Supporting Data Contents
Supporting Data 1- Agreement between parentage methods.xlsx
Data Columns
ID: The individual that was assigned parentage by Cervus.
Cervus assigned father: the ID of the male assigned as the father to an individual by Cervus.
Males present in colony: Adult males present in the same colony as the individual, making them candidate fathers. 
Reason for assignment: The reason why one of the adult males present in the colony was assigned as the father by observation.
Father assigned by observation: The father assigned to the individual (ID) using observation method. 
Observed and Cervus match?: whether the same parent is assigned by Cervus and observation method. 
Cervus assigned mother: the ID of the female assigned as the mother to an individual by Cervus.
Females present in colony: Adult females present in the same colony as the individual, making them candidate mothers. 
Reason for assignment: The reason why one of the adult females present in the colony was assigned as the mother by observation.
Mother assigned by observation: The mother assigned to the individual (ID) using observation method. 
Observed and Cervus match?: whether the same parent is assigned by Cervus and observation method. 

Supporting Data 2- Fitness trait GLMs data.xlsx 
Different calculation methods for the inbreeding coefficients FH and F^III are provided with values for each fitness trait measured. 
Data columns
ID: The unique identifier assigned to each individual. 
PHt- Proportion of loci that were heterozygous for each individual. 
Cluster- the genetic cluster to which the individual had majority probability of membership, as calculated using the program Structure. 2=Northern cluster, 1= Southern cluster. 
Period: The period during which the individual was genetically sampled. 1=1997 to 2001, 2=2011-2017. 
Bred: whether an individual bred during their lifetime. 0= no, 1=yes. 
Survival: whether an individual survived to 3 years: 0=no, 1=yes.
Longevity (years): How long an individual lived.
Offspring: The number of offspring produced by an individual. 

Supporting Data 3- Population monitoring data for Yellingbo 1997 to 2017.xlsx
Each sampling year is shown in a separate tab. 
Data Columns
Box: The nest box or colony being surveyed.
Date: The date on which the colony or nest box was inspected. 
Animals present: A unique identifier given to each individual (either a tattoo or each notch position). 
Genotype: The name of the DNA sample obtained from an individual. These are the same as those listed in Supporting Data 4. 
Sex: the sex of the individual. 
First detection?: Whether this is the first time the individual has been identified during surveys. 
Weight: Weight of the individual. 
Fluffy rump fur: Whether there is elongated fur on the rump of the individual, indicative of being juvenile or subadult. 
Tail base staining: Whether there is staining at the base of the tail, indicative of pair-bonding between mates. 
Pouch condition: Whether there is evidence of prior breeding (stretched or stained) or pouch young present. Enlarged nipples are also indicative of current or recent lactation. 
Breeding: Whether the individual has been identified as currently breeding. 
Lactating: Whether the individual is currently lactating. 
Notes: Other observations of an individual. 


Supporting Data 4- DArT genotypes and metadata.xlsx
First sheet contains the genotype of each individual, given in one row format- o=homozygous for reference allele, 1=heterozygous, 2=homozygous for alternate allele. Metrics for each locus are given in the first 22 columns. Individual IDs are give in row 6, beginning column 23. 
Second sheet gives the metadata for each individual in the dataset.
Data columns
ID: Unique identifier assigned to each individual. 
Sex: The sex of each individual.
Pop: The location where the sample was collected. 
Year collected: The year when the genetic sample was collected.