Phylogenetics reconstructs the evolutionary relationships between different species, mapping out which species share more recent common ancestors and which diverged from each other longer ago. Cladistics is the specific, now-dominant method for doing this rigorously: it groups species strictly according to shared common ancestry, evidenced by shared derived traits inherited from a common ancestor, rather than by overall physical resemblance. This distinction matters because ancestry and surface-level similarity don't always line up the way intuition might suggest.
Shared ancestry and shared appearance are genuinely different things
Two species can look strikingly similar to each other for two entirely different underlying reasons: they might share that similarity because they inherited it from a relatively recent common ancestor, or they might have evolved that similarity entirely independently, in response to similar environmental pressures, without sharing anything close to a recent common ancestor at all. Cladistics is specifically designed to distinguish between these two cases, since only the first kind of similarity, inherited from shared ancestry, actually reflects genuine evolutionary relatedness, while the second kind, convergent similarity arrived at independently, doesn't.
Convergent similarity can mislead a purely appearance-based classification
A classification system based purely on overall physical resemblance risks grouping species together based on convergent similarity, traits that evolved independently in unrelated lineages facing similar environmental pressures, mistaking that superficial resemblance for genuine close relatedness. Cladistics avoids this specific trap by focusing analysis on shared derived traits, features that trace back to a specific shared ancestor, rather than on overall appearance, which is exactly why two species that look remarkably alike can still end up placed quite far apart on a rigorously constructed cladogram, once their apparent similarity is properly traced back to independent evolutionary origins rather than to shared ancestry.
What we're still unsure about
The basic distinction cladistics draws between shared-ancestry similarity and independently evolved convergent similarity, and the method's now-dominant status in modern evolutionary biology, are well established, extensively confirmed findings, especially since genetic sequence data became widely available to test earlier appearance-based classifications directly. What remains more genuinely an active area of ongoing research is resolving specific, still-contested branches of the tree of life where different lines of evidence, morphological, genetic, and from different genes within the same genome, sometimes point toward genuinely conflicting evolutionary relationships — researchers continue actively working through these specific unresolved or disputed branches, rather than treating every part of the tree of life as already fully, uncontroversially settled.
This sits inside Phylogenetics & Cladistics, one of seven topics in Evolution, one of six domains in Biology, one of seventeen subjects the app can quiz you on.