Ecology

The goal of ecology is to explain where organisms live, how many there are, and how their interactions with one another and their surroundings change those patterns. Living partners include prey, predators and parasites; nonliving conditions include light, temperature and water. An ecosystem brings these interacting parts into one study system. See Clark, Douglas and Choi, Biology 2e, 44.1: the scope of ecology.

Start with an invented aquatic food web: photosynthetic algae feed zooplankton, which feed small fish, which feed large fish. That food chain has four feeding positions and three feeding arrows. Dead material also reaches decomposers through detritus, so the food web branches rather than forming a single ladder.

The appeal of ecology is that an organism's surroundings include other organisms that change those surroundings. Photosynthesis links light to living material; predation transfers that material between organisms; decomposers return its constituent chemical elements to forms that can be used again. These connections help explain why changing one part of an ecosystem can affect distant parts of its food web, although an arrow alone does not predict the size or even the direction of an indirect change. Population dynamics supplies quantitative tools when the question concerns changing counts.

In 1866, Ernst Haeckel's Generelle Morphologie der Organismen included a section titled Oecologie und Chorologie in volume 2, beginning on page 286. This places the terminology of ecology in an early systematic treatment of organisms and their relationships. See Haeckel, Generelle Morphologie der Organismen, volume 2 (1866), contents and p. 286. A later quantitative landmark is Raymond L. Lindeman's 1942 treatment of ecosystems through feeding relationships and energy flow. See Lindeman, The Trophic-Dynamic Aspect of Ecology, Ecology 23 (1942), 399–417.

The mass of living material in a stated system or volume. Dry mass, organic carbon and pigment proxies are distinct measures and require stated conversion assumptions.

Formation of biomass from inorganic carbon, using light or chemical free energy.

Increase in the concentration of some substances along feeding relationships between successive trophic levels. It depends on uptake, transfer and elimination and is not a universal property of all chemicals.

Increase of a substance within an organism when uptake from its surroundings and food exceeds elimination. This is distinct from biomagnification across a food chain.

Introduction of substances or other agents that cause harmful environmental change; the relevant effect depends on the agent, exposure and system.

A substance or other agent contributing to pollution. Its effect cannot generally be inferred from the human biological population alone.

Conversion of molecular nitrogen into biologically accessible reduced nitrogen. Symbiotic fixation costs energy and must be distinguished from nitrate uptake.

Reduction in detection through resemblance to the visual or other sensory background. It is distinct from recognition as a defended organism after detection.

Acceptability of an item as food to a specified consumer. Chemical concentration, willingness to attack, willingness to swallow and subsequent illness are different measurements.

Complete removal of a target population from a defined area, requiring sustained surveillance to distinguish absence from nondetection.

Measures reducing introduction or spread of organisms through a specified pathway.

Establishment and spread of organisms into a new region, with effects dependent on community context and introduction history.

A species moved by humans beyond its natural geographic range. Introduction is defined relative to location, not only national boundaries.

An introduced species whose establishment and spread cause adverse effects under the specified ecological definition. Presence outside the native range does not alone establish an impact.

Evolutionary divergence associated with interactions between coexisting lineages. Testing it requires alternatives to pre-existing differences and environmental sorting.

Overlap in a stated dimension of resource use or environmental requirements. Similarity of potential resource use is not a direct estimate of its demographic cost.

Differential use of resources by coexisting organisms. It can reduce competition, but does not by itself measure the strength of competition that produced or currently accompanies it.

Movement potentially connecting populations or colonizing habitat. Movement alone is not gene flow: migrants must contribute inherited material to later generations.

Movement between the natal site and the site of reproduction.

Use of metabolites released or supplied by another organism. An initially incidental exchange can become specialized, but cross-feeding alone does not establish reciprocal dependence.

A persistent close association between organisms of different species. Such associations can be mutualistic, commensal or parasitic; symbiosis does not by itself mean mutual benefit.

A root-fungus association with branched fungal exchange structures, arbuscules, within root cortical cells. Nutrient transfer and host carbon allocation are regulated and context-dependent.

A close biological association on which at least one partner depends for persistence or reproduction under the specified conditions. Obligacy does not itself imply mutual benefit, reciprocity or coevolution.

Dependence of interacting organisms on one another’s presence or activities in a specified environment. One-sided reliance should be distinguished from reciprocal dependence.

An interaction providing net benefits to both participants under specified conditions. It need not be obligatory or free of evolutionary conflict.

Conditional resource allocation in which a partner providing more service receives more resource. Reciprocal reward can help stabilize cooperation without guaranteeing equal exchange or universal host control.

A host response reducing the success of an established symbiont that provides less benefit. It differs from exclusion of a partner before association and need not imply conscious choice.

A mutual benefit arising as a consequence of actions favoured for an actor’s own immediate returns. It does not require delayed repayment.

Study of the ecological and evolutionary consequences of animal behaviour.

The number or rate of social or ecological encounters. It differs from the fraction of a particular strategy in a population and from the probability of meeting the same partner again.

A social interaction in which a participant provides a benefit to another; classifications distinguish immediate actor benefits from evolutionary altruism. Group benefit alone does not explain persistence of an individually costly contribution.

A resource or service whose effects can benefit others as well as its producer. The spatial scale of benefits, production cost and competitive setting determine exploitation incentives.

Discrimination among potential or previous partners. Repeat interactions support partner-specific responses only if the relevant information can be retained or reliably associated with a location.

Information about an individual’s past behaviour that can alter its later interactions, including interactions with different partners. Reputation-based explanations require a mechanism for acquiring and using that information.

A mechanism in which helping a persistent partner improves the actor’s later direct returns through that partner’s survival or productivity, without requiring an explicit repayment rule.

Conditional cooperation based on previous interaction with the same partner. Repeated-game support for cooperation depends on encounter continuation, observation and the competing strategies.

Selection of interaction partners in a way that can favour useful contributions through access to future benefits. Its effects depend on available alternatives, information and switching costs.

An interaction in which access to partners and exchange alternatives change the terms of cooperation. Encounter rate and partner availability can have effects different from relationship persistence.

In evolutionary analysis, an action with a direct fitness cost to its actor and a benefit to another. The comparison depends on the specified alternative and timescale.

Biological disturbance and mixing of sediment, including burrowing. It modifies habitats and can destroy or change surfaces that otherwise preserve body impressions and trace fossils.

An interaction in which members of different species reduce one another's access to limiting resources. Shared location or a correlated population decline alone does not prove this mechanism.

A model-specific parameter describing how one population affects another. It cannot be read directly from the distance between skeletal forms.

Division of habitat into smaller or more isolated patches. Effects of changed connectivity must be distinguished from effects of reduced total habitat area.

An organism consuming plant material. Plant-part selection and digestive strategy can differ substantially among herbivores.

Loss of all members of a lineage. Local disappearance is an extirpation and must be distinguished from global extinction, especially when interpreting a regional fossil record.

A delayed future loss of species caused by past environmental change. Habitat loss or fragmentation can leave surviving populations that are not viable in the long term, so present species richness exceeds what the altered system can sustain. The delay provides a potential opportunity for restoration or reconnection before losses are realized.^[ref]

Systematic variation in extinction probability with biological or ecological traits. Associations can change between events and taxonomic levels: geographic range, body size and sexual dimorphism have each been linked to survival differences in particular datasets, but none is a universal predictor across all mass extinctions.

The difference between saturation and actual water-vapour pressure. It quantifies atmospheric drying demand and can increase under warming even when the change in rainfall is small.

Experimental elevation of atmospheric carbon dioxide around vegetation without enclosing it in a chamber. Replicated ambient controls and complete carbon and nutrient budgets are needed to connect photosynthetic responses to net storage.

An atmospheric flux method using covariance of rapid vertical-velocity and concentration fluctuations. Its footprint and transport assumptions matter; the measured exchange is not automatically a complete budget including harvested or dissolved exports.

Variation among living organisms and their biological organization. For ecosystem-function experiments, distinguish the number of species from their identities, relative abundances and functional differences.

The number of species in a defined assemblage or sample. It differs from evenness, abundance and functional diversity; controlled richness experiments need replication of composition to separate these effects.

Variation among species in their responses to environmental change, especially among species contributing similar ecosystem effects. Different responses can support persistence of functions across changing conditions.

A mixture yielding more than its best monoculture comparator under matched conditions. It is stronger evidence against a pure best-species sampling explanation than exceeding a weighted monoculture average, but does not identify the physiological cause.

The component of a biodiversity-effect partition reflecting covariance between monoculture yield and mixture relative-yield change. The name does not imply evolutionary natural selection.^[ref]

The average-relative-yield component of a biodiversity-effect partition. A positive value can arise from resource partitioning, facilitation or other mechanisms and is not uniquely diagnostic of one interaction.^[ref]

The hypothesis that abundant species' traits strongly influence ecosystem processes. It motivates separating effects of dominant-species identity from effects of species interactions or richness.

Differences in ecological use or response that can reduce competition among species. Stable coexistence requires the relevant recovery-when-rare conditions, not merely the observation of different traits.

A measurable characteristic relevant to plant performance or ecological effects. A convenient trait measurement is not automatically a direct assay of lifetime genotype fitness.

A ratio expressing carbon gain or biomass production relative to water use, under a specified measurement convention. Higher leaf-level efficiency does not guarantee greater whole-ecosystem carbon storage.

Mass of wood per specified reference volume, with measurement conventions stated. It can associate with mechanical investment, transport and demographic performance without uniquely determining any one mechanism.

Leaf dry mass divided by leaf area. Its construction-mass meaning must be kept distinct from whole-plant growth rate.

Leaf area per unit dry mass. It is the reciprocal of leaf mass per area when the same tissue and units are used.

Coordinated variation in leaf construction, physiological rates and longevity, contrasting rapid returns with persistent, conservative tissues. Mass-based and area-based measurements differ.^[ref]

A constraint on jointly improving components such as growth, survival and reproduction under specified conditions. Variation in resource acquisition can mask negative relationships arising from allocation.

A biological population is a set of organisms of a species occupying a specified area or experimental setting at a specified time. State the boundary for the question being studied: a flask, a breeding locality, or a wider region connected by gene flow. A biological population need not be perfectly mixed or isolated.

An ecosystem is a system of interacting organisms and their nonliving surroundings. A pond study might include algae, fish, bacteria, water, dissolved chemical compounds and incoming light. The useful step is to state the boundary and time interval: the pond surface, bottom and shoreline might enclose the study region, but water, organisms and energy can cross them. The chosen boundary specifies what counts as internal storage, input or output; it does not make the ecosystem sealed. See Clark, Douglas and Choi, Biology 2e, 46.1: ecosystems and their components.

For a toy pond water budget over one day, begin with $1000{\mathrm{m}}^3$, add $120{\mathrm{m}}^3$ crossing inward, and remove $90{\mathrm{m}}^3$ crossing outward. With all other transfers omitted by assumption, the final amount is $1000+120-90=1030{\mathrm{m}}^3$. The same bookkeeping asks whether a change inside an ecosystem came from internal processes or exchanges with its surroundings. Changing the boundary to include an upstream reservoir changes which transfers are internal, while preserving the accounting.

The difference between gross primary production and both autotrophic and heterotrophic respiration. A full storage budget must additionally account for disturbance and lateral transfers.

Carbon production remaining after subtracting autotrophic respiration from gross primary production. It need not remain stored, because consumers, decomposers and disturbance can return or export carbon.

The amount of carbon held in a specified pool or system. It is a stock, distinct from gross uptake or its rate of net change; large old stocks can coexist with small current fluxes.

Transfer of carbon into storage over a specified time horizon. Net sequestration requires uptake to exceed relevant losses under an explicit boundary; high photosynthesis alone does not establish it.

Maintenance or assessment of multiple ecosystem functions together. Functions can depend on different traits or conflict, so performance in one process cannot stand in for every other process.

A primary producer builds organic chemical compounds from inorganic sources. Photosynthetic algae, plants and cyanobacteria use light energy for this role through photosynthesis and carbon fixation. The role supplies new living material to a food web; it does not mean that the organism creates energy.

A consumer obtains organic material by feeding on other organisms or their products. A consumer feeding on primary producers is a primary consumer; one feeding on primary consumers is a secondary consumer. These names describe positions in a food chain, rather than permanent labels for a species.

A decomposer breaks down dead organic material and absorbs products of that breakdown; many bacteria and fungi perform this role. Decomposers connect detritus from different trophic levels to material recycling, so placing all decomposers at one final step of every food chain is misleading. See Clark, Douglas and Choi, Biology 2e, 46.1: grazing and detrital food webs.

An omnivore feeds on both primary producers and consumers. Its mixed diet explains why a trophic level need not be a whole number or a fixed label throughout an organism's life.

Detritus is nonliving organic material, including dead remains and organic wastes. It is a resource for decomposers, not itself an organism or a predator. In the illustrative food web, the dashed arrow from algae to detritus denotes a material transfer; the solid arrow from detritus to decomposers denotes resource use.

A trophic level describes feeding position relative to primary producers. Assign primary producers level 1; in the illustrated food chain, zooplankton occupy level 2, small fish level 3, and large fish level 4. Following a single feeding path adds one level at each step. The labels make dependence on the initial resource visible, but a branching food web can give an organism several feeding paths. See Clark, Douglas and Choi, Biology 2e, 46.1: feeding positions and branching food webs.

An omnivore can obtain food from more than one trophic level. As an explicitly assumed diet-weighted example, suppose an omnivore gets half its assimilated food energy from level-1 primary producers and half from level-2 consumers. Define its trophic level as one plus the weighted mean level of its food: $1+(1/2)1+(1/2)2=2.5$. This computed position depends on the specified diet and weighting convention; it is not an immutable property of the species. A different life stage or diet can change it.

Energy flow tracks energy entering an ecosystem, passing through organisms and leaving its boundary. To see its quantitative effect, assume net production at one trophic level is $P_1=1000\mathrm{kJ}{\mathrm{m}}^{-2}\mathrm{da}{\mathrm{y}}^{-1}$ and assume a transfer efficiency $\epsilon =0.10$ at each of two successive steps. Here $P_i$ measures the energy incorporated into new living material per unit area per day, after that level's own cellular respiration; it is not a count of organisms or a standing stock. The joule supplies the energy unit, with $1\mathrm{kJ}=1000\mathrm{J}$.

Only $10/1000=0.01$, or one percent, of the initial production reaches level 3 in this toy food chain. The first step leaves $1000-100=900$ and the second $100-10=90$ outside the next level's new production. These differences can include uneaten material, wastes, and energy released as heat during cellular respiration; their separate amounts have not been assigned. Detritus can still carry energy to decomposers. The 10 percent efficiency is an assumption, not a universal law: transfer efficiencies vary with the organisms, food and conditions. The production ratio $P_{i+1}/P_i$ also differs from the fraction of an individual meal converted into growth. See Clark, Douglas and Choi, Biology 2e, 46.2: production and transfer efficiency.

The shrinking budget explains why supporting another trophic level requires enough production below it. It does not prove an exact maximum length for every food chain, particularly when a food web imports resources or has branching diets. Lindeman's 1942 paper grouped feeding relationships into trophic levels, compared transfers and cellular respiration, and emphasized the ecosystem as a unit connecting living and nonliving components. That viewpoint made different organisms comparable through a common energy budget. See Lindeman, The Trophic-Dynamic Aspect of Ecology (1942).

Material recycling and energy flow describe different bookkeeping. Carbon, nitrogen and phosphorus can be reused through chemical reactions and transfers between organisms and their surroundings. Energy transferred as heat is conserved, but is no longer the same store of chemical energy available to a consumer; photosynthetic primary producers need continuing light input. A decomposer helps recycle material and also releases heat through metabolism. Thus loss from one feeding budget means transfer into other forms or routes, never destruction of energy. See Clark, Douglas and Choi, Biology 2e, 46.3: material cycles. Conservation of energy applies to the whole accounting.

Zooplankton are drifting aquatic consumers, including small animals. In the illustrative food web, the chosen zooplankton feed on algae and serve as prey for small fish; this assumed diet is not a claim about every kind of zooplankton.

Phytoplankton are drifting aquatic organisms that carry out photosynthesis, including many algae. They can supply food to zooplankton in an ecosystem.

The standing stock of living phytoplankton, often expressed as carbon mass per water volume. Chlorophyll a is an accessible proxy, but its ratio to carbon is variable.

Endosymbiosis is an ecological association in which one organism, the endosymbiont, lives inside another. The definition specifies location, not that both partners benefit, nor that the internal partner has become an organelle. An intracellular association can remain an association between distinct organisms. Endosymbiotic theory addresses a different question: how particular ancestral bacteria became inherited, functionally integrated organelles during evolution.

The striking consequence is that a eukaryotic biological cell can combine histories: its nuclear lineage and its mitochondria need not have the same ancestry. Mitochondria have bacterial ancestry related to Alphaproteobacteria; the plastids of plants and many algae, including chloroplasts, have ancestry within cyanobacteria. These are ancestral lineages, not a claim that a named living bacterial species is the literal ancestor. Present-day bacteria and organelles have both evolved since their shared ancestors. ^[ref]

An endosymbiont is the internal partner in an endosymbiosis. Calling an organism an endosymbiont does not by itself classify it as an organelle or imply an irreversible evolutionary transition.

Endosymbiotic theory explains the bacterial origins of mitochondria and plastids through enduring internal associations and subsequent integration. Survival inside a biological cell is only part of the problem: exchange through membrane transport, inherited division, gene expression and delivery of required proteins must work together. The elegance is evolutionary reuse of an existing cellular capability, followed by changes that make the partners operate as one system. ^[ref]

The historical On the origin of mitosing cells by Lynn Sagan (1967, abstract and Introduction, pp. 225–226) synthesized a symbiotic account of eukaryotic origins and proposed tests using molecular evidence. Its Introduction explicitly acknowledged earlier proposals. It also hypothesized origins for other structures; the modern evidence for mitochondria and plastids should be assessed separately from the rest of that historical scheme.

Resemblance is a clue, not sufficient evidence of common descent. A small size, two surrounding membranes, division, retained DNA or bacterial-looking ribosomes does not uniquely identify an ancestor. Internal membranes exist outside these organelles, and a similar function can favor similar structures. The stronger question is whether independently examined molecular characters support the same historical relationship.

A concrete genomic observation is the mitochondrial sequence reported in 1997 for Reclinomonas americana: $69,034$ base pairs containing 97 identified genes, including four for a bacterial-type multisubunit RNA polymerase. This is a reported genome inventory, not a calculation from the pictured shape of a mitochondrion. Retention of such bacterial features strengthens the ancestry argument; a living Reclinomonas americana is not itself an ancestral eukaryote. The inspected abstract supplies these observations but not the detailed sequencing protocol or contamination controls, so those details are not attributed to this report here. ^[ref]

A sequence-based investigation obtains nucleotide sequences by DNA sequencing, identifies comparable genes, makes a sequence alignment and uses phylogenetics to infer relationships. The readout is a proposed relationship with support and uncertainty, not a photograph of an ancient encounter. Comparisons of plastid sequences with bacterial sequences support cyanobacterial ancestry, while the exact closest sampled cyanobacterial group has depended on the chosen data and inference. A bacterial affinity in one gene is weaker than coherent evidence across several genes and cellular systems. ^[ref]

For such an analysis, useful checks include distinguishing organelle DNA from bacterial contamination, verifying sequence quality, comparing corresponding rather than unrelated genes, sampling several bacterial groups and testing sensitivity to the sequence alignment and evolutionary mathematical model. These are methodological requirements, not a claim that this article has rerun a particular published analysis. Horizontal gene transfer, gene loss and unequal evolutionary change can make an individual gene's history differ from a whole organism's history. A supported bacterial origin therefore need not identify an extant donor species, an exact date or the original mode of entry. ^[ref]

Endosymbiotic gene transfer moves genetic material from an endosymbiont or its descendant organelle into the host genome, notably the nuclear genome. A transferred DNA segment can remain silent. For a transferred gene to replace an organelle-encoded function, nuclear gene expression must work and its protein must reach the right compartment through organelle protein import. Transfer of DNA and transport of proteins are distinct processes in opposite directions. ^[ref]

Gene loss and endosymbiotic gene transfer are different: absence from an organelle genome does not by itself show that a functional nuclear copy exists. Conversely, an imported protein may derive from a host gene rather than a transferred gene. The surviving organelle genome is therefore a partial record, not a complete inventory of either ancestral bacteria or the modern organelle's machinery. ^[ref]

Experimental Reconstruction of Functional Gene Transfer from the Tobacco Plastid Genome to the Nucleus by Sandra Stegemann and Ralph Bock (2006, Results, pp. 2870–2874) separated relocation of DNA from activation of a relocated gene. Engineered tobacco chloroplasts carried an nptII gene with nuclear expression signals beside an aadA gene with plastid expression signals. Selection on kanamycin recovered plants with the segment in the nuclear genome. Crosses then replaced the engineered chloroplasts with ordinary chloroplasts: the nuclear segment remained, but the plants were initially sensitive to spectinomycin and streptomycin. The transferred aadA gene was not yet functional in its new setting.

Leaf pieces were cultured on regeneration medium containing both drugs. Resistant regenerated plants supplied the functional readout. Using both drugs reduced selection of spontaneous plastid mutations conferring resistance mainly to one drug. Reciprocal crosses and selfing distinguished maternal plastid inheritance from nuclear Mendelian segregation; eight of sixteen initial candidates had the latter pattern. ^[ref]

The molecular readout came from RNA hybridization and DNA sequencing. A Northern blot detected aadA messenger RNA in activated lines, with different transcript sizes. Thermal asymmetric interlaced polymerase chain reaction recovered upstream DNA; products present in activated lines but absent in original-line and ordinary-plant controls were sequenced. The mapped rearrangements connected aadA to the upstream nuclear gene promoter. Thus resistance, inheritance, RNA detection and changed nucleotide sequences supported activation of the transferred nuclear gene, rather than resistance alone. ^[ref]

This engineered test demonstrates one route to functional nuclear gene expression after plastid DNA transfer. It does not establish a natural transfer rate, replay ancient endosymbiosis or demonstrate that the resulting protein is imported into a chloroplast. The authors explicitly identify acquisition of targeting information as an additional step not reproduced by this experiment. ^[ref]

Parasitism is an interaction in which a parasite obtains resources from a host, reducing some component of the host's performance. Its demographic effects depend on exposure, within-host processes and transmission opportunities.

A parasitic worm; the term groups several distinct animal lineages rather than one taxon.

A genus of parasitic roundworms, including Trichinella spiralis.^[ref]

A host in which a parasite reaches sexual maturity.

A host carrying developmental stages without the sexually mature adult stage of the parasite.