F-score

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/F-score

Precision and recall

In statistical analysis of binary classification and information retrieval systems, the F-score or F-measure is a measure of predictive performance. It is calculated from the precision and recall of the test, where the precision is the number of true positive results divided by the number of all samples predicted to be positive, including those not identified correctly, and the recall is the number of true positive results divided by the number of all samples that should have been identified as positive. Precision is also known as positive predictive value, and recall is also known as sensitivity in diagnostic binary classification.

The F₁ score is the harmonic mean of the precision and recall. It thus symmetrically represents both precision and recall in one metric. The more generic ${\displaystyle F_{\beta }}$ score applies additional weights, valuing one of precision or recall more than the other.

The highest possible value of an F-score is 1.0, indicating perfect precision and recall, and the lowest possible value is 0, if the precision or the recall is zero.

Etymology

The name F-measure is believed to be named after a different F function in Van Rijsbergen's book, when introduced to the Fourth Message Understanding Conference (MUC-4, 1992).

Definition

The traditional F-measure or balanced F-score (F₁ score) is the harmonic mean of precision and recall:

${\displaystyle F_1=\frac{2}{{\mathrm{r}\mathrm{e}\mathrm{c}\mathrm{a}\mathrm{l}\mathrm{l}}^{-1}+{\mathrm{p}\mathrm{r}\mathrm{e}\mathrm{c}\mathrm{i}\mathrm{s}\mathrm{i}\mathrm{o}\mathrm{n}}^{-1}}=2\frac{\mathrm{p}\mathrm{r}\mathrm{e}\mathrm{c}\mathrm{i}\mathrm{s}\mathrm{i}\mathrm{o}\mathrm{n}\cdot \mathrm{r}\mathrm{e}\mathrm{c}\mathrm{a}\mathrm{l}\mathrm{l}}{\mathrm{p}\mathrm{r}\mathrm{e}\mathrm{c}\mathrm{i}\mathrm{s}\mathrm{i}\mathrm{o}\mathrm{n}+\mathrm{r}\mathrm{e}\mathrm{c}\mathrm{a}\mathrm{l}\mathrm{l}}=\frac{2\mathrm{T}\mathrm{P}}{2\mathrm{T}\mathrm{P}+\mathrm{F}\mathrm{P}+\mathrm{F}\mathrm{N}}}$

F_β score

A more general F score, ${\displaystyle F_{\beta }}$, that uses a positive real factor ${\displaystyle \beta }$, where ${\displaystyle \beta }$ is chosen such that recall is considered ${\displaystyle \beta }$ times as important as precision, is:

${\displaystyle F_{\beta }=(1+{\beta }^2)\cdot \frac{\mathrm{p}\mathrm{r}\mathrm{e}\mathrm{c}\mathrm{i}\mathrm{s}\mathrm{i}\mathrm{o}\mathrm{n}\cdot \mathrm{r}\mathrm{e}\mathrm{c}\mathrm{a}\mathrm{l}\mathrm{l}}{({\beta }^2\cdot \mathrm{p}\mathrm{r}\mathrm{e}\mathrm{c}\mathrm{i}\mathrm{s}\mathrm{i}\mathrm{o}\mathrm{n})+\mathrm{r}\mathrm{e}\mathrm{c}\mathrm{a}\mathrm{l}\mathrm{l}}}$

In terms of Type I and type II errors this becomes:

${\displaystyle F_{\beta }=\frac{(1+{\beta }^2)\cdot \mathrm{t}\mathrm{r}\mathrm{u}\mathrm{e}\mathrm{p}\mathrm{o}\mathrm{s}\mathrm{i}\mathrm{t}\mathrm{i}\mathrm{v}\mathrm{e}}{(1+{\beta }^2)\cdot \mathrm{t}\mathrm{r}\mathrm{u}\mathrm{e}\mathrm{p}\mathrm{o}\mathrm{s}\mathrm{i}\mathrm{t}\mathrm{i}\mathrm{v}\mathrm{e}+{\beta }^2\cdot \mathrm{f}\mathrm{a}\mathrm{l}\mathrm{s}\mathrm{e}\mathrm{n}\mathrm{e}\mathrm{g}\mathrm{a}\mathrm{t}\mathrm{i}\mathrm{v}\mathrm{e}+\mathrm{f}\mathrm{a}\mathrm{l}\mathrm{s}\mathrm{e}\mathrm{p}\mathrm{o}\mathrm{s}\mathrm{i}\mathrm{t}\mathrm{i}\mathrm{v}\mathrm{e}}}$

Two commonly used values for ${\displaystyle \beta }$ are 2, which weighs recall higher than precision, and 0.5, which weighs recall lower than precision.

The F-measure was derived so that ${\displaystyle F_{\beta }}$ "measures the effectiveness of retrieval with respect to a user who attaches ${\displaystyle \beta }$ times as much importance to recall as precision". It is based on Van Rijsbergen's effectiveness measure

${\displaystyle E=1-{\left(\frac{\alpha }{p}+\frac{1-\alpha }{r}\right)}^{-1}}$

Their relationship is: ${\displaystyle F_{\beta }=1-E}$ where ${\displaystyle \alpha =\frac{1}{1+{\beta }^2}}$

Diagnostic testing

This is related to the field of binary classification where recall is often termed "sensitivity".

		Predicted condition
	Total population = P + N	Predicted positive	Predicted negative	Informedness, bookmaker informedness (BM) = TPR + TNR − 1	Prevalence threshold (PT) = ⁠√TPR × FPR - FPR/TPR - FPR⁠
Actual condition	Positive (P)	True positive (TP), hit	False negative (FN), miss, underestimation	True positive rate (TPR), recall, sensitivity (SEN), probability of detection, hit rate, power = ⁠TP/P⁠ = 1 − FNR	False negative rate (FNR), miss rate type II error  = ⁠FN/P⁠ = 1 − TPR
	Negative (N)	False positive (FP), false alarm, overestimation	True negative (TN), correct rejection	False positive rate (FPR), probability of false alarm, fall-out type I error  = ⁠FP/N⁠ = 1 − TNR	True negative rate (TNR), specificity (SPC), selectivity = ⁠TN/N⁠ = 1 − FPR
	Prevalence = ⁠P/P + N⁠	Positive predictive value (PPV), precision = ⁠TP/TP + FP⁠ = 1 − FDR	False omission rate (FOR) = ⁠FN/TN + FN⁠ = 1 − NPV	Positive likelihood ratio (LR+) = ⁠TPR/FPR⁠	Negative likelihood ratio (LR−) = ⁠FNR/TNR⁠
	Accuracy (ACC) = ⁠TP + TN/P + N⁠	False discovery rate (FDR) = ⁠FP/TP + FP⁠ = 1 − PPV	Negative predictive value (NPV) = ⁠TN/TN + FN⁠ = 1 − FOR	Markedness (MK), deltaP (Δp) = PPV + NPV − 1	Diagnostic odds ratio (DOR) = ⁠LR+/LR−⁠
	Balanced accuracy (BA) = ⁠TPR + TNR/2⁠	F1 score = ⁠2 PPV × TPR/PPV + TPR⁠ = ⁠2 TP/2 TP + FP + FN⁠	Fowlkes–Mallows index (FM) = √PPV × TPR	Matthews correlation coefficient (MCC) = √TPR × TNR × PPV × NPV - √FNR × FPR × FOR × FDR	Threat score (TS), critical success index (CSI), Jaccard index = ⁠TP/TP + FN + FP⁠

Type I error: A test result which wrongly indicates that a particular condition or attribute is present

Normalised harmonic mean plot where x is precision, y is recall and the vertical axis is F₁ score, in percentage points

Precision-Recall Curve: points from different thresholds are color coded, the point with optimal F-score is highlighted in red

Dependence of the F-score on class imbalance

Precision-recall curve, and thus the ${\displaystyle F_{\beta }}$ score, explicitly depends on the ratio ${\displaystyle r}$ of positive to negative test cases. This means that comparison of the F-score across different problems with differing class ratios is problematic. One way to address this issue (see e.g., Siblini et al., 2020) is to use a standard class ratio ${\displaystyle r_0}$ when making such comparisons.

Applications

The F-score is often used in the field of information retrieval for measuring search, document classification, and query classification performance. It is particularly relevant in applications which are primarily concerned with the positive class and where the positive class is rare relative to the negative class.

Earlier works focused primarily on the F₁ score, but with the proliferation of large scale search engines, performance goals changed to place more emphasis on either precision or recall and so ${\displaystyle F_{\beta }}$ is seen in wide application.

The F-score is also used in machine learning. However, the F-measures do not take true negatives into account, hence measures such as the Matthews correlation coefficient, Informedness or Cohen's kappa may be preferred to assess the performance of a binary classifier.

The F-score has been widely used in the natural language processing literature, such as in the evaluation of named entity recognition and word segmentation.

Properties

The F₁ score is the Dice coefficient of the set of retrieved items and the set of relevant items.

• The F₁-score of a classifier which always predicts the positive class converges to 1 as the probability of the positive class increases.
• The F₁-score of a classifier which always predicts the positive class is equal to 2 * proportion_of_positive_class / ( 1 + proportion_of_positive_class ), since the recall is 1, and the precision is equal to the proportion of the positive class.
• If the scoring model is uninformative (cannot distinguish between the positive and negative class) then the optimal threshold is 0 so that the positive class is always predicted.
• F₁ score is concave in the true positive rate.

Criticism

David Hand and others criticize the widespread use of the F₁ score since it gives equal importance to precision and recall. In practice, different types of mis-classifications incur different costs. In other words, the relative importance of precision and recall is an aspect of the problem.

According to Davide Chicco and Giuseppe Jurman, the F₁ score is less truthful and informative than the Matthews correlation coefficient (MCC) in binary evaluation classification.

David M W Powers has pointed out that F₁ ignores the True Negatives and thus is misleading for unbalanced classes, while kappa and correlation measures are symmetric and assess both directions of predictability - the classifier predicting the true class and the true class predicting the classifier prediction, proposing separate multiclass measures Informedness and Markedness for the two directions, noting that their geometric mean is correlation.

Another source of critique of F₁ is its lack of symmetry. It means it may change its value when dataset labeling is changed - the "positive" samples are named "negative" and vice versa. This criticism is met by the P4 metric definition, which is sometimes indicated as a symmetrical extension of F₁.

Difference from Fowlkes–Mallows index

While the F-measure is the harmonic mean of recall and precision, the Fowlkes–Mallows index is their geometric mean.

Extension to multi-class classification

The F-score is also used for evaluating classification problems with more than two classes (Multiclass classification). A common method is to average the F-score over each class, aiming at a balanced measurement of performance.

Macro F1

Macro F1 is a macro-averaged F1 score aiming at a balanced performance measurement. To calculate macro F1, two different averaging-formulas have been used: the F1 score of (arithmetic) class-wise precision and recall means or the arithmetic mean of class-wise F1 scores, where the latter exhibits more desirable properties.

Micro F1

Micro F1 is the harmonic mean of micro precision (number of correct predictions normalized by false positives) and micro recall (number of correct predictions normalized by false negatives). Since in multi-class evaluation the overall amount of false positives equals the amount of false negatives, micro F1 is equivalent to Accuracy.

the number of real positive cases in the data

A test result that correctly indicates the presence of a condition or characteristic

Type II error: A test result which wrongly indicates that a particular condition or attribute is absent

the number of real negative cases in the data

A test result that correctly indicates the absence of a condition or characteristic

Reticulate evolution

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Reticulate_evolution

Phylogenetic network depicting reticulate evolution: Lineage B results from a horizontal transfer between its two ancestors A and C (blue, dotted lines).

Reticulate evolution, or network evolution is the origination of a lineage through the partial merging of two ancestor lineages, leading to relationships better described by a phylogenetic network than a bifurcating tree. Reticulate patterns can be found in the phylogenetic reconstructions of biodiversity lineages obtained by comparing the characteristics of organisms. Reticulation processes can potentially be convergent and divergent at the same time. Reticulate evolution indicates the lack of independence between two evolutionary lineages. Reticulation affects survival, fitness and speciation rates of species. 

Reticulate evolution can happen between lineages separated only for a short time, for example through hybrid speciation in a species complex. Nevertheless, it also takes place over larger evolutionary distances, as exemplified by the presence of organelles of bacterial origin in eukaryotic cells.

Reticulation occurs at various levels: at a chromosomal level, meiotic recombination causes evolution to be reticulate; at a species level, reticulation arises through hybrid speciation and horizontal gene transfer; and at a population level, sexual recombination causes reticulation.

The adjective reticulate stems from the Latin words reticulatus, "having a net-like pattern" from reticulum, "little net."

Underlying mechanisms and processes

Since the nineteenth century, scientists from different disciplines have studied how reticulate evolution occurs. Researchers have increasingly succeeded in identifying these mechanisms and processes. It has been found to be driven by symbiosis, symbiogenesis (endosymbiosis), lateral gene transfer, hybridization and infectious heredity.

Symbiosis

Symbiosis is a close and long-term biological interaction between two different biological organisms. Often, both of the organisms involved develop new features upon the interaction with the other organism. This may lead to the development of new, distinct organisms. The alterations in genetic material upon symbiosis can occur via germline transmission or lateral transmission. Therefore, the interaction between different organisms can drive evolution of one or both organisms.

Symbiogenesis

Symbiogenesis (endosymbiosis) is a special form of symbiosis whereby an organism lives inside another, different organism. Symbiogenesis is thought to be very important in the origin and evolution of eukaryotes. Eukaryotic organelles, such as mitochondria, have been theorized to have been originated from cell-invaded bacteria living inside another cell.

Lateral gene transfer

Lateral gene transfer, or horizontal gene transfer, is the movement of genetic material between unicellular and/or multicellular organisms without a parent-offspring relationship. The horizontal transfer of genes results in new genes, which could give new functions to the recipient and thus could drive evolution.

Hybridization

In the neo-Darwinian paradigm, one of the assumed definition of a species is that of Mayr's, which defines species based upon sexual compatibility. Mayr's definition therefore suggests that individuals that can produce fertile offspring must belong to the same species. However, in hybridization, two organisms produce offspring while being distinct species. During hybridization the characteristics of these two different species are combined yielding a new organism, called a hybrid, thus driving evolution.

Infectious heredity

Infectious agents, such as viruses, can infect the cells of host organisms. Viruses infect cells of other organisms in order to enable their own reproduction. Hereto, many viruses can insert copies of their genetic material into the host genome, potentially altering the phenotype of the host cell. When these viruses insert their genetic material in the genome of germ line cells, the modified host genome will be passed onto the offspring, yielding genetically differentiated organisms. Therefore, infectious heredity plays an important role in evolution, for example in the formation of the female placenta.

Models

Reticulate evolution has played a key role in the evolution of some organisms such as bacteria and flowering plants. However, most methods for studying cladistics have been based on a model of strictly branching cladogeny, without assessing the importance of reticulate evolution. Reticulation at chromosomal, genomic and species levels fails to be modelled by a bifurcating tree.

According to Ford Doolittle, an evolutionary and molecular biologist: “Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree”.

Reticulate evolution refers to evolutionary processes which cannot be successfully represented using a classical phylogenetic tree model, as it gives rise to rapid evolutionary change with horizontal crossings and mergings often preceding a pattern of vertical descent with modification. Reconstructing phylogenetic relationships under reticulate evolution requires adapted analytical methods. Reticulate evolution dynamics contradict the neo-Darwininan theory, compiled in the Modern Synthesis, by which the evolution of life occurs through natural selection and is displayed with a bifurcating or branching pattern. Frequent hybridisation between species in natural populations challenges the assumption that species have evolved from a common ancestor by simple branching, in which branches are genetically isolated. The study of reticulate evolution is said to have been largely excluded from the modern synthesis. The urgent need for new models which take reticulate evolution into account has been stressed by many evolutionary biologists, such as Nathalie Gontier who has stated "reticulate evolution today is a vernacular concept for evolutionary change induced by mechanisms and processes of symbiosis, symbiogenesis, lateral gene transfer, hybridization, or divergence with gene flow, and infectious heredity". She calls for an extended evolutionary synthesis that integrates these mechanisms and processes of evolution.

Applications

Reticulate evolution has been extensively applied to plant hybridization in agriculture and gardening. The first commercial hybrids appeared in the early 1920s. Since then, many protoplast fusion experiments have been carried out, some of which were aimed at improvement of crop species. Wild types possessing desirable agronomic traits are selected and fused in order to yield novel, improved species. The newly generated plant will be improved for traits such as better yield, greater uniformity, improved color, and disease resistance.

Examples

Reticulate evolution is regarded as a process that has shaped the histories of many organisms. There is evidence of reticulation events in flowering plants, as the variation patterns between angiosperm families strongly suggests there has been widespread hybridisation. Grant states that phylogenetic networks, instead of phylogenetic trees, arise in all major groups of higher plants. Stable speciation events due to hybridisation between angiosperm species supports the occurrence of reticulate evolution and highlights the key role of reticulation in the evolution of plants.

Genetic transfer can occur across wide taxonomic levels in microorganisms and become stably integrated into the new microbial populations, as has been observed through protein sequencing. Reticulation in bacteria usually only involves the transfer of only a few genes or parts of these. Reticulate evolution driven by lateral gene transfer has also been observed in marine life. Lateral genetic transfer of photo-response genes between planktonic bacteria and Archaea has been evidenced in some groups, showing an associated increase in environmental adaptability in organisms inhabiting photic zones.

Moreover, in the well-studied Darwin finches signs of reticulate evolution can be observed. Peter and Rosemary Grant, who carried out extensive research on the evolutionary processes of the Geospiza genus, found that hybridization occurs between some species of Darwin finches, yielding hybrid forms. This event could explain the origin of intermediate species. Jonathan Weiner commented on the observations of the Grants, suggesting the existence of reticulate evolution: "To the Grants, the whole tree of life now looks different from a year ago. The set of young twigs and shoots they study seems to be growing together in some seasons, apart in others. The same forces that created these lines are moving them toward fusion and then back toward fission."; and "The Grants are looking at a pattern that was once dismissed as insignificant in the tree of life. The pattern is known as reticulate evolution, from the Latin reticulum, diminutive for net. The finches' lines are not so much lines or branches at all. They are more like twiggy thickets, full of little networks and delicate webbings."

Keystone species

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Keystone_species

The jaguar: a keystone, flagship, and umbrella species, and an apex predator

The beaver: a keystone species, and habitat creator, responsible for the creation of lakes, canals and wetlands irrigating large forests and creating ecosystems

A keystone species is a species that has a disproportionately large effect on its natural environment relative to its abundance. The concept was introduced in 1969 by the zoologist Robert T. Paine. Keystone species play a critical role in maintaining the structure of an ecological community, affecting many other organisms in an ecosystem and helping to determine the types and numbers of various other species in the community. Without keystone species, the ecosystem would be dramatically different or cease to exist altogether. Some keystone species, such as the wolf and lion, are also apex predators.

The role that a keystone species plays in its ecosystem is analogous to the role of a keystone in an arch. While the keystone is under the least pressure of any of the stones in an arch, the arch still collapses without it. Similarly, an ecosystem may experience a dramatic shift if a keystone species is removed, even though that species was a small part of the ecosystem by measures of biomass or productivity. It became a popular concept in conservation biology, alongside flagship and umbrella species. Although the concept is valued as a descriptor for particularly strong inter-species interactions, and has allowed easier communication between ecologists and conservation policy-makers, it has been criticized for oversimplifying complex ecological systems.

History

Ochre seastars (Pisaster ochraceus), a keystone predator

 

California mussels (Mytilus californianus), the seastar's prey

The concept of the keystone species was introduced in 1969 by zoologist Robert T. Paine. Paine developed the concept to explain his observations and experiments on the relationships between marine invertebrates of the intertidal zone (between the high and low tide lines), including starfish and mussels. He removed the starfish from an area, and documented the effects on the ecosystem. In his 1966 paper, Food Web Complexity and Species Diversity, Paine had described such a system in Makah Bay in Washington. In his 1969 paper, Paine proposed the keystone species concept, using Pisaster ochraceus, a species of starfish generally known as ochre starfish, and Mytilus californianus, a species of mussel, as a primary example. The ochre starfish is a generalist predator and feeds on chitons, limpets, snails, barnacles, echinoids, and even decapod crustacea. The favourite food for these starfish is the mussel which is a dominant competitor for the space on the rocks. The ochre starfish keeps the population numbers of the mussels in check along with the other preys allowing the other seaweeds, sponges, and anemones, that ochre starfish do not consume, to co-exist. When Paine removed the ochre starfish, the mussels quickly outgrew the other species crowding them out. At the start, the rock pools held 15 rock-clinging species. Three years later there were 8 such species; and ten years later the pools were largely occupied by a single species, mussels. The concept became popular in conservation, and was deployed in a range of contexts and mobilized to engender support for conservation, especially where human activities had damaged ecosystems, such as by removing keystone predators.

Definitions

A keystone species was defined by Paine as a species that has a disproportionately large effect on its environment relative to its abundance. It has been defined operationally by Davic in 2003 as "a strongly interacting species whose top-down effect on species diversity and competition is large relative to its biomass dominance within a functional group."

A classic keystone species is a predator that prevents a particular herbivorous species from eliminating dominant plant species. If prey numbers are low, keystone predators can be even less abundant and still be effective. Yet without the predators, the herbivorous prey would explode in numbers, wipe out the dominant plants, and dramatically alter the character of the ecosystem. The exact scenario changes in each example, but the central idea remains that through a chain of interactions, a non-abundant species has an outsized impact on ecosystem functions. For example, the herbivorous weevil Euhrychiopsis lecontei is thought to have keystone effects on aquatic plant diversity by foraging on nuisance Eurasian watermilfoil in North American waters. Similarly, the wasp species Agelaia vicina has been labeled a keystone species for its unparalleled nest size, colony size, and high rate of brood production. The diversity of its prey and the quantity necessary to sustain its high rate of growth have a direct impact on other species around it.

The keystone concept is defined by its ecological effects, and these in turn make it important for conservation. In this it overlaps with several other species conservation concepts such as flagship species, indicator species, and umbrella species. For example, the jaguar is a charismatic big cat which meets all of these definitions:

The jaguar is an umbrella species, flagship species, and wilderness quality indicator. It promotes the goals of carnivore recovery, protecting and restoring connectivity through Madrean woodland and riparian areas, and protecting and restoring riparian areas. ... A reserve system that protects jaguars is an umbrella for many other species. ... the jaguar [is] a keystone in subtropical and tropical America ...

— David Maehr et al, 2001

Predators

Sea otters and kelp forests

Sea urchins like this purple sea urchin can damage kelp forests by chewing through kelp holdfasts

 

The sea otter is an important predator of sea urchins, making it a keystone species for the kelp forests.

Sea otters protect kelp forests from damage by sea urchins. When the sea otters of the North American west coast were hunted commercially for their fur, their numbers fell to such low levels – fewer than 1000 in the north Pacific ocean – that they were unable to control the sea urchin population. The urchins, in turn, grazed the holdfasts of kelp so heavily that the kelp forests largely disappeared, along with all the species that depended on them. Reintroducing the sea otters has enabled the kelp ecosystem to be restored. For example, in Southeast Alaska some 400 sea otters were released, and they have bred to form a population approaching 25,000.

The wolf, Yellowstone's apex predator

Riparian willow recovery at Blacktail Creek, Yellowstone National Park, showing effect of the reintroduction of wolves

Further information: Apex predator

Keystone predators may increase the biodiversity of communities by preventing a single species from becoming dominant. They can have a profound influence on the balance of organisms in a particular ecosystem. Introduction or removal of a keystone predator, or changes in its population density, can have drastic cascading effects on the equilibrium of many other populations in the ecosystem. For example, grazers of a grassland may prevent a single dominant species from taking over.

The elimination of the gray wolf from the Greater Yellowstone Ecosystem had profound impacts on the trophic pyramid. Without predation, herbivores began to over-graze many woody browse species, affecting the area's plant populations. In addition, wolves often kept animals from grazing in riparian areas, which protected beavers from having their food sources encroached upon. The removal of wolves had a direct effect on beaver populations, as their habitat became grazing territory. Increased browsing on willows and conifers along Blacktail Creek due to a lack of predation caused channel incision because the beavers helped slow the water down, allowing soil to stay in place. Furthermore, predation keeps hydrological features such as creeks and streams in normal working order. When wolves were reintroduced, the beaver population and the whole riparian ecosystem recovered dramatically within a few years.

Sea stars and other non-apex predators

As described by Paine in 1966, some sea stars (e.g., Pisaster ochraceus) may prey on sea urchins, mussels, and other shellfish that have no other natural predators. If the sea star is removed from the ecosystem, the mussel population explodes uncontrollably, driving out most other species.

These creatures need not be apex predators. Sea stars are prey for sharks, rays, and sea anemones. Sea otters are prey for orca.

The jaguar, whose numbers in Central and South America have been classified as near threatened, acts as a keystone predator by its widely varied diet, helping to balance the mammalian jungle ecosystem with its consumption of 87 different species of prey. The lion is another keystone species.

Acorn banksia, Banksia prionotes, is periodically the sole source of nectar for important pollinators, honeyeaters.

Mutualists

Keystone mutualists are organisms that participate in mutually beneficial interaction, the loss of which would have a profound impact upon the ecosystem as a whole. For example, in the Avon Wheatbelt region of Western Australia, there is a period of each year when Banksia prionotes (acorn banksia) is the sole source of nectar for honeyeaters, which play an important role in pollination of numerous plant species. Therefore, the loss of this one species of tree would probably cause the honeyeater population to collapse, with profound implications for the entire ecosystem. Another example is frugivores, such as the cassowary, which spreads the seeds of many different trees. Some seeds will not grow unless they have been through a cassowary.

Ecosystem engineers

Prairie dog town. Drawing by Josiah Gregg, 1844

Further information: Ecosystem engineer and Niche construction

A term used alongside keystone is ecosystem engineer. In North America, the prairie dog is an ecosystem engineer. Prairie dog burrows provide the nesting areas for mountain plovers and burrowing owls. Prairie dog tunnel systems also help channel rainwater into the water table to prevent runoff and erosion, and can also serve to change the composition of the soil in a region by increasing aeration and reversing soil compaction that can be a result of cattle grazing. Prairie dogs also trim the vegetation around their colonies, perhaps to remove any cover for predators. Grazing species such as plains bison, which is another keystone species, the pronghorn, and the mule deer have shown a proclivity for grazing on the same land used by prairie dogs.

Beaver dam, an animal construction which has a transformative effect on the environment

The beaver is a well known ecosystem engineer and keystone species. It transforms its territory from a stream to a pond or swamp. Beavers affect the environment first altering the edges of riparian areas by cutting down older trees to use for their dams. This allows younger trees to take their place. Beaver dams alter the riparian area they are established in. Depending on topography, soils, and many factors, these dams change the riparian edges of streams and rivers into wetlands, meadows, or riverine forests. These dams have been shown to be beneficial to a myriad of species including amphibians, salmon, and song birds.

In the African savanna, the larger herbivores, especially the elephants, shape their environment. The elephants destroy trees, making room for the grass species and creating habitat for various small animal species. Without these animals, much of the savanna would turn into woodland. In the Amazon river basin, peccaries produce and maintain wallows that are utilized by a wide variety of species. Australian studies have found that parrotfish on the Great Barrier Reef are the only reef fish that consistently scrape and clean the coral on the reef. Without these animals, the Great Barrier Reef would be under severe strain.

In the Serengeti, the presence of sufficient gnus in these grasslands reduces wildfire likelihood, which in turn promotes tree growth. The documentary The Serengeti Rules documents this in detail.

Limitations

Depends on context

The community ecologist Bruce Menge states that the keystone concept has been stretched far beyond Paine's original concept. That stretching can be quantified: the researcher Ishana Shukla has listed 230 species identified as keystones in some 157 studies in the 50 years since Paine's paper. Menge's own work has shown that the purple Pisaster sea star that Paine had studied was a powerful keystone species in places exposed to strong wave action, but was far less important in sheltered places. Paine had indeed stated that in Alaska, without the relevant mussel species as prey, the predatory Pisaster was "just another sea star". In other words, the extent to which a species could be described as a keystone depended on the ecological context.

Multiple meanings

Although the concept of the keystone species has a value in describing particularly strong inter-species interactions, and for allowing easier communication between ecologists and conservation policy-makers, it has been criticized by L. S. Mills and colleagues for oversimplifying complex ecological systems. The term has been applied widely in different ecosystems and to predators, prey, and plants (primary producers), inevitably with differing ecological meanings. For instance, removing a predator may allow other animals to increase to the point where they wipe out other species; removing a prey species may cause predator populations to crash, or may allow predators to drive other prey species to extinction; and removing a plant species may result in the loss of animals that depend on it, like pollinators and seed dispersers. Beavers too have been called keystone, not for eating other species but for modifying the environment in ways that affected other species. The term has thus been given quite different meanings in different cases. In Mills's view, Paine's work showed that a few species could sometimes have extremely strong interactions within a particular ecosystem, but that does not automatically imply that other ecosystems have a similar structure.

Perennial

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Perennial

Common chicory, Cichorium intybus, is a herbaceous perennial plant.

In horticulture, the term (per- + -ennial, "through the year") is used to differentiate a plant from shorter-lived annuals and biennials. It has thus been defined as a plant that lives more than 2 years. The term is also loosely used to distinguish plants with little or no woody growth (secondary growth in girth) from trees and shrubs, which are also technically perennials. Notably, it is estimated that 94% of plant species fall under the category of perennials, underscoring the prevalence of plants with lifespans exceeding two years in the botanical world.

Perennials (especially small flowering plants) that grow and bloom over the spring and summer, die back every autumn and winter, and then return in the spring from their rootstock or other overwintering structure, are known as herbaceous perennials. However, depending on the rigours of the local climate (temperature, moisture, organic content in the soil, microorganisms), a plant that is a perennial in its native habitat, may be treated by a gardener as an annual and planted out every year, from seed, from cuttings, or from divisions. Tomato vines, for example, live several years in their natural tropical/ subtropical habitat but are grown as annuals in temperate regions because their above-ground biomass does not survive the winter.

There is also a class of evergreen perennials which lack woody stems, such as Bergenia which retain a mantle of leaves throughout the year. An intermediate class of plants is known as subshrubs, which retain a vestigial woody structure in winter, e.g. Penstemon.

The symbol for a perennial plant, based on Species Plantarum by Linnaeus, is , which is also the astronomical symbol for the planet Jupiter.

Life cycle and structure

Perennial plants can be short-lived (only a few years) or long-lived. They include a wide assortment of plant groups from non-flowering plants like ferns and liverworts to highly diverse flowering plants like orchids, grasses, and woody plants. Plants that flower and fruit only once and then die are termed monocarpic or semelparous; these species may live for many years before they flower. For example, a century plant can live for 80 years and grow 30 meters tall before flowering and dying. However, most perennials are polycarpic (or iteroparous), flowering over many seasons in their lifetime. Perennials invest more resources than annuals into roots, crowns, and other structures that allow them to live from one year to the next. They often have a competitive advantage because they can commence their growth and leaf out earlier in the growing season, and can grow taller than annuals. In doing so they can better compete for space and collect more light.

Perennials typically grow structures that allow them to adapt to living from one year to the next through a form of vegetative reproduction rather than seeding. These structures include bulbs, tubers, woody crowns, rhizomes, turions, woody stems, or crowns which allows them to survive periods of dormancy over cold or dry seasons; these structures typically store carbohydrates which are used once the dormancy period is over and new growth begins. In climates that are warm all year long, perennials may grow continuously. Annuals which complete their life cycle in one growing season, in contrast with perennials, produce seeds as the next generation and die; the seeds may survive cold or dry periods or germinate soon after dispersal depending on the climate.

Some perennials retain their foliage year-round; these are evergreen perennials. Deciduous perennials shed all their leaves part of the year. Deciduous perennials include herbaceous and woody plants; herbaceous plants have stems that lack hard, fibrous growth, while woody plants have stems with buds that survive above ground during dormancy. Some perennials are semi-deciduous, meaning they lose some of their leaves in either winter or summer. Deciduous perennials shed their leaves when growing conditions are no longer suitable for photosynthesis, such as when it is too cold or dry. In many parts of the world, seasonality is expressed as wet and dry periods rather than warm and cold periods, and deciduous perennials lose their leaves in the dry season.

Some perennial plants are protected from wildfires because they have underground roots that produce adventitious shoots, bulbs, crowns, or stems; other perennials like trees and shrubs may have thick cork layers that protect the stems. Herbaceous perennials from temperate and alpine regions of the world can tolerate the cold during winter.

Perennial plants may remain dormant for long periods and then recommence growth and reproduction when the environment is more suitable, while most annual plants complete their life cycle during one growing period, and biennials have two growing periods.

The meristem of perennial plants communicates with the hormones produced due to environmental situations (i.e., seasons), reproduction, and stage of development to begin and halt the ability to grow or flower. There is also a distinction between the ability to grow and the actual task of growth. For example, most trees regain the ability to grow during winter but do not initiate physical growth until the spring and summer months. The start of dormancy can be seen in perennial plants through withering flowers, loss of leaves on trees, and halting of reproduction in both flowering and budding plants.

Perennial species may produce relatively large seeds that have the advantage of generating larger seedlings that can better compete with other plants. Perennials also produce seeds over many years.

An important aspect of cold acclimation is overexpression of DNA repair genes. In Thinopyrum intermedium a perennial relative of common wheat Triticum aestivum, conditions of freezing stress were shown to be associated with large increases in expression of two DNA repair genes (one gene product a photolyase and the other, a protein involved in nucleotide excision repair).

Cultivation

Perennials that are cultivated include: woody plants like fruit trees grown for their edible fruits; shrubs and trees grown as landscaping ornamentals; herbaceous food crops like asparagus, rhubarb, strawberries; and subtropical plants not hardy in colder areas such as tomatoes, eggplant, and coleus (which are treated as annuals in colder areas). Perennials also include plants grown for their flowering and other ornamental value including bulbs (like tulips, narcissus, and gladiolus); lawn grass, and other groundcovers, (such as periwinkle and Dichondra).

Each type of plant must be separated differently; for example, plants with fibrous root systems like daylilies, Siberian iris, or grasses can be pried apart with two garden forks inserted back to back, or cut by knives. However, plants such as bearded irises have a root system of rhizomes; these root systems should be planted with the top of the rhizome just above ground level, with leaves from the following year showing. The point of dividing perennials is to increase the amount of a single breed of plant in your garden. In the United States more than 900 million dollars worth of potted herbaceous perennial plants were sold in 2019.

Dahlia plants are tender perennials that originate from climates that are warm all year round and need special care to survive cold winters.

Benefits in agriculture

Switchgrass is a deep-rooted perennial. These roots are more than 3 meters long.

Although most of humanity is fed by the re-sowing of the seeds of annual grain crops, (either naturally or by the manual efforts of humans), perennial crops provide numerous benefits. Perennial plants often have deep, extensive root systems which can hold soil to prevent erosion, capture dissolved nitrogen before it can contaminate ground and surface water, and out-compete weeds (reducing the need for herbicides). These potential benefits of perennials have resulted in new attempts to increase the seed yield of perennial species, which could result in the creation of new perennial grain crops. Some examples of new perennial crops being developed are perennial rice and intermediate wheatgrass. A perennial rice developed in 2018, was reported in 2023, to have provided a similar yield to replanted annual rice when evaluated over eight consecutive harvests.

Location

Perennial plants dominate many natural ecosystems on land and in fresh water, with only a very few (e.g. Zostera) occurring in shallow sea water. Herbaceous perennial plants are particularly dominant in conditions too fire-prone for trees and shrubs, e.g., most plants on prairies and steppes are perennials; they are also dominant on tundra too cold for tree growth. Nearly all forest plants are perennials, including trees and shrubs.

Perennial plants are usually better long-term competitors, especially under stable, resource-poor conditions. This is due to the development of larger root systems which can access water and soil nutrients deeper in the soil and to earlier emergence in the spring. Annual plants have an advantage in disturbed environments because of their faster growth and reproduction rates.

Types

• Herbaceous – plants that have foliage and stems that die to the ground at the end of the growing season and which show only primary growth. Examples include frost-tender plants such as Rudbeckias, Mirabilis jalapa, Momordica charantia, mint, tobacco, common purslane, alfalfa, petunias, Thinopyrum intermedium, Red clover, Hylotelephium telephium and Cochliasanthus caracalla.
• Evergreen – plants that have persistent foliage without woody stems. Examples include many Senecios, Begonia, Gaillardias, Dimorphothecas, Gazanias, Thunbergias, Dietes, Osteospermums, Tradescantias and Vincas, among others.
• Woody – plants with persistent above ground stem that survive from one growing season to the next, with primary and secondary growth, or growth in width protected by an outer cortex. Some may be deciduous. Examples of many shrubs, lianas and trees such as Ipomeas, banana, lilacs, Geraniums, Lantanas, Hydrangeas, Nandinas, Pandoreas, grape, Hederas, pine, apple, Jasmines, Trachelospermums, Gardenias, Plumbagos, Cistus and Rosas, among others.
• Monocarpic – plants that flower, set seeds once and then die. Examples include, Agave and some species of Streptocarpus

List of perennials

Each section contains a short list of species related to that topic, these are an example as the true lists would fill several books.

Perennial flowers

Perennials grown for their decorative flowers include very many species and types. Some examples include:

• Achillea
• Aster
• Bergenia
• Dahlia
• Foxglove
• Hollyhock
• Kniphofia
• Lupin
• Salvia
• Phlox

Perennial fruits

The majority of fruit bearing plants are perennial even in temperate climates. Examples include:

• Apple
• Blackcurrant
• Blueberry
• Blackberry
• Currant
• Grape
• Pear
• Plum
• Raspberries
• Strawberry

Perennial herbs

Many herbs are perennial, including these examples:

• Fennel
• Mint
• Rosemary
• Sage
• Thyme

Perennial vegetables

Main article: Perennial vegetables

Many vegetable plants can grow as perennials in tropical climates, but die in cold weather. Examples of some of the more completely perennial vegetables are:

• Asparagus
• Chives
• Globe artichoke
• Jerusalem artichoke
• Kale
• Leek
• New Zealand spinach
• Rhubarb
• Sea kale
• Sweet potato

Aquatic plants

Main article: Aquatic plant

Many aquatic plants are perennial even though many do not have woody tissue. Examples include:

• Crassula helmsii – New Zealand Stonecrop
• Pontederia cordata – Pickerell weed
• Stratiotes aloides – Water Soldier which sinks to the bottom of the pond in winter
• Utricularia vulgaris – Common bladderwort which produces turions as its overwintering stage