Geographical distribution of some Danish surnames: reflections of social and natural selection.

Geographical differences in the frequencies of eight common surnames in Jutland (Denmark) are analysed using data from telephone directories of 121 exchanges. All the names showed a significant geographical surplus variance, which was divided into trend and patchiness components reflecting the history of the names. The surplus variance of surnames with restricted areas of origin was dominated by a large trend component; for surnames with an originally more even distribution, the patchiness component was dominant. The patterns of distribution were affected by processes which modelled natural selection with linkage disequilibrium. The combined patchiness within the clusters of exchanges gave information about patterns of local migration and level of social integration in the communities. Areas situated in boundary regions show high levels of patchiness.     

Genetic diversity assessed by amplified fragment length polymorphism analysis of the parasitic nematode Dictyocaulus viviparus the lungworm of cattle

We have examined the population genetic structure in a collection of nine isolates of the parasitic lungworm Dictyocaulus viviparus. Eight of the isolates were sampled from cattle in geographically separated farms throughout south-central Sweden, and one isolate was a laboratory strain that has been maintained in experimentally infected calves for almost four decades. A total of 72 worms were examined, with eight individual worms from the same individual host representing each isolate. The genetic variation as revealed by amplified fragment length polymorphism analysis using four selective primer combinations was high. Depending on the primer combination a total of 66-79 restriction fragments were amplified, with 26-44 peaks of similar complexity from each of the isolates. The heterozygosity within populations was relatively small, as were the population mutation and immigration rates, which seemed to be in neutral equilibrium. The genetic diversity was therefore reasonably well structured in the field; and the laboratory isolate was quite distinct from the field samples. There was no relationship between the patterns of genetic diversity and the geographical proximity of the farms. The estimates of heterozygosity were much larger and more consistent than those previously estimated for this nematode species using mitochondrial sequencing, and the genetic structuring was thus much less pronounced and the gene flow greater. We attribute these differences in estimation to the broader sampling of loci available using amplified fragment length polymorphism markers, which may therefore constitute a superior technique for the study of patterns of lungworm diversity. Furthermore, the data estimating gene flow for D. viviparus was less than previously reported for closely related species in North America. This might be related to different rates of movements of infected hosts. It seems likely that lungworm infections are rather persistent on different farms, and the sudden outbreaks of disease that can be observed with host movements are most likely to be related to the introduction of susceptible stock.     

Seed set and germination in crosses within and between two geographically isolated small populations of Saxifraga hirculus in Denmark

Dahlgaard, J. & Warncke, E. 1995. Seed set and germination in crosses within and between two geographically isolated small populations of Saxifraga hirculus in Denmark. - Nord. J. Bot. 15: 337–341. Copenhagen. ISSN 0107–055X.
Seed set and germination were studied in two geographically isolated populations of Saxifraga hirculus in Jutland, Denmark. The size of the populations differed, but both were assumed to exhibit significant genetic homogeneity and inbreeding due to (1) small population size (2) limited pollen flow and seed dispersal and (3) absence of gene flow between populations. Crosses within populations, as well as reciprocal crosses between populations, were carried out in the field. Seed number, proportion of developing seeds, germination percent, and germination rate were found to be greater for crosses between populations than for crosses within populations. Variation in seed size was found to be larger for maternal plants from the smaller population.     

Health status of a recently discovered population of feral swine in Kansas.

Twenty feral hogs (Sus scrofa) from a newly discovered population on Fort Riley Army Base (Kansas, USA) were shot and examined from November 1993 through February 1994 to assess the health of the population. The hogs were generally healthy, although serologic evidence indicated that some individuals had been exposed to parvovirus, enterovirus, and swine influenza. We found no indications of brucellosis, pseudorabies, or porcine respiratory and reproductive syndrome. Lung worms (Metastrongylus spp.), round worms (Ascaris suum), and whipworms (Trichuris suis) were found in nine, four and two of the hogs, respectively. Seven hogs had infestations of lice (Haematopinus suis). Fence-line contacts were documented between four wild boars and domestic sows, and in three cases wild boars entered pens containing domestic sows. We recommend that hogs be examined periodically from this and other wild populations to monitor health status since new animals may enter populations through deliberate translocation, escape from shooting preserves or domestic swine producers, or dispersal from other feral populations.     

Parapatric diversification after post-glacial range expansion in the gall fly Urophora cardui (Tephritidae)

Aim Primary and secondary genetic clines in post-glacial colonized regions have different implications for biogeographic distributions and the origin of species. Primary clines arise in situ after colonization as adaptive responses to environmental gradients, while secondary clines are caused by contact between vicariant lineages. Here we analyse primary versus secondary origin of a genetic cline in the tephritid fly Urophora cardui in Jutland, Denmark, in a post-glacial landscape. Location Western Palaearctic. Methods Phylogeographic and demographic analyses of U. cardui based on mitochondrial DNA (mtDNA) genealogies, hierarchical genetic variance tests based on allozymes and distribution analysis of a rare allele from the Jutland cline. Results There was no phylogeographic divergence between the Jutland population of U. cardui north of the cline and neighbouring western European regional populations, which all shared the common western European mtDNA haplotype H1. At nuclear loci, by contrast, the North Jutland population was diverged above the mean level of divergence among regional populations and had no loss of genetic variation. A rare allozyme allele that was frequent in the cline area (up to 45%) and was missing north of the cline also occurred at low frequency (0–14%) elsewhere in the sampling range. Shallow phylogeographic divergence was observed between Russian and western European populations and between English and continental populations. Main conclusions The genetic variation patterns support primary cline evolution and parapatric divergence in Jutland following a demographic expansion of a western European ancestral source population of U. cardui, and suggest cryptic refugia and/or selection in other European population assemblages. The patterns of intra-specific regional divergence are discussed with respect to the interpretation of cryptic refugia in Europe after the most recent ice age.     

Detection of differential gene flow from patterns of quantitative variation

A major goal in anthropological genetics is the assessment of the effects of different microevolutionary forces. Harpending and Ward (1982) developed a model that aids in this effort by comparing observed and expected heterozygosity within populations in a local region. The expected heterozygosity within a population is a function of the total heterozygosity of the entire region and the distance of the population from the regional mean centroid of allele frequencies. Greater than average gene flow from an external source will result in a population having greater heterozygosity than expected. Less than average gene flow from an external source will result in a population having less heterozygosity than expected. We extend the Harpending-Ward model to quantitative traits using an equal and additive effects model of inheritance. Here the additive genetic variance within a population is directly proportional to heterozygosity, and its expectation is directly proportional to the genetic distance from the centroid. Under certain assumptions the expectations for phenotypic variances are similar. Observed and expected genetic or phenotypic variance can then be compared to assess the effects of differential external gene flow. When the additive genetic covariance matrix or heritabilities are not known, the phenotypic covariance matrix can be used to provide a conservative application of the model. In addition, we develop new methods for estimation of the genetic relationship matrix (R) from quantitative traits. We apply these models to two data sets: (1) six principal components derived from twenty dermatoglyphic ridge count measures for nine villages in Nepal and (2) ten anthropometric measurements for seven isolated populations in western Ireland. In both cases both the univariate and multivariate analyses provide results that can be directly interpreted in terms of historically known patterns of gene flow.     

Salmonella enterica in swine production: assessing the association between amplified fragment length polymorphism and epidemiological units of concern

The aims of this study were to determine the ability of amplified fragment length polymorphism (AFLP) to differentiate Salmonella isolates from different units of swine production and to demonstrate the relatedness of Salmonella between farms and abattoirs by AFLP. Twenty-four farms in the midwestern United States were visited four times from 2006 to 2009. At each farm or abattoir visit, 30 fecal samples or 30 mesenteric lymph nodes were collected, respectively. A total of 220 Salmonella isolates were obtained, serotyped, and genotyped by multilocus sequence typing (MLST) and AFLP. These 220 isolates clustered into 21 serotypes, 18 MLST types, and 14 predominant AFLP clusters based on a genetic similarity threshold level of 60%. To assess genetic differentiation between farms, harvest cohorts, and pigs, analysis of molecular variance was conducted using AFLP data. The results showed 65.62% of overall genetic variation was attributed to variance among pigs, 27.21% to farms, and 7.17% to harvest cohorts. Variance components at the farm (P = 0.003) and pig (P = 0.001) levels were significant, but not at the harvest cohort level (P = 0.079). A second analysis, a permutation test using AFLP data, indicated that on-farm and at-abattoir Salmonella from pigs of the same farms were more related than from different farms. Therefore, among the three subtyping methods, serotyping, MLST, and AFLP, AFLP was the method that was able to differentiate among Salmonella isolates from different farms and link contamination at the abattoir to the farm of origin.     

Optimising profitability and productivity of pasture-based dairy farms with automatic milking systems

There is a large variability in profitability and productivity between farms operating with automatic milking systems (AMS). The objectives of this study were to identify the physical factors associated with profitability and productivity of pasture-based AMS and quantify how changes in these factors would affect farm productivity. We utilised two different datasets collected between 2015 and 2019 with information from commercial pasture-based AMS farms. One contained annual physical and economic data from 14 AMS farms located in the main Australian dairy regions; the other contained monthly, detailed robot-system performance data from 23 AMS farms located across Australia, Ireland, New Zealand, and Chile. We used linear mixed models to identify the physical factors associated with different profitability (Model 1) and partial productivity measures (Model 2). Additionally, we conducted a Monte Carlo simulation to evaluate how changes in the physical factors would affect productivity. Our results from Model 1 showed that the two main factors associated with profitability in pasture-based AMS were milk harvested/robot (MH; kg milk/robot per day) and total labour on-farm (full-time equivalent). On average, Model 1 explained 69% of the variance in profitability. In turn, Model 2 showed that the main factors associated with MH were cows/robot, milk flow, milking frequency, milking time, and days in milk. Model 2 explained 90% of the variance in MH. The Monte Carlo simulation showed that if pasture-based AMS farms manage to increase the number of cows/robot from 54 (current average) to ～ 70 (the average of the 25% highest performing farms), the probability of achieving high MH, and therefore profitability, would increase from 23% to 63%. This could make AMS more attractive for pasture-based systems and increase the rate of adoption of the technology.     

Airborne Detection and Quantification of Swine Influenza A Virus in Air Samples Collected Inside,Outside and Downwind from Swine Barns

Airborne transmission of influenza A virus (IAV) in swine is speculated to be an important route of virus dissemination, but data are scarce. This study attempted to detect and quantify airborne IAV by virus isolation and RRT-PCR in air samples collected under field conditions. This was accomplished by collecting air samples from four acutely infected pig farms and locating air samplers inside the barns, at the external exhaust fans and downwind from the farms at distances up to 2.1 km. IAV was detected in air samples collected in 3 out of 4 farms included in the study. Isolation of IAV was possible from air samples collected inside the barn at two of the farms and in one farm from the exhausted air. Between 13% and 100% of samples collected inside the barns tested RRT-PCR positive with an average viral load of 3.20E+05 IAV RNA copies/m³ of air. Percentage of exhaust positive air samples also ranged between 13% and 100% with an average viral load of 1.79E+04 RNA copies/m³ of air. Influenza virus RNA was detected in air samples collected between 1.5 and 2.1 Km away from the farms with viral levels significantly lower at 4.65E+03 RNA copies/m³. H1N1, H1N2 and H3N2 subtypes were detected in the air samples and the hemagglutinin gene sequences identified in the swine samples matched those in aerosols providing evidence that the viruses detected in the aerosols originated from the pigs in the farms under study. Overall our results indicate that pigs can be a source of IAV infectious aerosols and that these aerosols can be exhausted from pig barns and be transported downwind. The results from this study provide evidence of the risk of aerosol transmission in pigs under field conditions.     

The Pleistocene glacial cycles shaped the historical demography and phylogeography of a pine fungal endophyte

The fungal endophyte Lophodermium nitens is an obligate symbiont of soft pines inhabiting only two pine species in Mexico with a broad distribution of geographically isolated populations. A previous study for the hosts indicated a main east–west subdivision with recurrent gene flow within these regions and demographic expansion of populations. We took these patterns as null hypotheses to test for the demography and phylogeographical patterns of the fungus, given the obligatory relationship of the endophyte to the host and its reduced capacity for long-distance dispersal. For this purpose, we employed two nuclear DNA loci, fragments of the actin and chitin synthase I genes. Both loci showed high genetic variation, consisting of private single-copy alleles, as well as few ones at high frequency that were shared among almost all populations. In order to distinguish between shared polymorphism due to incomplete lineage sorting and gene flow posterior to population divergence, we applied the coalescent-based Isolation–Migration (IM) model. We found patterns of gene flow and isolation similar to those of the hosts as well as signs of population expansion. Mean migration time and divergence time estimates fell within the Pleistocene, previous to Last Glacial Maximum. The results presented here for L. nitens emphasize the potential use of endophytic fungi to deepen the knowledge of historical patterns and processes of their host plants.     

Genetic variation within and among populations of Fomitopsis pinicola (Basidiomycetes)

RAPD polymorphisms were used to reveal the genetic population structure of Fomitopsis pinicola from 5 populations in southwestern Sweden with outliers in Finland and Norway. Eleven primers were used on 35 isolates. Using the Analysis of Molecular Variance (AMOVA), the total variance was divided into 3 hierarchical components: 84% within populations, 11% among regions, and 5% among populations within regions. The 3 large Swedish populations contained 95% of the variation within them. The statistical significance of these patterns was supported by permutation tests. The similarity index between all genets ranged from 0.10 to 0.72, with an average of 0.45. Genets from the same population could form more than one cluster in the neighbor-joining analysis. Some of these clusters were also supported by parsimony jack-knifing. This pattern is tentatively explained by establishment of spores from different basidiomata. The result of somatic incompatibility tests and RAPD markers were compared and this comparison indicated that compatible reactions do not necessarily imply genetic identity. Sampling from cut sections of infected trees revealed that multiple infections were present in a single tree and that the fungus probably infects host-trees by basidiospores, arriving via the air. Each somatically incompatible genet characteristically monopolized only part of a resource unit. Spore trapping showed no evidence of long distance spore dispersal, but this is probably due to the limited experiment, since the genetic analysis suggested a high rate of gene flow.     

Borrelia burgdorferi infection in Ixodes ricinus from habitats in Denmark

A total of 2647 ticks of the genus Ixodes was sampled by flagging the vegetation in thirty-one sites in eastern Jutland, Denmark. All ticks were identified as Ixodes ricinus Linnaeus. A total of 317 ticks (202 nymphs and 115 adults) from three different sites were examined for the spirochaete Borrelia burgdorferi Johnson et al. by indirect fluorescent antibody staining; the frequency of infection varied from 7% to 22%. It is concluded that I. ricinus, known to be the most common tick in Denmark, is the vector largely responsible for the transmission of B. burgdorferi in this country.     

Hybridisation between the digeneans Schistosoma haematobium and S. mattheei : viability of hybrids and their development in sheep

The F1 and F2 hybrids of Schistosoma haematobium male × S. mattheei female were studied with regard to infectivity to intermediate and definitive hosts, isoenzymes (phosphoglucomutase) of individual male worms, randomly amplified polymorphic DNAs of individual adult worms and scanning electron micrographs of the tubercles of male worms. The infection rate of the F1 hybrid miracidia in Bulinus globosus (41.7%) was greater than that achieved in B. wrighti (16.3%); the infection rate of the F2 in B. wrighti was 15.4%. In the definitive hosts: in sheep only male F1 hybrids (i.e. no females and no F2 worms)were recovered; but in hamsters both paired F1 worms and unpaired F1 males were recovered, as were one pair of worms and unpaired males of the F2 generation. The S. mattheei and S. haematobium male worms showed very distinctive PGM patterns, and the F1 hybrids showed additive patterns and a polymorphism with two distinct types of band patterns which are the result of polymorphism in the S. haematobium. The RAPD profiles of the F1 hybrids were also composite of the two parental species. Scanning electron micrographs of the tubercles of male S. haematobium showed them to be heavily spined, whereas those of S. mattheei males were devoid of spines. The F1 hybrids did show variation ranging from non-spined, some with partial spination, to those with heavily spined tubercles. Male worms of the F2 generation possessed tubercles either with or without spines. The potential significance of hybridisation in areas of sympatry between S. haematobium and S. mattheei is discussed.     

The persistence of African swine fever virus in field-infected Ornithodoros erraticus during the ASF endemic period in Portugal

African swine fever (ASF) is an important disease of pigs and outbreaks of ASF have occurred in Europe on multiple occasions. To explore the period for which the European soft tick species Ornithodoros erraticus (Acari: Argasidae) is able to act as a reservoir of African swine fever virus (ASFV) after infected hosts are removed, we collected specimens from farms in the provinces of Alentejo and Algarve in Portugal during the endemic period and tested them subsequently using cell culture and experimental infection. We show that ticks from previously infected farms may contain infectious virus for at least five years and three months after the removal of infectious hosts. Furthermore, in two cases infectious virus was successfully isolated from ticks on restocked farms that had not yet suffered a re-emergence of disease. Experimental transmission to pigs was demonstrated in batches tested up to 380 days after an outbreak. These results clarify the epidemiological role of O. erraticus ticks in the persistence of ASFV in the field, provide additional evidence to support its role in the re-emergence of a sporadic outbreak of ASF in Portugal in 1999 and suggest that the current quarantine legislation and restocking advice when these ticks are present on the pig farm premises is appropriate.     

断奶仔猪源大肠杆菌LEE及HPI毒力岛的检测

应用Duplex_PCR方法,对240株断奶仔猪源大肠杆菌分离株的LEE毒力岛的eaeA基因和耶尔森菌强毒力岛核心区的irp2基因进行了检测,并对HPI毒力岛的fyuA基因及其在大肠杆菌染色体中的插入位置进行了分析,以及随机选取部分PCR产物进行了克隆和序列分析。结果表明:其中29株(12.08%)为LEE HPI ,39株(16.25%)为LEE ,11株(4.58%)为HPI ;另外还发现:不同病例来源的分离株之间,两种毒力岛的携带率不同;在断奶仔猪腹泻源分离株中,29株(20.71%)为LEE HPI ,22株(15.71%)为LEE ,9株(6.43%)为HPI ;断奶仔猪水肿病源分离株中,仅5株(6.58%)为LEE ,2株(2.63%)为HPI ,未发现LEE HPI 菌株;断奶仔猪水肿病并发腹泻源分离株中,仅12株(50%)为LEE ,未发现HPI 及LEE HPI 菌株。本实验克隆的eaeA(425bp)与已发表序列完全一致,irp2(280bp)f、yuA(948bp)、asn_tRNA_intB(1391bp)均与已发表的序列高度同源,同源性分别在98.2%、98.3%、95.8%以上;40株LEE HPI 或HPI 分离株中,29株(72.5%)为fyuA ,且其HPI毒力岛位于大肠杆菌染色体asn_tRNA位点。     

Ascaris and ascariasis

Ascaris lumbricoides and Ascaris suum are widespread parasitic nematodes of humans and pigs respectively. Recent prevalence data suggests that approximately 1.2 billion people are infected. Adult worms exhibit an overdispersed frequency distribution in their hosts and individuals harbouring heavy burdens display associated morbidity. In this review, we describe the parasite, its distribution and measures undertaken to control infection.     

Experimental infection of Dirofilaria immitis in raccoon dogs

Canine heartworm (Dirofilaria immitis) is a nematode that naturally parasitizes in the pulmonary arteries and the right ventricle of domestic dogs (Canis familiaris) as final hosts. Japanese raccoon dogs (Nyctereutes procyonoides viverrinus) also are known to be susceptible to infection by the parasite. However, prevalence of this infection among free-ranging raccoon dogs is low and so is the worm burden. To examine the susceptibility of the raccoon dog to D. immitis infection, 3 raccoon dogs and 2 beagles were inoculated 4 times with 25 third-stage larvae (L3s) of D. immitis at 3-wk intervals. Worms were recovered from 2 raccoon dogs and both domestic dogs. The average percentage of recovery (2.3%) of the raccoon dogs was almost 10 times lower (24.5%) than that of the domestic dogs, but there was no significant difference in the body length of worms recovered from 2 types of hosts. To examine microfilaremia, 2 raccoon dogs were infected with 100 L3s. Microfilaremia was observed for 180 days postinoculation (PI) but disappeared at about 300 days PI. The raccoon dog was mildly susceptible to infection with D. immitis, but surviving worms developed and matured normally.     

North‐south population subdivision of Juniperus seravschanica in Kyrgyzstan revealed through novel plastid DNA markers

Abstract Junipers are main components of semiarid forests in Central Asia. Conservation of these plant genetic resources should be based on an understanding of factors that have shaped species‐level genetic variation. We used Juniperus seravschanica Kom. as a model species to investigate patterns and processes that may be associated with these factors. Novel plastid DNA markers (two minisatellites, one transversion, one indel) were identified and applied to investigate haplotype diversity and population structure in Kyrgyzstan. In total, 540 individuals from 15 populations were analyzed and 11 haplotypes detected. Strong divergence between populations from northern and southern Kyrgyzstan was evident from the haplotype distribution. Gene diversity within populations ranged from 0.083 to 0.765, and was on average higher in southern (0.687) than in northern populations (0.540). A similar pattern was detected in allelic richness. Analysis of molecular variance (AMOVA) revealed that 11.9% of the total genetic variation was due to differences among regions, 1.5% among populations, and 86.6% within populations. N_ST was not significantly different from G_ST (0.125), suggesting no evidence of a phylogeographic pattern. A Mantel test detected a weak but significant isolation‐by‐distance pattern for the whole dataset and southern populations separately. These results suggest that the north of Kyrgyzstan was relatively recently colonized by migrants from southern populations, probably associated with favorable conditions during the early Holocene. The humid Fergana Valley and Fergana Range are probable ecological barriers to gene flow between northern and southern populations.     

Genetic diversity and microgeographic differentiation of Yushan cane (Yushania niitakayamensis; Poaceae) in Taiwan

Yushan cane ( Yushania niitakayamensis ) is distributed in southeast Asia. In Taiwan, the species occurs in mountains 1000–3600 m above sea level. The species appears to spread mainly by rhizomes and flowers only rarely. Nine locations across its distribution range in Taiwan were sampled. Locations at higher altitudes generally consist of grassland and forest undergrowth habitats while those of lower altitudes generally consist of forest undergrowth only. Thus two sampling sites (montane grassland and forest undergrowth) were selected from each location at higher altitudes while only one sampling site was selected from each location at lower altitudes, resulting in a total of 13 sampling sites. Within each sampling site, 20 individual plants were sampled. The results of the cluster analysis and the principal coordinate analysis based on random amplified polymorphic DNA (RAPD) indicated that the populations are generally differentiated according to geographical separation and altitudinal differences that interrupt gene flow. The populations at higher altitudes, where the species is distributed somewhat contiguously, were found to be more similar genetically. Analysis of molecular variance ( AMOVA ) revealed that the among-location, between sampling sites within location, and among individuals within sampling site components accounted for 15.27%, 4.80% and 79.93% of the total variance, respectively. For locations with two sampling sites, two-level AMOVA revealed that the diversities between sampling sites (sun and shade habitats) within locations ranged from 2.91% to 7.99% of the total diversity. Random permutation tests revealed that these diversities were significant, implying that there is microgeographic differentiation due to habitat differences.