Restoration genetics of the vernal pool endemic Lasthenia conjugens (Asteraceae)

Restoration of habitat for endangered species often involves translocation of seeds or individuals from source populations to an area targeted for revegetation. Long-term persistence of a species is dependent on the maintenance of sufficient genetic variation within and among populations. Thus, knowledge and maintenance of genetic variability within rare or endangered species is essential for developing effective conservation and restoration strategies. Genetic monitoring of both natural and restored populations can provide an assessment of restoration protocol success in establishing populations that maintain levels of genetic diversity similar to those in natural populations. California’s vernal pools are home to many endangered plants, thus conservation and restoration are large components of their management. Lasthenia conjugens (Asteraceae) is a federally endangered self-incompatible vernal pool annual with gravity- dispersed seeds. Using the molecular technique of intersimple sequence repeats (ISSRs), this study assessed levels and patterns of genetic variability present within natural and restored populations of L. conjugens. At Travis Air Force Base near Fairfield, California, a vernal pool restoration project is underway. Genetic success of the ecologically based seeding protocol was examined through genetic monitoring of natural and restored populations over a three-year period. Genetic diversity remained constant across the three sampled generations. Diversity was also widely distributed across all populations. We conclude that the protocol used to establish restored populations was successful in capturing similar levels and patterns of genetic diversity to those seen within natural pools. This study also demonstrates how genetic markers can be used to inform conservation and restoration decisions.     

Population genetic diversity and structure of two rare vernal pool grasses in central California

Vernal pool ecosystems are declining throughout California, with only 10% of historic habitat remaining. This has endangered many specialist endemic plant species, leaving extant populations fragmented, isolated, and threatened or endangered. Recovery plans for the increasing number of endangered vernal pool species require information on their genetic and ecological status to guide conservation and restoration efforts. Federally threatened Neostapfia colusana (Colusa grass) and federally endangered Tuctoria greenei (Greene’s tuctoria) are two endemic vernal pool grasses of high conservation concern in central California. Remaining populations are highly fragmented due to range-wide habitat destruction. Using five polymorphic microsatellite markers for each species, we performed genetic surveys of 240 individuals from eight vernal pools for N. colusana, and 317 individuals from 13 vernal pools for T. greenei. We detected high within-population genetic diversity for both species, with average allelic diversities of 24 alleles/locus (mean Hobs = 0.68, mean Hexp = 0.71) for N. colusana, and 19 alleles/locus (mean Hobs = 0.77, and mean Hexp = 0.79) for T. greenei. Bayesian clustering and AMOVA indicated two genetically distinct population groups for N. colusana (Fst = 0.268, P < 0.0001), and three for T. greenei (Fst = 0.11, P < 0.0001). We found very slight temporal genetic structure at one N. colusana (Fst = 0.013, P < 0.05) and two T. greenei (Fst = 0.015, Fst = 0.018, P < 0.05) pools. These estimates of population genetic diversity and structure are critical measures for both species that will help inform recovery management actions.     

Conservation Genetics of Jacquemontia reclinata (Convolvulaceae), an Endangered Species from Southern Florida: Implications for Restoration Management

Guidelines designed to aid in the restoration of rare species have been previously proposed using two primary strategies to select individuals for augmentation and reintroduction: mixing progeny from different populations or separating individuals from different populations. Understanding the genetic structure and diversity of an endangered species can offer insights into conservation management strategies. We used random amplified polymorphic DNA markers to assess the genetic structure and diversity of Jacquemontia reclinata , a federally endangered species endemic to Southeastern Florida. We sampled 20 percent of total number of individuals from eight of the ten known wild populations. Across individuals high levels of polymorphic loci (94.7%) were found and larger populations had greater genetic diversity. Cluster and ordination analyses found that one population was genetically differentiated from all the others; this population grows in a unique habitat. Most genetic variation (77.5%) was found within populations, and genetic distances between populations were not explained by their geographic distances. We recommend the use of two management units in restoration programs for J. reclinata , one consisting of the genetically differentiated population and the second consisting of the other seven populations sampled.     

鹅掌楸贵州烂木山居群的微卫星遗传多样性及空间遗传结构

濒危植物鹅掌楸(Liriodendron chinense)目前仅零散分布于我国亚热带及越南北部地区, 残存居群生境片断化较为严重。研究濒危植物片断化居群的遗传多样性及小尺度空间遗传结构(spatial genetic structure)有助于了解物种的生态进化过程以及制定相关的保育策略。本研究采用13对微卫星引物, 对鹅掌楸的1个片断化居群进行了遗传多样性及空间遗传结构的研究, 旨在揭示生境片断化条件下鹅掌楸的遗传多样性及基因流状况。研究结果表明: 鹅掌楸烂木山居群内不同生境斑块及不同年龄阶段植株的遗传多样性水平差异不显著(P>0.05), 居群内存在寨内和山林2个遗传分化明显的亚居群。烂木山居群个体在200 m以内呈现显著的空间遗传结构, 而2个亚居群内的个体仅在20 m的距离范围内存在微弱或不显著的空间遗传结构。鹅掌楸的空间遗传结构强度较低(Sp = 0.0090), 且寨内亚居群的空间遗传结构强度(Sp = 0.0067)要高于山林亚居群(Sp = 0.0053)。鹅掌楸以异交为主, 种子较轻且具翅, 借助风力传播, 在一定程度上降低了空间遗传结构的强度。此外, 居群内个体密度及生境特征也对鹅掌楸的空间遗传结构产生了一定影响。该居群出现显著的杂合子缺失, 近交系数(F_IS)为0.099 (P < 0.01), 表明生境片断化的遗传效应正逐渐显现。因此, 对鹅掌楸的就地保护应注意维护与强化生境的连续性, 促进基因交流。迁地保护时, 取样距离应不小于20 m, 以涵盖足够多的遗传变异。     

Conservation genetics of Amorpha georgiana (Fabaceae), an endangered legume of the Southeastern United States

Amorpha georgiana (Fabaceae) is an endangered legume species found in longleaf pine savannas in the Southeastern United States. Approximately 900 individuals and 14 populations remain, most of which are concentrated in North Carolina. Eleven microsatellite loci were used to explore genetic diversity, population structure and recent population bottlenecks using genotypic data from 132 individuals collected at ten different localities. Although A. georgiana is quite rare, it exhibited high levels of genetic diversity (17.7 alleles/locus; H _o = 0.65, H _E = 0.75). Most of the genetic variation was found within rather than between populations of this species. The single remaining Georgia population was well differentiated from populations of the Carolinas ( F _ST > 0.1), which had weaker structure among them ( F _ST < 0.1). Only a geographically disjunct population showed strong evidence of a recent population bottleneck, perhaps due to a recent founder event. Hybridization with A. herbacea was also detected. For conservation management plans, A. georgiana populations in each geographic region (North Carolina, South Carolina and Georgia) plus a disjunct population in North Carolina (Holly Shelter) should be treated as separate management units for which in situ conservation, including habitat restoration and use of prescribed burns, should ensure persistence of this species and preservation of its evolutionary potential.     

Does Species Range and Rarity Affect Population Genetics? A Case Study of Four Graptophyllum Species from Queensland,Australia

There are four species of Graptophyllum (Acanthaceae) in Australia which span a gradient in rarity and conservation status from the most endangered, Graptophyllum reticulatum (endangered), to G. ilicifolium (vulnerable), to G. excelsum (rare), to the least endangered G. spinigerum (widespread). Graptophyllum reticulatum and G. ilicifolium are each only known from three locations. All species were found to have quite high levels of genetic diversity (H_e, A, A_p, P) and there was no significant difference among species in genetic diversity ( P > 0.05), thus, genetic diversity was unrelated to conservation status or species geographic range. All species had high allelic fixation values ( F  ), indicating that populations were effectively inbred regardless of conservation status and geographic range. The genetic diversity among populations (F_ST) was not related to rarity and contrasted among the most restricted species, where diversity among populations was twice as high among G. reticulatum populations (F_ST, 0.22) compared with among G. ilicifolium populations (F_ST, 0.11).     

Ecosystem engineers maintain a rare species of butterfly and increase plant diversity

We evaluated whether ecosystem engineers can accomplish two conservation goals simultaneously: (1) indirectly maintain populations of an endangered animal through habitat modification and (2) increase riparian plant diversity. We tested for effects of a prominent ecosystem engineer, the beaver Castor canadensis, on populations of St. Francis' satyr butterfly Neonympha mitchellii francisci and plant species richness and composition. We performed our test by surveying riparian vegetation communities in all stages of beaver‐influenced wetland succession. We found that beavers created wetland habitats that supported plant species not found elsewhere in riparian zones and increased plant species diversity across the landscape by creating a novel combination of patch types. Our results confirmed what others have found about engineering effects on plant diversity, but these results further demonstrated a case where ecosystem engineers indirectly maintain populations of rare animals by modifying the composition and diversity of plant communities within wetlands. Our research demonstrates how an ecosystem engineer can influence habitat availability and composition of plant communities important for an endangered insect, and maintain overall plant species diversity by increasing habitat heterogeneity.     

Genetic diversity pattern of Stipa purpurea populations in the hinterland of Qinghai–Tibet Plateau

Stipa purpurea is among constructive endemic species in alpine meadow and steppe on the Qinghai–Tibet Plateau. To reveal the genetic diversity of this species and its relationship with geographic distribution pattern, we sampled eight populations across a northward transect with an increasing aridity gradient in the hinterland of Qinghai–Tibet Plateau. Their genetic diversity was quantified using eight intersimple sequence repeat (ISSR) primers. We found that S. purpurea had relatively low genetic diversity ( H _e = 0.135) but significant genetic differentiation among populations ( G _st = 0.391), indicating relatively more genetic diversity retained within populations. A Mantel test revealed a significant relationship between genetic and geographic distance in the S. purpurea populations. The genetic diversity tended to decrease with increasing latitude and longitude, while no significant relationship was found between genetic diversity and altitude, suggesting the possible influences of humidity and temperature on genetic diversity of alpine plant. We propose conservation measures for this plant on the plateau.     

Management units of the endangered herb Primula sieboldii based on microsatellite variation among and within populations throughout Japan

To promote programs for the conservation and restoration of the endangered species Primula sieboldii, we examined genetic variation at eight microsatellite loci among and within 32 remnant wild populations throughout Japan. Total allelic diversity within a population was higher in larger populations, but not so after rarefaction adjustment. The positive relationship between population size and the inbreeding coefficient may suggest that more heterozygous genets tend to survive the habitat contraction possibly because of the higher fitness associated with heterozygosity. By principal coordinate analysis and Bayesian analysis, we detected four genetic groups (Hokkaido, northern Honshu, central Honshu, and western Japan), which could be recognized as management units of P. sieboldii. If supplementation with plants from other populations were planned, it should be conducted among populations which belong to the same management unit and which are likely to represent the same adaptive variation.     

Weak genetic structuring indicates ongoing gene flow across White-ruffed Manakin (<Emphasis Type="Italic">Corapipo altera</Emphasis>) populations in a highly fragmented Costa Rica landscape

We explored the effects of recent forest fragmentation on fine-scale patterns of population structuring and genetic diversity in populations of White-ruffed Manakins (Corapipo altera) inhabiting premontane forest fragments of varying size in southwestern Costa Rica. Habitat fragmentation is a major conservation concern for avian populations worldwide, but studies of the genetic effects of fragmentation on Neotropical birds are limited. We sampled 159 manakins from nine forest fragments of varying size within an 18 km radius, and genotyped these birds at 13 microsatellite loci. Bayesian clustering methods revealed that birds from all fragments comprised a single genetic population, and an MCMC approach showed that the fragments were likely to be at migration-drift equilibrium. F-statistics showed only modest levels of differentiation between forest fragments. We calculated allelic diversity indices for each fragment but found no correlation between genetic diversity and fragment size. These results suggest that manakins may retain substantial connectivity via inter-fragment dispersal despite habitat fragmentation.     

Genetic diversity and structure in fragmented populations of the endangered species Ranunculus cabrerensis (Ranunculaceae): implications for conservation

Ranunculus cabrerensis is an endemic and endangered species of the Northwestern Iberian Peninsula. The molecular markers AFLP and ISSR were used to investigate the genetic diversity and population structure of four populations across its known distribution. Fifteen selective primer combinations of AFLP and seventeen ISSR primer combinations produced a total of 2830 and 103 unambiguously repeatable fragments respectively, of which 97.57 and 81.38% were polymorphic for both markers. The genetic diversity of R. cabrerensis at species level was high (H _E = 0.294 by ISSR and H _E = 0.191 by AFLP) and differentiation between sampled locations was also relatively high (G _ST = 0.316 and 0.158 by ISSR and AFLP analysis respectively) compared to other studies of endangered and rare species using the same techniques. The analysis of molecular variance (AMOVA) indicated that the main genetic variation was within sampled locations (73% by AFLP; 52% by ISSR), even though the variation among locations was also significant. Principal Coordinates, NeighborNet and Bayesian analyses revealed a weak but significant relationship between the genetic structures of different populations in R. cabrerensis, with gene flow acting as a homogenizing force that prevents stronger differentiation of populations. Finally, suggestions for conservation strategies to preserve the genetic resources of this species are outlined.     

Conservation genetics in hypersaline inland waters: mitochondrial diversity and phylogeography of an endangered Iberian beetle (Coleoptera: Hydraenidae)

Saline inland waters are globally threatened habitats harbouring many specialised endemic species, which often have restricted geographic ranges, and occur as highly isolated populations. We studied the genetic variation and phylogeography of Ochthebius glaber Montes and Soler, a rare and endangered water beetle endemic to hypersaline streams in the South and Southeast of the Iberian Peninsula. We used a 633 bp fragment of cytochrome oxidase subunit 1 gene to determine the genetic diversity and phylogeographic structure within this species, and interpret this in the light of the speciesȁ9 conservation requirements. Thirteen populations were sampled across the speciesȁ9 geographic range, and genetic diversity found to be very high, with 37 haplotypes across the 71 specimens examined (p-distance 0.2–7.3%, average 3.1±0.4). Phylogeographic analyses revealed a surprisingly high degree of geographical structure, detectable among populations separated by relatively short geographical distances, with three main groups of haplotypes which have apparently been isolated for significant periods of time. Past fragmentation and contiguous range expansion events were inferred as the main causes of the detected geographical associations of haplotypes. The establishment of independent evolutionary lineages as conservation units is particularly important for species inhabiting saline habitats such as O. glaber, which is endangered by habitat loss across most of its distribution. However, given the natural instability of hypersaline environments, the conservation of a network of populations and potential habitats would be necessary to enable the preservation of the process generating and maintaining the diversity of the species.     

武夷山地伯乐树种群遗传多样性的ISSR分析

伯乐树（Bretschneidera sinensis Hemsl.）为我国特有单型科珍稀濒危植物,具重要的科研价值。本研究采用ISSR分子标记对武夷山脉分布的5个伯乐树天然种群和1个移栽种群进行遗传多样性分析。结果表明伯乐树物种水平遗传多样性较高（PPB：75.70%;H_ES：0.304 5;H：0.450 1）,种群水平则较低（PPB：60.13%;H_EP：0.238 1;H：0.347 5）,MJY种群和BSZ种群分别是所有种群中遗传多样性最高和最低的。5个地理种群间遗传分化程度较高（G_st=0.218 1）,原因可能源于伯乐树的繁殖方式及生境片段化,Mantel检验也证实了地理距离与遗传距离具有显著相关性（r=0.626 7,P＜0.05）。针对伯乐树种群遗传多样性现状,建议加强现有自然种群的就地保护,促进种群自然更新。     

The genetic status of the violet copper Lycaena helle– a relict of the cold past in times of global warming

Rising temperatures and agricultural changes (intensification and succession on fallow land) during the last few decades have caused a strong decline of moist and cool sites on nutrient-poor grasslands and species depending on these habitats. We tested the effects of habitat deterioration on a local and regional scale in such a species, the highly endangered butterfly Lycaena helle , which was more widely distributed over central Europe during the postglacial period, but has recently become restricted to some remnants. We analysed five polymorphic microsatellite loci in 220 individuals sampled at ten different localities. The study sites in Germany, Luxembourg and Belgium are geographically split into three mountain regions: the Ardennes, the Eifel and the Westerwald; the latter is separated from the other two by the river Rhine. A comparatively high genetic diversity was detected in all local populations and genetic differentiation was found among the Ardennes, the Eifel and the Westerwald (F_CT: 0.084). The genetic differentiation among all populations (F_ST: 0.137) underlines natural and anthropogenic habitat fragmentation. While ongoing gene flow seems to exist among the Eifel populations indicating the only intact metapopulation, a high genetic differentiation in the Ardennes and the Westerwald indicates a disruption of population connectivity. Our genetic data obtained on different spatial scales show the genetic consequence of long-term isolation and should trigger necessary conservation measures at the metapopulation level.     

Biotechnological approaches for conservation and improvement of rare and endangered plants of Saudi Arabia

Genetic variation is believed to be a prerequisite for the short-and long-term survival of the plant species in their natural habitat. It depends on many environmental factors which determine the number of alleles on various loci in the genome. Therefore, it is important to understand the genetic composition and structure of the rare and endangered plant species from their natural habitat to develop successful management strategies for their conservation. However, rare and endangered plant species have low genetic diversity due to which their survival rate is decreasing in the wilds. The evaluation of genetic diversity of such species is very important for their conservation and gene manipulation. However, plant species can be conserved by in situ and in vitro methods and each has advantages and disadvantages. DNA banking can be considered as a means of complimentary method for the conservation of plant species by preserving their genomic DNA at low temperatures. Such approach of preservation of biological information provides opportunity for researchers to search novel genes and its products. Therefore, in this review we are describing some potential biotechnological approaches for the conservation and further manipulation of these rare and endangered plant species to enhance their yield and quality traits.     

Genetic variability and the effect of habitat fragmentation in spotted suslik Spermophilus suslicus populations from two different regions

Endangered species worldwide exist in remnant populations, often within fragmented landscapes. Although assessment of genetic diversity in fragmented habitats is very important for conservation purposes, it is usually impossible to evaluate the amount of diversity that has actually been lost. Here, we compared population structure and levels of genetic diversity within populations of spotted suslik Spermophilus suslicus, inhabiting two different parts of the species range characterized by different levels of habitat connectivity. We used microsatellites to analyze 10 critically endangered populations located at the western part of the range, where suslik habitat have been severely devastated due to agriculture industrialization. Their genetic composition was compared with four populations from the eastern part of the range where the species still occupies habitat with reasonable levels of connectivity. In the western region, we detected extreme population structure (F _ST = 0.20) and levels of genetic diversity (Allelic richness ranged from 1.45 to 3.07) characteristic for highly endangered populations. Alternatively, in the eastern region we found significantly higher allelic richness (from 5.09 to 5.81) and insignificant population structure (F _ST = 0.03). As we identified a strong correlation between genetic and geographic distance and a lack of private alleles in the western region, we conclude that extreme population structure and lower genetic diversity is due to recent habitat loss. Results from this study provide guidelines for conservation and management of this highly endangered species.     

Genetic diagnosis of a rare myrmecochorous species,Plagiorhegma dubium (Berberidaceae): Historical genetic bottlenecks and strong spatial structures among populations

Distribution of genetic variation over time and space is relevant to demographic histories and tightly linked to ecological disturbances as well as evolutionary potential of an organism. Therefore, understanding the pattern of genetic diversity is a primary step in conservation and management projects for rare and threatened plant species. We used eight microsatellite markers to examine the level of genetic diversity, spatial structure, and demographic history of Plagiorhegma dubium, a rare myrmecochorous herb, populations sampled across northeast Asia and Siberia. We found low within‐population genetic variation associated with historical bottlenecks. Although pairwise F_ST values were not much higher than the ones found in similar life form species, STRUCTURE and PCoA revealed a clear broadscale spatial pattern of genetic structure. Bayesian clustering (best K = 6) and PCoA identified three populations that are distinctive from neighboring populations in the Korean peninsula, which suggests potential units for conservation and management plans in Korea. MIGRATE‐N and BAYESASS showed that both contemporary (0.003–0.045) and historical migration rates (2 × e^?5?4.6 × e^?4) were low. Our findings provide a good example, where genetic considerations should be integrated for conservation and management plans of rare and threatened species.     

Genetic population structure, fitness variation and the importance of population history in remnant populations of the endangered plant Silene chlorantha (Willd.) Ehrh. (Caryophyllaceae)

Habitat fragmentation can lead to a decline of genetic diversity, a potential risk for the survival of natural populations. Fragmented populations can become highly differentiated due to reduced gene flow and genetic drift. A decline in number of individuals can result in lower reproductive fitness due to inbreeding effects. We investigated genetic variation within and between 11 populations of the rare and endangered plant Silene chlorantha in northeastern Germany to support conservation strategies. Genetic diversity was evaluated using AFLP techniques and the results were correlated to fitness traits. Fitness evaluation in nature and in a common garden approach was conducted. Our analysis revealed population differentiation was high and within population genetic diversity was intermediate. A clear population structure was supported by a Bayesian approach, AMOVA and neighbour-joining analysis. No correlation between genetic and geographic distance was found. Our results indicate that patterns of population differentiation were mainly caused by temporal and/or spatial isolation and genetic drift. The fitness evaluation revealed that pollinator limitation and habitat quality seem, at present, to be more important to reproductive fitness than genetic diversity by itself. Populations of S. chlorantha with low genetic diversity have the potential to increase in individual number if habitat conditions improve. This was detected in a single large population in the investigation area, which was formerly affected by bottleneck effects.     

Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, <Emphasis Type="Italic">Ambystoma californiense</Emphasis>

Maintaining genetic diversity and population viability in endangered and threatened species is a primary concern of conservation biology. Genetic diversity depends on population connectivity and effective population size (N_e), both of which are often compromised in endangered taxa. While the importance of population connectivity and gene flow has been well studied, investigating effective population sizes in natural systems has received far less attention. However, N_e plays a prominent role in the maintenance of genetic diversity, the prevention of inbreeding depression, and in determining the probability of population persistence. In this study, we examined the relationship between breeding pond characteristics and N_e in the endangered California tiger salamander, Ambystoma californiense. We sampled 203 individuals from 10 breeding ponds on a local landscape, and used 11 polymorphic microsatellite loci to quantify genetic structure, gene flow, and effective population sizes. We also measured the areas of each pond using satellite imagery and classified ponds as either hydrologically-modified perennial ponds or naturally occurring vernal pools, the latter of which constitute the natural breeding habitat for A. californiense. We found no correlation between pond area and heterozygosity or allelic diversity, but we identified a strong positive relationship between breeding pond area and N_e, particularly for vernal pools. Our results provide some of the first empirical evidence that variation in breeding habitat can be associated with differences in N_e and suggest that a more complete understanding of the environmental features that influence N_e is an important component of conservation genetics and management.     

High genetic diversity vs. low genetic differentiation in Nouelia insignis (Asteraceae), a narrowly distributed and endemic species in China, revealed by ISSR fingerprinting

BACKGROUND AND AIMS: Nouelia insignis Franch., a monotypic genus of the Asteraceae, is an endangered species endemic in Yunnan and Sichuan Provinces of China. Most of the populations are seriously threatened. Some of them are even at the brink of extinction. In this study, the genetic diversity and differentiation between populations of this species were examined in two drainage areas. METHODS: DNA fingerprinting based on inter-simple sequence repeat polymorphisms was employed to detect the genetic variation and population structure in the species. KEY RESULTS: Genetic diversity at species level was high with P=65.05% (percentage of polymorphic loci) and Ht=0.2248 (total genetic diversity). The coefficient of genetic differentiation among populations, Gst, which was estimated by partitioning the total gene diversity, was 0.2529; whereas, the genetic differentiation between populations in the Jinsha and Nanpan drainage areas was unexpectedly low (Gst=0.0702). CONCLUSIONS: Based on the genetic analyses of the DNA fingerprinting, recent habitat fragmentation may not have led to genetic differentiation or the loss of genetic diversity in the rare species. Spatial apportionment of fingerprinting polymorphisms provides a footprint of historical migration across geographical barriers. The high diversity detected in this study holds promise for conservation and restoration efforts to save the endangered species from extinction.