Evolutionary dynamics ofmicrosatellitesBennet McComish, Michael Charleston, Matthew Parks, Barbara Hollandand David Lambert

Phylomania, 11-13 November 2015

Microsatellites

Tandem repeats of motifs up to 6bp,e.g. (AAC)6 = AACAACAACAACAACAAC

Locus length is highly polymorphic.

Ubiquitous in eukaryote genomes.

Most evolve neutrally, widely used as genetic markers inpopulation genetics, ecology.

Some implicated in disease in humans and other mammals.

Thought to mutate by slipped-strand mispairing.

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Microsatellites

Repeats can be imperfect, e.g. one locus has three alleles:

or compound, e.g. (AGG)8(CTC)6

Point mutation may be important in these cases.

(AAAG)121.

(AAAG)22A(AAAG)122.

(AAAGAGAG)6(A)4(AG)3(AAAG)3 (AG)9AA(AG)3(AAAG)2(AG)2(AAAG)2(AGAGAAAG)15(AAAG)24

3.

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Microsatellite evolution

Three embedded processes:

Availability of ancient genomes allows us to examine themutation process within a species.

Availability of complete genome alignments allows us to examinethe birth and death of microsatellite loci across a phylogeny.

Mutation process: birth and death of repeat units.

Birth and death of microsatellites.

Phylogeny: birth and death of species.

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Ancient Adélie genomes

Adélie penguins breed inmultiple locations around thecoast of Antarctica.

Have been nesting on exposedareas of coastline forthousands of years.

High-coverage (~30x) genomesequence reads for 26 modernsamples from five sites.

Lower-coverage reads for 23ancient genomes ranging from329 to 46,500 years old fromseveral sites. 5/20

Microsatellite genotyping

Numbers of loci detected inAdélie reference genome:

Motif length Loci

dinucleotide 63,965

trinucleotide 32,338

tetranucleotide 44,004

pentanucleotide 23,252

hexanucleotide 14,415

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Does length change with sample age?

No!

Model testing using BayesFactor: models in which allele lengthdepends on sample age are less plausible than the null model.

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Genomic data

48 avian genomes, andpairwise alignments betweenchicken and each othergenome (from Jarvis et al. 2014,Science 346:1320-31).

15 additional chordategenomes for which pairwisealignments to chicken are alsoavailable.

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Microsatellite homology

Microsatellites detected in each genome are mapped tocoordinates in the chicken genome.

These coordinates are clustered into sets of putativehomologues.

Homologues are converted to presence/absence matrix, which isused for ancestral state reconstruction and locus age estimation.

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Microsatellite frequencies

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Loci aligned to chicken

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Microsatellite gain and loss rates

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Age distribution of Adélie microsats

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Allele lengths in Adélie samples

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Effect of age on length

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Heterozygosity in Adélie samples

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Effect of age on heterozygosity

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GC content in Adélie samples

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Conclusions

Some microsatellite loci have persisted for over 500 million years,and remain variable (at least in Adélie).

Loci in coding and regulatory regions are more likely to persist.

Despite variable allele lengths, average is stable at theintraspecific level, and increases very slowly over evolutionarytime.

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Acknowledgements

Barbara HollandMike Charleston

Griffith University Ancient DNA Lab:

Human Frontier Science Program

BGI:

Dave Lambert

Matt Parks

Sankar Subramanian

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Cao Li

Guojie Zhang

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