Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Outlier scans

To establish the diploma of genetic parallelism between ‘Balchen’ and ‘Albeli’ whitefish species from throughout the radiation, we subsetted 24 people representing three ‘Balchen’ species and three ‘Albeli’ species from 4 of the lakes we sampled: Lake Brienz, Lake Lucerne, Lake Walen and Lake Neuchâtel out of our full 99 particular person dataset. ‘Albeli’ species included C. candidus, C. albellus, C. muelleri and C. heglingus (for lakes Neuchâtel, Brienz, Lucerne, and Walen), and ‘Balchen’ species included C. palea, C. alpinus, C. litoralis, and C. duplex (for lakes Neuchâtel, Brienz, Lucerne, and Walen). To first affirm the impartial evolution of every ‘Balchen’ and ‘Albeli’ species pair inside every of those 4 lakes, as indicated by the phylogeny, F4 statistics had been calculated throughout a four-taxon tree (as utilized in ref. 81), permitting us to estimate the diploma of correlated allele frequencies between ‘Balchen’ and ‘Albeli’ people inside and between lake techniques. First, loci had been pruned primarily based on linkage disequilibrium utilizing the script ldPruning.sh (https://github.com/joanam/scripts/raw/master/ldPruning.sh), leading to 1,315,105 SNPs. Then the script plink2treemix.py (from https://speciationgenomics.github.io/Treemix/) was used to transform information into the treemix format earlier than F4 calculations had been applied utilizing f4.py (https://raw.githubusercontent.com/mmatschiner/F4/master/f4.py). We calculated F4 for 2 completely different topologies, inserting ‘Balchen’ and ‘Albeli’ species from all pairwise combos of the 4 lakes on a four-taxon tree. Within the first four-taxon tree ((A,B),(C,D)) we positioned sympatric ‘Balchen’ and ‘Albeli’ species from a primary lake as A and B, and ‘Balchen’ and ‘Albeli’ species from a second lake as C and D. On this context, the ensuing F4 (F4¹) represents the correlated allele frequency between A or B and C or D that may point out introgression, or in our case, consultant of a single evolution of ‘Balchen’ and ‘Albeli’ adopted by sorting into lakes. We then calculated F4 the place allopatric ‘Balchen’ species from two completely different lakes had been positioned as A and B and allopatric ‘Albeli’ species from the identical two lakes as C and D (F4²). F4 on this second association represents the correlated allele frequencies of sympatric species, once more between A or B and C or D. The place F4¹ < F4² there’s stronger help for the situation wherein ‘Balchen’ and ‘Albeli’ are really sympatric species pairs, and due to this fact independently originated throughout lakes somewhat than for a single origin of the 2 ecomorphs.

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