Comparing cortex-wide gene expression patterns between species in a common reference frame

Abstract

Advances in sequencing techniques have made comparative studies of gene expression a current focus for understanding evolutionary and developmental processes. However, insights into the spatial expression of genes have been limited by a lack of robust methodology. We therefore developed a set of algorithms for quantifying and comparing tissue-wide spatial patterns of gene expression within and across species. Here we apply these algorithms to compare cortex-wide expression of Id2 and RZRβ mRNA in early postnatal mice and voles. We show that neocortical patterns of Id2 expression are moderately conserved between species, but that the degree of conservation varies by cortical layer and area. By comparison, patterns of RZRβ expression are highly conserved in somatosensory areas, and more variable between species in visual and auditory areas. We consider if these differences reflect independent evolution in the 35 million years since the last common ancestor.

Whole-brain comparison of rodent and human brains using spatial transcriptomics

“…Importantly, these patterns appear to be conserved across mammalian species ( Fulcher et al, 2019 ), which opens up the possibility of using the expression of homologous genes as a common space across species. In fact, a recent study demonstrated how the expression of homologous genes can be used to directly register mouse and vole brains into a common reference frame, which allows for direct point-by-point comparisons of brain maps ( Englund et al, 2021 ). However, this specific approach is only feasible because of the large degree of morphological similarity between mouse and vole brains.…”

Whole-brain comparison of rodent and human brains using spatial transcriptomics

“…Importantly, these patterns appear to be conserved across mammalian species (28) , which opens up the possibility of using the expression of homologous genes as a common space across species. In fact, a recent study demonstrated how the expression of homologous genes can be used to directly register mouse and vole brains into a common reference frame, which allows for direct point-by-point comparisons of brain maps (29) . However, this specific approach is only feasible because of the large degree of morphological similarity between mouse and vole brains.…”

Evolution of cortical geometry and its link to function, behaviour and ecology

“…The recent availability of large open image datasets of rodents 25 , non-human primates 26,27 , human subjects 28,29 and fossil taxa 30 has facilitated comparative analyses of brain organisation and function 31,32 . However, studies are either limited to phylogenetically closely related species 33,34 , a-priori defined spatial homologies 6,35 , or avoid establishing correspondences between morphologically and functionally divergent domains altogether by focusing on global descriptions of brain organisation 5,[36][37][38] .…”