Evolutionary relationships are reconstructed by comparing evidence across species. Extant organisms provide abundant molecular and genetic data, while extinct organisms contribute fossil and occasionally molecular snapshots that reveal ancestral features and branching patterns.

Key idea: combining living and fossil evidence

Comparisons among species work best when multiple, independent lines of evidence converge on the same pattern of relatedness.

This diagram contrasts monophyletic, paraphyletic, and polyphyletic groupings on a branching tree. It helps clarify how phylogenetic hypotheses aim to identify true clades (monophyletic groups) rather than groupings produced by shared ancestral traits or convergent evolution. Source

Using both types helps resolve cases where living species have diverged greatly, where key intermediate forms are missing from modern ecosystems, or where rapid evolution obscures earlier history.

Evidence from extant (living) species

Molecular and genetic data

Living organisms supply large, comparable datasets:

• DNA nucleotide sequences (nuclear, mitochondrial, chloroplast)

• Protein amino acid sequences (conserved proteins can be compared across distant lineages)

• Gene order and shared genomic features (e.g., conserved regulatory regions)

• Shared derived molecular changes (specific substitutions or insertions unlikely to arise independently)

Closely related species generally show higher overall sequence similarity, and patterns across many genes reduce the chance that a single gene’s history misleads the overall relationship.

The image on this page shows a phylogenetic tree that summarizes inferred relationships among taxa using molecular data. It reinforces the idea that sequence comparisons (typically via alignment and counting differences) can be translated into a branching pattern that represents hypothesized common ancestry. Source

Morphology and observable traits

Extant species also provide:

• Comparative anatomy (structures can be measured consistently across taxa)

• Developmental comparisons (timing and pattern of trait formation can reveal deep similarity)

• Trait-function links that help interpret whether similarity is likely inherited or a response to similar environments

Because natural selection can produce superficial similarity in unrelated groups, morphological comparisons are strongest when paired with molecular evidence.

Evidence from extinct species

Fossil morphology and transitional forms

Fossils extend the record beyond what is alive today by preserving:

This 3D fossil model highlights skeletal anatomy of Tiktaalik, a classic transitional vertebrate with a mix of fish-like and tetrapod-like features. It provides a concrete example of how fossil morphology can reveal intermediate character combinations and help infer the order in which traits evolved. Source

• Ancestral character states that may be absent in modern descendants

• Mosaic traits (combinations of features that bridge major groups)

• Ordered appearances of features through stratigraphic context, supporting sequences of change

Extinct taxa can reduce “long-branch” gaps between living groups, clarifying which traits are likely inherited from common ancestors versus evolved later in separate lineages.

Molecular data from extinct organisms (when preserved)

Some extinct organisms yield informative molecules:

• Ancient DNA (aDNA) from relatively recent fossils (often fragmented)

• Ancient proteins that persist longer than DNA in some contexts

• Biomolecular signatures that support placement of fossils when morphology is incomplete

These data can directly test whether a fossil aligns more closely with one living lineage than another, strengthening evolutionary hypotheses when morphology alone is ambiguous.

Integrating extant and extinct evidence to infer relationships

How multiple datasets deepen understanding

Evolutionary relationships are best treated as testable hypotheses supported by converging evidence:

• Compare morphological datasets (extant + fossil) with molecular/genetic datasets (mostly extant, sometimes extinct).

• Check whether independent datasets support the same branching pattern.

• Use extinct taxa to interpret which traits are ancestral versus derived, improving character coding and comparisons among living groups.

Common challenges and how scientists address them

Both evidence sources have limits that must be considered:

• Fossil record incompleteness and preservation bias can omit key lineages.

• DNA degradation limits genetic sampling from most extinct organisms.

• Trait evolution rates differ (some genes/traits change quickly, others slowly), so broad sampling across characters is important.

• Homoplasy risk (similar traits evolving independently) is reduced by emphasizing many independent characters and prioritizing consistent patterns across data types.

When molecular, morphological, and genetic evidence from extant and extinct organisms align, confidence in inferred evolutionary relationships increases substantially.