Low impact of present and historical landscape configuration on the genetics of fragmented Anthyllis vulneraria populations

Decreasing habitat fragment area and increasing isolation may cause loss of plant population genetic diversity and increased genetic differentiation between populations. We studied the relation between the historical and the present landscape configuration (i.e., patch area and patch connectivity), and the present management of calcareous grassland fragments on the one hand, and the within and between population genetic structure of 18 Anthyllis vulneraria populations on the other hand. Despite the long-time fragmentation history and the mainly selfing breeding system of the species, we detected very low genetic differentiation (Φ_st = 0.056) among habitat fragments and no significant isolation-by-distance relation. Average within fragment genetic diversity measured as molecular variance and expected heterozygosity, were relatively high (16.46 and 0.28, respectively), and weakly positively correlated with the current fragment area, most likely because larger fragments contained larger populations. We found no effects of the historical landscape configuration on the genetic diversity of the populations. Our data suggest that the consequences of habitat fragmentation for genetic differentiation and genetic diversity of A. vulneraria are relatively minor which is very likely due to the historical high levels of seed exchange among fragments through grazing and roaming livestock. This study provides indirect evidence that nature management by grazing not only positively affects habitat quality but that it might also mitigate the genetic consequences of habitat fragmentation. From the conservation point of view, this study illustrates the importance of grazing and of the regular transport of livestock between fragments to prevent the long-term effects of fragmentation on the genetic diversity of the populations studied.     

Genetic diversity and relatedness of boreal caribou populations in western Canada

We studied genetic diversity within and gene flow among six ‘threatened’ populations of boreal caribou (Rangifer tarandus caribou) inhabiting Alberta and British Columbia, Canada. Mean expected heterozygosity (H_E) across 11 loci spanned a narrow range between 0.74 and 0.79. Estimates of H_E were in the mid to high range of those typically observed in natural populations of large mammals, including caribou, and were not suggestive of any immediate threat to survival. We concluded that recent anthropogenic fragmentation of caribou range in western Canada has yet to affect genetic diversity of populations. Analysis of population structure identified a region of relatively low gene flow corresponding with the valley of the Peace River. The highest value of F_ST observed between populations on the same side of the river was 0.025, whereas the lowest value that spanned the river was 0.044. Confirming this result, an assignment test demonstrated that 96.5% of animals could be assigned to the correct side of the Peace River, though only 66.0% of animals could, on average, be assigned to populations of actual origin. Taken as a whole, our results support the existence of two discrete metapopulations bisected by the Peace River, within each of which there exist multiple populations, or at least multiple regions, which experience considerably higher levels of interchange. For caribou inhabiting the boreal plains, large rivers such as the Peace and Mackenzie may serve as biologically meaningful boundaries for managing metapopulations.     

Potential factors controlling the population viability of newly introduced endangered marble trout populations

While several population viability analyses (PVAs) have been performed on anadromous salmonids, less attention has been given to stream-living salmonids. In this work, we explore the role of PVA as a tool in the recovery of threatened stream-living salmonid species. The analysis has been performed with reference to marble trout Salmo marmoratus, a salmonid with a limited geographic distribution and at risk of extinction due to hybridization with the non-native introduced brown trout. Demographic parameters, such as survival, fecundity and density-dependent patterns were estimated from an eight year on-going monitoring program of two translocated marble trout populations in pristine, previously fishless streams (Zakojska and Gorska) in the Soca and Idrijca river basins (Slovenia). To explore the importance of disturbance events such as floods on marble trout population dynamics, we performed a PVA under three scenarios: (1) occurrence of both severe and moderate floods; (2) occurrence of only moderate floods; (3) no flood events. Our analysis shows that population viability is threatened only by severe flood events, otherwise the two populations prove to be fairly stable with population abundance fluctuating around stream carrying capacity. A sensitivity analysis performed on model parameters highlighted that density-dependence in first-year survival and the magnitude of reduction in population size after a severe flood are the two most crucial parameters affecting population abundance and quasi-extinction probability, respectively. While only extreme floods can drive the population to extinction, the increase in juvenile survival when population abundance collapses after a major flood may allow the populations to quickly recover from few reproductive individuals back to stream carrying capacity.     

Responses of flood peaks to land use and landscape patterns under extreme rainstorms in small catchments - A case study of the rainstorm of Typhoon Lekima in Shandong,China

Investigations of the formation mechanisms of flood peaks in small catchments facilitate flood prediction and disaster prevention under extreme rainstorms. However, there have been few studies on the responses of flood peaks to land use landscape patterns using field surveys during extreme rainstorm events. Based on field data from 17 small catchments near the rainstorm center of Typhoon Lekima, 7 landscape indices were chosen. The flood peak and its sensitivity to the land use landscape were investigated by combining remote sensing interpretation and related analysis. The conclusions are as follows: (1) The peak discharge of the small catchment was 2.36–56.50 m³/s, the peak modulus was 8.00–48.89 m³/(s·km²), and the flood index K ranged from 3.61 to 4.55. (2) Under similar rainfall conditions, the flood peak modulus, K and the proportion of sloping cropland had significantly positive correlations (p < 0.05). The flood peak modulus was significantly negatively correlated with the proportion of forest-grassland and terrace (p < 0.05), and K and the proportion of forest-grassland and terraced land exhibited a negative correlation. (3) The flood peak modulus and K were positively correlated with the landscape fragmentation. (4) The sensitivities of small catchments to floods were evaluated to be moderate compared to K values from other studies. The ability of small catchments to cope with extreme rainstorms can be improved by increasing the areas of forest-grassland, and terraces and reducing landscape fragmentation. Our results could be applied to provide a basis for land use planning and support for the response against disasters caused by extreme floods.     

Population isolation exacerbates conservation genetic concerns in the endangered Amargosa vole, Microtus californicus scirpensis

The ability of a taxon to maintain adaptive flexibility in a stochastic environment is a function of the genetic diversity within the population. In small, fragmented populations, genetic variation can become depleted more quickly than in larger, more contiguous populations. Characterizing the patterns of genetic variation and differentiation associated with these processes is an important step in establishing conservation priorities. The Amargosa vole, Microtus californicus scirpensis, is an endangered rodent persisting in the small, fragmented marsh complex surrounding the Amargosa River near Death Valley, California. This naturally patchy system has existed since the end of the Pleistocene (approximately 10,000 y.b.p.), however, fragmentation has been exacerbated by recent anthropogenic changes. For this study, I used five nuclear microsatellite loci and the cytochrome-b region of the mitochondrial genome to quantify levels of genetic variation, population substructure, and patterns of gene flow in M.c. scirpensis. These data were compared to a broadly distributed subspecies, Microtus californicus sanctidiegi. Overall levels of nuclear genetic variation were significantly lower in M.c. scirpensis, whether measured in terms of diversity or heterozygosity, compared to more broadly distributed conspecifics. Moreover, only two haplotypes were recovered from the mitochondrial data with over 90% of the observed haplotypes being identical. Despite low genetic diversity, significant genetic subdivision among M.c. scirpensis populations was detected using both pairwise F_ST and Bayesian clustering methods. Furthermore, isolation by distance analyses reveal that an important landscape feature, ephemeral tributaries, is critical for dispersal among population clusters. Recommendations for conservation management are presented.     

Sediment toxicity in a connected oxbow lake of the Upper Rhine (Germany): EROD induction in fish cells

Purpose  

Although the water quality of the Rhine River in Europe has improved, contaminated sediments may still threaten fish populations. This is particularly likely in Upper Rhine oxbow lakes, which are connected to the main river channel only at one end, except for extreme flood events. The impact of such extreme flood events on the sediment toxicity has, however, not yet been investigated, although numerous oxbow lakes exist with varying degrees of connection to their main river channels.     

Unexpected high levels of genetic variability and the population structure of an island endemic rodent (Oryzomys couesi cozumelae)

Oryzomys couesi cozumelae is an endemic, threatened rodent from Cozumel Island, Mexico. We estimated its genetic diversity and structure by analyzing microsatellite loci in 228 samples from 12 sampling sites widely distributed throughout the island. Unexpected high levels of genetic and allelic diversity were found: a total of 54 alleles, an average of 10.8 alleles per locus, and high heterozygosity values (mean H_O = 0.624, H_E = 0.690 and H_Nei = 0.689). These values are higher than those reported for small sized insular mammals, higher than that found in 37 individuals of the mainland O. couesi from southern Mexico (H_O = 0.578) that we analyzed for comparative purposes, and similar to those of other mainland small mammal populations. Despite factors that affect Cozumel’s biota, such as exotic predators and competitors, hurricanes, seasonal population fluctuations and anthropogenic activities, no evidence of genetic bottlenecks was found. A significant population structure was observed and a model of isolation-by-distance was supported. Our findings render O. c. cozumelae a high conservation value, not only for its high genetic diversity and structure, but because available data suggests that its population has declined significantly in recent years. Further habitat fragmentation and population isolation could result in a higher genetic structure and loss of genetic diversity. The protection of habitat, the maintenance of habitat connectivity and the removal of introduced competitors and predators are a conservation priority. Acknowledging that the genetic structure of populations has crucial conservation implications, the present genetic information should be taken into account in management plans for the conservation of O. c. cozumelae.     

Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implications for conservation

The endangered fish species Anaecypris hispanica is restricted to eight disjunct populations in the Portuguese Guadiana drainage. The genetic structure of these populations was studied in order to determine levels of genetic variation within and among populations and suggest implications for conservation of the species. Based on five microsatellite loci, the null hypothesis of population homogeneity was tested. Tests for genetic differentiation revealed highly significant differences for pairwise comparisons between all populations, and substantial overall population subdivision (F_ST=0.112). All sampled populations contained unique alleles. Our findings indicate marked genetic structuring and emphasise limited dispersal ability. The high levels of genetic diversity detected within and among A. hispanica populations suggest, however, that the observed fragmentation and reduction in population size of some populations during the last two decades, has impacted little on levels of genetic variability. Data imply that most A. hispanica populations should be managed as distinct units and that each has a high conservation value containing unique genetic variation. It is argued that geographic patterns of genetic structuring indicate the existence of eight management units.     

Genetic variation in the endangered Rutaceae species <Emphasis Type="Italic">Citrus hongheensis</Emphasis> based on ISSR fingerprinting

Citrus hongheensis is a critically endangered species endemic to the Honghe river region in southeastern Yunnan, China. Its genetic diversity and differentiation were investigated using Inter-Simple Sequence Repeat (ISSR) markers. One hundred primers were screened, and a total of 245 loci were amplified from seven natural populations by 13 informative and reliable primers. Of these 245 ISSR loci, 233 were polymorphic and the detected variations revealed a relatively high level of intraspecific genetic diversity. At the population level, the mean percentage of polymorphic loci (PPB) was 36.50%, while the average expected heterozygosity (He) and Shannon diversity index (Ho) were 0.1327 and 0.1972, respectively. At the species level (across all populations), PPB was 95.10%, while He and Ho were 0.3520 and 0.5195, respectively. A high Gst value (0.6247) indicated that there is significant differentiation among populations, which was confirmed by AMOVA analysis (Φst = 0.6420). Pairwise genetic identity (I) values among populations ranged from 0.6341 to 0.7675, with a mean of 0.7008. We propose that the high level of genetic differentiation may be the result of habitat fragmentation and limited gene flow (Nm = 0.1502). For effective in situ conservation and population restoration of C. hongheensis it will be important to maintain historical processes, including high outbreeding rates, sufficient gene flow, and large effective population sizes.     

汉江上游与渭河流域特大洪水发生规律的对比研究

以汉江上游安康水库和渭河流域临潼站1960-2000年发生的特大洪水资料为依据,对其发生规律进行了对比研究.结果表明,汉江上游和渭河流域特大洪水的发生具有一些共同特征.主要表现在两大流域特大年径流量年份,完全与华西秋雨多雨年份相对应,但特大洪水并不都是发生在华西秋雨异常多雨年份,而是错前错后发生.受到季风活动及地理环境的影响,汉江上游和渭河流域特大洪水的发生又表现出各自的特殊性,汉江上游特大洪水主要发生在初夏和秋季,渭河流域特大洪水主要发生在盛夏和秋季;一年中汉江上游特大洪水发生时间早于渭河流域;渭河流域秋季特大洪水发生时间早于汉江上游特大洪水.     

Sedimentary records and luminescence chronology of Late Holocene palaeofloods in the Luni River, Thar Desert, northwest India

River Luni is the only well-integrated river system in the Thar Desert of India. This river catastrophically flooded due to unusually heavy rainfall in the catchment area during July 1979. In order to establish whether floods of this magnitude have occurred in the recent geological past, sedimentary records of palaeofloods occurring in the Sindari Gorge, in the lower Luni Basin were investigated. The principal slackwater flood deposits were observed in a back-flooded tributary near Bhuka. Analysis of the slackwater flood deposits preserved in the back-flooded tributary and their luminescence dating suggests that the Luni River has experienced at least 17 extreme floods during the past millennium. Evidence from the Bhuka site also suggests that no floods comparable in magnitude to the July 1979 megaflood have occurred during this period. This observation is in conformity with the palaeoflood record of central India. Comparison of the long-term monsoon rainfall series for the Luni Basin and the Indian region reveals a clear link between the two, and indicates that the clustering of large floods in the last few decades and during the Medieval warming period is a regional phenomenon associated with wetter conditions. This correlates with a regionally extended episode of landscape stability denoted by stabilization of dunes in this region.     

From genetic diversity and structure to conservation: Genetic signature of recent population declines in three mouse lemur species (Microcebus spp.)

The exceptional biodiversity of Madagascar is threatened by anthropogenic landscape changes that took place during the 2000 years of human colonization. This study focuses on the influence of geographic distance and forest fragmentation on genetic diversity and population differentiation of three rare, nocturnal, arboreal lemur species in northwestern Madagascar. Historic declines in population sizes as a consequence of forest fragmentation are quantified and dated. Eighteen sites were visited, and a total of 205 Microcebus ravelobensis, 45 M. bongolavensis and 78 M. danfossi were genotyped with eight microsatellite loci. Genetic differentiation among the sites, as measured by F_ST, ranged from 0.01 to 0.19. These values were significant in almost all cases and indicated genetic structure in the samples. Isolation-by-distance was detected in one species and a STRUCTURE analysis indicated that fragmentation further promoted genetic differentiation. Bayesian methods revealed that populations from all three species underwent a major demographic collapse of around two orders of magnitude. This decrease probably began after the arrival of humans, most likely within the last 500 years. This result suggests that anthropogenic changes may have been limited during the first 1500 years of human colonization in all three ranges. Two of the study species (M. danfossi, M. bongolavensis) lack effectively protected areas in their ranges. Consequently, quick conservation actions are now needed in order to secure the remaining genetic diversity of these species.     

Influence of habitat fragmentation on the genetic structure of Polyommatus coridon (Lepidoptera: Lycaenidae): implications for conservation

Conservation biologists pay increasing attention to the interdependence between habitat structure and genetic patterns of species and to the importance of conserving genetic diversity. A suitable model species for such a study is Polyommatus coridon, a butterfly of dry calcareous grassland. We studied the population genetic structure of 22 western German populations of this species (874 individuals). We observed no congruence between the observed genetic structure and the geographic arrangement of the studied populations. Genetic diversity was slightly higher in large populations than in small populations. Differentiation among populations was weak or even missing. Populations of an area with high habitat density showed no significant differentiation, whereas areas with low habitat densities showed significant genetic differentiation among populations. At present, hierarchical variance analysis revealed no differentiation between four distinguished limestone areas. The combination of all analytical results allow the definition of management units for P. coridon. Conservation measures are proposed from which a large number of rarer species occurring together with P. coridon will benefit.     

Genetic diversity and local population structure of fragmented populations of Trillium camschatcense (Trilliaceae)

Trillium camschatcense, a long-lived common woodland herb, has been experiencing intensive habitat fragmentation over the last century in eastern Hokkaido, Japan. We examined the genetic diversity and population genetic structure of 12 fragmented populations with different population sizes using allozyme electrophoresis. The percentage of polymorphic loci and mean number of alleles per locus were positively related to population size, probably due to the stochastic loss of rare alleles (frequency of q<0.1) in small populations. Populations with 350 flowering plants or fewer had lost almost all of their rare alleles. While the heterozygosity and inbreeding coefficient were not related to population size, some small populations showed relatively high inbreeding coefficients. In spite of the low genetic differentiation among overall populations (F_ST=0.130), local population structuring was recognized between the two geographically discontinuous population groups. Within groups, sufficient historical gene flow was inferred, whereas a low dispersal ability of this species and geographical separation could produce apparent differentiation between groups.     

Influence of forest fragmentation on an endangered large-bodied lemur in northwestern Madagascar

Madagascar’s diverse and mostly endemic fauna and flora suffer from recent landscape changes that are primarily caused by high levels of human activities. The loss and fragmentation of forest habitats are well known consequences of human activities. In this study, we investigate the effects of forest fragmentation on presence, abundance and genetic diversity in a larger-bodied lemur species, Lepilemur edwardsi, in northwestern Madagascar. In addition, we characterized the genetic differentiation among populations and demographic changes. We found L. edwardsi at only 13 (76.5%) of 17 visited sites, 11 of which were situated in the Ankarafantsika National Park (ANP). We captured between two and 17 individuals per site. We sequenced the mtDNA d-loop of all samples and genotyped 14 microsatellite loci in two exemplary populations for demographic analyses. A negative influence on forest fragmentation could be detected, since the fragments had a lower genetic diversity than sites in the ANP. Genetic differentiation between populations ranged from low to high but was almost always significant. A typical pattern of isolation-by-distance could not be detected and the data could rather be interpreted as results of random genetic drift. The data furthermore revealed signals of a demographic collapse of about two orders of magnitude in the two exemplary sites. This decline probably started during the last few hundred years of intensified human disturbances and population growth. Given the results of this study, urgent conservation actions are needed and should concentrate on an effective protection of the few remaining populations in order to ensure the long-term survival of L. edwardsi.     

Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest

Tropical rainforests are becoming increasingly fragmented and understanding the genetic consequences of fragmentation is crucial for conservation of their flora and fauna. We examined populations of the toad Rhinella ornata, a species endemic to Atlantic Coastal Forest in Brazil, and compared genetic diversity among small and medium forest fragments that were either isolated or connected to large forest areas by corridors. Genetic differentiation, as measured by F_ST, was not related to geographic distance among study sites and the size of the fragments did not significantly alter patterns of genetic connectivity. However, population genetic diversity was positively related to fragment size, thus haplotype diversity was lowest in the smallest fragments, likely due to decreases in population sizes. Spatial analyses of genetic discontinuities among groups of populations showed a higher proportion of barriers to gene flow among small and medium fragments than between populations in continuous forest. Our results underscore that even species with relatively high dispersal capacities may, over time, suffer the negative genetic effects of fragmentation, possibly leading to reduced fitness of population and cases of localized extinction.     

Genetic diversity of core and peripheral Sitka spruce (Picea sitchensis (Bong.) Carr) populations: implications for conservation of widespread species

This study investigated levels of genetic diversity and population differentiation among Sitka spruce (Picea sitchensis) populations classified as core or peripheral based on ecological niche, and continuous or disjunct based on species distribution. Large numbers of trees (N = 200) were sampled from each of eight populations to evaluate the distribution of rare as well as common alleles across the species range. Codominant alleles for eight sequence-tagged site loci were classified based on frequency and geographic distribution in order to develop appropriate sampling strategies to target specific classes of alleles. An important finding of this study is the similarity in genetic diversity as measured by expected heterozygosity between core populations (mean H_E = 0.58) and peripheral populations (mean H_E = 0.56). However, there was significant inbreeding in peripheral (F_IS = 0.17) but not in core (F_IS = 0.03) populations. Large differences in gene flow estimates were observed between core (Nm = 9.0) and peripheral populations (Nm = 3.5). Irrespective of population classification, over 75% of the alleles were common and widespread. Only one allele was classified as rare and localized, and this allele was limited to one core, disjunct and two peripheral, disjunct populations. There was stronger evidence of past bottlenecks in peripheral, disjunct populations than in core, continuous populations. Results are used to suggest sampling strategies for capture of maximum level of genetic diversity and conservation of rare alleles. The conservation of peripheral, particularly disjunct, populations as well as populations in putative glacial refugia may present the best opportunity for conserving rare alleles.     

ISSR analysis shows low genetic diversity versus high genetic differentiation for giant bamboo, Dendrocalamus giganteus (Poaceae: Bambusoideae), in China populations

Dendrocalamus giganteus Munro is a high-value woody bamboo widely grown in Southeast Asia and China’s Yunnan Province. We investigated its genetic diversity in Yunnan as a prelude to considering effective breeding programs and the protection of germplasm resources. Inter-simple sequence repeat (ISSR) markers were used to assess the genetic structure and differentiation of seven populations. Seven ISSR primers generated 140 bands, of which 124 were polymorphic (88.57%). Genetic diversity within populations was relatively low, averaging 11.33% polymorphic bands (PPB), while diversity was considerably higher among populations, with PPB = 88.57%. Greater genetic differentiation was detected among populations (G _ST = 0.8474). We grouped these seven populations into two clusters within an UPGMA dendrogram—one comprised the Xinping and Shiping populations from central Yunnan, the other included the remaining five populations. Mantel tests indicated no significant correlation between genetic and geographic distances among populations. Breeding system characteristics, genetic drift, and limited gene flow (N _m = 0.0901) might be important factors for explaining this differentiation. Based on the overall high genetic diversity and differentiation among D. giganteus populations in Yunnan, we suggest the implementation of in situ conservation measures for all populations and sufficient sampling for ex situ conservation collections.     

Geochemical traces of flood layers in the fluvial sedimentary archive; implications for contamination history analyses

We studied three cores from a well-dated sediment archive from an oxbow lake of the River Morava, Czech Republic, using a high-resolution (1 cm) multiproxy stratigraphic analysis and a concentration of selected heavy metals. The objective was to investigate how the vertical distribution of pollutants could be affected by episodic flood sedimentation in archives with high sedimentation rates. Stratigraphic proxies (magnetic susceptibility/MS/, X-ray densitometry and visible-light diffuse reflectance spectrometry), supported by grain-size analyses, enabled us to identify relatively coarse-grained flood layers and correlate them in the proximal-to-distal direction in the oxbow-lake delta. A correlation of the flood layers with the time series of the river discharge was used to improve the age model based primarily on ¹³⁷Cs dating. The refined age model is nonlinear and shows periods of lower and higher sediment accumulation rates, which coincided with periods of lower and higher frequency of floods in the river, respectively. Concentrations of most heavy metals, normalized to lithogenic aluminium, revealed vigorous short-term variation related to floods, whose magnitude exceeds that of long-term trends. There is a substantial risk that temporal contamination trends, even if normalized to lithogenic elements, can be strongly influenced by facies, which may lead to potential misinterpretations. Element normalizing to MS, which proved to be a good proxy of grain size, provided smoother long-term trends whose interpretation was less affected by short-term variations. The long-term trends exhibit decreasing concentrations of most heavy metals for the last ~ 25 years, most notably between ~ 1987 and ~ 1992. These historical patterns correspond well to the significant improvement in environmental pollution reported elsewhere in Central Europe. In contrast, concentrations of Na have systematically increased up until the present, partly being driven by the widespread use of de-icing salt for winter road treatment.     

Genetic diversity,genetic structure and migration routes of wild <Emphasis Type="Italic">Brassica juncea</Emphasis> in China assessed by SSR markers

The wild Brassica juncea (L.) Czern. et Coss., systematically belonging to the genus Brassica L. in the Cruciferae family, has become a noxious weed for cropping systems nowadays. Here, simple sequence repeat (SSR) markers were applied to investigate the genetic diversity, genetic structure and migration routes of the wild B. juncea populations in China. The results showed that a total of 90 alleles, with extensive allelic diversity, were observed at the 11 SSR loci of the wild B. juncea. The STRUCTURE analysis indicated that all the 25 wild populations were best described as belonging to two lineages. High Fst value (0.568), together with the partitioning, provided significant evidence for lineage differentiation in wild B. juncea. The high differentiation between the two lineages was, perhaps, due to limited gene flow (Nm?=?0.301) of this species. The analysis of molecular variance with distances among individuals corrected for the dominant nature of SSRs showed that most of the variation (59%) occurred within populations, and the remaining 41% variance was attributed to differences among populations. The distribution of diversity across China was significantly geographically dependent. NJ cluster analysis, based on genetic distance, grouped populations geographically, which further corroborated spatial pattern of two lineages. Based on these results, two routes were proposed for the migration of wild B. juncea in China after its origin from northwest China, heading east along the Yellow River or Yangtze River, respectively. We concluded that China, especially the northwest, is one of the primary origins of B. juncea.