AP Syllabus focus:
‘Eukaryotes share linear chromosomes and genes containing introns, reflecting their common evolutionary origin.’
Eukaryotic genomes carry distinctive features that are shared across diverse lineages. Linear chromosomes and intron-containing genes are especially informative because they depend on complex, conserved cellular machinery that likely evolved once and was inherited.
What these shared features suggest
Across animals, plants, fungi, and protists, two genomic traits recur:
Linear nuclear chromosomes
Genes with introns that are removed from RNA before translation
Because both traits require coordinated molecular systems, their broad distribution supports common ancestry among eukaryotes and helps reconstruct evolutionary history.
Linear chromosomes in eukaryotes
Eukaryotic nuclear DNA is typically organised as multiple linear DNA molecules, each with specialised end structures and packaging.
Telomeres cap the ends of linear chromosomes using repeated DNA sequences plus the shelterin protein complex, which helps hide chromosome ends from being mistaken for DNA breaks. The diagram shows key structural features (including the single-stranded overhang and higher-order end structures) that prevent end-to-end fusion and support stable inheritance of linear chromosomes. Source
Linear chromosome: A chromosome consisting of a DNA molecule with two physical ends that must be protected and fully replicated to maintain genome stability.
Key shared features and implications:
Ends create unique problems:
DNA ends resemble double-strand breaks, so cells need end-protection mechanisms to prevent inappropriate repair.
Replicating the extreme ends is difficult; without dedicated solutions, chromosomes would shorten across cell divisions.
Telomeres (repetitive end DNA plus associated proteins) help:
Protect chromosome ends from degradation and fusion
Provide a buffer against end-replication limitations
Conserved chromosome architecture:
Eukaryotes package linear DNA with proteins into chromatin, enabling regulated access to genes.
Many lineages share similar strategies for chromosome segregation, reflecting inherited systems rather than independent invention.
Why this is evidence for evolutionary history:
The widespread presence of linear chromosomes with comparable end-maintenance strategies across eukaryotes is best explained by inheritance from a common ancestral eukaryote, not repeated convergent evolution of the same complex suite.
Introns in eukaryotic genes
Many eukaryotic genes are interrupted by non-coding segments that are transcribed but removed from the RNA.
Intron: A non-coding nucleotide sequence within a gene that is transcribed into pre-mRNA but removed during RNA processing, leaving coding exons joined to form mature mRNA.
Introns matter because they require a conserved processing pathway:
Transcription produces pre-mRNA containing both introns and exons.
RNA splicing removes introns and ligates exons to form mature mRNA.
Pre-mRNA splicing occurs through two catalytic steps that remove an intron and join adjacent exons. This diagram highlights hallmark features of the process, including recognition of splice sites, formation of a lariat intermediate, and exon–exon ligation to produce mature mRNA. Source
Splicing relies on recognisable sequence signals at intron boundaries and a large, multi-component molecular machine that must function accurately to preserve reading frames.
Splicing depends on specific sequence landmarks in the intron—most notably the 5′ splice site, branch point, and 3′ splice site—that guide spliceosome assembly. The figure illustrates how these signals are read by splicing factors in an ordered pathway to ensure precise intron excision and correct joining of exons. Source
Shared biological consequences:
Introns enable alternative splicing, where different exon combinations can be produced from the same gene, increasing protein diversity without increasing gene number.
Introns can facilitate evolutionary change by allowing:
Recombination within introns with less risk of disrupting coding sequences
New exon combinations that may be selected for if they improve function
Why introns inform evolutionary history:
The presence of introns across many eukaryotic groups, together with broadly similar splicing signals and splicing machinery, supports the idea that intron-containing genes arose early in eukaryotes and were inherited.
Using these traits to infer common ancestry
When biologists compare genomes across eukaryotes, they look for shared, complex features unlikely to evolve repeatedly in the same way.
What makes linear chromosomes strong evidence
They require coordinated solutions for:
End protection
End replication
Accurate segregation of multiple chromosomes
Similar solutions appearing across eukaryotes indicate descent from an ancestor that already had these systems.
What makes introns strong evidence
Introns are not merely “extra DNA”; they imply:
A functional splicing process
Tolerance of intron insertion/retention over evolutionary time
Shared patterns of intron presence across related organisms can help infer:
Which introns were present in ancestral genes
Where introns were gained or lost in specific lineages
Interpreting variation without leaving the core claim
Not every eukaryote has the same intron density, and chromosome structures can differ in number and size. These differences fit evolutionary history as modifications of inherited systems, rather than separate origins of linear chromosomes and intron-containing genes.
FAQ
Many bacteria and archaea have streamlined genomes under selection for rapid replication.
Group I/II introns exist in some prokaryotes, but widespread spliceosome-type introns are uncommon, partly because they require extensive processing machinery.
They compare homologous genes across multiple species and map intron positions onto an evolutionary tree.
Shared intron positions in distant descendants suggest ancestral presence, whereas lineage-specific introns suggest later gain.
Intron phase refers to where an intron interrupts a codon: phase 0, 1, or 2.
Phase patterns can affect how easily exons can be recombined without frameshifts, influencing how exon shuffling might occur over evolutionary time.
Telomeres combine repetitive DNA with multiple binding proteins and regulated length control.
Because failure is catastrophic (end-to-end fusions, instability), the shared reliance on dedicated telomere systems across eukaryotes suggests inheritance rather than repeated, identical innovation.
Some introns contain regulatory elements, encode small RNAs, or influence transcription and mRNA export.
Even when not directly functional, introns can shape evolution by altering recombination patterns and enabling new splicing outcomes.
Practice Questions
State two genomic features shared by eukaryotes that support their common ancestry. (2 marks)
Linear nuclear chromosomes (1)
Genes containing introns (1)
Explain how linear chromosomes and intron-containing genes can be used as evidence for common ancestry among eukaryotes. (5 marks)
Linear chromosomes have DNA ends that require specialised maintenance (1)
The need for conserved end-protection/replication solutions makes independent origin unlikely (1)
Introns are transcribed into pre-mRNA and must be removed by splicing (1)
Splicing requires conserved sequence signals and complex molecular machinery, supporting inheritance (1)
Similarity and broad distribution of these features across eukaryotes supports descent from a common ancestral eukaryote (1)
