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PubMed2025

The role of stochasticity in fungal community assembly: explaining apparent stochasticity with field experiments.

Stochasticity is a main process in community assembly. However, experimental studies rarely target stochasticity in natural communities, and hence experimental validation of stochasticity estimates in observational studies is lacking. Here, we combine experimental and observational data to unravel the role of stochasticity in the assembly of wood-inhabiting fungi. We carried out a replicated field experiment where the natural colonization of a focal fungal species was simulated through inoculation, and the local fungal communities were monitored through DNA metabarcoding before and after the inoculations. The amount of stochasticity in fungal colonization was less pronounced than expected from the amount of unpredictability in observational data, suggesting that stochasticity may play a smaller role in fungal occurrence than previously anticipated, or that it may be a stronger influence in the dispersal and establishment phases than in colonization per se. Stochasticity was more prominent in the initial phase of community succession, with the earliest successional stage involving a higher level of stochasticity than the later stage after 2 years. We conclude that experimentally measuring the role of stochasticity in community assembly is feasible for species-rich communities under natural conditions and highlight the importance of experimentally testing the accuracy of stochasticity estimates based on observational data.

Stochastic Processes↗
PubMed2026

Reproduction on the Rocks: Life History of a Freshwater Macrobioeroding Bivalve.

Macrobioerosion, the excavation and removal of consolidated mineral substrates by macrofauna, is well established in marine systems, where macrobioeroders drive carbonate cycling, sediment production and habitat formation. In freshwater ecosystems, however, it has been documented in only a small number of invertebrate taxa and remains a poorly resolved ecological process. Among these, the teredinid shipworm Lithoredo abatanica represents a remarkable departure from the wood-boring ecology of its family, having evolved to excavate and ingest limestone in fresh water. Despite this remarkable ecological transition, its reproductive biology and life history remain unknown. Here, we investigate the reproductive mode and life history strategy of this species using population size structure, in&#xa0;situ observations of siphonal morphology, and sperm morphometrics. We show that L.&#x2009;abatanica reaches exceptional dimensions, with measured body lengths exceeding 100&#x2009;mm, one intact empty burrow exceeding 200&#x2009;mm and in-water observations indicating burrows possibly exceeding 500&#x2009;mm, establishing it as the largest known freshwater macrobioeroder. Its large size and dense aggregations indicate considerable capacity for local rock breakdown and habitat modification within the Abatan River system (Bohol, Philippines). Recently settled juveniles (<&#x2009;10&#x2009;mm) alongside reproductively mature individuals indicate ongoing recruitment. The morphology of the siphons and calcareous tube appears to preclude direct sperm transfer via pseudocopulation, while sperm morphometrics are consistent with external fertilisation. Together, these findings indicate that L.&#x2009;abatanica reproduces via broadcast spawning with external fertilisation and likely possesses a planktotrophic larval phase. This raises a fundamental question: how does a broadcast-spawning species with planktotrophic larvae maintain populations up to 15&#x2009;km upstream in a flowing freshwater river subject to persistent downstream advection? By resolving the life history of the largest known freshwater macrobioeroder, this study provides critical insight into the persistence, dispersal and ecological role of a globally unique riverine ecosystem engineer.

broadcast spawning↗
PubMed1992

Surveillance and control of emerging zoonoses.

"Emerging zoonoses" are defined as zoonotic diseases caused either by apparently new agents, or by previously known microorganisms, appearing in places or in species in which the disease was previously unknown. New animal diseases with an unknown host spectrum are also included in this definition. Natural animal reservoirs represent a more frequent source of new agents of human disease than the sudden appearance of a completely new agent. Factors explaining the emergence of a zoonotic or potentially zoonotic disease are usually complex, involving mechanisms at the molecular level, such as genetic drift and shift, and modification of the immunological status of individuals and populations. Social and ecological conditions influencing population growth and movement, food habits, the environment and many other factors may play a more important role than changes at the molecular level. Diseases associated with changing farming practices, trade and consumer habits. Bacterial enteric diseases due to Salmonella enteritidis and Echerichia coli 0:157 are examples of diseases associated with changing farming practices and consumer habits. The increasing trade in live animals for animal production and research led to the introduction of the New World screwworm to the Libyan Arab Jamahiriya in 1989 and an Ebola-like virus in monkeys in quarantine facilities in the United States of America. The development of the epidemics of bovine spongiform encephalopathy (BSE) in the United Kingdom is due to multiple factors including the increasing use of ruminant proteins as feed for animals. Diseases associated with changing environmental conditions which influence reservoirs, vectors and/or victim species population parameters.(ABSTRACT TRUNCATED AT 250 WORDS)

Adaptation, Biological↗
PubMed2026

A guide to understanding tumour evolution through the lens of population genetics.

Every cancer carries the history of its own evolution, hidden in its genome. Modern DNA&#xa0;sequencing can catalogue millions of mutations and profile tumours across space and time, but sequencing alone struggles to answer the questions that matter most: when did key adaptations emerge, how strongly were they selected, why do some tumours relapse whereas others do not, and&#xa0;how will the cancer evolve next? The reason is fundamental: sequencing&#xa0;is a snapshot, whereas evolution is a dynamic process. Bridging this gap requires moving beyond descriptive cancer genomics towards quantitative evolutionary inference. In this Review, we argue that population genetics provides the mathematical framework needed to extract evolutionary dynamics from cancer genomes. We show how models of mutation, selection and drift transform allele frequencies from descriptive measurements into quantitative estimates of clonal fitness and evolutionary timings. We discuss how these principles extend to epigenetic inheritance, plasticity and ecological interactions within the tumour ecosystem, and examine the assumptions and limitations for their application to modern sequencing data. By reframing cancer genomes as quantitative records of evolutionary processes rather than catalogues of mutations, researchers have used population genetics to provide a foundation for understanding - and ultimately predicting - the trajectories of cancer evolution.

Journal Article↗
PubMed1976

Influenza: its antigenic variation and ecology.

Influenza viruses have two surface antigens, the glycoprotein structures hemagglutinin (HA) and neuraminidase (NA). Antibodies to each of these are associated with immunity, but the structures themselves are antigenically variable. When an antigenic change is gradual over time it is referred to as a drift, while a sudden complete or major change in either or both antigens is termed a shift. The mechanism of antigenic drift is usually attributed to selection of preexisting mutants by pressure from increasing immunity in the human population. The mechanism of antigenic shift is less clear, but one tentative hypothesis is that shifts arise from mammalian or avian reservoirs, or through genetic recombination of human and animal influenza strains.

Animals↗
PubMed1976

Population genetics and molecular evoulution.

Recent studies of evolution and polymorphism at the molecular level (i.e, at the level of internal structure of the gene) have brought many puzzling as well as enlightening results. It appears that, in addition to natural selection, chance (in the form of random gene frequency drift) is playing a much larger part than previously considered. Futhermore, natural selection is likely to be based more directly on the secondary and the higher order structure of informational macromolecules rather than ecological conditions, usually in the form of negative selection. In this respect, there is growing evidence suggesting that very slightly deleterious mutations whose selective disadvantages are not excessively large as compared with the mutation rates are playing a significant role in variation and evoulution at the molecular level.

Alleles↗
PubMed2024

Rapid vertebrate speciation via isolation, bottlenecks, and drift.

Speciation is often driven by selective processes like those associated with viability, mate choice, or local adaptation, and "speciation genes" have been identified in many eukaryotic lineages. In contrast, neutral processes are rarely considered as the primary drivers of speciation, especially over short evolutionary timeframes. Here, we describe a rapid vertebrate speciation event driven primarily by genetic drift. The White Sands pupfish (Cyprinodon tularosa) is endemic to New Mexico's Tularosa Basin where the species is currently managed as two Evolutionarily significant units (ESUs) and is of international conservation concern (Endangered). Whole-genome resequencing data from each ESU showed remarkably high and uniform levels of differentiation across the entire genome (global FST &#x2248; 0.40). Despite inhabiting ecologically dissimilar springs and streams, our whole-genome analysis revealed no discrete islands of divergence indicative of strong selection, even when we focused on an array of candidate genes. Demographic modeling of the joint allele frequency spectrum indicates the two ESUs split only ~4 to 5 kya and that both ESUs have undergone major bottlenecks within the last 2.5 millennia. Our results indicate the genome-wide disparities between the two ESUs are not driven by divergent selection but by neutral drift due to small population sizes, geographic isolation, and repeated bottlenecks. While rapid speciation is often driven by natural or sexual selection, here we show that isolation and drift have led to speciation within a few thousand generations. We discuss these evolutionary insights in light of the conservation management challenges they pose.

Animals↗
PubMed2025

Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series.

MOTIVATION: The lineage dynamics and history of cells in a population reflect the interplay of evolutionary forces they experience, including mutation, drift, and selection. When the population is polyclonal, lineage dynamics also manifest the extent of clonal competition among co-existing mutational variants. If the population exists in a community of other species, the lineage dynamics could also reflect the population's ecological interaction with the rest of the community. Recent advances in high-resolution lineage tracking via DNA barcoding, coupled with next-generation sequencing of bacteria, yeast, and mammalian cells, allow for precise quantification of clonal dynamics in these organisms. RESULTS: In this work, we introduce Doblin, an R suite for identifying dominant barcode lineages based on high-resolution lineage tracking data. We first benchmarked Doblin's accuracy using lineage data from evolutionary simulations, showing that it recovers the clones' identity and relative fitness in the simulation. Next, we applied Doblin to analyze clonal dynamics in laboratory evolutions of Escherichia coli populations undergoing antibiotic treatment and in colonization experiments of the gut microbial community. Doblin's versatility allows it to be applied to lineage time-series data across different experimental setups. AVAILABILITY AND IMPLEMENTATION: Doblin is available on CRAN (https://CRAN.R-project.org/package=doblin) and Github (https://github.com/dagagf/doblin).

DNA Barcoding, Taxonomic↗
PubMed2024

Environmental stress mediates groundwater microbial community assembly.

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

Phylogeny↗
PubMed1977

Where did our infectious diseases come from? The evolution of infectious disease.

Infectious diseases have been evolving from the earliest days of life on earth. Major factors influencing their developments include the splitting of continents (continental drift), the radiation of early primates into present-day forms, migrations of man around the world, the ending of the Ice Age, the invention of agriculture, the domestication of animals, the increase in populations, and the urbanization of societies. The impact of such basic changes on infectious diseases is reviewed.

Agriculture↗
PubMed2014

Serial founder effects and genetic differentiation during worldwide range expansion of monarch butterflies.

Range expansions can result in founder effects, increasing genetic differentiation between expanding populations and reducing genetic diversity along the expansion front. However, few studies have addressed these effects in long-distance migratory species, for which high dispersal ability might counter the effects of genetic drift. Monarchs (Danaus plexippus) are best known for undertaking a long-distance annual migration in North America, but have also dispersed around the world to form populations that do not migrate or travel only short distances. Here, we used microsatellite markers to assess genetic differentiation among 18 monarch populations and to determine worldwide colonization routes. Our results indicate that North American monarch populations connected by land show limited differentiation, probably because of the monarch's ability to migrate long distances. Conversely, we found high genetic differentiation between populations separated by large bodies of water. Moreover, we show evidence for serial founder effects across the Pacific, suggesting stepwise dispersal from a North American origin. These findings demonstrate that genetic drift played a major role in shaping allele frequencies and created genetic differentiation among newly formed populations. Thus, range expansion can give rise to genetic differentiation and declines in genetic diversity, even in highly mobile species.

Animal Distribution↗
PubMed1976

A contribution to the study of linkage disequilibrium in Drosophila melanogaster.

Linkage disequilibrium was detected in 12 out of 30 cases involivng gene alleles and inversions in three cage populations and in a natural population of Drosophila melanogaster from Greece. The cage populations possessed practically the same gene pool at their origin and were maintained simultaneously under the effects of the ecological factors "food medium" and "humidity". It is dicussed that the correlation of the same direction found between the frequencies of nonallelic elements of Adh locus and In (2L) 22D-34A or In (2R)52A-56F in such different populations as American, Japanese (Mukai et al;, 1971, 1974; Langley et al., 1974) and Greek, as well as cage populations under different environmental conditions, could be attributed to the effect of epistatic selection. Moreover, it seems that the In(2L)22D-34A has a tendency to interact genetically with the alpha-Gpdh locus, particularly when the populations are maintained under crowding conditions. However, further data are needed to assess whether other cases of the observed nonrandom associations can be better explained as transient associations generated by random drift, or as the result of epistatic selection.

Alcohol Oxidoreductases↗
PubMed2025

The distribution of fitness effects varies phylogenetically across animals.

The distribution of fitness effects (DFE) describes the selection coefficients () of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (), and the proportion of new beneficial mutations (). These findings align with Fisher's Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGM's predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals.

Fisher&#x2019;s geometric model↗
PubMed1976

Darwin's finches: population variation and natural selection.

Van Valen's model, which relates morphological variation to ecological variation in an adaptive scheme, was investigated with individually marked and measured Darwin's finches on two adjacent Galápagos islands, Santa Cruz and Daphne Major. Results show that environmental heterogeneity is correlated with large continuous, morphological variation: variation in bill dimensions of Geospiza fortis is greater on Santa Cruz than on Daphne, as is environmental heterogeneity. Within populations of this species, different phenotypes distribute themselves in different habitat patches, select foods of different sizes and hardness, and exploit them with efficiencies that are phenotype- (bill size) dependent. These data constitute indirect evidence that natural selection has a controlling influence over the level of phenotypic variation exhibited by a population. Further evidence is that phenotypes did not survive equally well during the study period; on Daphne island G. fortis was apparently subjected to directional selection on bill tip length and G. scandens to normalizing selection on body weight and bill depth. Other factors which may have contributed to the establishment of a difference in variation between Santa Cruz and Daphne populations are the founder effect, genetic drift, and assortative mating. Annual climatic unpredictability is considered a source of environmental heterogeneity which, through its effect upon food supply, favors large morphological variation. It is predicted that species of large individual size are more influenced by this than are small species, and consequently exhibit greater size-corrected variation. The prediction is tested with data from six Geospiza species, and found to be correct.

Adaptation, Biological↗
PubMed1975

Conditions for the existence of clines.

A very general partial differential equation in space and time satisfied by the gene frequency in a monoecious population distributed continuously over an arbitrary habitat is derived. The treatment is restricted to a single diallelic locus in the absence of mutation and random drift, and it is supposed that time is continuous, births and deaths occur at random, and migration is independent of genotype. With the further assumptions that migration is isotropic and homogeneous, the population density is constant and uniform (as permitted by the population regulation mechanism included in the formulation), and Hardy-Weinberg proportions obtain locally, this partial differential equation reduces to the simplest multidimensional generalization of the classical Fisher-Haldane cline model. The efficacy of migration and selection in maintaining genetic variability at equilibrium in this model is investigated by deducing conditions for the existence of clines under various circumstances. The effects of the degree of dominance, a neutral belt between the regions where a particular allele is advantageous and deleterious, finiteness of the habitat, and habitat dimensionality are evaluated. Provided at least one of the alleles is favored only in a finite region, excluding the special case in which its total effective selective coefficient is zero, if conditions for supporting a cline are too unfavorable because migration is too strong, selection is too weak, or both, a cline cannot exist at all. Thus, unless there is overdominance, the population must be monomorphic. It is possible for a cline which can barely exist under the prevailing ecological circumstances to show a large amount of variation in gene frequency.

Alleles↗
PubMed1992

Fate and effects of the insecticide Dursban 4E in indoor Elodea-dominated and macrophyte-free freshwater model ecosystems: I. Fate and primary effects of the active ingredient chlorpyrifos.

The fate of the insecticide Dursban 4E (active ingredient chlorpyrifos) and its effect on crustaceans and insects was studied in indoor experimental freshwater ecosystems that intended to mimick drainage ditches. A single dose (simulating aerial drift) was applied to achieve nominal chlorpyrifos concentrations of 5 or 35 micrograms/L. Two experiments were performed, one in which all model ecosystems were dominated by the macrophyte Elodea nuttallii, and one using systems devoid of macrophytes. In macrophyte-dominated systems, Elodea vegetation adsorbed a large proportion of the dose applied and hampered the mixing of the insecticide in the water (at least up till day 8). Only a small proportion became incorporated in the sediment. In open water systems the insecticide was rapidly mixed in the water, and the sediment played a very significant role as sink for chlorpyrifos. In both Elodea-dominated and open water systems 50% of the dose applied had disappeared on day 8 post-treatment. The rate of disappearance of chlorpyrifos was relatively rapid in water and macrophytes, and relatively slow in the sediment. Of the arthropods in the zooplankton Cladocera were more susceptible than Copepoda. Significant effects (p less than or equal to 0.05) on Cladocera occurred relatively late in Elodea-dominated systems (in week 4 post-application) in contrast to open water systems (week 1), which is in accordance with the observed differences in the fate of chlorpyrifos. Daphnia pulex, D. longispina and Simocephalus vetulus recovered in the model ecosystems when chlorpyrifos concentrations were lower than 0.1-0.2 micrograms/L, which is in agreement with results of laboratory protocol tests performed with these cladocerans. Among the macroscopic Arthropoda the apparent order of susceptibility was amphipods greater than insects greater than isopods. The isopod Asellus aquaticus was more sensitive to the application of the insecticide than the closely related species Proasellus coxalis. In treated open water systems the latter even increased significantly in numbers. Cage experiments in the model ecosystems performed with several species of Arthropoda indicate that laboratory protocol tests may give a reasonable prediction of short-term direct effects of chlorpyrifos for the same species inhabiting more complex aquatic systems.

Animals↗