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Speciation: A splitting event that creates two or more distinct species from an ancestral species. It can be rapid or gradual and results from a two-step process of genetic isolation and genetic divergence. This process leads to the formation of evolutionarily independent populations.

• Genetic Isolation: The first step in speciation, where a barrier to gene flow isolates two populations within a species.

• Genetic Divergence: The second step in speciation, where mutation, natural selection, and genetic drift act independently in each of the isolated populations, causing their allele frequencies to diverge. If gene flow stops, allele frequencies in isolated populations can diverge, leading them to evolve independently.

• Species: An evolutionarily independent population or group of populations. Biologists commonly use three criteria for identifying species: the biological species concept, the morphological species concept, and the phylogenetic species concept.

Species Concepts

• Biological Species Concept: Defines species based on reproductive isolation, meaning members of populations either do not interbreed or fail to produce viable, fertile offspring after mating, resulting in a lack of gene flow.

◦ Prezygotic isolation: Occurs when individuals of different species are prevented from mating successfully.

◦ Postzygotic isolation: Occurs when hybrid offspring do not survive or reproduce.

• Morphospecies Concept: Identifies species based on individual lineages differing in size, shape, or other morphological features.

◦ Cryptic species: Species that differ in non-morphological traits and cannot be identified by the morphospecies concept.

• Phylogenetic Species Concept: Identifies species based on their evolutionary history, defining a species as the smallest monophyletic group on a phylogenetic tree.

◦ Monophyletic group (clade or lineage): Consists of an ancestral population plus all of its descendants.

◦ Synapomorphies: Homologous traits found in a common ancestor and its descendants but missing in more distant ancestors, used to identify monophyletic groups.

Speciation Mechanisms

• Allopatry / Allopatric speciation: Populations that live in different geographic areas are in allopatry. Speciation that begins with geographic isolation is called allopatric speciation. It starts via:

◦ Dispersal: The movement of individuals from one place to another.

◦ Vicariance: The physical splitting of a habitat by a physical barrier, splitting a population into physically isolated subgroups.

• Sympatry / Sympatric speciation: Populations or species that live in the same geographic area—close enough to interbreed—live in sympatry. Speciation that occurs among populations within the same geographical area is called sympatric speciation. It can be initiated by:

◦ External (extrinsic) events: Such as disruptive selection based on different ecological niches or mate preferences.

◦ Internal (intrinsic) events: Such as chromosomal mutations.

• Disruptive selection (divergent selection): Acts on diverse traits, including morphology and behaviors, and can involve survival in an environment (ecological selection).

• Niche: The range of ecological resources that a species can use and the range of conditions that it can tolerate.

• Polyploidy: The condition of possessing more than two complete sets of chromosomes, caused by massive errors in meiosis or mitosis.

◦ Autopolyploid: Individuals produced when a mutation results in a doubling of the chromosome number, with chromosomes all from the same species.

◦ Allopolyploid: Individuals created when parents of different species mate and an error in mitosis occurs, resulting in viable, nonsterile offspring with two different sets of chromosomes.

Outcomes of Secondary Contact

• Reinforcement: If two populations have diverged extensively and hybrid offspring have low fitness, natural selection favors traits that prevent interbreeding among the populations.

• Hybrid zone: A geographic area where interbreeding between two populations occurs and hybrid offspring are common.

• Hybridization (leading to new species): When two species interbreed and produce viable hybrid offspring, a new species might result if the combination of genes allows them to occupy distinct habitats or use novel resources.

Phylogenetics and Life's History

• Phylogeny: The branching evolutionary history of a group of organisms.

• Phylogenetic tree: A simplified diagram of a phylogeny, showing evolutionary relationships.

◦ Nodes: Represent speciation events on a phylogenetic tree.

◦ Branches: Connect nodes and tips, representing lineages.

• Systematics: The discipline of biology that characterizes and classifies relationships among organisms.

• Taxonomy: The practice of describing, naming, and classifying individual species.

• Taxa: Higher-level groups of organisms that can be classified and named.

• Character or trait: Any genetic, morphological, physiological, developmental, or behavioral characteristic to be studied.

◦ Outgroup: A group closely related to the study group, used to distinguish ancestral versus derived traits.

◦ Ancestral trait: A character that existed in an ancestor.

◦ Derived trait: A modified form of the ancestral trait, found in a descendant and originating via mutation, selection, and genetic drift.

• Homology: Similarity in traits due to common ancestry.

• Homoplasy: Traits that are similar due to independent evolution, not common ancestry.

• Convergent evolution: The independent evolution of similar traits in distantly related organisms, often occurring as adaptations to similar environmental pressures. This is a common cause of homoplasy.

• Fossil: The physical evidence from an organism that lived in the past.

• Fossil record: The total collection of fossils that have been found throughout the world.

• Adaptive radiation: The rapid production of many descendant species from a single lineage, with these descendant species having a wide range of adaptive forms. It typically involves a monophyletic group that speciated rapidly and diversified ecologically into many niches.

• Cambrian explosion: A period approximately 541 million years ago (mya) where animals became larger and more complex, with the sudden appearance of diverse animal groups and the filling of many ecological niches.

• Mass extinction: The rapid extinction of a large number of diverse species around the world, where at least 60% of species are wiped out within 1 million years. Caused by catastrophic events.

• Background extinction: The lower, average rate of extinction due to normal environmental change, emerging disease, predation pressure, or competition