5.4 Non-Mendelian Genetics

Non-Mendelian genetics means inheritance patterns that don’t match Mendel’s simple predictions (like 3:1 or 9:3:3:1) because one or more Mendelian assumptions break down. Mendel assumed single genes with complete dominance, independent assortment, and autosomal (nuclear) inheritance. Deviations include: genetic linkage (genes on same chromosome → recombination frequencies and gene mapping), codominance (both alleles expressed—e.g., AB blood), incomplete dominance (blended heterozygote), sex-linked traits (X or Y linkage gives different parent/offspring patterns), pleiotropy (one gene affects many traits), and non-nuclear (mitochondrial/chloroplast) maternal inheritance. On the AP exam you’ll be asked to identify these patterns quantitatively (chi-square, recombination % → map units) and interpret pedigrees/data (LO 5.4.A). For a focused review and sample problems on each type, check the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and practice questions (https://library.fiveable.me/practice/ap-biology).

Mendel’s 3:1 ratio assumes simple dominant/recessive alleles that segregate independently. Real traits break those assumptions for several reasons (all in the CED): linked genes on the same chromosome don’t assort independently (use recombination frequency/map units), so offspring ratios shift; codominance and incomplete dominance change heterozygote phenotypes so you won’t see a 3:1 phenotype ratio; sex-linked (X- or Y-linked) genes give different patterns in males and females; pleiotropy means one gene affects many traits so segregation patterns are complicated; and non-nuclear (mitochondrial/chloroplast) inheritance is usually maternal and doesn’t follow Mendel’s laws. On the AP exam you should identify which mechanism fits the data and use quantitative tests (chi-square) when observed ratios differ from expected (EK 5.4.A.1). For a focused review, check the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and try practice problems (https://library.fiveable.me/practice/ap-biology).

Codominance vs. incomplete dominance—quick and AP-friendly: - Codominance: both alleles are fully expressed in the heterozygote, so the heterozygote shows a phenotype that includes both parental traits (different from either homozygote). Example: AB blood (both A and B antigens). This matches EK 5.4.A.1.ii—heterozygote ≠ either homozygote. - Incomplete dominance: neither allele completely masks the other, so the heterozygote has an intermediate (blended) phenotype between the two homozygotes. Example: red × white flowers → pink offspring (EK 5.4.A.1.iii). On the AP exam you should describe the heterozygote phenotype and predict genotypic/phenotypic ratios (use quantitative analysis when ratios deviate from Mendelian expectations). For more examples and practice questions on Topic 5.4, check the Fiveable study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and the Unit 5 overview (https://library.fiveable.me/ap-biology/unit-5). For extra practice, try the 1000+ AP problems at (https://library.fiveable.me/practice/ap-biology).

X-linked genes are on the X chromosome; Y-linked genes are on the Y. Because males are XY, they’re hemizygous for X-linked loci (only one X). That means a single recessive X allele will show in males, so X-linked recessive traits (like colorblindness) appear much more often in males. Key pedigree clues: affected males often have unaffected parents, affected fathers don’t pass the trait to sons but do pass the mutant X to all daughters (who may be carriers). Autosomal vs X-linked shows different father→son transmission. Y-linked traits occur only in males and transmit father → son in every generation (useful pedigree hallmark). For the AP exam you should be able to predict inheritance from pedigrees and data (EK 5.4.A.2); practice identifying hemizygous patterns and using pedigrees on free-response. For targeted review, check the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and drill pedigrees in the practice question bank (https://library.fiveable.me/practice/ap-biology).

Map distance (map units or centimorgans, cM) comes from recombination frequency. Formula: (number of recombinant offspring ÷ total offspring) × 100 = recombination frequency (%) = map units. So 10 recombinants out of 200 total → (10/200)×100 = 5% → genes are 5 map units apart (5 cM). Remember: 1% recombination ≈ 1 map unit. This is LO 5.4.A stuff—useful on AP free-response questions where you calculate genetic maps. For genes far apart, double crossovers make observed recombination lower than actual distance, so you need three-point crosses to detect double crossovers and get more accurate maps (topic links with meiosis and recombination). For more practice and examples, check the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and Unit 5 overview (https://library.fiveable.me/ap-biology/unit-5). For extra problems, see the practice bank (https://library.fiveable.me/practice/ap-biology).

"Linked" genes are genes located on the same chromosome, so they tend to be inherited together instead of assorting independently like Mendel’s unlinked genes (EK 5.4.A.1). During meiosis, crossing over (recombination) can separate linked genes, but the closer two genes are, the less likely a crossover will occur between them. That’s why linked genes deviate from Mendelian 9:3:3:1 or 3:1 ratios—you see fewer recombinant phenotypes. You can quantify this: recombination frequency = (number of recombinants / total offspring) × 100 = map units (centimorgans). Lower recombination frequency → smaller map distance → stronger linkage. This idea is tested on the AP exam under non-Mendelian genetics and gene mapping. For a quick review, check the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and try practice questions (https://library.fiveable.me/practice/ap-biology) to see mapping problems.

Pleiotropy means one gene influences more than one phenotypic trait. In other words, a single mutant allele can cause multiple, seemingly unrelated effects—so those traits won’t segregate independently (CED EK 5.4.A.3). Classic examples: the sickle-cell mutation in the HBB gene alters red blood cell shape (anemia, pain crises) and also gives some malaria resistance. PKU (phenylketonuria) is one mutant enzyme that causes mental retardation, lighter skin/hair, and a musty odor if untreated. Marfan syndrome (FBN1) affects connective tissue and shows up in long limbs, lens dislocation, and aortic problems—all from one gene. On the AP exam you might be asked to explain how pleiotropy deviates from Mendelian ratios or to interpret data showing one genotype with multiple phenotypes. For a quick topic review, see the Non-Mendelian Genetics study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and practice problems (https://library.fiveable.me/practice/ap-biology).

Mitochondrial traits are usually inherited only from the mother because mitochondria (and their DNA) come from the egg’s cytoplasm—sperm contribute almost no cytoplasm at fertilization and their mitochondria are typically destroyed or excluded. That makes mitochondrial inheritance a form of non-nuclear (cytoplasmic) inheritance and explains why these traits don’t follow Mendel’s rules (EK 5.4.A.4 ii). Because mitochondria are passed maternally, all children of an affected mother can inherit a mitochondrial mutation, while children of an affected father usually won’t. Remember also that mitochondria are randomly assorted to daughter cells, so phenotype can vary in severity (heteroplasmy). This is exactly the kind of deviation from Mendelian patterns the AP CED highlights—see Topic 5.4 (study guide: https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs). For extra practice, check the Unit 5 overview (https://library.fiveable.me/ap-biology/unit-5) and lots of practice questions (https://library.fiveable.me/practice/ap-biology).

Nuclear inheritance: genes are on chromosomes in the nucleus and follow Mendel-based patterns (segregation, independent assortment) unless modified by linkage, dominance types (codominance/incomplete), sex-linkage, or pleiotropy. These nuclear genes recombine during meiosis and you can map them by recombination frequency (EK 5.4.A.1, EK 5.4.A.2, EK 5.4.A.3). Non-nuclear inheritance: genes are in organelles (mitochondria or chloroplasts). These genomes are inherited outside the nucleus, often show maternal inheritance because eggs transmit most organelles (EK 5.4.A.4). Organelle DNA is randomly assorted to gametes/daughter cells, so traits don’t follow Mendel’s ratios and won’t recombine like nuclear genes (no standard linkage mapping). In plants both mitochondria and chloroplasts are usually maternally inherited; in animals mitochondrial inheritance is typically maternal. For AP prep, focus on recognizing maternal (mitochondrial/chloroplast) inheritance patterns and that they’re non-Mendelian (see Topic 5.4 study guide: https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs and the unit overview: https://library.fiveable.me/ap-biology/unit-5). Practice problems: https://library.fiveable.me/practice/ap-biology.

Quick rules to read sex-linked pedigrees: - Remember sex chromosomes: females XX, males XY. For X-linked traits males are hemizygous (only one X), so any recessive allele on X shows in males. - X-linked recessive patterns: more affected males than females; affected males usually have unaffected parents; an affected male won’t pass the trait to his sons but will pass the mutant X to all daughters (they become carriers if heterozygous). A carrier (heterozygous) mother has a 50% chance to pass the affected X to each son (affected) and 50% to each daughter (carrier). - X-linked dominant: affected males pass the trait to all daughters and no sons; affected females often pass to ~50% of offspring of either sex. - Y-linked: only males affected; trait passes father → son every time. - On pedigrees use symbols (squares, circles), count affected by sex, and test hypotheses with expected ratios (50% from heterozygote mother, etc.)—this aligns with EK 5.4.A.2 in the CED. For more examples and practice, check the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and try practice questions (https://library.fiveable.me/practice/ap-biology).

Look at the heterozygote’s phenotype, not just the numbers. Per the CED: incomplete dominance = heterozygote is a blended intermediate (e.g., red × white → pink in F1). Codominance = heterozygote shows both alleles’ phenotypes simultaneously (e.g., A and B both expressed in AB blood). Practically: cross two true-breeding parents and inspect the F1. If F1 is intermediate → incomplete dominance. If F1 clearly shows both parent traits together → codominance. With F1 × F1 (or F2) both can give a 1:2:1 phenotypic split, so don’t rely on ratio alone—describe the heterozygote’s appearance or use genotyping. On the exam, state which genotype produces which phenotype (use terms heterozygote/homozygote) and, when needed, test with chi-square for expected ratios. For more examples and practice, see the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and practice problems (https://library.fiveable.me/practice/ap-biology).

Chloroplasts and mitochondria have their own DNA because they evolved from free-living prokaryotes that were engulfed by ancestral eukaryotic cells (endosymbiotic theory). Their genomes encode some proteins needed for organelle function, so traits can be determined by genes outside the nucleus (mitochondrial/chloroplast inheritance). That matters for inheritance: these organelle genes are randomly assorted to daughter cells and gametes, so they don’t follow Mendel’s laws of segregation and independent assortment (EK 5.4.A.4.i). In animals, mitochondria come almost entirely from the egg (maternal inheritance), and in plants mitochondria and chloroplasts are usually transmitted in the ovule, not pollen (EK 5.4.A.4.ii–iii). So expect maternal patterns in pedigrees, no typical Mendelian ratios, and possible heteroplasmy (mixed organelle genotypes) in cells. For a focused review, see the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and practice questions (https://library.fiveable.me/practice/ap-biology).

If a trait shows incomplete dominance, the heterozygote has a blended phenotype. Cross two heterozygotes (Rr × Rr) gives Mendelian genotypes 1 RR : 2 Rr : 1 rr (25% : 50% : 25%). Because of incomplete dominance, those genotypes map to three distinct phenotypes in the same 1:2:1 ratio—e.g., RR = red, Rr = pink (blend), rr = white. So half the offspring show the heterozygote (blended) phenotype and one quarter each show the two homozygote phenotypes. This is a classic EK 5.4.A.3 example (heterozygote phenotype differs from either homozygote). For more practice and AP-style questions on non-Mendelian inheritance, see the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and Fiveable’s practice problems (https://library.fiveable.me/practice/ap-biology).

Recombination frequency = (number of recombinant offspring ÷ total offspring) × 100. Example: if 20 recombinants appear out of 200 total offspring, RF = (20/200)×100 = 10%. On AP exams you’ll convert that percentage directly into map units (centiMorgans): 10% = 10 map units. Practically: - RF < 50% means the genes are linked (closer on the same chromosome). - RF ≈ 50% means they assort independently (unlinked or far apart). Recombination frequency estimates physical distance but isn’t perfectly linear for large distances (double crossovers can hide true distances), so map distances are best for nearby genes. This calculation is exactly what EK 5.4.A.1 expects you to use for genetic mapping. For more examples and practice problems, check the Topic 5.4 study guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and the AP practice bank (https://library.fiveable.me/practice/ap-biology).

Short answer: maternal inheritance usually applies to organelles that have their own genomes—mainly mitochondria (animals) and mitochondria plus chloroplasts (plants)—not to all organelles. Why: Mendel’s laws describe nuclear genes. EK 5.4.A.4 in the CED explains that mitochondria and chloroplasts carry DNA and are transmitted in the egg (ovule) rather than sperm (pollen), so traits from those genomes are typically maternally inherited. In animals, mitochondria are usually passed only by the egg; in plants both mitochondria and chloroplasts are often inherited through the ovule. Exceptions exist: “paternal leakage,” biparental inheritance, and heteroplasmy (mixed organelle genomes) can occur in some species, so it’s not absolutely universal. For AP review, this is covered under non-nuclear (maternal) inheritance—study the examples in the Topic 5.4 guide (https://library.fiveable.me/ap-biology/unit-5/non-mendelian-genetics/study-guide/5oRHoGlMbML8IgtaHaHs) and practice related questions (https://library.fiveable.me/practice/ap-biology).