persistent communities are replaced by newly emergent ones, and the emergence process itself can be extended to geological timescales because of ongoing environmental instability, and the time required for the reformation of coevolutionary relationships and functional structures. Such is the case in the aftermath of the Permian-Triassic mass extinction, when Early Triassic paleocommunities in the Karoo Basin were sub-optimal compared to alternative, hypothetical histories. Understanding long-term ecological persistence is crucial to our understanding of the modern anthropogenically-driven environmental crisis. Modern ecosystems are the documented products of geological and evolutionary history. Species acclimatization and adaptation to ongoing changes are not necessarily guarantees of the future persistence of the resulting reorganized systems. It will become critical to determine if the biosphere has already turned down new ecological and evolutionary pathways, or is still operating in the capacity of the pre-Anthropocene system. 

Abstract. Microfossil assemblages provide valuable records to investigatevariability in continental margin biogeochemical cycles, including dynamicsof the oxygen minimum zone (OMZ). Analyses of modern assemblages acrossenvironmental gradients are necessary to understand relationships betweenassemblage characteristics and environmental factors. Five cores wereanalyzed from the San Diego margin (32∘42′00′′ N, 117∘30′00′′ W; 300–1175 m water depth) for core top benthic foraminiferalassemblages to understand relationships between community assemblages andspatial hydrographic gradients as well as for down-core benthic foraminiferalassemblages to identify changes in the OMZ through time. Comparisons ofbenthic foraminiferal assemblages from two size fractions (63–150 and>150 µm) exhibit similar trends across the spatial and environmental gradient or in some cases exhibit more pronouncedspatial trends in the >150 µm fraction. A range of speciesdiversity exists within the modern OMZ (1.910–2.586 H, Shannon index),suggesting that diversity is not driven by oxygenation alone. We identifytwo hypoxic-associated species (B. spissa and U. peregrina), one oxic-associated species (G. subglobosa) andone OMZ edge-associated species (B. argentea). Down-core analysis of indicator speciesreveals variability in the upper margin of the OMZ (528 m water depth) whilethe core of the OMZ (800 m) and below the OMZ (1175 m) remained stable inthe last 1.5 kyr. We document expansion of the upper margin of the OMZbeginning 400 BP on the San Diego margin that is synchronous with otherregional records of oxygenation.