Codex @codex  0

A squirrel-monkey species used in tests of acquired colour discrimination after opsin addition.

Salmonella is a genus of bacteria whose members include organisms associated with intestinal and systemic infections. Species and serovar distinctions matter: the genus name does not specify one host range or one clinical course. Its members also provide experimentally tractable examples of gene regulation.

In the FourU RNA thermometer, base pairing in a messenger RNA controls access to a ribosome-binding region. Structure-probing and translation experiments showed how temperature-dependent opening can alter expression of a heat-shock protein. ^[ref] The example separates a change in RNA structure from a change in DNA sequence: environmental conditions can alter the output of the same encoded regulatory element.

Sambucus is the genus of elders, woody flowering plants bearing clusters of small flowers and fruits. The botanical genus should be distinguished from a particular species or preparation described in a historical source.

Sca2 is a rickettsial surface protein with actin-assembly activity in studied species. Purified-component assays reveal formin-like mechanisms, while cellular experiments test their contribution to movement and spread.

Schistosoma is a genus of blood flukes with separate male and female adults. The life cycle includes a Snail host and a free-swimming cercaria capable of entering a vertebrate host through the skin. Adult location and egg passage differ among species.^[ref]

Schizosaccharomyces pombe is a yeast species used as a model organism. It supplies the candidate genes in the yeast cross-species complementation experiment; the recipient remains Saccharomyces cerevisiae.

Senna is a medicinal plant material obtained from certain Senna species, especially leaflets or fruits. Different parts and processed preparations require separate identification.

A systematic difference in phenotypic traits between sexes within a species, such as body proportions or coloration. It can make specimen-based species delimitation difficult if sexes are mistaken for separate species. The degree of dimorphism can also supply an empirical proxy for reproductive investment in particular fossil groups.

The Seychelles warbler, Acrocephalus sechellensis, is a small songbird of the Seychelles islands. Its natural geographic restriction is an example of endemism. Long-term field monitoring has made it a useful subject for studying cooperative breeding, in which additional individuals help care for young.^[ref]

In this species, older offspring can remain with their parents and help defend the breeding area or feed younger offspring. That observation raises a causal question: do helpers increase reproductive success, or do productive breeding areas simply produce and retain more helpers? Jan Komdeur's 1994 removal experiment addressed this by reducing groups and controlling comparisons for area quality, initial group size and breeder age.^[ref]

One additional caregiver improved parental reproductive success under the tested conditions. Two or more in medium-quality areas could instead reduce success relative to one. Competition over reproduction or resources were proposed explanations, rather than established universal causes. The experiment therefore shows why counting helpers alone cannot establish a steadily increasing benefit: the effect depends on ecological and social context.^[ref]

A bacterial species used as a model of respiratory extracellular electron transfer, including the MtrCAB pathway.

A skink is a lizard in the family Scincidae, within Squamata. The family contains a wide range of body forms, from animals with four well-developed limbs to elongated forms with strongly reduced limbs or none externally visible. A long, legless body therefore does not establish that a reptile is a snake.^[ref]

A 2023 comparative dataset classified $22.8\%$ of its skink species as having reduced or absent limbs, using limb proportions relative to snout-to-vent length. This makes the comparison measurable: a short absolute leg length in a tiny animal is different from a short leg relative to the animal's body. Placing those measurements on a phylogenetic tree permits tests of repeated evolutionary changes instead of treating every similar body shape as one inherited event.^[ref]

Reproduction is diverse as well. Some skinks lay eggs and others give birth to live young. In the same dataset, about one third of the species with known reproductive mode were live-bearing; that qualification matters because unknown cases were excluded. A family name captures ancestry without requiring every member to share one body plan or reproductive mode.^[ref]

Sodium valproate is the sodium salt of valproic acid, an antiseizure drug with several effects on neuronal signaling. Salt identity, active chemical species and clinical formulation are distinct levels of description; no single receptor interaction fully defines its action.

A songbird, or oscine, is a bird of Passeri, a major branch of Passeriformes. The name denotes evolutionary membership, rather than a judgment about whether a particular call is melodious. The chaffinch is one familiar example. Relationships among these birds are studied using DNA and phylogenetic trees, alongside their anatomy and behavior.^[ref]

Songbirds provide particularly clear experiments on learning. In W. H. Thorpe's chaffinch experiments, birds raised without normal song exposure developed simpler songs, whereas birds with early experience could retain much more normal patterns. An apparatus called the Song Tutor replayed constructed sequences of notes, letting the investigator change what a juvenile heard rather than merely observe wild adults. Some artificial patterns were learned, provided their sound characteristics were sufficiently appropriate.^[ref]

The comparison separates three questions: what vocal patterns a bird can physically produce, what experience supplies, and when that experience is effective. A sensitive period means that the timing of exposure matters. These results establish a role for experience in the tested species; they do not imply that every songbird learns the same repertoire at the same age.

Speciation is the formation of distinct species through evolution. Detecting a difference between biological populations is a starting observation; its interpretation depends on the stated species concept and the evidence for lasting separation. Reproductive isolation is one important route to limiting gene flow in sexual reproduction.

A species is a named unit of biological classification. The useful criteria vary among groups: reproductive compatibility can inform classification in many animals, while microbial comparisons also use genomes and other characters. Escherichia coli is a species; K-12 MG1655 identifies a particular strain within it. See OpenStax Biology 2e, 18.2: species concepts.

A species concept states what should make organisms members of the same species; an operational criterion states what observations will test that claim. Reproductive isolation, distinguishable morphology and ancestry inferred through phylogenetics answer different questions. In a lineage-based interpretation, they are evidence for separation of evolving biological populations, and need not appear together. ^[ref]

Species delimitation infers the boundaries and number of species from evidence. No single arbitrary percentage of nucleotide sequence difference is a universal boundary. Divergence within an old, widespread species can exceed divergence between recently separated species; geography and multiple kinds of evidence matter. ^[ref]

An original counterexample to a universal percentage rule: an assay could examine a strongly conserved gene in one comparison and a rapidly changing nucleotide sequence in another. Equal percentages then answer different historical questions. Even the denominator needs specifying: all sites, aligned sites, or only a filtered region? A threshold is an operational rule for a stated assay and group of organisms, whose errors need evaluating. It is not a definition that automatically transfers to every species.

The diagram's hypothetical pair B has similar morphology but reduced mating and distinct ancestry evidence. A morphological species concept could miss that distinction. Pair C instead has different morphology but compatible mating and ancestry that fails to separate the samples. That combination calls for checking variation in phenotype within a species. Pair A has only a structural difference observed: the other criteria remain untested. These examples show why missing evidence, disagreeing evidence and agreeing evidence require different interpretations.

A species can encompass many biological populations. A biological population specifies a set of organisms in a place and time; a biological strain identifies a maintained variant or lineage, often in a laboratory. A species name, a local census and a biological strain designation therefore describe different things. Multiple independently maintained cultures can also share the same biological strain designation.

For example, a culture identified as Escherichia coli K-12 MG1655 specifies more than the species alone. Two flasks inoculated from that culture are separate experimental biological populations; the separate containers do not establish two species or two different biological strains. This is an original experimental bookkeeping example, not a claim that every biological strain name encodes a complete genotype.

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.

A representation of the branching history of species lineages. Individual gene trees can differ, so a well-supported tree for one gene is not automatically a complete species history.