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.     

Genetic diversity of Andean Polylepis (Rosaceae) woodlands and inferences regarding their fragmentation history

There is a long‐standing debate on whether the occurrence of the iconic high‐Andes Polylepis woodlands as small and isolated fragments is of natural or anthropogenic origin. We make inferences regarding the fragmentation history based on both a new population genetic study on P. besseri and a synthesis of available studies on the population genetics of Polylepis woodlands. We infer the timing of the main woodland fragmentation event by analysing: (1) the remaining levels of population genetic diversity and the relation to population size; (2) among‐population genetic differentiation; and (3) the difference in genetic diversity between the offspring and adult generation. We retrieved seven publications on the population genetics of five Polylepis spp. We did not find a relationship between population size and genetic diversity, and genetic differentiation was low compared with that reported for similar plant species. These findings do not support a history of long‐term fragmentation. The offspring showed a loss of genetic diversity and increasing differentiation compared with adults, suggesting that the main habitat fragmentation event is of relatively recent origin. For P. besseri, no significant differences were found between the adult and offspring genetic variation. We discuss the conservation and restoration consequences for this important high‐Andean genus. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 544–554.     

Conservation genetics of the rare Iberian endemic Cheirolophus uliginosus (Asteraceae)

Cheirolophus uliginosus is a rare species, endemic to the south‐western Iberian Peninsula, and listed as a characteristic taxon from the temperate Atlantic wet heaths, a priority habitat for conservation by the European Union. The conservation status of this species in most of its distribution area is poorly known, but, in recent times, some populations have disappeared and there has been a reduction in the number of individuals in others. In this context, we analysed the effects of population size on genetic diversity, revealing that genetic erosion and inbreeding depression could be having a significant impact on smaller populations. Furthermore, we studied the patterns of genetic structure and variability at the species level, finding a strikingly low within‐population diversity and high among‐population genetic differentiation. Finally, the genetic structure analyses suggested a long and complex phylogeographical history of C. uliginosus in the region, in agreement with the climate relict status proposed for this species. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 157–171.     

Phylogeography and genetic effects of habitat fragmentation on endangered Taxus yunnanensis in southwest China as revealed by microsatellite data

It is not known how the profoundly complex topography and habitat heterogeneity generated by the uplift of the Qinghai‐Tibetan Plateau (QTP) during the late Tertiary affected population genetic structure of endangered Taxus yunnanensis. In addition, the effects of habitat fragmentation due to anthropogenic disturbance on genetic diversity and population differentiation of this species have not been studied. T. yunnanensis is an ancient tree/shrub mainly distributed in southwest China. Recently, the species has suffered a sharp decline due to excessive logging for its famous anticancer metabolite taxol, resulting in smaller and more isolated populations. To understand the phylogeography and genetic consequences of habitat fragmentation of this endangered species, using 11 polymorphic microsatellites, we genotyped 288 individuals from 14 populations from a range‐wide sampling in China. Our results suggest that two different population groups that were once isolated have persisted in situ during glacial periods in both areas, and have not merged since. Habitat fragmentation has led to significant genetic bottlenecks, high inbreeding and population divergence in this species. The two different population groups of T. yunnanensis could be attributed to restricted gene flow caused through isolation by geographical barriers and by habitat heterogeneity during uplift of the QTP, or the existence of two separate glacial refugia during the Pleistocene. In situ and ex situ conservation of the two Evolutionarily Significant Units (ESUs), artificial gene flow between populations and a comprehensive understanding of the pollination system in this endangered species are suggested from this study.     

Habitat fragmentation,genetic diversity,and inbreeding depression in a threatened grassland legume: is genetic rescue necessary?

Kincaid’s lupine (Lupinus oreganus), a threatened perennial legume of western Oregon grasslands, is composed of small, fragmented populations that have consistently low natural seed set, suggesting they may have accumulated high enough levels of genetic load to be candidates for genetic rescue. We used simple sequence repeat (SSR) loci, both nuclear DNA and chloroplast DNA, to screen populations throughout the species’ range for evidence of severe inbreeding and recent genetic bottlenecks due to habitat fragmentation. After genotyping about 40% of the known populations, only one of 24 populations had strong statistical evidence for a recent genetic bottleneck (H _e > H _eq). Both mean nSSR fixation coefficients and genetic diversity did not statistically differ between very small, small, medium, and large lupine population size classes. Within population chloroplast DNA haplotype number was high for an animal pollinated species, ≈4.2 haplotypes/population, and within population haplotype diversity was also relatively evenly distributed. Within population patterns of nSSR and cpSSR genetic diversity suggest that genetic diversity has not been lost over the last century of habitat fragmentation. With genet lifespan thought to exceed 100 years, overlap of several to many generations, and substantial reductions in seed set from inbreeding depression that shifts cohort composition towards those generated by outcrossing events, Kincaid’s lupine is likely maintain the currently high levels of within population genetic diversity. The case of Kincaid’s lupine provides an example of how the assumptions of severe inbreeding depression with small population size and habitat fragmentation can be inaccurate.     

Long‐term ‘islands’ in the landscape: low gene flow,effective population size and genetic divergence in the shrub Hakea oldfieldii (Proteaceae)

The genetic structure of disjunct populations is determined by founding genetic properties, demographic processes, gene flow, drift and local selection. We aim to identify the genetic consequences of natural population disjunction at regional and local scales in Hakea oldfieldii using nuclear and plastid markers to investigate long‐term effective population sizes and gene flow, and patterns of diversity and divergence, among populations. Regional divergence was significant as shown by a consistent pattern in principal coordinates, neighbor‐joining and Bayesian analyses, but divergence at the local level was also significant with localized distribution of plastid haplotypes and populations clustering separately in Bayesian analyses. Historical, recent and first‐generation gene flow was low, suggesting that recent habitat fragmentation has not reduced gene migration significantly. Genetic bottlenecks were detected in three populations. Long‐term effective population size was significantly correlated with the number of alleles/locus and observed heterozygosity, but not with census population size, suggesting that the loss of diversity is associated with long‐term changes rather than recent fragmentation. Inbreeding coefficients were significant in only three populations, suggesting that the loss of diversity is linked to drift and bottlenecks associated with demographic processes (local extinction by fires) rather than inbreeding. Historical disjunction as a result of specific ecological requirements, contraction of habitats following drying during the Pleistocene, low gene flow and changes in population size are likely to have been important forces driving divergence through isolation by distance and drift. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 319–334.     

Rapid genetic differentiation between ex situ and their in situ source populations: an example of the endangered Silene otites (Caryophyllaceae)

Ex situ cultivation in botanic gardens could be one possibility to preserve plant species diversity and genetic variation. However, old ex situ populations are often sparsely documented. We were able to retrieve three different ex situ populations and their source in situ populations of the endangered plant species Silene otites after 20–36 years of isolation. Furthermore, three additional wild populations were included in the analysis. Population genetic diversity and differentiation were analysed using AFLP markers. Genetic variation in the ex situ populations was lower than the variation found in the in situ populations. Strong differentiation (F_ST = 0.21–0.36) between corresponding in situ and ex situ populations was observed. Bayesian clustering approach also showed a distinct genetic separation between in situ and ex situ populations. The high genetic differentiation and loss of genetic diversity during spatial and temporal isolation in the ex situ populations can be attributable to small population sizes and unconscious selection during cultivation. Therefore, adequate sampling prior to ex situ cultivation and large effective population sizes are important to preserve genetic diversity. Near‐natural cultivation allowing for generation overlap and interspecific competition without artificial selection is recommended as being best for the maintenance of the genetic constitution. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, ??, ??–??.     

Limited genetic impacts of habitat fragmentation in an “old rare” relict tree, Euptelea pleiospermum (Eupteleaceae)

Euptelea pleiospermum is an ??old rare?? tree species distributed along the high-elevation streamsides in Burma, China, and India. Deforestation and construction of roads for timber transport have highly fragmented the natural habitats of this species in the Shennongjia Forestry District. In this study, we used this fragmentation to test the hypothesis that ??old rare?? tree species are insusceptible to the genetic consequences of habitat fragmentation. Using eight microsatellite loci, we estimated allelic richness (A _R), observed heterozygosity (H _O), expected heterozygosity (H _E), Wright??s inbreeding coefficient (F _IS), and genetic differentiation (F _ST and D _EST) between pre- and post-fragmentation cohorts. We found no significant differences in either genetic diversity or genetic differentiation between the two cohorts. The limited genetic effects of fragmentation may result from too few fragmented generations, because the time between the start of fragmentation (year 1970) and our study (year 2008) was less than one generation of this tree species. It should be mentioned that clonal reproduction by sprouting, a common phenomenon in many ??old rare?? tree species, can help E. pleiospermum buffer the genetic impacts of fragmentation by delaying the time between generations. Therefore, we conclude that this ??old rare?? tree species show limited genetic impacts from recent habitat fragmentation. However, the elimination of rare alleles and increase of inbreeding coefficient in the post-fragmentation cohort are early warnings of deleterious genetic consequences of fragmentation. Our results provide valuable information to formulate conservation and restoration guidelines for E. pleiospermum.     

Effects of population size and isolation on the genetic structure of the East African mountain white‐eye Zosterops poliogaster (Aves)

Habitat size, quality and isolation determine the genetic structure and diversity of populations and may influence their evolutionary potential and vulnerability to stochastic events. Small and isolated populations are subject to strong genetic drift and can lose much of their genetic diversity due to stochastic fixation and loss of alleles. The mountain white‐eye Zosterops poliogaster, a cloud forest bird species, is exclusively found in the high mountains of East Africa. We analysed 13 polymorphic microsatellites for 213 individuals of this species that were sampled at different points in time in three mountain massifs differing in habitat size, isolation and habitat degradation. We analysed the genetic differentiation among mountain populations and estimated the effective population sizes. Our results indicate three mountain‐specific genetic clusters. Time cohorts did not show genetic divergences, suggesting that populations are large enough to prevent strong drift effects. Effective population sizes were higher in larger and geographically interconnected habitat patches. Our findings underline the relevance of ecological barriers even for mobile species and show the importance of investigating different estimators of population size, including both approaches based on single and multiple time‐points of sampling, for the inference of the demographic status of a population. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 828–836.     

The impact of habitat fragmentation on fitness‐related traits in a native prairie plant,Chamaecrista fasciculata (Fabaceae)

Loss and fragmentation of the native prairies in the Midwestern United States have resulted in isolated and smaller habitats and populations. The populations remaining in these prairies are expected to show a decline in the extent of genetic variation and an increase in genetic drift load (accumulation of deleterious recessive alleles due to genetic drift) in fitness‐related traits. Using complementary greenhouse experiments, we tested whether these expected changes have occurred in the native annual prairie plant Chamaecrista fasciculata. In the first experiment, open pollinated C. fasciculata seeds from 12 prairie fragments representing a range in area of habitat were grown in competition with Schizachyrium scoparium to determine if there are changes in plant vigour with changes in fragment size and corresponding changes in population size. Plants from smaller prairie fragments exhibited a slight but significant decline in biomass, suggesting an increase in genetic drift load. In the second experiment, a formal genetic crossing design of four prairie fragment populations was used to estimate quantitative genetic diversity and genetic drift load. We did not find extensive quantitative genetic variation, but we did find a strong effect of genetic drift load on five traits in this experiment. Our overall conclusion is that a decline in relative‐fitness traits in smaller prairie fragments is probably associated with fixation of deleterious alleles due to more isolated and smaller populations, i.e. genetic drift load. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Extreme population differentiation in a vulnerable slavemaking ant with a fragmented distribution

Understanding levels of population differentiation and inbreeding are important issues in conservation biology, especially for social Hymenoptera with fragmented and small population sizes. Isolated populations are more vulnerable to genetic loss and extinction than those with extended continuous distributions. However, small populations are not always a consequence of a recent reduction of their habitat. Thus, determining the history of population isolation and current patterns of genetic variation of a species is crucial for its conservation. Rossomyrmex minuchae is a slave-making ant with patchy distribution in South Eastern Spain and is classified as vulnerable by the IUCN. In contrast, the other three known species of the genus are presumed to show more uniform distributions. Here we investigate the genetic diversity and population structure of R. minuchae and compare it with that found in two other species of the genus: R. anatolicus and R. quandratinodum. We conclude that although genetic diversity of R. minuchae is low, there is no evidence of a recent bottleneck, suggesting a gradual and natural fragmentation process. We also show extreme population differentiation at nuclear and mitochondrial markers, and isolation by distance at a local scale. Despite some evidence for inbreeding and low genetic variation within populations, we found almost no diploid males, a finding which contrasts with that expected in inbred Hymenoptera with single locus complementary sex determination. This could mean that sex is determined by another mechanism. We argue that continued low population size means that detrimental effects of inbreeding and low genetic variation are likely in the future. We suggest that a policy of artificial gene flow aimed at increasing within population variation is considered as a management option.     

A comparison of the population genetic structure of parasitic Viscum album from two landscapes differing in degree of fragmentation

Parasite populations do not necessarily conform to expected patterns of genetic diversity and structure. Parasitic plants may be more vulnerable to the negative consequences of landscape fragmentation because of their specialized life history strategies and dependence on host plants, which are themselves susceptible to genetic erosion and reduced fitness following habitat change. We used AFLP genetic markers to investigate the effects of habitat fragmentation on genetic diversity and structure within and among populations of hemiparasitic Viscum album. Comparing populations from two landscapes differing in the amount of forest fragmentation allowed us to directly quantify habitat fragmentation effects. Populations from both landscapes exhibited significant isolation-by-distance and sex ratios biased towards females. The less severely fragmented landscape had larger and less isolated populations, resulting in lower levels of population genetic structure (F _ST = 0.05 vs. 0.09) and inbreeding (F _IS = 0.13 vs. 0.27). Genetic differentiation between host-tree subpopulations was also higher in the more fragmented landscape. We found no significant differences in within-population gene diversity, percentage of polymorphic loci, or molecular variance between the two regions, nor did we find relationships between genetic diversity measures and germination success. Our results indicate that increasing habitat fragmentation negatively affects population genetic structure and levels of inbreeding in V. album, with the degree of isolation among populations exerting a stronger influence than forest patch size.     

Genetic diversity in adult and seedling populations of <Emphasis Type="Italic">Primula vulgaris</Emphasis> in a fragmented agricultural landscape

Habitat fragmentation is known to generally reduce the size of plant populations and increase their isolation, leading to genetic erosion and increased between-population genetic differentiation. In Flanders (northern Belgium) Primula vulgaris is very rare and declining. Populations have incurred strong fragmentation for the last decades and are now restricted to a few highly fragmented areas in an intensively used agricultural landscape. Previous studies showed that small populations of this long-lived perennial herb still maintained high levels of genetic variation and low genetic differentiation. This pattern can either indicate recent gene flow or represent historical variation. Therefore, we used polymorphic microsatellite loci to investigate genetic variation and structure in adult (which may still reflect historical variation) and seedling (recent generation, thus affected by current processes) life stages. The recent generation (seedlings) showed a significant loss of observed heterozygosity (H _o) together with lower expected heterozygosity (H _e), a trend for higher inbreeding levels (F _IS) and higher differentiation (F _ST) between populations compared to the adult generation. This might result from (1) a reduction in effective population size, (2) higher inbreeding levels in the seedlings, (3) a higher survival of heterozygotes over time due to a higher fitness of heterozygotes (heterosis) and/or a lower fitness of homozygotes (inbreeding depression), (4) overlapping generations in the adult life stage, or (5) a lack of establishment of new (inbred) adults from seedlings due to degraded habitat conditions. Combining restoration of both habitat quality and gene flow between populations may be indispensable to ensure a sustainable conservation of fragmented populations.     

Genetic diversity and structure of the endangered lady's slipper orchid Cypripedium japonicum Thunb. (Orchidaceae) in Japan

Cypripedium japonicum Thunb. (Orchidaceae), once a common perennial herb, is now designated as endangered throughout most of its distribution due to habitat destruction and fragmentation, and the impacts of horticultural collection. We investigated the genetic characteristics of this species for conservation purposes, using microsatellite markers to examine the genetic diversity and structure of 15 native and 5 ex situ populations in Japan. The results imply that although allelic variation is low in Japanese C. japonicum, sexual reproduction by seed, as well as clonal propagation, may occur in some populations. Both native and ex situ populations were found to be genetically differentiated, indicating that some populations may have experienced recent population declines, genetic fragmentation, or bottlenecks. The degree of genetic drift from the putative ancestral population, inferred through STRUCTURE analysis, was more pronounced in northern populations than in southern populations. Some of the ex situ conserved populations exhibited a low degree of differentiation from ancestral native populations. Our results imply that conservation of C. japonicum in Japan is best supported by maintaining individual populations and their unique genetic characteristics.     

Ex situ conservation genetics: a review of molecular studies on the genetic consequences of captive breeding programmes for endangered animal species

Captive breeding has become an important tool in species conservation programmes. Current management strategies for ex situ populations are based on theoretical models, which have mainly been tested in model species or assessed using studbook data. During recent years an increasing number of molecular genetic studies have been published on captive populations of several endangered species. However, a comprehensive analysis of these studies is still outstanding. Here, we present a review of the published literature on ex situ conservation genetics with a focus on molecular studies. We analysed 188 publications which either presented empirical studies using molecular markers (105), studbook analyses (26), theoretical work (38), or tested the genetic effects of management strategies using model species (19). The results show that inbreeding can be minimized by a thorough management of captive populations. There seems to be a minimum number of founders (15) and a minimum size of a captive population (100) necessary in order to minimize a loss of genetic diversity. Optimally, the founders should be unrelated and new founders should be integrated into the captive population successively. We recommend that genetic analyses should generally precede and accompany ex situ conservation projects in order to avoid inbreeding and outbreeding depression. Furthermore, many of the published studies do not provide all the relevant parameters (founder size, captive population size, H_o, H_e, inbreeding coefficients). We, therefore, propose that a general standard for the presentation of genetic studies should be established, which would allow integration of the data into a global database.     

Genetic evidence of fragmented populations and inbreeding in the Colombian endemic Dahl’s toad-headed turtle (<Emphasis Type="Italic">Mesoclemmys dahli</Emphasis>)

Population fragmentation is one of the most concerning consequences of habitat fragmentation, as small and isolated populations suffer increased genetic drift and inbreeding. However, the extent to which habitat fragmentation leads to population fragmentation depends not only on the landscape structure, but also on the response of organisms to it. This behavioral component makes it difficult to detect population fragmentation even if the habitat is fragmented, unless appropriate tools are used. In this study, we used a molecular approach to evaluate if Dahl’s toad-headed turtle (Mesoclemmys dahli) population was fragmented, given that it occurs in a very restricted area within the most degraded biome of Colombia, the tropical dry forest. We developed a panel of 15 microsatellite loci in order to perform the first genetic assessment of M. dahli across its complete geographic range. We found that M. dahli has significant genetic structure with at least four subpopulations, with surprisingly moderate to high levels of genetic diversity. Despite high levels of genetic diversity, subpopulations are very small (effective population sizes?<?50) and isolated, with little to no contemporary gene flow among them. As a consequence, mating among related individuals has been occurring, and all four populations are showing high degrees of inbreeding. To counteract this threat, we recommend an urgent genetic rescue strategy accompanied by habitat restoration, and advocate for a new conservation status assessment, not based on geographic range, but on adult population size and level of fragmentation.     

Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis

Australian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.

     

A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and the isolation level is high, and because such populations provide insight into the consequences of population declines in a broader conservation context. The harbour seal (Phoca vitulina) population in Svalbard is the world's northernmost P. vitulina population. Nothing is known about the genetic diversity, distinctiveness, or origin of this small, marginalized mammalian population. Thus, the present study investigated its genetic status in the context of nearby P. vitulina in Iceland, south‐east Greenland, and northern Norway: this species is depleted/threatened in all of these regions. A total of 174 samples distributed between the four locations were analysed using 15 polymorphic microsatellites and variation in the displacement loop region (D‐loop). Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size, and showed an indication of having experienced a bottleneck resulting from a recent population decline. The significant heterozygote excess observed in the Svalbard sample might be attributed to the low effective population size, which could initiate future population inbreeding effects. This phenomenon has not been reported earlier from other P. vitulina populations, but if the Svalbard population is experiencing inbreeding, this could reduce its resilience to climate change, disease outbreaks, or other perturbations. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 420–439.     

Genetic diversity through life history of Dioon edule Lindley (Zamiaceae, Cycadales)

The distribution of genetic diversity and structure for three populations of Dioon edule Lindley (Zamiaceae) at Monte Oscuro (MO), El Farallón (EF) and Rancho del Niño (RN) in Veracruz, Mexico was studied using 20 allozyme loci, considering four life history classes: seeds, seedlings, juveniles and adults. The MO population is genetically less diverse than the EF and RN populations. Total and local inbreeding differ significantly between life history classes. An increment of inbreeding among all classes was observed, and genetic differentiation among populations was higher in seeds and seedlings than in juveniles and adults. In terms of percentage of polymorphic loci, the MO seeds showed least (80%), followed by RN (95%) and EF had the highest values (100%), probably because of a reduction in effective population size and habitat fragmentation processes. In this context, the mean effective population size was 23.2 ± 11.3 for all populations. We conclude that seed cohorts in EF and RN represent a reservoir of genetic diversity within these two populations. Also, preservation of adult plants is an essential aspect to consider in management and conservation efforts for populations of Dioon edule in natural conditions.     

Conservation genetics and population diversity of Erigeron breviscapus (Asteraceae), an important Chinese herb

Erigeron breviscapus (Vant.) Hand.-Mazz. is an important Chinese herb in treating cerebral infarction and heart diseases, which is increasingly endangered because of over-harvesting and habitat fragmentation. We applied AFLP method to investigate its genetic diversity and population structure in order to make efficient conservation strategies. The results indicated a relatively low intraspecific genetic diversity and feeble genetic differentiation among populations, and no Evolutionarily Significant Units (ESUs) was detected. The relationships between population genetic diversity and populations' distributions (latitude, longitude and altitude) were tested, and the genetic diversity of each population (H_POP) positively correlated with the populations' distribution altitudes. The suitable germinating and growing conditions and less human disturbance at the higher latitude regions might be attributable for this phenomenon. For conservation purpose, an ex situ conservation measure for the populations of E. breviscapus with large size in higher altitude regions should be conserved in priority.