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Evolutionary theory* -->
Evolutionary theory* -->
Evolution is not just change over time, since all individuals change over time.
Darwin described evolution simply as "descent with modification".
Evolution is, by definition, the change in allele frequency in a population over time.
What does this mean? If the alleles within a population change over time, then organisms will exhibit differing attributes and features, which will confer varying degrees of success in survival and reproduction. This success will lead to some reproducing more and thus changing the allele frequency.
Population: a group of organisms of the same species in an area
Allele: one of many alternative forms of a gene; found at the same place on a chromosome (e.g., wrinkled and smooth pods, yellow and green seeds)
An allele is a gene that codes for the same function (e.g., flower color), but with different variants (e.g., red vs. white flowers)
Alleles bring variability into the gene pool
Frequency: the ratio of a particular allele to the total of all other alleles of the same gene in a given population
If the frequency of the alleles does not change, then the organisms in the population would remain the same.
If the frequency changes, organisms within the population will have different expressions of genes, which may confer more or less success in survival and reproduction
*A theory is a well-substantiated explanation of natural phenomena based on evidence.
While we may use the term “theory” in common verbiage to mean a guess or an idea, this is not how it is used in science.
Theories are confirmed ideas with many lines of evidence.
Testability and falsifiability are needed through observation and sometimes experimentation for an idea to become a scientific theory (Popper, 1959).
For example, a population of flowering plants will all have genes that determine flower color, but some individuals may have different variants of the gene (alleles), such as red petals versus pink petals.
In the population, red may be preferred by pollinators, with fewer pollinators choosing the pink variants.
Over time, pollinators may start to prefer the pink color over the red, allowing those pink-flowered plants to have more successful pollination interactions, and thus making more seeds.
The plants with the pink petals will increase in the population, and therefore the frequency of those "pink alleles" will change in relation to the "red alleles".
To put a fine point on this: The allele frequency, in this plant population, changes over time. That IS the definition of evolution
Over an extended period of time, the red-flowered plants might not receive pollinators anymore, and the "red group" goes extinct. The pink-flowered plants continue as the dominant species.
Another possibility is that the pink and red flower variants may become discrete populations, with their own pollinators. The gene pools of these two groups become different enough that they can no longer interbreed. New species are formed.
Speciation
Speciation
Speciation is the origin of new species
The definition of a species can be challenging. For simplicity, it can be defined as a group of individuals that actually or potentially interbreed in nature.
Note that many plants can form hybrids in nature, which involves different species interbreeding, blurring the lines between species.
Allopatric speciation
Allopatric speciation
A geographic barrier separates populations that evolve “away” from each other.
e.g., islands, mountains, waterfalls
This may lead to an adaptive radiation of species (e.g., Galapagos Islands), which is a rapid speciation of organisms in this new environment.
Sympatric speciation
Sympatric speciation
genetic changes create a reproductive barrier that allows a new species to arise even though it is within breeding distance. e.g., polyploidy - having more than two sets of chromosomes
Autopolyploidy: doubling of chromosomes within an individual
Non-disjunction of chromosomes happens during meiosis. Homologous or sister chromosomes do not separate properly, creating daughter cells with abnormal chromosome numbers.
Allopolyploidy: a cross between two close species
Offspring are usually sterile, but these taxa can still spread vegetatively
If autopolyploidy occurs in this “sterile” offspring, then it becomes fertile and can produce gametes
Modern synthesis
Modern synthesis
Population Genetics merged Darwinian evolution and Gregor Mendel's principles
Mendel and Darwin were contemporaries, with much overlap in their scientifically productive years. Available evidence shows that Mendel knew much about Darwin, whereas Darwin knew nothing of Mendel or the method of inheritance he described.
Evolutionary theory needed an explanation for inheritance of information, and Gregor Mendel provided this method of inheritance (i.e. genetic information)
Terminology
Population: localized group of individuals belonging to the same species
Species: a group of individuals (populations) that actually or potentially interbreed in nature
Allele: one of many forms of a gene
Genotype: all genes in an organism
Gene pool: sum total of all alleles of all the genes of all individuals in a population.
Phenotype: the physical appearance of an organism
Above: Peas plants and an image of Gregor Mendel
Mechanisms of Evolution
Mechanisms of Evolution
A mutation is a change in am organism's genetic information (DNA)
Most are detrimental, but these changes are the raw material for evolution
Mutations can creates new alleles and allele frequencies [Remember, evolution is the change in allele frequency in a population over time]
Appearance of new members into the population will introduce new alleles, and change proportions or frequencies within population.
For plants, this could be the appearance of pollen into a flowering population from a distant location
The change in the frequency of a gene variant (allele) in a population due to random sampling of organisms
Genetic drift is the effect of chance on individuals within the population
Laws of probability will greatly affect small populations more than large populations
Founder effect: loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population
Bottleneck effect: a population's size (and its genetic variation) is reduced for at least one generation
If and when the population recovers, the descendants will only carry the alleles from "bottleneck individuals", which is usually reduced genetic variation
This is a big concern with endangered species, since their reduced variability many further impact their success in the environment, leading to extinction
the process by which favorable traits that are heritable become more common in successive generations of a population of reproducing organisms
Unfavorable traits that are heritable become less common.
Acts on the physical traits (phenotype) of an organism, such that favorable traits allow the organism to survive and reproduce
Over time this creates adaptations that specialize organisms to a particular ecological niche and new species
Artificial selection: a similar process that is controlled by humans to breed favorable plants and animals
Negative selection or purifying selection: selective removal of alleles that are deleterious
Sexual selection, a type of natural selection, favors alleles that allow an organism to successfully mate. This is common in animals that display different morphologies for sexual display
Plants tend not to have these behaviors, but inbreeding can result in similar changes in allele frequencies
Inbreeding is mating of closely-related individuals, or the same individual (e.g. self-pollination)
There are many mechanisms in nature to insure cross-pollination and "mixing of alleles" in plant populations. This reduces the accumulations of damaging alleles in a population.
In certain environments, such as constantly changing landscapes (e.g. stream edges), the need to flower and wait for cross-pollination is selected against.
Self-pollination, with all of its evolutionary limitations, allows for the production of seeds in these environments.
Hardy-Weinberg equilibrium
Hardy-Weinberg equilibrium
The H-W equilibrium is a mathematical calculation, or test, for whether the process of evolution is occurring.
Remember, all ideas in science need to be testable, and researchers compare null hypotheses against alternative hypotheses to show evidence
The H-W equilibrium is a mathematical way that can show if a population is experiencing a change in allele frequency over time (i.e., evolution)
The frequency of alleles in a population’s gene pool remains constant, unless…
Mutations occur and accumulate, or...
Mating occurs between populations, or...
Population size is small, or...
Natural selection occurs, or...
Mating is selective and not random
Looking back at the Mechanisms of Evolution, we see that we could have just said "The frequency of alleles in a population’s gene pool remains constant, unless... one of the mechanisms of evolution is occurring"
One or more of these conditions usually occurs, therefore the frequency of alleles changes within a population… that is evolution!
Conversely, if none of these occur, then allele frequencies do not change, and the populations will not evolve. This is the null hypothesis
In other words, the Hardy-Weinberg Equilibrium can be used as a null hypothesis, compared to values from a real population, to describe significant deviations from the Equilibrium. If the deviation is significant, then the gene frequencies are changing (not at equilibrium), supporting the alternate hypothesis that evolution is occurring.
Micro-evolution and Macro-evolution
Micro-evolution and Macro-evolution
What is micro-evolution? Evolution on a small scale; within a single population of a species. Usually takes place over thousands and millions of years.
What is macro-evolution? Evolution "above the species level" (i.e. at levels such as family, order, class, etc.). Usually takes place over tens and hundreds of millions of years.
Macro-evolution evolves geologic time, usually the fossil record, and major changes in plant evolution from ancestor groups to descendant groups
e.g. the origin of angiosperms from gymnosperms; the extinction of many spore-bearing groups during the Permian Period.
Are they separate processes? Of course not...
Modes of Macroevolution
Modes of Macroevolution
Phyletic Gradualism
Phyletic Gradualism
Evolution occurs at a slow, but constant rate
Species continue to adapt to new challenges over the course of their history, gradually becoming new species
There is no clear line of demarcation between the old species and the new species
Punctuated Equilibrium
Punctuated Equilibrium
Abrupt changes in form followed by long periods of stasis
Most sexually-reproducing species will show little change for most of their geological history
When phenotypic evolution occurs, it is localized in rare events
Branching speciation occurs relatively quickly compared to the species' full and stable duration on earth
e.g. Colorado blue columbines (Aquilegia coerulea) have a recessive spurless trait that appears in 25% of the population (UC Santa Barbara 16Feb2022)
This trait is controlled by one gene, and a mutation can create a morphologically different "hopeful monster"
This shows that adaptation can occur in large jumps, rather than gradual change over time.
Above: Colorado blue columbines (Aquilegia coerulea) with spurred wild-type (right), and recessive spurless type (left)
Convergent Evolution
Convergent Evolution
Species from uncommon ancestors, evolve a similar form or function
There are many examples of convergence in the plant kingdom
Plant form in arid environments: cacti (Cactaceae) and spurges (Euphorbiaceae) look alike, but evolved from different ancestors.
Carnivorous "pitcher plants" (i.e. Sarracenia, Cephalotus, Nepenthes) have a similar form for catching insects, but originate from different orders
Conifers and the She-oaks, a flowering plant in the Casuarinaceae
Ancient horsetails (Calamites) and modern day bamboo (e.g. Bambusa)
Tree-like gymnosperm cycads (Cycadaceae) and modern day palms (Arecaeae)
Gnetophytes and angiosperms share several features: netted veins in leaves, vessels in wood, flower-like cones, double fertilization, angiosperm-like seed
There is a debate whether these features are convergence or homologous
Grass-like morphology, or linear leaves from the ground, can be found in the quillworts (Isoetales), the curlygrass ferns (Schizaeaceae), as well as true grasses (Poales),
Above: Stem succulent plants display convergent evolution. Plants in the New World deserts evolved from the cactus family. Plants in the Old World deserts evolved from the euphorb family.
Below: Pine (left) a well-known conifer, and the She-Oak or Casuarina (right) an angiosperm with pine-like leaves and cone-like fruits
Taxonomy is the science of classification that involves naming, describing, and arranging all living organisms, including plants and animals. It encompasses the processes of identification, characterization, and classification based on various criteria such as genetic, biochemical, and morphological traits.
Taxonomy plays a crucial role in organizing biological diversity and understanding the relationships between different organisms.
Cladistics is a method of biological classification that categorizes organisms based on shared traits and their common evolutionary history. It involves analyzing characteristics to hypothesize relationships among organisms and reconstruct evolutionary trees.
In cladistics, groups of organisms, known as "clades," are recognized by unique features that were not present in distant ancestors, indicating a shared lineage.
Questions for thought
Questions for thought
What is taxonomy and how are plants ordered?
What is evolution?
How does evolution occur? What are the agents?
What is cladistics?
Could you make a cladogram from a character chart?
Additional Resources
Additional Resources
Polyploid plants maintain several distinct flower types through ancient genetic architecture (Phys.org 18Sep2025)
└Luo et al. (2025) Genetic architecture of the S‐locus supergene revealed in a tetraploid distylous species
Tomatoes in the Galápagos are quietly de-evolving (Phys.org 24Jun2025)
└Jozwiak et al. (2025) Enzymatic twists evolved stereo-divergent alkaloids in the Solanaceae family
Solving the evolutionary puzzle of polyploidy: How genome duplication shapes adaptation (Phys.org 23Jan2025)
└Hatakeyama et al. (2025) Evolutionary Innovation by Polyploidy
Evolution in real time: Scientists predict—and witness—evolution in a 30-year marine snail experiment (Phys.org 11Oct2024)
└Castillo et al. (2024) Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails
How fast does evolution happen? (LiveScience 9Sep2024)
└Stroud et al. (2024) Fluctuating selection maintains distinct species phenotypes in an ecological community in the wild
Interaction with insects accelerates plant evolution (Phys.org 19June2024)
└Dorey et al. (2024) Biotic interactions promote local adaptation to soil in plants
Microevolution can predict how evolution works on much longer timescales (Phys.org, 10May2024)
└Holstad et al. (2024) Evolvability predicts macroevolution under fluctuating selection
Does Urbanization trigger evolution (Phys.org 20Oct2023)
└Fukano et al. (2023) From green to red: Urban heat stress drives leaf color evolution
Ancestral bottleneck could have spelled doom for humans (Phys.org 31Aug2023)
Humans continue to evolve (Phys.org 20Dec2022)
Evidence of punctuated equilibrium in Colorado blue columbine (Cabin et al. 2022)
Play the PBS Evolution Lab Game!
Evolution is unpredictable and irreversible (Univ. of Penn. 2015)
Speciation through genome duplication more common in plant evolution than previously thought (Univ of Indiana)
Phylogeny of Life, Cladistics, Modern Synthesis, and Macroevolution (Univ of Califronia Berkeley Museum of Paleontology)
Hardy-Weinberg (Kansas State University)
Agents of Evolution (Univ. of Maryland)
Biological Classification (Univ. of Buffalo)
Are viruses alive? (LiveScience 14Sep2012)
A case of sympatric speciation (In Defense of Plants 1May2017)
Does inbreeding counteract the benefits of self-pollination? (Am.J. Bot 16Nov2021)
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