Rao Golla, T. | bioRxiv Science

bioRxiv2020

Reorganization of 3D genome structure in the Drosophila melanogaster species group

Topologically associating domains, or TADs, are functional units that organize chromosomes into 3D structures of interacting chromatin. TADs play an important role in regulating gene expression by constraining enhancer-promoter contacts; there is evidence that deletion of TAD boundaries leads to aberrant expression of neighboring genes. While the mechanisms of TAD formation have been well-studied, current knowledge on the extent of TAD conservation across species is inconclusive. Due to the integral role TADs play in gene regulation, their structure and organization is expected to be conserved during evolution. However, more recent research suggests that TAD structures diverge relatively rapidly. We use Hi-C chromosome conformation capture to measure evolutionary conservation of whole TADs and TAD boundary elements between D. melanogaster and D. triauraria, two early-branching species from the melanogaster species group which diverged ~15 million years ago. We find that 75% of TAD boundaries are orthologous while only 25% of TAD domains are conserved and these are enriched for Polycomb-repressed chromatin. Our results show that TADs have been reorganized since the common ancestor of D. melanogaster and D. triauraria, yet the sequence elements that specify TAD boundaries remain highly conserved. We propose that evolutionary divergence in 3D genome organization results from shuffling of conserved boundary elements across chromosomes, breaking old TADs and creating new TAD architectures. This result supports the existence of distinct TAD subtypes: some may be evolutionarily flexible while others remain highly conserved due to their importance in restricting gene-regulatory element interactions.

genomics↗

bioRxiv2018

Thermal selection drives biodiversity origination across the Atlantic/Indian Ocean boundary

Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive the evolution of new biodiversity. Ecological speciation scenarios are often invoked to explain such patterns, but the fact that adaptation is usually only identified when phylogenetic splits are already evident makes it impossible to rule out the alternative scenario of allopatric speciation with subsequent adaptation. We integrated large-scale genomic and environmental datasets along one of the worlds best defined marine thermal gradients (the South African coastline) to test the hypothesis that incipient speciation in the sea is due to divergence linked to the thermal environment. We identified temperature-associated gene regions in a coastal fish species that is spatially homogeneous throughout several temperature-defined biogeographical regions on the basis of selectively neutral markers. Based on these gene regions, the species is divided into geographically distinct regional populations. Importantly, the ranges of these populations are delimited by the same ecological boundaries that define distinct infraspecific genetic lineages in co-distributed marine the species, and biogeographical disjunctions in species assemblages. Our results indicate that ecologically-mediated selection represents an early stage of marine speciation in coastal regions that lack physical dispersal barriers.

evolutionary biology↗