Microsatellite evolution in ancient and modern penguins Bennet - PowerPoint PPT Presentation

Faculty of Science, Engineering & Technology Microsatellite evolution in ancient and modern penguins Bennet McComish School of Mathematics and Physics •

Faculty of Science, Engineering & Technology Microsatellites T andem repeats of motifs up to Repeats can be imperfect, e.g. 6bp, e.g. (AC) 6 = ACACACACACAC one locus has three alleles: 1. (AAAG) 12 Length is highly polymorphic. Ubiquitous in eukaryote genomes. 2. (AAAG) 22 A(AAAG) 12 Most evolve neutrally, and are 3. (AAAGAGAG) 6 (A) 4 (AG) 3 widely used as genetic markers in (AAAG) 3 (AG) 9 AA(AG) 3 (AAAG) 2 population genetics, ecology. (AG) 2 (AAAG) 2 (AGAGAAAG) 15 Some are also involved in disease (AAAG) 24 in humans and other mammals. Thought to mutate by replication or compound, e.g. (AGG) 8 (CTC) 6 slippage. Point mutation may be important in these cases. M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology Microsatellite models Symmetric models: Asymmetric models Constant rate of mutation in Difgerent rates up and down ● ● both directions – biased upwards if the current number of repeats is Rate proportional to current ● small, downwards if large. length Can be generalised to allow ● Can change by multiple ● multi-step changes, point repeat units mutations. Very simplistic, and don't have a These models have stationary stationary distribution. distributions. M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology Adélie penguin data Adélie penguins breed in multiple locations around the coast of Antarctica. Same nesting sites used for thousands of years – dead chicks preserved. We have high-coverage (~30x) genome sequence reads for 22 modern samples from fjve sites. 32 ancient genomes up to 25,000 years old from several sites currently being sequenced at lower coverage (up to 10x). M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology Africa 4 6 Adelie Genomic Sequencing Efforts South America Scott Base / McMurdo Station Modern Samples Ancient Samples ca. 60 samples 4 1-30 KYA 4 Australia 4 M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology Microsatellite detection Run T andem Repeat Finder Map reads to reference using (Benson, 1999) on best available Bowtie2 (Langmead, 2012). reference genome – numbers of Use RepeatSeq (Highnam, loci detected: 2013) to genotype samples based on read mapping. Motif Number length of loci Convert ouput for easy 1 175,604 processing in R – we have: motif, position and length in 2 41,411 reference, lengths observed in 3 61,014 samples, quality scores. 4 105,862 5 232,325 6 529,492 M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology What now? Analyse ancient samples. Ascertainment bias is a problem: Need to choose summary 1. can't detect long loci (but statistics that can distinguish these are rare). models. Any suggestions would 2. AT-rich motifs less likely to be be most welcome! observed (lower coverage). Look at purity of loci, for models Difgerent motifs will have to be that incorporate point mutation. analysed independently. M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s

Faculty of Science, Engineering & Technology Thanks! Barbara Holland Human Frontier Science Program Griffjth University Ancient DNA Lab: Dave Lambert ● Matt Parks ● Sankar Subramanian ● All of you for listening! M i c r o s a t e l l i t e e v o l u t i o n i n a n c i e n t a n d m o d e r n p e n g u i n s