DOI: 10.5061/dryad.xsj3tx9q5
title: Data from: Assessment of conservation status of Ferula huber-morathii: Association with population genetic structure and regional climate

description: Ferula huber-morathii is an endemic and medicinally important plant. This
 species is distributed in eight Turkish localities, including three newly
 identified ones. Its extent of occurrence and area of occupancy is
 determined to be 3963 km2 and 32 km2 respectively. All localities are
 characterized by East Mediterranean and sub-Mediterranean precipitation
 regimes; however, temperatures increase excessively and precipitation
 decreases during the flowering period of the species. The population sizes
 are quite small, and the number of reproducing individuals in some
 populations is below ten. Analyses of ISSR markers showed the percentage
 of polymorphic loci to be 94% at the species level and 56% at the
 population level. The level of genetic differentiation (measured by GST)
 was 0.37 and the estimated level of gene flow among populations (NM) was
 0.84. The percentage of variance occurring within and among populations,
 determined by AMOVA, was 75% and 25%, respectively. STRUCTURE analysis
 revealed two genetic clusters of individuals with a geographic structure
 similar to that found in UPGMA and an ordination analysis. Some
 populations turned out to have both low numbers of individuals and low
 genetic diversity. Since many of the populations are subject to
 anthropogenic disturbance, the species should remain in the EN category.
 At the same time, it is suggested that a new in-situ conservation area
 should be created around nearby dams, situated in the same climate area as
 the currently known populations.
description: The area of occupancy and other distributional data were
 determined by the Geospatial Conservation Assessment Tool (GeoCat) program
 (http://geocat.kew.org; Bachman et al. 2011), based on the 2x2 km cell
 sizes recommended by IUCN and interpopulation distances obtained with the
 Google Earth program. In accordance with the ICUN criteria (2012; 2019)
 and the updated population data collected from the field study, these data
 resulted in a reassessment of the Red List category for the
 species.  The data obtained using the ISSR markers were
 scored in a binary matrix as present (1) or absent (0). Allele number
 observed (Na), effective allele number (Ne), polymorphic locus number
 (P<sub>LS</sub>), polymorphic locus percentage
 (P<sub>LY</sub>), Nei’s genetic diversity (H) (1973, 1987) as
 well as Shannon’s information index (Lewontin, 1972), served as general
 estimators of genetic diversity, calculated using POPGENE ver. 1.32 (Yeh
 et al. 1997) and GenAlEx ver. 6.5 (Peakall and Smouse, 2012).
 Finally, individuals were classified into genetic clusters using
 STRUCTURE version 2.3.4 (Pritchard et al. 2000). In order to account for
 potential recombination across inferred clusters, the Admixture model was
 used to calculate the probabilities of the data for each K ((Pr(X|K)) or
 L(K) cluster for K=1 through K=10 clusters. After 100,000 or 300,000 McMC
 replications had been performed as a burn-in period for each K, 10 runs
 with ten iterations were performed. The amount of variance in each
 K.'s likelihood was estimated (Evanno et al. 2005). The bestfit
 number of groups in CLUMPAK (Kopelman et al. 2015) was determined using
 K.
description: # Assessment of conservation status of Ferula huber-morathii: Association
 with population genetic structure and regional climate This dataset
 includes the raw data of *Ferula huber-morathii*, FR GEN-DIVERSITY data,
 and Figure 4, and their explanations. ### The Raw Data of *Ferula
 huber-morathii* This data was obtained by amplifying plant DNA with
 diversity primers. The data includes populations and their individuals,
 presence (1) and absence analyses (0), and primers mentioned in the
 article. The data was also used in STRUCTURE analysis after being
 evaluated in GenAlEx and POPGENE programs for studies on population
 diversity, differentiation among populations, distance among populations,
 etc. ### FR GEN-DIVERSITY data set Table 4 contains genetic diversity data
 of *F. huber-morathii* and its populations. * N = Sample sizes * Na =
 Observed number of alleles * Ne = Effective number of alleles [Kimura and
 Crow (1964)] * H = Nei's (1973) gene diversity * I = Shannon's
 Information index [Lewontin (1972)] **Formulas from which data is
 obtained** N = Sample sizes Na = Number of Different Alleles Ne = Number
 of Effective Alleles = 1 / (p^2 + q^2) H = Σ(1- pi2– qi2)/n)  I =
 Shannon's Information Index = -1* (p * Ln (p) + q * Ln(q)) He =
 Expected Heterozygosity = 2 * p * q polymorphic locus percentage (PLY)
 Where for Diploid Binary data and assuming Hardy-Weinberg Equilibrium, q =
 (1 - Band Freq.)^0.5 and p = 1 - q. ### Figure 4 This was obtained by
 loading the data generated as a result of structure analysis into the
 CLUMPACK program. In this data set account for potential recombination in
 clustering of population individuals, the Mixture model was used to
 calculate the probabilities of the data from K=1 to K=10 clusters for each
 cluster K ((Pr(X|K)) or L(K). After performing 100,000 or 300,000 McMC
 iterations as burn-in time for each K, 10 runs with ten iterations were
 performed. The amount of variance in the probability of each K was
 estimated (Evanno et al. 2005). MCMC: integrates over possible chunk sizes
 and breakpoints to find different values of K. The optimal number of
 groups was determined using K in CLUMPAK (Kopelman et al. 2015).
 Retrieving data from files for each K K: number of populations K=1 mean:
 -754.21 K=1 standard deviation: 0.128668393770775 K=1 median: -754.2 K=2
 mean: -630.77 K=2 standard deviation: 0.494525586350747 K=2 median: -630.7
 K=3 mean: -640.63 K=3 standard deviation: 6.97982011866271   K=3 median:
 -638.1 K=4 mean: -718.74 K=4 standard deviation: 21.814072929597     K=4
 median: -722 K=5 mean: -743.32 K=5 standard deviation: 15.4657902050515  
 K=5 median: -748 K=6 mean: -743.11 K=6 standard deviation:
 17.6488872800022   K=6 median: -739.1 K=7 mean: -728.84 K=7 standard
 deviation: 18.4378957584644   K=7 median: -732.6 K=8 mean: -882.44 K=8
 standard deviation: 502.315585176402   K=8 median: -723.3 K=9 mean:
 -704.89 K=9 standard deviation: 10.4891954992851   K=9 median: -705.25
 K=10 mean: -707.07 K=10 standard deviation: 12.1466090375508 K=10 median:
 -709.7 \* Calculating Best K by Evanno Delta(K=2) = 269.55127030668
 Delta(K=3) = 9.77818895611831 Delta(K=4) = 2.45392046559867 Delta(K=5) =
 1.60289255649564 Delta(K=6) = 0.796650790326652 Delta(K=7) =
 9.1046181299151 Delta(K=8) = 0.659246915231004 Delta(K=9) =
 17.1347745413125 Max Delta K: 269.55127030668 \* Optimal K by Evanno is: 2
 ## Change log **Oct 2024**: In addition to the previous version, the raw
 data of Ferula huber-morathii has been added. In particular, it was
 desired to emphasize the importance of the raw data used in reaching the
 obtained results in determining both genetic diversity and the
 relationships among populations.