ResearchPad - 60 https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Coexisting attractors in the context of cross-scale population dynamics: measles in London as a case study]]> https://www.researchpad.co/article/elastic_article_9535 Patterns of measles infection in large urban populations have long been considered the paradigm of synchronized nonlinear dynamics. Indeed, recurrent epidemics appear approximately mass-action despite underlying heterogeneity. However, using a subset of rich, newly digitized mortality data (1897–1906), we challenge that proposition. We find that sub-regions of London exhibited a mixture of simultaneous annual and biennial dynamics, while the aggregate city-level dynamics appears firmly annual. Using a simple stochastic epidemic model and maximum-likelihood inference methods, we show that we can capture this observed variation in periodicity. We identify agreement between theory and data, indicating that both changes in periodicity and epidemic coupling between regions can follow relatively simple rules; in particular we find local variation in seasonality drives periodicity. Our analysis underlines that multiple attractors can coexist in a strongly mixed population and follow theoretical predictions.

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<![CDATA[The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases]]> https://www.researchpad.co/article/Nc9e55dae-0ecc-4336-855c-b5ad1fdaf2ed There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 60 859 fossil occurrences, we show that the spatial extent of the worldwide terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic. Changes in spatial sampling explain up to 67% of the change in known fossil species counts, and these changes are decoupled from variation in habitable land area that existed through time. Spatial sampling therefore represents a real and profound sampling bias that cannot be explained as redundancy. To address this bias, we estimate terrestrial tetrapod diversity for palaeogeographical regions of approximately equal size. We find that regional-scale diversity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. Although the Cretaceous/Palaeogene mass extinction catalysed an abrupt two- to three-fold increase in regional diversity 66 million years ago, no further increases occurred, and recent levels of regional diversity do not exceed those of the Palaeogene. These results parallel those recovered in analyses of local community-level richness. Taken together, our findings strongly contradict past studies that suggested unbounded diversity increases at local and regional scales over the last 100 million years.

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<![CDATA[Intestinal microbes: an axis of functional diversity among large marine consumers]]> https://www.researchpad.co/article/N11c9ff5b-6314-46a5-963a-c9aec1a1f5de Microbes are ubiquitous throughout the world's oceans, yet the manner and extent of their influence on the ecology and evolution of large, mobile fauna remains poorly understood. Here, we establish the intestinal microbiome as a hidden, and potentially important, ‘functional trait’ of tropical herbivorous fishes—a group of large consumers critical to coral reef resilience. Using field observations, we demonstrate that five common Caribbean fish species display marked differences in where they feed and what they feed on. However, in addition to space use and feeding behaviour—two commonly measured functional traits—we find that interspecific trait differences are even more pronounced when considering the herbivore intestinal microbiome. Microbiome composition was highly species specific. Phylogenetic comparison of the dominant microbiome members to all known microbial taxa suggest that microbiomes are comprised of putative environmental generalists, animal-associates and fish specialists (resident symbionts), the latter of which mapped onto host phylogeny. These putative symbionts are most similar to—among all known microbes—those that occupy the intestines of ecologically and evolutionarily related herbivorous fishes in more distant ocean basins. Our findings therefore suggest that the intestinal microbiome may be an important functional trait among these large-bodied consumers.

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<![CDATA[Phylogenetic clustering and rarity imply risk of local species extinction in prospective deep-sea mining areas of the Clarion–Clipperton Fracture Zone]]> https://www.researchpad.co/article/N01777460-8e8b-4c0c-b411-8f7e1d52e262 An understanding of the forces controlling community structure in the deep sea is essential at a time when its pristineness is threatened by polymetallic nodule mining. Because abiotically defined communities are more sensitive to environmental change, we applied occurrence- and phylogeny-based metrics to determine the importance of biotic versus abiotic structuring processes in nematodes, the most abundant invertebrate taxon of the Clarion–Clipperton Fracture Zone (CCFZ), an area targeted for mining. We investigated the prevalence of rarity and the explanatory power of environmental parameters with respect to phylogenetic diversity (PD). We found evidence for aggregation and phylogenetic clustering in nematode amplicon sequence variants (ASVs) and the dominant genus Acantholaimus, indicating the influence of environmental filtering, sympatric speciation, affinity for overlapping habitats and facilitation for community structure. PD was associated with abiotic variables such as total organic carbon, chloroplastic pigments equivalents and/or mud content, explaining up to 57% of the observed variability and providing further support of the prominence of environmental structuring forces. Rarity was high throughout, ranging from 64 to 75% unique ASVs. Communities defined by environmental filtering with a prevalence of rarity in the CCFZ suggest taxa of these nodule-bearing abyssal plains will be especially vulnerable to the risk of extinction brought about by the efforts to extract them.

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<![CDATA[Underwater caustics disrupt prey detection by a reef fish]]> https://www.researchpad.co/article/Nedd18f8c-0807-4d5b-a2ae-88d3646a98e9 Natural habitats contain dynamic elements, such as varying local illumination. Can such features mitigate the salience of organism movement? Dynamic illumination is particularly prevalent in coral reefs, where patterns known as ‘water caustics’ play chaotically in the shallows. In behavioural experiments with a wild-caught reef fish, the Picasso triggerfish (Rhinecanthus aculeatus), we demonstrate that the presence of dynamic water caustics negatively affects the detection of moving prey items, as measured by attack latency, relative to static water caustic controls. Manipulating two further features of water caustics (sharpness and scale) implies that the masking effect should be most effective in shallow water: scenes with fine scale and sharp water caustics induce the longest attack latencies. Due to the direct impact upon foraging efficiency, we expect the presence of dynamic water caustics to influence decisions about habitat choice and foraging by wild prey and predators.

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<![CDATA[Global shifts in mammalian population trends reveal key predictors of virus spillover risk]]> https://www.researchpad.co/article/Ndff64f7e-baec-4f05-b52b-09b447dda302 Emerging infectious diseases in humans are frequently caused by pathogens originating from animal hosts, and zoonotic disease outbreaks present a major challenge to global health. To investigate drivers of virus spillover, we evaluated the number of viruses mammalian species have shared with humans. We discovered that the number of zoonotic viruses detected in mammalian species scales positively with global species abundance, suggesting that virus transmission risk has been highest from animal species that have increased in abundance and even expanded their range by adapting to human-dominated landscapes. Domesticated species, primates and bats were identified as having more zoonotic viruses than other species. Among threatened wildlife species, those with population reductions owing to exploitation and loss of habitat shared more viruses with humans. Exploitation of wildlife through hunting and trade facilitates close contact between wildlife and humans, and our findings provide further evidence that exploitation, as well as anthropogenic activities that have caused losses in wildlife habitat quality, have increased opportunities for animal–human interactions and facilitated zoonotic disease transmission. Our study provides new evidence for assessing spillover risk from mammalian species and highlights convergent processes whereby the causes of wildlife population declines have facilitated the transmission of animal viruses to humans.

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<![CDATA[What makes a pair bond in a Neotropical primate: female and male contributions]]> https://www.researchpad.co/article/N83ea953f-5c33-488f-a14d-34442f3aac35

Pair living and pair bonding are rare in mammals, and the mechanisms of their maintenance remain a puzzle. Titi monkeys, a ‘textbook example’ for ‘monogamous’ primates, have strong pair bonds and extensive male care. To investigate mechanisms of pair-bond maintenance, we studied seven wild groups of red titis (Plecturocebus cupreus) in Peruvian Amazonia over a period of 14 months. We analysed pair bonds by measuring proximity, grooming and approaches/leaves within pairs, and collected data on intergroup encounters. Females contributed to grooming more than males, especially during infant dependency, when most of the grooming within pairs was done by females. Females were also more active in controlling proximity between pair mates, making most of the approaches and leaves. Males, on the other hand, invested more in territorial defences. They participated in more intergroup encounters than females and were more active during these encounters. Our data is most consistent with the ‘male-services’ hypothesis for pair-bond maintenance, where a female contributes more to the proximity and affiliation maintenance while a male provides beneficial services.

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<![CDATA[An experimental approach to evaluate the potential of drones in terrestrial mammal research: a gregarious ungulate as a study model]]> https://www.researchpad.co/article/N5745988f-3513-4c72-b094-70620994866c

Research on the use of unmanned aircraft systems (UAS) in wildlife has made remarkable progress recently. Few studies to date have experimentally evaluated the effect of UAS on animals and have usually focused primarily on aquatic fauna. In terrestrial open arid ecosystems, with relatively good visibility to detect animals but little environmental noise, there should be a trade-off between flying the UAS at high height above ground level (AGL) to limit the disturbance of animals and flying low enough to maintain count precision. In addition, body size or social aggregation of species can also affect the ability to detect animals from the air and their response to the UAS approach. To address this gap, we used a gregarious ungulate, the guanaco (Lama guanicoe), as a study model. Based on three types of experimental flights, we demonstrated that (i) the likelihood of miscounting guanacos in images increases with UAS height, but only for offspring and (ii) higher height AGL and lower UAS speed reduce disturbance, except for large groups, which always reacted. Our results call into question mostly indirect and observational previous evidence that terrestrial mammals are more tolerant to UAS than other species and highlight the need for experimental and species-specific studies before using UAS methods.

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<![CDATA[An atypical mating system in a neotropical manakin]]> https://www.researchpad.co/article/N3f9e6cbc-e8a0-42c4-bf6d-f36b51f0c46c

Most of the diversity in the mating systems of birds and other animals comes at higher taxonomic levels, such as across orders. Although divergent selective pressures should lead to animal mating systems that diverge sharply from those of close relatives, opportunities to examine the importance of such processes are scarce. We addressed this issue using the Araripe manakin (Antilophia bokermanni), a species endemic to a forest enclave surrounded by xeric shrublands in Brazil. Most manakins exhibit polygynous lekking mating systems that lack territoriality but exhibit strong sexual selection. In sharp contrast, we found that male Araripe manakins defended exclusive territories, and females nested within male territories. However, territoriality and offspring paternity were dissociated: males sired only 7% of nestlings from the nests within their territories and non-territorial males sired numerous nestlings. Moreover, female polyandry was widespread, with most broods exhibiting mixed paternity. Apparently, territories in this species function differently from both lekking arenas and resource-based territories of socially monogamous species. The unexpected territoriality of Araripe manakins and its dissociation from paternity is a unique evolutionary development within the manakin clade. Collectively, our findings underscore how divergences in mating systems might evolve based on selective pressures from novel environmental contexts.

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<![CDATA[Limited thermal plasticity and geographical divergence in the ovipositor of Drosophila suzukii]]> https://www.researchpad.co/article/Nf42216b8-039f-48a2-bf6a-eb018e9931d0

Phenotypic plasticity has been repeatedly suggested to facilitate adaptation to new environmental conditions, as in invasions. Here, we investigate this possibility by focusing on the worldwide invasion of Drosophila suzukii: an invasive species that has rapidly colonized all continents over the last decade. This species is characterized by a highly developed ovipositor, allowing females to lay eggs through the skin of ripe fruits. Using a novel approach based on the combined use of scanning electron microscopy and photogrammetry, we quantified the ovipositor size and three-dimensional shape, contrasting invasive and native populations raised at three different developmental temperatures. We found a small but significant effect of temperature and geographical origin on the ovipositor shape, showing the occurrence of both geographical differentiation and plasticity to temperature. The shape reaction norms are in turn strikingly similar among populations, suggesting very little difference in shape plasticity among invasive and native populations, and therefore rejecting the hypothesis of a particular role for the plasticity of the ovipositor in the invasion success. Overall, the ovipositor shape seems to be a fairly robust trait, indicative of stabilizing selection. The large performance spectrum rather than the flexibility of the ovipositor would thus contribute to the success of D. suzukii worldwide invasion.

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<![CDATA[Functional differences in seasonally absorbed nitrogen in a winter-green perennial herb]]> https://www.researchpad.co/article/N929b15d8-b308-4438-95e8-3d0d03661e0f

Nitrogen (N) uptake in response to its availability and effective N-use are important for determining plant fitness, as N is a major limiting resource and its availability changes both seasonally and annually. Storage organs such as bulbs are considered an adaptive trait with respect to plant N-use strategies. It is well known that N is remobilized from storage organs to satisfy the high demand for new growth that is not completely satisfied by external uptake alone. However, little is known about how this N absorbed during different seasons contributes to plant performance. By manipulating seasonal N availability in potted Lycoris radiata var. radiata (Amaryllidaceae), a winter-green perennial, we found that the N absorbed during different seasons had different effects on leaf growth and leaf N concentrations, effectively increasing the growth and survival of the plants. N absorbed during the summer (leafless period; N was thus stored in the bulb) enhanced plant growth by increasing leaf growth. Compared with the plants supplied with N during autumn (leaf flush period), the leafy plants also showed greater growth per unit leaf area despite the lower area-based photosynthetic capacity of the latter. By contrast, N absorbed during the autumn increased the leaf N concentration and thus the photosynthetic capacity, which was considered to enhance survival and growth of the plant during winter by reducing the potentially fatal risk caused by the absorption of photons under low temperature. Our findings have important implications for estimating plant responses to environmental changes. We predict that changes in seasonal N availability impact the performance of plants, even that of perennials that have large storage organs, via an altered relative investment of N into different functions.

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<![CDATA[Parasite diversity and ecology in a model species, the guppy (Poecilia reticulata) in Trinidad]]> https://www.researchpad.co/article/N5822ac7a-9048-4d5a-bf46-3a73d89eebf9

The guppy (Poecilia reticulata) is a model species in ecology and evolution. Many studies have examined effects of predators on guppy behaviour, reproduction, survival strategies, feeding and other life-history traits, but few have studied variation in their parasite diversity. We surveyed parasites of 18 Trinidadian populations of guppy, to provide insight on the geographical mosaic of parasite variability, which may act as a source of natural selection acting on guppies. We found 21 parasite species, including five new records for Trinidad. Spatial variation in parasite diversity was significantly higher than that of piscine predators, and significant variation in parasite richness among individuals and populations was correlated with: (i) host size, (ii) snail species richness, and (iii) the distance between populations. Differences in parasite species richness are likely to play an important, yet underestimated role in the biology of this model species of vertebrate ecology and evolution.

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<![CDATA[Field assessment of behavioural responses of southern stingrays (Hypanus americanus) to acoustic stimuli]]> https://www.researchpad.co/article/Nae95d22c-f704-412e-9ad7-93e2cb0e14f4

The ability of elasmobranchs to detect and use sound cues has been heavily debated in previous research and has only recently received revived attention. To properly understand the importance of sound to elasmobranchs, assessing their responses to acoustic stimuli in a field setting is vital. Here, we establish a behavioural audiogram of free-swimming male and female southern stingrays (Hypanus americanus) exposed to low-frequency tones. We demonstrate that female stingrays exposed to tones (50–500 Hz) exhibit significant changes in swimming behaviours (increased time spent swimming, decreased rest time, increased surface breaches and increased side swimming with pectoral flapping) at 140 dB re 1 µPa (−2.08 to −2.40 dB re 1 m s−2) while males exposed to the same tones did not exhibit a change in these behaviours until 160 dB re 1 µPa (−1.13 to −1.21 dB re 1 m s−2). Our results are the first demonstration of field responses to sound in the Batoidea and show a distinct sensitivity to low-frequency acoustic inputs.

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<![CDATA[Spatial heterogeneity of the shorebird gastrointestinal microbiome]]> https://www.researchpad.co/article/N8a8feae3-4d3d-4f89-a789-641d12d54567

The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestine. To understand birds as hosts of microbial ecosystems, we characterized the microbial communities in six sections of the GIT of two shorebird species, the Dunlin and Semipalmated Sandpiper, identified potential host species effects on the GIT microbiome and used microbial source tracking to determine microbial origin throughout the GIT. The upper three GIT sections had higher alpha diversity and genus richness compared to the lower sections, and microbial communities in the upper GIT showed no clustering. The proventriculus and gizzard microbiomes primarily originated from upstream sections, while the majority of the large intestine microbiome originated from the caeca. The heterogeneity of the GIT sections shown in our study urges caution in equating data from faeces or a single GIT component to the entire GIT microbiome but confirms that ecologically similar species may share many attributes in GIT microbiomes.

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<![CDATA[Individual-based model of juvenile eel movement parametrized with computational fluid dynamics-derived flow fields informs improved fish pass design]]> https://www.researchpad.co/article/N5d440b70-3c15-487a-b956-3c6ff4f8e7b6

European eel populations have declined markedly in recent decades, caused in part by in-stream barriers, such as weirs and pumping stations, which disrupt the upstream migration of juvenile eels, or elvers, into rivers. Eel passes, narrow sloping channels lined with substrata that enable elvers to ascend, are one way to mitigate against these barriers. Currently, studded eel tiles are a popular substrate. This study is the first to evaluate the flow fields within studded eel tiles and to model the swimming performance of elvers using cellular automata (CA) and individual- (or agent-) based models. Velocities and flow depths predicted by a computational fluid dynamics model of studded eel tiles are first validated against published values for a single installation angle–discharge combination. The validated model is then used to compute three-dimensional flow fields for eel passes at five different installation angles and three inflow discharges. CA and individual-based models are employed to assess upstream passage efficiency for a range of elver sizes. The individual-based model approximates measured passage efficiencies better than the CA model. Passage efficiency is greatest for shallow slopes, low discharges and large elvers. Results are synthesized into an easy-to-understand graphic to help practitioners improve eel pass designs.

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<![CDATA[Extinction debt in local habitats: quantifying the roles of random drift, immigration and emigration]]> https://www.researchpad.co/article/Nbae7afa5-fad1-4203-8c7c-4653b8f5da69

We developed a time-dependent stochastic neutral model for predicting diverse temporal trajectories of biodiversity change in response to ecological disturbance (i.e. habitat destruction) and dispersal dynamic (i.e. emigration and immigration). The model is general and predicts how transition behaviours of extinction may accumulate according to a different combination of random drift, immigration rate, emigration rate and the degree of habitat destruction. We show that immigration, emigration, the areal size of the destroyed habitat and initial species abundance distribution (SAD) can impact the total biodiversity loss in an intact local area. Among these, the SAD plays the most deterministic role, as it directly determines the initial species richness in the local target area. By contrast, immigration was found to slow down total biodiversity loss and can drive the emergence of species credits (i.e. a gain of species) over time. However, the emigration process would increase the extinction risk of species and accelerate biodiversity loss. Finally but notably, we found that a shift in the emigration rate after a habitat destruction event may be a new mechanism to generate species credits.

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<![CDATA[A framework for experimental scenarios of global change in marine systems using coral reefs as a case study]]> https://www.researchpad.co/article/N4ce00ac2-4865-4800-ae4b-da305104e125

Understanding the consequences of rising CO2 and warming on marine ecosystems is a pressing issue in ecology. Manipulative experiments that assess responses of biota to future ocean warming and acidification conditions form a necessary basis for expectations on how marine taxa may respond. Although designing experiments in the context of local variability is most appropriate, local temperature and CO2 characteristics are often unknown as such measures necessitate significant resources, and even less is known about local future scenarios. To help address these issues, we summarize current uncertainties in CO2 emission trajectories and climate sensitivity, examine region-specific changes in the ocean, and present a straightforward global framework to guide experimental designs. We advocate for the inclusion of multiple plausible future scenarios of predicted levels of ocean warming and acidification in forthcoming experimental research. Growing a robust experimental base is crucial to understanding the prospect form and function of marine ecosystems in the Anthropocene.

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<![CDATA[Burrowing detritivores regulate nutrient cycling in a desert ecosystem]]> https://www.researchpad.co/article/N5b0c604a-06ed-46e0-8d20-cc32ec50d55f

Nutrient cycling in most terrestrial ecosystems is controlled by moisture-dependent decomposer activity. In arid ecosystems, plant litter cycling exceeds rates predicted based on precipitation amounts, suggesting that additional factors are involved. Attempts to reveal these factors have focused on abiotic degradation, soil–litter mixing and alternative moisture sources. Our aim was to explore an additional hypothesis that macro-detritivores control litter cycling in deserts. We quantified the role different organisms play in clearing plant detritus from the desert surface, using litter baskets with different mesh sizes that allow selective entry of micro-, meso- or macrofauna. We also measured soil nutrient concentrations in increasing distances from the burrows of a highly abundant macro-detritivore, the desert isopod Hemilepistus reaumuri. Macro-detritivores controlled the clearing of plant litter in our field site. The highest rates of litter removal were measured during the hot and dry summer when isopod activity peaks and microbial activity is minimal. We also found substantial enrichment of inorganic nitrogen and phosphorous near isopod burrows. We conclude that burrowing macro-detritivores are important regulators of litter cycling in this arid ecosystem, providing a plausible general mechanism that explains the unexpectedly high rates of plant litter cycling in deserts.

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<![CDATA[New application of strontium isotopes reveals evidence of limited migratory behaviour in Late Cretaceous hadrosaurs]]> https://www.researchpad.co/article/Nb9091ab0-5d82-4a73-8c59-6c096c056520

Dinosaur migration patterns are very difficult to determine, often relying solely on the geographical distribution of fossils. Unfortunately, it is generally not possible to determine if a fossil taxon's geographical distribution is the result of migration or simply a wide distribution. Whereas some attempts have been made to use isotopic systems to determine migratory patterns in dinosaurs, these methods have yet to achieve wider usage in the study of dinosaur ecology. Here, we have used strontium isotope ratios from fossil enamel to reconstruct the movements of an individual hadrosaur from Dinosaur Provincial Park in Alberta, Canada. Results from this study are consistent with a range or migratory pattern between Dinosaur Provincial Park and a contemporaneous locality in the South Saskatchewan River area, Alberta, Canada. This represents a minimum distance of approximately 80 km, which is consistent with migrations seen in modern elephants. These results suggest the continent-wide distribution of some hadrosaur species in the Late Cretaceous of North America is not the result of extremely long-range migratory behaviours.

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<![CDATA[Effects of niche overlap on coexistence, fixation and invasion in a population of two interacting species]]> https://www.researchpad.co/article/N7d27642e-fda8-4f63-a458-0c8771ec3304

Synergistic and antagonistic interactions in multi-species populations—such as resource sharing and competition—result in remarkably diverse behaviours in populations of interacting cells, such as in soil or human microbiomes, or clonal competition in cancer. The degree of inter- and intra-specific interaction can often be quantified through the notion of an ecological ‘niche’. Typically, weakly interacting species that occupy largely distinct niches result in stable mixed populations, while strong interactions and competition for the same niche result in rapid extinctions of some species and fixations of others. We investigate the transition of a deterministically stable mixed population to a stochasticity-induced fixation as a function of the niche overlap between the two species. We also investigate the effect of the niche overlap on the population stability with respect to external invasions. Our results have important implications for a number of experimental systems.

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