Brendan Epstein
YOU?
Author Swipe
View article: Genetic variation in host selectivity and adaptive strain enrichment within legume-rhizobia symbiosis: processes are host-dependent, far from perfect, and correlate with nodule morphology
Genetic variation in host selectivity and adaptive strain enrichment within legume-rhizobia symbiosis: processes are host-dependent, far from perfect, and correlate with nodule morphology Open
Mutualism breakdown can be prevented if partner species preferentially select and reward partners that provide greater benefit. We examined these two components using the legume Medicago truncatula and its nitrogen-fixing symbiont Sinorhiz…
View article: Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia
Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia Open
Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansi…
View article: Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria
Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria Open
View article: Adaptation to mercury stress by nitrogen-fixing bacteria is driven by horizontal gene transfer and enhanced gene expression of the Mer operon
Adaptation to mercury stress by nitrogen-fixing bacteria is driven by horizontal gene transfer and enhanced gene expression of the Mer operon Open
Background: Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms …
View article: Local adaptation to mercury contamination by nitrogen-fixing rhizobia is driven by horizontal gene transfer, copy number, and enhanced gene expression
Local adaptation to mercury contamination by nitrogen-fixing rhizobia is driven by horizontal gene transfer, copy number, and enhanced gene expression Open
Mercury (Hg) is highly toxic and has the potential to cause severe health problems for foraging animals and humans when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent h…
View article: Discordant population structure among rhizobium divided genomes and their legume hosts
Discordant population structure among rhizobium divided genomes and their legume hosts Open
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. …
View article: Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype
Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype Open
Legume crops establish beneficial associations with rhizobial bacteria that perform biological nitrogen fixation, providing nitrogen to plants without the economic and greenhouse gas emission costs of chemical nitrogen inputs. Here, we exa…
View article: Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis
Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis Open
The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhiz…
View article: Discordant population structure within rhizobium divided genomes and between rhizobia and legume hosts in their native range
Discordant population structure within rhizobium divided genomes and between rhizobia and legume hosts in their native range Open
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Bacterial symbionts often have genomes comprised of multiple replicons with distinct rates of evolution and horizontal transmissio…
View article: Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range
Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range Open
Coevolution is predicted to depend on how the genetic diversity of interacting species is geographically structured. Plant-microbe symbioses such as the legume-rhizobium mutualism are ecologically and economically important, but distinct l…
View article: Contemporary and historical selection in Tasmanian devils ( <i>Sarcophilus harrisii</i> ) support novel, polygenic response to transmissible cancer
Contemporary and historical selection in Tasmanian devils ( <i>Sarcophilus harrisii</i> ) support novel, polygenic response to transmissible cancer Open
Tasmanian devils ( Sarcophilus harrisii ) are evolving in response to a unique transmissible cancer, devil facial tumour disease (DFTD), first described in 1996. Persistence of wild populations and the recent emergence of a second independ…
View article: Genomic signatures of divergent selection are associated with social behaviour for spinner dolphin ecotypes
Genomic signatures of divergent selection are associated with social behaviour for spinner dolphin ecotypes Open
Understanding the genomic basis of adaptation is critical for understanding evolutionary processes and predicting how species will respond to environmental change. Spinner dolphins in the eastern tropical Pacific (ETP) present a unique sys…
View article: Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes
Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes Open
Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia–legume symbiosis. To gain insight into the extent of HT of symbiosis genes with…
View article: Comparison of Nodule Endophyte Composition, Diversity, and Gene Content Between <i>Medicago truncatula</i> Genotypes
Comparison of Nodule Endophyte Composition, Diversity, and Gene Content Between <i>Medicago truncatula</i> Genotypes Open
Leguminous plants form symbiotic relationships with rhizobia. These nitrogen-fixing bacteria live in specialized root organs called nodules. Although rhizobia form the most notable host relationship within root nodules, other bacterial end…
View article: Table S5 from Contemporary and historical selection in Tasmanian devils (<i>Sarcophilus harrisii</i>) support novel, polygenic response to transmissible cancer
Table S5 from Contemporary and historical selection in Tasmanian devils (<i>Sarcophilus harrisii</i>) support novel, polygenic response to transmissible cancer Open
Annotated Tasmanian devil gene IDs of within 1000 bp of SNPs in the top 1% of DCMS scores; i.e. candidates for contemporary selection.
View article: Table S6 from Contemporary and historical selection in Tasmanian devils (<i>Sarcophilus harrisii</i>) support novel, polygenic response to transmissible cancer
Table S6 from Contemporary and historical selection in Tasmanian devils (<i>Sarcophilus harrisii</i>) support novel, polygenic response to transmissible cancer Open
All PAML (16, 17) branch site test results for the 1,773 genes with inferred historical positive selection.
View article: Host-associated rhizobia fitness: Dependence on nitrogen, density, community complexity, and legume genotype
Host-associated rhizobia fitness: Dependence on nitrogen, density, community complexity, and legume genotype Open
The environmental context of the nitrogen-fixing mutualism between leguminous plants and rhizobial bacteria varies over space and time. Variation in resource availability, population density, and composition likely affect the ecology and e…
View article: Contemporary and historical selection in Tasmanian devils (<i>Sarcophilus harrisii</i>) support novel, polygenic response to transmissible cancer
Contemporary and historical selection in Tasmanian devils (<i>Sarcophilus harrisii</i>) support novel, polygenic response to transmissible cancer Open
Tasmanian devils ( Sarcophilus harrisii ) are evolving in response to a unique transmissible cancer, devil facial tumour disease (DFTD), first described in 1996. Persistence of wild populations and the recent emergence of a second independ…
View article: Host plants and <i>Wolbachia</i> shape the population genetics of sympatric herbivore populations
Host plants and <i>Wolbachia</i> shape the population genetics of sympatric herbivore populations Open
Changing climate and land‐use practices have the potential to bring previously isolated populations of pest insects into new sympatry. This heightens the need to better understand how differing patterns of host–plant association, and uniqu…
View article: Disease swamps molecular signatures of genetic‐environmental associations to abiotic factors in Tasmanian devil ( <i>Sarcophilus harrisii</i> ) populations
Disease swamps molecular signatures of genetic‐environmental associations to abiotic factors in Tasmanian devil ( <i>Sarcophilus harrisii</i> ) populations Open
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found onl…
View article: Hybridizing salamanders experience accelerated diversification
Hybridizing salamanders experience accelerated diversification Open
View article: Table S1 from Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes
Table S1 from Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes Open
NCBI accession numbers, species names, assembly completeness, and genome size statistics for all strains included in the OrthoFinder analysis.
View article: Table S3 from Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes
Table S3 from Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes Open
The 143 symbiosis genes from all four categories with their annotations.
View article: Table S5 from Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes
Table S5 from Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes Open
Table of summary statistics and annotations for all genes, both symbiosis and non-symbiosis.
View article: A Select and Resequence Approach Reveals Strain-Specific Effects of <i>Medicago</i> Nodule-Specific PLAT-Domain Genes
A Select and Resequence Approach Reveals Strain-Specific Effects of <i>Medicago</i> Nodule-Specific PLAT-Domain Genes Open
Genetic studies of legume symbiosis with nitrogen-fixing rhizobial bacteria have traditionally focused on nodule and nitrogen-fixation phenotypes when hosts are inoculated with a single rhizobial strain. These approaches overlook the poten…
View article: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (<i>Sarcophilus harrisii</i>) populations
Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (<i>Sarcophilus harrisii</i>) populations Open
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil ( Sarcophilus harrisii ) is found o…
View article: Hybridizing salamanders experience accelerated diversification
Hybridizing salamanders experience accelerated diversification Open
Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays…
View article: Genome-Wide Association Analyses in the Model Rhizobium <i>Ensifer meliloti</i>
Genome-Wide Association Analyses in the Model Rhizobium <i>Ensifer meliloti</i> Open
Genome-wide association analyses are a powerful approach for identifying gene function. These analyses are becoming commonplace in studies of humans, domesticated animals, and crop plants but have rarely been conducted in bacteria. We appl…
View article: Large‐effect loci affect survival in Tasmanian devils ( <i>Sarcophilus harrisii</i> ) infected with a transmissible cancer
Large‐effect loci affect survival in Tasmanian devils ( <i>Sarcophilus harrisii</i> ) infected with a transmissible cancer Open
Identifying the genetic architecture of complex phenotypes is a central goal of modern biology, particularly for disease‐related traits. Genome‐wide association methods are a classical approach for identifying the genomic basis of variatio…
View article: The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements
The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements Open
Ensifer meliloti (formerly Rhizobium meliloti and Sinorhizobium meliloti ) is a model bacterium for understanding legume–rhizobial symbioses. The tripartite genome of E. meliloti consists of a chromosome, pSymA and pSymB, and in some insta…