Concerted evolution Concerted evolution: the observation that paralogous genes appear "homogenized" (e.g., little difference in known non-functional region where one expects accumulation of neutral mutations) Mechanisms of concerted evolution Unequal cross-over Gene conversion: non-reciprocal transfer of information between homologous sequences; the main mechanism invoked to explain concerted evolution

Concerted evolution … … - maintenance of homogeneous nt sequences among multi-gene family members (especially when in tandem arrays) - exchange of sequence info so members kept very similar - eg. eukaryotic nuclear ribosomal RNA gene copies (~100-200) … rDNA Aside: Rapid evolution of non-transcribed rRNA spacers vs. slow for rRNAs 45S precursor rRNA 18S 28S NTS 5.8S 5S rRNA gene cluster … 5S NTS: non-transcribed spacer ETS: external transcribed spacer ITS: internal transcribed spacer 28S LSU rRNA 5.8S 18S SSU rRNA Fig. 6.26

Hypotheses Shared premise: certain genes such as rRNA are so important and functionally constrained that it is crucial for them to be identical for optimal functioning. Different mechanisms: Selection eliminates mutants: Prediction 1: Functionally more important sites should be more conserved than functionally less important sites, e.g., ETS, ITS and loop regions in rRNA genes Gene conversion, mainly through non-reciprocal recombination. Prediction 2: Same sequence conservation regardless of functional importance. Corroborative evidence: gene in single copy in some organisms (pattern consistent with Prediction 1) and multi-copy in others (pattern consistent with Prediction 2)

Possible evolutionary scenarios resulting in “homogenized” tandem array 1. Beneficial mutations fixed by positive selection but spacers with no known function can show concerted evolution also unlikely because expect neutral mutations too 2. Recent amplification … can determine from tests 3. Mutation in one repeat “spreads” to others Fig. 6.27

- homologous recombination between misaligned arrays 1. Unequal crossing over - homologous recombination between misaligned arrays - end up with identical tandem copies 4 - and change in number of repeats - array expands or contracts Fig. 6.31

Example of unequal crossing over in human b-globin array 5 genes 3 genes “Lepore” b - thalassemia misalignment (of sister chromatids during mitosis in germ cell or homologous chromosomes during meiosis…) Page & Holmes Fig. 3.15

2. gene conversion Holiday model (1964, Genet. Res. 5, 282–304) Meselson-Radding model PNAS 72:358-361) DSBR (double-strand break and repair) model (Szostak et al. 1983. Cell 33:25–35. SDSA (synthesis-dependent strand annealing) model (Allers et al. 2001. Cell 106:47–57). Most studies use yeasts. Santoyo, G. and Romero, D. (2005), Gene conversion and concerted evolution in bacterial genomes. FEMS Microbiology Reviews, 29: 169–183

Haliday model Pair of homologous sequences, differing at the dotted region. A single-strand nick made in both of the DNA participating molecules Unwinding and strand exchange. Resulting heteroduplex DNA with mismatches The repair system will recognize the mismatch and probably correct them. Some repair preference will lead to gene conversion. The length of the gene conversion tract will depend on both the migration of the Holliday structure and the capacity to repair the mismatches before replication. Gene conversion results essentially from reciprocal heteroduplex formation and DNA repair. Problem: gene conversion often occurs without reciprocal heteroduplex formation Filled dots mark the sequence difference between participating homologues, triangles mark the cuts

Meselson-Radding model One single-strand cut is made in one of the chains, which is then displaced by the action of a DNA polymerase. The displaced chain invades a homolog sequence Ligation of the newly synthesized strand with a strand of the same polarity in the other homolog generates the Holliday junction. Migration of Holiday junction. Resolution of the heteroduplex and subsequent repair lead to gene conversion. Problem: Recombination is mainly associated with double-strand breaks Filled dots mark the sequence difference between participating homologues, triangles mark the cuts

DSBR model Recombination initiates with a double-strand break, continued by extensive single chain degradation in the 5′ to 3′ direction leading to exposed 3′ overhangs. One of these 3′ overhangs can invade the uncut homolog, thus displacing a D-loop that can pair with the remaining 3′ overhang; the paired D-loop can act as a template for DNA synthesis, primed by the 3′ overhang. The length of synthesis depends on the migration of the two Holliday junctions. DNA synthesis, or DNA repair, leads to gene conversion. Problem (shared with the other two): gene conversion often occurs without the expected cross-over. Filled dots mark the sequence difference between participating homologues, triangles mark the cuts

SDSA model A double-strand cut is made in one DNA duplex and is degraded to generate 3′ overhangs. One of these 3′ ends invades a homologous region and starts DNA synthesis using as template the homologous strand. A D-loop is formed as a consequence of strand displacing and DNA synthesis. The newly synthesized strand is kicked off, making it available to pair with the other 3′ end in its original duplex. A full duplex is then restored by DNA synthesis. Gene conversion may result from DNA synthesis or mismatch repair. Filled dots mark the sequence difference between participating homologues, triangles mark the cuts

Watson Fig. 10-21 - example of yeast mating-type switching strand invasion

Example of concerted evolution in primate b -globin gene cluster Exon 3 used in sequence comparisons Exons 1 - 2 How do you interpret these data? ... and panel 3 of Fig.6.33 ? Ex3 Fig. 6.33

6 3.5 C_Gr H_Gr G_Gr H_Ar C_Ar G_Ar Anc H_Ar H_Gr C_Gr C_Ar G_Gr G_Ar 4 0.5 3.5 2 2 0.5 2 1 2 0.5 2.5 4 0.5 2 2 0.5 2 4 2 0.5 H_Gr C_Gr G_Gr H_Ar C_Ar G_Ar 4 8 12 Anc H_Gr C_Gr G_Gr H_Ar C_Ar G_Ar 4 8 1 12 10 Anc ((H_Ar:0.500000,H_Gr:0.500000):4.000000,((C_Gr:0.500000,C_Ar:0.500000):2.500000,(G_Gr:0.500000,G_Ar:0.500000):3.500000):1.000000,Anc:3.500000); Gene conversion homogenizes paralogues Gene conversion could start earlier in chimp and gorilla than human and reduce chimp-gorilla divergence Gene conversion reduces divergence Gene conversion brings all closer to root

“Resurrection” of ribonuclease pseudogene by gene conversion What is predicted status of SR gene in giraffe? or sheep? How did they deduce time of SR gene inactivation? - in ancestor of ruminants, duplications so that 3 forms: pancreatic (PR), seminal (SR) and cerebral (CR) ribonucleases - then SR became y gene (frameshift near 5’end) … but in some bovine species, gene conversion of ySR with PR gene, so functional again Fig. 6.34

Factors affecting rate of concerted evolution (p. 317-320) 1. Number, arrangement, structure of repeats - non-coding regions evolve more rapidly, and if divergent enough may “escape” homogenization 2. Functional requirement - selective advantage of high amount of same gene product vs. diversity 3. Population size - time for variant to be fixed or eliminated

Evolutionary implications of concerted evolution (p.320-322) “molecular drive” 1. Spread of advantageous mutations (or removal of deleterious ones) 2. Retards paralogous gene divergence (preventing redundant copy from becoming non-functional) or even “resurrecting” a pseudogene 3. Generates increased genetic variation at a particular locus within a population Methodological implications - degree of sequence divergence of paralogous genes undergoing concerted evolution is not correlated with evolutionary time so gene duplications can appear younger than they really are…