Data standards

Proportion of trees with reproductive structures (cones, flowers, fruits...) inferred either by total visual counts, estimated based on incomplete counts (e.g. counting of reproductive trees in transects) or remote sensing (e.g. drones, LIDAR).

Unique identifier of the genetic index descriptor. This field is used to indicate which descriptors represent genetic indexes.

Number of trees measured for a single trait or descriptor.

Number of loci used in genetic analysis to calculate genetic indices.

Type of molecular markers used for calculation of genetic indices.

A measure used to quantify genetic diversity in a population. It can be used for comparisons of populations when analysing the same loci across all compared populations.

Genetic diversity (Hs) is a measure of the genetic variation within a single subpopulation under random mating. It quantifies the probability that two randomly selected alleles from the subpopulation are different. The value ranges from 0 (no genetic variability) to 1 (high genetic variability). Hs was calculated in R packege hierfstat.

Nucleotide diversity (π) measures the degree of polymorphism within a population and is defined as the average number of nucleotide differences per site between any two DNA sequences of the same genomic region, chosen randomly from the selected population. This parameter is a measure of genetic variation, in a similar way to Hs. One commonly used measure of nucleotide diversity was first introduced by: Nei M, Li WH. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U.S.A.76:5269–5273.

A molecular diversity partition of total gene diversity into diversity per se and distinctivness using molecular markers. Then the contribution of each population to the total (global) diversity is computed by removing one population at a time. This index refers to the population diversity per se (variation within populations). The measure is relative to the dataset analysed simultaneously and changes when new GCUs are added to the dataset. The index was calculated with metapop2 (https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13015). Reference: Petit et al. 1998 (https://doi.org/10.1111/j.1523-1739.1998.96489.x)

A molecular diversity partition into diversity per se and distinctiness is defined by using molecular markers. Then the contribution of each population to the total (global) diversity is computed by removing one population at a time. This statistics refers to the population distinctiveness (variation between populations). The measure is relative to the dataset analysed simultaneously and changes when new GCUs are added to the dataset. The index was calculated with metapop2 (https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13015). Reference: Petit et al. 1998 (https://doi.org/10.1111/j.1523-1739.1998.96489.x)

Genetic differentiation of a population is determined by the accumulation of independent genetic changes (mutations) or maintenance of unique variants through time. For instance a population living in an ecologically distinct environment can exhibit genetic divergence from the other studied populations. Fst ranges from 0 (complete similarity of alleles/variants) to 1 (no overalp of alleles/variants). Population-specific Fst values can identify the source/ancestral population and trace the evolutionary history of its derived populations. The measure is relative to the dataset analysed simultaneously and changes when new GCUs are added to the dataset. Population specific Fst was calculated with BayeScan (Foll & Gagiotti 2008) in R.

Genetic differentiation of a population is determined by the accumulation of independent genetic changes (mutations) or maintenance of unique variants through time. For instance a population living in an ecologically distinct environment can exhibit genetic divergence from the other studied populations. Fst ranges from 0 (complete similarity of alleles/variants) to 1 (no overalp of alleles/variants). Pairwise Fst provides insight into the current population genetic structure. The measure is relative to the dataset analysed simultaneously and changes when new GCUs are added to the dataset. Pairwise Fst was calculated with package hierfstat in R.

Number of genetically identical individuals, reproducing asexually, divided by the total number of individuals of a specific population.

Area occupied by genetically identical individuals which reproduce asexually by means of vegetative propagation.

Measurement of the extent of admixture of individuals in a population belonging to different gene pools when individuals from two or more parental (ancestral) populations interbreed. The gene pool is the set of all genes, or genetic information in a group of individuals. The value given is the average population ancestry in each of the gene pools detected in the target tree species and is calculated with the R package LEA using the function sNMF. Depending on the number and distribution of populations in the analysis, the proportion of population's ancestry in each of the detected gene pools may change. The number of gene pools detected may also change.

Measurement of the extent of hybridisation between two species in a population. The value given is the average population ancestry in each of the two hybridising species and is calculated with the R package LEA using the function sNMF.

Inbreeding is the production of offspring from the mating or breeding of individuals that are closely related genetically. The degree of inbreeding can be measured using a calculation called the inbreeding coefficient. This calculates the probability that two copies of a gene variant have been inherited from an ancestor common to both the mother and the father. The lower the degree of inbreeding, the lower the inbreeding coefficient. Negative values indicate no inbreeding. Reference: Wright (1921) Systems of Mating. II. the Effects of Inbreeding on the Genetic Composition of a Population. Genetics, 6: 124-143.

Genetic load is a measure of the reduction of fitness caused by genetic erosion. It can be due to the increase in frequency of deleterious mutations due to random genetic drift and/or inbreeding. It is calculated by first identifying deleterious mutations via prediction of their effects, and then deriving deleterious scores that can be summarized to produce a load index, in this case the counts of derived deleterious mutations in homozygosis corrected by the number of synonymous ones. Reference: Bertorelle, G., Raffini, F., Bosse, M. et al. Genetic load: genomic estimates and applications in non-model animals. Nat Rev Genet 23, 492–503 (2022). doi.org/10.1038/s41576-022-00448-x

Genomic offset measures population vulnerability to new environmental conditions. It refers to the expected change in allele frequencies that would be required to mantain optimal fitness under future conditions (e.g. changing climate). It assumes equilibrium between current conditions and allele frequencies and it is usually calculated based on a set of genetic markers under natural selection. It is sensitive to the environmental variables used in the analysis. Reference: Capblancq, T., Fitzpatrick, M. C., Bay, R. A., Exposito-Alonso, M., & Keller, S. R. (2020). Genomic prediction of (mal) adaptation across current and future climatic landscapes. Annual Review of Ecology, Evolution, and Systematics, 51, 245-269.

Evolvability is the ability of a population to produce phenotypic variation that is both heritable and adaptive. References: Houle, 1992. Comparing evolvability and variability of quantitative traits. Genetics. 130(1):195-204. doi: 10.1093/genetics/130.1.195; Payne, J.L., Wagner, A. The causes of evolvability and their evolution. Nat Rev Genet 20, 24–38 (2019). doi.org/10.1038/s41576-018-0069-z