5 research outputs found
Strong, recent selective sweeps reshape genetic diversity in freshwater bivalve Megalonaias nervosa
Freshwater Unionid bivalves have recently faced ecological upheaval through
pollution, barriers to dispersal, human harvesting, and changes in fish-host
prevalence. Currently, over 70% of species are threatened, endangered or
extinct. To characterize the genetic response to these recent selective
pressures, we collected population genetic data for one successful bivalve
species, Megalonaias nervosa. We identify megabase sized regions that are
nearly monomorphic across the population, a signal of strong, recent selection
reshaping genetic diversity. These signatures of selection encompass a total of
73Mb, greater response to selection than is commonly seen in population genetic
models. We observe 102 duplicate genes with high dN/dS on terminal branches
among regions with sweeps, suggesting that gene duplication is a causative
mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect
functional classes known to be important for Unionid survival, including
anticoagulation genes important for fish host parasitization, detox genes,
mitochondria management, and shell formation. We identify selective sweeps in
regions with no known functional impacts, suggesting mechanisms of adaptation
that deserve greater attention in future work on species survival. In contrast,
polymorphic transposable element insertions appear to be detrimental and
underrepresented among regions with sweeps. TE site frequency spectra are
skewed toward singleton variants, and TEs among regions with sweeps are present
only at low frequency. Our work suggests that duplicate genes are an essential
source of genetic novelty that has helped this successful species succeed in
environments where others have struggled. These results suggest that gene
duplications deserve greater attention in non-model population genomics,
especially in species that have recently faced sudden environmental challenges.Comment: 6 figures, 4 supplementary tables, 31 pages tota
Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater Bivalve \u3ci\u3eMegalonaias nervosa\u3c/i\u3e
Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, harvesting, and changes in fish–host prevalence. Currently, over 70% of species in North America are threatened, endangered or extinct. To characterize the genetic response to recent selective pressures, we collected population genetic data for one successful bivalve species, Megalonaias nervosa. We identify megabase-sized regions that are nearly monomorphic across the population, signals of strong, recent selection reshaping diversity across 73 Mb total. These signatures of selection are greater than is commonly seen in population genetic models. We observe 102 duplicate genes with high dN/dS on terminal branches among regions with sweeps, suggesting that gene duplication is a causative mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect functional classes important for Unionid survival, including anticoagulation genes important for fish host parasitization, detox genes, mitochondria management, and shell formation. We identify sweeps in regions with no known functional impacts, suggesting mechanisms of adaptation that deserve greater attention in future work on species survival. In contrast, polymorphic transposable elements (TEs) appear to be detrimental and underrepresented among regions with sweeps. TE site frequency spectra are skewed toward singleton variants, and TEs among regions with sweeps are present at low frequency. Our work suggests that duplicate genes are an essential source of genetic novelty that has helped this species succeed in environments where others have struggled. These results suggest that gene duplications deserve greater attention in non-model population genomics, especially in species that have recently faced sudden environmental challenges
Complete Genome Sequence of \u3ci\u3eRickettsia parkeri\u3c/i\u3e Strain Black Gap
A unique genotype of Rickettsia parkeri, designated R. parkeri strain Black Gap, has thus far been associated exclusively with the North American tick, Dermacentor parumapertus. The compete genome consists of a single circular chromosome with 1,329,522 bp and a G+C content of 32.5%