Habitat fragmentation reduces plant progeny quality: a global synthesis

Most of the world's land surface is currently under human use and natural habitats remain as fragmented samples of the original landscapes. Measuring the quality of plant progeny sired in these pervasive environments represents a fundamental endeavour for predicting the evolutionary potential of plant populations remaining in fragmented habitats and thus their ability to adapt to changing environments. By means of hierarchical and phylogenetically independent meta‐analyses we reviewed habitat fragmentation effects on the genetic and biological characteristics of progenies across 179 plant species. Progeny sired in fragmented habitats showed overall genetic erosion in contrast with progeny sired in continuous habitats, with the exception of plants pollinated by vertebrates. Similarly, plant progeny in fragmented habitats showed reduced germination, survival and growth. Habitat fragmentation had stronger negative effects on the progeny vigour of outcrossing‐ than mixed‐mating plant species, except for vertebrate‐pollinated species. Finally, we observed that increased inbreeding coefficients due to fragmentation correlated negatively with progeny vigour. Our findings reveal a gloomy future for angiosperms remaining in fragmented habitats as fewer sired progeny of lower quality may decrease recruitment of plant populations, thereby increasing their probability of extinction.     

Microsatellite variation and structure of 28 populations of the common wetland plant, Lychnis flos-cuculi L., in a fragmented landscape

Habitat fragmentation is known to cause genetic differentiation between small populations of rare species and decrease genetic variation within such populations. However, common species with recently fragmented populations have rarely been studied in this context. We investigated genetic variation and its relationship to population size and geographical isolation of populations of the common plant species, Lychnis flos-cuculi L., in fragmented fen grasslands. We analysed 467 plants from 28 L. flos-cuculi populations of different sizes (60 000-54 000 flowering individuals) in northeastern Switzerland using seven polymorphic microsatellite loci. Genetic differentiation between populations is small (F(ST) = 0.022; amova; P < 0.001), suggesting that gene flow among populations is still high or that habitat fragmentation is too recent to result in pronounced differentiation. Observed heterozygosity (H(O) = 0.44) significantly deviates from Hardy-Weinberg equilibrium, and within-population inbreeding coefficient F(IS) is high (0.30-0.59), indicating a mixed mating breeding system with substantial inbreeding in L. flos-cuculi. Gene diversity is the only measure of genetic variation which decreased with decreasing population size (R = 0.42; P < 0.05). While our results do not indicate pronounced effects of habitat fragmentation on genetic variation in the still common L. flos-cuculi, the lower gene diversity of smaller populations suggests that the species is not entirely unaffected.     

Comparison of contemporary mating patterns in continuous and fragmented Eucalyptus globulus native forests

While habitat fragmentation is a central issue in forest conservation studies in the face of broad-scale anthropogenic changes to the environment, its effects on contemporary mating patterns remain controversial. This is partly because of the inherent variation in mating patterns which may exist within species and the fact that few studies have replication at the landscape level. To study the effect of forest fragmentation on contemporary mating patterns, including effective pollen dispersal, we compared four native populations of the Australian forest tree, Eucalyptus globulus . We used six microsatellite markers to genotype 1289 open-pollinated offspring from paired fragmented and continuous populations on the island of Tasmania and in Victoria on mainland Australia. The mating patterns in the two continuous populations were similar, despite large differences in population density. In contrast, the two fragmented populations were variable and idiosyncratic in their mating patterns, particularly in their pollen dispersal kernels. The continuous populations showed relatively high outcrossing rates (86–89%) and low correlated paternity (0.03–0.06) compared with the fragmented populations (65–79% and 0.12–0.20 respectively). A greater proportion of trees contributed to reproduction in the fragmented ( de/d ≥ 0.5) compared with the continuous populations ( de/d  =   0.03–0.04). Despite significant inbreeding in the offspring of the fragmented populations, there was little evidence of loss of genetic diversity. It is argued that enhanced medium- and long-distance dispersal in fragmented landscapes may act to partly buffer the remnant populations from the negative effects of inbreeding and drift.     

Mitosis, stature and evolution of plant mating systems: low-Phi and high-Phi plants

There is a long-recognized association in plants between small stature and selfing, and large stature and outcrossing. Inbreeding depression is central to several hypotheses for this association, but differences in the evolutionary dynamics of inbreeding depression associated with differences in stature are rarely considered. Here, we propose and test the Phi model of plant mating system evolution, which assumes that the per-generation mutation rate of a plant is a function of the number of mitoses (Phi) that occur from zygote to gamete, and predicts fundamental differences between low-Phi (small-statured) and high-Phi (large-statured) plants in the outcomes of the joint evolution of outcrossing rate and inbreeding depression. Using a large dataset of published population genetic studies of angiosperms and conifers, we compute fitted values of inbreeding depression and deleterious mutation rates for small- and large-statured plants. Consistent with our Phi model, we find that populations of small-statured plants exhibit a range of mating systems, significantly lower mutation rates, and intermediate inbreeding depression, while large-statured plants exhibit very high mutation rates and the maximum inbreeding depression of unity. These results indicate that (i) inbred progeny typically observed in large-statured plant populations are completely lost prior to maturity in nearly all populations; (ii) evolutionary shifts from outcrossing to selfing are generally not possible in large-statured species, rather, large-statured species are more likely to evolve mating systems that avoid selfing such as self-incompatibility and dioecy; (iii) destabilization of the mating system-high selfing rate with high-inbreeding depression-might be a common occurrence in large-statured species; and (iv) large-statured species in fragmented populations might be at higher risk of extinction than previously thought. Our results help to unify and simplify a large and diverse field of research, and serve to emphasize the importance that developmental and genetic constraints play in the evolution of plant mating systems.     

The biogeography of plant reproduction: potential determinants of species' range sizes

Aim A major biogeographical hypothesis, the ‘niche‐breadth’ hypothesis, explains species range sizes based on the extent of a species’ niche (e.g. diversity of habitats occupied; range of environmental conditions tolerated). An alternative hypothesis explains range sizes using metapopulation theory (e.g. colonization dynamics; dispersal ability). Both niche breadth and colonization ability may be related to plant species’ reproductive characteristics. We evaluate both hypotheses by examining the relationship of plant range size to mating system and genomic structure (ploidy status). Location Western North America. Methods Using a data set of 60 taxa in the genus Clarkia (Onagraceae), we use three analytical techniques to examine the effect of reproductive characteristics on range size. We conduct cross‐species analyses of present‐day taxa to examine both mating system and polyploidy in relation to range size. We also conduct a phylogenetically independent contrasts analysis (using caic software) on the relationship of mating system to range size in diploid species. Third, we compare closely related taxon pairs that differ in mating system as an alternative method to control for phylogeny. Results Polyploid species have significantly larger ranges compared with diploid species. When considering only diploid taxa, no significant relationship is found for mating system in both cross‐species and phylogenetically independent contrasts analyses. The diploid pairwise analysis, comparing only the range sizes of direct sister taxa with alternative mating systems, does show a relationship, with outcrossing species having larger ranges than self‐fertilizing species. Main conclusions We argue that genetic diversity, colonization ability, or a combination of both factors may influence plant species’ range sizes. The significant pairwise analysis suggests that both the independent contrast and the cross‐species analysis may be confounded by polytomies of species at the terminal nodes of the phylogeny, indicating the importance of comparing the results of multiple analytical techniques. We propose that the range sizes of self‐fertilizing species have a bimodal distribution, obscuring the effect of mating system on range size, and that a broader survey of plant taxa will resolve the two modes from that of the outcrossing species. Lastly, polyploid species appear to show significantly larger range sizes than diploid species, irrespective of mating system.     

Forest fragmentation effects on patch occupancy and population viability of herbaceous plant species

Habitat fragmentation is one of the major threats to species diversity. In this review, we discuss how the genetic and demographic structure of fragmented populations of herbaceous forest plant species is affected by increased genetic drift and inbreeding, reduced mate availability, altered interactions with pollinators, and changed environmental conditions through edge effects. Reported changes in population genetic and demographic structure of fragmented plant populations have, however, not resulted in large-scale extinction of forest plants. The main reason for this is very likely the long-term persistence of small and isolated forest plant populations due to prolonged clonal growth and long generation times. Consequently, the persistence of small forest plant populations in a changing landscape may have resulted in an extinction debt, that is, in a distribution of forest plant species reflecting the historical landscape configuration rather than the present one. In some cases, fragmentation appears to affect ecosystem integrity rather than short-term population viability due to the opposition of different fragmentation-induced ecological effects. We finally discuss extinction and colonization dynamics of forest plant species at the regional scale and suggest that the use of the metapopulation concept, both because of its heuristic power and conservation applications, may be fruitful.     

Conservation Genetics of the Endemic Mexican Heliconia uxpanapensis in the Los Tuxtlas Tropical Rain Forest

Heliconia uxpanapensis (Heliconiaceae) is an outcrossing endemic herb that grows within continuous and fragmented areas of the tropical rain forest of southeast Veracrúz (México). The genetic diversity, population differentiation, and genetic structure of seven populations of the studied species were assessed using inter‐simple sequence repeat) markers. Population differentiation was moderately high (F_ST range: 0.18–0.22) and indirect estimates of gene flow were rather low (Nm=0.65–0.83). Analysis of molecular variance indicated that the populations explained 22.2 percent of the variation, while individuals within the populations accounted for 77.8 percent. The similar and high level of genetic diversity found within populations of the continuous and fragmented forest suggests that H. uxpanapensis has not suffered yet the expected negative effect of fragmentation. Genetic structure analyses indicated the presence of fewer genetic clusters (K=4) than populations (N=7). Three of the four fragmented forest populations were assigned each to one of the clusters found within the continuous forest, suggesting the absence of a negative fragmentation effect on the amount and distribution of genetic variation. Given the significant genetic structure combined with high genetic diversity and low levels of gene flow, theoretical simulations indicated that H. uxpanapensis might be highly susceptible to changes in the mating system, which promotes inbreeding within fragmented populations. Thus, future conservation efforts in this species should be directed to ensure that levels of gene flow among populations are sufficient to prevent an increment in the magnitude of inbreeding within fragments.     

Inbreeding and soil conditions affect dispersal and components of performance of two plant species in fragmented landscapes

During habitat fragmentation, plant populations become smaller and more isolated from each other, resulting in increasing inbreeding rates within populations. Furthermore, fragmentation is often accompanied by a progressive deterioration of soil conditions. Overall, high inbreeding rates and poor soil conditions decrease plant performance and so increase the probability of extinction of fragmented plant populations. The goal of this study was to investigate the effects of inbreeding and soil acidification on seed and offspring traits of Succisa pratensis and Hypochaeris radicata, two plant species differing in mating system, lifespan and dispersal ability. For each species, plants from four populations of different sizes were hand-pollinated. The selfed and outcrossed progeny were grown at two soil pH levels. Overall, results showed that the dispersal potential of H. radicata was reduced by selfing, indicating that dispersal capacity is not independent from the genetic erosion process. Variation among seed families and its interactions with pollination treatments indicate that dispersal capacity may have a genetic basis. The performance of both species decreased sharply as soil conditions became more acidic, but inbreeding did not aggravate the process. These results suggest that S. pratensis and H. radicata populations may decline in the long term; however, family level variation suggests a potential for adaptation to new conditions.     

Genetic Connectivity of the Moth Pollinated Tree Glionnetia sericea in a Highly Fragmented Habitat

Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.     

生境片断化对植物种群遗传结构的影响及植物遗传多样性保护

生境片断化是指大而连续的生境变成空间隔离的小种群的现象。生境片断化对植物种群遗传效应包括生境片断化过程中的取样效应及其后的小种群效应（遗传漂变、近交等）。理论研究表明,生境片断化后,植物种群的遗传变异程度将降低,而残留的小种群间的遗传分化程度将升高。然而对一些植物的研究表明,生境片断化对植物种群的遗传效应要受其他一些因素的影响,如世代长度、片断化时间、片断种群的大小、基因流的改变等。最后,针对生境     

Inbreeding depression in Vriesea gigantea,a perennial bromeliad from southern Brazil

Inbreeding depression is a reduction of fitness in the progeny of closely related individuals and its effects are assigned to selfing or biparental inbreeding. Vriesea gigantea is a self‐compatible bromeliad species distributed in the Brazilian Atlantic rainforest and habitat destruction and fragmentation and collection have decreased the natural populations. We aim to describe the occurrence of inbreeding depression (δ) in three natural populations of V. gigantea and to correlate this phenomenon with previous studies of fertility, genetic diversity, population genetic structure, gene flow, mating system and seed dispersal in this species. Fifty‐four adult plants were sampled and 108 flowers were used for pollination treatments (selfing, outcrossing and control). For adult plants, we analysed plant and inflorescence height, flower numbers and seed set. In the progenies, evaluated parameters included seed germination and seedling survival rate. The results indicated low to moderate levels of inbreeding depression in V. gigantea (δ = 0.02 to 0.39), in agreement with molecular data from a previous study. Vriesea gigantea populations tolerate some degree of inbreeding, which is consistent with previous results on fertility, mating system, genetic diversity and gene flow. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 312–319.     

Fine-scale genetic structure enhances biparental inbreeding by promoting mating events between more related individuals in wild soybean (Glycine soja; Fabaceae) populations

Outcrossing between genetically distant individuals in a plant population enhances allelic heterozygosity-an important source for genetic diversity and adaptive evolution. Fine-scale spatial genetic structure (FSGS) can interfere with outcrossing by promoting mating between more related individuals. To test the influence of FSGS on outcrossing, FSGS and outcrossing rates were analyzed with four wild soybean (Glycine soja) populations from different habitats, using simple sequence repeat (SSR) fingerprints. Spatial autocorrelation analysis indicated variable FSGS (15.44-25.87 m) in all four populations. Multilocus mixed-mating analysis of 1605 progeny indicated substantial variation in single-locus outcrossing (T(s) = 6.3-12.6%) although the total outcrossing rates as estimated by multilocus outcrossing (T(m) = 12.8-17%) did not vary significantly among populations. The comparison between FSGS and outcrossing rates demonstrated that strong FSGS with large genetic patch size can enhance biparental inbreeding by promoting mating between more related individuals in a population. The results suggest that patch size management can aid in situ conservation by avoiding formation of strong FSGS and encouraging true outcrossing among individuals.     

Contemporary pollen-mediated gene immigration reflects the historical isolation of a rare,animal-pollinated shrub in a fragmented landscape

Fragmentation is generally considered to have negative impacts on widespread outbreeders but impacts on gene flow and diversity in patchy, naturally rare, self-compatible plant species remain unclear. We investigated diversity, gene flow and contemporary pollen-mediated gene immigration in the rare, narrowly distributed endemic shrub Calothamnus quadrifidus ssp. teretifolius. This taxon occurs in an internationally recognized biodiversity hotspot subjected to recent human-induced fragmentation and the condition of the remnants ranges from intact to highly degraded. Using microsatellites, we found that inbreeding, historically low gene flow and significant population differentiation have characterized the genetic system of C. quadrifidus ssp. teretifolius. Inbreeding arises from self-pollination, a small amount of biparental inbreeding and significant correlation of outcross paternity but fecundity was high suggesting populations might have purged their lethals. Paternity analyses show that pollinators can move pollen over degraded and intact habitat but populations in both intact and degraded remnants had few pollen parents per seed parent and low pollen immigration. Genetic diversity did not differ significantly between intact and degraded remnants but there were signs of genetic bottlenecks and reduced diversity in some degraded remnants. Overall, our study suggests human-induced fragmentation has not significantly changed the mating system, or pollen immigration to, remnant populations and therefore genetic connectivity need not be the highest conservation priority. Rather, for rare species adapted to higher levels of inbreeding, conservation efforts may be best directed to managing intact habitats and ecosystem processes.     

Isozyme variability of the wetland specialist Swertia perennis (Gentianaceae) in relation to habitat size, isolation, and plant fitness

We examined the effects of size and spatial isolation of fens on the isozyme variability of 17 populations of Swertia perennis. This long-lived perennial is a locally abundant fen specialist in Switzerland, where wetlands have been strongly fragmented. Isozyme variability was comparable to other outcrossing plants (A = 1.53, AP(p) = 2.01, P(p) = 42.5, H(o) = 0.113, H(e) = 0.139). F statistics indicated both inbreeding within and differentiation between populations (F(IS) = 0.076, F(IT) = 0.194, F(ST) = 0.128), with moderate gene flow between populations (N(e)m = 1.703). Populations in small, isolated fens had reduced genetic variability and the highest within-population inbreeding coefficients (F(IS)). Isozyme variability was significantly associated with vegetative fitness traits (MANOVA), and the magnitude of leaf herbivory decreased as the percentage of polymorphic loci increased. These data suggest that the reduced genetic variability of S. perennis in small, isolated populations may reduce plant fitness, thereby increasing susceptibility to herbivore damage. Our study also shows that habitat fragmentation can reduce the genetic variability of populations of fairly common habitat specialists, which so far have attracted less conservation attention than rare species.     

Within-population spatial genetic structure in four naturally fragmented species of a neotropical inselberg radiation, Alcantarea imperialis, A. geniculata, A. glaziouana and A. regina (Bromeliaceae)

Studies of organisms on 'terrestrial islands' can improve our understanding of two unresolved issues in evolutionary genetics: the likely long-term effects of habitat fragmentation and the genetic underpinnings of continental species radiations in island-like terrestrial habitats. We have addressed both issues for four closely related plant species of the adaptive radiation Bromeliaceae, Alcantarea imperialis, A. geniculata, A. regina and A. glaziouana. All four are adapted to ancient, isolated inselberg rock outcrops in the Brazilian Atlantic rainforest and are thus long-term fragmented by nature. We used eight nuclear microsatellites to study within-population spatial genetic structure (SGS) and historical gene dispersal in nine populations of these species. Within-population SGS reflected known between-species differences in mating systems. The strongest SGS observed in A. glaziouana (Sp=0.947) was stronger than literature estimates available for plants. Analysis of short- and long-distance components of SGS identified biparental inbreeding, selfing and restricted seed dispersal as main determinants of SGS, with restricted pollen dispersal by bats contributing in some localities. The ability of Alcantarea spp. to colonize isolated inselbergs probably stems from their flexible mating systems and an ability to tolerate inbreeding. Short-ranging gene dispersal (average sigma=7-27 m) is consistent with a loss of dispersal power in terrestrial island habitats. Population subdivision associated with sympatric colour morphs in A. imperialis is accompanied by between-morph differences in pollen and seed dispersal. Our results indicate a high potential for divergence with gene flow in inselberg bromeliads and they provide base-line data about the long-term effects of fragmentation in plants.     

Plant reproductive susceptibility to habitat fragmentation: review and synthesis through a meta-analysis

The loss and fragmentation of natural habitats by human activities are pervasive phenomena in terrestrial ecosystems across the Earth and the main driving forces behind current biodiversity loss. Animal-mediated pollination is a key process for the sexual reproduction of most extant flowering plants, and the one most consistently studied in the context of habitat fragmentation. By means of a meta-analysis we quantitatively reviewed the results from independent fragmentation studies throughout the last two decades, with the aim of testing whether pollination and reproduction of plant species may be differentially susceptible to habitat fragmentation depending on certain reproductive traits that typify the relationship with and the degree of dependence on their pollinators. We found an overall large and negative effect of fragmentation on pollination and on plant reproduction. The compatibility system of plants, which reflects the degree of dependence on pollinator mutualism, was the only reproductive trait that explained the differences among the species' effect sizes. Furthermore, a highly significant correlation between the effect sizes of fragmentation on pollination and reproductive success suggests that the most proximate cause of reproductive impairment in fragmented habitats may be pollination limitation. We discuss the conservation implications of these findings and give some suggestions for future research into this area.     

Skewed morph ratios lead to lower genetic diversity of the heterostylous Primula veris in fragmented grasslands

• Populations of heterostylous plant species are ideally composed of equal frequencies of two (distylous) or three (tristylous) morphologically different floral morphs. Intra-morph incompatibility helps to avoid inbreeding and to maintain genetic diversity, supporting plant fitness and long-term viability. Habitat fragmentation can lead to skewed morph ratios and thereby reduce the abundance of compatible mates. This, in turn, can result in a loss of genetic diversity. We tested whether the genetic diversity of heterostylous plants is affected by morph ratio bias using populations of the distylous grassland plant Primula veris in recently fragmented grasslands.
• We recorded morph frequencies and population sizes in 30 study populations of P. veris on two Estonian islands characterised by different degrees of habitat fragmentation. Examining variation of thousands of single nucleotide polymorphisms (SNPs) and heterostyly-specific genetic markers, we quantified overall and morph-specific genetic diversity and differentiation in these populations.
• Morph frequencies deviated more in smaller populations. Skewed morph ratios had a negative effect on the genetic diversity of P. veris in more fragmented grasslands. In the populations of better-connected grassland systems, genetic differentiation among S-morphs was higher than among L-morphs.
• Our study shows that deviations from morph balance are stronger in small populations and have a negative impact on the genetic diversity of the distylous plant P. veris. Together with the direct negative effects of habitat loss and decreased population size on the genetic diversity of plants, morph ratio bias may intensify the process of genetic erosion, thus exacerbating the local extinction of heterostylous species.

     

普通野生稻小种群的交配系统与遗传多样性

小种群的遗传动态是保育遗传学关注的核心问题之一,而种群遗传动态又与交配系统密切相关.普通野生稻(Oryza rufipogon Griff.)是具有重要经济价值的濒危物种,目前其种群规模都较小,研究其小种群交配系统与遗传变异性对普通野生稻的保护具有重要意义.运用7对SSR引物,对采自江西东乡普通野生稻小种群的36份种茎和其中20个家系共计601份子代进行了分析.结果显示:该种群的表观异交率为0.318,多位点法估计(MLTR)的多位点异交率为0.481;50%以上的子代共享亲本,非随机交配明显;东乡普通野生稻种群交配系统属于混合交配类型.比较亲本和子代种群的遗传变异性显示:子代种群比亲本种群遗传变异性更丰富;子代种群的杂合子不足与种群变小自交比例上升有关;而亲本种群杂合子过剩可能与杂合基因型的选择优势有关.这些结果说明创造条件扩大种群规模对普通野生稻的原生境保护显得尤为重要.     

Large-scale plant conservation in European semi-natural grasslands: a population genetic perspective

During the last century, unprecedented landscape fragmentation has severely affected many plant species occurring in once widespread semi-natural grasslands in Europe. Fragmentation reduces population size and increases isolation, which can jeopardize the persistence of populations. Recent large-scale ecological and genetic studies across several European countries indicate that fragmented populations of common plant species exhibit a strong genetic differentiation and local adaptation to their home sites, reducing their capacity to establish new populations elsewhere. We discuss the main genetic processes that determine the performance of plant populations in severely fragmented landscapes: namely inbreeding depression, genetic differentiation and genetic introgression. We stress the need for large-scale genetic studies to detect the geographical structure of genetic variation of fragmented plant populations, since nuclei of genetically independent groups of populations may become important targets of conservation. A thorough knowledge on the large-scale geographical structure of genetic variation for a sufficiently wide array of plant species can provide the basis to develop comprehensive conservation plans to preserve the ecological and evolutionary processes that generate and maintain biodiversity of fragmented semi-natural grasslands.     

Population genetics of threatened wild plants in Japan

Approximately one-fourth of Japan's native plant species are threatened with extinction. To conserve these species, it is critical to evaluate genetic diversity at species-level and population-level. Some factors, including population size and geographic distribution, are known to influence the population genetic diversity of wild plant species. This article briefly reviews the population genetic studies that have been conducted on wild threatened plants in Japan. A large population size or wide geographic distribution does not always lead to large genetic diversity, suggesting that historical factors such as speciation processes and population expansion often play more important roles in determining genetic diversity than the number of remnant individuals. The mating system of a species also affects genetic diversity; predominantly selfing species tend to have smaller genetic diversity than outcrossing congeners. Another issue of concern in the conservation genetics of wild plants in Japan is the genetic diversity of insular endemics, because Japan consists of many islands, and the insular flora contains many endemic and threatened species. Previous studies on endemic plants on the Bonin and the Ryukyu Islands are reviewed. Compared to the cases of the Bonin Islands or other oceanic islands, there is much larger genetic diversity in plants endemic to the Ryukyu Islands. This difference is probably the result of the differences in the geological history of these islands. Electronic Publication