Amac_ILMO_Dryad

Excel spreadsheet with haplotype and genotype scores for 489 field-collected Ambystoma maculatum embryos across one mitochondrial and seven microsatellite loci. Sample ID's, population names, and names of loci are given as column headings

Data analyses R

Scripts of data analyses using

Cline_data

Summary file of cline dat

DIST1UTDAT

R input file for concordance and geographic cline analyse

alldata

R input file for genomic cline analyses and figure

Individual_data

Summary file of individual dat

RAW_MICROSAT_DATA_FOR_DRYAD

Microsatellite data for the loci and populations described in the manuscript. Data are in CONVERT format, which can easily be converted to many other formats using either the program CONVERT or PGDSpider

Chickadee SNP data

Genotypes of 1425 SNPs for the 167 chickadees described in the manuscript. Chickadees were sampled in southeastern Pennsylvania. SNPs were identified using GBS (genotyping by sequencing), in conjunction with the UNEAK pipeline (part of Tassel) and a Perl script to call genotypes in a max likelihood framework

High fat diet and exercise lead to a disrupted and pathogenic DNA methylome in mouse liver

<p>High-fat diet consumption and sedentary lifestyle elevates risk for obesity, non-alcoholic fatty liver disease, and cancer. Exercise training conveys health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms in many tissues; however, such effects are poorly documented in the liver, a central metabolic organ. To dissect the consequences of diet and exercise on the liver epigenome, we measured DNA methylation, using reduced representation bisulfite sequencing, and transcription, using RNA-seq, in mice maintained on a fast food diet with sedentary lifestyle or exercise, compared with control diet with and without exercise. Our analyses reveal that genome-wide differential DNA methylation and expression of gene clusters are induced by diet and/or exercise. A combination of fast food and exercise triggers extensive gene alterations, with enrichment of carbohydrate/lipid metabolic pathways and muscle developmental processes. Through evaluation of putative protective effects of exercise on diet-induced DNA methylation, we show that hypermethylation is effectively prevented, especially at promoters and enhancers, whereas hypomethylation is only partially attenuated. We assessed diet-induced DNA methylation changes associated with liver cancer-related epigenetic modifications and identified significant increases at liver-specific enhancers in fast food groups, suggesting partial loss of liver cell identity. Hypermethylation at a subset of gene promoters was associated with inhibition of tissue development and promotion of carcinogenic processes. Our study demonstrates extensive reprogramming of the epigenome by diet and exercise, emphasizing the functional relevance of epigenetic mechanisms as an interface between lifestyle modifications and phenotypic alterations.</p

Distribution of <i>Crocidura russula</i> in Ireland.

<p>Positive (filled shapes) and negative (empty shapes) <i>Crocidura russula</i> records in Ireland from 2006 to 2013 (A). Localities O1–3 are outlier records (see main text). Dashed squares represent sites that were used for the estimation of range expansion between 2012 and 2013 (A). The 100% minimum convex polygon (MCP) from the 2012 summer live-trapping survey is shown in red (A). Inset map (B) shows this same MCP, highlighting the three ‘Zones’ used for the analyses of species interactions and habitat associations, and the four transects used to measure changes in species abundance and expansion rate. Black circles are <i>C. russula</i> positive and white circles are <i>C. russula</i> negative sites in 2012. Zone 1 (dark grey) is the MCP of <i>C. russula</i> sites which contained no <i>Sorex minutus</i> observations, Zone 2 (light grey) is the MCP of all <i>C. russula</i> observations, Zone 3 (the rest of the region) is outside the observed range of <i>C. russula</i>. The white diamond represents the centroid of Zone 1.</p