https://doi.org/10.5061/dryad.nvx0k6f37

Description of the data and file structure

Description of dataset

This dataset was generated to compare genetic diversity and relatedness of the UK breeding population of black-tailed godwits (42 pairs) with the much larger breeding population in the Netherlands (~30,000_ pairs).

Individuals were genotyped at 9 loci microsatellite loci. The UK dataset consisted of 59 individuals, the Netherlands dataset of 38 individuals.

METHODOLOGICAL INFORMATION

Description of methods used for collection/generation of data:

Sampling: Individual eggshell and its membrane were air dried. Of 9 chicks that died of naturla causes, a leg was removed and stored in ethanol

DNA extraction: salt extraction protocol modified from Richardson et al. (2001)

PCR: microsatellite loci were amplified using a 2µl PCR technique (Kenta et al., 2008), using primers from Verkuil et al. (2009), tagged with FAM or HEX dyes and arranged into multiplex reactions 

Genotyping: on an ABI 3730 sequencer

Allele sizes calling: Gene Mapper Version 3.7 (Applied Biosystems)	

	

Methods for processing the data:

Hardy-Weinberg equilibrium (HWE) test: chi-squared tests (UK dataset) and GENEPOP (Raymond and & Rousset, 1995; Netherlands dataset, see Trimbos et al. 2011)

Genetic diversity summary statistics for UK and The Netherlands: allelic richness (Na), rarefacted allelic richness (Ra), expected and observed heterozygosity (Ho and He), and the inbreeding coefficient (Fis); in Pegas 1.2 (Paradis, 2010)

Ritland estimator (Ritland, 1996): pairwise relatedness between all individuals, using the related package (version 1.0) in R (Pew et al., 2015)

Wilcoxon tests: Statistical differences in genetic diversity and relatedness values between countries 

Kruskal-Wallis test: Statistical differences in relatedness between pairs with zero, one or two individuals that recruited into the UK breeding population between 2019-2023

The .r codes have been uploaded and can be accessed on Zenoda: Godwit microsatellite analysis.r, aux_functions.R

FILE LIST

Genotypes_Godwits_UK.csv
Samples_metadata_Godwits_UK.xlsx
Genotypes_Godwits_Netherlands_Trimbos.xlsx
GenoptypeTableUK.xlsx
OneSibperNest.csv
Table2.xls
aux_functions.R
Godwit microsatellite analysis.r

Files and variables

FILE 1

DATA-SPECIFIC INFORMATION FOR: Genotypes_Godwits_UK.csv

1. Number of variables: 22

2. Number of cases/rows: 789

Row 1: variable names
Row 2-789: 788 cases

3. Variable List:

1. Sample File (fasta with allele call; value = [ID].fsa)
2. Sample Name (value = sample DNA extraction ID)
3. Run Name (plate name for sequencing run; value = Plate [#])
4. Panel (Panel is group of markers; value = panel ID)
5. Marker (value = name of PCR primer set)
6. Dye (value = color label of marker for sequencing)
7. Allele 1 (value = allele of microsatellite locus)
8. Allele 2 (value = allele of microsatellite locus)
9. Size 1 (value = exact length of allele 1)
10. Size 2 (value = exact length of allele 2)
11. Height 1 (value = height of the peak indicating allele 1)
12. Height 2 (value = height of the peak indicating allele 2)
13. Peak Area 1 (value = width of the peak indicating allele 1)
14. Peak Area 2 (value = width of the peak indicating allele 2)
15. Data Point 1 (value = size standard allele 1)
16. Data Point 2 (value = size standard allele 2)
17. AE (value = Process Quality Values (PQV))
18. OS (value = Process Quality Values (PQV))
19. BIN (value = Process Quality Values (PQV))
20. PHR (value = Process Quality Values (PQV))
21. XTLK (value = Process Quality Values (PQV))
22. GQ (value = overall Genotype Quality)

4. Missing data codes: ""

FILE 2 (three sheets):

DATA-SPECIFIC INFORMATION FOR: Samples_metadata_Godwits_UK.xlsx; sheet: Master

1. Number of variables: 18

2. Number of cases/rows: 261

Row 1: variable names
Row 2-261: 260 cases 

3. Variable List:

1. Year (value = collection year of sample)
2. Sample type (value = description of sample type)
3. Sample # (value = sample ID)
4. Sample (value = sample process status)
5. SUCCESSFUL Extractions-SampleID (value = sample ID)
6. UNSUCCESSFUL Extractions-SampleID (value = sample ID)
7. Location (value = storage location sample: UEA = University of East Anglia)
8. Colour combo (value = colour ring ID for individual bird) 
9. Source location (nest location; value =  area name)
10. Source location FIELD (nest location; value = field ID)
11. Nest # (value = nest ID)
12. Egg # (value = egg ID)
13. year:nest (value = variable of combined collection year and nest ID)
14. year:nest:egg (value = variable of combined collection year and nest ID and egg ID)
15. Wild or H-S (value = nest in wild Wild)  or headstarted (H-S)
16. Parent Male (value = colour ring ID father)
17. Parent Female (value = colour ring ID mother)
18. RECRUIT:STATUS (recruited in population; value = RECRUITED/NOT-RECRUITED/NA)

4. Missing data codes: ""

DATA-SPECIFIC INFORMATION FOR: Samples_metadata_Godwits_UK.xlsx; sheet: Extractions

1. Number of variables: 3

2. Number of cases/rows: 213

Row 1: variable names
Row 2-213: 212 reactions 

3. Variable List:

1. Extraction (value = ID DNA extraction)
2. SampleID (value = sample ID)
3. Worked? (value = sample process status) 

4. Missing data codes: ""

DATA-SPECIFIC INFORMATION FOR: Samples_metadata_Godwits_UK.xlsx; sheet: Extraction details

1. Number of variables: 9

2. Number of cases/rows: 37

Row 1: variable names
Row 2-37: 36 extractions

3. Variable List:

1. Extraction Number (value = ID DNA extraction)
2. Sample ID (value = sample ID)
3. Ring# (value = metal ring ID for individual bird
4. Colours (value = colour ring ID for individual bird)
5. Source location (nest location, value = field ID)
6. Nest (value = nest ID)
7. Egg (value = egg ID)
8. Wild or HS (nest type; value = nest in wild (Wild), or headstarted nest (HS))
9. Parent Female (value = colour ring ID mother)

4. Missing data codes: ""

FILE 3 (two sheets):

DATA-SPECIFIC INFORMATION FOR: Genotypes_Godwits_Netherlands_Trimbos.xlsx; sheet: Sample info Godwit Ned

1. Number of variables: 12

2. Number of cases/rows: 39

Row 1: variable names
Row 2-39: 38 samples

3. Variable List:

1. Sample Number (value = field sample ID)
2. Ringnumber (value = metal ring ID for individual bird)
3. Location ID (value = code assigned to location)
4. Loc (nest location; value = area name)
5. Nest ID (value = code assigned to nest)
6. Age (age of chicks; value = days)
7. Year of 1st Bloodsample (value = year bird was sampled)
8. Remarks
9. Min dis between samples km (minimum distance between sampling locations; value = kilometer (km))
10. Max dis between samples km (maximum distance between sampling locations' value = kilometer (km))
11. Longitude (value = longitude of nest location)
12. Latitude (value = latitude of nest location)

4. Missing data codes: 99

DATA-SPECIFIC INFORMATION FOR: Genotypes_Godwits_Netherlands_Trimbos.xlsx; sheet: Gescoorde Msats Friesland

1. Number of variables: 20

2. Number of cases/rows: 39

Row 1: variable names
Row 2-39: 38 samples

3. Variable List:

1. Sample Name (value = field sample ID)
2. Popinfo (population location information; Friesland only; value = FRS)
3. Lim10 (marker ID, allele 1; value = length in base pairs)
4. Lim10-2 (marker ID, allele 2; value = length in base pairs)
5. Lim11 (marker ID, allele 1; value = length in base pairs)
6. Lim11-2 (marker ID, allele 2; value = length in base pairs)
7. Lim12a (marker ID, allele 1; value = length in base pairs)
8. Lim12a-2 (marker ID, allele 2; value = length in base pairs)
9. Lim25 (marker ID, allele 1; value = length in base pairs)
10. Lim25-2 (marker ID, allele 2; value = length in base pairs)
11. Lim3 (marker ID, allele 1; value = length in base pairs)
12. Lim3-2 (marker ID, allele 2; value = length in base pairs)
13. Lim30 (marker ID, allele 1; value = length in base pairs)
14. Lim30-2 (marker ID, allele 2; value = length in base pairs)
15. Lim33 (marker ID, allele 1; value = length in base pairs)
16. Lim33-2 (marker ID, allele 2; value = length in base pairs)
17. Lim5 (marker ID, allele 1; value = length in base pairs)
18. Lim5-2 (marker ID, allele 2; value = length in base pairs)
19. Lim8 (marker ID, allele 1; value = length in base pairs)
20. Lim8-2 (marker ID, allele 2; value = length in base pairs)

4. Missing data codes: 999

FILE 4:

DATA-SPECIFIC INFORMATION FOR: GenoptypeTableUK.xlsx

1. Number of variables: 22

2. Number of cases/rows: 60

Row 1: variable names
Row 2-60: 59 samples 

3. Variable List:

1. Sample Name (sample ID; value = extraction ID)
2. PopInfo (population location information; UK only; value = 1)
3. LIM10_Allele 1 (marker ID, allele 1; value = length in base pairs)
4. LIM10_Allele 2  (marker ID, allele 2; value = length in base pairs)
5. LIM11_Allele 1 (marker ID, allele 1; value = length in base pairs)
6. LIM11_Allele 2  (marker ID, allele 2; value = length in base pairs)
7. LIM12a_Allele 1 (marker ID, allele 1; value = length in base pairs)
8. LIM12a_Allele 2  (marker ID, allele 2; value = length in base pairs)
9. LIM22_Allele 1 (marker ID, allele 1; value = length in base pairs)
10. LIM22_Allele 2  (marker ID, allele 2; value = length in base pairs)
11. LIM25_Allele 1 (marker ID, allele 1; value = length in base pairs)
12. LIM25_Allele 2 (marker ID, allele 2; value = length in base pairs)
13. LIM3_Allele 1 (marker ID, allele 1; value = length in base pairs)
14. LIM3_Allele 2 (marker ID, allele 2; value = length in base pairs)
15. LIM30_Allele 1 (marker ID, allele 1; value = length in base pairs)
16. LIM30_Allele 2  (marker ID, allele 2; value = length in base pairs)
17. LIM33_Allele 1 (marker ID, allele 1; value = length in base pairs)
18. LIM33_Allele 2  (marker ID, allele 2; value = length in base pairs)
19. LIM5_Allele 1 (marker ID, allele 1; value = length in base pairs)
20. LIM5_Allele 2  (marker ID, allele 2; value = length in base pairs)
21. LIM8_Allele 1 (marker ID, allele 1; value = length in base pairs)
22. LIM8_Allele 2  (marker ID, allele 2; value = length in base pairs)

4. Missing data codes: NA

FILE 5:

DATA-SPECIFIC INFORMATION FOR: OneSibperNest.csv

1. Number of variables: 2

2. Number of cases/rows: 60

Row 1: variable names
Row 2-60: 59 samples 

3. Variable List:

1. Sample Name (sample ID; value = extraction ID)
2. InAnalyses (selected for analyses (no/yes; value = 0 or 1)

4. Missing data codes: no missing data

FILE 6:

DATA-SPECIFIC INFORMATION FOR: Table2.xls

1. Number of variables: 11

2. Number of cases/rows: 10

Row 1: variable names
Row 2-10: summary stats for 9 loci

3. Variable List:

1. Locus (value = marker name)
2. NaUK (value = number of alleles (Na) in UK sample)
3. ArUK (value = number of alleles after rarefaction (Ar) in UK sample)
4. HeUK (value = expected heterozygosity (He) in UK sample)
5. HoUK (value = observed heterozygosity (Ho) in UK sample)
6. FisUK (value = inbreeding coefficient (Fis) in UK sample)
7. NaFRS (value = number of alleles (Na) in UK sample)
8. ArFRS (value = number of alleles after rarefaction (Ar) in Friesland sample)
9. HeFRS (value = expected heterozygosity (He) in Friesland sample)
10. HoFRS (value = observed heterozygosity (Ho) in Friesland sample)
11. FisFRS (value = inbreeding coefficient (Fis) in Friesland sample)

4. Missing data codes: no missing data

FILE 7:

DATA-SPECIFIC INFORMATION FOR: aux_functions.R

R script

FILE 8:

DATA-SPECIFIC INFORMATION FOR: Godwit microsatellite analysis.r

R script

Code/software

SOFTWARE

• Gene Mapper Version 3.7 (Applied Biosystems)
• R version 4.0.2 'related' package (version 1.0) (Pew et al., 2015)
• 'Pegas' package (version 1.2) (Paradis, 2010)
• 'adegenet' package (in R version 4.0.2)
• 'ape' package (in R version 4.0.2)
• GENEPOP (Raymond and & Rousset, 1995; Netherlands dataset, see Trimbos et al. 2011).

CODE

SEE FILE 7: aux_functions.R

SEE FILE 8: Godwit microsatellite analysis.r

Access information

Other publicly accessible locations of the data:

• NA

Data was derived from the following sources:

• NA