arXiv subjects

Cathy C. Moore

Publications and source records attributed to Cathy C. Moore.

3 recordsLinked to original sources

arXiv2021

Chromosomal rearrangements and transposable elements in locally adapted island Drosophila

Chromosomal rearrangements, particularly those mediated by transposable elements (TEs), can drive adaptive evolution by creating chimeric genes, inducing de novo gene formation, or altering gene expression. Here, we investigate rearrangements evolutionary role during habitat shifts in two locally adapted populations, Drosphila santomea and Drosphila yakuba, who have inhabited the island S\~ao Tom\'e for 500,000 and 10,000 years respectively. Using the D. yakuba- D. santomea species complex, we identified 16,480 rearrangements in the two island populations and the ancestral mainland African population of D. yakuba. We find a disproportionate association with TEs, with 83.5% of rearrangements linked to TE insertions or TE-facilitated ectopic recombination. Using significance thresholds based on neutral expectations, we identify 383 and 468 significantly differentiated rearrangements in island D. yakuba and D. santomea, respectively, relative to the mainland population. Of these, 99 and 145 rearrangements also showed significant differential gene expression, highlighting the potential for adaptive solutions from rearrangements and TEs. Within and between island populations, we find significantly different proportions of rearrangements originating from new mutations versus standing variation depending on TE association, potentially suggesting adaptive genetic mechanisms differ based on the timing of habitat shifts. Functional analyses of rearrangements most likely driving local adaptation revealed enrichment for stress response pathways, including UV tolerance and DNA repair, in high-altitude D. santomea. These findings suggest that chromosomal rearrangements may act as a source of genetic innovation, and provides insight into evolutionary processes that SNP-based analyses might overlook.

q-bio.PE↗

arXiv2021

New gene formation in hybrid Drosophila

The origin of new genes is among the most fundamental processes underlying genetic innovation. The substrate of new genetic material available defines the outcomes of evolutionary processes in nature. Historically, the field of genetic novelty has commonly invoked new mutations at the DNA level to explain the ways that new genes might originate. In this work, we explore a fundamentally different source of epistatic interactions that can create new gene sequences in hybrids. We observe "bursts" of new gene creation in F1 hybrids of D. yakuba and D. santomea, a species complex known to hybridize in nature. The number of new genes is higher in the gonads than soma. We observe asymmetry in new gene creation based on the direction of the cross. Greater numbers of new transcripts form in the testes of F1 male offspring in D. santomea female x D. yakuba male crosses and greater numbers of new transcripts appear in ovaries of F1 female offspring of D. yakuba female x D. santomea male. These loci represent wholly new transcripts expressed in hybrids, but not in either parental reference strain of the cross. We further observe allelic activation, where transcripts silenced in one lineage are activated by the transcriptional machinery of the other genome. These results point to a fundamentally new model of new gene creation that does not rely on the formation of new mutations in the DNA. These results suggest that bursts of genetic novelty can appear in response to hybridization or introgression in a single generation. Ultimately these processes are expected to contribute to the substrate of genetic novelty available in nature, with broad impacts on our understanding new gene formation and on hybrid phenotypes in nature.

q-bio.PE↗

arXiv2020

Gene family amplification facilitates adaptation in freshwater Unionid bivalve Megalonaias nervosa

As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new regulatory patterns that can facilitate evolutionary change. With advances in genome sequencing it is possible to gain a broader view of how gene family proliferation and TE content evolve in non-model species when populations become threatened. Freshwater bivalves (Unionidae) currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways, and overfishing. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Gene family expansion is common, with a duplication rate of 1.16 x 10^-8 per gene per generation. Cytochrome P450, ABC transporters, Hsp70 genes, von Willebrand proteins, chitin metabolism genes, mitochondria eating proteins, and opsin gene families have experienced significantly greater amplification and show signatures of selection. We use evolutionary theory to assess the relative contribution of SNPs and duplications in evolutionary change. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv=0.185 compared with Psgv=0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of "hopeful monsters" within the genome that facilitate adaptation.

q-bio.GN↗