Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test

BACKGROUND: Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals. RESULTS: We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8). The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes. CONCLUSION: We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution

Tomato diseases, quality, yield and pesticide use : a field study in Nicaragua

Nicaraguan farmers have for a long time struggled with tomato production. The primary problem has been Begomovirus infection, which devastated the tomato production in the country in the 1990's. In the battle against the Begomovirus other problems in the native tomato production have been neglected. The overall goal with these projects was to identify common tomato diseases and to evaluate their effect on yield and quality of the tomato fruits at different nitrogen levels. This report contains two separate theses (chapter 2 and 3). The results of the studies are based on the same field experiments. To increase the understanding about local farming conditions (chapter 1), interviews were made at two locations. During the interviews the farmers were asked questions about the farms, their production and pesticide use. Today, the farmers overuse chemical products to control different pests. The Nicaraguan farmers in general have a strong belief that pesticides are the solution of all their agricultural problems. The thesis in chapter 2 deals with the effect of nitrogen on some diseases of tomato. The symptoms that appeared in the field experiment indicated that the plants were not infected by the suspected pathogens and lab results showed that symptoms on the plants were caused by two other diseases: bacterial wilt and powdery mildew (causing agents: Ralstonia solanacearum and Leveilulla taurica). The results showed that plants fertilised with double the normal amount of nitrogen were significantly more resistant to powdery mildew. There was also a significant difference between the varieties in severity of powdery mildew. Regarding bacterial wilt the results are ambiguous, one of the field experiments show no difference between the treatments but in the other experiment there was a considerably higher rate of infection in the to highest levels of nitrogen fertilisation. The aim of the study in chapter 3 was to evaluate the effects of nitrogen fertilization on the yield and quality of the tomato fruits and to evaluate the relations between the incidence of diseases and nitrogen fertilization on one hand and fruit quality on the other. The harvest was divided in good (marketable) and bad (not marketable) fractions. To evaluate the fruit quality, taste tests were carried out on the two first harvests and laboratory analyses of acid (% titratable acids) and sugar content (ºBrix) were measured on the second harvest. The results showed that the unfertilized plots had significantly lower foliar nitrogen content. The total harvest levels of the experiment were in similar range as the average harvest for the region (12-18 t/ha), but the marketable fraction was only between 39 and 50 % of the total yield. In the taste test, one of the varieties was significantly the most preferred variety, independent of fertilizing level. The high not marketable fraction was probably due to poor pollination and fruit set caused by high temperatures and heavy infections of Begomovirus and other diseases. It is also very important to identify the pathogen to know which diseases that are present in the field and how to treat them properly. A solution to many disease and quality problem could be a break in tomato production some time during the year to create a host free period for diseases and vectors.Nicaraguanska bönder har länge tvingats kämpa med problem i tomatodlingen. Det största problemet har varit infektion av Begomovirus, vilket fick katastrofala följder för tomatproduktionen på 1990-talet. I kampen mot Begomovirus glömdes andra problem i den inhemska tomatodlingen bort. Det övergripande målet med de här projekten var att identifiera vanliga tomatsjukdomar och utvärdera deras effekt på skörd och kvalitet på tomaterna vid olika kvävegivor. Rapporten innehåller två separata examensarbeten (kapitel 2 och 3). Resultaten från studierna bygger på samma fältexperiment. För att öka förståelsen om den inhemska tomatproduktionen (kapitel 1), intervjuades bönder i två byar. I intervjuerna ställdes frågor om gårdarna, produktionen och bekämpningsmedel. Idag finns en överanvändning av kemiska preparat för att kontrollera olika skadegörare och Nicaraguanska bönder har generellt sett en övertro på att bekämpningsmedel som en lösning på alla problem inom jordbruket. Examensarbetet i kapitel 2 handlar om effekten av kväve på vissa tomatsjukdomar. Symptomen som uppträdde i fält tydde på att det inte var de förväntade sjukdomarna och laboratorieresultaten visade att plantorna hade infekterats av två andra sjukdomar: bacterial wilt och mjöldagg (orsakad av Ralstonia solanacearum och Leveilulla taurica). Resultaten visade att plantorna som gödslats med dubbla normalgivan av kväve var mer motståndskraftiga mot mjöldagg, det fanns också en skillnad mellan sorterna när det gäller angrepp av mjöldagg. Angående bacterial wilt var resultaten tvetydiga, ett av fältförsöken visade ingen skillnad mellan behandlingarna, medan i det andra var det högre infektionsgrad i de högsta kvävegivorna. Syftet med studien i kapitel 3 var att utvärdera effekterna av kvävegödsling på skörden och kvalitén på tomaterna samt att utvärdera sambandet mellan förekomsten av sjukdom och mängden kväve å ena sidan och kvalitén å anda sidan. Skörden delades in i en bra (säljbar) och en dålig (icke säljbar) del. För att utvärdera fruktkvalitén gjordes smaktest på två skördar och laboratorieanalyser av syra (% titrerbar syra) och sockerinnehåll (ºBrix) på den andra skörden. Resultaten visade att ogödslade rutor hade signifikant lägre kväveinnehåll i blasten. Den totala skördenivån i fältförsöket var jämförbar med normala skördar i området (12-18 t/ha), men andelen säljbara frukter var endast 39 till 50 % av den totala skörden. Smaktesten visade att den ena sorten föredrogs av panelen oberoende av kvävegiva. Den höga andelen icke säljbara frukter berodde troligen på dålig pollination och fruktbildning orsakad av hög temperatur och kraftiga infektioner av Begomovirus och andra sjukdomar. Det är också mycket viktigt att identifiera patogener för att veta vilka sjukdomar som finns i fält och hur de bäst skall bekämpas. En lösning till många sjukdoms- och kvalitetsproblem skulle kunna vara att införa ett uppehåll i tomatodlingen någon gång under året, för att skapa en värdfri period för sjukdomar och vektorer

Polymorphism and Divergence in Two Willow Species, Salix viminalis L. and Salix schwerinii E. Wolf

We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (πi = 0.00849) than in S. viminalis (πi = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus

<p><b>Abstract</b></p> <p>Background</p> <p><it>Salix </it>(willow) and <it>Populus </it>(poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the <it>Populus trichocarpa </it>genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya.</p> <p>Results</p> <p>We constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S₁, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S₃consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41).</p> <p>Conclusions</p> <p>The relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 × 10^-9and 1.68 × 10^-9per site and year, which are close to rates found in other perennials but much lower than rates in annuals.</p

A calibration method for non-overlapping cameras based on mirrored phase target

A novel calibration method for non-overlapping cameras is proposed in this paper. A LCD screen is used as a phase target to display two groups of orthogonal phase-shifted sinusoidal patterns during the calibration process. Through a mirror reflection, the phase target is captured by the cameras respectively. The relations between each camera and the phase target can be obtained according the proposed algorithm. Then the relation between the cameras can be calculated by treating the phase target as an intermediate value. The proposed method is more flexible than conventional mirror-based approach, because it do not require the common identification points and is robust to out-of-focus images. Both simulation work and experimental results show the proposed calibration method has a good result in calibrating a non-overlapping cameras system

Трансформация культуры чтения в цифровую эпоху как показатель цивилизационных сдвигов

Материалы X Международной научной конференции 25–26 мая 2017 г

A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus)

<p>Abstract</p> <p>Background</p> <p>There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (~10^-3) and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (<it>Lagopus lagopus</it>) has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance.</p> <p>Results</p> <p>We sequenced 18 autosomal protein coding loci from approximately 15–18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (<it>π</it>_<it>t</it>) was between 1.30 × 10^-4and 7.66 × 10^-3(average <it>π</it>_{<it>t </it>}= 2.72 × 10^-3± 2.06 × 10^-3) and silent nucleotide diversity varied between 4.20 × 10^-4and 2.76 × 10^-2(average <it>π</it>_{<it>S </it>}= 9.22 × 10^-3± 7.43 × 10^-4). The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 × 10^-3(average <it>π</it>_{<it>a </it>}= 5.08 × 10^-4± 7.43 × 10³), which suggest that purifying selection is strong in these genes. <it>F</it>_STvalues based on synonymous SNP's varied between -5.60 × 10^-4and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of <it>F</it>_ST= 0.03 (95% CI: 0.006 – 0.057) over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low levels of linkage disequilibrium were observed within genes, with an average r²= 0.084 ± 0.110, which is expected for a large outbred population with no population differentiation. The mean per site per generation recombination parameter (ρ) was comparably high (0.028 ± 0.018), indicating high recombination rates in these genes.</p> <p>Conclusion</p> <p>We found unusually high levels of nucleotide diversity in the Scandinavian willow grouse as well as very little population structure among localities with up to 1647 km distance. There are also low levels of linkage disequilibrium within the genes and the population recombination rate is high, which is indicative of an old panmictic population, where recombination has had time to break up any haplotype blocks. The non-synonymous nucleotide diversity is low compared with the silent, which is in agreement with effective purifying selection, possibly due to the large effective population size.</p

Diversity and evolution of potato mop-top virus

Nearly complete sequences of RNA-CP and 3'-proximal RNA-TGB were determined for 43 samples of potato mop-top virus (PMTV) originating from potato tubers and field soil from Sweden, Denmark and the USA. The results showed limited diversity and no strict geographical grouping, suggesting only a few original introductions of PMTV from the Andes. Two distinguishable types of RNA-CP and RNA-TGB were found in the samples, but no specific combination of them correlated with spraing symptoms in tubers. Lack of positive selection in the coding sequences indicates that there is no specific molecular adaptation of PMTV to new vectors or hosts