A review on Q ST – F ST comparisons of seed plants: Insights for conservation

Abstract Increased access to genome‐wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable because genomic data are not available to most rare plant species. In the hope of bridging the gap between conservation science and practice, we outline how conservation practitioners can more efficiently employ population genetic information in plant conservation. We first review the current knowledge about neutral genetic variation (NGV) and adaptive genetic variation (AGV) in seed plants, regarding both within‐population and among‐population components. We then introduce the estimates of among‐population genetic differentiation in quantitative traits (Q ST) and neutral markers (F ST) to plant biology and summarize conservation applications derived from Q ST–F ST comparisons, particularly on how to capture most AGV and NGV on both in‐situ and ex‐situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials (n = 18) to capture 99% of NGV and AGV, respectively, whereas four populations would be needed in case of herbaceous perennials (n = 14). On average, Q ST is about 3.6, 1.5, and 1.1 times greater than F ST in woody plants, annuals, and herbaceous perennials, respectively. Hence, conservation and management policies or suggestions based solely on inference on F ST could be misleading, particularly in woody species. To maximize the preservation of the maximum levels of both AGV and NGV, we suggest using maximum Q ST rather than average Q ST. We recommend conservation managers and practitioners consider this when formulating further conservation and restoration plans for plant species, particularly woody species.


| INTRODUC TI ON
Genetic diversity is a prerequisite for evolutionary change in all organisms; preservation of genetic diversity in a species likely increases its chances of surviving over evolutionary time when facing environmental changes. Plant evolutionary biologists, foresters, and conservation geneticists have long been interested in the genetic differences among populations and the degree to which these may reflect local adaptation (see Table 1 for the definition of population genetic terms cited in this mini review). This interest traces back to the common garden experiments of Turesson (1922) and the reciprocal transplants of Clausen et al. (1941). For decades, common garden and reciprocal transplant experiments have been instrumental in advancing our understanding of how natural selection shapes geographic phenotypic variation (reviewed in Flanagan et al., 2018;Sork, 2018). As putatively neutral molecular genetic markers (i.e., allozymes and DNA-based dominant and codominant loci) became available, plant biologists were able to compare the levels of genetic diversity at single gene markers and the degree of divergence seen at phenotypic traits (De Kort et al., 2013;Leinonen et al., 2013;Marin et al., 2020;Reed & Frankham, 2001).
Applications of traditional marker-based neutral genetic variation (NGV) to the conservation and restoration of plant species have been somewhat controversial due to the assumed evolutionary neutrality of used markers and their limitations to be informative about the adaptive potential (García-Dorado & Caballero, 2021;Teixeira & Huber, 2021). Although levels of NGV might not be always predictive of adaptive genetic variation (AGV; Teixeira & Huber, 2021), it is possible that NGV under current conditions may become AGV under changed environmental conditions. However, NGV, largely corresponding to within-population genetic variation from allozymes to nucleotide sequences-as reflected in the percentage of polymorphic loci (%P), allelic richness (AR), or gene diversity (Hardy-Weinberg expected heterozygosity, H e )-is considered a poor "proxy" of levels of AGV in quantitative traits (i.e., narrow-and broad-sense heritabilities [h 2 and H 2 ]; Depardieu et al., 2020;Reed & Frankham, 2001).
The comparison between F ST ( [Wright, 1951] or its analogs estimated from neutral genetic markers [Meirmans & Hedrick, 2010]; see Holsinger & Weir, 2009 for different definitions and interpretations of F ST ) and Q ST (F ST analog for quantitative traits ;Depardieu et al., 2020;Spitze, 1993), i.e., Q ST -F ST comparisons or relationships, was formalized with the adoption of Q ST in the 1990s. Q ST creates an explicit prediction of the expectation for quantitative trait differentiation under neutrality (De Kort et al., 2013;Leinonen et al., 2013;Merilä & Crnokrak, 2001). Under the reasonable assumption that the genetic markers used commonly to estimate F ST are neutral, the common finding that Q ST > F ST supports the view that the divergence of quantitative traits among populations exceeds neutral divergence and hence is predominantly driven by natural selection. Although F ST is generally a poor predictor of Q ST , many researchers still assume that levels of NGV would be indicative of those of AGV (e.g., DeWoody et al., 2021;García-Dorado & Caballero, 2021;Hamrick & Godt, 1996;Oostermeijer et al., 1994;Ottewell et al., 2016, but see Teixeira & Huber, 2021).
Although there is already an ongoing transition from conservation genetics to conservation genomics (Allendorf et al., 2010(Allendorf et al., , 2022Sork, 2018), conservation managers and practitioners need to continuously utilize information on NGV, if any, to support their decision making because genomic data are still scarce for many rare plant species. Comparative (i.e., Q ST -F ST comparisons) and theoretical studies of NGV and AGV within and among populations in a variety of organisms are abundant in the literature (e.g., Hendry, 2002;Leinonen et al., 2013;Li et al., 2019;McKay & Latta, 2002;Frankham, 2001, 2003 andreferences therein). However, few studies have so far described or considered the application of Q ST -F ST comparisons in the field of conservation biology (Reed & Frankham, 2003; but see Gravuer et al., 2005;McKay et al., 2001;Petit et al., 2001;Rodríguez-Quilón et al., 2016).
On a different but related note, there have been increasing recommendations for lowering the gap between conservation science and practice (also coined as "the conservation genetics gap", "the research-implementation gap", or "the science-practice gap" ;Britt et al., 2018;Dubois et al., 2019;Fabian et al., 2019;Holderegger et al., 2019;Taylor et al., 2017). It is generally agreed that conservation researchers should communicate with practitioners to integrate their genetic findings into conservation implementation (Chung et al., 2021;Ottewell et al., 2016). To achieve this, a generally and clearly written narrative covering Q ST -F ST in seed plants might be needed to lower the threshold for plant conservation practitioners to employ population genetics information in conservation practice.
With this in mind, we first introduce the current knowledge about within-population genetic variation and among-population differentiation both in NGV and AGV in seed plants to highlight the distinction between the approaches used to identify the two types of genetic variation. Next, we introduce the known general application of Q ST -F ST comparisons to plant biology. We also provide management suggestions as to how to capture germplasms (e.g., seeds) covering most AGV and NGV based on the analyses of molecular and quantitative trait data.

| COMPARISON OF WITHIN -P OPUL ATION G ENE TIC VARIATION: NEUTR AL MARK ER S VER SUS ADAP TIVE TR AITS
As neutral genetic markers reflect demographic processes (including past demographic histories) within local populations, they are informative for management and conservation purposes. Small populations are generally susceptible to the loss of NGV and less adaptive to novel environments due to the loss of AGV through genetic drift (Reed & Frankham, 2003). It is known that the degree of individuals' heterozygosity (estimated as the number of loci at which each individual is heterozygous) is often correlated with fitness TA B L E 1 Definitions of terms used in this mini review.

Term Definition
Adaptation A trait that increases the ability of a population or an organism to survive in its environment.

Allelic richness (AR)
A measurement of the number of alleles per locus with rarefaction adjusting for differences in sample sizes.
Balancing selection A process in which more than one allele is maintained at a locus at a frequency higher than expected by chance. Balancing selection can come about due to overdominance (heterozygote advantage) or frequency-dependent selection.
Broad-sense heritability (H 2 ) The ratio of total genetic variance to total phenotypic variance within a population.

Common garden experiment
A traditional experiment in which genotypes from different populations (provenances) are grown under a common environment to test the relative contribution of genetic and environmental variation on a given phenotypic trait.

Conservation genetics
A branch of (population) genetics aimed to reduce the risk of population and species extinctions and to design strategies for their preservation or restoration.

Conservation genomics
The use of genome-scale data with the same aims of conservation genetics, i.e., ensuring the viability of populations and the biodiversity of living organisms.
F ST The probability of identity by descent (ibd; describing the pair of homologous DNA sequences [for simplicity, alleles] carried by the gametes that produced it from a recent ancestor) resulting from population subdivision (independent of inbreeding within subdivisions); F ST measures the probability of ibd of alleles within subpopulations relative to the total population.

G ST
The proportion of total genetic diversity found among populations averaged over all polymorphic loci; it is regarded as a multiallelic variant of Wright's F ST (1951).
Gene diversity (H e ) Hardy-Weinberg expected heterozygosity both at monomorphic and polymorphic loci. The probability that an individual will be heterozygous at a given locus, based on allele frequencies at that locus.

Gene flow
The movement of alleles from one population to another population, which for plants is achieved by the transport of pollen and seeds by wind, water, or animals.
Genetic drift A change in allele frequencies in a population over time resulting from a random sampling of gametes (i.e., error) to produce zygotes in the next generation and from chance variation in individuals' survival and/or reproductive success. Thus, it results in nonadaptive evolution.
Genetic markers Any type of neutral (see below) genetic information (e.g., allozymes, amplified fragment length polymorphism, inter-simple sequence repeats, microsatellites, DNA sequences [e.g., single nucleotide polymorphisms, SNPs]) that can be used to identify differences between individuals, populations, and/or species.

Isolation by distance
A process by which geographically restricted gene flow results in genetic differentiation being an increasing function of geographic distance.

Linkage disequilibrium
A state in which genes are combined in a dependent manner (i.e., linkage). It arises when genotypes at one locus within a population are non-randomly distributed with respect to genotypes at another locus.
Local adaptation A situation in which resident genotypes have a relatively higher fitness in their local environments than in other environments.
Narrow-sense heritability (h 2 ) The ratio of additive genetic variance to the phenotypic variance in a trait within a population.
Neutral Molecular markers that do not affect fitness, i.e., individuals with different genotypes A 1 A 1 vs. A 1 A 2 have the same fitness.

Non-additive genetic variation
Results from interactions between alleles at the same locus (dominance) or at different loci (epistasis).

Percentage of polymorphic loci (%P)
A measure used to quantify genetic diversity.

Q ST
The proportion of total additive genetic variance that is due to among-population differences in a quantitative trait.
The comparison of the degree of genetic differentiation in quantitative traits (Q ST ) with that in neutral molecular markers (F ST ). This comparison allows the identification of a trait divergence caused by natural selection, as opposed to genetic drift.

Reciprocal transplant experiment
A traditional experimental approach in which living organisms from two different environments are reciprocally grown in their respective environments. If the phenotype of the transplanted individuals does not converge towards that of individuals in receiving population would be evidence for the strong genetic basis of the focal trait. The opposite outcome would be evidence for plasticity in determining the trait value.

Translocation
The deliberate (human-mediated) transfer of plants (entire plants, seeds, or propagules) from an ex situ collection or a natural population to a new location, usually in the wild. (Oostermeijer et al., 1994;Reed & Frankham, 2003). Even when there is a real relationship between an individual's heterozygosity and fitness, this does not imply that there should be a relationship between H e and h 2 at the population level. These two estimates are determined by somewhat different processes.
In a meta-analysis of 71 (60 out of these with allozymes) published datasets, H e was only weakly correlated with h 2 or H 2 : r = 0.217 (−0.88 to 0.90, SD ± 0.433), indicating that neutral markerbased measures only explain 4% of the variation in quantitative traits (Reed & Frankham, 2001). In addition, the correlation between allozyme-based H e and h 2 for 17 metric characters in seven populations of the annual Phlox drummondii was found to be highly variable, The studies listed above suggest that NGV has a limited ability to predict AGV within populations. Reed and Frankham (2001) listed six factors that could be responsible for the low correlation between NGV and AGV, namely, differential selection, non-additive genetic variation, different mutation rates (μ), low-statistical power, environmental effects on quantitative characters, and impact of regulatory variation. In addition, various forms of natural selection affecting the level of neutral polymorphism at linked sites may also contribute to the lack of a relationship between NGV and AGV. The most dramatic effect on neutral variation occurs when beneficial alleles at loci contributing to AGV spread into a population, a process known as a "selective sweep" (Nielson, 2005;Stephan, 2019). Selective sweep can lead to a very large reduction of local H e and AR along the chromosome segment (Kreitman, 2001). H e and AR for non-neighboring or unlinked neutral regions are likely not affected by such events (Nielson, 2005), because linkage disequilibrium between NGV and AGV decays gradually under the influence of recombination.
It should be noted that, however, invoking selective sweep as a factor that lowers the correlation between NGV and AGV could be problematic. The sweeping of one beneficial allele means that the AGV in that gene also disappears. Therefore, because AGV and NGV can be both high in the absence of a selective sweep, they can be both reduced after a sweep, and a positive correlation between AGV and NGV can be still maintained. Therefore, we need to ask whether there are other forms of natural selection in which NGV is lowered without reducing AGV. One such scenario, the hitchhiking effect of fluctuating selection, was provided by Barton (2000): fluctuating environment causing the adaptive alleles to oscillate between low and high frequencies, thus maintaining AGV without fixation or loss, is expected to reduce the levels of the surrounding NGV. The feasibility of such an evolutionary scenario is receiving growing attention, as fitness is indeed found to fluctuate rapidly and widely in natural populations (Bell, 2010;Messer et al., 2016) and population genomic studies have revealed seasonal oscillations of allele frequencies at a large number of sites (Bergland et al., 2014;Machado et al., 2021).
Under balancing selection, different alleles affecting fitness are maintained via heterozygote advantage, rare-allele advantage, or temporally/spatially heterogeneous selection. By definition, such loci harbor high levels of AGV (Aguilar et al., 2004;Charlesworth, 2006). The level of NGV is also expected to be elevated at sites closely linked to the loci of stable balanced polymorphism (Charlesworth, 2006). However, only very closely neighboring neutral sites may experience such an increase in polymorphism because meiotic recombination quickly erodes linkage disequilibrium around the selected loci (Fijarczyk & Babik, 2015). This suggests that The neutrality expectation depends on the assumption that mutation rates (μ) are substantially lower than migration rates (m; Hendry, 2002). Neutral markers having high μ (e.g., microsatellites) are not recommended to be used in Q ST -F ST comparisons (Edelaar et al., 2011;Hendry, 2002), unless hypervariable loci are excluded (Li et al., 2019).  (Lande, 1992). Finally, if Q ST < F ST , trait divergence among populations is less than expected due to genetic drift alone probably under strong spatially uniform or stabilizing selection. The R package "driftsel" (Karhunen et al., 2013(Karhunen et al., , 2014Ovaskainen et al., 2011) can be used to differentiate between stabilizing selection, diversifying selection, and random genetic drift, allowing one to circumvent a lot of the problems with the traditional

| APPLI C ATI ON OF Q S T -F S T COMPARISONS TO PL ANT B IOLOGY
Q ST -F ST comparisons have been used to estimate ecological and evolutionary processes in various plant species, including local adaptation, sexual selection, evolutionary stasis, human-induced evolution, and artificial selection, among others. Perhaps, the most commonly studied issue has been to identify natural selection as a cause of broad-scale clinal variation in morphological and life-history traits (local adaptation; e.g., in Campanulastrum americanum [Prendeville et al., 2013], in Helianthus maximiliani [Kawakami et al., 2011], in two subspecies of Antirrhinum majus [Marin et al., 2020] or various tree species [Savolainen et al., 2007]  e.g., Oryza sativa [Sreejayan et al., 2011] and Zea mays [Pressoir & Berthaud, 2004]). By performing Q ST -F ST comparisons between the invasive species' native and invasive ranges (biological invasions), several researchers have provided information on the evolution of invasiveness and the adaptive potential of invasive plant species (e.g., Hypericum canariense [Dlugosch & Parker, 2007], Ambrosia artemisiifolia [Chun et al., 2011], Lythrum salicaria [Chun et al., 2009], and Geranium carolinianum [Shirk & Hamrick, 2014]).

| IN S I G HTS INTO CON S ERVATI ON AND RE S TOR ATION DERIVED FROM Q S T -F S T COMPARISONS
The Q ST -F ST comparisons, along with geographic and environmental data, have been used to establish translocation schemes for population augmentation of rare plants (e.g., Liatris scariosa [Gravuer et al., 2005]). Furthermore, it has been suggested that setting conservation priorities should not be based only on neutral marker diversity and that Q ST -F ST comparisons could be used to identify populations suitable for translocations (e.g., Arabis fecunda [McKay et al., 2001] and Araucaria araucana [Bekessy et al., 2003]).  (Kremer et al., 1997;Savolainen et al., 2007).

Conservation practitioners may also need information
It has been suggested that more populations would be needed to preserve enough AGV for adaptively significant quantitative traits than for NGV, particularly in trees (Chung et al., 2020;Hamrick et al., 2006;McKay et al., 2001).
Population(s) to be protected in situ or to be sampled for seed banking purposes could be estimated using the following formu-  As F ST appears to be more closely related to AGV than withinpopulation genetic diversity metrics (e.g., H e , %P, or AR), the former should be considered as a more predictable parameter for plant conservation and restoration purposes; estimating the value of F ST (i.e., low, moderate, or high) is important for prioritizing populations for both in situ and ex situ collection and for identifying appropriate sources for reintroductions (Chung et al., 2021;Hamrick & Godt, 1996;Ottewell et al., 2016). Thus, the importance of the proper consideration of F ST information (and Q ST , if available) in conservation management cannot be overstated, particularly when it comes to annuals and herbaceous perennials.

| CON CLUS I ON S AND PER S PEC TIVE
Within-population genetic variation, both natural and restored, is crucial for the response to short-term environmental stresses and long-term evolutionary change. Although the levels of H e are often correlated with fitness (Oostermeijer et al., 1994;Reed & Frankham, 2003;Szulkin et al., 2010), H e of NGV is poorly correlated with heritability (h 2 or H 2 ) of quantitative traits (AGV). As discussed above, the relationship of H e to h 2 or H 2 is often very weak, while the relationship between F ST and Q ST is comparatively stronger; thus, F ST could be considered a weak proxy of Q ST .
However, whenever logistically possible, common garden and/ or transplant studies are strongly recommended to quantify patterns of adaptive genetic variation and differentiation (Capblancq et al., 2020;de Villemereuil et al., 2016;Sork, 2018). The most comprehensive studies conducted so far are generally those carried out with many commercially important tree species (e.g., eucalypts, oaks, poplars, pines, and spruces), and plants with welladapted genotypes are already used to replant clear-cut areas (Depardieu et al., 2020).

FU N D I N G I N FO R M ATI O N
This work was supported by the research fund of Chungnam National University, the Republic of Korea to MYC.

CO N FLI C T O F I NTER E S T S TATEM ENT
All the authors state that there is no conflict of interest.

DATA AVA I L A B I L I T Y S TAT E M E N T
There was no new data created or analyzed for this manuscript.