Striking differentiation of sub-populations within a genetically homogeneous isolate (Ogliastra) in Sardinia as revealed by mtDNA analysis

Since the reduced genetic diversity found in isolates should simplify the study of complex traits, analyses of patterns of homogeneity within populations are of particular interest. We analysed the mtDNA haplogroups and hypervariable segment I (HVS-I) sequences of 475 individuals from a geographically restricted and isolated area (Ogliastra) within Sardinia, comprehending 175 random samples from 20 out of 23 villages. The remaining 300 subjects were chosen from the other three villages, Talana, Urzulei and Perdasdefogu, by sampling all maternal lineages. A comparison with other European populations reveals that Ogliastra ranks among the most genetically homogenous population and that it has been small and isolated throughout its history. The lack of variation and the high genetic homogeneity indicate that an important founder event and a demographic expansion took place during the Neolithic (~ 7,700 years before present) in Ogliastra's mtDNA gene pool. We present highly resolved phylogenetic networks for Ogliastra and for the three sub-isolates. MtDNA differentiation in the sub-populations versus Ogliastra is revealed by a strong demarcation in their genetic pools due to distinctive founder effects and genetic drift. We found that genetic homogeneity strictly depends on a scale factor in population size and on sampling methodology. The outstanding homogeneity and the reduced female gene pool observed in Ogliastra, in the European context, hide an extremely marked differentiation in sub-isolates originated from the same archaic population. Although Ogliastra can be considered a genetically homogeneous isolate, small villages' divergent genetic histories underline the importance of more systematic analysis of DNA variation between and within populations.C. Fraumene and E. Petretto contributed equally to this work     

On Nonrandom Mating Systems for Attaining Hardy-Weinberg Equilibrium

LI (1988) showed that random mating is a sufficient, not a necessary condition for the Hardy-Weinberg principle. A nonrandom mating population that behaves like a random mating population is thus called a ‘pseudo-random mating population’ by him. The pseudo-random mating system studied by him has been focused on those populations in which the parental generation is in Hardy-Weinberg proportions. In other words, the mating type frequency deviations from random mating for each parental genotype add up to zero. In this article these restrictions are relaxed and new pseudo-random mating systems that immediately yield Hardy-Weinberg offspring are also obtained. This is possible because reciprocal crosses have identical segregation probabilities for an autosomal locus, and the manipulation of the combined frequency of reciprocal crosses does not change the gene frequency of the population. A comparison of these new patterns with that of Li is given in the Discussion.     

Rabies emergence among foxes in Turkey

Sixteen rabies isolates recently collected from mainland Turkey and two isolates held within a British archive were used to form a representative cohort from a range of vectors, and were analyzed to identify potential causes for an increase of rabies within the fox (Vulpes vulpes) population in Turkey. Each isolate was characterized by sequence analysis of the nucleoprotein gene and compared phylogenetically to the cohort, to isolates from neighboring countries and to isolates from continental Europe and Russia. From this analysis the isolates could be divided into three groups associated with geographic location. This included a western group, an eastern group, and one isolate that did not group with any other Turkish isolate. This observation was also found using the heteroduplex mobility assay as an alternative method for typing rabies virus isolates. Further comparison with isolates from neighboring countries suggests that this isolate was related to viruses present in Georgia and could represent a recent import to Turkey from that country. Within the two larger groups, sequence data were obtained from both infected dogs and foxes suggesting that there has been transmission of virus between these two species. The direction of transmission could not be identified by the phylogenetic analysis, although absence of rabies within the fox population in previous years suggests that this could represent a recent spillover from the domestic dog to the fox.     

Modes of speciation and the lifespans of species under neutrality: a response to the comment of Robert E. Ricklefs

Ricklefs (2003) has presented a thoughtful critique of the two modes of speciation discussed in my recent book ( Hubbell 2001a ). His main point is that under point mutation speciation, a plethora of species is produced with extremely short lifespans, whereas under random fission speciation, lifespans are too long, particularly in large metacommunities. The issue is easily resolved if one regards point mutation speciation and random fission speciation as the theoretical extremes of a speciation continuum. The mean lifespan of a species in the theory depends upon the size of the species population at its origination. If initial population sizes are fairly small, but not as small as the extreme of individual-founded lineages as under point mutation, then intermediate distributions of species lifespans are obtained. To examine this further, I consider a third model of speciation that I call "peripheral isolate speciation." There should be a signature of peripheral isolate speciation in the distribution of metacommunity relative species abundance, just as there is in the case of point mutation speciation and random fission speciation. Other points made by Ricklefs and several others are addressed in the body of the text.     

Searching for a Needle in a Haystack: Evaluating Survey Methods for Non-indigenous Plant Species

The control and management of non-indigenous plant species (NIS) can be conceptually divided into three phases: inventory/survey, monitoring and management. Here we focus on phase one, determining which species are present and where they are located within the environment. Sampling for NIS is inherently time-consuming and thus costly. Many management areas are large and therefore can only be surveyed (partial observation of the total area by sampling) and not inventoried (total observation of area). Survey data should reflect the spatial distribution of the target species populations over the landscape. Such data can then be used in combination with environmental data, to create probability maps of target species occurrence for the entire area of interest. We used a GIS model to evaluate seven different survey methods for consistency and reliability of intersecting NIS species’ patches and producing samples which reflect the spatial distribution of the population, and which can be performed in a cost and time-efficient manner. The GIS model was developed to create NIS populations which were then sampled using the different survey methods, and the results recorded. To improve the applicability of the model, four patch sizes and levels of occurrence were used, along with random and weighted distribution patterns in relation to patch proximity to roads and trails. Grid and random points, and targeted (stratified continuous) transects (starting on a road or trail (rights of way (RoW)) and finishing 2 km from any RoW) methods provided the most consistent samples of the population. Logistically, point methods required an unrealistic distance and time commitment in comparison with transect methods. The importance of collecting information on the size of NIS patches was demonstrated as more small patches were intersected than larger ones when the area infested was held constant. Thus, if frequency of patches is used to explain the results of a survey then comparisons between species and methods are difficult to interpret thus leading to erroneous conclusions. However, use of percentage of area infested estimates provides for easier comparison between species and sample methods. The targeted transect method provided the most reliable, efficient and consistent sample with the expected spatial distribution.     

Genetic stability of the D1Z2 region: implications for DNA genotyping and paternity testing.

The aim of the present study was to examine a single locus variable number tandem repeat for the purpose of DNA genotyping ("fingerprinting"). DNAs of 175 individuals from five ethnic groups (Black, Chinese, Japanese, Caucasian, and Melanesian) were analyzed. Restriction fragment length polymorphic analysis of random individuals revealed individual specific DNA patterns in all but one group. Among 20 Melanesian inhabitants of the Vanuatu islands in the southwest Pacific, three individuals were found to share a common pattern. This island population represents a "genetic isolate" and illustrates the importance of carrying out population studies on individual ethnic groups of interest. The complexity and the genetic stability of the D1Z2 region as revealed by the probe hMF1 make it an excellent candidate for DNA genotyping in paternity testing as 101 Caucasian individuals each had unique patterns for PstI and SinI digests.     

Mortality rate in the capital city of Warsaw in the eighties

Percentage of the elderly is higher in the Warsaw metropolitan area than that in other parts of Poland. This difference became more pronounced in the eighties. An analysis has shown that considering changes in the population age structure overall mortality rate in the Warsaw metropolitan area tended to decrease. It resulted from the decrease in mortality rate in the youngest (under 30 years) and the oldest population groups (over 74 years). An increase in mortality rate was noted in some subgroups of middle age and an advanced age (up to 74 years). It did not change the general trend, i.e. decrease in overall mortality rate. Mortality rate of males inhabiting Warsaw metropolitan area was lower in nearly all age groups in comparison with indices for the whole country. The same was seen in the groups of the youngest and oldest women. It may be assumed that health conditions favor men over women inhabiting Warsaw metropolitan area in comparison with the values for the whole country.     

Inbreeding avoidance in an isolated indigenous Zapotec community in the valley of Oaxaca, southern Mexico

We analyzed inbreeding using surname isonymy in an indigenous genetic isolate. The subjects were residents of a rural Zapotec-speaking community in the valley of Oaxaca, southern Mexico. The community can be classified as a genetic isolate with an average gene flow of < or = 3% per generation. Surnames were collected for individuals in each household in pedigree form using the culturally traditional patronym-matronym naming. Estimation of inbreeding from surname isonymy is facilitated by the traditional patronym-matronym name assignment among indigenous Mexican populations. A total of 2,149 individuals had valid surname patronym-matronym pairings, including 484 deceased ancestors. Surname isonymy analysis methods were used to estimate total inbreeding and to segregate it into random and nonrandom components. The surname isonymy coefficient computed from 119 isonymous surname pairings (119/2,149) was 0.0554. The estimated inbreeding coefficient from surname isonymy was 0.0138 (0.0554/4). The random and nonrandom components of inbreeding were F(r) = 0.0221 and F(n) = -0.0091, respectively. The results suggest that consanguinity is culturally avoided. Nonrandom inbreeding decreased total inbreeding by about 41%. Total estimated inbreeding by surname isonymy was 0.0138, which is similar to inbreeding estimated from a sample of pedigrees, 0.01. Socially prescribed inbreeding avoidance substantially lowered total F through negative nonrandom inbreeding. Even in the situation of genetic isolation and small effective population size (N(e)), estimated inbreeding is lower than may have otherwise occurred if inbreeding were only random. However, among the poorest individuals, socially prescribed jural rules for inbreeding avoidance failed to operate. Thus the preponderance of inbreeding appears to occur among the poor, economically disadvantaged in the community.     

Biophysical aspects of microsphere engulfment by human neutrophils.

A quantitative investigation into the mechanism of neutrophil phagocytosis of opsonized microspheres possessing well defined dimensions was undertaken. Three aspects were documented: membrane conservation, cell adhesion to the spheres, and active cell cytoplasmic projection around the microspheres. The physical act of internalizing a particle by a cell involves a reduction in its plasma membrane area and an increase in its volume. As a consequence, a cell can internalize only a finite number of particles. A store of membrane area exists on cytoplasmic granules and may be recruited during phagocytosis. Previous measurements of neutrophil membrane area and volume served as a basis for estimates of the maximum number of internalized microspheres. A comparison with experimental prediction based on membrane conservation and degranulation agrees within 10% for a range of microsphere diameters, from 0.5 to 8 microns. This suggests that the limitation for additional particle uptake in the population of engorged neutrophils is the lack of excess plasma membrane area. In a random population of neutrophils, there was a sub-group, approximately 40%, which could no longer phagocytose before depleting their membrane stores. Several aspects of the engulfment process were investigated to elucidate the cause of this phagocytosis deficiency. It could be shown by single cell observation that these cases were associated with a lack of pseudopod projection, although adhesion was still evident between the cell membrane and the microspheres.     

MUTATIONS DO NOT ACCUMULATE IN ASEXUAL ISOLATES CAPABLE OF GROWTH AND EXTINCTION–MULLER'S RATCHET RE-EXAMINED

The rarity of exclusively asexual species is often attributed to Muller's Ratchet. This supposes that because asexual populations cannot recreate individuals with fewer mutations than the currently least-loaded line, mutations will accumulate in such isolates. However, because the computer models that corroborate this theory have assumed isolate immortality, it is possible that mutations will accumulate only if there is “soft” selection acting on relative, rather than absolute, fitness. Here we, therefore, describe several models in which 200 asexual organisms randomly selected from an infinite population in genetic equilibrium under “hard” selection (acting through absolute fitness), were followed for 100 generations. When there were no limits to the fluctuations in population size, the deterministic distribution of mutations per individual was maintained for 100 (as well as for 200) generations. If population growth was limited by a proportional decrease in fertility of the whole isolate, then the isolates tended to become extinct. The rate of extinction was inversely related to maximum isolate size. When resource limitation at maximum population size had an extra deleterious effect on mutants, then isolates shed the mutant classes. Mutations accumulated (ad inifinitum) in immortal isolates whose population numbers were kept constant by proportionately increasing or decreasing each class's size whenever isolate size ≠ 200. Muller's Ratchet, therefore, operates only when mutations affect the outcome of intraspecific contests, but not the organisms' intrinsic ability to survive in the ecosystem.     

Allele-sharing methods for estimation of population size

Genetic data are becoming increasingly important in ecology and conservation biology. This article presents a novel method for estimating population size from DNA profiles obtained from a random sample of individuals. The underlying idea is that the degree of biological relationship between individuals in the sample reflects the size of the population and that DNA profiles provide information about relatedness. A pseudolikelihood approach is taken, involving pairwise comparison of individuals. The main field of applications is seen to be catch data, and as an example, the method is applied to DNA profiles (10 microsatellite loci) from 334 North Atlantic minke whales. It is concluded that the sample size is too small for the method to give useful results. The question about the required sample size is investigated by simulation.     

Whole-Genome Sequence of Livestock-Associated ST398 Methicillin-Resistant Staphylococcus aureus Isolated from Humans in Canada

Despite reports of high colonization rates of ST398 livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) among pigs and pig farmers, the incidence of LA-MRSA infection in the general population in Canada appears to be rare in comparison to that in some European countries. In this study, the complete genome sequence of a Canadian representative LA-MRSA isolate (08BA02176) from a human postoperative surgical site infection was acquired and compared to the sequenced genome of an LA-MRSA isolate (S0385) from Europe to identify genetic traits that may explain differences in the success of these particular strains in some locales.     

Salmonella Amager, Campylobacter jejuni, and urease-positive thermophilic Campylobacter found in free-flying peregrine falcons (Falco peregrinus) in Sweden

Rare species with small population sizes are vulnerable to perturbations such as disease, inbreeding, or random events. The threat arising from microbial pathogens could be large and other species could act as reservoirs for pathogens. We report finding three enteric bacterial species, Salmonella Amager, Campylobacter jejuni, and urease-positive thermophilic Campylobacter, in nestling free-flying peregrine falcons (Falco peregrinus) in Sweden in 2000. Campylobacter jejuni isolates exhibited marked genetic similarities to an isolate from a human, providing a possible association between a human-associated strain of this bacterium and peregrine falcons.     

Genetic variation and heavy metal tolerance in the ectomycorrhizal basidiomycete Suillus luteus

Twenty-one isolates of the ectomycorrhizal fungus Suillus luteus were screened for their tolerance to the heavy metals Zn, Cd, Cu and Ni, measured as inhibition of radial growth and biomass production. Two populations from even-aged pine stands were investigated: 10 isolates were obtained from an area polluted with high levels of Zn, Cd and Cu, and 11 isolates were obtained from a control population located in a nearby unpolluted area. RFLP patterns of the internal transcribed spacer region of the isolates confirmed the morphological identification of the carpophores. All isolates were maintained on basic medium without elevated metals to avoid phenotypically acquired metal tolerance. The in vitro Zn and Cd tolerance of the S. luteus isolates from the polluted habitat were significantly higher than the tolerances measured in the isolates from the nonpolluted site. This observation suggests that the elevated soil metal concentrations might be responsible for the evolution of adaptive Zn and Cd tolerance. Tolerance was maintained in an isolate not exposed to elevated metals for 3 yr. The two S. luteus populations did not differ in tolerance to Cu and Ni. The mechanisms for the adaptive Zn and Cd tolerance are not identical as there was no correlation between response to the two metals; the most Zn-tolerant isolate was the most sensitive for Cd in the metal-tolerant population. Zinc did not accumulate in basidiocarp tissue, whereas Cd levels in basidiocarps were significantly higher in the population on the polluted site. Inter-simple sequence-repeat fingerprints showed that 90% of the isolates were from different individuals. The genetic variation in the population from the unpolluted site was considerably larger than that observed at the polluted site.     

Laser Capture Microdissection - A Demonstration of the Isolation of Individual Dopamine Neurons and the Entire Ventral Tegmental Area

Laser capture microdissection (LCM) is used to isolate a concentrated population of individual cells or precise anatomical regions of tissue from tissue sections on a microscope slide. When combined with immunohistochemistry, LCM can be used to isolate individual cells types based on a specific protein marker. Here, the LCM technique is described for collecting a specific population of dopamine neurons directly labeled with tyrosine hydroxylase immunohistochemistry and for isolation of the dopamine neuron containing region of the ventral tegmental area using indirect tyrosine hydroxylase immunohistochemistry on a section adjacent to those used for LCM. An infrared (IR) capture laser is used to both dissect individual neurons as well as the ventral tegmental area off glass slides and onto an LCM cap for analysis. Complete dehydration of the tissue with 100% ethanol and xylene is critical. The combination of the IR capture laser and the ultraviolet (UV) cutting laser is used to isolate individual dopamine neurons or the ventral tegmental area when using PEN membrane slides. A PEN membrane slide has significant advantages over a glass slide as it offers better consistency in capturing and collecting cells, is faster collecting large pieces of tissue, is less reliant on dehydration and results in complete removal of the tissue from the slide. Although removal of large areas of tissue from a glass slide is feasible, it is considerably more time consuming and frequently leaves some residual tissue behind. Data shown here demonstrate that RNA of sufficient quantity and quality can be obtained using these procedures for quantitative PCR measurements. Although RNA and DNA are the most commonly isolated molecules from tissue and cells collected with LCM, isolation and measurement of microRNA, protein and epigenetic changes in DNA can also benefit from the enhanced anatomical and cellular resolution obtained using LCM.     

A comparison of biological performances among a laboratory-isolated population and two wild populations of Moniliformis moniliformis

Divergence of biological performance of a laboratory-reared population of Moniliformis moniliformis (Acanthocephala) was investigated after 31 yr, or approximately 60 generations, of genetic isolation. An isolate of the laboratory-reared population and isolates of 2 wild populations were used to begin 3 independent life cycles that were maintained for 1 generation for interbreeding and life history trait comparison. Both wild population isolates represented populations with open gene flow. One wild population isolate represented a present-day sample of descendants of the parent population of the laboratory isolate. All 3 populations hybridized, and egg production occurred in all mixed-sex pairs of different populations. The 3 populations did not differ significantly in prepatent period, mean daily egg production, or establishment within the definitive host Rattus norvegicus. The 3 populations varied in patent period, but the laboratory-isolated worms differed from the 2 wild population isolates no more than they did from each other. A positive correlation between mean daily egg production and duration of patent period resulted in different cumulative egg productions. A 31-yr period of isolation did not produce greater divergence in a laboratory population of M. moniliformis than occurs between wild populations with respect to the biological parameters measured.     

A Genomewide Screen for Schizophrenia Genes in an Isolated Finnish Subpopulation, Suggesting Multiple Susceptibility Loci

Schizophrenia is a severe mental disorder affecting approximately 1% of the world's population. Here, we report the results from a three-stage genomewide screen performed in a study sample from an internal isolate of Finland. An effort was made to identify genes predisposing for schizophrenia that are potentially enriched in this isolate, which has an exceptionally high lifetime risk for this trait. Ancestors of the local families with schizophrenia were traced back to the foundation of the population in the 17th century. This genealogical information was used as the basis for the study strategy, which involved screening for alleles shared among affected individuals originating from common ancestors. We found four chromosomal regions with markers revealing pairwise LOD scores>1.0: 1q32.2-q41 (Z(max)=3.82, dominant affecteds-only model), 4q31 (Z(max)=2. 74, dominant 90%-penetrance model), 9q21 (Z(max)=1.95, dominant 90%-penetrance model), and Xp11.4-p11.3 (Z(max)=2.01, recessive 90%-penetrance model). This finding suggests that there are several putative loci predisposing to schizophrenia, even in this isolate.     

Environmental drivers of habitat use by common bottlenose dolphins (Tursiops truncatus) in the Indian River Lagoon,Florida, USA

Anthropogenic impacts in estuarine systems can influence marine mammal habitat use, population dynamics, fitness, and mortality events. The objective was to examine habitat use among the resident common bottlenose dolphin (Tursiops truncatus) population inhabiting the Indian River Lagoon, Florida, and the influences of variation in environmental factors and prey availability in 2003–2015. We utilized photo-identification surveys, stratified random samples of prey, and environmental variables collected monthly. Kernel density estimation was used to determine the magnitude-per-unit area of dolphins across the IRL by wet and dry seasons each year, the values were used as a response variable in classification and regression tree analyses with fish community and environmental variables as predictors. Spatial patterns in dolphin density in the IRL were associated with salinity and dissolved oxygen levels, which are in part associated with freshwater discharges of nutrient and algae laden waters from the region's storm water management system. These findings isolate locations of concern for management of dolphin habitat, and anthropogenic drivers of dolphin distributions requiring further research.     

Host range extension of <Emphasis Type="Italic">Cydia pomonella</Emphasis> granulovirus: adaptation to Oriental Fruit Moth, <Emphasis Type="Italic">Grapholita molesta</Emphasis>

Among various Cydia pomonella granulovirus (CpGV) isolates, the Mexican isolate (CpGV-M) has demonstrated a significant ability to reduce damage induced by the oriental fruit moth, Grapholita molesta (Busck) (=Cydia molesta) in peach crops. To obtain a more efficient virus for G. molesta control, an experimental virus population was constructed by mixing various CpGV isolates. This mixture was then selected for replication in a G. molesta laboratory colony. After 12 successive passages on this alternative host, the insecticidal efficacy of the virus population had improved. The concentration of virus occlusion bodies required to kill 90 % of neonate larvae was 450-fold lower than that of the original isolate mixture, and 120-fold lower than that of the CpGV-M isolate alone. Following adaptation to this alternative host, the efficacy against its natural host, the codling moth, C. pomonella, was conserved. This mixed isolate population can be produced on C. pomonella without loss of efficacy, which is useful from a commercial production perspective. This adapted virus isolate mixture is likely to prove more effective than individual component isolates at controlling G. molesta.     

Effects of clear-cutting on the composition of bacterial populations of northern spruce forest soil.

This paper concerns the microbiological part of an investigation, the goal of which is to describe the biological changes in coniferous forest soil upon clear-cutting in a northern (66 degrees 20'N) moraine area where reforestation after clear-cutting had been met with difficulty. The zoological part of the work has been published elsewhere. Clear-cut sites of increasing age (4, 7, and 13 years) were investigated and compared with a forest area where no cutting of timber had been done for 120 years. A total of 684 random isolates of heterotrophic bacteria from pooled samples of the sites investigated were passed through 36 biochemical tests. The data were condensed by the aid of factor analysis, and a comparison of the populations was based on squared Euclidean distances between population centroids in a seven-dimensional factor space. The most marked population changes followed a course in which frequencies of some population characteristics became increasingly different until 7 years after clear-cutting, with regression towards the control clearly evident after 13 years. Disturbances of shorter duration were also relatively common, with maximal changes observed in the 4-year samples, and with a complete recovery after 7 years. The mineral soil populations seemed to undergo greater changes than the humus populations. The most distinct changes believed to be due to clear-cutting were the short-term relative increase of organisms producing acid from sucrose and dissolving CaHPO4, and a long-term increase of lipolytic and caseolytic, rhamnose-negative organisms; both in the mineral soil layer. In the humus layer, a short-term increase of lipolytic and of rhamnose-positive organisms seemed to take place.