Organisms share fundamental characteristics because they—and their genes—have descended from a common ancestor in the distant past. Common ancestry between humans and all other living things is a fundamental principle that explains countless facts. It is one of the two greatest principles of evolution.
All species, extant and extinct, form a great “Tree of Life” or phylogenetic tree. Closely adjacent twigs represent living species derived only recently from their common ancestors (shared ancestors). Twigs on more distant branches represent species derived from more ancient common ancestors. All the organisms we know of have descended from a single ancestral form of life that lived between 4 and 3.7 billion years ago. The first cellular organisms that we know of were prokaryotes that evolved into two great groups, the Bacteria and Archaea. Eukaryotes evolved from a symbiotic association between an archaean and a bacterium that evolved into the mitochondrion. Complex multicellular life forms evolved many times. Among these groups are plants, brown algae, some fungi, and animals.
There are two major processes in the evolution of a higher taxon. Anagenesis is the evolutionary change of features within a single lineage (species). Cladogenesis is the branching of a lineage into two more descendant lineages. Anagenesis in descendant lineages results in divergent evolution. A phylogeny is the history of the events by which species or other taxa have successively arisen from common ancestors. The branching diagram that portrays this history is called a phylogenetic tree. All the descendants of any one ancestor form a clade. Two clades that originate from a common ancestor are called sister groups. The lineage leading to the most recent common ancestor (MRCA) of all the species in the phylogeny is called the root of the tree. Our estimate of how taxa are related to one another is based on characteristics that are homologous among the taxa. Features are homologous among species if they have been inherited from common ancestors. Each trait of an organism is called a character, which may have various character states. Homologous character states that are shared among species provide evidence of common ancestry if they evolved only once. Parsimony, which minimizes the fewest evolutionary changes, is one method for inferring phylogenies.
Branches sometimes rejoin, so that relationships among organisms may form a network rather than just a branching tree. In these cases of hybrid speciation, various phenotypic features and DNA markers through the genome reveal two ancestral sources. Horizontal gene transfer (HGT) is the nonreproductive passage of genes among organisms. HGT has played a major evolutionary role among prokaryotes. A branching tree that portrays the history of DNA sequences of a gene (haplotypes) is often called a gene tree or a gene genealogy. Different genes sometimes have had different phylogenetic histories. Thus, a gene tree can differ from the species tree, the phylogeny of the species from which the genes are sampled. One of the most important processes by which genomes have increased in size is gene duplication. The genes that originate from an ancestral gene duplication are paralogous, whereas the genes that diverge from a common ancestral gene by phylogenetic splitting at the organismal level are orthologous. This process may occur repeatedly over evolutionary time, generating a gene family.
One of the most important uses of phylogenetic information is to reconstruct the history of evolutionary change in interesting characteristics by “mapping” character states on the phylogeny and inferring the state in each common ancestor, right back to the root of the entire tree. In the simplest methods, we assign to ancestors those character states that require us to postulate the fewest evolutionary changes for which we lack independent evidence. The proportion of base pairs that differ between homologous DNA sequences in two species increases with the amount of time that has elapsed since the species originated from their common ancestor. As long as the increase is linear with time, the difference in sequence can serve as a molecular clock. Rates of evolution differ among the different positions in codons and among different genes in the genome. Rates of sequence evolution also differ among groups of organisms, especially distantly related taxa. There is not a universal clock.
A phylogenetic perspective on the diversity of organisms and their characteristics enables biologists to trace patterns of evolution of various characteristics.
- Most features of organisms have been modified from pre-existing features. A character may be homologous among species, but a given character state may not be. The most common criteria for hypothesizing homology of anatomical characters are correspondence of position relative to other parts of the body and correspondence of structure. Correspondence of shape or of function is not a useful criterion for homology.
- Rates of character evolution differ. Some characters, often called conservative characters, are retained with little or no change over long periods among the many descendants of an ancestor. Evolution of difference characters at different rates within a lineage is called mosaic evolution. This principle says that a species evolves not as a whole, but piecemeal: many of its features evolve more or less independently. Every species is a mosaic of plesiomorphic (ancestral, or “primitive”) and apomorphic (derived, or “advanced”) characters. It is inaccurate or even wrong to consider one living species more “advanced” than another.
- Evolution is often gradual. Many higher taxa that diverged in the distant past are very different and are not bridged by intermediate forms, either among living species or in the fossil record. However, the fossil record does document intermediates in the evolution of some higher taxa. Gradations among living species are very common, as we would expect if characters evolve gradually.
- Homoplasy is common. Homoplasy—the independent evolution of a character or character state in different taxa—includes convergent evolution (convergence), parallel evolution (parallelism), and evolutionary reversal. Dollo’s law is the principle that complex characters, once lost, are unlikely to be regained; however, there are exceptions.
- Phylogenies describe patterns of diversification. Divergent evolution of numerous related lineages within a relatively short time is called evolutionary radiation. In most cases, the lineages become modified for different ways of life, and the evolutionary radiation may be called an adaptive radiation. Evolutionary radiation, rather than sustained, directional evolutionary trends, is probably the most common pattern of long-term evolution.
We can identify several patterns that confirm the historical reality of evolution and which make sense only if evolution has occurred.
- The hierarchical organization of life. A historical process of branching and divergence will yield objects that can be hierarchically ordered, but few other processes will do so.
- Homology. Similarity of structure despite differences in function follows from the hypothesis that the characteristics of organisms have been modified from the characteristics of their ancestors, but it is hard to reconcile with the hypothesis of intelligent design. Likewise, the nearly universal, arbitrary genetic code makes sense only as a consequence of common ancestry.
- Embryological similarities. Homologous characters include some features that appear during development, but would be unnecessary if the development of an organism were not a modification of its ancestors’ ontogeny.
- Vestigial characters. Some features, displayed by almost every species, served a function in the species’ ancestors, but do so no longer.
- Convergence. There are many examples in which functionally similar features actually differ profoundly in structure. Likewise, evolutionary history is a logical explanation (and creation is not) for cases in which different organisms use very different structures for the same function.
- Suboptimal design. Evolutionary history explains many features that no intelligent engineer would be expected to design.
- Geographic distributions. The distributions of many taxa make sense only if they have arisen from common ancestors.
- Intermediate forms. The hypothesis of evolution by successive small changes predicts the innumerable cases in which characteristics vary by degrees among species and higher taxa.
Even if there were no fossil record, the evidence from living species would be more than sufficient to demonstrate the historical reality of evolution: all organisms have descended, with modification, from common ancestors.
—November 2021
—January 2022
Lance Jones 