dd.site: Genetic data for the freshwater snail _Drepanotrema...

In hhwagner1/LandGenCourse: Interface for course "Landscape Genetic Data Analysis with R"

Genetic data for the freshwater snail Drepanotrema depressissimum

Description

Site-level data from Lamy et al. (2012).

Usage

dd.site

Format

An 'sf' object with 42 populations (combinations of site x year) and 22 variables:

proj4string

Projection: "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"

bbox

Boundary box: spatial extent

SiteID

Combination of SITE and YEAR

SITE

Site name (abbreviated)

YEAR

Year of sampling

Spatial

Logical: population included in spatial study?

MultiYear

Logical: population sampled in multiple years?

APE

Logical: population extinct between sampling years? Based on Table 5.

Cluster

Cluster name for populations that belong to a cluster.

n

Number of individuals sampled per population.

RA

Allelic richness based on a sample size of 14 individuals. From Table 2.

He

Gene diversity (expected heterozygosity). From Table 2.

f

Inbreeding coefficient. From Table 2

s

Estimate of selfing rate based on a multilocus maximum-likelihood method. From Table 2.

Type

Habitat type (p = pond, r = small river and s = swamp grasslands). From Table 4.

FST.GESTE

Population-specific FST as returned by GESTE. From Table 4.

Size

Patch size: Largest diameter in meter, tranformed with log(1 + X). From Table 4.

V

Vegetation cover: Fraction of site covered by aquatic vegetation (macrophytes and algae), tranformed with log(1 + X). From Table 4.

C

Connectivity to neighbouring sites, see paper. From Table 4.

Stab

Temporal stability, see paper. From Table 4.

D

Density of favourable habitats: Number of water bodies within a radius of 2 km. From Table 4.

APA

Apparent population age: Time in years since the most recent potential founder effect. From Table 4.

NLT

Long-term population size: Combination of observed density and site size averaged over years. From Table 4.

Fst.temp

Mean pairwise FST between temporal samples within site. From Table 5.

geometry

Spatial coordinates (Longitude, Latitude: WGS84)

References

Lamy, T., Pointier, J. P., Jarne, P. and David, P. (2012), Testing metapopulation dynamics using genetic, demographic and ecological data. Molecular Ecology, 21: 1394–1410. doi:10.1111/j.1365-294X.2012.05478.x

hhwagner1/LandGenCourse documentation built on Feb. 17, 2024, 4:42 p.m.