The genetic structure of the loggerhead sea turtle (Caretta caretta) in the Mediterranean as revealed by nuclear and mitochondrial DNA and its conservation implications

The population genetic structure of the loggerhead sea turtle (Caretta caretta) nesting in the eastern Mediterranean was assessed by sequencing a fragment of the control region of the mitochondrial DNA (n = 190) and seven microsatellites (n = 112). The two types of markers revealed genetic structuring (mtDNA: γ_st = 0.212, P < 0.001; nDNA F _st = 0.006, P < 0.001), thus indicating that both females and males are philopatric and that gene flow between populations is restricted. Mitochondrial DNA data indicate that the female populations nesting on the islands of Crete and Cyprus have suffered a recent bottleneck or colonization event. However, no bottleneck or founder effect was revealed by nuclear markers, thus indicating male-mediated gene flow from other populations that would increase nuclear genetic variability. Crete, and to a lower extent Cyprus, are thought to play a central role in such male-mediated gene flow that may reduce the negative effect of genetic drift or inbreeding on the small populations of Lebanon and Israel. This population structure indicates that assessing population relevance only on the basis of genetic variability and size would be misleading, as some populations not fulfilling those requirements may play a relevant role in genetic exchange and hence contribute to the overall genetic variability.     

Allopolyploid origin and population genetics of the rare orchid Spiranthes diluvialis

The process of becoming and the attributes of being polyploid play a major role in the development and maintenance of genetic variation in allopolyploid species. A genetic survey employing protein electrophoresis on 12 populations of S. diluvialis, as well as on populations of eight congeneric species, was conducted to assess the putative allopolyploid origin of S. diluvialis and to determine the genetic variability within and among populations. Genetic identity values indicated S. diluvialis was more similar to S. magnicamporum (0.619) and S. romanzoffiana (0.727) than to any of the other congeneric species assayed. Similar to most allopolyploids, S. diluvialis showed high levels of fixed, or nearly fixed, heterozygosity and a high percentage of polymorphic loci (57.1-71.4%). The mean number of alleles per polymorphic locus in populations of S. diluvialis (2.6-3.3), however, was similar to mean values for both animal-pollinated, outcrossing, diploid species, and geographically restricted, diploid species (2.6 and 2.5, respectively). Genetic divergence among populations (mean Fst = 0.083) was low, leading to relatively high estimates of interpopulational gene flow (mean Nm = 5.41). Thus, each population harbors most of the genetic variability found within the species. The genetic variation observed within S. diluvialis supports the occurrence of at least two separate hybridization events giving rise to S. diluvialis.     

Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis

In the past decade much attention has focused on the role that genetics can play in the formation of management strategies in conservation. Here, we describe genetic diversity in the world''s largest lizard, the Komodo dragon (Varanus komodoensis), examining the evolutionary relationships and population genetic history of the four islands in south-east Indonesia, which form the vast majority of its range. We identify distinct genetic groups for conservation. The population on the island of Komodo shows by far the largest values of genetic divergence and is proposed that it should be a separate conservation management unit. Other populations, surviving either on small islands with substantially reduced genetic variability, or in isolated patches, are identified as particularly vulnerable to stochastic threats and habitat loss. Our results provide an example of how data defining intraspecific levels of genetic divergence can provide information to help management plans, ensure the maintenance of genetic variability across populations and identify evolutionary potential within endangered species.     

Microevolution in Solatopupa landsnails (Pulmonata Chondrinidae): genetic diversity and founder effects

Enzyme variability at 28 presumptive gene loci was studied, by standard starch gel electrophoresis, in 30 populations belonging to the five recognized species of the landsnail Solatopupa from its entire NW Mediterranean range.
Six genetically differentiated groups can be identified among the 30 populations sampled. These are distinguished by two to 19 diagnostic loci, different levels of genetic variability and populations genetics. They are also significantly different as far as the D values are considered. There is no evidence of gene flow among them. Genetically inferred groups correspond in four cases to morphologically distinguished species. In contrast, S. similis , as identified by morphological features, is likely to be a complex of at least two cryptic species.
Populations and species of Solatopupa are characterized by: high fixation of alternative alleles both within and between species; medium-lo-low levels of genie variation; heterozygote deficiency; sharp genetic differentiation among population within species; restricted gene flow; and high genetic distances. Genetic variability is partly associated with climatic factors related to moisture.
Both deterministic and stochastic processes may play a part in the genetic differentiation of Solatopupa snails. Founder events seem to be the main factor affecting the genetic structure of populations and perhaps also speciation. Solatopupa populations display many attributes of populations that may be expected to undergo speciation events involving reorganization of the whole genome after a founder event.     

THE INFLUENCE OF SELF-FERTILIZATION AND POPULATION DYNAMICS ON THE GENETIC STRUCTURE OF SUBDIVIDED POPULATIONS: A CASE STUDY USING MICROSATELLITE MARKERS IN THE FRESHWATER SNAIL BULINUS TRUNCATUS

The distribution of neutral genetic variability within and among sets of populations results from the combined actions of genetic drift, migration, extinction and recolonization processes, mutation, and the mating system. We here analyzed these factors in 38 populations of the hermaphroditic snail Bulinus truncatus. The sampling area covered a large part of the species range. The variability was analyzed using four polymorphic microsatellite loci. A very large number of alleles (up to 55) was found at the level of the whole study. Observed heterozygote deficiencies within populations are consistent with very high selfing rates, generally above 0.80, in all populations. These should depress the variability within populations, because of low effective size, genetic hitchhiking, and background selection, whatever the model of mutation assumed. However, that some populations exhibit much more variability than others suggests that historical demographic processes (e.g., population size variation, bottlenecks, or founding events) may play a significant role. A hierarchical analysis of the distribution of the variability across populations indicates a strong pattern of isolation by distance, whatever the geographical scale considered. Our analysis also illustrates how the mutation rate may affect population differentiation, as different mutation rates result in different levels of homoplasy at microsatellite loci. The effects of both genetic drift and gene flow vary with the temporal and spatial scales considered in B. truncatus populations.     

Fertilization and defoliation frequency affect genetic diversity of Festuca pratensis Huds. in permanent grasslands

Permanent pastures and meadows are species-rich vegetation systems that play an important role in the ecology and agriculture of temperate climates. Intensive management reduces species diversity and may also influence the genetic diversity within individual species and populations. The objective of this study was to assess genetic variability of meadow fescue, an important component of species-rich grasslands, and to determine whether fertilization and defoliation frequency influence genetic variability within natural populations. Genetic diversity of six natural populations and three cultivars of Festuca pratensis was investigated using randomly amplified polymorphic DNA (RAPD) markers and agronomic traits. Samples of natural populations were taken from two unrelated long-term experiments, where treatments had been applied for 11–38 years. RAPD analysis detected a clear genetic distinction of the cultivars from the natural populations. Genetic variability within cultivars was lower than within natural populations. Analysis of molecular variance ( AMOVA ) showed a significant effect of management on genetic variability. Fertilization and frequent defoliation led to a reduction in genetic variability within natural populations. Analysis of agronomic traits was only partially congruent with the results of RAPD analysis. This study shows that significant genetic variability exists within cultivars and natural populations of Festuca pratensis and can be reduced by intensive management.     

The importance of control populations for the identification and management of genetic diversity

A fundamental criterion for recognizing species or populations as potentially endangered is the presence/absence of genetic diversity. However, the lack of control populations in many studies of natural systems deprives one from unambiguous criteria for evaluating the genetic effects of small population size and its potential effects on fitness. In this study, I present an example of how the lack of adequate controls may lead to erroneous conclusions for understanding the role that population size may play in the preservation of genetic diversity and fitness of natural populations. The genetic analysis of a population of greater prairie chickens from Illinois, USA, between two time periods (1974–1987 and 1988–1993) in which the studied population experienced a substantial reduction in size and fitness showed no apparent associations between population size and genetic diversity. However, genetic analysis of museum specimens from early this century indicated that Illinois prairie chickens had originally higher levels of genetic diversity, which suggest the Illinois population was already bottlenecked by the 1970s. This study emphasizes the importance of using historical controls to evaluate the temporal dynamics of genetic variability in natural populations. The large number of museum collections worldwide may provide a valuable source of genetic information from past populations, particularly in species currently endangered as a result of human activities. This revised version was published online in July 2006 with corrections to the Cover Date.     

Ecological significance of individual variability in copepod bioenergetics

High interstage variability in body length and mass, reproductive state, and metabolic activity is characteristic of copepod populations from the Barents Sea and coastal waters in Sweden and Norway. The dry weight of a given copepodite stage, sampled at a given time from a homogeneous water mass, may vary by a factor of 4–5 between extreme individuals, protein and particularly lipid content being even more variable. Similarly, high variability in gut fullness and grazing rate within defined copepodite stages typically occurs at all times of the year, both when measured as in situ rate or experimentally determined rate, using homogeneous food suspensions. In accordance with this, maturation state (measured as length of gonads) and spawning (measured as rate of egg production over 24 h) are highly variable factors at the individual level. Since all these factors also influence the metabolic rate of the animals the respiratory rate (measured as ETS activity) of comparable individuals may vary by a factor of 5 or more. The results indicate that high individual variability in size and activity parameters is universal. This can not be explained by existing models of feeding behaviour, growth and development, and calls for new models, in which the nutritional history of the individual may play an important role.     

Perforated synapses and plasticity

Against a background of existing models relating perforated synapses to synaptic plasticity, the numerical density and frequency of perforated synapses in rat neocortex have been assessed from 1 d to 22 mo of age using the disector procedure, and changes in their morphology were assessed using 3-D computer reconstructions. The data point toward perforated and nonperforated synapses being separate synaptic populations from early in development, and with perforated synapses playing a part in the maintenance of neuronal postsynaptic density surface area from mid-adulthood onwards. This suggests that they play a crucial role in synaptic plasticity, although its nature may be different from that postulated by most recent workers.     

The Influence of Translocation Strategy and Management Practices on the Genetic Variability of a Reestablished Elk (Cervus elaphus) Population

Reintroduction of terrestrial vertebrates with the goal of ecosystem restoration typically establishes small and isolated populations that may experience reduced genetic variability due to founder effects and genetic drift. Understanding the genetic structure of these populations and maintaining adequate genetic diversity is important for long‐term restoration success. We quantified genetic variability at six microsatellite loci for a reintroduced population of Cervus elaphus (elk) restored to the tallgrass prairie ecosystem of northeastern Kansas. Allelic richness, observed and expected heterozygosity were intermediate to levels reported in other North American elk populations. Current levels of genetic variability in restored North American elk populations were not well explained by founding population size, number of founding populations, or number of years since the last translocation. Simulation results suggest that the retention of genetic variability in isolated populations is strongly influenced by mating system while also being impacted by temporal variability in population size and population growth rate. Our results have implications for understanding how translocation strategies and post‐reintroduction management may influence genetic variability in restored populations.     

Common Factors in Biofeedback Administered by Psychotherapists

Common factors are nonspecific therapeutic elements common across different varieties of psychotherapy. In a recent study, 68 expert psychotherapy researchers with a variety of allegiances collectively rated biofeedback as being negatively associated with many common factors (Tschacher et al. in Clin Psychol Psychother 21(1):82–96, 2014), including the therapeutic alliance. However, it seems implausible that biofeedback could benefit so many people while being incompatible with the therapeutic alliance and other common factors. The present study investigated the experiences of biofeedback clients who participated in a brief heart rate variability biofeedback protocol in order to explore the potential roles of common factors in biofeedback. The results of this study offer preliminary evidence that many common factors—including therapeutic alliance, self-efficacy expectation, mastery experiences, provision of explanatory scheme, mindfulness, and even cognitive restructuring—may play a role in biofeedback outcomes. Future research on this topic should include mediation and moderation models investigating the role of specific common factors on outcome and process studies to help determine what clinician behaviors are most helpful. Deeper investigation of common factors in biofeedback may benefit future biofeedback research and practice and address the concerns of colleagues outside of the biofeedback community who believe that biofeedback is at odds with common factors.

     

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

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

Allelic diversity at the Mhc-DQA locus of woodmouse populations (Apodemus sylvaticus) present in the islands and mainland of the northern Mediterranean

Aim Polymorphism at neutral markers and at MHC loci in rodent populations living on islands is generally low. The main genetic factors that may contribute to a reduced level of genetic variability are genetic drift, reduced gene flow and founder events. We investigated the pattern of polymorphism at the second exon of the Mhc‐DQA gene in island populations of Apodemus sylvaticus and in their mainland counterparts to investigate the pattern of MHC polymorphism in a phylogeographical context and to assess the impact of insularity on diversity at this locus. Location Eight north Mediterranean populations of Apodemus sylvaticus were studied, including five island populations (Majorca, Minorca, Porquerolles, Port‐Cros and Sicily) and three mainland populations. Methods cDNA sequencing and nucleotide sequences analyses. Synonymous and non‐synonymous substitutions were examined at the PBR and non‐PBR sites. The DQA allelic distribution in populations was compared with the woodmouse phylogeography. Results This study presents novel DQA alleles. High polymorphism of the DQA locus is recorded in natural populations of A. sylvaticus with 13 alleles being widely distributed irrespective of the geographical origin and palaeoclimatic history of populations. The DQA locus does not show the expected pattern for non‐synonymous substitutions at the PBR sites. However, island populations show a weak loss of polymorphism in comparison with their mainland counterparts. Main conclusions The DQA locus in the woodmouse seems to be subject to weak selection and does not allow resolution of phylogeographical relationships among European woodmouse populations. The presence of at least three alleles in island populations and the maintenance of five alleles between the two European lineages over 1.5 Myr suggest that balancing selection may act within populations, and more precisely within island populations, to maintain genetic variability. This study shows that phylogeographical studies are a prerequisite for any genetic investigation of selected genes in natural populations.     

Extent of adaptation is not limited by unpredictability of the environment in laboratory populations of Escherichia coli

Environmental variability is on the rise in different parts of the earth, and the survival of many species depends on how well they cope with these fluctuations. Our current understanding of how organisms adapt to unpredictably fluctuating environments is almost entirely based on studies that investigate fluctuations among different values of a single environmental stressor such as temperature or pH . How would unpredictability affect adaptation when the environment fluctuates between qualitatively very different kinds of stresses? To answer this question, we subjected laboratory populations of Escherichia coli to selection over ~ 260 generations. The populations faced predictable and unpredictable environmental fluctuations across qualitatively different selection environments, namely, salt and acidic pH . We show that predictability of environmental fluctuations does not play a role in determining the extent of adaptation, although the extent of ancestral adaptation to the chosen selection environments is of key importance.     

Somatic variation in living, wild ring-tailed lemurs (Lemur catta)

While understanding somatic variability among wild primates can provide insight into natural patterns of developmental plasticity, published data for living populations are rare. Here we provide such information for two distinct wild populations of Lemur catta. Variants observed include microtia, athelia, and female virilization. Dental variants observed include individuals with supernumerary teeth, rotated teeth, maxillary incisor agenesis, and severe malocclusion. There was a sex bias in incisor agenesis, with 5 of 7 examples (71%) found in males. The frequency of dental variants in our sample is lower than that seen in many other lemuriformes, as well as other primates. This may be a product of their less derived dental formula and/or their relatively fast dental development. Amassing such data is a critical first step to assess if wild primate populations are exhibiting normal variability or are being affected by potential inbreeding and/or environmental effects.     

Diseases of Mites

An overview is given of studies on diseases of mites. Knowledge of diseases of mites is still fragmentary but in recent years more attention has been paid to acaropathogens, often because of the economic importance of many mite species. Most research on mite pathogens concerns studies on fungal pathogens of eriophyoids and spider mites especially. These fungi often play an important role in the regulation of natural mite populations and are sometimes able to decimate populations of phytophagous mites. Studies are being conducted to develop some of these fungi as commercial acaricides.Virus diseases are known in only a few mites, namely, the citrus red mite and the European red mite. In both cases, non-occluded viruses play an important role in the regulation of mite populations in citrus and peach orchards, respectively, but application of these viruses as biological control agents does not seem feasible. A putative iridovirus has been observed in association with Varroa mites in moribund honeybee colonies. The virus is probably also pathogenic for honeybees and may be transmitted to them through this parasitic mite.Few bacteria have been reported as pathogens of the Acari but in recent years research has been concentrated on intracellular organisms such as Wolbachia that may cause distorted sex ratios in offspring and incompatibility between populations. The role of these organisms in natural populations of spider mites is in particular discussed. The effect of Bacillus thuringiensis on mites is also treated in this review, although its mode of action in arthropods is mainly due to the presence of toxins and it is, therefore, not considered to be a pathogen in the true sense of the word.Microsporidia have been observed in several mite species especially in oribatid mites, although other groups of mites may also be affected. In recent years, Microsporidia infections in Phytoseiidae have received considerable attention, as they are often found in mass rearings of beneficial arthropods. They affect the efficacy of these predators as biological control agent of insect and mite pests. Microsporidia do not seem to have potential for biological control of mites.     

Genetic Variation Within and Among Populations of Rhodiola alsia (Crassulaceae) Native to the Tibetan Plateau as Detected by ISSR Markers

Genetic variation of 10 Rhodiola alsia (Crassulaceae) populations from the Qinghai–Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai–Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible.     

Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility

Variations in gene expression level might lead to phenotypic diversity across individuals or populations. Although many human genes are found to have differential mRNA levels between populations, the extent of gene expression that could vary within and between populations largely remains elusive. To investigate the dynamic range of gene expression, we analyzed the expression variability of ∼18, 000 human genes across individuals within HapMap populations. Although ∼20% of human genes show differentiated mRNA levels between populations, our results show that expression variability of most human genes in one population is not significantly deviant from another population, except for a small fraction that do show substantially higher expression variability in a particular population. By associating expression variability with sequence polymorphism, intriguingly, we found SNPs in the untranslated regions (5′ and 3′UTRs) of these variable genes show consistently elevated population heterozygosity. We performed differential expression analysis on a genome-wide scale, and found substantially reduced expression variability for a large number of genes, prohibiting them from being differentially expressed between populations. Functional analysis revealed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling in HIV-1 infection, and for HIV-interacting proteins that control viral entry, replication, and propagation. This observation combined with the finding that known human HIV host factors show substantially elevated expression variability, collectively suggest that gene expression variability might explain differential HIV susceptibility across individuals.     

Complex social behaviour can select for variability in visual features: a case study in Polistes wasps

The ability to recognize individuals is common in animals; however, we know little about why the phenotypic variability necessary for individual recognition has evolved in some animals but not others. One possibility is that natural selection favours variability in some social contexts but not in others. Polistes fuscatus wasps have variable facial and abdominal markings used for individual recognition within their complex societies. Here, I explore whether social behaviour can select for variability by examining the relationship between social behaviour and variability in visual features (marking variability) across social wasp taxa. Analysis using a concentrated changes test demonstrates that marking variability is significantly associated with nesting strategy. Species with flexible nest-founding strategies have highly variable markings, whereas species without flexible nest-founding strategies have low marking variability. These results suggest that: (i) individual recognition may be widespread in the social wasps, and (ii) natural selection may play a role in the origin and maintenance of the variable distinctive markings. Theoretical and empirical evidence suggests that species with flexible nesting strategies have reproductive transactions, a type of complex social behaviour predicted to require individual recognition. Therefore, the reproductive transactions of flexible species may select for highly variable individuals who are easy to identify as individuals. Further, selection for distinctiveness may provide an alternative explanation for the evolution of phenotypic diversity.     

Influence of hydrologic attributes on brown trout recruitment in low-latitude range margins

Factors controlling brown trout Salmo trutta recruitment in Mediterranean areas are largely unknown, despite the relevance this may have for fisheries management. The effect of hydrological variability on survival of young brown trout was studied during seven consecutive years in five resident populations from the southern range of the species distribution. Recruit density at the end of summer varied markedly among year-classes and rivers during the study period. Previous work showed that egg density the previous fall did not account for more than 50% of the observed variation in recruitment density. Thus, we expected that climatic patterns, as determinants of discharge and water temperature, would play a role in the control of young trout abundance. We tested this by analyzing the effects of flow variation and predictability on young trout survival during the spawning to emergence and the summer drought periods. Both hatching and emergence times and length of hatching and emergence periods were similar between years within each river but varied considerably among populations, due to differences in water temperature. Interannual variation in flow attributes during spawning to emergence and summer drought affected juvenile survival in all populations, once the effect of endogenous factors was removed. Survival rate was significantly related to the timing, magnitude and duration of extreme water conditions, and to the rate of change in discharge during hatching and emergence times in most rivers. The magnitude and duration of low flows during summer drought appeared to be a critical factor for survival of young trout. Our findings suggest that density-independent factors, i.e., hydrological variability, play a central role in the population dynamics of brown trout in populations from low-latitude range margins. Reported effects of hydrologic attributes on trout survival are likely to be increasingly important if, as predicted, climate change leads to greater extremes and variability of flow regimes.