Conservation genetics of the endangered terrestrial orchid Liparis japonica in Northeast China based on AFLP markers

Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.     

High genetic diversity detected in the endemic Primula apennina Widmer (Primulaceae) using ISSR fingerprinting

Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population percentage of polymorphic band (PPB = 75.92%, H _S = 0.204, H _pop = 0.319) and at species level (PPB = 96.95%, H _T = 0.242, H _sp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and Bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability.     

Multi-annual density fluctuations and habitat size enhance genetic variability in two northern voles

In order to gain a better understanding of the consequences of population density cycles and landscape structure for the genetic composition in time and space of vole populations, we analyzed the multiannual genetic structure of the two numerically dominant, sympatric small rodent species of northernmost Fennoscandia. Red voles Myodes rutilus and grey-sided voles M. rufocanus were trapped in the subarctic birch forest along three fjords over five years. Along each fjord, there were four or five altitudinal transects each with five trapping stations. Spring and fall population densities were estimated from mark–recapture data. Grey-sided voles exhibited higher amplitude density fluctuations than red voles. Polymorphism at eight or nine microsatellite loci, determined in 1228 voles, was used to estimate local genetic diversity and differentiation among samples. Genetic diversity was higher in grey-sided voles than in red voles. Spring densities had no effect on local genetic diversity or on differentiation. The amplitude of density fluctuations and the extent of favorable habitat (sub-arctic birch forest) surrounding each site had a positive effect on genetic diversity, and the amplitude of density fluctuations had a negative effect on differentiation in red voles, for which fluctuating populations were compared with more stable populations. The harmonic mean of densities, reflecting average population sizes, had a negative effect on genetic diversity in red voles, but a positive effect in grey-sided voles, for which only fluctuating populations were compared. No other effects were significant for grey-sided voles. A temporal assignment test showed that the spatial structure was more stable in time for populations with more stable population dynamics. Altogether our results suggest that high amplitude density fluctuations lead to more gene flow and higher genetic diversity in vole populations.     

Genetic diversity and population structure of the serpentine endemic Ni hyperaccumulator Alyssum lesbiacum

Alyssum lesbiacum is a well-established Ni hyperaccumulator, endemic to serpentine soils of Lesbos Island (Greece). A total of 95 individuals were collected from 17 plots encompassing the only four large populations of this species. ISSR (Inter-simple sequence repeat) markers were used to assess genetic diversity and population structure of A. lesbiacum to provide initial guidance for the development of successful management and conservation measures. A total of ten primers produced 82 bands, 96.34 % being polymorphic. The largest part of total diversity was found within populations, rather than among them. AMOVA analysis partitioned the largest part of diversity within plots (66 %), while 15 % contained among plots within populations and 19 % among populations. Principal coordinates analysis along with dendrogram based on genetic distances among populations showed a high degree of genetic differentiation of the isolated population Loutra. At a smaller scale, distance was not the most significant factor influencing the patterns of genetic diversity, but topography, ecosystem types and connectivity through streams. According to our results, conservation efforts should be organized at the level of watersheds and ecosystem types, considering them as management units. For ex situ conservation and restoration, seed samplings should be representative of the different habitats and watersheds as well as the patches of large and small populations while keeping the east population of Loutra separate from the other three central populations, to avoid any loss of genetic diversity and to preserve the character of the local adapted populations.     

Long-term genetic monitoring of a translocated population of collared brown lemurs

Post-release monitoring is important to improve translocation success because it provides an opportunity to identify factors relevant to the survival of local populations. We studied a population of the endangered collared brown lemur (Eulemur collaris) translocated from a degraded forest fragment to a nearby littoral forest within the Mandena Conservation Area in southeast Madagascar from 2000–2011. We compared genetic surveys of mitochondrial and nuclear markers with the genetic profile of nearby populations to examine the dispersal capacity of the collared brown lemur. We also performed a landscape analysis to assess changes in connectivity between forest fragments. There was a fluctuating trend characterized by a phase of demographic and genetic stability shortly after translocation, followed by an increase in genetic diversity coinciding with a population decrease and a gradual recovery of initial conditions. These results demonstrated the ability of the collared brown lemur to disperse through unfavorable landscapes and to recover after translocation. Our study revealed the importance of monitoring translocated populations over time using a multidisciplinary approach.     

Variation in pika (Ochotona collaris,O. princeps) vocalizations within and between populations

Understanding geographic call variation can resolve evolutionary and behavioural questions, yet the factors influencing divergent acoustic signals remain poorly understood in mammals. We explored call variation between collared pikas in Yukon and Alaska and American pikas in Alberta, and between individuals within a population of collared pikas. Classification trees were used to determine the extent of call divergence between populations and the elements of calls driving these differences. Pika populations had significant differences in call structure, and individual pikas were classified to their correct populations with up to 94% accuracy. To investigate possible mechanisms responsible for interspecific variability, we tested the acoustic adaptation hypothesis by using a playback experiment to explore whether American and collared pika calls transmit with less degradation across their own species' habitat than the habitat of their congener. We found no support for the acoustic adaptation hypothesis. Geographic call variation in these two species of pikas likely reflects genetic divergence, and may be a result of separate evolutionary histories. We calculated the potential for individual coding for both time and frequency measurements of calls. High frequency harmonics showed greater between‐ than within‐individual variation, and may act as sources of information regarding individual identity.     

Population genetic structure of wild daffodils (Narcissus pseudonarcissus L.) at different spatial scales

We studied the population genetic and clonal structure of the endangered long-lived perennial plant Narcissus pseudonarcissus using random amplified polymorphic markers. Estimates for mean gene diversity within 15 populations of N. pseudonarcissus of three neighbouring geographical regions were high in comparison to other long-lived perennials (H _eN = 0.33). The genetic diversity of the two smallest populations (<200 plants) was significantly reduced, indicating loss of genetic variability due to drift. The analysis of the population genetic structure revealed a significant genetic differentiation both between regions (Φ_ST = 0.06) and between populations within regions (Φ_ST = 0.20). However, there was incomplete correspondence between geographical regions and the population genetic structure. In order to preserve the overall genetic variation in wild populations of N. pseudonarcissus, management measures should thus aim to protect many populations in each region. The spatial genetic structure within populations of N. pseudonarcissus was in agreement with an isolation by distance model indicating limited gene flow due to pollinator behaviour and restricted seed dispersal. The very restricted spatial extent of clonal growth (<5 cm) and the high level of clonal diversity indicate that clonal growth in N. pseudonarcissus is not an important mode of propagation and that management measures should favour sexual reproduction in order to avoid further reductions in the size and number of populations.     

Genetic diversity and population structure of Chinese <Emphasis Type="Italic">Lentinula edodes</Emphasis> revealed by InDel and SSR markers

Genetic diversity and population structure of 88 Chinese Lentinula edodes strains belonging to four geographic populations were inferred from 68 Insertion-Deletion (InDel) and two simple sequence repeat (SSR) markers. The overall values of Shannon’s information index and gene diversity were 0.836 and 0.435, respectively, demonstrating a high genetic diversity in Chinese L. edodes strains. Among the four geographic populations, the Central China population displayed a lower genetic diversity. Multiple analyses resolved two unambiguous genetic groups that corresponded to two regions from which the samples were collected—one was a high-altitude region (region 1) and the other was a low-altitude region (region 2). Results from analysis of molecular variance suggested that the majority of genetic variation was contained within populations (74.8 %). Although there was a strong genetic differentiation between populations (F _ST ?=?0.252), the variability of ITS sequences from representative strains of the two regions (<3 %) could not support the existence of cryptic species. Pairwise F _ST values and Nei’s genetic distances showed that there were relatively lower genetic differentiations and genetic distances between populations from the same region. Geographic distribution could play a vital role in the formation of the observed population structure. Mycelium growth rate and precocity of L. edodes strains displayed significant differences between the two regions. Strains from region 2 grew faster and fructified earlier, which could be a result of adaptation to local environmental factors. To the best of our knowledge, this was the first study on the genetic structure and differentiation between populations, as well as the relationship between genetic structure and phenotypic traits in L. edodes.     

Multiple geographic origins and high genetic differentiation of the Alpine marmots reintroduced in the Pyrenees

Reintroductions inherently involve a small number of founders leading reintroduced populations to be prone to genetic drift and, consequently, to inbreeding depression. Assessing the origins as the genetic diversity and structure of reintroduced populations compared to native populations are thus crucial to foresee their future. Here, we aim to clarify the origins of the Alpine marmots reintroduced in the Pyrenees and to evaluate the genetic consequences of this reintroduction after almost 30 years without monitoring. We search for the origins and compare the genetic structure and the genetic variability of three reintroduced Pyrenean and eight native Alpine populations using pairwise genetic distances, Bayesian clustering method and multivariate analyses. Our results reveal that the Alpine marmots reintroduced in the Pyrenees originated both from the Northern and the Southern Alps, and that, despite these multiple origins, none of the current Pyrenean marmots are admixed. The reintroduction led to a strong genetic differentiation and to a decrease in genetic diversity. This pattern likely results from the small number of founders and the low dispersal capacities of Alpine marmots and thus, highlight the necessity to consider both genetic characteristics and natural history when reintroducing a species.     

Within-river gene flow in the hellbender (Cryptobranchus alleganiensis) and implications for restorative release

Understanding how populations are genetically and demographically connected is beneficial for species management, since gene flow and dispersal contribute to genetic diversity and population persistence. For hellbenders (Cryptobranchus alleganiensis), an aquatic salamander species experiencing dramatic declines in population size, fine-scale (i.e. within river) patterns of genetic diversity and gene flow are not well understood. Previous findings indicate that hellbenders are habitat specialists that exhibit extreme site fidelity and low vagility, suggesting that gene flow is restricted among the several, discrete habitat patches within a river. Using 15 polymorphic microsatellite loci and 497 hellbender samples from four Missouri rivers, we assessed fine-scale patterns of genetic diversity in order to infer population connectivity and aid in population management. Results indicate moderate levels of genetic variation (H_O = 0.66–0.78) with little differentiation among habitat patches (avg. F_ST = 0.002) and no evidence of isolation by distance. Our data suggest that hellbender gene flow has been extensive even among habitat patches separated by distances greater than >100 km. These results are useful for hellbender management, especially in terms of making informed decisions regarding restorative releases of captively propagated individuals.     

Local genetic structure of a montane herb among isolated grassland patches: implications for the preservation of genetic diversity under climate change

Habitat loss, fragmentation of meadow patches, and global climate change (GCC) threaten plant communities of montane grasslands. We analyzed the genetic structure of the montane herb Geranium sylvaticum L. on a local scale in order to understand the effects of habitat fragmentation and potential GCC impacts on genetic diversity and differentiation. Amplified fragment length polymorphism (AFLP) fingerprinting and cpDNA sequencing was performed for 295 individuals of 15 G. sylvaticum populations spanning the entire distribution range of the species in the Taunus mountain range in Germany. We found patterns of substantial genetic differentiation among populations using 150 polymorphic AFLP markers (mean F _ST = 0.105), but no variation in 896 bp of plastid DNA sequences. While populations in the center of their local distribution range were genetically diverse and less differentiated, higher F _ST values and reduced genetic variability was revealed for the populations at the low-altitudinal distribution margins. Projections of GCC effects on the distribution of G. sylvaticum in 2050 showed that GCC will likely lead to the extinction of most edge populations. To maintain regional genetic diversity, conservation efforts should focus on the diverse high-altitude populations, although a potential loss of unique variations in genetically differentiated peripheral populations could lower the overall genetic diversity and potentially the long-term viability in the study region. This study documents the usefulness of fine-scale assessments of genetic population structure in combination with niche modeling to reveal priority regions for the effective long-term conservation of populations and their genetic variation under climate change.     

Fine-scale spatial genetic structure and within population male-biased gene-flow in the grasshopper <Emphasis Type="Italic">Mioscirtus wagneri</Emphasis>

Dispersal is a life history trait that plays a key role in population dynamics, determining gene flow and influencing the size, structure and persistence of populations. For these reasons, the study of the genetic consequences of dispersal can be considered a central topic in both conservation and population genetics. In this study we examine the patterns of fine-scale genetic structure within two populations of the grasshopper Mioscirtus wagneri (Orhoptera: Acrididae). For this purpose, we have used seven species-specific microsatellite markers to type 266 individuals from two populations (Peña Hueca and El Salobral) located in Central Spain. We have found subtle genetic differentiation between some sampling patches and significant kinship structures up to 25 m distance which were particularly patent for females. In Peña Hueca locality, patterns of isolation-by-distance at both the patch scale and the individual level have also revealed an association between genetic differentiation/similarity and geographical distance in females but not in males. Overall, these data suggest a fine-scale spatial genetic substructure in the studied populations which seems to be mainly driven by female philopatry. Such pattern of within population genetic structure together with the inferred restricted dispersal distances is likely to contribute to reduce effective population sizes and inter-population gene flow. This can erode genetic variability and limit the colonization ability of this orthoptera, factors which can ultimately compromise the long-term persistence of their small size and isolated populations.     

Negligence in the Atlantic forest,northern Brazil: a case study of an endangered orchid

Currently, many Brazilian orchids are threatened with extinction resulting from habitat loss and intense harvesting pressure stemming from their value as ornamental plants. Therefore, the genetic diversity in remaining populations is fundamental to the survival of these species in natural environments. In order to inform conservation strategies, this study evaluated the genetic diversity and structure of Cattleya granulosa populations. The sample consisted of 151 individuals from 12 populations in the Atlantic Forest, northeastern Brazil, evaluated using 91 ISSR markers. Genetic variability was assessed through molecular variance, diversity indexes, clusters of genotypes through Bayesian analysis, and tests for genetic bottlenecks. From all polymorphic loci, genetic diversity (H_E) varied between 0.210 and 0.321 and the Shannon index ranged from 0.323 and 0.472. Significant genetic differentiation between populations (Φ_ST = 0.391; P < 0.0001) resulted in the division of the populations into five groups based on the log-likelihood Bayesian analysis. We found significant positive correlation between geographical and genetic distances between populations (r = 0.794; P = 0.017), indicating isolation by distance. Patterns of allelic diversity within populations suggest the occurrence of bottlenecks in most C. granulosa populations (n = 8). Therefore, in order to maintain the genetic diversity of the species, the conservation of spatially distant groups is necessary.     

Effects of population size and forest management on genetic diversity and structure of the tuberous orchid Orchis mascula

Due to societal changes and altered demands for firewood, the traditional forest management of coppicing has been largely abandoned. As a result, many forest herbs that are specifically adapted to regular opening of the canopy, have suffered significant declines in abundance, and the remaining populations of these species often tend to be small and isolated. Reduced population sizes and pronounced spatial isolation may cause loss of within-population genetic diversity and increased between-population differentiation through random genetic drift and inbreeding. In this study, we investigated genetic diversity and genetic structure of 15 populations of the food-deceptive orchid Orchis mascula using AFLP markers. Within-population genetic diversity significantly increased with increasing population size, indicating genetic impoverishment in small populations. Genetic differentiation, on the other hand, was rather low (Φ_ST = 0.083) and there was no significant relationship between genetic and geographic distances, suggesting substantial gene flow within the study area. However, strong differences in levels of within-population diversity and among-population differentiation were found for populations located in forests that have been regularly coppiced and populations found in forests that were neglected for more than 50 years and that were totally overgrown by shrubs. Our data thus indicate that a lack of coppicing leads to decreased genetic diversity and increased differentiation in this orchid species, most likely as a result of genetic drift following demographic bottlenecks. From a conservation point of view, this study combined with previous results on the demography of O. mascula in relation to forest management illustrates the importance of coppicing in maintaining viable populations of forest herbs in the long-term.     

Contrasting coarse and fine scale genetic structure among isolated relic populations of Kmeria septentrionalis

Trees of the Magnoliaceae family are of scientific, cultural and socio-economic importance. Kmeria septentrionalis Dandy (Magnoliaceae) is a dioecious tree, found in small, isolated, relic populations in Southern China, and is subject to extensive protection due to its rarity and high economic values. To improve conservation outcomes and in particular, germplasm collection guidelines, information on spatial genetic structure of the species is required. In this study, we investigated the spatial genetic structure and genetic diversity of 161 individuals of K. septentrionalis collected from five natural populations using AFLP molecular markers. Within-population genetic variation was measured, with percentage of polymorphic bands (PPB) ranged from 63% to 87%, while H _S (genetic diversity within population) varied from 0.185 to 0.244 with a mean of 0.215 ± 0.025. Significant genetic differentiations were revealed between pairwise populations, indicating each population existing as an independent evolutionarily significant unit. Mantel test results showed no pattern of isolation-by-distance among populations separated by large distance. Fine scale spatial patterns of genetic variation suggested significant effects of isolation-by-distance within population at distances of 22 m. The results of contrasting genetic structure at coarse and fine scale in K. septentrionalis may indicate restricted pollen flow and seed dispersal at fine scales, and separated evolution in isolated populations over long period of time at coarser scales. Finally, we make several suggestions for improved management practices that may assist in the conservation of this species.     

Inbreeding and strong population subdivision in an endangered salamander

Studies of genetic population structure and genetic diversity are often critical components of endangered species conservation and management plans. Genetic studies are thus particularly important for amphibians, which are in global decline. We studied genetic variation and population structure among 276 individuals from approximately half of the known localities of the endangered Sonora tiger salamander, Ambystoma mavortium stebbinsi, using ten microsatellite loci. Allelic diversity was generally low (2.7 alleles per locus per population) and overall observed heterozygosity (0.191) was significantly lower than expected (0.332). Most populations showed significant departures from Hardy–Weinberg equilibrium, which are likely due to inbreeding. In addition, evidence of recent bottlenecks was suggested by shifted allele frequency distributions in 5 of 16 populations, and ratios of allele number to allele size range (M) values lower than critical values in all populations. A high degree of genetic subdivision (θ = 0.133) was found over all populations, and nearly all pairwise population combinations were genetically subdivided. Thus, gene flow is limited even over small distances, perhaps because high desert grassland throughout the study area limits the efficacy of inter-pond movement of salamanders. Further, population sizes and gene flow of Sonora tiger salamanders are likely compromised by several contemporary ecological threats, including: frequent die-offs due to an infectious virus, introductions of non-native species, and continuing cattle grazing. Overall, these genetic data support the endangered status of the Sonora tiger salamander and suggest the subspecies exists in small, inbred populations.     

Comparing the genetic population structure of two species of arctic lemmings: more local differentiation in Lemmus trimucronatus than in Dicrostonyx groenlandicus

Collared and brown lemmings ( Dicrostonyx groenlandicus and Lemmus trimucronatus ) are two largely sympatric and ecologically comparable species of arctic microtine rodents, differing however in some respects which allow us to hypothesise differences in the genetic structure of their populations. Collared lemmings are particularly well adapted to life at high latitude, they occasionally emerge to the surface of the snow and may disperse over larger distances than brown lemmings – possibly even over snow and ice. This should result in more local differentiation among populations of brown lemmings than among populations of collared lemmings. We compared the genetic population structure between the two lemming species in a fragmented landscape with small islands in the central Canadian Arctic using four microsatellite loci and partial mitochondrial control region sequences. Both types of genetic markers showed higher differentiation ( F _ST values) among local populations for brown lemmings than for collared lemmings. We discuss to what extent the observed genetic differences may be explained by differences in dispersal rates in addition to differences in average effective population size.     

Fine-Scale Genetic Response to Landscape Change in a Gliding Mammal

Understanding how populations respond to habitat loss is central to conserving biodiversity. Population genetic approaches enable the identification of the symptoms of population disruption in advance of population collapse. However, the spatio-temporal scales at which population disruption occurs are still too poorly known to effectively conserve biodiversity in the face of human-induced landscape change. We employed microsatellite analysis to examine genetic structure and diversity over small spatial (mostly 1-50 km) and temporal scales (20-50 years) in the squirrel glider (Petaurus norfolcensis), a gliding mammal that is commonly subjected to a loss of habitat connectivity. We identified genetically differentiated local populations over distances as little as 3 km and within 30 years of landscape change. Genetically isolated local populations experienced the loss of genetic diversity, and significantly increased mean relatedness, which suggests increased inbreeding. Where tree cover remained, genetic differentiation was less evident. This pattern was repeated in two landscapes located 750 km apart. These results lend support to other recent studies that suggest the loss of habitat connectivity can produce fine-scale population genetic change in a range of taxa. This gives rise to the prediction that many other vertebrates will experience similar genetic changes. Our results suggest the future collapse of local populations of this gliding mammal is likely unless habitat connectivity is maintained or restored. Landscape management must occur on a fine-scale to avert the erosion of biodiversity.     

Microsatellite Polymorphisms in Cassava Landraces from the Cerrado Biome, Mato Grosso do Sul, Brazil

Using nine microsatellite loci, we investigated genetic structure and diversity in 83 Brazilian cassava accessions, including several landraces, in the Cerrado biome in Mato Grosso do Sul, Brazil. All nine loci were polymorphic, averaging 6.00 alleles per locus. Treating each of seven municipalities as a cassava group or population, they averaged 3.5 alleles per locus, with 97% polymorphic loci, high values for observed heterozygosity (0.32) and gene diversity (0.56). Total genetic variability was high (0.668), and most of this genetic variability was concentrated within municipalities (0.577). Cluster and structure analyses divided accessions into two major clusters or populations (K = 2). Also, a significant genetic versus geographic correlation was found (r = 0.4567; P < 0.0260). Migratory routes in the Cerrado are considered main contributors to the region’s high cassava diversity and spatial genetic structure, amplifying interactions between traditional farmers and the evolutionary dynamics of this crop.     

Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density

The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.