A Method for Detecting Population Genetic Structure in Diverse, High Gene-Flow Species

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and UST under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (5 Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements UST/FST, SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

Background The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. Results Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. Conclusion ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.

DOWNREGULATION OF PAX2 SUPPRESSES OVARIAN CANCER CELL GROWTH

PAX2 is one of nine PAX genes regulating tissue development and cellular differentiation in embryos. PAX2 promotes cell proliferation, oncogenic transformation, cell-lineage specification, migration, and survival. Unattenuated PAX2 has been found in several cancer types. We therefore sought to elucidate the role of PAX2 in ovarian carcinomas. We found that PAX2 was expressed in low-grade serous, clear cell, endometrioid and mucinous cell ovarian carcinomas, which are relatively chemoresistant compared to high grade serous ovarian carcinomas. Four ovarian cancer cell lines, RMUGL (mucinous), TOV21G (clear cell), MDAH-2774 (endometrioid) and IGROV1 (endometrioid), which express high-levels of PAX2, were used to study the function of PAX2. Lentiviral shRNAs targeting PAX2 were used to knock down PAX2 expression in these cell lines. Cellular proliferation and motility assays subsequently showed that PAX2 stable knockdown had slower growth and migration rates. Microarray gene expression profile analysis further identified genes that were affected by PAX2 including the tumor suppressor gene G0S2. Reverse phase protein array (RPPA) data showed that PAX2 knockdown affected several genes that are involved in apoptosis, which supports the fact that downregulation of PAX2 in PAX2-expressing ovarian cancer cells inhibits cell growth. We hypothesize that this growth inhibition is due to upregulation of the tumor suppressor gene G0S2 via induction of apoptosis. PAX2 represents a potential therapeutic target for chemoresistant PAX2-expressing ovarian carcinomas.

Helium transfer from water into quartz crystals: A new approach for porewater dating

Several important fundamental and applied problems require a quantification of slow rates of groundwater flow. To resolve these problems helium appears to be a promising tracer. In this contribution we discuss a new approach, which gives the helium inventory in a rock – pore water system by using the relevant mineral record, i.e., without extraction and investigation of the porewater samples. Some U- and Th-poor minerals such as quartz (quartz separates from Permo-Carboniferous Formation, sandstone–shale interlayering, Molasses Basin, Northern Switzerland, hereafter PCF, are used in this study) contain excessive helium having migrated into their internal helium-accessible volume (HAV) from the surrounding porewater [I.N. Tolstikhin, B.E. Lehmann, H.H. Loosli, A. Gautschi, Helium and argon isotopes in rocks, minerals and related groundwaters: a case study in Northern Switzerland, Geochim. Cosmochim. Acta 60 (1996) 1497–1514]. These volumes are estimated by using helium as a nano-size penetrating tool, i.e., by saturation of the minerals with helium under controlled pressure–temperature conditions and subsequent measurements of the helium-saturated concentrations. In the quartz separates HAV/total volume ratios vary from 0.017% to 0.16%; along with the measured initial (unsaturated) He concentration the HAV gives the internal helium pressure, the mean value obtained for 7 samples (25 sample aliquots) is P=0.45F0.15 atm (1 r). The product of helium pressure and solubility (7.35_10_3 cc STP He/cc H2O for the temperature and salinity of PCF aquifers reported in [F.J. Pearson, W. Balderer, H.H. Loosli, B.E. Lehmann, A. Matter, T. Peters, H. Schmassmann, A. Gautschi, Applied Isotope Hydrogeology–A Case Study in Northern Switzerland, Elsevier Amsterdam, 1991, 439 pp.]) is the mineral-derived He concentration in the respective porewater, CPW=0.0035F0.0017 cc He/cc H2O. This value is in full accord with measured He concentrations in PCF aquifers, CPCF, varying from 0.0045 to 0.0016 cc He/cc H2O. This agreement validates the proposed approach and also shows that the mineral–porewater helium–concentration equilibrium has been established. Indeed, estimates of the He-migration rates through our quartz samples show that in ~6000 years the internal pressure should equilibrate with He-concentration in related porewater of PCF, and this time interval is short compared to independent estimates [I.N. Tolstikhin, B.E. Lehmann, H.H. Loosli, A. Gautschi, Helium and argon isotopes in rocks, minerals and related groundwaters: a case study in Northern Switzerland, Geochim. Cosmochim. Acta 60 (1996) 1497–1514]. The helium inventory in the rock–porewater assemblage shows that helium abundance in pore waters is indeed important. In shale samples (with ~15% porosity) porewaters contain more helium than the host minerals altogether. Porewater heliumconcentration profiles, available from the mineral record, along with helium production rates are input parameters allowing model(s) of helium migration through a hydrological structure to be developed. Quite high helium concentrations in PCF porewaters imply slow removal mechanisms, which will be discussed elsewhere.

Central European vegetation response to abrupt climate change at 8.2 ka

Oxygen isotope records show a major climatic reversal at 8.2 ka in Greenland and Europe. Annually laminated sediments from two lakes in Switzerland and Germany were sampled contiguously to assess the response of European vegetation to climate change ca. 8.2 ka with time resolution and precision comparable to those of the Greenland ice cores. The pollen assemblages show pronounced and immediate responses (0–20 yr) of terrestrial vegetation to the climatic change at 8.2 ka. A sudden collapse of Corylus avellana (hazel) was accompanied by the rapid expansion of Pinus (pine), Betula (birch), and Tilia (linden), and by the invasion of Fagus silvatica (beech) and Abies alba (fir). Vegetational changes suggest that climatic cooling reduced drought stress, allowing more drought-sensitive and taller growing species to out-compete Corylus avellana by forming denser forest canopies. Climate cooling at 8.2 ka and the immediate reorganization of terrestrial ecosystems has gone unrecognized by previous pollen studies. On the basis of our data we conclude that the early Holocene high abundance of C. avellana in Europe was climatically caused, and we question the conventional opinion that postglacial expansions of F. silvatica and A. alba were controlled by low migration rates rather than by climate. The close connection between climatic change and vegetational response at a subcontinental scale implies that forecasted global warming may trigger rapid collapses, expansions, and invasions of tree species.

Sediment wave layer summary in ODP Site 172-1062

Abyssal mud waves (or fine-grained sediment waves) are often cited as evidence for deep current activity because subbottom profiles show that the wave form has migrated with time. The migration history of a fine-grained sediment wave on the Blake-Bahama Outer Ridge (ODP Site 1062) has been studied through the analysis of multiple ODP holes spaced across the wave. Additional information about wave migration patterns comes from 3.5-kHz records and watergun seismic profiles. These data suggest that wave migration has varied during the last not, vert, similar ~10 Myr, although the only sediments sampled are younger than 4.8 Ma. Seismic profiles suggest wave migration was initiated about 8-10 Ma, and wave migration was pronounced from about 5 Ma to about 1 Ma (with an episode of wave reorganization about 4.5 Ma). Analysis of ODP cores suggests that migration rates have been somewhat lower and more variable during the last 1 Myr. Intervals of no wave migration are observed for several time intervals and appear to characterize deglaciations, especially during the last 500 kyr. Comparisons between seismic profiles and the core record show that most of the seismic horizons correlate closely with time horizons, and thus that the seismic profiles give a reasonable representation of sediment wave migration. Models suggest that wave migration is more pronounced during periods of higher bottom current flow and less pronounced during periods of lower current flow. Thus the migration record is consistent with generally higher bottom flow speeds at this site prior to 1 Ma and lower bottom flow speeds after 1 Ma. The Mid-Pleistocene Transition from a dominant climatic periodicity of 40 kyr to a dominant climatic periodicity of 100 kyr starts at about this time, suggesting an overall reduction in bottom flow speed at this site coincident with changing climate patterns. These changes in flow speed could be related to changes in the depth of the Western Boundary Undercurrent as well as to changes in the speed of thermohaline circulation.

Occurrence of mammalia relicts at site Nörre-Lyngby

Investigations at a Late Weichselian freshwater basin in northwestern Jutland, Denmark, yielded a fairly rich assemblage of vertebrate remains, mostly bones and teeth of small mammals. The remains are primarily allochthonous and the bones have been subjected to different taphonomic pathways and agents. AMS 14C-dates on terrestrial organic remains provided ages of Middle to Late Allerød time. Identifications revealed the first fossil record in Scandinavia of Rana arvalis, Sorex minutus, Ochotona cf. pusilla, Microtus gregalis, Microtus oeconomus, and Sicista cf. betulinu. Spermophilus cf. major and Desmana moschata, previously found only once and twice respectively, were retrieved, and Sorex araneus and Arvicola terrestris were recovered for the first time beyond the Atlantic chronozone. Ecologically, the Nørre Lyngby small mammal fauna can be characterized by its very high and almost equal proportions of boreal forest and steppe elements followed by a relatively high proportion of tundra elements. The fossil species share a modern area of sympatry north of the Caspian Sea from the river Volga in the west to the southern and western slopes of the Urals. If, however, the large Allerød mammals are added, the fauna is without modern analogues. The Nørre Lyngby fauna can be seen as a last expansion of the North European glacial fauna. Provided that an absolute chronology and a differentiated sea-level curve for the area can be established, the Nørre Lyngby fauna could become important for studies in mammalian dispersal and migration rates.

Ligand occupancy of the alpha-V-beta3 integrin is necessary for smooth muscle cells to migrate in response to insulin-like growth factor.

Smooth muscle cells (SMCs) have been shown to migrate in response to insulin-like growth factor I (IGF-I). However, the mechanism mediating this response has not been determined. The migration rates of porcine and human vascular SMCs were assessed in a monolayer wounding assay. IGF-I and IGF-II induced increases of 141% and 97%, respectively, in the number of cells that migrated in 4 days. The presence of 0.2% fetal bovine serum in the culture medium was necessary for the IGFs to stimulate migration over uncoated plastic surfaces. However, if vitronectin was used as the substratum, IGF-I stimulated migration by 162% even in the absence of serum. To determine the role of integrins in mediating this migration, SMC surface proteins were labeled with 125I and immunoprecipitated with specific anti-integrin antibodies. Integrins containing alpha-V (vitronectin receptor), alpha5 (fibronectin receptor), and alpha3 (collagen/laminin receptor) subunits were the most abundant. IGF-I treatment caused a 73% reduction in alpha5-integrin subunit protein and a 25% increase in alpha-V subunit. More importantly, ligand binding of alpha-V-beta3 was increased by 2.4-fold. We therefore examined whether the function of the alpha-V-beta3 integrin was important for IGF-I-mediated migration. The disintegrin kistrin was shown by affinity crosslinking to specifically bind with high affinity to alpha-V-beta3 and not to alpha5-beta1 or other abundant integrins. The related disintegrin echistatin specifically inhibited 125I-labeled kistrin binding to alpha-V-beta3, while a structurally distinct disintegrin, decorsin, had 1000-fold lower affinity. The addition of increasing concentrations of either kistrin or echistatin inhibited IGF-I-induced migration, whereas decorsin had a minimal effect. The potency of these disintegrins in inhibiting IGF-I-induced migration paralleled their apparent affinity for the alpha-V integrin. Furthermore, an alpha-V-beta3 blocking antibody inhibited SMC migration by 80%. In summary, vitronectin receptor activation is a necessary component of IGF-I-mediated stimulation of smooth muscle migration, and alpha-V-beta3 integrin antagonists appear to be important reagents for modulating this process.

An investigation into effects of long-distance seed dispersal on organelle population genetic structure and colonization rate: a model analysis

A simulation-based modelling approach is used to examine the effects of stratified seed dispersal (representing the distribution of the majority of dispersal around the maternal parent and also rare long-distance dispersal) on the genetic structure of maternally inherited genomes and the colonization rate of expanding plant populations. The model is parameterized to approximate postglacial oak colonization in the UK, but is relevant to plant populations that exhibit stratified seed dispersal. The modelling approach considers the colonization of individual plants over a large area (three 500 km x 10 km rolled transects are used to approximate a 500 km x 300 km area). Our approach shows how the interaction of plant population dynamics with stratified dispersal can result in a spatially patchy haplotype structure. We show that while both colonization speeds and the resulting genetic structure are influenced by the characteristics of the dispersal kernel, they are robust to changes in the periodicity of long-distance events, provided the average number of long-distance dispersal events remains constant. We also consider the effects of additional physical and environmental mechanisms on plant colonization. Results show significant changes in genetic structure when the initial colonization of different haplotypes is staggered over time and when a barrier to colonization is introduced. Environmental influences on survivorship and fecundity affect both the genetic structure and the speed of colonization. The importance of these mechanisms in relation to the postglacial spread and genetic structure of oak in the UK is discussed.

Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations

Human social organization can deeply affect levels of genetic diversity. This fact implies that genetic information can be used to study social structures, which is the basis of ethnogenetics. Recently, methods have been developed to extract this information from genetic data gathered from subdivided populations that have gone through recent spatial expansions, which is typical of most human populations. Here, we perform a Bayesian analysis of mitochondrial and Y chromosome diversity in three matrilocal and three patrilocal groups from northern Thailand to infer the number of males and females arriving in these populations each generation and to estimate the age of their range expansion. We find that the number of male immigrants is 8 times smaller in patrilocal populations than in matrilocal populations, whereas women move 2.5 times more in patrilocal populations than in matrilocal populations. In addition to providing genetic quantification of sex-specific dispersal rates in human populations, we show that although men and women are exchanged at a similar rate between matrilocal populations, there are far fewer men than women moving into patrilocal populations. This finding is compatible with the hypothesis that men are strictly controlling male immigration and promoting female immigration in patrilocal populations and that immigration is much less regulated in matrilocal populations.

Phylogeography of the scarab beetle Antitrogus parvulus Britton (Coleoptera : Scarabaeidae) in south-eastern Queensland, Australia

This study surveys the population genetic structure of Childers canegrub, Antitrogus parvulus, to elucidate its population dynamics and gene flow. Antitrogus parvulus is a pest of sugarcane in the Bundaberg region and this knowledge can be used to optimise integrated pest management practices. Here, base-pair differences in the cytochrome oxidase II gene (COII) were used to characterise haplotypic diversity, infer levels of gene flow, and phylogenetic relationships of alleles and their phylogeographical structure. There were 28 unique haplotypes among the 70 sequenced individuals from the seven locations. All three variance components (among regions, among populations, within populations) are highly significant, with highest genetic diversity among regions and lowest among populations within regions. A positive correlation between migration rates and geographical distance and significant phylogeographical structure between four main geographical regions. The main implication of these findings for pest management is that if a grower can eliminate an existing infestation within a field, then reinvasion will be slow and further outbreaks within that field are unlikely to occur. The low dispersal ability of females also means that any resistance to insecticides that develops is likely to remain localised, but will rapidly become dominant within the affected population.

The genetic structure of Australasian green turtles (Chelonia mydas): exploring the geographical scale of genetic exchange

Ecological and genetic studies of marine turtles generally support the hypothesis of natal homing, but leave open the question of the geographical scale of genetic exchange and the capacity of turtles to shift breeding sites. Here we combine analyses of mitochondrial DNA (mtDNA) variation and recapture data to assess the geographical scale of individual breeding populations and the distribution of such populations through Australasia. We conducted multiscale assessments of mtDNA variation among 714 samples from 27 green turtle rookeries and of adult female dispersal among nesting sites in eastern Australia. Many of these rookeries are on shelves that were flooded by rising sea levels less than 10 000 years (c. 450 generations) ago. Analyses of sequence variation among the mtDNA control region revealed 25 haplotypes, and their frequency distributions indicated 17 genetically distinct breeding stocks (Management Units) consisting either of individual rookeries or groups of rookeries in general that are separated by more than 500 km. The population structure inferred from mtDNA was consistent with the scale of movements observed in long-term mark-recapture studies of east Australian rookeries. Phylogenetic analysis of the haplotypes revealed five clades with significant partitioning of sequence diversity (Phi = 68.4) between Pacific Ocean and Southeast Asian/Indian Ocean rookeries. Isolation by distance was indicated for rookeries separated by up to 2000 km but explained only 12% of the genetic structure. The emerging general picture is one of dynamic population structure influenced by the capacity of females to relocate among proximal breeding sites, although this may be conditional on large population sizes as existed historically across this region.

The morphology of spray-dried particles

Samples of Various industrial or pilot plant spray-dried materials were obtained from manufacturers together with details of drying conditions and feed concentrations. The samples were subjected to qualitative and semi-quantitative examination to identify structural and morphological features. The results were related to measured bulk physical properties and to drying conditions. Single particles were produced in a convective drying process Analogous to spray drying, in which different solids or mixtures of solids were dried from solutions, slurries or pastes as single suspended droplets. The localized chemical and physical structures were analysed and in some cases the retention of volatiles monitored. The results were related to experimental conditions, viz.; air temperature, initial solids concentration and the degree of feed aeration. Three distinct categories of particle morphology were identified, i.e.; crystalline, skin-forming and agglomerate. Each category is evidence of a characteristic drying behaviour which is dependent on initial solids concentration. the degree of feed aeration, and drying temperature. Powder flow ability, particle and bulk density, particle-size, particle friability, and the retention of volatiles bear a direct relationship to morphological structure. Morphologies of multicomponent mixtures were complex, but the respective migration rates of the solutes were dependent on drying temperature. Gas-film heat and SDSS transfer coefficients of single pure liquid droplets were also measured over a temperature range of 50•C to 200•C under forced convection. Balanced transfer rates were obtained attributed to droplet instability or oscillation within the airflow, demonstrated in associated work with single free-flight droplets. The results are of relevance to drier optimisation and to the optimisation of product characteristics, e.g.; particle strength and essential volatiles-retention, in convective drying.

(Table 1) Radiocarbon ages of samples taken from five sites in north-eastern European Russia

Aim: Concepts about patterns and rates of post-glacial tree population migration are changing as a result of the increasing amount of palaeobotanical information being provided by macroscopic plant remains. Here we combine macrofossil, pollen and stomata records from five sites in north-eastern European Russia and summarize the results for the late-glacial-early Holocene transition. The late-glacial-early Holocene transition encompasses the first indications of trees (tree-type Betula, Picea abies, Abies sibirica and Larix sibirica) and subsequent forest development. Considerable time-lags between the first macrobotanical and/or stomata finds of spruce (Picea abies) and the establishment of a closed forest are reconsidered. Location: Pechora basin, north-eastern European Russia. Methods: We used plant macrofossil, stomata, pollen and radiocarbon analyses to reconstruct late-glacial and early Holocene tree establishment and forest development. The data were derived from lake sediment and peat archives. Results: Palaeobotanical data reveal an early Holocene presence (11,500-10,000 cal. yr bp) of arboreal taxa at all five sites. One site presently located in the northernmost taiga zone, shows the presence of spruce and reproducing tree birch during the late-glacial. Given the current view of post-glacial population dynamics and migration rates, it seems likely that the source area of these early tree populations in north-eastern European Russia was not located in southern Europe but that these populations had local origins. Results thus support the emerging view that the first post-glacial population expansions in non-glaciated regions at high latitudes do not reflect migration from the south but were a result of an increase in the size and density of small persisting outlying tree populations. Main conclusions: Results suggest that the area east of the margin of the Scandinavian ice sheet to the Ural Mountains had isolated patches of trees during the late-glacial and early Holocene and that these small populations acted as initial nuclei for population expansion and forest development in the early Holocene.

Plant Migrations Impact on Potential Vegetation and Carbon Redistribution in Northern North America from Climate Change

Forests have a prominent role in carbon storage and sequestration. Anthropogenic forcing has the potential to accelerate climate change and alter the distribution of forests. How forests redistribute spatially and temporally in response to climate change can alter their carbon sequestration potential. The driving question for this research was: How does plant migration from climate change impact vegetation distribution and carbon sequestration potential over continental scales? Large-scale simulation of the equilibrium response of vegetation and carbon from future climate change has shown relatively modest net gains in sequestration potential, but studies of the transient response has been limited to the sub-continent or landscape scale. The transient response depends on fine scale processes such as competition, disturbance, landscape characteristics, dispersal, and other factors, which makes it computational prohibitive at large domain sizes. To address this, this research used an advanced mechanistic model (Ecosystem Demography Model, ED) that is individually based, but pseudo-spatial, that reduces computational intensity while maintaining the fine scale processes that drive the transient response. First, the model was validated against remote sensing data for current plant functional type distribution in northern North America with a current climatology, and then a future climatology was used to predict the potential equilibrium redistribution of vegetation and carbon from future climate change. Next, to enable transient calculations, a method was developed to simulate the spatially explicit process of dispersal in pseudo-spatial modeling frameworks. Finally, the new dispersal sub-model was implemented in the mechanistic ecosystem model, and a model experimental design was designed and completed to estimate the transient response of vegetation and carbon to climate change. The potential equilibrium forest response to future climate change was found to be large, with large gross changes in distribution of plant functional types and comparatively smaller changes in net carbon sequestration potential for the region. However, the transient response was found to be on the order of centuries, and to depend strongly on disturbance rates and dispersal distances. Future work should explore the impact of species-specific disturbance and dispersal rates, landscape fragmentation, and other processes that influence migration rates and have been simulated at the sub-continent scale, but now at continental scales, and explore a range of alternative future climate scenarios as they continue to be developed.