Landmark-based estimates of genomic disparity
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Genomic architecture has played a key role in the evolution of biodiversity. Structural comparisons of genome sequences have informed the study of supergenes, sex chromosomes, and some of the earliest divergences in the tree of life. However, multi-species comparisons of whole genome sequences still have many computational and analytical limitations. Here we present a computationally non-intensive approach, based on geometric morphometrics, that generates disparity scores using conserved sequences as landmarks. This ‘geno-metric’ method captures structural differences in homologous chromosomal regions and can be applied at micro- and macroevolutionary scales. Using ultraconserved elements (UCEs) as landmarks, we provide empirical demonstrations with chromosome 5 from the Drosophila virilis group and 40 placental mammal genomes. These examples identify chromosomal rearrangements while also confirming that UCE landmark placement has strong parallels with morphometrics regarding chromosome size, landmark orientation, phylogenetic signal of landmarks, and landmark availability. Using simulations, we show that UCE-inferred disparity is correlated with overall levels of chromosome evolution which can be further studied using macroevolutionary models of continuous trait evolution. Landmark-based estimates of disparity are a valuable addition to the comparative genomic toolkit in that they offer an intuitive, rapid mechanism for detecting chromosomal expansions, contractions, and rearrangements. We also highlight the potential for this approach to identify translocations and genome duplications.
Significance Statement
The increased throughput of genome sequencing has outpaced the development of analytical tools to extract information from these big data, creating an urgent need for novel methodological perspectives in genomics. We describe and validate a morphometric approach based on conserved genomic landmarks that effectively captures multi-species variation of chromosome structure. Using the principles of morphological disparity, the throughput of comparative genomics can be greatly increased, and the syntenic organization of chromosomes placed in quantitative and macroevolutionary contexts.
