Speciation & Phylogenetic Inference

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Abstractions about speciation, common ancestry, homology, phylogenetic comparison, evolutionary tempo, and inference from related organisms.

14 abstractions in this family — domain-specific abstractions that sit near one another in structural-signature space (k-means over structural-signature embeddings). Each is shown with its short description.

• Allopatric speciation — The evolution of reproductive isolation after geographic separation reduces gene flow between formerly connected populations.
• Breeding back — Select among living domestic descendants for inherited traits associated with an extinct or altered ancestral form, producing a new lineage that resembles the target without recreating its lost genome.
• Disk-covering method — A divide-and-conquer metatechnique for large phylogenetic inference that solves overlapping local subsets and combines their results into a global tree.
• Emergent evolution — Explain evolutionary history through the appearance of qualitatively novel levels or properties that depend on lower-level processes yet are not exhaustively characterized in the vocabulary used for those processes.
• Lamarckism — The evolutionary doctrine that characteristics acquired through use, disuse or environmental response can be inherited by offspring.
• Most recent common ancestor — The latest ancestral individual, population or gene lineage from which every member of a specified descendant set is inferred to descend.
• Phenetics — A taxonomic method that classifies organisms by quantified overall observable similarity without privileging inferred evolutionary ancestry.
• Phylogenetic autocorrelation — Statistical dependence among species or cultural units caused by shared ancestry, violating independent-sample assumptions when traits are inherited along a phylogeny.
• Phylogenetic bracketing — Inference of an unknown organismal trait from its distribution among close relatives positioned on a phylogenetic tree.
• Pithecometra principle — The nineteenth-century evolutionary thesis that humans belong within the ape lineage rather than forming a biologically separate creation.
• Punctuated gradualism — An evolutionary tempo hypothesis in which a lineage shows long relative stasis interrupted by comparatively rapid morphological change without requiring branching speciation.
• Push of the past — A survivorship bias in birth-death diversification histories whereby long-lived clades are disproportionately those with unusually strong early growth, creating an apparent later slowdown.
• Quartet distance — The number or normalized fraction of four-leaf subsets on which two phylogenetic trees induce different quartet topologies.
• Sequence homology — The shared evolutionary ancestry of DNA, RNA or protein sequences, inferred from statistically and structurally supported similarity but treated as a historical relation rather than a percentage-valued resemblance.