Browsing by Author "Aiden, Erez L."

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    Chromosome size affects sequence divergence between species through the interplay of recombination and selection
    (Wiley, 2022) Tigano, Anna; Khan, Ruqayya; Omer, Arina D.; Weisz, David; Dudchenko, Olga; Multani, Asha S.; Pathak, Sen; Behringer, Richard R.; Aiden, Erez L.; Fisher, Heidi; MacManes, Matthew D.; Center for Theoretical and Biological Physics
    The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades—Peromyscus rodents, Mus mice, and great apes—from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.
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    The Australian dingo is an early offshoot of modern breed dogs
    (AAAS, 2022) Field, Matt A.; Yadav, Sonu; Dudchenko, Olga; Esvaran, Meera; Rosen, Benjamin D.; Skvortsova, Ksenia; Edwards, Richard J.; Keilwagen, Jens; Cochran, Blake J.; Manandhar, Bikash; Bustamante, Sonia; Rasmussen, Jacob Agerbo; Melvin, Richard G.; Chernoff, Barry; Omer, Arina; Colaric, Zane; Chan, Eva K. F.; Minoche, Andre E.; Smith, Timothy P. L.; Gilbert, M. Thomas P.; Bogdanovic, Ozren; Zammit, Robert A.; Thomas, Torsten; Aiden, Erez L.; Ballard, J. William O.; Center for Theoretical Biological Physics
    Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.