Linkage mapping reveals strong chiasma interference in Sockeye salmon: Implications for interpreting genomic data

Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in nonmodel species. Salmonid females generally produce thousands of embryos, providing large families for conducting inheritance studies. Further, salmonid genomes are currently rediploidizing after a whole genome duplication and can serve as models for studying the role of homeologous crossovers on genome evolution. Here, we present a detailed interrogation of recombination patterns in sockeye salmon (Oncorhynchus nerka). First, we use RAD sequencing of haploid and diploid gynogenetic families to construct a dense linkage map that includes paralogous loci and location of centromeres. We find a nonrandom distribution of paralogs that mainly cluster in extended regions distally located on 11 different chromosomes, consistent with ongoing homeologous recombination in these regions. We also estimate the strength of interference across each chromosome; results reveal strong interference and crossovers are mostly limited to one per arm. Interference was further shown to continue across centromeres, but metacentric chromosomes generally had at least one crossover on each arm. We discuss the relevance of these findings for both mapping and population genomic studies

Breed Locally, Disperse Globally: Fine-Scale Genetic Structure Despite Landscape-Scale Panmixia in a Fire-Specialist

An exciting advance in the understanding of metapopulation dynamics has been the investigation of how populations respond to ephemeral patches that go \u27extinct\u27 during the lifetime of an individual. Previous research has shown that this scenario leads to genetic homogenization across large spatial scales. However, little is known about fine-scale genetic structuring or how this changes over time in ephemeral patches. We predicted that species that specialize on ephemeral habitats will delay dispersal to exploit natal habitat patches while resources are plentiful and thus display fine-scale structure. To investigate this idea, we evaluated the effect of frequent colonization of ephemeral habitats on the fine-scale genetic structure of a fire specialist, the black-backed woodpecker (Picoides arcticus) and found a pattern of fine-scale genetic structure. We then tested for differences in spatial structure between sexes and detected a pattern consistent with male-biased dispersal. We also detected a temporal increase in relatedness among individuals within newly burned forest patches. Our results indicate that specialist species that outlive their ephemeral patches can accrue significant fine-scale spatial structure that does not necessarily affect spatial structure at larger scales. This highlights the importance of both spatial and temporal scale considerations in both sampling and data interpretation of molecular genetic results

Women’s Access to Land and Economic Empowerment in Selected Nigerian Communities

Despite various land policies that prescribe rights to land in many societies, women remain marginalized in access to and economic utilization of land. This is widespread in rural communities where informal institutions such as customs and traditions subsist. In most of these communities, the patriarchal structure of families is championed by the informal institutions that support male dominance. This study focuses on economic empowerment of women as it encapsulates sustainable wealth of women. It provides answers to two main research questions: a) what kind of relationship exists between land access and empowerment of women? And b) how important are individual and household attributes in informing women’s empowerment through land rights? The empirical results of this study provide some new insights as they demonstrate how land rights influence women’s economic empowerment. The study also finds that women’s earning capacity reduces when they take up the responsibility of becoming the heads of households and that their income increases as they become more educate

The Decline And Isolation Of Fisher Populations Prior To European Settlement: Insights From Dna Analysis

Historical and contemporary genetic information can provide insights into the nature of population expansions or contractions and temporal changes in abundance and connectivity. Fisher (Martes pennanti) populations in California are thought to have declined precipitously over the last 150 yrs and currently only two populations remain in the state that are both geographically and genetically isolated from each other. In this study we looked at whether the isolation of these two populations is a result habitat alteration and trapping that accompanied European settlement in the mid-1800s or if it is the result of a more ancient demographic event. We collected both historical and contemporary genetic samples from each of the two extant fisher populations. We successfully obtained microsatellite genotypes at 10 loci for 21 museum specimens (dated 1882-1920) and 275 contemporary individuals (2006-2009). We found significant temporal shifts in allele frequencies between historical and contemporary samples between regions indicating large amounts of genetic drift likely due to isolation and small population size. We found a strong genetic signal for a 90 percent contraction in effective population size of fisher and estimated that this decline occurred over a thousand years ago. As a decline in abundance of this magnitude likely resulted in contraction of the geographic range, our analyses suggest that fisher populations in California became isolated from one another far prior to the European settlement of the state

Historical and Contemporary DNA Indicate Fisher Decline and Isolation Occurred Prior to the European Settlement of California

Establishing if species contractions were the result of natural phenomena or human induced landscape changes is essential for managing natural populations. Fishers (Martes pennanti) in California occur in two geographically and genetically isolated populations in the northwestern mountains and southern Sierra Nevada. Their isolation is hypothesized to have resulted from a decline in abundance and distribution associated with European settlement in the 1800s. However, there is little evidence to establish that fisher occupied the area between the two extant populations at that time. We analyzed 10 microsatelliteloci from 275 contemporary and 21 historical fisher samples (1880-1920) to evaluate the demographic history of fisher in California. We did not find any evidence of a recent (post-European) bottleneck in the northwestern population. In the southern Sierra Nevada, genetic subdivision within the population strongly influenced bottleneck tests. After accounting for genetic subdivision, we found a bottleneck signal only in the northern and central portions of the southern Sierra Nevada, indicating that the southernmost tip of these mountains may have acted as a refugium for fisher during the anthropogenic changes of the late 19th and early 20th centuries. Using a coalescent-based Bayesian analysis, we detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. We hypothesize that fisher distribution in California contracted to the two current population areas pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement

Removing exogenous information using pedigree data

Management of certain populations requires the preservation of its pure genetic background. When, for different reasons, undesired alleles are introduced, the original genetic conformation must be recovered. The present study tested, through computer simulations, the power of recovery (the ability for removing the foreign information) from genealogical data. Simulated scenarios comprised different numbers of exogenous individuals taking partofthe founder population anddifferent numbers of unmanaged generations before the removal program started. Strategies were based on variables arising from classical pedigree analyses such as founders? contribution and partial coancestry. The ef?ciency of the different strategies was measured as the proportion of native genetic information remaining in the population. Consequences on the inbreeding and coancestry levels of the population were also evaluated. Minimisation of the exogenous founders? contributions was the most powerful method, removing the largest amount of genetic information in just one generation.However, as a side effect, it led to the highest values of inbreeding. Scenarios with a large amount of initial exogenous alleles (i.e. high percentage of non native founders), or many generations of mixing became very dif?cult to recover, pointing out the importance of being careful about introgression events in populatio

A multiscale analysis of gene flow for the New England cottontail, an imperiled habitat specialist in a fragmented landscape

Landscape features of anthropogenic or natural origin can influence organisms\u27 dispersal patterns and the connectivity of populations. Understanding these relationships is of broad interest in ecology and evolutionary biology and provides key insights for habitat conservation planning at the landscape scale. This knowledge is germane to restoration efforts for the New England cottontail (Sylvilagus transitionalis), an early successional habitat specialist of conservation concern. We evaluated local population structure and measures of genetic diversity of a geographically isolated population of cottontails in the northeastern United States. We also conducted a multiscale landscape genetic analysis, in which we assessed genetic discontinuities relative to the landscape and developed several resistance models to test hypotheses about landscape features that promote or inhibit cottontail dispersal within and across the local populations. Bayesian clustering identified four genetically distinct populations, with very little migration among them, and additional substructure within one of those populations. These populations had private alleles, low genetic diversity, critically low effective population sizes (3.2-36.7), and evidence of recent genetic bottlenecks. Major highways and a river were found to limit cottontail dispersal and to separate populations. The habitat along roadsides, railroad beds, and utility corridors, on the other hand, was found to facilitate cottontail movement among patches. The relative importance of dispersal barriers and facilitators on gene flow varied among populations in relation to landscape composition, demonstrating the complexity and context dependency of factors influencing gene flow and highlighting the importance of replication and scale in landscape genetic studies. Our findings provide information for the design of restoration landscapes for the New England cottontail and also highlight the dual influence of roads, as both barriers and facilitators of dispersal for an early successional habitat specialist in a fragmented landscape

Activated Microglia Desialylate and Phagocytose Cells via Neuraminidase, Galectin-3, and Mer Tyrosine Kinase

Activated microglia can phagocytose dying, stressed, or excess neurons and synapses via the phagocytic receptor Mer tyrosine kinase (MerTK). Galectin-3 (Gal-3) can cross-link surface glycoproteins by binding galactose residues that are normally hidden below terminal sialic acid residues. Gal-3 was recently reported to opsonize cells via activating MerTK. We found that LPS-activated BV-2 microglia rapidly released Gal-3, which was blocked by calcineurin inhibitors. Gal-3 bound to MerTK on microglia and to stressed PC12 (neuron-like) cells, and it increased microglial phagocytosis of PC12 cells or primary neurons, which was blocked by inhibition of MerTK. LPS-activated microglia exhibited a sialidase activity that desialylated PC12 cells and could be inhibited by Tamiflu, a neuraminidase (sialidase) inhibitor. Sialidase treatment of PC12 cells enabled Gal-3 to bind and opsonize the live cells for phagocytosis by microglia. LPS-induced microglial phagocytosis of PC12 was prevented by small interfering RNA knockdown of Gal-3 in microglia, lactose inhibition of Gal-3 binding, inhibition of neuraminidase with Tamiflu, or inhibition of MerTK by UNC569. LPS-induced phagocytosis of primary neurons by primary microglia was also blocked by inhibition of MerTK. We conclude that activated microglia release Gal-3 and a neuraminidase that desialylates microglial and PC12 surfaces, enabling Gal-3 binding to PC12 cells and their phagocytosis via MerTK. Thus, Gal-3 acts as an opsonin of desialylated surfaces, and inflammatory loss of neurons or synapses may potentially be blocked by inhibiting neuraminidases, Gal-3, or MerTK.This work was supported by the Medical Research Council U.K. (Grant MR/ L010593)

Genetic variation and effective population size in isolated populations of coastal cutthroat

Abstract Following glacial recession in southeast Alaska, waterfalls created by isostatic rebound have isolated numerous replicate populations of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in short coastal streams. These replicate isolated populations offer an unusual opportunity to examine factors associated with the maintenance of genetic diversity. We used eight microsatellites to examine genetic variation within and differentiation among 12 population pairs sampled from above and below these natural migration barriers. Geological evidence indicated that the above-barrier populations have been isolated for 8,000-12,500 years. Genetic differentiation among below-barrier populations (F ST = 0.10, 95% C.I. 0.08-0.12) was similar to a previous study of more southern populations of this species. Above-barrier populations were highly differentiated from adjacent below-barrier populations (mean pairwise F ST = 0.28; SD 0.18) and multiple lines of evidence were consistent with asymmetric downstream gene flow that varied among streams. Each above-barrier population had reduced within-population genetic variation when compared to the adjacent belowbarrier population. Within-population genetic diversity was significantly correlated with the amount of available habitat in above-barrier sites. Increased genetic differentiation of above-barrier populations with lower genetic diversity suggests that genetic drift has been the primary cause of genetic divergence. Long-term estimates of N e based on loss of heterozygosity over the time since isolation were large (3,170; range 1,077-7,606) and established an upper limit for N e if drift were the only evolutionary process responsible for loss of genetic diversity. However, it is likely that a combination of mutation, selection, and gene flow have also contributed to the genetic diversity of above-barrier populations. Contemporary above-barrier N e estimates were much smaller than long-term N e estimates, not correlated with withinpopulation genetic diversity, and not consistent with the amount of genetic variation retained, given the approximate 10,000-year period of isolation. The populations isolated by waterfalls in this study that occur in larger stream networks have retained substantial genetic variation, which suggests that the amount of habitat in headwater streams is an important consideration for maintaining the evolutionary potential of isolated populations

Analytical models for high-temperature corrosion of silica refractories in glass-melting furnaces

Corrosion of refractory silica brick used to line the crown of many glass-melting furnaces is a serious problem in furnaces using oxygen-fuel rather than air-fuel mixtures. To better understand and to quantify this process analytical models are utilized to evaluate the importance of four potential rate-limiting processes: a) gas-phase transport of NaOH to the crown surface; b) diffusion of sodium-containing reactants through a liquid product layer that forms on the brick face; c) gas-phase diffusion of NaOH into refractory pores; and d) chemical-kinetic limitations at the silica grain surface. Predictions are compared with reported corrosion rates and product compositions previously determined by post-mortem analysis of refractory samples. It is concluded that corrosion occurs largely by reaction and removal of material from the exposed brick face, rather than by transport of reactants into the porous bricks. The observed presence of corrosion products deep within the brick pores is shown to be consistent with capillary suction of high-viscosity liquid products from the hot face into the interior. The results further suggest that mechanisms (b) and (c) do not substantially limit the rate of corrosion, but that mechanisms (a) and (d) may both be important. Comparison of measurements with equilibrium predictions of corrosion-product composition indicate that the corrosion reactions are likely to be close to equilibrium at the conditions and lifetimes typical of full-scale furnaces, but that significant departures from equilibrium may occur in short-duration tests. Although computed corrosion rates based on mass transport through a gas boundary layer are somewhat greater than those observed, the results are very sensitive to the gas-phase concentration of NaOH and to the refractory temperature, both of which contain significant uncertainties