Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power

Genetic assignment methods use genotype likelihoods to draw inference about where individuals were or were not born, potentially allowing direct, real-time estimates of dispersal. We used simulated data sets to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F-0 immigrants in populations with ongoing gene flow, and hence for providing direct, real-time estimates of migration rates. The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set being analysed. A novel Monte Carlo resampling method taking into account these aspects was proposed and its efficiency was evaluated. Power and error were relatively insensitive to the frequency assumed for missing alleles. Power to identify F-0 immigrants was improved by using large sample size (up to about 50 individuals) and by sampling all populations from which migrants may have originated. A combination of plotting genotype likelihoods and calculating mean genotype likelihood ratios (D-LR) appeared to be an effective way to predict whether F-0 immigrants could be identified for a particular pair of populations using a given set of markers.

Evolution in heterogeneous populations: from migration models to fixation probabilities.

Although dispersal is recognized as a key issue in several fields of population biology (such as behavioral ecology, population genetics, metapopulation dynamics or evolutionary modeling), these disciplines focus on different aspects of the concept and often make different implicit assumptions regarding migration models. Using simulations, we investigate how such assumptions translate into effective gene flow and fixation probability of selected alleles. Assumptions regarding migration type (e.g. source-sink, resident pre-emption, or balanced dispersal) and patterns (e.g. stepping-stone versus island dispersal) have large impacts when demes differ in sizes or selective pressures. The effects of fragmentation, as well as the spatial localization of newly arising mutations, also strongly depend on migration type and patterns. Migration rate also matters: depending on the migration type, fixation probabilities at an intermediate migration rate may lie outside the range defined by the low- and high-migration limits when demes differ in sizes. Given the extreme sensitivity of fixation probability to characteristics of dispersal, we underline the importance of making explicit (and documenting empirically) the crucial ecological/ behavioral assumptions underlying migration models.

Cell proliferation and migration in the jejunum of suckling rats submitted to progressive fasting

Cell proliferation and migration in the intestinal crypts, and cell migration in the villus are controlled by different mechanisms in adult rats. In the present study, weanling rats and fasting rats were used to quantitatively study the correlation of cell cycle parameters and epithelial cell migration in crypts and intestinal villi. Eighteen-day-old rats received a single injection of tritiated thymidine [3H]TdR (23:00 h); half of the pups were submitted to fasting 5 h earlier. Cell proliferation was determined in radioautographs of jejunal crypts, on the basis of the labeling indices (LI) taken 1, 8, 13 and 19 h after [3H]TdR. The results showed that the labeling index did not differ 1 h or 19 h after [3H]TdR between the fed (38.7% or 48%) and fasting groups (34.6% or 50.4%). The modified method of grain count halving indicated that cell cycle time did not differ between fed (16.5 h) and fasting rats (17.8 h); the growth fraction, however, had lower values in fasting (59%) than in fed rats (77%). Cell migration in the crypt, estimated by the LI obtained for each cell position, did not change with treatment. As for the villi, the cell migration rate was significantly retarded by 3 cell positions (8%). These results suggest that the cell migration in the villi of weanling pups does not depend directly on the cell proliferation and migration in the intestinal crypt, but is directly affected by the absence of food in the lumen

Growth, migration and unemployment across Swedish municipalities

Fundamental questions in economics are why some regions are richer than others, why their economic growth rates vary, whether their growth tends to converge and the key factors that contribute to the variations. These questions have not yet been fully addressed, but changes in the local tax base are clearly influenced by the average income growth rate, net migration rate, and changes in unemployment rates. Thus, the main aim of this paper is to explore in depth the interactive effects of these factors (and local policy variables) in Swedish municipalities, by estimating a proposed three-equation system. Our main finding is that increases in local public expenditures and income taxes have negative effects on subsequent local income growth. In addition, our results support the conditional convergence hypothesis, i.e. that average income tends to grow more rapidly in relatively poor local jurisdictions than in initially “richer” jurisdictions, conditional on the other explanatory variables.

DAPK loss in colon cancer tumor buds: implications for migration capacity of disseminating tumor cells.

Defining new therapeutic strategies to overcome therapy resistance due to tumor heterogeneity in colon cancer is challenging. One option is to explore the molecular profile of aggressive disseminating tumor cells. The cytoskeleton-associated Death-associated protein kinase (DAPK) is involved in the cross talk between tumor and immune cells at the invasion front of colorectal cancer. Here dedifferentiated tumor cells histologically defined as tumor budding are associated with a high risk of metastasis and poor prognosis. Analyzing samples from 144 colorectal cancer patients we investigated immunhistochemical DAPK expression in different tumor regions such as center, invasion front, and buds. Functional consequences for tumor aggressiveness were studied in a panel of colon tumor cell lines using different migration, wound healing, and invasion assays. DAPK levels were experimentally modified by siRNA transfection and overexpression as well as inhibitor treatments. We found that DAPK expression was reduced towards the invasion front and was nearly absent in tumor buds. Applying the ECIS system with HCT116 and HCT116 stable lentiviral DAPK knock down cells (HCTshDAPK) we identified an important role for DAPK in decreasing the migratory capacity whereas proliferation was not affected. Furthermore, the migration pattern differed with HCTshDAPK cells showing a cluster-like migration of tumor cell groups. DAPK inhibitor treatment revealed that the migration rate was independent of DAPK's catalytic activity. Modulation of DAPK expression level in SW480 and DLD1 colorectal cancer cells significantly influenced wound closure rate. DAPK seems to be a major player that influences the migratory capability of disseminating tumor cells and possibly affects the dynamic interface between pro- and anti-survival factors at the invasion front of colorectal cancer. This interesting and new finding requires further evaluation.

Sphingosine kinase 2 deficiency increases proliferation and migration of renal mouse mesangial cells and fibroblasts

Both of the sphingosine kinase (SK) subtypes SK-1 and SK-2 catalyze the production of the bioactive lipid molecule sphingosine 1-phosphate (S1P). However, the subtype-specific cellular functions are largely unknown. In this study, we investigated the cellular function of SK-2 in primary mouse renal mesangial cells (mMC) and embryonic fibroblasts (MEF) from wild-type C57BL/6 or SK-2 knockout (SK2ko) mice. We found that SK2ko cells displayed a significantly higher proliferative and migratory activity when compared to wild-type cells, with concomitant increased cellular activities of the classical extracellular signal regulated kinase (ERK) and PI3K/Akt cascades, and of the small G protein RhoA. Furthermore, we detected an upregulation of SK-1 protein and S1P3 receptor mRNA expression in SK-2ko cells. The MEK inhibitor U0126 and the S1P1/3 receptor antagonist VPC23019 blocked the increased migration of SK-2ko cells. Additionally, S1P3ko mesangial cells showed a reduced proliferative behavior and reduced migration rate upon S1P stimulation, suggesting a crucial involvement of the S1P3 receptor. In summary, our data demonstrate that SK-2 exerts suppressive effects on cell growth and migration in renal mesangial cells and fibroblasts, and that therapeutic targeting of SKs for treating proliferative diseases requires subtype-selective inhibitors.

Rural to Urban Migration: A District Level Analysis for India

Based on the recent census data this paper analyses the district level rural to urban migration rates (both intra-state and the inter-state) among males and females separately. Both the rates are closely associated irrespective of whether the migrants originate from the rural areas within the state or outside the state. This would suggest that women usually migrate as accompanists of the males. Though many of the relatively poor and backward states actually show large population mobility, which is primarily in search of a livelihood, the mobility of male population is also seen to be prominent in the relatively advanced states like Maharashtra and Gujarat. Rapid migration of rural females within the boundaries of the states is, however, evident across most of the regions. The social networks, which play an important role in the context of migration are prevalent among the short distance migrants and tend to lose their significance with a rise in the distance between the place of origin and destination though there are some exceptions to this phenomenon. Besides the north-south divide in the Indian context is indeed a significant phenomenon with a few exceptions of metropolitan cities. As regards the effect of factors at the place of destination, prospects for better job opportunities are a major determinant of male migration. Low castes and minority groups tend to pull migration through network effects. Among females also these effects are evident though with the inclusion of the male migration rate they become less significant. Finally the paper brings out the policy implications.

Channel Migration and Avulsion Hazards at Sunshine Point Campground, Mount Rainier National Park, Washington

In November 2006, the flood of record on the upper Nisqually River destroyed part of Sunshine Point Campground in Mount Rainier National Park, Washington. The Nisqually River migrated north and reoccupied five acres of its floodplain; Tahoma Creek partially avulsed into the west floodplain, topping banks of an undersized channel and flooding the campground. I assessed hazards to infrastructure at the old campground location, where the Park proposes to rebuild the remaining campground roads and sites. This assessment focuses on two major hazards: northward Nisqually River migration, which may reincorporate the floodplain into the river destroying infrastructure; and Tahoma Creek avulsions, which may flood the campgroud and deposit sediment burying campground infrastructure. I quantify northward migration by: estimating migration rates and changes to channel width; evaluating river occupation of the pre- and post-2006 campground; and estimating scour depths at revetments protecting the campground. I digitized the Nisqually River channels and channel centerlines from maps and images between 1955 and 2013 into a GIS, which I used to estimate migration rate and river width changes. Centerline migration rates average 9 ft/yr along the length of the Nisqually River study reach; at Sunshine Point lateral migration rates average 11 ft/yr. Maximum migration along the study reach was 19 ft/yr between 2006 and 2009. Greater than average migration rates and channel widths correspond to river confluences and include the Tahoma Creek confluence at Sunshine Point. To determine historical channel locations and the frequency that the river occupied different parts of its floodplain, I digitized the river from maps and images between 1903 and 2013. The Nisqually River flows through Sunshine Point Campground in eight out of 15 historical images. I assess scour at revetments protecting infrastructure from the Nisqually River during a 100-year recurrence interval flood using measured cross-sections. During a 100-year flood, the Nisqually River may scour up to 10 feet below the bed elevation. These scour depths can destabilize critical revetments leaving loose unconsolidated riverbanks exposed to Nisqually River flows. To determine the causes, locations, and frequency of flood hazards from Tahoma Creek avulsions, I field map avulsion channels and compare the results with imagery and channel width changes between 1955 and 2013. Mapped avulsion channels occur with swaths of dead vegetation or nascent vegetation; both dead and recent vegetation are visibly distinct from surrounding vegetation in aerial images. Times of changes to these vegetation anomalies correspond to increases in Tahoma Creek channel width. Avulsions have occurred at least three times in the study period: pre-1955, between 1979 and 1984, and in 2006. The 1984 and 2006 avulsions both occur after increases in Tahoma Creek reach averaged width. The NPS is considering two options to rebuild Sunshine Point Campground, both at the same location. The hazards posed by the Nisqually River and Tahoma Creek at Sunshine Point will affect both construction options equally. Migration hazards to the campground may be reduced by limiting the proposed campground infrastructure to an elevated ridge that has not been occupied by the Nisqually River since 1903. The hazards of damage from migration may be reduced by revetments, which were effective in preventing northward Nisqually River migration in 1959 and 1965. Tahoma Creek avulsions are related increased of Tahoma Creek reach averaged widths, which are near a 58- year maximum, and occurred during a 10-year flood in 1984. The campground may be as susceptible to flooding from avulsions during as little as a 10-year flood. A large avulsion may occur with the next significant Tahoma Creek width increase. Glacial retreat has been shown to increase debris flow activity and increase sediment delivery to Mount Rainier rivers. Increased sediment discharge has been correlated with aggradation, which will further encourage Tahoma Creek avulsions.

The effect of iron on liquid film migration and sintering of an Al-Cu-Mg alloy

Analytical transmission electron microscopy indicates that liquid film migration occurs during sintering of an Al-Cu-Mg alloy, that intragranular liquid pools develop from migrating films and that iron segregates to these pools. It is suggested that a high localised iron concentration retards the liquid film migration rate by reducing the coherency strain in the retreating grain, causing a region of the film to detach from the boundary, thus forming an intragranular pool in the advancing grain. Alloys with low iron levels develop few intragranular pools and have high sintered densities. (C) 2003 Acta Materialia Inc. Published by Elsevier Science Ltd. All rights reserved.

Nondestructive measurement of water content and moisture migration of unsaturated red clays in South China

To reveal the moisture migration mechanism of the unsaturated red clays, which are sensitive to water content change and widely distributed in South China, and then rationally use them as a filling material for highway embankments, a method to measure the water content of red clay cylinders using X-ray computed tomography (CT) was proposed and verified. Then, studies on the moisture migrations in the red clays under the rainfall and ground water level were performed at different degrees of compaction. The results show that the relationship between dry density, water content, and CT value determined from X-ray CT tests can be used to nondestructively measure the water content of red clay cylinders at different migration time, which avoids the error reduced by the sample-to-sample variation. The rainfall, ground water level, and degree of compaction are factors that can significantly affect the moisture migration distance and migration rate. Some techniques, such as lowering groundwater table and increasing degree of compaction of the red clays, can be used to prevent or delay the moisture migration in highway embankments filled with red clays.

Tracking rates of ecotone migration due to salt-water encroachment using fossil mollusks in coastal South Florida

We determined the rate of migration of coastal vegetation zones in response to salt-water encroachment through paleoecological analysis of mollusks in 36 sediment cores taken along transects perpendicular to the coast in a 5.5 km2 band of coastal wetlands in southeast Florida. Five vegetation zones, separated by distinct ecotones, included freshwater swamp forest, freshwater marsh, and dwarf, transitional and fringing mangrove forest. Vegetation composition, soil depth and organic matter content, porewater salinity and the contemporary mollusk community were determined at 226 sites to establish the salinity preferences of the mollusk fauna. Calibration models allowed accurate inference of salinity and vegetation type from fossil mollusk assemblages in chronologically calibrated sediments. Most sediments were shallow (20–130 cm) permitting coarse-scale temporal inferences for three zones: an upper peat layer (zone 1) representing the last 30–70 years, a mixed peat-marl layer (zone 2) representing the previous ca. 150–250 years and a basal section (zone 3) of ranging from 310 to 2990 YBP. Modern peat accretion rates averaged 3.1 mm yr)1 while subsurface marl accreted more slowly at 0.8 mm yr)1. Salinity and vegetation type for zone 1 show a steep gradient with freshwater communities being confined west of a north–south drainage canal constructed in 1960. Inferences for zone 2 (pre-drainage) suggest that freshwater marshes and associated forest units covered 90% of the area, with mangrove forests only present along the peripheral coastline. During the entire pre-drainage history, salinity in the entire area was maintained below a mean of 2 ppt and only small pockets of mangroves were present; currently, salinity averages 13.2 ppt and mangroves occupy 95% of the wetland. Over 3 km2 of freshwater wetland vegetation type have been lost from this basin due to salt-water encroachment, estimated from the mollusk-inferred migration rate of freshwater vegetation of 3.1 m yr)1 for the last 70 years (compared to 0.14 m yr)1 for the pre-drainage period). This rapid rate of encroachment is driven by sea-level rise and freshwater diversion. Plans for rehydrating these basins with freshwater will require high-magnitude re-diversion to counteract locally high rates of sea-level rise.

Mitochondrial DNA Variability Among Eight Tikuna Villages: Evidence for an Intratribal Genetic Heterogeneity Pattern

To study the genetic structure of the Tikuna tribe, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 187 Amerindians from eight Tikuna villages located in the Brazilian Amazon. The central position of these villages in the continent makes them relevant for attempts to reconstruct population movements in South America. In this geographic region, there is particular concern regarding the genetic structure of the Tikuna tribe, formerly designated ""enigmatic"" due to its remarkable degree of intratribal homogeneity and the scarcity of private protein variants. In spite of its large population size and geographic distribution, the Tikuna tribe presents marked genetic and linguistic isolation. All individuals presented indigenous mtDNA haplogroups. An intratribal genetic heterogeneity pattern characterized by two highly homogeneous Tikuna groups that differ considerably from each other was observed. Such a finding was unexpected, since the Tikuna tribe is characterized by a social system that favors intratribal exogamy and patrilocality that would lead to a higher female migration rate and homogenization of the mtDNA gene pool. Demographic explosions and religious events, which significantly changed the sizes and compositions of many Tikuna villages, may be reflected in the genetic results presented here. Am J Phys Anthropol 140:526-531,2009. (C) 2009 Wiley-Liss, Inc

Influence of seaward boundary condition on contaminant transport in unconfined coastal aquifers

Contaminant transport in coastal aquifers is complicated partly due to the conditions at the seaward boundary including seawater intrusion and tidal variations of sea level. Their inclusion in modelling this system will be computationally expensive. Therefore, it will be instructive to investigate the consequence of simplifying the seaward boundary condition by neglecting the seawater density and tidal variations in numerical predictions of contaminant transport in this zone. This paper presents a comparison of numerical predictions for a simplified seaward boundary condition with experimental results for a corresponding realistic one including a saltwater interface and tidal variations. Different densities for contaminants are considered. The comparison suggests that the neglect of the seawater intrusion and tidal variations does not affect noticeably the overall migration rate of the plume before it reaches the saltwater interface. However, numerical prediction shows that a more dense contaminant travels further seaward and part of the solute mass exits under the sea if the seawater density is not included. This is not consistent with the experimental result, which shows that the contaminant travels upwards to the shoreline along the saltwater interface. Neglect of seawater density, therefore, will result in an underestimation of the exit rate of solute mass around the coastline and fictitious migration paths under the seabed. For a less dense contaminant, neglect of seawater density has little effect on numerical prediction of migration paths. (C) 2001 Elsevier Science B.V. All rights reserved.

Numerical modelling of contaminant transport in coastal aquifers

This paper employs a two-dimensional variable density flow and transport model to investigate the transport of a dense contaminant plume in an unconfined coastal aquifer. Experimental results are also presented to show the contaminant plume in a freshwater-seawater flow system. Both the numerical and experimental results suggest that the neglect of the seawater interface does not noticeably affect the horizontal migration rate of the plume before it reaches the interface. However, the contaminant will travel further seaward and part of the solute mass will exit under the sea if the higher seawater density is not included. If the seawater density is included, the contaminant will travel upwards towards the beach along the freshwater-saltwater interface as shown experimentally. Neglect of seawater density, therefore, will result in an underestimate of solute mass rate exiting around the coastline. (C) 2002 IMACS. Published by Elsevier Science B.V. All rights reserved.

Genetic variability of Triatoma flavida and Triatoma bruneri (Hemiptera: Reduviidae) by RAPD-PCR technique

The Triatominae (Hemiptera:Reduviidae) contains the principal and potential Chagas disease vectors present in Mexico, Central America and South America. Triatoma flavida and T. bruneri are Cuban species. These species are closely related according to morphology and were considered synonyms until 1981, when they were separated on the grounds of external characters of the body and the morphology of male genitalia. The present study seeks to analyze genetic polymorphism of T. flavida and T. bruneri populations using RAPD techniques, and to assess the genetic relationship between these species. Ten random primers were used to evaluate the genetic variability among species using RAPD-PCR. The genetic flow among them was calculated. The dendrogram based on calculated Jaccard distances showed two clearly distinguishable clusters which coincided with the studied species. Within each species, moderate genetic differentiation (Fst 0.05-0.15) and migration rates (N > 1) were found among populations, that reveal gene flow and genetic homogeneity. Between species, the Fst value showed a high genetic differentiation and the migration rate was insufficient to maintain genetic homogeneity, and confirmed the absence of gene flow between them. Our results confirm the genetic variability among T. flavida and T. bruneri species.