Effect of stand age and management regime on genetic diversity of Thuidium cymbifolium in western China

Using random amplified polymorphic DNA (RAPD) markers, we examined genetic variability of the moss Thuidium cymbifolium (Thuidiaceae) sampled from three types of spruce (Picea asperata) stands: an intact stand, naturally regenerated stands after clearcut harvests, and planted stands after clearcut harvests in the Miyaluo area, western Sichuan of China. Stands of the latter two types were of various age since the last clearcut. Results showed that the population of T. cymbifolium from the intact stand displayed the highest level of genetic diversity, and populations from the planted stands exhibited significantly higher levels than the naturally regenerated stands. In planted stands, genetic variation within populations increased over time. These findings indicated that habitat destruction by forest harvesting led to the reduction in genetic variation within populations, but that given time, artificial reforestation after clearcut was effective in promoting the recovery of genetic diversity in the recolonized moss species. Therefore, lengthening the normal felling rotation of plantations should be favored to restore and conserve genetic diversity in recolonized species. In addition, thinning young plantations via selective logging may provide heterogenous microhabitats similar to those in the old stands, and thereby facilitate the development of bryophyte communities and the increase of genetic variation of the recolonized mosses.     

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.     

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.     

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 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.     

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.     

High genetic diversity and heterogeneous parasite load in the earthworm Lumbricus terrestris on a German meadow

In parasite-host dynamics, parasites exert frequency-dependent selection on their hosts by favouring rare alleles that may confer resistance against infection. Therefore host populations that suffer strong parasite stress should maintain higher levels of genetic variability. We studied the Lumbricus terrestris-Monocystis sp. host-parasite system at a microgeographical scale. Using three polymorphic microsatellite loci on one large earthworm population sampled at 26 different sites (281 genotypes), we tested the relationship between parasite load and genetic variation in natural samples of the common earthworm L. terrestris. Our analysis yielded the following: (1) parasite load varied significantly across sites in this population; (2) there was no consistent evidence for heterozygote deficiency (observed heterozygosities ranged between 0.74 and 0.87), indicating a low level of inbreeding; (3) there was no significant genetic structuring among sample sites; (4) we could not identify a significant association between parasite load and population genetic diversity; (5) there was considerable population differentiation (15.17%) between our German samples and a Canadian L. terrestris reference population. Our study provides insight into the population genetics of one of the most economically important soil organisms on a microgeographic scale.     

Novel microsatellite loci for the compost earthworm Eisenia fetida: A genetic comparison of three North American vermiculture stocks

Earthworms are important components of soil ecosystems worldwide, and have been used extensively as indicator species in ecotoxicology studies. Our understanding of mating systems, population structure, and genetic diversity in earthworms is limited by the current lack of available genetic tools. To address this gap, we developed 16 novel microsatellite markers for the compost earthworm Eisenia fetida, one of the most widely studied earthworm species. We tested the new markers in 3 putative populations of worms from commercial vermiculture operations in Canada and the U.S.A. All 16 loci were variable in at least one population, with the number of alleles per locus ranging from 3 to 10, observed heterozygosity from 0.000 to 0.783, and polymorphic information content from 0.032 to 0.587. One group had significantly reduced heterozygosity compared to the other 2, but overall there were only minor genetic differences among the tested suppliers, suggesting a possible bottleneck for this species in North America. The microsatellite loci we describe here will be extremely useful tools for future field and laboratory studies of E. fetida. Body size and condition in adult worms varied significantly by supplier, and breeding success and cocoon production were significantly higher in breeding pairs from one supplier compared to the other two. In the absence of evidence for genetic divergence among populations, our results suggest that the early rearing environment may be an important factor affecting adult breeding performance. We caution that the source of worms may affect the outcome of laboratory experiments involving growth and reproduction.     

The importance of understanding spatial population structure when evaluating the effects of silviculture on spotted salamanders (Ambystoma maculatum)

Current silvicultural practices in the northeastern United States create diverse vegetation patterns and microclimates that provide a mosaic of terrestrial habitats for amphibian species. We inferred patterns of habitat use by the spotted salamander, Ambystoma maculatum, by studying colonization of four newly created breeding pools each surrounded by four different forest treatments: a control, partial cut, clearcut with coarse woody debris (CWD) removed, and clearcut with CWD retained. Created pools were rapidly colonized, indicating that breeding salamanders readily bred in new pools they encountered. This suggests that in our study area pool-specific philopatry and site fidelity may not be high and that particular pools may not define local breeding populations. In the experimental silvicultural treatments, juvenile salamanders preferred the control forest to the clearcuts, whereas adult salamanders showed no significant preferences among the treatments. Although silvicultural practices such as clearcutting may reduce juvenile movement between pools, inter-pool movement by adults that are more tolerant of habitat change may ameliorate this effect in our study area. If juveniles are the primary life-history stage dispersing between local populations (i.e., moving between more isolated groups of pools), however, there is potential for clearcutting to reduce the connectivity between local populations.     

Genetic diversity and gene flow dynamics revealed in the rare mixed populations of wild soybean (Glycine soja) and semi-wild type (Glycine gracilis) in China

Thus far, there is little knowledge of the genetic diversity, structure and gene flow dynamics in rare wild and semi-wild soybean mixed populations, and such information is vital for understanding of the origin of semi-wild soybean (Glycine gracilis) and the biosafety protection of wild soybean from transgenic soybeans. Population eco-genetic data are necessary to provide a more coherent and comprehensive understanding of the genetic events that occurred in the natural habitats of wild soybean (Glycine soja). We tested genetic diversity and structure of 11 wild mixed populations of wild soybean (Glycine soja) and semi-wild soybean (G. gracilis), 1 wild soybean population, and 1 cultivated soybean variety population were studied using 20 nuclear microsatellite markers (SSRs). We found based on microsatellite polymorphisms that the mixed populations were characterized by higher mean heterozygosity (H _o = 0.029) and outcrossing rate (t _m = 6.35 %), and lower fixation index (F _is = 0.891), and the semi-wild plants had distinctly higher heterozygosity (H _o = 0.081) than that of the wild plants (H _o = 0.007). The occurrence of semi-wild plants influenced population genetic structure but not geographical population differentiation. These mixed populations exhibited strong ecogeographical differentiation, which suggests that their original populations were colonized over a long phytogeographical history. The introgression occurred through pollen gene flow from the soybean fields into wild populations and created the semi-wild plants, with significant genetic differentiation from the typical wild ones. Introgressive genes could become established by two possible modes in wild soybean populations by both self-segregation and/or intrapopulation secondary hybridization. The latter deserves attention because of the possibility of rapid transgene escape.     

Ecological and genetic measurements of dispersal in a threatened dragonfly

Leucorrhinia caudalis is a rare dragonfly, threatened throughout its European distribution. The species was formerly widespread in the Swiss lowlands, but only a single population remained in the 1980s. However, a spread has recently been observed, with additional ponds being colonised, sometimes at considerable distance. Despite this evidence of recent long-distance dispersal, it is unknown whether L. caudalis regularly moves among ponds or whether this is a rather rare event. A combination of an ecological mark-resight and a population genetic study was applied to investigate contemporary dispersal and the genetic footprint of the recent population history of L. caudalis in Switzerland. DNA for genetic microsatellite analysis was extracted from exuviae. The mark-resight study and the genetic analysis gave congruent results. They showed that L. caudalis is mostly a sedentary species, with only a few contemporary dispersal events over distances up to 5 km being observed. The genetic analysis was in agreement with the recent population history of the Swiss populations. The oldest and largest population showed large genetic diversity and acted as source population for the recent spread of L. caudalis in Switzerland. Recurrent gene flow among this source population and close populations caused substantial local genetic variation in the latter, as well as low population differentiation. The two recently founded distant populations (?30 km distance) were genetically less diverse and highly differentiated. These distant populations and another recently colonised population also expressed signatures of genetic bottlenecks.     

Core terrestrial habitat for conservation of local populations of salamanders and wood frogs in agricultural landscapes

Pond-breeding amphibians require aquatic and terrestrial habitats to complete their lifecycles, and preservation of both habitats is necessary for maintaining local populations. Current wetland regulations focus primarily on aquatic habitats, and criteria to define critical upland habitats and regulations to protect them are often ambiguous or lacking. We examined the association between the presence of seven pond-breeding amphibian species and the landscape composition surrounding 54 wetlands located within the Till Plains and the Glaciated Plateau ecoregions of Ohio, USA. We quantified landscape composition within 200 m of the wetland (“core terrestrial zone”) and the area extending from 200 m to 1 km from the wetland (“broader landscape context zone”). We constructed binary logistic regression models for each species, and evaluated them using Akaike Information Criterion. Presence of spotted salamanders (Ambystoma maculatum), Jefferson's salamander complex (A. jeffersonianum) and smallmouth salamanders (A. texanum) was positively associated with the amount of forest within the core zone. Presence of wood frogs (Rana sylvatica) was positively associated with the amount of forest within the core zone and the amount of forest within the broader landscape context zone. Presence of tiger salamanders (A. tigrinum tigrinum) was negatively associated with the cumulative length of paved roads within 1 km of the site, and presence of red-spotted newts (Notophthalmus v. viridescens) was negatively associated with the average linear distance to the five nearest wetlands. Overall salamander diversity was positively associated with the amount of forest within the core zone, and negatively associated with the presence of predatory fish and cumulative length of paved roads within 1 km of the site. Our results confirm the strong association between the structure of surrounding upland areas and amphibian diversity at breeding ponds, and stress the importance of preserving core terrestrial habitat around wetlands for maintaining amphibian diversity.     

Cross-amplification and characterization of microsatellite loci for three species of <Emphasis Type="Italic">Theobroma</Emphasis> (Sterculiaceae) from the Brazilian Amazon

This study reports on the cross-species amplification of 23 microsatellite markers previously developed for Theobroma cacao L. (Sterculiaceae), source of chocolate in three economically important Amazonian species of Theobroma (T. grandiflorum, T. subincanum, T. sylvestre). Thirteen of the 23 microsatellite loci tested were polymorphic across the three species at 2–13 alleles per locus. The observed heterozygosity per locus varied from 0.18 to 0.84 and expected heterozygosity ranged from 0.28 to 0.87. The high level of transferability and genetic information content of these microsatellite loci indicate their usefulness for population genetic, mating system and breeding studies of these economically important Amazonian fruit trees.     

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.     

Presence of phylogeographic structure among wild diploid alfalfa accessions (Medicago sativa L. subsp. microcarpa Urb.) with evidence of the center of origin

The genetic structure of wild germplasm on a macrogeographic scale has implications for collection and conservation of wild genetic resources of economically important plants. Cultivated alfalfa is derived from a taxonomic group called the Medicago sativa–falcata complex, which includes a number of morphologically and genetically differentiated diploid and tetraploid subspecies representing the primary gene pool for alfalfa improvement. Although the origin of the taxa included in M. sativa–falcata complex has been described broadly, the center of diversity for each taxon is not clear. In this study, 60 individual genotypes from 16 accessions of the diploid taxon M. sativa subsp. microcarpa Urb. [M. sativa subsp. caerulea (Less. ex Ledeb.) Schmalh.] were obtained from the two proposed centers of diversity, Caucasia and Central Asia, and were genotyped with 89 simple sequence repeat markers. Phylogenetic reconstructions together with population genetics statistics (heterozygosity, allelic diversity, and F_ST) were used to describe the pattern of present genetic diversity, to deduce biogeographic history, and to infer the center of diversity. Our results revealed that the Central Asian accessions were distinct from the Caucasian accessions, and that overall accessions, genetic distance was positively correlated with geographical distance, indicating a spatial genetic structure. The accessions from the Caucasian region had higher mean F_ST values, higher allele diversity and higher heterozygosity, suggesting that the Caucasian region is the likely center of diversity for M. sativa subsp. microcarpa [M. sativa subsp. caerulea] and the accessions recolonized Central Asia from Caucasia after the glacial retreat.     

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.     

Evaluation of genetic diversity in a Camelina sativa (L.) Crantz collection using microsatellite markers and biochemical traits

A genomic DNA library enriched with GA/TC repeats from Camelina sativa variety Calena has been analysed. After sequencing of about 200 randomly selected clones, approximately 60 % of them showed to contain simple or compound microsatellites with a high number of repeats. Among all microsatellite markers analysed 15 primer pairs amplified polymorphic fragments. Forty C. sativa accessions of different origin were genotyped with 15 microsatellite markers that generated 134 alleles with an average of 8.93 alleles per locus. The observed heterozygosity (Ho) among the accessions ranged from 0.0 to 0.15 with an average of 0.0370, whereas the average of expected heterozygosity (He) among accessions was 0.2769. The analysis of the average total heterozygosity (H_T = 0.651), the intrapopulation genetic diversity (H_S = 0.260), the interpopulation genetic diversity (D_ST = 0.391) and the coefficient of genetic differentiation among populations (G_ST = 0.574) demonstrated that 57.4 % of the genetic diversity is among the accessions, while 42.6 % resides within them. Phylogenetic tree of the 40 C. sativa accessions was constructed based on Nei’s genetic distance. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram shows, except for CAM108 and CAM170, a clear discrimination among C. sativa accessions grouping them in five subgroups. ANOVA analysis indicates significant differences in some biochemical and agronomic parameters among the C. sativa accessions grouped according to Nei’s genetic distance. The result of the Tukey HSD test demonstrated that the A4 subgroup showed a significant higher TWS and linoleic acid (LA) content, while the subgroup A1 showed a significant higher linolenic and lower LA content compared to the remaining groups.     

Long-term effects of experimental forest harvesting on abundance and reproductive demography of terrestrial salamanders

Both observational and experimental studies have documented drastic reductions in salamanders after forest harvesting. Yet, the amount of time until salamander populations rebound and the factors limiting recovery after harvesting are unknown. We compared the effects of six oak regeneration practices to a control, representing a disturbance gradient from no treatment to silvicultural clearcut, on the relative abundance and reproductive demography of terrestrial salamanders through 13-years post-harvest. Following the experimental disturbance, relative abundance of terrestrial salamanders in treatments that opened the canopy were significantly and persistently lower than in either untreated control stands or midstory herbicide treatments. In general, this trend persisted through 9-13 years after treatment. Changes to demography of commonly captured salamanders varied by species, but Plethodon cinereus had a greater proportion of juveniles in unharvested treatments 7-13-years post-harvest, and Desmognathus ochrophaeus had a greater proportion of juveniles and a greater number of eggs/female in unharvested treatments 1-6-years post-harvest. Population modeling of P. cinereus indicated that adult survival had the greatest elasticity of the vital rates. Further, >60 years may be needed before P. cinereus reduced by the observed decline could reach pre-harvest levels of abundance. Of the treatments with canopy disturbance, the group selection harvest had the greatest abundances of salamanders 7-13-years post-harvest, but when coupled with future stand entries, the volume of wood fiber extracted, costs of harvesting, reduced sprouting of oaks, and soil disturbances, this method may not have the best balance of ecological and economic sustainability in central Appalachian hardwood forest.     

Ecological effects on estimates of effective population size in an annual plant

Effective population size (N_e) is a critical indicator of the vulnerability of a population to allele loss via genetic drift, and it can also be used to assess the evolutionary potential of a population. While some plant conservation plans have focused on outcrossing through cross-pollination as a way to increase estimated N_e, variance in reproductive output determined by ecological factors such as competition can also strongly affect estimated N_e. We examined the effects of intraspecific and interspecific competition, stressful soils, and local adaptation on estimates of N_e in an annual plant species. While ecological influences on plant growth rate variance have been predicted to influence estimates of N_e/N, we found a significant effect on the estimate of N_e/N, but no significant ecological effects on growth rate variance. Lower survivorship on stressful soil was the most important effect reducing estimates of N_e/N. If stochastic mortality is greater in environments that are abiotically stressful, then populations in these stressful environments may be slower to adapt because of lower census sizes and reduction of N_e/N. In populations of conservation concern, increasing survivorship may be of greater benefit for maximizing N_e than the reduction of variability in reproductive output among surviving adults.