The diversity of living organisms provides tangible evidence of evolutionary processes. Contemporary species are the result of a hereditary transformation process that has affected all living beings over time, gradually modifying their morphology and interactions with the environment. The phenotype, i.e., the set of observable characteristics of an organism, is influenced by the genotype—the genetic information encoded in DNA—and by interactions with environmental factors.
Charles Darwin was the first to correctly conceptualize the mechanism underlying these processes, formulating the theory of evolution by natural selection: individuals possessing advantageous traits tend to have higher reproductive success (and a greater chance of survival) and pass these traits on to their offspring, whereas individuals with disadvantageous traits have a lower probability of reproducing. In geographically isolated populations, natural selection can lead to population differentiation and the formation of new species.
In the centuries following Darwin, his evolutionary theory has been consolidated by extensive empirical evidence, including biogeographic distribution (vicariance), structural homologies, evolutionary convergences, and the universality of cellular structure and genetic mechanisms. At the same time, complementary perspectives and refinements have emerged concerning selection mechanisms, reproductive isolation processes, and the pace of evolution. Studies on mutations, genome evolution, and molecular gene regulation mechanisms have further clarified how variation, selection, and genetic drift interact to drive evolutionary change, providing an integrated framework for population dynamics and species formation.
Once evolutionary theory was widely accepted, biological classifications increasingly emphasized evolutionary relationships, grouping species not only based on morphological similarity but above all according to evolutionary affinities. This study, which aims to reconstruct relationships of common ancestry between species, is known as phylogenetics.
Phylogenetics aims to reconstruct the evolutionary history of species by integrating paleontological, morphological, embryological, genetic, and biochemical data. This approach provides a coherent framework to define natural species, understand processes of speciation and adaptation, interpret geographic distributions, and construct taxonomic classifications based on actual evolutionary relationships, avoiding misleading interpretations arising from convergence or superficial similarity.
Each species combines ancestral characters and derived characters. The sharing of derived characters among multiple species indicates the existence of a common ancestor, according to the principle of phylogenetic relatedness. Relationships among taxa are represented using dendrograms or cladograms (phylogenetic trees).
A crucial step toward the desired objectivity of classifications has been achieved in recent decades through molecular genetic techniques. Specific techniques have made it possible to quantify the number of mutations in a given gene (DNA segment) and compare differences among individuals from different populations, allowing the reconstruction of relatedness levels. These relationships are represented as phylogenetic trees, graphically derived from statistical analyses.
The arrangement of branches in the tree depends on numerous variables; however, the method tends to produce internally consistent results under controlled conditions. The resulting evolutionary framework may still vary depending on the number of sequenced samples per population, the number of populations analyzed, the number of genes considered, the precision in sample localization and identification, and the statistical algorithm employed.
Important: Phylogenetic trees are a reliable tool for assessing relatedness among taxa, but they do not determine taxonomic status. They indicate sets and subsets, but do not specify whether a particular dichotomy corresponds to a taxonomic rank, such as species or subspecies.
Additional biological criteria are needed to define species or subspecies. Taxa within the ‘species group’ are defined primarily by reproductive isolation criteria rather than by strictly phylogenetic criteria. Therefore, analyses aimed at defining them should focus not only on genetic distance but also on the presence of unique haplotypes - specific combinations of alleles not shared with other populations - which suggest reproductive isolation.